10 gel gel5 Full Text Measure the levels of FasL and Fas gene under E2 treatment. Mice treatment with E2, RNA extraction from thymi, RT-PCR, PCR with specific primers. Increased levels of Fas and FasL genes in thymi. E2 treatment upregulates Fas and FasL genes compared with vehicle treatment. none no no no no no no no no 10 gel gel5 Image+Caption+Title+Abstract Examine the upregulation of Fas and FasL genes after estradiol-17-valerate treatment. E2 treatment in mice, RNA extraction from thymi, cDNA synthesis, PCR with specific primers. Fas and FasL genes, after E2 treatment are upregulated compared with the vehicle. Treatment with 1 mg/kg body weight of E2 induces the expression of Fas and FasL genes. None. no no no no no no no no 10 gel gel5 Image+Caption Examine whether Fas and FasL genes are upregulated following E2 treatment. treatment with E2, RNA extraction, cDNA synthesis, PCR with specific primers. Genes Fas and FasL are upregulated after treatment. E2 induces the expression of Fas and FasL genes in mice. none no no no no no no no no 10 graph graph5 Full Text &#921;dentify a gene required for the reconstitution of heterologous elongase activity.Examine the requirement of YBR159w for yeast viability. they used a “loss-of-heterologous-function” screen to genetically identify a component of the microsomal fatty acid elongase. ybr159&#948; cells are able to grow at 30 °C in rich medium(in the absence of fatty acid supplements) but at a slower rate than wild type. Th&#949; initial slow growth may be related to some form of adaptive response to the loss of this microsomal elongase component. After this “adaptation” the mutant spore colonies formed are viable in the absence of fatty acid supplement, although growing at a much slower rate than wild type cells. none no no no no no no no no 10 graph graph5 Image+Caption+Title+Abstract Examine effect of Ybr159w disruption in S. cerevisiae mutant cells. Disruption of Ybr159w gene, compare growth between wild type and mutant cells via optical method. Mutants are slow growing and display high temperature sensitivity. Disruption of YBR159w is not lethal since there is some growth in mutant cells. What type of cells are they using? (S. cerevisiae isn't mentioned) no yes no no yes no no no 10 graph graph5 Image+Caption Compare growth rates between wild type and ybr159 mutant cells Measure the growth rate with photometer Growth rate of the mutant cells is lower The maximum growth in wild type cells occurs earlier none no no no no no no no no 10 mixed mixed5 Full Text Confirm the cross-overs and test whether there is an auxotrophy in Leptospira spp. PCR and Southern blot analysis to confirm the allelic exchange.Photometer to examine the growth of the mutants. There is an increase in size in PCR product or the hybridizing fragment due to the insertion of the kanamycin-resistant cassette.Addition of tryptophan restored growth of the L. meyeri trpE mutant at the wild-type rate. L. meyeri is able to acquire amino acids from its environment by taking up free amino acids. none no no no no no no no no 10 mixed mixed5 Image+Caption+Title+Abstract To investigate whether trpE deficiency mutants can grow. PCR, Southern blot analysis, photometer trpE mutant is able to grow when tryptophan or anthranilate is added to the media.trpE mutant was not able to grow. trpE is essential for bacteria viability. Label each growth curve. no no yes no no no no no 10 mixed mixed5 Image+Caption Expression of trpE gene in wild-type strain, single cross-over recombinant strain, double cross-over recombinant strain.Examine the growth of parental, trpe mutant, trpE mutant supplemented with tryptophan strains. PCR, Southern blot analysis, Photometer The size of the bands in PCR are different with the bands in Southern blot analysis. Do not know Name its curve. no no no yes no no yes yes 10 model model5 Full Text Construction of T1 Domain Constructs in order to efficiently separate T1 domain proteins into different molecular weight species. Do not know. Synthesize of soluble N-terminal peptides from the Shaker type K1 channel subunit protein AKv1.1, containing the T1 domain. Synthesize of soluble N-terminal peptides from the Shaker type K1 channel subunit protein AKv1.1, containing the T1 domain. Information about T1 domain.The procedure the constructs were designed. yes yes yes no yes yes yes yes 10 model model5 Image+Caption+Title+Abstract Determine the N of the assembled protein peak on HPLC SEC. Cross-link the T1 domain proteins. Three constructs are full N-terminal and two are T1 domain only constructs. Five constructs are going to be used to determine the assembly properties of the Shaker channel T1 domain. Provide information about T1 domain, meaning definition. yes no no no no yes yes yes 10 model model5 Image+Caption Schematic description of constructs originated from the parent AKv1.1a clone that are used in the experiments. Schematic There are three full terminal constructs and two T1 domain only constructs. Five constructs derived from AKv1.1a clone and used in the experiments. Each construct what is made from.What is Tag1, T7tag mean?More information about the constructs meaning in which experiments they were used. no no yes no no yes yes yes 10 thing thing5 Full Text Stydy the delay in excitation-contraction coupling in porcine ASM cells after ACh addition. Real-time confocal. Exposure of single ASM cells to ACh resulted in the initiation of propagating [Ca21]i oscillations that typically initiated from one end at the long axis of the cell.The ACh-induced elevation of [Ca21]i did not result in an immediate initiation of contraction.and propagated toward the other end In porcine ASM cells ACh-induced propagating [Ca21]i oscillations lead to a stable force generation. Define the method that was used.More detailed explanation for each image. no yes yes no no yes no no 10 thing thing5 Image+Caption+Title+Abstract To study the hypothesis that in ASM, coupling of elevations and reductions in [Ca2+]i to force generation and relaxation is slower than ACh-induced [Ca2+]i oscillations. Real-time confocal imaging. The delay between elevated [Ca2+]i and contraction in intact porcine ASM cells was found to be ~450 ms. Addition of ACh leads to stable force generation. Which method was used.What 50ms, 200ms, 300ms, 400ms mean. no yes no no no yes yes no 10 thing thing5 Image+Caption To study the effect of ACh addition to Ca2+ oscillations and to the shortening of the cell. Do not know. Do not know. Do not know. Explain what we see in the above pictures.What 50ms, 200ms, 300ms. 400ms mean? no yes yes yes no yes yes yes 11 gel gel4 Full Text study the interactions between RNase R and Rnase E co-sediments;SDS-PAGE;silver staining;sulfopropyl-Sepharose (SP) fractions;Western blot analysis; RNase R and Rnase E peaked in the same glycerol density gradient fractions;but they can be seperated by different glycerol density gradient,and verified through Westblot array and migrate behavior of different molecular weight marker protein. there was an interactions between RNase R and Rnase E. none no no no no no no no yes 11 gel gel4 Image+Caption+Title+Abstract study exoribonuclease R interacts with endoribonuclease E sulfopropyl-Sepharose ;SDS-PAGE ;silver staining;Western blot analysis;co-sediments ;cation exchange chromatography the hydrolytic exoribonuclease RNase R was found to co-purify with RNase E;Co-immunoprecipitation and Ni2+-affinity pull-down experiments confirmed the specific interaction between RNase R and RNase E The identification of RNase R instead of polynucleotide phosphorylase in this complex underlines the importance of the interaction between endo- and exoribonucleases for the bacterial RNA metabolism. The physical association of RNase E with an exoribonuclease and an RNA helicase apparently is a common theme in the composition of bacterial RNA-degrading complexes. none no no no no no no no no 11 gel gel4 Image+Caption maybe study the relation between RNase E and RNase R glycerol density gradients;SDS-PAGE ;silver staining;Western blot analysis ; at same SP,RNase E and RNase R reached their peaks and hard to distinguish them;but at the different SP gradients,they can be seperated easily. there is an certain relationship between RNase E and RNase R. molecular weight of RNase E and RNase R should be provided. yes no yes no yes no yes yes 11 graph graph3 Full Text microcirculatory adjustments associated with changes at the opposite values of the hematocrit scale, i.e., in polycythemia. animal models;Cobalt irritate,EPO injection;aortic clamp Baseline left ventricular hemodynamic parametersin both types of experimental polycythemia did not differ from those in control animals. On the other hand,maximal left ventricular function after aortic clampingwas characterized by small but significant decreases insystolic pressure and developed pressure in both modelsof polycythemia. In the case of cobalt-induced polycythemia,a decrease in functional reserve was alsoobserved (see Fig. 1). Maximal rates of pressure developmentwere similar in all three experimental groups. Only rats with cobalt-induced polycythemia had anincreased coronary capillary and arteriolar supply.Chronic polycythemia induced by EPO injections wascharacterized by even larger increases in hematocritbut the coronary microvascular bed remained unchanged. Therefore, a hypoxic stimulus seemed to be more effective in inducing angiogenesis than mechanical stimuli. none no no no no no no no no 11 graph graph3 Image+Caption+Title+Abstract the effect of polycythemia on the coronary microcirculation Cobalt irritate,EPO injection;aortic clamp;Morphometric analysis In both models, baseline left ventricular function was normal, whereas maximal systolic and developed pressures were decreased. In cobalt-treated rats the left ventricular functional reserve was also compromised; polycythemia induced by Cobalt and EPO can affect the coronary microcirculation capillary angiogenesis's methods,doses of Cobalt and EPO; no yes no no no yes no no 11 graph graph3 Image+Caption the relation between left ventricular maximal systolic and developed pressure under different levels polycythemia Cobalt irradiate and EPO injection;aortic clamp In maximal systolic of LV and developed pressure, there were significant differences between Cobalt group and EPO group and control group,but under reserve conditions, there was an significant difference between Cobalt group and control group; the maximal rate of pressure development was no difference among different groups. polycythemia affected the left ventricular maximal systolic and developed pressure,irradiation may be an important cause. experimental conditions,include doses of Cobalt and EPO, the time of aortic clamp, etc no yes no no no yes no no 11 mixed mixed2 Full Text the mechanism of ODC degration IP,Westblot;SAS-PAGE GAr can inhibit proteasome inhibitor action and regulate the ODC degration GAr can inhibit ODC degration and play an important role in ATP degration none no no no no no no no no 11 mixed mixed2 Image+Caption+Title+Abstract the mechanism of GAr control ODC degration IP; SAS-PAGE;immunoflurescence GAr can inhibit ODC degration or stop transfer GAr play an important role in ODC degration ATP degration mechanism;GFP fluorescence(Westblot analysis) no no yes yes no yes no no 11 mixed mixed2 Image+Caption GAr maybe can inhibitor ODC degration IP SDS-PAGE the speed of ODC::GAr degration slowed, especially with ODCCA441;rpn4 may be more susceptible to proteasome inhibitor GAr maybe play an important role in ODC degration GAr MW(molecular weight),expression no no yes no no no yes yes 11 model model2 Full Text the interaction of hRad1, hHus1, hRad9, and hRad17 during a DNA damage response westblot and IP, mutational analysis endogenous humanRad17 (hRad17) interacts with the PCNA-related checkpointproteins hRad1, hRad9, and hHus1. Mutationalanalysis of hRad1 and hRad17 demonstrates that thisinteraction has properties similar to the interaction between RFC and PCNA;DNA damage affects the association of hRad17 with the clamp-likecheckpoint proteins hRad17 interacts with the PCNA-like proteins hRad1, hHus1, and hRad9 in manner similar to the interaction between RFC and PCNA. none no no no no no no no no 11 model model2 Image+Caption+Title+Abstract Model for the interaction of hRad1, hHus1, hRad9, and hRad17 during a DNA damage response westlot and mutational analysis demonstrate that endogenous human Rad17 (hRad17) interacts with the PCNA-related checkpoint proteins hRad1, hRad9, and hHus1. Mutational analysis of hRad1 and hRad17 demonstrates that this interaction has properties similar to the interaction between RFC and PCNA, a well characterized clamp-clamp loader pair. Moreover, we show that DNA damage affects the association of hRad17 with the clamp-like checkpoint proteins hRad17 interacts with the PCNA-like proteins hRad1, hHus1, and hRad9 in manner similar to the interaction between RFC and PCNA. molecular weight of these four proteins and the order of expression, no no no yes no no no yes 11 model model2 Image+Caption the interaction of hRad1, hHus1, hRad9, and hRad17 during a DNA damage response do not know hRad17 recognizes DNA damage and loads an hRad1-containing clamp onto the DNA hRad17,maybe play an important role in the interaction of these four genes Westblot no yes no yes no yes no no 11 thing thing3 Full Text whether the N-terminal selfassociation domain of RAD52 is an uinique region in the earliest stages of chromosomal double-strand break repair via the homologous recombination pathway electron micrograph;Westblot,PCR;Protein Purification;ELIA;DLS analisis; there are in fact two experimentally separable self-association domains in RAD52.N-terminal identified and unidentified C-terminal. thereare in fact two experimentally separable self-associationdomains in RAD52. The N-terminal self-association domainmediates the assembly of monomers into rings,and the previously unidentified domain in the C-terminalhalf of the protein mediates higher order self-associationof the rings. none no no no no no no no no 11 thing thing3 Image+Caption+Title+Abstract whether self-association domain of RAD52 has a unique region in the N-terminal half of the protein in the earliest stages of chromosomal double-strand break repair via the homologous recombination pathway electron micrographs there are in fact two experimentally separable self-association domains in RAD52:The N-terminal self-association domain and unidentified domain in the C-terminal half of the protein The N-terminal self-association domain of RAD52 mediates the assembly of monomers into rings, and the previously unidentified domain in the C-terminal half of RAD52 mediates higher order self-association of the rings. RAD52 molecular weight,westbolt analysis no yes no no no yes no no 11 thing thing3 Image+Caption wt RAD52 and RAD52-(1-192) go in for certain mechanism of regulation. electron micrographs wt RAD52 and RAD52-(1-192) formed different shape and size materials wt RAD52 and RAD52-(1-192)maybe play an important role in certain mechanism of regulation. wt RAD52 and RAD52-(1-192) expression no no yes no no no no no 12 gel gel3 Full Text To understand an essential role for metazoan REF1 or the additional EJC proteins. West plotting analysis (using antibodies) on gene-deleted cells. REF1 and the additional components of the EJC are dispensable for export of bulk mRNA in Drosophila cells. Only when REF1 and RNPS1 are codepleted, or when all EJC proteins are simultaneously depleted is a partial nuclear accumulation of polyadenylated RNAs observed. A significant fraction of bulk mRNA is detected in the cytoplasm of cells depleted of all EJC proteins. REF1 and the additional components of the EJC are dispensable for export of bulk mRNA in Drosophila cells. Only when REF1 and RNPS1 are codepleted, or when all EJC proteins are simultaneously depleted is a partial nuclear accumulation of polyadenylated RNAs observed. A significant fraction of bulk mRNA is detected in the cytoplasm of cells depleted of all EJC proteins none no no no no no no no no 12 gel gel3 Image+Caption+Title+Abstract To understand an essential role for metazoan REF1 or the additional EJC proteins. West plotting REF1 and the additional components of the EJC are dispensable for export of bulk mRNA in Drosophila cells. Only when REF1 and RNPS1 are codepleted, or when all EJC proteins are simultaneously depleted is a partial nuclear accumulation of polyadenylated RNAs observed. A significant fraction of bulk mRNA is detected in the cytoplasm of cells depleted of all EJC proteins Additional adaptor protein(s) mediate the interaction between NXF1 and cellular mRNAs in metazoa. The essential role of UAP56 in mRNA export is not restricted to the recruitment of REF1. none no no no no no no no no 12 gel gel3 Image+Caption Do not know West plotting. Depletion of EJC proteins reduces, but does not abolish, incorporation of [35S]Met into newly synthesized proteins. Do not know none yes no no yes yes no no yes 12 graph graph4 Full Text To examine polyol accumulation and metabolism in Aspergillus oryzae cultured on whole wheat grains or on wheat dough as a model for solid-state culture. Rapid frozen techniques. Enzyme activity analysis. Northern analysis. NADP+-dependent glycerol dehydrogenase activity correlated very well with glycerol accumulation. NADP+- ependent glycerol and erythritol dehydrogenases are involved in biosynthesis of glycerol and erythritol, respectively, and that these enzymes are induced by osmotic stress. none no no no no no no no no 12 graph graph4 Image+Caption+Title+Abstract To examine polyol accumulation and metabolism in Aspergillus oryzae cultured on whole wheat grains or on wheat dough as a model for solid-state culture. Do not know. NADP+-dependent glycerol dehydrogenase activity correlated very well with glycerol accumulation. NADP+- ependent glycerol and erythritol dehydrogenases are involved in biosynthesis of glycerol and erythritol, respectively, and that these enzymes are induced by osmotic stress. none no yes no no no yes no no 12 graph graph4 Image+Caption Do not know Chromatography Do not know Do not know none yes no yes yes yes no yes yes 12 mixed mixed1 Full Text Examining how mutations in Parkin, involved in autosomal recessive juvenile parkinsonism, cause nigral cell death. Use west plotting and enzyme activity analysis to examine the effect of Parkin overexpression on cellular levels of oxidative damage, antioxidant defenses, nitric oxide production, and proteasomal enzyme activity. Increasing expression of Parkin by gene transfection in NT-2 and SK-N-MC