| accession_id (string) | pmid (string) | figure_idx (int16) | figure_fn (string) | figure (image) | caption (string) | license (string) | retracted (string) | last_updated (string) | citation (string) |
|---|---|---|---|---|---|---|---|---|---|
"PMC176545" | "12929205" | 1 | "pbio.0000005.g001" |  | "Figure 1 Parasite Culturing and Data Characteristics of the P. falciparum IDC Transcriptome Analysis (A) Giemsa stains of the major morphological stages throughout the IDC are shown with the percent representation of ring-, trophozoite-, or schizont-stage parasites at every timepoint. The 2-h invasion window during the initiation of the bioreactor culture is indicated (gray area). (B–D) Example expression profiles for three genes, encoding EBA175, DHFR-TS, and ASL, are shown with a loess fit of the data (red line). (E) MAL6P1.147, the largest predicted ORF in the Plasmodium genome, is represented by 14 unique DNA oligonucleotide elements. The location of each of the oligonucleotide elements within the predicted ORF and the corresponding individual expression profiles are indicated (oligo 1–14). A red/green colorimetric representation of the gene expression ratios for each oligonucleotide is shown below the graph. The pairwise Pearson correlation for these expression profiles is 0.98 ± 0.02. (F) The percentage of the power in the maximum frequency of the FFT power spectrum was used as an indicator of periodicity. A histogram of these values reveals a strong bias toward single-frequency expression profiles, indicating that the majority of P. falciparum genes are regulated in a simple periodic manner. This bias is eliminated when the percent power was recalculated using random permutations of the same dataset (inset). For reference, the locations of EBA175 (peak B), DHFR-TS (peak C), and ASL (peak D) are shown." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 18; 1(1):e5" |
"PMC176545" | "12929205" | 2 | "pbio.0000005.g002" |  | "Figure 2 Overview of the P. falciparum IDC Transcriptome (A) A phaseogram of the IDC transcriptome was created by ordering the transcriptional profiles for 2,712 genes by phase of expression along the y-axis. The characteristic stages of intraerythrocytic parasite morphology are shown on the left, aligned with the corresponding phase of peak gene expression. (B–M) The temporal ordering of biochemical processes and functions is shown on the right. Each graph corresponds to the average expression profile for the genes in each set and the mean peak-to-trough amplitude is shown in parentheses." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 18; 1(1):e5" |
"PMC176545" | "12929205" | 3 | "pbio.0000005.g003" |  | "Figure 3 Coregulation of Gene Expression along the Chromosomes of P. falciparum Is Rare, While Plastid Gene Expression Is Highly Coordinated Expression profiles for oligonucleotides are shown as a function of location for Chromosome 2 ([A], Oligo Map). With the exception of the SERA locus (B), coregulated clusters of adjacent ORFs are seldom observed, indicating that expression phase is largely independent of chromosomal position. (C) In contrast to the nuclear chromosomes, the polycistronic expression of the circular plastid genome is reflected in the tight coregulation of gene expression. This is an expanded view of the plastid-encoded genes from Figure 2 J. Genomic differences between strain 3D7, from which the complete genome was sequenced, and strain HB3 were measured by CGH. The relative hybridization between the gDNA derived from these two strains is shown as a percent reduction of the signal intensity for 3D7 ([A], CGH Data). Differences between the two strains are predominately located in the subtelomeric regions that contain the highly polymorphic var, rifin, and stevor gene families. Intrachromosomal variations, as observed for the msp2 gene, were rare." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 18; 1(1):e5" |
"PMC176545" | "12929205" | 4 | "pbio.0000005.g004" |  | "Figure 4 Temporal Distribution of the Apicoplast-Targeted Proteins and P. falciparum Proteases, Potential Antimalarial Drug Candidates (A) The expression profiles of all putative plastid-targeted genes represented on our microarray are shown. The yellow box encompasses a highly synchronized group of genes, which are in-phase with plastid genome expression. The average expression profile for this in-phase group of genes is shown and includes most of the known apicoplast-targeted genes as well as many hypothetical genes. For reference, the average expression profile for the plastid genome is shown (dashed gray line). (B) Proteases represent an attractive target for chemotherapeutic development. The broad range of temporal expression for various classes of proteases and their putative functions are displayed. Abbreviations: HAP, histo-aspartyl protease (PM III); Clp, caseineolytic protease; sub1, 2, subtilisin-like protease 1 and 2." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 18; 1(1):e5" |
"PMC176545" | "12929205" | 5 | "pbio.0000005.g005" |  | "Figure 5 Phaseogram of Putative Vaccine Targets The similarity of all expression profiles to seven known vaccine candidates (boxed) was calculated. The top 5% of similar profiles correspond to 262 ORFs, 28 of which have been previously associated with plasmodial antigenicity and the process of merozoite invasion." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 18; 1(1):e5" |
"PMC176546" | "12929206" | 1 | "pbio.0000006.g001" |  | "Figure 1 Asian Elephant Range and Sampling Locations in Borneo Solid lines demarcate country borders and the dotted line the boundary between the Malaysian states of Sabah and Sarawak. Black dots indicate areas of sample collection." | "CC BY" | "no" | "2022-01-13 00:01:35" | "PLoS Biol. 2003 Oct 18; 1(1):e6" |
"PMC176546" | "12929206" | 2 | "pbio.0000006.g002" |  | "Figure 2 Asian Elephant Range and Sampling Locations Central sampling locations denote the countries sampled and represent a number of actual sampling locations within each country. 1. Sri Lanka, 2. India, 3. Bhutan, 4. Bangladesh, 5. Thailand, 6. Laos, 7. Vietnam, 8. Cambodia, 9. Peninsular Malaysia, 10. Sumatra (Indonesia) 11. Borneo (Sabah–Malaysia)." | "CC BY" | "no" | "2022-01-13 00:01:35" | "PLoS Biol. 2003 Oct 18; 1(1):e6" |
"PMC176546" | "12929206" | 3 | "pbio.0000006.g003" |  | "Figure 3 A Neighbour-Joining Phylogram of Asian Elephant Haplotypes Rooted with an African Elephant Out-Group Sunda Region haplotypes are in bold." | "CC BY" | "no" | "2022-01-13 00:01:35" | "PLoS Biol. 2003 Oct 18; 1(1):e6" |
"PMC176546" | "12929206" | 4 | "pbio.0000006.g004" |  | "Figure 4 Network of Asian Elephant Haplotypes Based on Statistical Parsimony Grey circles with letters denote haplotypes unique to the Sunda region (BD: Borneo; BQ, BV: peninsular Malaysia; BR, BS, BT, BU: Sumatra). White circles with letters denote haplotypes found in mainland Asia (excluding peninsular Malaysia) and Sri Lanka. The small open circles denote hypothetical haplotypes. Haplotypes beginning with the letters A and B belong to the two clades α and β, respectively." | "CC BY" | "no" | "2022-01-13 00:01:35" | "PLoS Biol. 2003 Oct 18; 1(1):e6" |
"PMC176547" | "0" | 1 | "pbio.0000007.g001" |  | "Borneo elephant" | "CC BY" | "no" | "2022-01-13 00:01:35" | "PLoS Biol. 2003 Oct 18; 1(1):e7" |
"PMC176548" | "0" | 1 | "pbio.0000011.g001" |  | "Gene expression profile of P. falciparum
" | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 18; 1(1):e11" |
"PMC193604" | "12975658" | 1 | "pbio.0000013.g001" |  | "Figure 1 Rescuing Molecular Oscillations within the LN v s Is Not Sufficient to Rescue Locomotor Activity Rhythms The rescued mutant genotype is y w ; pdf–GAL4;UAS–CYC , cyc 01 / cyc 01 . The flies were entrained in standard LD conditions and timepoints taken. Molecular oscillations were examined by whole-mount in situ hybridization of the tim gene. Double staining with a Pdf probe was used to label the LN v s neuronal group. (A and B) These show representative duplicate experiments. No tim mRNA signal is detectable in the dorsal region of the brain. The lower arrows point to the s-LN v s and the upper arrows to the l-LN v s. (A) Brain taken at timepoint ZT3. Panels shown from left to right are Pdf (green, FITC labeled), tim (red, Cy3 labeled), and an image overlay. (B) Brain taken at timepoint ZT15. Panels shown from left to right are Pdf (green, FITC labeled), tim (red, Cy3 labeled), and an image overlay. (C) The double-plotted actograms of rescue mutant and control flies in a standard LD:DD behavior assay. The colors on the background indicate the lighting conditions of the behavior monitors (white, lights on; light blue, lights off). In the actogram, the average locomotor activity of the group of flies is plotted as a function of time. The left panel shows the actogram of the rescued mutant flies ( y w;pdf–GAL4/+;UAS–CYC,cyc 01 / cyc 01 , n = 30). RI (rhythm index; Levine et al. 2002a ) = 0.14. The right panel shows the actogram for the rescued wild-type (control) flies ( y w;pdf–GAL4/+;UAS–CYC/+ , n = 32, RI = 0.61)." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 15; 1(1):e13" |
"PMC193604" | "12975658" | 2 | "pbio.0000013.g002" |  | "Figure 2 All Brain Clock Neuronal Groups Maintain Robust Oscillations of tim RNA Levels in DD Wild-type flies were entrained for at least 3 days and then released into DD. tim RNA was assayed at trough (left panels) and peak (right panels) timepoints by whole-mount in situ hybridization. Wild-type flies in LD (A) were compared with the eighth day of DD (B). On the eighth day of DD, the locomotor activities of the fly population were still in close synchrony, without any obvious phase spreading (data not shown). Left panels, brains at ZT3 (A) or CT3 (B); right panels, brains from ZT15 (A) or CT15 (B). Both (A) and (B) are representative of three replicate experiments." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 15; 1(1):e13" |
"PMC193604" | "12975658" | 3 | "pbio.0000013.g003" |  | "Figure 3 Molecular Oscillations of tim RNA Damp in DD in the Pdf 01 Mutant
tim RNA oscillations were examined in the Pdf 01 mutant under both LD (A) and different days in DD ([B] and [C]), by whole-mount in situ hybridization. (A), (B), and (C) are representative images from replicas of three experiments. (A) The left panel is from ZT3, and the right panel is from ZT15. A normal tim oscillation profile is observed compared to that of wild-type (see Figure 2 A). (B) Brains from the Pdf 01 mutant in the first day of DD. Left panel, CT3; right panel, CT15. Oscillations are comparable to those in LD. (C) Brains taken in the fourth day of DD. Six timepoints were taken throughout the circadian day. The sequence of panels from left to right is CT2, 6, 10, 14, 18, and 20, respectively. Wild-type brains (top row) were assayed in parallel with those from the Pdf 01 mutant (bottom row). See text for details. (D) Quantification of (C). Relative intensities are taken from normalized mean pixel intensities. Different clock neuronal groups were quantified independently and compared between wild-type (blue curves) and Pdf 01 mutant (purple curves). The panels from left to right are quantification of tim RNA oscillation in the DNs, in the LN d s, and in the LN v s. Reduced cycling amplitude and a significant advanced phase were observed in the fourth day of DD. See text for details." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 15; 1(1):e13" |
"PMC193604" | "12975658" | 4 | "pbio.0000013.g004" |  | "Figure 4
cry RNA Oscillation Amplitude Is Also Reduced by the Fourth Day of DD in the Pdf 01 Mutant
cry RNA expression in the brain was examined at the fourth day of DD by whole-mount in situ hybridization using a cry probe. Timepoints were taken every 4 hours throughout the circadian day. The sequence of panels from left to right is CT2, 6, 10, 14, 18, and 20, respectively. Wild-type brains (top row) were analyzed in parallel with those from the Pdf 01 mutant (bottom row). Shown are representative images from duplicate experiments. Quantification of cry RNA oscillations in different cell groups is as shown in Figure 3 . Ubiquitous damping of the cycling amplitude in the different cell groups was observed in the Pdf 01 mutant." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 15; 1(1):e13" |
"PMC193604" | "12975658" | 5 | "pbio.0000013.g005" |  | "Figure 5 A PDF Peptide Binds to Many Cells, Including Several Clock Neuronal Groups In vitro biontinylated PDF peptide was used to visualize the peptide binding locations (middle panels, with Cy3) in the brain (see Materials and Methods for details). We used membrane-bound GFP (green panels on the left) to label specific circadian neurons as well as their projections (right panels show the overlay of both channels). (A) The brain is from flies with labeled LN v s (y w,UAS–mCD8iGFP;pdf–GAL4) . Numerous cells at the periphery of the medulla have the vast majority of the bound PDF peptide signal within the brain. This region receives widespread dendritic arborizations from the l-LN v s. (B) Bound PDF peptide was also detected on the surface of LN v s at a lower intensity. LN v cell bodies were labeled using UAS–mCD8iGFP;pdf–GAL4 . Since the signal from the Cy3 channel was much weaker than the GFP signal, we reduced the output gain from the GFP channel. Sequential scanning was used to prevent cross-talk between the two channels. (C) y w,UAS–mCD8iGFP;tim–GAL4/+ flies were used to label all circadian neurons. In the dorsal region shown in this series, the arrow points to a group of DN3 neurons." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 15; 1(1):e13" |
"PMC193605" | "12975657" | 1 | "pbio.0000019.g001" |  | "Figure 1 Number of Genes and Species within the Gene Families (A) Distribution of the number of genes contained in the homolog families. (B) Number of orphan genes in each species in parentheses. Abbreviations: Ba, Buchnera aphidicola ; Ec, Escherichia coli ; Hi, Haemophilus influenzae ; Pa, Pseudomonas aeruginosa ; Pm, Pasteurella multocida ; St, Salmonella typhimurium ; Vc, Vibrio cholerae ; Wb, Wigglesworthia brevipalpis ; Xa, Xanthomonas axonopodis ; Xc, Xanthomonas campestris ; Xf, Xylella fastidiosa ; Yp CO92, Yersinia pestis CO_92; Yp KIM, Yersinia pestis KIM. (C) Distribution of the number of species contained in the homolog families." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 15; 1(1):e19" |
"PMC193605" | "12975657" | 2 | "pbio.0000019.g002" |  | "Figure 2 The 13 Candidate Topologies Topologies 1–4 correspond to tree reconstructions based on SSU rRNA. Topologies 5 and 6 correspond to the trees based on the concatenation of the proteins. Topologies 7–13 correspond to additional topologies constructed to test the sister relationship of the two symbiont species. Species abbreviations as in Figure 1 . Abbreviations: ML, maximum likelihood; NJ, neighbor joining; K, Kimura distance; G&G, Galtier and Gouy distance; γ, gamma-based method for correcting the rate heterogeneity among sites. The position of the root corresponds to the one obtained repeatedly using SSU rRNA." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 15; 1(1):e19" |
"PMC193605" | "12975657" | 3 | "pbio.0000019.g003" |  | "Figure 3 Result of the SH Test The graph shows the number of alignments accepting or rejecting each topology. The “Other Topologies” are those built to test the sister relationship of Wigglesworthia and Buchnera . The “Proteins” topologies are those obtained using both the protein concatenation and the consensus of trees from all 205 alignments. The “SSU rRNA” topologies were obtained using the SSU rRNA sequences with different methods." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 15; 1(1):e19" |
"PMC193605" | "12975657" | 4 | "pbio.0000019.g004" |  | "Figure 4 Phylogenies for the Laterally Transferred Genes (A) ML trees obtained for BioB (left) and MviN (right). (B) NJ trees obtained for BioB (left) and MviN (right). Abbreviations: Pf, Pseudomonas fluorescens ; Pp, Pseudomonas putida ; Ps, Pseudomonas syringae . Other species abbreviations as in Figure 1 ." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 15; 1(1):e19" |
"PMC193605" | "12975657" | 5 | "pbio.0000019.g005" |  | "Figure 5 Tree Based on the Concatenation of the 205 Proteins (NJ) The topology shown agrees with almost all individual gene alignments (topology 5 of Figure 2 ). The same tree is obtained after removing the two genes showing evidence for LGT. The position of the root corresponds to the one obtained repeatedly using SSU rRNA." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 15; 1(1):e19" |
"PMC193605" | "12975657" | 6 | "pbio.0000019.g006" |  | "Figure 6 Similarity Levels for Pairwise Comparisons of Genes from Two Representative Genome Pairs Frequency distribution of the ratio (bit score/maximal bit score) in a BLASTP query of the proteins from E. coli on the proteins from the genomes of Salmonella enterica (solid line) and Vibrio cholerae (dashed line). The ratio of 0.3 allows identification of most homologs but excludes probable nonspecific matches (NS)." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 15; 1(1):e19" |
"PMC193606" | "0" | 1 | "pbio.0000023.g001" |  | "
Drosophila lateral neuron (green)" | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 15; 1(1):e23" |
"PMC193607" | "0" | 1 | "pbio.0000031.g001" |  | "Electron micrograph of Proteobacteria in eukaryotic cell" | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 15; 1(1):e31" |
"PMC212689" | "14551906" | 1 | "pbio.0000008.g001" |  | "Figure 1 Crossing for Kernels Over time, selective breeding modifies teosinte's few fruitcases (left) into modern corn's rows of exposed kernels (right). (Photo courtesy of John Doebley.)." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 13; 1(1):e8" |
"PMC212689" | "14551906" | 2 | "pbio.0000008.g002" |  | "Figure 2 Biotech Bridge to Africa In an effort to reduce corn stem-borer infestations, corporate and public researchers partner to develop local Bt corn varieties suitable for Kenya. (Photo courtesy of Dave Hoisington/CIMMYT.)." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 13; 1(1):e8" |
"PMC212690" | "14551907" | 1 | "pbio.0000009.g001" |  | "" | "CC BY" | "no" | "2022-01-13 00:05:08" | "PLoS Biol. 2003 Oct 13; 1(1):e9" |
"PMC212691" | "14551908" | 1 | "pbio.0000010.g001" |  | "Figure 1 Reaction Scheme for Wnt Signaling The reaction steps of the Wnt pathway are numbered 1 to 19. Protein complexes are denoted by the names of their components, separated by a slash and enclosed in brackets. Phosphorylated components are marked by an asterisk. Single-headed solid arrows characterize reactions taking place only in the indicated direction. Double-headed arrows denote binding equilibria. Blue arrows mark reactions that have only been taken into account when studying the effect of high axin concentrations. Broken arrows represent activation of Dsh by the Wnt ligand (step 1), Dsh-mediated initiation of the release of GSK3β from the destruction complex (step 3), and APC-mediated degradation of axin (step 15). The broken arrows indicate that the components mediate but do not participate stoichiometrically in the reaction scheme. The irreversible reactions 2, 4, 5, 9–11, and 13 are unimolecular, and reactions 6, 7, 8, 16, and 17 are reversible binding steps. The individual reactions and their role in the Wnt pathway are explained in the text." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 13; 1(1):e10" |
"PMC212691" | "14551908" | 2 | "pbio.0000010.g002" |  | "Figure 2 Kinetics of β-Catenin Degradation: Simulation and Experimental Results (A) Simulated timecourses of β-catenin degradation. The straight line for t < 0 corresponds to the reference state of β-catenin using the parameters given in the legends of Table 1 and 2. In vitro conditions are simulated by switching off synthesis of β-catenin and axin ( ν
12 = 0, ν
14 = 0 for t ≥ 0). Curve a: reference case (no addition of further compounds); curve b: addition of 0.2 nM axin; curve c: addition of 1 μM activated Dsh (deactivation of Dsh was neglected, k
2 = 0); curve d: inhibition of GSK3β (simulated by setting k
4 = 0, k
9 = 0); curve e: addition of 1μM TCF. Addition of compounds (axin, Dsh, TCF) and inhibition of GSK3β was performed at t = 0. (B) Experimental timecourse of β-catenin degradation in Xenopus egg extracts in the presence of buffer (curve a′), axin (curve b′: 10 nM), Dsh (curve c′: 1 μM), Li + (curve d′: 25 mM), or Tcf3 (curve e′: 1 μM)." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 13; 1(1):e10" |
"PMC212691" | "14551908" | 3 | "pbio.0000010.g003" |  | "Figure 3 Preincubation of Dsh in Xenopus Egg Extracts Abolishes the Lag in Dsh Activity Labeled β-catenin was incubated in Xenopus extracts on ice 30 min prior to (B) or 30 min after (A) the extract had been preincubated with 1 μM Dsh. No degradation of the labeled β-catenin was detected while the reactions were on ice. The reactions were started by shifting to 20°C." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 13; 1(1):e10" |
"PMC212691" | "14551908" | 4 | "pbio.0000010.g004" |  | "Figure 4 The Effect of Dsh versus Axin or GSK3β on the Half-Life of β-Catenin in Xenopus Extracts (A and B) Predicted effects of Dsh, axin, and GSK3β on the half-life of β-catenin degradation. The half-lives are calculated from simulated degradation curves. Data are plotted as function of added Dsh (logarithmic scale) for various concentrations of axin (A) and GSK3β (B). (C and D) Measured effects of Dsh, axin, and GSK3β on the half-life of β-catenin degradation. Stimulation of β-catenin degradation by axin occurs throughout the range of Dsh concentrations tested. (C) Axin increases the rate of β-catenin degradation even in the absence of added Dsh. (D) Stimulation of β-catenin degradation by GSK3β is detected only at high concentrations of Dsh. No effects of GSK3β on β-catenin degradation can be detected at less than 30 nM added Dsh. There is a disparity between the concentrations of axin in the experimental and theoretical curves. We assume that this is most likely due to the specific activity of the expressed axin protein." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 13; 1(1):e10" |