cells led to increased proteasomal activity, decreased levels of protein carbonyls, 3-nitrotyrosine- ontaining proteins, and a trend to a reduction in ubiquitinated protein levels. Transfection of these cells with DNA encoding three mutant Parkins associated with autosomal recessive juvenile parkinsonism (Del 3–5, T240R, and Q311X) gave smaller increases in proteasomal activity and led to elevated levels of protein carbonyls and lipid peroxidation. Turnover of the mutant proteins was slower than that of the wild-type protein, and both could be blocked by the proteasome inhibitor, lactacystin. A rise in levels of nitrated proteins and increased levels of NO2-/NO3- was also observed in cells transfected with mutant Parkins, apparently because of increased levels of neuronal nitricoxide synthase. The presence of mutant Parkin in substantia nigra in juvenile parkinsonism may increase oxidative stress and nitric oxide production, sensitizing cells to death induced by other insults. none no no no no no no no no 12 mixed mixed1 Image+Caption+Title+Abstract Studying the effect of Parkin overexpression on cellular levels of oxidative damage, antioxidant defenses, nitric oxide production, and proteasomal enzyme activity. West blotting. Enzyme activity analysis. One-way ANOVA. Increasing expression of Parkin by gene transfection in NT-2 and SK-N-MC cells led to increased proteasomal activity, decreased levels of protein carbonyls, 3-nitrotyrosine-containing proteins, and a trend to a reduction in ubiquitinated protein levels. Transfection of these cells with DNA encoding three mutant Parkins associated with autosomal recessive juvenile parkinsonism (Del 3-5, T240R, and Q311X) gave smaller increases in proteasomal activity and led to elevated levels of protein carbonyls and lipid peroxidation. Turnover of the mutant proteins was slower than that of the wild-type protein, and both could be blocked by the proteasome inhibitor, lactacystin. A rise in levels of nitrated proteins and increased levels of NO /NO was also observed in cells transfected with mutant Parkins, apparently because of increased levels of neuronal nitric-oxide synthase. The presence of mutant Parkin in substantia nigra in juvenile parkinsonism may increase oxidative stress and nitric oxide production, sensitizing cells to death induced by other insults. none no no no no no no no no 12 mixed mixed1 Image+Caption Do not know. Western blot analysis. Measuring enzyme activities. One-way ANOVA. Wild-type and mutant Parkin proteins, in NT-2 and SK-N-MC cell lines show different overexpression, enzyme activity, and turnover. Do not know. none yes no no yes yes no no yes 12 model model4 Full Text To present a model relating changes in functional properties of FBPase to deletion and point mutations in residues 1-10. Deleting of the first 10 residues of FBPase and checking its activity. Changes in the relative stability of the known conformational states for loop 52-72, in response to changes in the quaternary structure of FBPase, can account for the phenomena above. The observation of corresponding conformational states in mammalian and chloroplast FBPases infers a common, early mechanism of FBPase regulation that has diverged through evolution. none no no no no no no no no 12 model model4 Image+Caption+Title+Abstract To investigate how residues 1-10 of porcine fructose-1,6-bisphosphatase(FBPase) are in different conformations correpsonding to the state of ligation of the enzyme. Deleting of the first 10 residues of FBPase and checking its activity. Changes in the relative stability of the known conformational states for loop 52-72, in response to changes in the quaternary structure of FBPase, can account for the phenomena above. Some aspects of the proposed model may be relevant to all forms of FBPase, including the thioredoxin-regulated FBPase from the chloroplast. none no no no no no no no no 12 model model4 Image+Caption To understand allosteric regulation mechanism of FBPase. Do not know. Do not know. Do not know. Background of this protein. no yes yes yes yes yes yes yes 12 thing thing2 Full Text To understand whether and how glu gene expression is regulated in a cell type-specific manner. Cell culture, cell transfection, and LUC reporter gene analysis in GLUTage, STC-1, InR1-G9, and a-TC-1 cell lines. Also applied techniques like antibodies, western blotting, and immuno-histochemical staining, northern blotting analysis and RT-PCR. Catenin and the glycogen synthase kinase-3 inhibitor lithium do not activate glu mRNA or glu promoter expression in pancreatic cell lines. In the intestinal GLUTag cell line, but not in the pancreatic InR1-G9 cell line, the glu promoter G2 enhancer-element was activated by lithium treatment via a TCF-binding motif. TCF-4 is abundantly expressed in the gut but not in pancreatic islets. Furthermore, both TCF-4 and -catenin bind to the glu gene promoter, as detected by chromatin immunoprecipitation. Finally, stable introduction of dominant-negative TCF-4 into the GLUTag cell line repressed basal glu mRNA expression and abolished the effect of lithium on glu mRNA expression and GLP-1 synthesis. TCF-4 Mediates Cell Type-specific Regulation of Proglucagon Gene Expression by B-Catenin and Glycogen Synthase Kinase-3B. none no no no no no no no no 12 thing thing2 Image+Caption+Title+Abstract To understand whether and how glu gene expression is regulated in a cell type-specific manner. Do not know. We now show that -catenin and the glycogen synthase kinase-3 inhibitor lithium do not activate glu mRNA or glu promoter expression in pancreatic cell lines. In the intestinal GLUTag cell line, but not in the pancreatic InR1-G9 cell line, the glu promoter G2 enhancer-element was activated by lithium treatment via a TCF-binding motif. TCF-4 is abundantly expressed in the gut but not in pancreatic islets. Furthermore, both TCF-4 and -catenin bind to the glu gene promoter, as detected by chromatin immunoprecipitation. Finally, stable introduction of dominant-negative TCF-4 into the GLUTag cell line repressed basal glu mRNA expression and abolished the effect of lithium on glu mRNA expression and GLP-1 synthesis. TCF-4 Mediates Cell Type-specific Regulation of Proglucagon Gene Expression by B-Catenin and Glycogen Synthase Kinase-3B. none no yes no no no yes no no 12 thing thing2 Image+Caption Do not know. Detection of TCF-4 expression in cultivated cell lines and in paraffin-embedded pancreatic and intestine tissue samples. Do not know. Do not know. none yes no yes yes yes no yes yes 13 gel gel1 Image+Caption+Title+Abstract Demonstrate the presence of various isoforms of PECAM-1 RNA extraction, RT-PCR, agarose gel electrophoresis Figure 2 might be showing one of these isoforms If the figure shows an isoform, then it means that they have been able to establish the presence of this isoform in the above mentioned picture Name of product and expected product size no no yes yes no no yes yes 13 gel gel1 Image+Caption One can guess that he study is trying establish the presence of an (unidentified) RNA product in different tissues RNA extraction, RT-PCR and agarose gel electrophoresis. There is a product present in all the tissues, with a size of approx 400bp (if the figure is oriented the way I think it is). Whether it is the expected product is not clear, THMVEC might be the positive control There is a product of the same size in all the tissues... Expected size of product. yes no yes yes yes no yes yes 14 model model3 Image+Caption to depict the organization of the doublecortin gene, with a clear representation of the exons, introns, splice sites and the possible mutations in the doublecortin gene cDNA sequence of the doublecortin gene and aligning the sequences for annotating the possible reading frames and mutations There are 9 exons, with multiple splicing sites and the open reading frame comprises of exons E2 through E7, with most of the mutations in the exon 3. Do not know It is not good to show the aminoacid substitutions in the gene sequence and it is not clear what the / stands for. no no yes yes no no no yes 15 gel gel5 Full Text to explain the mechanism by which estradiol increase apoptosis of T-cells expression analysis of Fas and FasL by RT-PCR in tymocytes Fas and FasL are upregulated by estradiol which may lead to activation of apoptosis and death of T-cells estradiol increases thymocytes death by activating the death receptor pathway, an event mediated by upregulation of Fas receptors and Fas ligand none no no no no no no no no 15 gel gel5 Image+Caption+Title+Abstract to show estrogen effect on expression of apoptotic genes Fas and FasL in T-cells expression of Fas and FasL was assesed by RT-PCR and gel electrophoresis of the PCR product. Those two gene were chosen because: 1)cDNA array showed they are upregulated after estradiol treatment and 2)are involved in apoptosis Estradiol upregulates Fas and FasL in T-cells and increases apoptosis estradiol may increase cell death of thymic cells (T-cells) by upregulation of Fas and FasL apoptotic genes none no no no no no no no no 15 gel gel5 Image+Caption to show the effect (upregulation) of estradiol on Fas and FasL genes expression this figure shows agarose gel electrophoresis of the PCR products. it demonstrates the presence of Fas and FasL genes in the template (qualitative value) and the ammount (quantitative value) of those genes (can be approximately determined by comparing with the marker bands). b-actin is the positive control. the group treated with estradiol showed increase expression of Fas and FasL genes comparing with the control group. estradiol treatment is positively corelated with increase of Fas and FasL genes expression. none no no no no no no no no 15 graph graph5 Full Text to identify a yeast gene involved in a microsomal FA elongation activity deletion of ybr159 to asses the importance of that gene in FA elongation activity deletion of ybr159 adversely affects the growth rate of yeast ybr159 gene is involved in the fatty acid elongation activity on ER none no no no no no no no no 15 graph graph5 Image+Caption+Title+Abstract to show YBR159 encodes gene involved in fatty acid elongase activity mutation of the target gene to show loss of function (FA elongase activity) the mutant cells for YBR159 show a slow growth when compared with wild type YBR159 is important in cell growth by being involved in FA elongase activity none no no no no no no no no 15 graph graph5 Image+Caption do not know cell culture and growth assesment by measuring density figure shows that wild type cells grow better than mutants do not know (what gene is mutated?) none yes yes yes yes yes no no yes 15 mixed mixed5 Full Text fig a to confirm the crossing-over, i.e. insertion of the kanamycin-resistant cassette into the trpE gene. figure b shows that inactivation of trpE gene stops the growth and results in tryptophan auxotrophy. trpE gene cloning, insertion of the gene into a vector (inactivation of the gene), and subsequently transformation were performed; that was followed by crossing over and allelic exchange. that event wae demonstrated by PCR and southern analysis (the recombinant has larger number of bp). to demonstrate tryptophan auxotrophy, tryptophan was added to the mutants and growth was restored trpE gene is inactivated by recombination with kanamycin-resistant cassetts. when this gene is inactivated, L. meyeri lose its growth capability that is restored by adding tryptophan in the growth media or by transfection of a plasmid that contains functional trpE gene in Leptospira, trpE gene is essential for tryptophan syntehsis. moreover, tryptophan prototrophy is essential for survival of Leptospira when cultured in environment lacking amino acids. none no no no no no no no no 15 mixed mixed5 Image+Caption+Title+Abstract the purpose of figure a is to demonstrate that the recombination of the target gene was succesful. figure b shows that inactivation of trpE gene stops the growth and results in tryptophan auxotrophy. to demonstrate that recombination was succesfull 1) PCR with specific primers was used followed by gel electrophoresis of products and 2) southern blot with TrpE probe was performed. to demonstrate tryptophan auxotrophy, simple experiment of adding tryptophan to the mutant colony was done figure a demonstrates that the trpE gene was recombined with another sequence, that would finally result in trpE inactivation. figure b shows that when trpE is inactivated L. meyeri doesn't grow, but when tryptophan is added the growth is recovered and equals the wild type. in L meyeri trpE gene activity is necessary for tryptophan synthesis and so is for growth. by blocking trpE gene activity, tryptophan auxotrophic mutant of L meyeri was created. none no no no no no no no no 15 mixed mixed5 Image+Caption do not know agarose gel electrophoresis of PCR products with specific primers gives positive results. however I cannot say anything about those results as there are no information. for southern blot the same thing. figure b shows measurement of growth, however three growth curves are not assignet to groups (which one reppresents parental strain, which one mutants??) do not know do not know none yes yes yes yes yes yes yes yes 15 model model5 Full Text to determine the importance of the K channel T1 domain in assembling its subunits different lenght constructs containing T1 domain were created and their assembly analysed by size-chromatography, affinity column analysis and co-immunoprecipitation T1 domains form stabile tetramers T1 domain of the Shaker K channel forms tetramers and has a central role in the regulated assembly (tetramerization) of channel subunits none no no no no no no no no 15 model model5 Image+Caption+Title+Abstract to determine the assembly properties of T1 domain of a K channel create different constructs of the channel that contain T1 region of interest described by the picture and perform the coassemble assay do not know do not know none no no yes yes no no yes yes 15 model model5 Image+Caption do not know do not know do not knoe do not know none yes yes yes yes yes yes yes yes 15 thing thing5 Full Text to examine the steps in the excitation-contraction coupling, focusing on time delay real-time confocal measurements of intercellular Ca2+, and assesment of the effects of releasing different caged compounds involved in excitation-contraction coupling AcH stimulus results in immediate increase in Ca2+, but the contraction is delayed AcH induced increase in intracellular Ca2+ is delayed and non-oscillatory. the step that contributes most to the delay is CaM recruitment. none no no no no no no no no 15 thing thing5 Image+Caption+Title+Abstract to explain the role of intracellular Ca2+ oscillations in regulating the stable contraction force and the temporal aspect of excitation-contraction copuling real-time confocal imaging was used to monitor Ca2+ oscillations and cell contractions. the same was done when cells were perturbed with exogenous Ca2+ and calmodulin AcH treatment results in Ca2+ oscillations but the cell shortening was visible only after ~450 ms. Ca2+ concentration in the cell is temporally modulated in order to produce stable force none no no no no no no no no 15 thing thing5 Image+Caption to show that in Ca2+ propagation is possible to see a direction and that the contraction has a delay from the rise in Ca2+ confocal microscopy was used to measure the Ca2+ signal (some Ca2+ dye was used) through time. Ca2+ wave spreads in one direction in the cell. contraction happens later after the rise in Ca2+. rise in intracellular Ca2+ concentration is necessary for contraction none no no no no no no no no 17 gel gel4 Full Text To characterize the degradosome of P. syringae Lz4W. Sequenced and identified P. syringae proteins and RNAse R P. syringae RNase R is in a complex with RNase E and RhlE (from heading of first Results paragraph) RNase R interacts with RNase E in P. syringae Lz4W. What does "N" (far right in diagram, above a gel image) signify? no no yes no no no no no 17 gel gel4 Image+Caption+Title+Abstract Do not know. Do not know. Do not know. Do not know. Methods, results, conclusion yes yes yes yes yes yes yes yes 17 gel gel4 Image+Caption Do not know. Do not know. Do not know. Do not know. Purpose, methods, results, conclusions yes yes yes yes yes yes yes yes 17 graph graph3 Full Text To investigate the microcirculatory adjustments associated with changes resulting from polycythemia. Polycythemia was induced in rats by exposure to either EPO or cobalt. Resulting blood pressures were measured, morphometric analyses of heart and RBC spacing in capillary bed tissues were made, and capillary hematocrit was measured. In both models, baseline left ventricular function was normal, whereas maximal systolic and developed pressures were decreased. In cobalt-treated rats the left ventricular functional reserve was also compromised. Morphometric analysis of the left ventricle confirmed previously described improved geometric conditions for oxygen supply at the distal portions of capillaries (smaller domain areas and shorter capillary segments). In cobalt-treated but not in erythropoietin-treated rats, increased capillary angiogenesis was also detected. In the hearts from rats with both types of polycythemia, a small but significant increase in the formation of arterioles was found. Capillary linear hematocrit was within the normal range in both types of polycythemia despite sizeable increases in systemic hematocrit. Significant differences in red blood cell distribution within capillaries were found between proximal and distal portions in all experimental groups. Only rats with cobalt-induced polycythemia had an increased coronary capillary and arteriolar supply. EPO-induced polycythemia results in larger increases in hematocrit, but no change in coronary microvascular bed. Hypoxic stimulus is more effective in inducing angiogenesis than mechanical stimuli. Also, capillary hematocrit was lower than systemic hematocrit in both types of polycythemia. None no no no no no no no no 17 graph graph3 Image+Caption+Title+Abstract What is the effect of polycythemia on the coronary microcirculation in young male rats, and the differences in blood pressure induced by cobalt or EPO Rats with polycythemia were exposed to cobalt or EPO and then their blood pressure was measured and a morphometric analysis of their hearts was conducted. In both models, baseline left ventricular function was normal, whereas maximal systolic and developed pressures were decreased. In cobalt-treated rats the left ventricular functional reserve was also compromised. Morphometric analysis of the left ventricle confirmed previously described improved geometric conditions for oxygen supply at the distal portions of capillaries (smaller domain areas and shorter capillary segments). In cobalt-treated but not in erythropoietin-treated rats, increased capillary angiogenesis was also detected. In the hearts from rats with both types of polycythemia, a small but significant increase in the formation of arterioles was found. Capillary linear hematocrit was within the normal range in both types of polycythemia despite sizeable increases in systemic hematocrit. Significant differences in red blood cell distribution within capillaries were found between proximal and distal portions in all experimental groups. (directly from figure caption. Do not know. none no no no yes no no no yes 17 graph graph3 Image+Caption Do not know. Rats are exposed to cobalt or erythropoietin and then their blood pressure is measured? Cobalt exposure depresses blood pressure more than erythropoietin, and both depress blood pressure in comparison to no exposure. Cobalt exposure depresses blood pressure more than erythropoietin none yes yes no no yes yes no no 17 mixed mixed4 Full Text To determine the influence of cargo size on Ran and energy requirements for nuclear protein import (from article title) Used in vitro transport reactions containing permeabilized HeLa cells to examine energy requirements for the NPC transit of small vs. large cargo in two pathways of receptor-mediated protein transport (from article) Efficient transit of small, but not large, cargo can proceed without GTP hydrolysis. Efficient in vitro transport of large proteins requires hydrolyzable GTP and the small GTPase Ran, which allow large cargo to efficiently cross central regions of the NPC. RanGTP functions in pathways to promote the transport of large cargo by enhancing the ability of import complexes to traverse diffusionally restricted areas of the NPC. What do the "glowing" vs. "dim" particles in B, D, and F indicate? no no no yes no no no no 17 mixed mixed4 Image+Caption+Title+Abstract To determine the influence of cargo size on Ran and energy requirements for nuclear protein import (from the title) Do not know. Do not know. Morphological and biochemical analysis indicates that the presence of Ran and GTP allows large cargo to efficiently cross central regions of the NPC. We further demonstrate that this function of RanGTP at least partly involves its direct binding to importin ©¬ and transportin.RanGTP functions in these pathways to promote the transport of large cargo by enhancing the ability of import complexes to traverse diffusionally restricted areas of the NPC (from caption text) Methods of study, results. no yes yes no no yes yes no 17 mixed mixed4 Image+Caption Do not know. Do not know. Do not know. Do not know. Organism studied; aim of study; methods; results; conclusions. yes yes yes yes yes yes yes yes 17 model model2 Full Text To determine if Rad1, Hus1, and Rad9 interact with Rad17 as a clamp-clamp loader pair during the DNA damage response. Too complicated for me to summarize here. It's not my field of expertise, so even reading the Methods section doesn't allow me to summarize with confidence. Rad1, Hus1, and Rad9 do interact with Rad17 as a clamp-clamp loader pair during the DNA damage response. Also, the interaction between Rad17 and hRad1 has biochemical features similar to the RFC-PCNA interaction. And, DNA damage alters the interaction of hRad17 with jHus1, hRad1, and hRad9. Rad1, Hus1, and Rad9 do interact with Rad17 as a clamp-clamp loader pair during the DNA damage response. "RFC" means what? no yes yes no no yes yes no 17 model model2 Image+Caption+Title+Abstract To determine if Rad1, Hus1, and Rad9 interact with Rad17 as a clamp-clamp loader pair during the DNA damage response (from figure caption) Do not know. Endogenous human Rad17 (hRad17) interacts with the PCNA-related checkpoint proteins hRad1, hRad9, and hHus1. Mutational analysis of hRad1 and hRad17 demonstrates that this interaction has properties similar to the interaction between RFC and PCNA, a well characterized clamp-clamp loader pair. Moreover, we show that DNA damage affects the association of hRad17 with the clamp-like checkpoint proteins (from figure caption) hRad17 interacts with the PCNA-like proteins hRad1, hHus1, and hRad9 in manner similar to the interaction between RFC and PCNA (from figure caption) Methods. What does "RFC" mean? no yes no no no yes no no 17 model model2 Image+Caption Do not know. Do not know. Do not know. Do not know. Everything: purpose, methods, results, conclusion. Also, what do all the abbreviations mean? yes yes yes yes yes yes yes yes 17 thing thing3 Full Text To investigate the self-association properties of the RAD52 protein (from article) Compared full-length RAD52 protein with two different mutant RAD52 proteins. Cultures with the different proteins were grown up; proteins extracted and purified; also DNA binding assays were conducted. Two modes of RAD52 self-association exist: ring-shaped oligomers and larger aggregates. Protrusions on rings are produced by wild-type RAD52 but not the mutant RAD52. There are two experimentally separable self-association domains in RAD52. The N-terminal self-association domain mediates the assembly of monomers into rings, and the previously unidentified domain in the C-terminal half of the protein mediates higher order self-association of the rings (from figure caption) none. no no no no no no no no 17 thing thing3 Image+Caption+Title+Abstract Do not know. Do not know. Do not know. There are two experimentally separable self-association domains in RAD52. The N-terminal self-association domain mediates the assembly of monomers into rings, and the previously unidentified domain in the C-terminal half of the protein mediates higher order self-association of the rings. (taken directly from figure caption) Purpose, methods, results yes yes yes no yes yes yes no 17 thing thing3 Image+Caption Do not know. Do not know. Do not know. Do not know. Everything -- purpose, methods, results, conclusion. yes yes yes yes yes yes yes yes 18 gel gel3 Full Text depletion of EJC protein influenced the incorporation of [35S]Met into newly synthesized proteins transfection;SAD-PAGE;Westernblot;Coomassie staining The steady-state expression level of REF1 was reduced, while the expression levels of DEK, NXF1, and UAP56 were not affected Depletion of EJC proteins reduces, but does not abolish,incorporation of [35S]Met into newly synthesized proteins;REF1 and the additional exon junction complexproteins are dispensable for nuclear mRNA export none no no no no no no no no 18 gel gel3 Image+Caption+Title+Abstract Depletion of EJC proteins influenced incorporation of [35S]Met into newly synthesized proteins transfection;SDS-PAGE ;Western blot ;Coomassie staining Through Westernblot analysis,the steady-state expression level of REF1 was reduced, while the expression levels of DEK, NXF1, and UAP56 were not affected different level depletion of EJC protein influenced nuclear mRNA export none no no no no no no no no 18 gel gel3 Image+Caption depletion of EJC proteins influnced incorporation of [35S]Met into newly synthesized proteins transfection; SDS-PAGE ;Coomassie staining;Western blot the different efficiency of the depletion of EJC affected incorporation of [35S]Met into newly synthesized proteins under different level depletion of EJC proteins reduces, but does not abolish, incorporation of [35S]Met into newly synthesized proteins what relations exist between REF1, REF2, DEK, SRm160, RNPS1, and Y14 dsRNAs no no no yes no no yes no 18 graph graph2 Full Text levels changes of M1/M3 and M2/M4 mCHR after rat pups exposed to different doses chlorpyrifos through different poatnatal days. receptor binding; westernblot; SNK;Enzyme Assays;Hemicholinium-3 and AH5183 Binding;Protein Determinations M1/M3 mAChR levels decreased in low and high doses group,and increased with postnatal time prolonged.M2/M4 mAChR levels slightly increased in different timepoints but no significant difference. chlorpyrifos play an very important role in regulate the binding of M1/M3 and M2/M4 mAChR. none no no no no no no no no 18 graph graph2 Image+Caption+Title+Abstract Levels changes of M1/M3 and M2/M4 mAChR after rap pups exposed to different doses chlorpyrifos through different days. receptor binding; Westernblot;SNK M1/M3 mAChR levels decreased in low and high doses group,and increased with postnatal time prolonged.M2/M4 mAChR levels slightly increased in different timepoints but no significant difference. chlorpyrifos influenced the levels of M1/M3 and M2/M4 mAChR none no no no no no no no no 18 graph graph2 Image+Caption Levels of M1/M3 and M2/M4 mAChR after rat pups exposed to different doses of chlorpyrifos through different poatnatal day SNK;Receptor Binding;Westernblot M1/M3 mAChR levels decreased in low and high doses group,and increased with postnatal time prolonged.M2/M4 mAChR levels slightly increased in different timepoints but no significant difference. chlorpyrifos influenced M1/M3 and M2/M4 binding. westernblot analysis of M1/M3 and M2/M4 expression no no yes no no no no no 18 mixed mixed3 Full Text use the Ucp3 knockout mice model to study the effect of Ucp3 disfficiecy Southernblot,Northernblot, westernblot,geneknockout Ucp3 knockout mice model was generated successfully Ucp3 knockout mice model was setup and applied to study the influence of the Ucp3 disfficiency none no no no no no no no no 18 mixed mixed3 Image+Caption+Title+Abstract Ucp3 knockout mouse procedure Southern blot,Northern analysis,Western analysis;gene knock out generate Ucp3 knockout mouse generate Ucp3 knockout mouse and could be use to study the influnce of Ucp3 knockout mouse to skeletal muscle none no no no no no no no no 18 mixed mixed3 Image+Caption procedure of generation of Ucp3 ( / ) mice Southern analysis;Northern analysis;westblot;gene knochout Ucp3-/-mice genotypes showed decreased,and produced Ucp3-/- mice Ucp3-/-mice can be generated successfully. what the author wang to do using Ucp3-/- mice? no no no yes yes no no no 18 model model4 Full Text Structural elements important to allosteric regulationin the R-state of FBPase TransformerTM site-directed mutagenesis kit;Expression and Purification of gene;Circular Dichroism (CD) Spectroscopy;Steady-state Fluorescence Measurements;Kinetic Experiments Residues 1–10 of porcine fructose-1,6-bisphosphatase(FBPase) are poorly ordered or are in different conformations,sensitive to the state of ligation of the enzyme.Deletion of the first 10 residues of FBPase reduces kcatby 30-fold and Mg21 affinity by 20-fold and eliminatescooperativity in Mg21 activation;Deletionof the first seven residues reduces kcat and Mg21 affinitysignificantly but has no effect on AMP inhibition different residues play very important role to allosteric regulation in the R-state of FBPase none no no no no no no no no 18 model model4 Image+Caption+Title+Abstract Structural elements important to allosteric regulation in the R-state of FBPase Recombinant array;allosteric array;deletion mutant different Structural elements important to allosteric regulation in the R-state of FBPase different Structural elements was very important to allosteric regulation in the R-state of FBPase,especially residues 1-10 how did different residues affect the allosteric regulation in the R-state of FBPase? no no no yes no no yes yes 18 model model4 Image+Caption Structural elements important to allosteric regulation in the R-state of FBPase Do not know different structure elments locations in R-state of FBPase different structural elements important to allosteric regulation in the R-state of FBPase why and how structural elements influenced the allosteric regulation in the R-state of FBPase? no yes no yes no yes yes yes 18 thing thing1 Full Text C2C12 cell differentiation and localization of MyoD and Id1 in myoblasts and myotubes phase contrast microscopic images ;double staining ;immunofluorescent staining ;confocal laser scanning microscopy C2C12 cells had different morphometry during different timepoit and verified by double-staining and immunofluorescent staining and confocal laser scanning microscopy C2C12 cells had different morphometry and localization of MyoD and Id1 in myoblasts and myotubes none no no no no no no no no 18 thing thing1 Image+Caption+Title+Abstract C2C12 cell differentiation and localization of MyoD and Id1 in myoblasts and myotubes phase contrast microscopic images ;double staining ;immunofluorescent staining ;confocal laser scanning microscopy C2C12 cells had different morphometry during different timepoit and verified by double-staining and immunofluorescent staining and confocal laser scanning microscopy C2C12 cells had different morphometry during differentiation and localization of MyoD and Id1 in myoblasts and myotubes none no no no no no no no no 18 thing thing1 Image+Caption C2C12 cell differentiation and localization of MyoD and Id1 in myoblasts and myotubes phase contrast microscopic images ;double staining immunofluorescent staining ; confocal laser scanning microscopy C2C12 cells had different morphometry during different timepoit and verified by double-staining and immunofluorescent staining and confocal laser scanning microscopy C2C12 cell had different morphometry during differentiation and localization of MyoD and Id1 in myoblasts and myotubes MyoD and Id1 in details no no yes yes yes no no yes 19 gel gel1 Full Text Investigation into the differential expression of PECAM1 isoforms / isotypes in both human and murine models. Cell line work / RT-PCT / Western blotting / Electrophoresis with ethidium bromide staining. Again very confusing to read - the results do not flow nicely. Do not know None no no yes yes no no yes yes 19 gel gel1 Image+Caption+Title+Abstract Investigating the expression of PECAM-1 in endothelial / haematopoetic cells in human and murine systems. RT-PCR + electrophoresis From the gel produced, the expression seems to be similar across all samples analysed. However, the intro states that alternate expression is noted in murine systems. Do not know Do not know no no yes yes no no yes yes 19 gel gel1 Image+Caption Some assessment of a particular protein / produce Real time PCR / SDS page electrophoresis All the tissues prepared contained a similar amount of protuct measured Do not know Short introduction into the perpose of the study yes no no yes yes no yes yes 19 graph graph1 Full Text To assess the mechanisms by which CPT-2 affects the long chain ACoA binding site. Liver samples where taken from Wistar rats and separated using gradient centrifugation. Mitochondria were isolated by step-sucrose centrifugation. Assays were performed by;Western blotting and enzyme inhibition studies. The Km for palmityl CoA was 2.4 fold higher in CPT1 located within membranes than at the enzyme contact sites. This mechanism proposes another potent action relating to the regulation of CPT12 binding (specifically to the ACoA binding site). None no no no no no no no no 19 graph graph1 Image+Caption+Title+Abstract To assess the activity of Carnitine palmitoyltransferase in rat liver mitochondria at both enriched membrane sites and enriched contact sites. The study also aims to assess the ability of malonyl CoA to act as an inhibitor to Carnitine palmitoyltransferase . Do not know The Km was 2.4 fold higher in Carnitine palmitoyltransferase (CPT1) located within outer membrane regions when compared to CPT1 located at contact sites. In membrane sites, malonyl CoA acted as a competitive inhibitor whilst at enzyme contact sites, malonyl CoA acted non-competitively. do not know Samples not indicated on the graph - required a legend. no yes yes yes no yes yes yes 19 graph graph1 Image+Caption Do not know Does not state but would presume that it is a RIA or spectrophotometric assay. Not possible to interpret as the two samples are not marked on the graph in a legend. The sample designated by a diamond shape is more active at the higher concentrations of Malonyl-CoA Legend required to explain which sample is which on the graph. Difficult to understand in isolation as the use of abreviations is not explained. Use of non-S.i units is confusing. yes yes yes yes yes yes yes yes 19 mixed mixed1 Full Text The involvment of Parkin protein mutations on juvenile parkinism Cell culture / WB / Cell viability assays / enxyme activity assays. Over expression of the protein did not affect the viability of the cell lines tested.Transinfection of cell lines with the mutant protein form increased enzyme activity 2.4 fold Do not know None no no no yes no no no yes 19 mixed mixed1 Image+Caption+Title+Abstract Study into the effects of + type and mutant Parkin proteins on antioxidant defences / oxidtive damage and NO Western Blotting / enzyme activity studies / cell culture Do not know Do not know Intro / Legent to be placed next to each individual figure no no yes yes no no yes yes 19 mixed mixed1 Image+Caption Investigation into the turnover of parkin (mutant and * type) in various cell lines Do not know Do not know Do not know Explanation of abriviations although this may be fine when in context with the whole paper no yes yes yes no yes yes yes 19 model model3 Full Text Investigation in to the involvment of double cortin gene defects / mutations in the incidence of SCLH - an X-linked disorder PCR analysis of patient samples - although the exact source is not noted I found these very difficult to follow - I would not be confident in stating any results. Do not know (due to confusing layout) The paper seemed to be in a non standard format - i.e. not flowing as Intro, M and M , Results, Discussion. As such it did not seem to build on previous concepts nor lead the reader through a jounrney of research no yes yes yes no yes yes yes 19 model model3 Image+Caption+Title+Abstract To investigate the association of doublecortin gene mutations with the incidence of SCLH/LIS. Not stated although would presume SNP analysis / RtPCR Mutations in the double cortin gene were noted in 10 out of 11 cases of SCLH/LIS. Does not state whether the one case that did not exibit mutation of the double cortin gene was that of the familial case - in which case another heritable mutation may have been involved. Nothing - this is very well presented no yes no yes no yes no yes 19 model model3 Image+Caption Simple presentation of the doublecortin gene. The diagram also shows the location of any known mutations within the marked exons. Do not know Simply presents the location of the mutations none None - if taken in context with the whole paper. If taken in isolation, a small introductary paragraph would be welcome yes yes yes yes no yes yes yes 19 thing thing2 Full Text To investigate whether and / or how GLU geneexpression is regulated in a cell type-specific manner. Plasmid preparation / Cell culture / Western Blotting / Immuno staining / Northern Blotting / RIA GLU mRNA expression can be regulated differentlyin proglucagon producing cell lines of the gut compared with those of pancreas. GLU enhancement region was upregulated by lithium treatment in the intestinal cell line only - not in the pancreatic cell line. TCF factorsthus may play a role in the diversity of the Wnt pathway thus explaining the tissue specific / differential expression of the GLU gene product None no no no no no no no no 19 thing thing2 Image+Caption+Title+Abstract To investigate the methods by which GLU is expressed within different cell types. Immunohistochemistry / confocal microscopy glycogen synthase kinase-3 inhibitor lithium does not activate glu expression in pancreatic cell lines. In the intestinal GLUTag cell line, but not in the pancreatic InR1-G9 cell line, the GLU promoter G2 enhancer-element was activated by lithium treatment. Do not know None no no no yes no no no yes 19 thing thing2 Image+Caption Demonstration of TCF-4 expression in various cell / tissue types Immunohistochemistry on both cell lines and paraffin embedded murine tissue, Do not know Do no know None - just needs to be taken in context with the rest of the paper yes yes yes yes no no yes yes 1 gel gel4 Full Text To characterize the degradosome of the psychrotrophic bacterium Pseudomonas syringae Lz4W 1. Bacterial culture2. Protein fractionation3.Protein sequencing and identification4.Purification of recombinant protein5.Expression of His-tagged RNase and RNase Rin P.syringae6.Analysis of interacting proteins by Ni-NTA Resin7.Western Blotting8.Co-immunoprecipitation experiments9.In vitro transcription of RNAs and enzyme assays10. Polyadenylation of RNA for degradation assay11. Thin layer chromatography 1. The hydrolytic exoribonuclease RNase R was found to co-purify with RNase E.2.Co-immunoprecipitation and Ni2+-affinity pull-down experiments confirmed the specific interaction between RNase R and RNase E. 3.Additionally, the DEAD-box helicase RhlE was identified as part of this protein complex. Fractions comprising the three proteins showed RNase E and RNase R activity and efficiently degraded a synthetic stem-loop containing RNA in the presence of ATP. 4.The unexpected association of RNase R with RNase E and RhlE in an RNA-degrading complex indicates that the cold-adapted P. syringae has a degradosome of novel structure. 