"PMC212691" | "14551908" | 5 | "pbio.0000010.g005" |  | "Figure 5 Effect of the Regulatory Loop for Axin Degradation The case “with regulatory loop” takes into account that axin degradation is APC-dependent (black curves). Alternatively, the case without this regulatory loop is considered (red curves). For the regulatory loop, the rate law (5) is used assuming that in the reference state the APC activation is half of its maximum ( K M = 98.0 nM). The value of k ′ 15 was chosen such that in the reference state both cases, with and without regulatory loop, yield the same degradation rate of axin ( k ′ 15 = 0.33 min −1 )." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 13; 1(1):e10" |
"PMC212691" | "14551908" | 6 | "pbio.0000010.g006" |  | "Figure 6 Timecourse of β-Catenin and Axin Concentrations Following a Transient Wnt Stimulation Transient activation of the pathway is modeled assuming a Wnt stimulus that decays exponentially (Equation [6] with τ W = 1/ λ = 20 min) starting at t
0 = 0. The straight line for t < 0 corresponds to the steady state before pathway stimulation. The curves are obtained by numerical integration of the differential equation system (see Dataset S1). The various curves for β-catenin and for axin differ in the turnover rate of axin determined by the parameters ν
14 and k
15 (curves a: reference values of these parameters; curves b: increase by a factor of 5; curves c: reduction by a factor of 5). All other parameters are given in the legend of Table 2 ." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 13; 1(1):e10" |
"PMC212691" | "14551908" | 7 | "pbio.0000010.g007" |  | "Figure 7 Effects of Increasing Axin Concentration on β-Catenin Degradation (A) Effect of axin concentration on β-catenin half-life. Curve a: reference case ( K
18 , K
19 > 1 nM, ordered mechanism); curve b: K
18 = 1 nM, K
19 > 1 nM; curve c: K
18 > 1 nM, K
19 = 1 nM; curve d: K
18 = 1 nM. (B) High concentration of axin inhibits β-catenin degradation in Xenopus egg extracts. Labeled β-catenin was incubated in Xenopus extracts in the absence (0 nM) or presence of moderate (10 nM) and high (300 nM) concentrations of axin. Moderate concentrations of axin greatly accelerate, whereas high concentrations inhibit β-catenin degradation." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 13; 1(1):e10" |
"PMC212691" | "14551908" | 8 | "pbio.0000010.g008" |  | "Figure 8 Effects of APC Concentrations on β-Catenin Degradation Effect of APC concentration on β-catenin half-life assuming an ordered (curve a) or nonordered mechanism (curve b: K
17 = 1,200 nM), respectively." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 13; 1(1):e10" |
"PMC212691" | "14551908" | 9 | "pbio.0000010.g009" |  | "Figure 9 Effects of the Alternative β-Catenin Degradation Pathway and of Axin Degradation at Low Concentrations of APC (A) The alternative β-catenin degradation pathway (axin independent) can have profound effects on β-catenin levels at low APC concentrations. Variations of β-catenin and axin resulting from changes in APC concentration were calculated from the standard stimulated state. Relative variations were plotted since variation in the share of alternative degradation (1%, 5%, and 10%) results in changes of the standard stimulated state (all parameters are constant). β-Catenin and axin levels for varying contributions of the alternative degradation pathway are as follows: 1.5%, β-catenin 178 nM, axin 0.00728 nM; 5%, β-catenin 151 nM, axin 0.00679 nM; 10%, β-catenin 125 nM, axin 0.00629 nM. (B) Inhibition of axin degradation reduces β-catenin concentration after loss of APC. Plotted is the concentration of a potential proteasome inhibitor I (scaled to its inhibition constant, K
I ) necessary to reduce β-catenin concentration to its original level, depending on the concentration of APC." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 13; 1(1):e10" |
"PMC212692" | "14551910" | 1 | "pbio.0000012.g001" |  | "Figure 1 Comparison of Different RNAi Experiments of Chromosome I Using Wild-Type Bristol N2 and rrf-3
Differences between different laboratories or investigators and between experiments done within the same laboratory and by the same investigators are observed. Ovals represent the amount of bacterial clones that gave an RNAi phenotype in an experiment. Areas that overlap represent clones for which in both experiments an RNAi phenotype was detected. Differences and overlap between an RNAi experiment done with the rrf-3 mutant strain and the data obtained by Fraser et al. (2000 ) done with the standard laboratory strain, Bristol N2 (A); N2 and rrf-3 tested at the same time within our laboratory (B); experiments done with N2 in two different laboratories: this study (‘NL') and Fraser et al. (2000 ) (C); two experiments done with the same strain, rrf-3 , within our laboratory (D)." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 13; 1(1):e12" |
"PMC212693" | "14551911" | 1 | "pbio.0000014.g001" |  | "Figure 1 FRAP of HP1–GFP Reveals a Dynamic Association with Heterochromatin A fraction of a heterochromatic cluster (arrowhead) was bleached by a laser pulse, and recovery of fluorescence was monitored by time-lapse imaging. Images were kindly provided by Thierry Cheutin and Tom Misteli." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 13; 1(1):e14" |
"PMC212694" | "14551912" | 1 | "pbio.0000015.g001" |  | "Figure 1 Flow Diagram of Gene Expression Profiling" | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 13; 1(1):e15" |
"PMC212695" | "14551913" | 1 | "pbio.0000016.g001" |  | "Figure 1 V(D)J Recombination Takes Place within the BCR and TCR Loci (A) Schematic of a receptor locus.V, D, and J segments are found just upstream of the constant region. (B) A cartoon view of a VJ recombination reaction. V segments (red) are flanked by RSSs with 12 bp-long spacers (green), while the J segments are flanked by RSS with 23 bp-long spacers (orange). Breaks are introduced directly between the heptamer and the coding sequence, and a CJ is formed between a V and a J segment, while the RSS ends are put together to form an SJ within a circular DNA that is later lost. Symbols: P, promoter; E, enhancer." | "CC BY" | "no" | "2022-01-13 00:01:35" | "PLoS Biol. 2003 Oct 13; 1(1):e16" |
"PMC212695" | "14551913" | 2 | "pbio.0000016.g002" |  | "Figure 2 RSSs Consist of a Fairly Conserved Heptamer and Nonamer Sequence, Separated by a Spacer Element Heptamer is shown in red and nonamer in green. Conserved nucleotides are shown in bold. The spacer is either 12 or 23 bp long." | "CC BY" | "no" | "2022-01-13 00:01:35" | "PLoS Biol. 2003 Oct 13; 1(1):e16" |
"PMC212698" | "14551916" | 1 | "pbio.0000020.g001" |  | "Figure 1 Study Design Candidate genes were selected based on known or putative function. A de novo polymorphism discovery step was undertaken to identify novel variants for association studies. We selected 152 SNPs and tested them in a case-control study and a QT study. Association analysis with Type 2 diabetes was done for SNPs and haplotypes under multiple genetic models. Only SNPs and haplotypes associated with disease were evaluated for association with five diabetes-related QTs under the same model in the QT study." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 13; 1(1):e20" |