1.The identification of RNase R instead of polynucleotide phosphorylase in this complex underlines the importance of the interaction between endo- and exoribonucleases for the bacterial RNA metabolism. 2.The physical association of RNase E with an exoribonuclease and an RNA helicase apparently is a common theme in the composition of bacterial RNA-degrading complexes. None no no no no no no no no 1 gel gel4 Image+Caption+Title+Abstract To characterize the degradosome of the psychrotrophic bacterium Pseudomonas syringae Lz4W 1.SDS-PAGE 2.Western blot 3.silver staining 1. The hydrolytic exoribonuclease RNase R was found to co-purify with RNase E.2.Co-immunoprecipitation and Ni2+-affinity pull-down experiments confirmed the specific interaction between RNase R and RNase E. 3.Additionally, the DEAD-box helicase RhlE was identified as part of this protein complex. Fractions comprising the three proteins showed RNase E and RNase R activity and efficiently degraded a synthetic stem-loop containing RNA in the presence of ATP. 4.The unexpected association of RNase R with RNase E and RhlE in an RNA-degrading complex indicates that the cold-adapted P. syringae has a degradosome of novel structure. 1.The identification of RNase R instead of polynucleotide phosphorylase in this complex underlines the importance of the interaction between endo- and exoribonucleases for the bacterial RNA metabolism. 2.The physical association of RNase E with an exoribonuclease and an RNA helicase apparently is a common theme in the composition of bacterial RNA-degrading complexes. None no no no no no no no no 1 gel gel4 Image+Caption Do not know. 1.SDS-PAGE 2.Western blot 3.silver staining Do not know. Do not know. None yes no yes yes yes no yes yes 1 graph graph1 Full Text To measure the kinetic parameters of CPT I present in rat liver submitochondrial membrane fractions enriched in either outer membrane or contact sites. 1.Preparation of subfractionation of mitochondria2.Marker protein determination3. Assay of activity and immunodetection The Km for palmitoyl-CoA was 2.4-fold higher for CPT I in outer membranes than that for the enzyme in contact sites. In addition, whereas in contact sites malonyl-CoA behaved as a competitive inhibitor of CPT I with respect to palmitoyl-CoA, in outer membranes malonyl-CoA inhibition was non-competitive. As a result of the combination of these changes, the IC50 for malonyl-CoA was severalfold higher for CPT I in contact sites than for the enzyme in bulk outer membrane. The Ki for malonyl-CoA, the Km for carnitine, and the catalytic constant of the enzyme were all unaffected. It is concluded that the different membrane environments in outer membranes and contact sites result in an altered conformation of L-CPT I that specifically affects the long-chain acyl-CoA binding site. The accompanying changes in the kinetics of the enzyme provide an additional potent mechanism for the regulation of L-CPT I activity None no no no no no no no no 1 graph graph1 Image+Caption+Title+Abstract To measure the kinetic parameters of CPT I present in rat liver submitochondrial membrane fractions enriched in either outer membrane or contact sites. kinetics The Km for palmitoyl-CoA was 2.4-fold higher for CPT I in outer membranes than that for the enzyme in contact sites. In addition, whereas in contact sites malonyl-CoA behaved as a competitive inhibitor of CPT I with respect to palmitoyl-CoA, in outer membranes malonyl-CoA inhibition was non-competitive. As a result of the combination of these changes, the IC50 for malonyl-CoA was severalfold higher for CPT I in contact sites than for the enzyme in bulk outer membrane. The Ki for malonyl-CoA, the Km for carnitine, and the catalytic constant of the enzyme were all unaffected. It is concluded that the different membrane environments in outer membranes and contact sites result in an altered conformation of L-CPT I that specifically affects the long-chain acyl-CoA binding site. The accompanying changes in the kinetics of the enzyme provide an additional potent mechanism for the regulation of L-CPT I activity None no no no no no no no no 1 graph graph1 Image+Caption Do not know Do not know Do not know Do not know None yes yes yes yes yes yes yes yes 1 mixed mixed4 Full Text To demonstrate that in the importin /©¬ and transportin import pathways, efficient in vitro transport of large proteins, in contrast to smaller proteins, requires hydrolyzable GTP and the small GTPase Ran. 1.Subcloning2.Protein purification3.Stokes radius analysis4.Nuclear import assay5. Corecipitation assay6.GAP assay7.Electron microscopy 1.The presence of Ran and GTP allows large cargo to efficiently cross central regions of the NPC. 2.The function of RanGTP at least partly involves its direct binding to importin ©¬ and transportin. We suggest that RanGTP functions in these pathways to promote the transport of large cargo by enhancing the ability of import complexes to traverse diffusionally restricted areas of the NPC. None no no no no no no no no 1 mixed mixed4 Image+Caption+Title+Abstract To demonstrate that in the importin /©¬ and transportin import pathways, efficient in vitro transport of large proteins, in contrast to smaller proteins, requires hydrolyzable GTP and the small GTPase Ran. Confocal images Biochemical analysis 1.The presence of Ran and GTP allows large cargo to efficiently cross central regions of the NPC. 2.The function of RanGTP at least partly involves its direct binding to importin ©¬ and transportin. We suggest that RanGTP functions in these pathways to promote the transport of large cargo by enhancing the ability of import complexes to traverse diffusionally restricted areas of the NPC. None no no no no no no no no 1 mixed mixed4 Image+Caption Do not know. Confocal images Import of large, but not small, cargo requires hydrolyzable GTP. Do not know. None yes no no yes yes no no yes 1 model model3 Full Text To identify alternative splicing and mutations in doublecortin gene coden region between between normal and in 11 unrelated females with SCLH. GenotypingRT-PCR ( RT-real time PCR )Gel extractionTA CloningDNA extractionSequencingGeneBank databaseDatabase for alternative splicing and mRNA sequenceMutation analysis :DGGEMRI, CTPSORT There are 2 of alternative splicing in doublecortin gene , 5 of nonsense and splice site mutations and 7 of missense mutations. Doublecortin gene has 2 of alternative splicing and 7 of missense mutations which may cause changing of protein structure and inactive protein function in 11 unrelated females with SCLH comparing with normal individuals.These results provide strong evidence that loss of function of doublecortin is the major cause of SCLH. The absence of phenotype-genotype correlations suggests that X-inactivation patterns of neuronal precursor cells are likely to contribute to the variable clinical severity of this disorder in females. RNA and protein expression level to look at inactived overecpression. no no yes no no no no no 1 model model3 Image+Caption+Title+Abstract To identify alternative splicing and mutations in doublecortin gene coden region between between normal and in 11 unrelated females with SCLH. GenotypingRT-PCR ( RT-real time PCR )Gel extractionTA CloningDNA extractionSequencingGeneBank databaseDatabase for alternative splicing and mRNA sequence There are 2 of alternative splicing in doublecortin gene , 5 of nonsense and splice site mutations and 7 of missense mutations. Doublecortin gene has 2 of alternative splicing and 7 of missense mutations which may cause changing of protein structure and inactive protein function in 11 unrelated females with SCLH comparing with normal individuals.These results provide strong evidence that loss of function of doublecortin is the major cause of SCLH. The absence of phenotype-genotype correlations suggests that X-inactivation patterns of neuronal precursor cells are likely to contribute to the variable clinical severity of this disorder in females. RNA and protein expression level to look at inactived overecpression. no no yes no no no yes no 1 model model3 Image+Caption To identify alternative splicing and mutations in doublecortin gene coden region between 2 stains of animal models or between normal and certain disease patients. GenotypingRT-PCR ( RT-real time PCR )Gel extractionTA CloningDNA extractionSequencingGeneBank databaseDatabase for alternative splicing and mRNA sequence There are 2 of alternative splicing in doublecortin gene , 5 of nonsense and splice site mutations and 7 of missense mutations. Doublecortin gene has 2 of alternative splicing and 7 of missense mutations which may cause changing of protein structure and inactive protein function in animals model or patient with certain disease. RNA and protein expression level. no no yes no no no no no 1 thing thing4 Full Text The aim of this study was to determine whether calcitonin gene-related peptide (CGRP), a neuropeptide also found in sensory afferent neurons, participates in the enterotoxic effects of toxin A. 1.Measurement of mannitol permeability and fluid secretion in rat ileal loops.2.Histological evaluation3. Measurement of CGRP content in ileal mucosa and dorsal root ganglia.4. Immunohistochemistry5. Statistical analysis 1.Buffer-treated ileal loop showing normal mucosa.2.Ileal loop exposed to toxin A showing disruption of villus architecture, goblet cell discharge, and tissue necrosis. 3.Ileal loop pretreated with CGRP-(8 37) before challenge with toxin A, showing almost complete prevention of the intestinal effects of toxin A.4.Administration of toxin A was also found to increase CGRP content in dorsal root ganglia and ileal mucosa 60 min after toxin exposure. 5.Furthermore, immunohistochemical studies demonstrated increased neuronal staining for CGRP 2 h after toxin A treatment. Pretreatment of rats with CGRP-(8 37), a specific CGRP antagonist, before instillation of toxin A into ileal loops significantly inhibited toxin-mediated fluid secretion (by 48%), mannitol permeability (by 83%), and histological damage. We conclude that CGRP, like substance P, contributes to the secretory and inflammatory effects of toxin A via increased production of this peptide from intestinal nerves, including primary sensory afferent neurons. None no no no no no no no no 1 thing thing4 Image+Caption+Title+Abstract The aim of this study was to determine whether calcitonin gene-related peptide (CGRP), a neuropeptide also found in sensory afferent neurons, participates in the enterotoxic effects of toxin A. 1.Immunohistochemistry2.Injection and surgery 1.Buffer-treated ileal loop showing normal mucosa.2.Ileal loop exposed to toxin A showing disruption of villus architecture, goblet cell discharge, and tissue necrosis. 3.Ileal loop pretreated with CGRP-(8 37) before challenge with toxin A, showing almost complete prevention of the intestinal effects of toxin A.4.Administration of toxin A was also found to increase CGRP content in dorsal root ganglia and ileal mucosa 60 min after toxin exposure. 5.Furthermore, immunohistochemical studies demonstrated increased neuronal staining for CGRP 2 h after toxin A treatment. Pretreatment of rats with CGRP-(8 37), a specific CGRP antagonist, before instillation of toxin A into ileal loops significantly inhibited toxin-mediated fluid secretion (by 48%), mannitol permeability (by 83%), and histological damage. We conclude that CGRP, like substance P, contributes to the secretory and inflammatory effects of toxin A via increased production of this peptide from intestinal nerves, including primary sensory afferent neurons. None no no no no no no no no 1 thing thing4 Image+Caption To study the inhibition of toxin A-induced enteritis by CGRP-(8 37). 1. Injection2. H&E staining 1.Buffer-treated ileal loop showing normal mucosa.2.Ileal loop exposed to toxin A showing disruption of villus architecture, goblet cell discharge, and tissue necrosis. 3.Ileal loop pretreated with CGRP-(8 37) before challenge with toxin A, showing almost complete prevention of the intestinal effects of toxin A. CGRP-(8 37)can inhibate toxin A-induced enteritis . None no no no no no no no no 2 gel gel3 Full Text To study an essential role for metazoan REF1 orthe additional EJC proteins in the export of spliced mRNA. Cloning of Drosophila cDNAs;double-stranded RNA interference(dsRNAi);RNA isolation and Northern blots; Preparation of total cell extracts and Western blotting; FISH and indirect immunofluorescence. Drosophila cells depleted of EJC proteins display diversegrowth phenotypes.Depletion of REF1 or of individual EJC proteins leads to different effects on cell proliferation. REF1 is not essential for nuclear export of bulk mRNA. Simultaneous depletion of REF1 and RNPS1 partially inhibits protein synthesis. Codepletion of EJC proteins leads to a partial nuclear accumulation of poly(A)+ RNA. The recruitment of NXF1:p15 heterodimers by cellular mRNAs is mediated by additional adaptor protein(s) in higher eukaryotes.The essential role of UAP56 in mRNA export is not restricted to the recruitment of REF1. none no no no no no no no no 2 gel gel3 Image+Caption+Title+Abstract To study an essential role for metazoan REF1 or the additional EJC proteins in the export of spliced mRNA. Transfection;SDS-PAGE;Coomassie blue stain and fluorography;Western blotting. REF1 and the additional components of the EJC are dispensable for export of bulk mRNA in Drosophila cells. Only when REF1 and RNPS1 are codepleted, or when all EJC proteins are simultaneously depleted is a partial nuclear accumulation of polyadenylated RNAs observed. Additional adaptor protein(s) mediate the interaction between NXF1 and cellular mRNAs in metazoa.The essential role of UAP56 in mRNA export is not restricted to the recruitment of REF1. none no no no no no no no no 2 gel gel3 Image+Caption Do not know Transfection; SDS-PAGE; Coomassie blue stain and fluorography;Western blotting Depletion of EJC proteins reduces, but does not abolish, incorporation of [35S]Met into newly synthesized proteins. At 37şC the heat-shock proteins (HSPs) are induced, whereas translation of nonheat shock proteins is inhibited. The steady-state expression level of REF1 was reduced, while the expression levels of DEK, NXF1, and UAP56 were not affected. Do not know. Explain the abbreviations and give more background. yes no no yes yes no yes yes 2 graph graph2 Full Text To study the neurochemical effects in developing rats exposed during gestation to the anticholinesterase organophosphorus insecticide chlorpyrifos (CPS). Enzyme assays; Muscarinic receptor binding with 3H-4-DAMP or 3H-AF-DX 384; Hemicholinium-3 and AH5183 binding; Protein determinations by the bicinchoninic acid method. ChE activities were inhibited about 15 and 30% on PND 1, in the low- and high-dosage groups, respectively, and were not different from control values by PND 6. mAChR densities on PND 1 were reduced in the high-dosage group byabout 18, 21, and 17%, using 3H-N-methylscopolamine, 3H-quinuclidinyl benzilate, and 3H-4-DAMP, respectively, as ligands, and were not different from control levels by PND 6. ChAT activity was decreased by ~12% in the high-dosage group on PND 9, 12, and 30. HACU levels, using 3H-hemicholinium-3 as the ligand, were reduced by ~25% on PND 6 in the low- and high-dosage groups, and by a14 and 21% on PND 12 and 30, only in the high-dosage group. Levels of the VAChT were reduced by a range of 13–31% on PND 3 through 30 in the high-dosage group, using 3H-AH5183 (vesamicol) as the ligand. Gestational exposure to 7 mg/kg/day CPS results in long-term alterations of presynaptic cholinergic neurochemistry. none no no no no no no no no 2 graph graph2 Image+Caption+Title+Abstract To study the neurochemical effects in developing rats exposed during gestation to the anticholinesterase organophosphorus insecticide chlorpyrifos (CPS). Enzyme activity assays;Receptor binding assays;3H-N-methylscopolamine, 3H-quinuclidinyl benzilate, and 3H-4-DAMP. ChE activities were inhibited about 15 and 30% on PND 1, in the low- and high-dosage groups, respectively, and were not different from control values by PND 6. mAChR densities on PND 1 were reduced in the high-dosage group by about 18, 21, and 17%, using 3H-N-methylscopolamine, 3H-quinuclidinyl benzilate, and 3H-4-DAMP, respectively, as ligands, and were not different from control levels by PND 6. ChAT activity was decreased by ~12% in the high-dosage group on PND 9, 12, and 30. HACU levels, using 3H-hemicholinium-3 as the ligand, were reduced by ~25% on PND 6 in the low- and high-dosage groups, and by ~14 and 21% on PND 12 and 30, only in the high-dosage group. Levels of the VAChT were reduced by a range of 13~31% on PND 3 through 30 in the high-dosage group. Gestational exposure to 7 mg/kg/day CPS results in long-term alterations of presynaptic cholinergic neurochemistry. none no no no no no no no no 2 graph graph2 Image+Caption To study M1/M3 and M2/M4 mAChR binding of rat pups exposed to 0 (control), 3 (low), or 7 (high) mg/kg/day chlorpyrifos from gestation days 6 through 20. 3H-4-DAMP and 3H-AF-DX 384 binding M1/M3 mAChR levels were decreased on postnatal day 1 and returned to control values on postnatal day 3 in low dosage groups.Levels in the high dosage group were decreased on postnatal day 1 and 3 and returned to control values by postnatal day 6. M2/M4 mAChR levels were not significantly different from control at any time points studied. M1/M3 levels were changed only on the early time points of postnatal days. M2/M4 receptor levels were not altered at any time points studied. M1/M3 mAChR are sensitive to chlorpyrifos exposure. study one more longer time point of postnatal day such as 9 to make sure levels return. no no yes no no no no no 2 mixed mixed2 Full Text To examine the mechanism of Gly-Ala repeat (GAr) inhibits proteasome processing by embedding a GAr withinornithine decarboxylase, a natural proteasome substratethat does not require ubiquitin conjugation. Plasmid construction and protein purification;PCR;SDS-PAGE;Metabolic labeling, immunoprecipitation, and immunoblotting. GAr inhibits proteolysis by purified components.Neither proteasome interaction nor catalytic function are impaired by the GAr.GAr insert causes partial proteolysis.Partial proteolysis stops short of the GAr.A GAr also leads to partial proteolysis of destabilized GFP. The ATP motor of the proteasome slips when it encounters the GAr, impeding further insertion and, in this way, halting degradation. none no no no no no no no no 2 mixed mixed2 Image+Caption+Title+Abstract To study the mechanism of GAr inhibits proteasome processing by embedding a GAr within ornithine decarboxylase, a natural proteasome substrate that does not require ubiquitin conjugation. Plasmid Construction;mutation;embed;Immunoprecipitation(IP); Immunoblotting(SDS-7.5% PAGE);pulse-chase analysis. Inhibition in a purified system, excluding involvement of ubiquitin conjugation or of proteins extraneous to substrate and proteasome.GAr acts as a stop-transfer signal in proteasome substrate processing, resulting in vivo in partial proteolysis that halts just short of the GAr.Introducing a GAr into green fluorescent proteindestabilized by the ornithine decarboxylase degradationdomain also stops the progress of proteolysis, leadingto the accumulation of partial degradation products. The ATP motor of the proteasome slips when it encounters the GAr, impeding further insertion and, in this way, halting degradation. none no no no no no no no no 2 mixed mixed2 Image+Caption To study the effect of GAr on ODC degradation. Immunoprecipitation(IP);SDS-7.5% PAGE;Pulse-chase analysis. ODC::GAr and ODC::GAr7 have the same degradation rate as ODC. C441A mutation in ODC::GAr can stabilize the protein and prevent degradation.Proteasome inhibitor MG132 prevented ODC degradation. Do not know. Explain the meaning of ODC::GAr,ODC::GAr7 and ODCC441A::GAr no no no yes no no yes yes 2 model model2 Full Text To study the interaction of hRad17,homologous with replication factor C (RFC) subunits, and PCNA-like Proteins hRad1, hHus1, and hRad9. Cell culture; Transfections; Plasmid Construction and Mutagenesis; Coimmunoprecipitation; Cell Fractionation Studies hRad17 interacts with hRad1, hHus1, and hRad9.The nucleotide-binding region of hRad17 is required forinteraction with hRad1, hHus1, and hRad9.Mutant hRad1 associates with hRad9 and hHus1 but cannot bind hRad17.hRad17 does not interact with hRad9-hHus1-hRad1 complex that associates with DNA after DNA damage. This paper provides the first experimental evidence that hRad17 interacts with the PCNA-like proteins hRad1, hHus1, and hRad9 in manner similar to the interaction between RFC and PCNA. none no no no no no no no no 2 model model2 Image+Caption+Title+Abstract To study the interaction of hRad17,homologous with replication factor C (RFC) subunits, and PCNA-like Proteins hRad1, hHus1, and hRad9. Mutational analysis. Ehuman Rad17 (hRad17) interacts with the PCNA-related checkpoint proteins hRad1, hRad9, and hHus1.This interaction has properties similar to the interaction between RFC and PCNA, a well characterized clamp-clamp loader pair. DNA damage affects the association of hRad17 with the clamp-like checkpoint proteins. hRad17 interacts with the PCNA-like proteins hRad1, hHus1, and hRad9 in manner similar to the interaction between RFC and PCNA. Show PCNA and clamp-clamp loader pair in the sketch map. no no yes no no no no no 2 model model2 Image+Caption To show the interaction of hRad1, hHus1, hRad9, and hRad17 during a DNA damage response. sketch map hRad17 interacts with hRad1, hHus1, and hRad9 forming a clamp-like complex. hRad17, as part of an RFC-containing clamp, recognizes DNA damage and loads an hRad1-containing clamp onto the DNA. none no no no no no yes no no 2 thing thing2 Full Text To study the molecular mechanism that specifically regulates glu gene expression in a cell type-specific manner. Plasmids;Cell culture, cell transfection, and LUC reporter gene analysis;Western blotting and immuno-histochemical staining;Northern blotting analysis and RT-PCR; Radioimmunoassay for GLP-1;Chromatin immunoprecipitation (ChIP). Lithium treatment does not activate glu mRNA expressionin pancreatic islet cell lines.A TCF binding motif within the G2 enhancer element mediates the cell type-specific activation.TCF-4 binds to glu promoter and is expressed in gut but not in pancreatic endocrine cells. Dominant-negative TCF-4 represses basal glu mRNA expressionand disrupts the activation mediated by lithium inGLUTag cells. The paper identified a unique mechanism that regulates glu expression in gut endocrine cells only. Tissue-specific expression of TCF factors thus may play a role in the diversity of the Wnt pathway. none yes yes yes yes no no no no 2 thing thing2 Image+Caption+Title+Abstract To study whether and how glu gene expression is regulated in a cell type-specific manner. Cell Culture;Chromatin immunoprecipitation; Immunohistochemical Staining;Immunofluoresence. â-catenin and the glycogen synthase kinase-3â inhibitorlithium do not activate glu mRNA or glu promoter expressionin pancreatic cell lines. In the intestinal GLUTag cell line, but not in the pancreatic InR1-G9 cell line, the glu promoter G2 enhancer-element was activated by lithium treatment via a TCF-binding motif. TCF-4 is abundantly expressed in the gut but not in pancreatic islets. Both TCF-4 and â-catenin bind to the glu gene promoter.Stable introduction of dominant-negative TCF-4 into the GLUTag cell line repressed basal glu mRNA expression and abolishedthe effect of lithium on glu mRNA expression and GLP-1 synthesis. The paper identified a unique mechanism that regulates glu expression in gut endocrine cells only. Tissue-specific expression of TCF factors thus may play a role in the diversity of the Wnt pathway. none no no no no no no no no 2 thing thing2 Image+Caption To detection of TCF-4 expression in cultivated cell lines and in paraffin-embedded pancreatic and intestine tissue samples. Immunofluorescene and immunohistology. TCF-4 is expressed a lot in the GLUTag and STC-1 cell lines but not in the á-TC-1 and InR1-G9 cell lines.TCF-4 is expressed in the gut but not in pancreatic islets. The InR1-G9 cells only express GLP-1 but not TCF-4. TCF-4 and GLP-1 was co-expressed in the GLUTag cell line. Do not know. Put some arrows for histology. no no yes yes no no no yes 3 graph graph3 Full Text The effect of induced polycythemia on the coronary microcirculation in rats. 2 experimental models of induced polycytemia were used: - Co induced: injection with CoCl2- EPO induced: injection with humen recombinant EPO- control group: injection with saline solutionBlood pressure was measured in left ventricule with 1kHz frequency and the various parameters were derived using a computer program. Left ventricular pressure in both types of experimental polycythemia did not differ much from those in control animals.There was a small decreases in systolic pressure and developed pressure in both models under study. In the case of cobalt-induced polycythemia,a decrease in reserve was also observed. Maximal rates of pressure developmentwere similar in all three experimental groups. Both rats with cobalt and EPO-induced polycythemia had andecreased coronary pressure and rate of pressure development. Significance for the maximal rate of pressure development?? no no no yes no no yes no 3 graph graph3 Image+Caption+Title+Abstract The effect of polycythemia on the coronary microcirculation in young male rats Three rats groups were employed: 1. Control group (n=11) 2. Co treated group(n=10)3. EPO treated group (n=8)Coronary pressure and rate of pressure development were measured before and after the aortic clamp. In both models (Co and EPO treatment), maximal systolic and developed pressures were decreased. Cobalt-treated rats showed lowest pressure values for both maximal and reserve. Both Co and EPO induced polycythemia has as effect a slight reduction in coronary pressure. introduce P for all cases. no no yes no no no no no 3 graph graph3 Image+Caption Dummping effect on blood pressure Rats injection with Co and EPO In all cases (A,B,C)there is a decrease in blood pressure and maximum rate of pressure development of Co, EPO treatment with respect to control individuals: control>EPO>Co with very good significance (p) between control and rats injected with Co (p<0.01) and good correlation between control rats and rats injected with EPO (p<0.05).There is a consistent decrease in pressure after the aortic clamp in all 3 cases (A,B,C) Both Co and EPO reduce blood pressure after administration but Co proves having the strongest effect.This unveal the secondary effects dopping with Co and EPO has on blood pressure. None no no no no no no no no 3 model model4 Image+Caption+Title+Abstract Unveil the morphology of mutation in FBPase. Illustration drawn with MOLSCRIPT Mutation of some segments reduce the functionality of the enzime. Changes in the relative stability of the known conformational states can account for the phenomena above. Some aspects of the proposed model may be relevant to other forms of FBPase. do not know no no no no no no no no 3 model model4 Image+Caption Describe morphologic structure for allosteric regulation in chromosome MOLARSCRIPT for arquitecture drawing Do not know Do not know do not know no no yes yes no no yes yes 4 gel gel2 Full Text To understand why most EHEC strains do not express urease activity. Analysis the nucleotide sequence of the entire urease gene cluster derived from a urease-activity-positive EHEC strain and compared in whit that of the urease-activity negative EHEC O157:H7 strain RIMD0509952. Using mutliple methods including genetic manipulations, nucleotide sequence analysis etc. O157 Sakai express no urease activity in vitro. The ureD gene of O157 Sakai has a premature stop codon. ureD gene is transcribed in O157 Sakai irrespective of the lack of urease activity. These results suggest that the lack of urease activity in most EHEC strains is due to a premature stop codon in ureD. none no no no no no no no no 4 gel gel2 Image+Caption+Title+Abstract To check if the urease activity of E.Coli depends on a specific one-base substitution in ureD. Do not know This study compared the nucleotide sequences of the urease gene clusters of a urease-activity-positive and a urease-activity-negative strain. The results showed that in the urease-activity-negative strain, ureD, a gene encoding a chaperone protein, had a single base substitution that encoded a premature stop codon resulting in a short ORF. The premature stop codon in ureD was commonly found in urease-activity-negative EHEC strains, but not in urease-activity-positive strains. Urease activity was detected after complementing the urease-activity-negative strain with ureD from the urease-activity-positive strain. Furthermore, introduction of the urease gene cluster from the urease-activity-negative strain into an amber suppressor phenotype Escherichia coli strain, DH5 , conferred the ability to produce the active urease. These results suggest that the lack of urease activity in most EHEC strains is due to a premature stop codon in ureD. none no yes no no no yes no no 4 gel gel2 Image+Caption do not know Do not know Do not know Do not know none yes yes yes yes yes yes yes yes 4 graph graph4 Full Text To examinePolyol accumulation and metabolism in Aspergillus oryzae cultured on whole wheat grains or on wheat dough as a model for solid-state culture Preparation of cell extracts, enzyme assays and partial purification of polyol dehydrogenases. Then Product analysis after incubation of cell extracts with various sugars was performed as follows. A similar correlation was observed for erythritol and NADP+?erythritol dehydrogenase The results suggesting that NADP+-dependent glycerol and erythritol dehydrogenases are involved in biosynthesis of glycerol and erythritol, respectively, and that these enzymes are induced by osmotic stress. none no no no no no no no no 4 graph graph4 Image+Caption+Title+Abstract To examinePolyol accumulation and metabolism in Aspergillus oryzae cultured on whole wheat grains or on wheat dough as a model for solid-state culture Do no know A similar correlation was observed for erythritol and NADP+?erythritol dehydrogenase The results suggesting that NADP+-dependent glycerol and erythritol dehydrogenases are involved in biosynthesis of glycerol and erythritol, respectively, and that these enzymes are induced by osmotic stress. none no yes no no no yes no no 4 graph graph4 Image+Caption To check the differenct activity of different compound at different fraction number. Do not know Differnt compound show up similar behavior. Do not know none no yes no yes yes yes yes yes 4 mixed mixed1 Full Text Effect of Wild-type or Mutant Parkin on Oxidative Damage, Nitric Oxide, Antioxidant Defenses, and the Proteasome. They examined the effect of Parkin overexpression on cellular levels of oxidative damage, antioxidant defenses, nitric oxide production, and proteasomal enzyme activity. They choose two very differenct cell types, a hum,an neuroblastoma cell line, SK-N-MC cells, and a human teratocarcinoma cell line, NT-2 cells, with cholinergi characteristics, to examine whether the effects could be reproduced in different cell lines. They use DNA transfection and using western blotting. Increasing expression of Parkin by gene transfection in NT-2 and SK-N-MC cells led to increased proteasomal activity, decreased levels of protein carbonyls, 3-nitrotyrosine-containing proteins, and a trend to a reduction in ubiquitinated protein levels. Transfection of these cells with DNA encoding three mutant Parkins associated with autosomal recessive juvenile parkinsonism (Del 3-5, T240R, and Q311X) gave smaller increases in proteasomal activity and led to elevated levels of protein carbonyls and lipid peroxidation. Turnover of the mutant proteins was slower than that of the wild-type protein, and both could be blocked by the proteasome inhibitor, lactacystin. A rise in levels of nitrated proteins and increased levels of NO /NO was also observed in cells transfected with mutant Parkins, apparently because of increased levels of neuronal nitric-oxide synthase. We can get the detailed method from the section of the method in paper. The presence of mutant Parkin in substantia nigra in juvenile parkinsonism may increase oxidative stress and nitric oxide production, sensitizing cells to death induced by other insults. none no no no no no no no no 4 mixed mixed1 Image+Caption+Title+Abstract Effect of Wild-type or Mutant Parkin on Oxidative Damage, Nitric Oxide, Antioxidant Defenses, and the Proteasome. They examined the effect of Parkin overexpression on cellular levels of oxidative damage, antioxidant defenses, nitric oxide production, and proteasomal enzyme activity. Do not know Increasing expression of Parkin by gene transfection in NT-2 and SK-N-MC cells led to increased proteasomal activity, decreased levels of protein carbonyls, 3-nitrotyrosine-containing proteins, and a trend to a reduction in ubiquitinated protein levels. Transfection of these cells with DNA encoding three mutant Parkins associated with autosomal recessive juvenile parkinsonism (Del 3-5, T240R, and Q311X) gave smaller increases in proteasomal activity and led to elevated levels of protein carbonyls and lipid peroxidation. Turnover of the mutant proteins was slower than that of the wild-type protein, and both could be blocked by the proteasome inhibitor, lactacystin. A rise in levels of nitrated proteins and increased levels of NO /NO was also observed in cells transfected with mutant Parkins, apparently because of increased levels of neuronal nitric-oxide synthase. The presence of mutant Parkin in substantia nigra in juvenile parkinsonism may increase oxidative stress and nitric oxide production, sensitizing cells to death induced by other insults. none no yes no no no yes no no 4 mixed mixed1 Image+Caption Different mutant Parking protein expression and activity? Do not know Do not know Do not know none yes yes yes yes yes yes yes yes 4 model model1 Full Text To compare the capacity of the bisintercalating anthracycline WP631 (which displays a remarkably high DNA-binding affinity) and the monointercalating anthracycline daunomycin to inhibit transcription initiation of the adenovirus major late promoter linked to a G-less transcribed DNA template. And to explain the difference in the ability of each drug to inhibit transcription initiation were related to the competition between Sp1 and the drugs for the same binding site. Transcription in vivo, and using Gel retardation assays, then DNase I