"PMC212698" | "14551916" | 2 | "pbio.0000020.g002" |  | "Figure 2 Power Calculations Power of the current Cambridgeshire Case-Control Study to detect associations with risk allele of varying frequencies and with a Type 1 error rate of 5%. Abbreviations: p0, frequency of the predisposing allele; chr, number of chromosomes. Graphs were plotted with the PS power and sample-size program (available at http://www.mc.vanderbilt.edu/prevmed/ps ; DuPont and Plummer 1997 )." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 13; 1(1):e20" |
"PMC212698" | "14551916" | 3 | "pbio.0000020.g003" |  | "Figure 3 Genes with Haplotypes Associated with Type 2 Diabetes Genomic organization with exons (black boxes or vertical lines) and with genotyped SNPs and SNPs utilised in the haplotype reconstructions (in blue boxes) is shown. The most common haplotypes with population prevalence greater than 5% in the control population are shown, and the measure of LD ( r 2 ) is shown for a subset of the SNPs. (A) ABCC8–KCNJ11 . (B) HNF4A . (C) INSR ." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 13; 1(1):e20" |
"PMC212698" | "14551916" | 4 | "pbio.0000020.g004" |  | "Figure 4 Size of Case-Control Study Required to Detect Small Risk Effects The number is shown of the case chromosomes (assuming an equal number of control chromosomes) required to attain 80% power to detect associations with the OR varying between 1.0 and 1.5 and with a Type 1 error rate of 0.01%. Abbreviations: p0, frequency of the predisposing allele; chr, number of chromosomes. Graphs were plotted with the PS power and sample-size program ( DuPont and Plummer 1997 )." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 13; 1(1):e20" |
"PMC212699" | "14551917" | 1 | "pbio.0000021.g001" |  | "Figure 1 Expression of Three Transcription Factors during Early Bacteriocyte Development (A) Drawings of some stages of pea aphid embryonic development, approximately to scale. Embryos develop viviparously within a follicular epithelium of the ovariole (data not shown). For a complete description, see Miura et al. (2003 ). Bacteria are transferred at stage 7. Embryos are labeled with bacteria (b), head (h), thoracic (t), and abdominal (a) regions. The three thoracic segments (t1, t2, t2) and germ cells (gc) are indicated in the stage 14 embryo. (B) A drawing of a stage 7 embryo illustrates transovarial transfer of the bacteria (red arrowhead) to the embryo and the presumptive bacteriocyte nuclei (arrow). (C) Confocal micrograph of a stage 6 embryo stained with anti-Dll antibody (red, indicated by arrow). Anti-Dll labels syncytial nuclei (presumptive bacteriocyte nuclei) in the posterior of the embryo. (D) Confocal micrograph of stage 7 embryo stained with anti-Dll and FP6.87 antibodies. Soon after the bacteria begin to invade the embryo, we observe staining with the FP6.87 antibody localized to the nucleoli (blue), which recognizes both Ubx and Abd-A in diverse arthropods, in the same nuclei that are already expressing Dll (red). The region outlined with a broken white box is enlarged in (D′) to show the bacteria, and only the green channel is shown in monochrome. The red arrow indicates one bacterium. (E and F) In these two panels of the same focal plane from the same stage 9 embryo, Ubx/Abd-A staining (blue) is observed throughout the entire nucleus of all nuclei that also express Dll (red). (G) Confocal micrograph of a stage 8 embryo stained with anti-En (yellow). As the transfer of bacteria (arrowhead) is being completed, the bacteriocyte nuclei begin to express En (yellow, indicated with arrow). In (C)–(G), confocal micrographs show only one focal plane of the embryo, so not all bacteriocyte nuclei in each embryo can be seen. In all figures, F-actin is stained with phalloidin (green). Embryos in all figures, except Figure 2 , are oriented with anterior of the entire embryo (towards the germarium) to the left." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 13; 1(1):e21" |
"PMC212699" | "14551917" | 2 | "pbio.0000021.g002" |  | "Figure 2 The Second Wave of Bacteriocyte Determination In (A)–(D), the embryos, which are normally folded in upon themselves in a pretzel shape within the ovariole ( Miura et al. 2003 ), have been dissected flat, stained with anti-Dll antibody (red) and phalloidin (green), and examined with a confocal microscope. (A) Dll expression (red) in a stage 14 embryo is detected in the labrum (La) and all developing limbs on the ventral surface except the mandibular segment (Mn). (Other abbreviations: An, antenna; Mx, maxilla; Lb, labium; T1, T2, T3, first, second, and third thoracic leg, respectively.) The dorsal surface of the abdomen of the same embryo is shown illustrating Dll expression in the original bacteriocytes (white arrow) and in a more posterior population of nuclei or cells (blue arrow). Germ cells (gc) are labeled. (B) Dll expression is first observed in the new bacteriocyte nuclei at stage 13. (C) By stage 15, many of the new bacteriocytes have migrated to and begun intercalating between the original bacteriocytes. (D) By stage 16, all of the new bacteriocytes have intercalated between the original bacteriocytes. (E) The migration of the new bacteriocytes is seen in a confocal section of an undissected stage 14 embryo. Embryos in (A)–(D) are oriented with the anterior of the germband towards the left." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 13; 1(1):e21" |
"PMC212699" | "14551917" | 3 | "pbio.0000021.g003" |  | "Figure 3 Elimination of B. aphidicola by Treatment with Antibiotics Has No Effect on the Determination and Maintenance of the Bacteriocyte Cell Fate in A. pisum
(A–C) Confocal micrographs of control embryos stained with anti-Dll antibody (red) show expression of Dll, as described in Figure 1 . Enlarged views of the bacteria within the broken white boxes in each embryo are shown in (A′)–(C′). (D–F) Embryos within aposymbiotic aphids at comparable stages as the controls in (A)–(C) express Dll in bacteriocyte nuclei. No bacteria are observed within these embryos, as seen in the enlarged views of (D′)–(F′)." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 13; 1(1):e21" |
"PMC212699" | "14551917" | 4 | "pbio.0000021.g004" |  | "Figure 4 Expression of Dll in Bacteriocytes and the Pattern of Bacteriocyte Development Are Conserved in Parthenogenetic Females of P. spyrothecae
Confocal micrographs of P. spyrothecae parthenogenetic embryos stained with anti-Dll antibody (red). (A) Dll is first detected in stage 6 embryos in one or two nuclei posterior to the cellular blastoderm (arrow). (B) By stage 8, the bacteria have been transferred to and entirely fill the embryo (red arrowhead). The Dll-expressing nuclei (arrow) have become highly polyploid. (C and D) At stage 12, only the original bacteriocyte nuclei are observed expressing Dll (white arrow), but by stage 14 (D) additional nuclei (blue arrow) closely apposed to the dorsal germband express Dll. (E) By stage 15, these new nuclei surround the original bacteriocyte, and at later stages the bacteria are divided into individual cells." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 13; 1(1):e21" |