footprinting. They found that both drugs inhibited the basal RNA synthesis of an adenovius promoter in a concentration -deopendent way. However, WP631 was more efficient at inhibiting transcriotion initiation when we used a plasmid which contained an Sp1-binding site under experimental conditions in which Sp1acts as a gene activator. The two plasmids used in their experiments contained a G-less template. From a practical standpoint, their results means that they have been able to distinguish unambiguously between effects that are due to the decrease in transcriotion initiation and those due to elongation. none no no no no no no no no 4 model model1 Image+Caption+Title+Abstract To compare the capacity of the bisintercalating anthracycline WP631 (which displays a remarkably high DNA-binding affinity) and the monointercalating anthracycline daunomycin to inhibit transcription initiation of the adenovirus major late promoter linked to a G-less transcribed DNA template. And to explain the difference in the ability of each drug to inhibit transcription initiation were related to the competition between Sp1 and the drugs for the same binding site In vitro transcription assay. gel retardation and footprinting assays. Both drugs inhibit basal RNA synthesis in a concentration-dependent way, and the drug concentrations required to inhibit transcription initiation are similar. However, in this study WP631 was around 15 times more efficient at inhibiting transcription initiation when used with an adenovirus promoter containing an upstream Sp1-protein binding site under experimental conditions in which the Sp1 protein acted as a transactivator in vitro. The differences in the ability of each drug to inhibit transcription initiation were related to the competition between Sp1 and the drugs for the same binding site. Concentrations of WP631 as low as 60 nM could inhibit the Sp1-activated transcription initiation in vitro. In contrast, the concentration of daunomycin required to inhibit Sp1-activated transcription by 50% was almost the same as the concentration required to inhibit basal transcription. The efficiency of WP631 at displacing Sp1 from its putative binding site was confirmed using gel retardation and footprinting assays. Do not know none no no no yes no no no yes 4 model model1 Image+Caption Do not know. Do not know. Do not know Do not know none yes yes yes yes yes yes yes yes 4 thing thing3 Full Text Given that the formation of both ring-shaped oligomers and aggregates of these rings seem relevant to RAD52 function, they sought to investigate further the self-association properties of the RAD52 protein. Performed a series of analyses comparing full-length RAD52 with two different mutant RAD52 proteins. Using enzyme-linked immunosorbent assay and gel-shift DNA binding assays. They also used the dynamic light-sacttering analysis and Electron microscopy. In contract to previous studies, the results show that there are experimentally separable determinants for two different modes of self-association by RAD52, one in the N-terminal and on in the C-terminal portion of the protein. Their data support a model in which the selfassociationdomain within the N-terminal region of RAD52 promotes the formation of ring-shaped oligomers that are functional for DNA binding, whereas the Cterminal domain (residues 218–418) mediates higher order self-association events. Additionally, the protrusions extending from the 10-nm ring structure of wild-type RAD52, originally modeled by Stasiak et al. (21) and seen clearly in our electronmicrographs, correspond to the C-terminal region of the protein. Given the likely importance of higher order self-association to the ability of RAD52 to promote end-to-end joining of DNA breaks (20), these protrusions seem to mediate a critically important aspect of RAD52 function. Further studies of various mutant RAD52 proteins will clarify the contribution made by the different aspects of self-association toward the overall function of this important DNA repair protein. none no no no no no no no no 4 thing thing3 Image+Caption+Title+Abstract Self-association of Human RAD52 Do not know Here we show that there are in fact two experimentally separable self-association domains in RAD52. The N-terminal self-association domain mediates the assembly of monomers into rings, and the previously unidentified domain in the C-terminal half of the protein mediates higher order self-association of the rings. Do not know none no yes no yes no yes no yes 4 thing thing3 Image+Caption Do not know Do not know Do not know Do not know none yes yes yes yes yes yes yes yes 5 gel gel5 Full Text To understand the role of cell death-receptor pathway. 3 different types of mice were treated with estradiol Estradiol increased Fas and FasL genes. T-cell apoptosis was induced by estradiol. Caspase 8 inhibitor blocked estradiol induced apoptosis of thymocytes. Estradiol is possibly the factor that induces apoptosis by actifating death-receptors. none no no no no no no no no 5 gel gel5 Image+Caption+Title+Abstract The aim was to find the causes apoptosis in mice thymic cells. Mice were treated with E2. Thymi were removed RNA was extracted and converted to cDNA. Treatment with E2 caused decrease in Thymic cellularity at allo doses except at 0.1mg/kg in all groups of mice. In 2 types of mice the degree of thymic atrophy was significantly less than in the other group. Reverse transcriptase-polymerase chaine reactions resulted in increased expression of Fas and FasL after E2 treatment. Caspase8 inhibitor blocked E2 induced apoptosis. E2 induces apoptosis. It may trigger the death receptor pathway and may induce apoptosis none no no no no no no no no 5 gel gel5 Image+Caption A gene expression was altered after E2 treatment. Mice were treated with E2. Thymi were extracted. Extracted RNA was converted into cDNA by an enzyme called reverse transcriptase. cDNA was amplified. Fas has not changed, FasL has changed a little and B-actin came close to the control substrate. Do not now. none no no no yes yes no no yes 5 graph graph5 Full Text To investigate the role of oxidoreductase in fatty acid elongation Membrane bound oxidoreductases were examined for potential roles in microsomal fatty acid elongation by measure of cell density A yeast gene was identified to be required for the elongation of fatty acids in Caenorhabditis and Arabidopsis . The mutant type is limided homolog to human steroid dehydrogenase. do not know none no no no yes no no no yes 5 graph graph5 Image+Caption+Title+Abstract To investigate the role of oxidoreductases (enzyme) in microsomal fatty acid elongation. optical measuring of cell density growth The wild type cells grow faster than the mutant cells. The wild type was identified as being required for activity of both the Caenorhabditis elegans elongase and the Arabidopsis thaliana elongase.The mutant type has limited homology to human steroid dehydrogenases. A disruption of the wild type is not lethal, the mutant type growths slower than the wild type. none no no no no no no no no 5 graph graph5 Image+Caption To investigate cell growth rates in wild type and mutant cells. Cell culture growth for the two types were monitored by measuring optical densities. Wild type ybr159 density increased after 17 hours and was saturated at 36 hours.Mutant type ybr159HIS3 cell density started to increase after 36 hours and continued to increase at 72 hours. Wild type cell density increases faster than mutant type cell density. none no no no no no no no no 5 mixed mixed5 Full Text To identify factors that interrupt the biosynthetic pathway of tryptophan in bacteria. DNA manipulation of bacteria. RNA isolation, construction of mutants by use of primers.Southern Blot, PCR. The mutant of the bacteria were not able to grow or to produce tryptophan. Tryptophan prototrophy is essential for survival of the strain in an amino acid lacking environment. none no no no no no no no no 5 mixed mixed5 Image+Caption+Title+Abstract do not know 3 strains of bacteria were used for a gene expression analysis.An interruption of the biosinthesis of the gene trpE was induced by homologization of trpE in one group. Measures were made with PRC and southern blot. A disruption of the trpE gene in bacteria resulted in tryptophan auxotrophy. do not know. none yes no no yes yes no no yes 5 mixed mixed5 Image+Caption To test the homology of recombination of genes Supplementation of a parental strain, trpE mutant and trpE mutant supplemented with tryptophan. Measured with PCR and Southern Blot. do not know do not know none no no yes yes no no yes yes 5 model model5 Full Text To understand the mechanism of the T1 domain of a K+ channel protein. Forming constructs of the T1 domain, in vivo translation, electrophorese, autoradiography, immunoprecipitation, chemical cross-linking. T 1 domain co-assembles with T1 domain proteins from the same sub family. T1 is the primary site for tetramerization of K+ channel sub units. do not know. none no no no yes no no no yes 5 model model5 Image+Caption+Title+Abstract To determine if the T1 domain of the Shaker channel can self assemble the number of subunits of the channel protein and to understand the mechanism of assembly. Hith pressure liquid chromatography (HPCL) and size exclusion chromatography (SEC) was used to separate the T1 domain into two peaks. Cross- linking the T1 domains into two peaks. do not know do not know none no no yes yes no no yes yes 5 model model5 Image+Caption Constructing a T domain and an N domain of a gene with different amino acids and introduce a restriction enzyme fo incuce chimerization. do not know. do not now. do not know. none no yes yes yes no yes yes yes 5 thing thing5 Full Text To examine the effect of ACh on the release of Ca2+ in AMS cells Single cell imaging. Tracheal cells of porcines werde extracted and cleaned in solutions. Cells were microscoped and Ca2+ releases recorded with real time imaging. The delay between the Ca2+ release and the contraction of the cell was measured (in ms) and recorded. The delay between elevated Ca2+ concentration and contraction was ~450ms. ASM cells permeated with esc9in showed a Ca2+ release after 800ms, an addition of calmodulin resulted in a shorter delay of 500ms. Ca2+ and Calmodulin together resulted in a force generation after 80ms. do not know. none no no no yes no no no yes 5 thing thing5 Image+Caption+Title+Abstract do not know Airway smoot muscle (ASM)cells were supplied with Ca2+, escin and calmodulin in vitro. Cells were examined with realtime confocal imaging. Ca2+ release after escin supplementation was 800 ms. When calmodulin was added the Ca2+ force generation occured at ca. 80 ms. do not know none yes no no yes yes no no yes 5 thing thing5 Image+Caption To examine the propagation of Ca2+ oscillation induced by the neurotransmitter ACh. In vitro supplementation of ACh to a cell cells shorten after ACh application do not know none no no no yes no no no yes 6 gel gel4 Full Text to studythe degradosome of the Antarctic bacterium Pseudomonas syringaeLz4W Purification of Recombinant Proteins from E. coli and Antibody Production;Expression of His-tagged RNase E and RNase R in P. syringae.Analysis of Interacting Proteins by Ni-NTA Resin.Western Blot.Co-immunoprecipitation.In Vitro Transcription of RNAs and Enzyme Assays.Polyadenylation of RNA for Degradation Assay.Thin Layer Chromatography. P. syringae RNase R Is in a Complex with RNase E andRhlE. P. syringae degradation Protein Fractions Comprising RNase E, RNase R, and RNA Helicases. RNase E, RNase R, and RNA Helicases functional work together to fulfil the function the degradation played. For A, some extra unrelated protein need not to be mark out.For B, it looks as if not closely related with the main topic. no no yes no no no no no 6 gel gel4 Image+Caption+Title+Abstract To prove that RNase R and RNase E can interact together to form degradosome. Co-immunoprecipitation and Ni2+-affinity pull-down experiments .glycerol density gradient. RNase R with RNase E and RhlE can form an RNA-degrading complex. RNase R with RNase E and RhlE can form an RNA-degrading complex. none no no no no no no no no 6 gel gel4 Image+Caption To prove that the P. syringae RNase E co-sediments with RNase R in glycerol density gradients. glycerol density gradient,SDS-PAGE and silver staining. The image display a similar distribution of RNase E and RNase R. P. syringae RNase E co-sediments with RNase R For image A, I do not know why the unlated protein need be make out.For image B, I do not know it has related with the the purpose, image A looks enough. no no yes no no no yes yes 6 graph graph2 Full Text determination of the occurrence and persistence ofeffects on the neurochemical components of the cholinergicnervous system in the offspring of dams orally exposed to CPSduring gestation Enzyme assays.Muscarinic receptor binding assay.Hemicholinium-3 and AH5183 binding assay.protein concentration analysis. ChE activities were inhibited about 15 and 30% on PND 1, in the low- and high-dosage groups, respectively, and were not different from control values by PND 6. mAChR densities on PND 1 were reduced in the high-dosage group by about 18, 21, and 17%, using 3H-N-methylscopolamine, 3H-quinuclidinyl benzilate, and 3H-4-DAMP, respectively, as ligands, and were not different from control levels by PND 6. ChAT activity was decreased by ~12% in the high-dosage group on PND 9, 12, and 30. HACU levels, using 3H-hemicholinium-3 as the ligand, were reduced by ~25% on PND 6 in the low- and high-dosage groups, and by ~14 and 21% on PND 12 and 30, only in the high-dosage group. exposure to CPS during gestation results intransient reductions of total mAChR and mAChR subtypes, butmore persistent reductions of HACU and VAChT levels. what is the a,b in the image? Even though I know what it is , it still be speak out. no no yes no no no no no 6 graph graph2 Image+Caption+Title+Abstract to study Neurochemical Effects of Repeated Gestational Exposure to Chlorpyrifos in Developing Rats. chemical feeding. ChE activities were inhibited about 15 and 30% on PND 1, in the low- and high-dosage groups, respectively, and were not different from control values by PND 6. mAChR densities on PND 1 were reduced in the high-dosage group by about 18, 21, and 17%, using 3H-N-methylscopolamine, 3H-quinuclidinyl benzilate, and 3H-4-DAMP, respectively, as ligands, and were not different from control levels by PND 6. ChAT activity was decreased by ~12% in the high-dosage group on PND 9, 12, and 30. HACU levels, using 3H-hemicholinium-3 as the ligand, were reduced by ~25% on PND 6 in the low- and high-dosage groups, and by ~14 and 21% on PND 12 and 30, only in the high-dosage group. gestational exposure to 7 mg/kg/day CPS results in long-term alterations of presynaptic cholinergic neurochemistry what is the a,b in the image? Even though I know what it is , it still be speak out. no no yes no no no no no 6 graph graph2 Image+Caption to analysis the chlorpyrifos on the binding capability of the M1/M3 mAChR and M2/M4 mAChR for the rat pups. do not know the binding content for the M1/M3 mAChR and M2/M4 mAChR is increased follow the postnatal day. At the early stage, the higher the chlorpyrifos feeded, the lower the M1/M3 mAChR binding when compare to the no treated control. the depression effect for chlorpyrifos to the binding of M1/M3 mAChR is time-dependent. there should have some conclusion words toward the image. no yes no yes no yes no no 6 mixed mixed2 Full Text To examine the mechanism of GAr action, Plasmid Construction and Protein Purification,Metabolic Labeling, Immunoprecipitation, and Immunoblotting inYeast, We show here that a 30-residue GAr embedded in ODCstrongly inhibits degradation of ODC by the proteasome. However,biochemical competition experiments showed that therepeat sequence does not impair proteasome-ODC interaction. The GAr must, therefore, function at a step downstream ofsubstrate recognition by the proteasome. none no no no no no no no no 6 mixed mixed2 Image+Caption+Title+Abstract to analysis the GAr region in the process of Proteasome . [35S]methionine-labeled ,immunoprecipitated, recommibination protein For A,B: The FLAG remains decrease step by step follow the chase going for the cells expressing ODC::GAr (repeat length 30), ODC, ODC::GAr7 (repeat length 7),but not for ODCC441A::GAr.for C,D: For rpn4 cells, the MG132 can decrease the speed of FLAG degeneration. we now demonstrate inhibition in a purified system, excluding involvement of ubiquitin conjugation or of proteins extraneous to substrate and proteasome. We show further that the GAr acts as a stop-transfer signal in proteasome substrate processing, resulting in vivo in partial proteolysis that halts just short of the GAr. none no no no no no no no no 6 mixed mixed2 Image+Caption Pulse-chase analysis of processing [35S]methionine-label, immunoprecipitate For A,B: The FLAG remains decrease step by step follow the chase going for the cells expressing ODC::GAr (repeat length 30), ODC, ODC::GAr7 (repeat length 7),but not for ODCC441A::GAr.for C,D: For rpn4 cells, the MG132 can decrease the speed of FLAG degeneration. The FLAG remains decrease step by step follow the chase going for the cells expressing ODC::GAr (repeat length 30), ODC, ODC::GAr7 (repeat length 7),but not for ODCC441A::GAr.this effect is depressed by MG132. none no no no no no no no no 6 model model4 Full Text the structural-functional analysis for the FBPase. Mutagenesis, protein purification, circular dichroism spectroscopy, kinetic analysis, fluorescence measurement Mutations, which directly or indirectlyinfluence positions 9 and 10, cause large perturbations incatalysis and/or AMP inhibition. A simple model in which thequaternary states of FBPase differentially stabilize specificconformations of loop 52–72 accounts for the properties of wildtypeand mutant FBPases presented Mutations, which directly or indirectlyinfluence positions 9 and 10, cause large perturbations incatalysis and/or AMP inhibition. A simple model in which thequaternary states of FBPase differentially stabilize specificconformations of loop 52–72 accounts for the properties of wildtypeand mutant FBPases presented The annotation is hard to be understood, need more information. yes yes yes yes no no no yes 6 model model4 Image+Caption+Title+Abstract to study the role of different amino acid played in the FBPase, and its structural basis. recommbination technique, Catalysis analysis, computer analysis. The 1-10 position is important for the FBPase activity and Mg2+ affinity. position 9 is especially important for the Mg2+ affinity, and position 10 is important for the AMP inhibition effect. The crystal structual picture, especially the upper one, support the result. The 1-10 position is important for the FBPase activity and Mg2+ affinity. position 9 is especially important for the Mg2+ affinity, and position 10 is important for the AMP inhibition effect. The bottom one is hard to be understood, especially which amino acid belong to which subunit. no no yes no no no yes yes 6 model model4 Image+Caption Not clear, maybe for the research of FBPase , especially its function. computer analysis with software MOLSCRIPT. The Structural for the R-state of FBPase have been provided. the R-state of FBPase is a form of tetramer. The bottom pic is hard to understand and the annotation do not clear tell us which amino acid belong to which subunit. yes no yes yes yes no yes no 6 thing thing4 Full Text todetermine whether CGRP contributes to the secretoryand inflammatory effects of C. difficile toxin A. Histological evaluation.Immunohistochemistry. toxin Ainducedfluid secretion, mucosal permeability, and inflammationin ileal loops are markedly attenuated byCGRP-(8—37), a specific CGRP antagonist. CGRP contributes to the secretoryand inflammatory effects of C. difficile toxin A. none no no no no no no no no 6 thing thing4 Image+Caption+Title+Abstract to determine whether calcitonin gene-related peptide (CGRP), a neuropeptide also found in sensory afferent neurons, participates in the enterotoxic effects of toxin A hematoxylin and eosin staining Pretreatment of rats with CGRP-(8 37), a specific CGRP antagonist, before instillation of toxin A into ileal loops significantly inhibited toxin-mediated fluid secretion (by 48%), mannitol permeability (by 83%), and histological damage. We conclude that CGRP, like substance P, contributes to the secretory and inflammatory effects of toxin A via increased production of this peptide from intestinal nerves, including primary sensory afferent neurons none. no no no no no no no no 6 thing thing4 Image+Caption to prove that CGRP-(837)can inhibt toxin-a induced enteritis. hematoxylin and eosin staining. A: buffer-treated ileal loop showing normal mucosa. B: ileal loop exposed to toxin A showing disruption of villus architecture, goblet cell discharge, and tissue necrosis. C: ileal loop pretreated with CGRP-(8 37) before challenge with toxin A, showing almost complete prevention of the intestinal effects of toxin A. CGRP-(837)can inhibt toxin-a induced enteritis. none no no no no no no no no 7 gel gel3 Full Text to verify that REF1/Aly and the additional exon junction complex proteins are dispensable for nuclear mRNA export western blot,PCR, dsRNA transfection,RNA isolation and Northern blots The depletion of REF1 or other EJC proteins reduces, but does not abolish the incorporation of [35S]Met into newly synthesized proteins 11 d after transfection (Fig. 4 A). Moreover, induction of the heat shock response was not completely inhibited (Fig. 4 B). no inhibition of protein synthesis was observed in cells depleted of REF2, DEK, and SRm160 (Figs. 4, A and B, lanes 5–7). The expression level of NXF1, DEK and UAP56 are not affected in REF1-depleted cells REF1 and the Drosophila homologues of mammalian EJC proteins may contribute to, but are not essential for bulk mRNA export. The intracellular distribution of bulk poly(A)+ RNA in control cells and in cells depleted of EJC proteins was investigated by oligo(dT) in situ hybridization. Depletion of REF1 or RNPS1 occasionally resulted in a partial accumulation of poly(A)+ RNAs within the nucleus. This accumulation was observed in <20% of the cells. no no no no no no no no 7 gel gel3 Image+Caption+Title+Abstract to verify that the essential role of UAP56 in mRNA export is not restricted to the recruitment of REF1. REF1 is dispensable for nuclear mRNA export western blot, dsRNA transfection Depletion of EJC proteins reduces, but does not abolish, incorporation of [35S]Met into newly synthesized proteins. Induction of heat shock response was not completely inhibited after EJC protein depletion. Depletion of REF1 doesn't affection the expression of UAP56, DEK and NXF1. Depletion of EJC proteins reduces, but does not abolish, incorporation of [35S]Met into newly synthesized proteins. REF1 is dispensable for nuclear mRNA export. Of the depleted cells which were collected 11 d after transfection, The strongest inhibitory effects were occurred after depletion of REF1 and RNPS1. no no yes no no no no no 7 gel gel3 Image+Caption to measure the efficacy of the depletions of EJC western blot and dsRNA transfection After the stimuli of heat, The synthesis of HSPs was not affected with the depleted EJC. Expression level of REF1 was blocked after transfected with REF1 dsRNA, while reduced after transfection with REF2 dsRNA. Depletion of EJC proteins reduces, but does not abolish the incorporation of [35S]Met into newly synthesized proteins. The most inhibitory effect happens when REF1 and RNPS1 dsRNA were incorporated no no no yes no no no no 7 graph graph4 Full Text to elucidate the metabolic pathways for polyol biosynthesis in fungi A. oryzae culture, polyol extraction and polyol analysis with HPLC, enzyme assays and partial purification of polyol dehydrogenases,northern analysis Four enzymes bearing highest activities with mannitol, glycerol, erythritol and D-arabitol, respectively, were well separated. The major part of the mannitol dehydrogenase activity (70 %) did not bind to the anion-exchange column and eluted in the first two fractions, whereas glycerol dehydrogenase bound weakly. in this study accumulation of glycerol, erythritol and arabitol by A. oryzae at low aw on solid-state substrate. Accumulation of a mixture of polyols might be typical for SSF due to the specific growth conditions present during growth on a solid substrate. NADP+-dependent glycerol and erythritol dehydrogenases were induced at low aw suggesting that these enzymes are involved in biosynthesis of glycerol and erythritol, respectively no no no yes no no no no 7 graph graph4 Image+Caption+Title+Abstract to testify that A. oryzae mycelium can accumulat various polyols at low aw. culture of the A. oryzae ;anion-exchange chromatography Four enzymes with mannitol, glycerol, erythritol and D-arabitol were well separated. NADP+-dependent glycerol and erythritol dehydrogenases are involved in biosynthesis of glycerol and erythritol, respectively glycerol dehydrogenase and mannitol dehydrogenase bound to the anion-exchange column weakly no no no yes no no no no 7 graph graph4 Image+Caption show the percentage of the dehydrogenase activity against the fraction number anion-exchange chromatography do not know do not know none no no yes yes no no yes yes 7 mixed mixed3 Full Text to test the influnence of Ucp3 on metabolic efficiency and obesity gene. gene knockout, RNA analysis, western blotting, Preparation of Mitochondria and Measurement of Mitochondrial Oxygen Consumption;Biochemical Assays 1.Production of Ucp3-ablated Mice.2. Ucp2 mRNA levels in muscle were unchanged in Ucp3 (/) as compared with wild type mice. BAT Ucp2 levels appeared to be slightly elevated in the knockout mice.Ucp1 mRNA levels in BAT from Ucp3 (/) mice were unchanged at 84 ± 18% of the wild type level.3.there is decreased proton leak in the Ucp3 (/) mitochondria.4. The base-line metabolic rate and respiratory exchange ratio were the same in knockout and control mice Ucp3 is not a major determinant of metabolic rate but, rather, has other functions. The knockout mice were not obese and had normal serum insulin, triglyceride, and leptin levels, with a tendency toward reduced free fatty acids and glucose. Knockout mice showed a normal circadian rhythm in body temperature and motor activity and had normal body temperature responses to fasting, stress, thyroid hormone, and cold exposure. The phenotype of Ucp1/Ucp3 double knockout mice was indistinguishable from Ucp1 single knockout mice. no no no yes no no no no 7 mixed mixed3 Image+Caption+Title+Abstract to test the hypotheses that UCP3 can influence metabolic efficiency and is a candidate obesity gene. western blot, northern blot, southern blot, gene knockout. The successfully established modle of UCP3 knockout mice. In mitochondria from the knockout mice, proton leak was greatly reduced in muscle, minimally reduced in brown fat, and not reduced at all in liver. UCP3 accounts for much of the proton leak in skeletal muscle, but is not a major determinant of metabolic rate but, rather, has other functions. The phenotype of Ucp1/Ucp3 double knockout mice was indistinguishable from Ucp1 single knockout mice. no no yes no no no yes yes 7 mixed mixed3 Image+Caption To establish the modle of Ucp3 knockout mice and testify the model. biochemistry, northern blot, southern blot, westerblot, gene knockout BAT expression in the Ucp3 knockout group is increased while muscle protein synthesis is reduced compared with the wild type. Ucp3 gene play an important role in the muscle protein synthesis. But I don't know what BAT stands for. none no no no yes no no yes yes 7 model model2 Full Text to verify that hRad17 does indeed interact with the PCNA-like proteins hRad1, hHus1, and hRad9 in manner similar to the interaction between RFC and PCNA cell culture,gene transfection,western blot the interaction between hRad17 and hRad1 has biochemical features similar to the RFC-PCNA interaction. DNA damage alters the interaction of hRad17 with hHus1, hRad1, and hRad9. hRad17 may interact only transiently with DNA. no no no yes no no no no 7 model model2 Image+Caption+Title+Abstract to verify endogenous human Rad17 (hRad17) interacts with the PCNA-related checkpoint proteins hRad1, hRad9, and hHus1 biochemistry the interaction between Rad17 and PCNA-related checkpoint proteins has properties similar to the interaction between RFC and PCNA hRad17 interacts with the PCNA-like proteins hRad1, hHus1, and hRad9 in manner similar to the interaction between RFC and PCNA DNA damage affects the association of hRad17 with the clamp-like checkpoint proteins no no no yes no no no no 7 model model2 Image+Caption to elucidate how gene hRad17 responses to the repair of DNA damage do not know Rad17 homologs have extensive homology with replication factor C (RFC) subunits ), which form a clamp loader checkpoint Rad proteins are thought to function as damage sensors in the DNA damage checkpoint response pathway the hRad9, hHus1, and hRad1 proteins make a trimeric ring structure no yes no no no yes no no 7 thing thing1 Full Text To investigate how the morphological and biological changes involved in myogenic differentiation affect the ubiquitin-proteasome-mediated degradation of MyoD and Id1 in muscle cells and how their degradation and interaction contribute to their cellular abundance and thus regulate differentiation. Plasmids and Construction of Id1-HA; Cell Culture;protein assay; western blotting; rt-PCR MyoD and Id1 co-localize within the nucleus in proliferating myoblasts. In mature myotubes, in contrast, they reside in distinctive subcellular compartments, with MyoD within the nucleus and Id1 exclusively in the cytoplasm. Cellular abundance of Id1 was markedly diminished from the very onset of muscle differentiation, whereas MyoD abundance was reduced to a much lesser extent and only at the later stages of differentiation. These reductions in MyoD and Id1 protein levels seem to result from a change in the rate of protein synthesis rather than the rate of degradation. In vivo protein stability studies revealed that the rates of ubiquitin-proteasome-mediated MyoD and Id1 degradation are independent of myogenic differentiation state. The relative protein synthesis rates for MyoD and Id1 were significantly diminished during myoblast to myotube differentiation. The regulation of MyoD and Id1 protein abundance is essential for muscle differentiation. The ubiquitin-proteasome system contributes to the regulation of MyoD cellular abundance via interactions with phosphorylation, DNA binding, and possibly other MyoD posttranslational modifications. Id1 activity during muscle differentiation may also be regulated by nuclear translocation of Id1. During differentiation from myoblast to myotube the down-regulation of Id1 protein, and that of MyoD protein as well, is due predominantly to a reduction of the protein synthesis rate rather than a change of the protein degradation rates. no no no yes no no no no 7 thing thing1 Image+Caption+Title+Abstract To elucidate the interaction between MyoD and Id1 in the process of muscle differentiation. Cell culture and plasmids translation, Immunofluorescence MyoD and Id1 co-localize within the nucleus in proliferating myoblasts. In mature myotubes, in contrast, they reside in distinctive subcellular compartments, with MyoD within the nucleus and Id1 exclusively in the cytoplasm. Cellular abundance of Id1 was markedly diminished from the very onset of muscle differentiation, whereas MyoD abundance was reduced to a much lesser extent and only at the later stages of differentiation. The rates of ubiquitin-proteasome-mediated MyoD and Id1 degradation are independent of myogenic differentiation state. none no no no no no no no no 7 thing thing1 Image+Caption Do not know cell culture, plasmid transforlation, Immunofluorescence, DAPI are expressed in both of the myoblast and myotube while myosin only expressed in myoblasts When myoblast differentiated into myotubes, the expression level of Id1 was markedly reduced. Id1 and MyoD may participate in the regulation of myogenesis and differentiation yes no no yes yes no no no 8 gel gel2 Full Text To compare the nucleotide sequences of the urease gene clusters of a urease-activity-positive and aurease-activity-negative strain Genetic manipulationsPCRSouthern hybridizationsequencingurease activity test O157 Sakai expresses no urease activity in vitroThe ureD gene of O157 Sakai has a prematurestop codonO157 Sakai complemented with ureD from theUre+-1 strain expresses urease activity Urease activity of enterohaemorrhagic Escherichiacoli depends on a specific one-base substitution inureD none no no no no no no no no 8 gel gel2 Image+Caption+Title+Abstract compare the nucleotide sequences of the urease gene clusters of a urease-activity-positive and a urease-activity-negative strain. RT-PCR in the urease-activity-negative strain, ureD, a gene encoding a chaperone protein, had a single base substitution that encoded a premature stop codon resulting in a short ORF. The premature stop codon in ureD was commonly found in urease-activity-negative EHEC strains, but not in urease-activity-positive strains. Urease activity was detected after complementing the urease-activity-negative strain with ureD from the urease-activity-positive strain. Furthermore, introduction of the urease gene cluster from the urease-activity-negative strain into an amber suppressor phenotype Escherichia coli strain, DH5 , conferred the ability to produce the active urease lack of urease activity in most EHEC strains is due to a premature stop codon in ureD NONE no no no no no no no no 8 gel gel2 Image+Caption Do not know RT-PCR Do not know Do not know NONE yes no yes yes yes no yes yes 8 graph graph1 Full Text to study CPT I molecules in the two membrane microenvironmentsmay have different kinetic properties Assay of Activity and Immunodetection of CPT I the kinetic parameterswith respect to one of its substrates, palmitoyl-CoA, are markedlydifferent for the enzyme in the two microenvironments.Moreover, the kinetics of malonyl-CoA inhibition of CPT Iactivity is different for the enzyme resident within the twomembrane populations. different membrane environments inouter membranes and contact sites result in an alteredconformation of L-CPT I that specifically affects thelong-chain acyl-CoA binding site. The accompanyingchanges in the kinetics of the enzyme provide an additionalpotent mechanism for the regulation of L-CPT Iactivity none no no no no no no no no 8 graph graph1 Image+Caption+Title+Abstract to compare distinct Kinetics of Carnitine Palmitoyltransferase I in Contact Sites and Outer Membranes of Rat Liver Mitochondria CPT I activity assay the IC50 for malonyl-CoA was severalfold higher for CPT I in contact sites than for the enzyme in bulk outer membrane. The Ki for malonyl-CoA, the Km for carnitine, and the catalytic constant of the enzyme were all unaffected. the different membrane environments in outer membranes and contact sites result in an altered conformation of L-CPT I that specifically affects the long-chain acyl-CoA binding site. The accompanying changes in the kinetics of the enzyme provide an additional potent mechanism for the regulation of L-CPT I activity none no no no no no no no no 8 graph graph1 Image+Caption compare the difference of the inhibition of CPT I activity by malonyl-CoA in contact sites and outer membranes of rat liver mitochondria. CPT I activity assay deceased activity of CPT i activity with the increased concentration of malonyl-CoA. contact site always show higher activity compared with the outrer membrane fraction Do not know none no no no yes no no no yes 8 mixed mixed4 Full Text TO STUDY THE Influence of cargo size on Ran and energyrequirements for nuclear protein import Stokes radius analysisNuclear import assayCoprecipitation assayGAP assayElectron microscopy Distinct Ran and energy requirements for small versuslarge cargo importthe similarity of the rate profilesfor the large cargos under the different energy/Ran conditionsindicates that the differences in import levels obtainedwith the different conditions do not reflect a preferentialdepletion of a transport component in one of the caseEfficient import of large cargos requires Ran and hydrolyzable GTPLarge cargo requires RanGTP to traverse the centralchannel of the NPCImport of large cargo requires a functional Ran bindingdomain on the receptor RanGTP functions in these pathways topromote the transport of large cargo by enhancing the abilityof import complexes to traverse diffusionally restrictedareas of the NPC. NONE no no no no no no no no 8 mixed mixed4 Image+Caption+Title+Abstract To demonstrate that in the importin /©¬ and transportin import pathways, efficient in vitro transport of large proteins, in contrast to smaller proteins, requires hydrolyzable GTP and the small GTPase Ran Morphological and biochemical analysis the presence of Ran and GTP allows large cargo to efficiently cross central regions of the NPCthis function of RanGTP at least partly involves its direct binding to importin ©¬ and transportin RanGTP functions in these pathways to promote the transport of large cargo by enhancing the ability of import complexes