"PMC212699" | "14551917" | 5 | "pbio.0000021.g005" |  | "Figure 5 Bacteriocytes Are Retained in One Species That Has Evolutionarily Lost Bacteria, but Not in Males of Another Species That Do Not Inherit Bacteria (A and B) Confocal micrographs of embryos of T. styraci stained with anti-Dll antibody (red). In T. styraci , in which B. aphidicola has been evolutionarily lost ( Fukatsu and Ishikawa 1992a ), embryos still contain nuclei that express Dll in the correct time and place to be bacteriocyte nuclei. (A) Dll expression is first detected in posterior nuclei at blastoderm at approximately stage 6 (arrow). (B) By stage 14, the original nuclei have divided once or twice and become polyploid (original bacteriocytes), and new cells begin to express Dll (new bacteriocytes; blue arrow) and migrate towards the original bacteriocytes. (C–F) Confocal micrographs of embryos of P. spyrothecae stained with anti-Dll antibody (red). (C) Stage 16 male embryos of P. spyrothecae do not contain B. aphidicola, and no Dll-expressing cells are observed in the expected location for bacteriocytes. We believe that the cells in this location are sperm (marked with an asterisk). Sexual female embryos within the same ovary do contain Dll-expressing original and new bacteriocyte nuclei (white and blue arrows, respectively). (D and E) Transient expression of Dll in putative bacteriocytes is observed in stage 7 male embryos (arrow in male embryo of [D]), but this expression does not persist into stage 10 male embryos (E), where no Dll-expressing nuclei are observed. By contrast, stage 6 female embryos (D) contain polyploid Dll-expressing nuclei (arrow in female embryo of [D]). The sex of each embryo could be determined because males develop synchronously and earlier than females ( Lampel 1958 , 1968). (F) In stage 14 male embryos, we observe transient Dll expression in nuclei (blue arrow) adjacent to the germ cells (gc) in the correct location to be the second wave of bacteriocyte nuclei. This Dll expression does not persist (see stage 16 male in [C]), and the fate of the cells is unknown." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 13; 1(1):e21" |
"PMC212700" | "0" | 1 | "pbio.0000024.g001" |  | "Aphid host of Buchnera endosymbionts" | "CC BY" | "no" | "2022-01-13 00:05:08" | "PLoS Biol. 2003 Oct 13; 1(1):e24" |
"PMC212701" | "0" | 1 | "pbio.0000026.g001" |  | "
Caenorhabditis elegans worms" | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 13; 1(1):e26" |
"PMC212702" | "14551921" | 1 | "pbio.0000027.g001" |  | "Figure 1 Biochemistry and Histology of Different Skin Types (A) Activation of the melanocortin 1 receptor (MC1R) promotes the synthesis of eumelanin at the expense of pheomelanin, although oxidation of tyrosine by tyrosinase (TYR) is required for synthesis of both pigment types. The membrane-associated transport protein (MATP) and the pink-eyed dilution protein (P) are melanosomal membrane components that contribute to the extent of pigment synthesis within melanosomes. (B) There is a gradient of melanosome size and number in dark, intermediate, and light skin; in addition, melanosomes of dark skin are more widely dispersed. This diagram is based on one published by Sturm et al. (1998) and summarizes data from Szabo et al. (1969) , Toda et al. (1972) , and Konrad and Wolff (1973) based on individuals whose recent ancestors were from Africa, Asia, or Europe." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 13; 1(1):e27" |
"PMC212702" | "14551921" | 2 | "pbio.0000027.g002" |  | "Figure 2 Relationship of Skin Color to Latitude (A) A traditional skin color map based on the data of Biasutti. Reproduced from http://anthro.palomar.edu/vary/ with permission from Dennis O'Neil.
Erratum note: The source of this image was incorrectly acknowledged. Corrected 12/19/03.
(B) Summary of 102 skin reflectance samples for males as a function of latitude, redrawn from Relethford (1997) ." | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 13; 1(1):e27" |
"PMC212704" | "0" | 1 | "pbio.0000032.g001" |  | "Understanding Wnt signaling through molecular modeling" | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Oct 13; 1(1):e32" |
"PMC300675" | "0" | 1 | "pbio.0000029.g001" |  | "Ribbon diagram of transferrin receptor homodimer" | "CC BY" | "no" | "2022-01-13 00:01:34" | "PLoS Biol. 2003 Dec 22; 1(3):e29" |
"PMC300881" | "14737182" | 1 | "pbio.0020002.g001" |  | "Figure 1 Alignment of Eukaryotic JAMM Domains with AfJAMM Eukaryotic JAMM domain proteins were aligned with AfJAMM using ClustalX and manually refined. Sequences are named with a two-letter code corresponding to the genus and species of the respective organism followed by the name of the protein (see Supporting Information for accession numbers), and ‘hyp’ is an abbreviation for hypothetical. The JAMM motif comprises the residues highlighted in green (E22, H67, H69, S77, and D80), and the active site core is surrounded by a red box. Conserved residues are highlighted in gray. The disulfide cysteine residues are highlighted in yellow (C74, C95). Active site residues that were mutated in S. pombe Csn5 are marked with an asterisk beneath the alignment. The secondary structure of AfJAMM is indicated above the sequence; helices are blue, sheets are red arrows, and loops are yellow lines. The dashed yellow line indicates a loop (F42–G58) that is disordered in the crystal." | "CC BY" | "no" | "2022-01-13 00:06:56" | "PLoS Biol. 2004 Jan 24; 2(1):e2" |
"PMC300881" | "14737182" | 2 | "pbio.0020002.g002" |  | "Figure 2 Crystal Structure of AfJAMM (A) On the left, the AfJAMM protomer is presented. The amino and carboxyl termini are marked by N and C. The catalytic zinc atom is depicted as a gray sphere. The zinc ligands (H67, H69, and D80) are colored in green. Secondary structure elements are numbered α1–α2 and β1–β8. The amino acids that mark the beginning and end of the disordered loop (P41–M60) are labeled. On the right, the crystal structure of the cytidine deaminase protomer is shown in the same orientation as AfJAMM to highlight the fold likeness as well as the similarly situated zinc-binding sites. The zinc ligands (C53, C86, and C89) are colored in green. (B) The dimer in the asymmetric unit of AfJAMM crystals. The side view is obtained by rotating the monomer in (A) by 90° as indicated by the quarter-arrow around the y-axis. The gold protomer is related to the green protomer by a 180° rotation around the crystallographic c-axis (shown as a black bar in the side view) and a translation of 3.38 Å." | "CC BY" | "no" | "2022-01-13 00:06:56" | "PLoS Biol. 2004 Jan 24; 2(1):e2" |
"PMC300881" | "14737182" | 3 | "pbio.0020002.g003" |  | "Figure 3 Metalloprotease-Like Active Site of AfJAMM (A) The active site of AfJAMM is shown centered around the catalytic zinc ion, which is represented as a dark gray sphere surrounded by anomalous cross Fourier difference density (contoured at 9.5 σ) colored in red. The aqua ligand, which lies at 2.9 Å from the zinc, is shown as a red sphere surrounded by purple density (contoured at 3 σ) of an F obs – F calc map, in which the aqua ligand was omitted from the calculation. Residues that underlie isopeptide bond cleavage are shown in green. The carboxylate oxygen atoms of D80 lie 2.2 Å from the zinc. The N ɛ2 atoms of H67 and H69 lie 2.1 Å from the zinc. The carboxylate oxygen atoms of E22 lie 3.2–3.5 Å from the aqua ligand and 4.5–5.0 Å from the zinc. Ancillary active site residues and the backbone (ribbon diagram) are shown in grey. The disulfide bond that links C74 to C95 is shown in yellow. The JAMM motif is shown in the upper lefthand corner for reference. (B) Superimposition of active site residues in ScNP, thermolysin, and AfJAMM. AfJAMM is in green, ScNP in blue, and thermolysin in red. For clarity only, the sidechains from the residues that bind the zinc or aqua ligands are shown in their entirety. In addition, atoms that stabilize the putative tetrahedral intermediate are shown. These include O γ of S77 in AfJAMM, O η of Y95 in ScNP, and the N ɛ2 of H231 in thermolysin." | "CC BY" | "no" | "2022-01-13 00:06:56" | "PLoS Biol. 2004 Jan 24; 2(1):e2" |
"PMC300881" | "14737182" | 4 | "pbio.0020002.g004" |  | "Figure 4 Mutations in the JAMM Motif of Csn5 Abrogate the Deneddylating Activity of the CSN (A) Mutations in the glutamic acid (E56A) that positions the aqua ligand and in the proposed catalytic serine (S128A) of Csn5 disrupt deneddylation of Cul1 by CSN but have no effect on assembly with Csn1. A csn5Δ strain of S. pombe was transformed with an empty pREP-41 plasmid (lane 1) or with the plasmid encoding FLAG tagged: Csn5 (lane 2), Csn5 E56A (lane 3), or Csn5 S128A (lane 4). Whole-cell lysates were used for Western blot analysis with anti-Cul1 antibodies (top gel) and anti-FLAG antibodies (second from top). A strain with a myc13 -tagged Csn1 was transformed with the above plasmids, and whole-cell lysates were used for Western blot analysis. Antibodies to the Myc tag were used to detect Csn1 myc13 (third from top), and were used to pull down Csn1 myc13 and subsequently blot with anti-FLAG antibodies to detect coprecipitated Csn5 mutant proteins (bottom gel). (B) Mutations in the JAMM motif display a modest dominant-negative phenotype. Western blot analysis of crude cell lysates was performed as described in (A). (C) Selected JAMM motifs from proteins of diverse functions. The canonical JAMM motif residues are highlighted in green. The conserved proline is highlighted in blue, and semiconserved cysteine is highlighted in yellow." | "CC BY" | "no" | "2022-01-13 00:06:56" | "PLoS Biol. 2004 Jan 24; 2(1):e2" |
"PMC300882" | "14737187" | 1 | "pbio.0020009.g001" |  | "Figure 1 Using Expression Data to Identify and Refine Sequence-Based Functional Assignments (A) Starting from a set of coexpressed genes (yellow dots in left box) associated with a particular function in organism A, we first identify the homologues in organism B using BLAST (middle box). Only some of these homologues are coexpressed while others are not (blue dots). The signature algorithm selects this coexpressed subset and adds further genes (light yellow) that were not identified based on sequence, but share similar expression profiles (right box). (B) The 15 coexpressed genes associated with heat shock in yeast (center) have eight homologues in E. coli (left) and 14 in C. elegans (right). Among the ten genes whose expression profiles are the most similar to these homologues (bottom), many are known to be associated with heat-shock response (boldface). (C) For each of the six organisms, the distribution of the Z -scores for the average gene–gene correlation of all the “homologue modules” ( see Materials and Methods ) obtained from the yeast modules is shown (top). Rejecting the homologues that are not coexpressed gives rise to the “purified modules,” whose Z -scores generally are larger (except for the yeast modules, which contain only coexpressed genes from the beginning). Adding further coexpressed genes yields the “refined modules,” which have significantly larger Z -scores (bottom)." | "CC BY" | "no" | "2022-01-13 00:06:56" | "PLoS Biol. 2004 Jan 15; 2(1):e9" |
"PMC300882" | "14737187" | 2 | "pbio.0020009.g002" |  | "Figure 2 Regulatory Relations between Modules A selection of eight transcription modules whose function is known in yeast was used to generate the corresponding (refined) homologue modules in the other five organisms. Each module is associated with a “condition profile” generated by the signature algorithm based on the expression data. (A) Correlations between these profiles were calculated for all pairs of modules in each organism. Note that for E. coli there is no proteasome and that the mitochondrial ribosomal proteins (MRPs) correspond to ribosomal genes. Modules are represented by circles (legend). Significantly correlated or significantly anticorrelated modules are connected by colored lines indicating their correlation (color bar). Positively correlated modules are placed close to each other, while a large distance reflects anticorrelation. See Figure S11 for a numerical tabulation of all pairwise correlations. (B and C) Correlations between pairs of modules according to the cell-cycle data as a function their correlation in the full data. Each circle corresponds to a pair of S. cerevisiae modules (B) or human modules (C). (D) To check the sensitivity of our results with respect to the size of the dataset, we reevaluated the correlations between the sets of conditions for randomly selected subsets of the data. Shown are the mean and standard deviation of the correlation coefficient between the heat-shock and protein-synthesis modules as a function of the fraction of removed conditions (see Figures S4 and S5 for correlations between other module pairs)." | "CC BY" | "no" | "2022-01-13 00:06:56" | "PLoS Biol. 2004 Jan 15; 2(1):e9" |
"PMC300882" | "14737187" | 3 | "pbio.0020009.g003" |  | "Figure 3 Properties of Transcription Modules (A and B) Module trees summarize the transcription modules identified by the ISA at different resolutions. Branches represent modules (rectangles) that remain fixed points over a range of thresholds. Fixed points that emerge at a higher threshold converge into an existing module when iterated at a lower threshold (thin transversal lines). Modules are colored according to the fraction of homologues they possess in the other organism (see the color bar). Among the yeast modules, those associated with protein synthesis (arrow) have the largest fraction of worm homologues. Searchable trees for all six organisms are available at http://barkai-serv.weizmann.ac.il/ComparativeAnalysis . (C) Histogram for the number of yeast modules with a given fraction of genes possessing a homologue in C. elegans (black bars). The distribution indicates that a significant number of modules have either much less or much more homologues than expected; indicated p -value were computed according to Kolmogorov–Smirnov test against control distribution (gray) generated from random sets of modules preserving their size. (D) Same as in (C) for C. elegans modules considering yeast homologues (see Figure S12 for other organisms)." | "CC BY" | "no" | "2022-01-13 00:06:56" | "PLoS Biol. 2004 Jan 15; 2(1):e9" |
"PMC300882" | "14737187" | 4 | "pbio.0020009.g004" |  | "Figure 4 Global Properties of Transcription Networks (A) The number of genes n(k) with connectivity k is plotted as a function of k ( see Materials and Methods ). For each of the six organisms n(k) is distributed as a power-law, n(k) ∼ k
−γ , with similar exponents γ ≈ 1.1–1.8 (see Figure S13). (B) The fraction of lethal genes is shown as a function of k for S. cerevisiae , E. coli , and C. elegans . The control (gray line) is obtained from 10,000 random choices for the lethal genes (preserving their total number). The dashed lines indicate standard deviations. (C) The fraction of genes with at least one yeast homologue is shown as a function of k for all six organisms. Control (gray) as in (B). (D) Z -score quantifying the deviation of the number of connections between genes with connectivities k and k ′ from that expected by randomly rewired networks (see Maslov and Sneppen 2002 ). Note that connections between genes of similar connectivity are enhanced (red regions), while those between highly and weakly connected genes are suppressed (blue). (E) The clustering coefficient C is plotted against k . Each dot corresponds to a single gene and is colored according to the transcription module it is associated with (see also Figure 2 ). Note that genes associated with the same module correspond to a specific band in the k – C plane. Several genes with high connectivity belong to more than one module (green dots superimposed on orange ones)." | "CC BY" | "no" | "2022-01-13 00:06:56" | "PLoS Biol. 2004 Jan 15; 2(1):e9" |