to traverse diffusionally restricted areas of the NPC. none no no no no no no no no 8 mixed mixed4 Image+Caption to prove that import of large, but not small, cargo requires hydrolyzable GTP in vitro import assays, confocol microscope Do not know Do not know none no no yes yes no no yes yes 8 model model1 Full Text to determine the influence of wp631 on a sp1- transactivzted promotor in vitro transcription in vitro, gel retardation assay, DNAase I footprinting Dau and wp inhibit the basel transcription. WP is very potent in inhibiting sp1-activated transcription in vitro; sp1 and wp might bind into the same DNA we have been able to distinguish the unambigiously due to the difference in transcription initiation and those due to elongation none no no no no no no no no 8 model model1 Image+Caption+Title+Abstract compare the capacity of the bisintercalating anthracycline WP631 (which displays a remarkably high DNA-binding affinity) and the monointercalating anthracycline daunomycin to inhibit transcription initiation of the adenovirus major late promoter linked to a G-less transcribed DNA template in vitro transcription assay Both drugs inhibit basal RNA synthesis in a concentration-dependent way, and the drug concentrations required to inhibit transcription initiation are similar. However, in this study WP631 was around 15 times more efficient at inhibiting transcription initiation when used with an adenovirus promoter containing an upstream Sp1-protein binding site under experimental conditions in which the Sp1 protein acted as a transactivator in vitro. The differences in the ability of each drug to inhibit transcription initiation were related to the competition between Sp1 and the drugs for the same binding site. Concentrations of WP631 as low as 60 nM could inhibit the Sp1-activated transcription initiation in vitro. In contrast, the concentration of daunomycin required to inhibit Sp1-activated transcription by 50% was almost the same as the concentration required to inhibit basal transcription. The efficiency of WP631 at displacing Sp1 from its putative binding site was confirmed using gel retardation and footprinting assays a direct effect of an intercalator on activated transcription initiation. none no no no no no no no no 8 model model1 Image+Caption the possible binding modes for the interaction of WP631 with DNA Do not know Do not know Do not know none no yes yes yes no yes yes yes 8 thing thing2 Full Text whether and how glu geneexpression is regulated in a cell type-specific manner Chromatin Immunoprecipitation (ChIP) a-catenin and the glycogen synthase kinase-3a inhibitorlithium do not activate glu mRNA or glu promoter expressionin pancreatic cell lines. In the intestinalGLUTag cell line, but not in the pancreatic InR1-G9 cellline, the glu promoter G2 enhancer-element was activatedby lithium treatment via a TCF-binding motif.TCF-4 is abundantly expressed in the gut but not inpancreatic islets. Furthermore, both TCF-4 and a-cateninbind to the glu gene promoter, as detected by chromatinimmunoprecipitation. Finally, stable introductionof dominant-negative TCF-4 into the GLUTag cellline repressed basal glu mRNA expression and abolishedthe effect of lithium on glu mRNA expression andGLP-1 synthesis. TCF-4 Mediates Cell Type-specific Regulation of Proglucagon GeneExpression by a-Catenin and Glycogen Synthase Kinase-3a none no no no no no no no no 8 thing thing2 Image+Caption+Title+Abstract whether and how glu gene expression is regulated in a cell type-specific manner chromatin precipatation -catenin and the glycogen synthase kinase-3 inhibitor lithium do not activate glu mRNA or glu promoter expression in pancreatic cell lines. In the intestinal GLUTag cell line, but not in the pancreatic InR1-G9 cell line, the glu promoter G2 enhancer-element was activated by lithium treatment via a TCF-binding motif. TCF-4 is abundantly expressed in the gut but not in pancreatic islets. Furthermore, both TCF-4 and -catenin bind to the glu gene promoter, Tissue-specific expression of TCF factors thus may play a role in the diversity of the Wnt pathway none no no no no no no no no 8 thing thing2 Image+Caption Detection of TCF-4 expression in cultivated cell lines and in paraffin-embedded pancreatic and intestine tissue samples immunoflucence and IHC Do not know Do not know more details of description no no yes yes no no yes yes 9 gel gel1 Full Text after reading the full-test of the annotation provided, i would describe the purpose of the study as i did previously (for the figure+caption+title+abstract, i.e. without full-text). in addition however, i would summarize that this study also aims to prepare the way for another study which would tackle the identification of the intracellular proteins that specifically interact with the PECAM-1 isoforms described in this study. all additional information retrieved from the full-text did not help my understadning (as i am not a biologist). hence, please refer to my description provided for this annotation based on figure+caption+title+abstract. i would describe results the same way as i did before (see my text based on figure+caption+abstract+title). additionally, i understand that another important result is that the frequency at which human PECAM-1 mRNA undergoes alternative splicing is much lower than that detectedin murine PECAM-1 mRNA. after reading the full-test of the annotation provided, i would describe the conclusions of the study as i did previously (for the figure+caption+title+abstract).additionally, i have learned that the developmental and species-specific regulation of PECAM-1isoform expression may play an important role duringangiogenesis by influencing cell adhesive mechanisms. none no no no no no yes no no 9 gel gel1 Image+Caption+Title+Abstract to find out if human PECAM-1 isoform shows different cell adhesion properties depending on the tissue with which it is brought into contact. a range of tissue were used (as described in my text to previous annotation (the one without abstract+title), apparently excluding murine endothelium. largely unclear to my understanding; apparently RT-PCR cloning and DNA sequence analysis were employed. human tissue and endothelial cells express multiple isoforms of PECAM-1, including the full-length PECAM-1 and five other isoforms, which lack exon 12, 13, 14, or 15 or exons 14 and 15. The full-length PECAM-1 is the predominant isoform detected in human tissue and endothelial cells.Hence, human PECAM-1 undergoes alternative splicing, generating multiple isoforms in vascular beds of various tissues. To my understanding however, the annotation provided is not meant to illustrate these results - and in fact I cannot see any of these results examplified in the figure. the study concludes that the regulated expression of the isoforms of PECAM-1 may influence endothelial cell adhesive properties during angiogenesis and/or vasculogenesis. but again, the figure provided does not (and is probably not meant to) show this conclusion. none no yes yes yes no yes no no 9 gel gel1 Image+Caption do not know both RNA from various human tissues as well as poly(A)+ RNA from huamn ednothelial cells were studied using gene-specific primers and molecular markers. thats all i understand. if the photograph is any valid result and can be interpreted visually, then the lung tissue seems to show some weak response to the treatment (whatever that was). frankly speaking: "do not know". do not know none yes yes yes yes yes no yes yes 9 graph graph3 Full Text to test the effect of polycythemia on the coronary microcirculation in young male rats by means of two different inductors of polycythemia: cobalt and EPO. my understanding of the methods has essentially remained the same as described by me in my answer to the previous figure which provided figure+caption+title+abstract. the full text provides a wider range of results (addressing Cardiac function, microvascular structure, and capillary hematocrit), but my understanding of the results shown in the annotation provided has not increased significantly by reading about these "other" results. please see my prevous results-answer for a describtion of my understanding of results. whereas i could not find any overall conclusion(s) in the abstract, i did encounter those in the full text. with respect to the annotation provided, the main conclusion to my understanding is "a hypoxic stimulus seemed to be more effective in inducing angiogenesis than mechanical stimuli." none no no no no no yes yes no 9 graph graph3 Image+Caption+Title+Abstract to investigate the Cardiac function, microvascular structure, and capillary hematocrit in hearts of polycythemic rats. without the abstract+title i thought this study i was not aware that the blood pressure was measured in the heart, not why cobalt and EPO were chosen (i.e. their mimicking effects). my undestanding includes the text i wrote for previously for this figure (figure+capture only). however, some new points emerged:apparently, baseline left ventricular function was also measured, which i did not realize by looknig at the figure alone (or perhaps this is retrievable from the absolute axis values). the abstract also pointed me to the fact that "cobalt-treated rats the left ventricular functional reserve was also compromised", but so far i had just overlooked this obvious fact, it is clearly udnestandable by looking at the the figure alone. reading the title and abstract did not susbtantially increase my undestanding of results. i am confident i got the main message, except for the part about Capillary linear hematocrit, which the abstract couldnt shed much more light on either however. my understanding of conclusions & indication did not improve by also reading the abstract+title, as compared to my previous text for this figure+caption only. in fact, the abstract provided elaborates on results, but does not draw a clear (overall) conclusion. none yes yes yes yes no no yes yes 9 graph graph3 Image+Caption to investigate the (blood?) pressure observed in rats with polycythemia if induced a) by cobald and b) EPO. details are not available, but obviously rats had been divided in control and test group. the test group members were then treated with either cobalt or EPO. pressure values were measured at before (?) as left ventricular maximal systolic (A) and after the treatment (B); i tried to understand the meaning of "Reserve" but failed. in all cases, Cobalt reduced pressure more (as well faster) than EPO. Either treatment however, reduced the pressure compared to the one the control group animals exhibited. furthermore, based on visual analysis of the figures, the developed pressure (B) is generally a bit lower than the systolic one (A). blood (?) pressure of rats with polycythemia can be reduced by both cobald, EPO, whereas the former is more effective. none no yes no yes yes yes no yes 9 mixed mixed1 Full Text my understanding of the purpose of this study has remained the same. please refer to the text i wrote in my previous answer (figure+caption+title+abstract). the full text article did not help because i am just not educated enough in this area of science. understanding the same as described in my previous answer for (figure+caption+title+abstract). understanding the same as described in my previous answer for (figure+caption+title+abstract). Abnormal proteins such as mutated Parkins impact on the ubiquitin-proteasome system, leading to oxidative stress and excess NO production, rendering them very sensitive to other insults. none no no no no no no no no 9 mixed mixed1 Image+Caption+Title+Abstract to find out if wild-type and mutant Parkin have different effects on Oxidative Damage, Nitric Oxide, Antioxidant Defenses, and the Proteasome. The first treatment was to increase the expression of Parkin by gene transfection in NT-2 and SK-N-MC cells.The second treatment involved a transfection of these cells with DNA encoding three mutant Parkins. The first treatment lead to a incrase in proteasomal activity, decreased levels of protein carbonyls, 3-nitrotyrosine-containing proteins, and a general decrease inubiquitinated protein levels. The second treatment gave smaller increases in proteasomal activity and led to elevated levels of protein carbonyls and lipid peroxidation. Also, turnover of the mutant proteins was slower than that of the wild-type protein, and both could be blocked by the proteasome inhibitor, lactacystin (but i am not sure where these results taken from the abstract are shown in the figures: do the white dots represent mutants or presence of lactacystin?). The presence of mutant Parkin in substantia nigra in juvenile parkinsonism may increase oxidative stress and nitric oxide production, sensitizing cells to death induced by other insults. none no no yes no no no yes no 9 mixed mixed1 Image+Caption I am not sure at all. Apparently the authors compared a range of both wild-type and mutant Parkin proteins in NT-2 and SK-N-MC cell lines with respect to a) their temporal decay properties and b) their individual ubiquitin ligase activity - whatever that is. in line with the above goals, cells were extracted for a) Western blotting and b) to measure enzyme activities. Results were compared with non- or vector-only transfectants under normal conditions (using ANOVA).Again: I am not sure at all about this. I don't undestand the results shown in the Overexpression. The second figure shows that some proteins (e.g. C [NT-2/wild-type parkin] and D [NT-2/Del 3-5 mutant parkin] as well as I and J all showed a significanlty higher ubiquitin ligase activity - measured as relative density - than other proteins. Figures 3 and 4 show that turnover was different for differnt proteins (e.g. WT), but about the same for both cell lines under investigation. I have no clue. I would need to know the context of that study. none (supposing that the criterion "Purpose of study" is meant to include the criteria "Research questions / hypotheses" and "Context of study", which could be assessed separately). But isn't this question designed to improve your own study rather than to evaluate the 15 figures presented? Thats my impression at least, so I am going to leave this field blank in the future, because my comment here applies to all subsequent 14 figures. Hope thats OK. yes yes yes yes yes yes yes yes 9 model model3 Full Text reading the full-text just confirmed what i understood previously (based on figure+caption+title+abstract). so please see my previous text. although the full-text presented all the detailed steps of the analysis performed (PCR etc), this did not improve my understanding, since i lack the background knowledge to put this information into context. hence, please see the text on "methods of study", which i wrote based on figure+caption+title+abstract alone. please see the text on "results of study", which i wrote based on figure+caption+title+abstract alone. the full-text gave me more information but i couldnt place it into context. identical with the text about "conclusions & indication", which i wrote based on figure+caption+title+abstract alone. none no no no no no yes yes yes 9 model model3 Image+Caption+Title+Abstract to find evidence of a malfunctioning of the doublecortin gene, as it is hypothesized to be the major gene causing X-linked SCLH, which is associated with epilepsy and mental retardation. a systematic mutation analysis of the doublecortin gene was carried out. it remains unclear how this was done exactly. the analysis led to the identification of mutations in 10 out of 11 cases. The sequence differences include nonsense, splice site and missense mutations and these were found throughout the gene, as the various affected Exons shown in the annotation illustrate. the study supports the hypothesis that a loss of function of doublecortin is the major cause of SCLH. none no yes no no no no no no 9 model model3 Image+Caption do not know do not know the figure shows the schematic structure of the doublecortin gene and where nonsense and splice site mutations as well as missense mutations are located on the Exons, which make up the coublecortin gene. having said that, i don't know if this information is an essential result of this study or not (it could just be an introduction). do not know none yes yes yes yes yes yes yes yes 9 thing thing3 Full Text in addition to my understanding of the purpose of study as described previously (figure+caption+title+abstract), i learnd from the full-text that RAD52 is an important DNA repair protein and its modes of self-association are essential for its overall functionality, which justifies this study further. although the full-text describes the methods in painstaking detail, this is of little use to me, as i lack the background knowledge to understand the meaning of these preparation routines of proteins. so, please take the text i wrote previusly based on figure+caption+title+abstract. in addition to the text i wrote previously (based on figure+caption+title+abstract alone), i learned from the full-text that the fact that the C-terminal region of RAD52 contains a novel self-association domain distinct from that previously identified, is more important than i first assumed when reading the abstract only.within residues 65–165 identical to my text written previously based on figure+caption+title+abstract. none no no no no no yes no no 9 thing thing3 Image+Caption+Title+Abstract to better understand how the human RAD52 protein influences the earliest stages of chromosomal double-strand break repair via the homologous recombination pathway by means of self-organisation processes. to differently prepared human RAD52 proteins were studied. the experimental procedure however remains unclear. There are in fact two experimentally separable self-association domains in RAD52. The N-terminal self-association domain mediates the assembly of monomers into rings (see figures A and C), and the previously unidentified domain in the C-terminal half of the protein mediates higher order self-association of the rings (see figure B and D). Human RAD52 Exhibits Two Modes of Self-association. Perhaps there is a stronger, more significant statement resulting from this sentence, but at this point I can't tell, given the information provided. none no yes no yes no yes no yes 9 thing thing3 Image+Caption do not know do not know according to the annotation, there are two main results (but i dont know if they are central to the study):a) all proteins formed 10nm ring-shaped polimersb) protrusions observed on the 10-nm rings of wild-type RAD52 are missing in the RAD52-(1-192) rings do not know none yes yes no yes yes yes no yes