"PMC300883" | "14737191" | 1 | "pbio.0020015.g001" |  | "Figure 1 Caspase Activity Is Required for Spermatid Individualization (A–C) Testis of different genotypes were visualized with antibodies specific for activated Drice (green). (A) Wild-type testis. Active DRICE is present in multiple elongated cysts. Cystic bulges (cb) and waste bags (wb) are indicated by arrows. (B and C) Testes from β2tub-DIAP1 and β2tub-p35 males, respectively. Active DRICE is present in elongated cysts, but cystic bulges and waste bags are reduced in number and size. (D–F) Phalloidin-stained investment cones from testes of different genotypes (red). Spermatid axonemes in (D)–(F) are highlighted by the AXO49 antibody, which recognizes polyglycylated β2tub ( Bressac et al. 1995 ) (blue). (D) In wild-type testes, investment cones move as a coordinated group. (E and F) Coordinated investment cone movement is disrupted in cysts from β2tub-DIAP1 and β2tub-p35 males, respectively. (G–L) EM sections of elongated cysts of different genotypes. (G) A cyst from a wild-type male that has undergone individualization. The boxed region is shown at higher magnification in (J), along with the locations of the major mitochondrial derivative (mj), minor mitochondrial derivative (mi), and axoneme (ax). A single spermatid unit is outlined with a dashed line. (H and I) In cysts from β2tub-DIAP1 and β2tub-p35 males, respectively, many spermatid units are present in a common cytoplasm that contains organelles, often including an enlarged minor mitochondrial derivative. Boxed regions of β2tub-DIAP1 and β2tub-p35 cysts shown in (H) and (I) are shown at higher magnification in (K) and (L), respectively. Several examples of multiple spermatids present in a common cytoplasm are outlined by the dashed line in (K) and (L). Scale bar for EM micrographs = 1 μm." | "CC BY" | "no" | "2022-01-13 00:06:56" | "PLoS Biol. 2004 Jan 15; 2(1):e15" |
"PMC300883" | "14737191" | 2 | "pbio.0020015.g002" |  | "Figure 2 ARK and DRONC Are Required for Spermatid Individualization (A and C) Testis from β2tub-Ark-RNAi and β2tub-Dn-DRONC males, respectively. Active DRICE-positive cysts are present, but cystic bulges and waste bags are largely absent. (B and D) Investment cone movements in testis from β2tub-Ark-RNAi and β2tub-Dn-DRONC, respectively, are uncoordinated. (E, G, and H) EM images of an elongated cyst from a β2tub-Ark-RNAi male. Some individualization failures are observed (E, G, and H), two of which are highlighted by the dashed lines in (G) and (H). In addition, many spermatids that have apparently undergone individualization still contain large amounts of excess cytoplasm (E and G). (F) EM image of a cyst from a β2ub-Dn-DRONC male. A large region in which individualization did not occur is outlined. (I) Western blot from wild-type (Wt) and β2tub-Ark-RNAi (DArki) testis probed with anti-ARK and anti-DRICE antibodies. ARK, but not DRICE, levels are greatly reduced in β2tub-Ark-RNAi testis." | "CC BY" | "no" | "2022-01-13 00:06:56" | "PLoS Biol. 2004 Jan 15; 2(1):e15" |
"PMC300883" | "14737191" | 3 | "pbio.0020015.g003" |  | "Figure 3 DRONC Activation Occurs in Association with Individualization Complexes and Is ARK-Dependent (A and B) Wild-type testis stained for active DRICE (green), phalloidin-stained filamentous actin (red), and TOTO-3-stained DNA (blue). (A) Active DRICE is present throughout the length of cysts undergoing individualization. (B) Higher magnification of the testis in (A). The arrowhead points to a cyst in which the individualization complex has assembled around the spermatid nuclei, but DRICE activation has not occurred. The arrow points to a neighboring cyst in which the individualization complex has just begun to move away from the spermatid nuclei. Active DRICE is now present throughout the length of this cyst, indicating that DRICE activation within a cyst occurs rapidly and globally. (C) Active DRONC (green) is initially present in a punctate pattern, apical to the individualization complex (red) at the base of the testis (arrowheads). The individualization complex then moves through the region containing active DRONC (arrow). (D) Subsequently, active DRONC is found associated with the trailing edge of the individualization complex as it moves apical within the cyst. A higher magnification view of active DRONC staining in the left-most cyst is shown in the inset. (E and F) Active DRONC is eliminated in cysts from β2tub-Ark-RNAi and β2tub-Dn-DRONC testis, respectively." | "CC BY" | "no" | "2022-01-13 00:06:56" | "PLoS Biol. 2004 Jan 15; 2(1):e15" |
"PMC300883" | "14737191" | 4 | "pbio.0020015.g004" |  | "Figure 4 HID, dFADD, and DREDD Participate in Individualization (A) HID protein (green) is concentrated in the region of the cystic bulge, which is marked by the presence of the phalloidin-stained individualization complex (red). (B) HID immunoreactivity is absent in testis from hid 05014 /H99 flies. (C) Active DRONC (green) is associated with the trailing edge of the individualization complex in a wild-type cyst. (D) Active DRONC is absent from the individualization complex in cysts from hid 05014 /H99 males. (E) EM section from hid 05014 /H99 testis. Essentially all spermatids have failed to individualize. (F) Higher magnification view of boxed area in (E). Multiple spermatid units sharing a common cytoplasm are outlined by the dashed line. (G) Representative EM section of cyst from dFadd f02804 / dFadd f02804 testis. Essentially all spermatids have failed to individualize. (H) EM section of cyst from Dredd B118 / Dredd B118 testis in which individualization has failed to occur. In some other cysts from this same male, individualization proceeded apparently normally (data not shown)." | "CC BY" | "no" | "2022-01-13 00:06:56" | "PLoS Biol. 2004 Jan 15; 2(1):e15" |
"PMC300883" | "14737191" | 5 | "pbio.0020015.g005" |  | "Figure 5 The bln 1 P-Element Insertion, Which Inhibits Cyt-c-d Expression, Results in Pleiotropic Defects in Spermatogenesis (A) Genomic organization of the cyt-c-d region. Upper half of the panel illustrates the structure of the region, as described by Arama et al. (2003 ). The lower half of the panel indicates the relative locations of several other genes in the region, as annotated by the Berkeley Drosophila Genome Project ( http://flybase.bio.indiana.edu/search/ ) as of August 2002. The bln 1 P element is inserted within the cyt-c-d transcription unit. This P element is also inserted within the transcription unit of a second gene, CR31808-RA ( RE70695 ). Both of these genes and the bln 1 P element reside within the intron of a third gene, CG31782 . (B and D) Wild-type and bln 1 testis, respectively, stained with anti-active DRICE antibodies. Active DRICE immunoreactivity is eliminated in bln 1 testis, as described in Arama et al. (2003 ). (C and E) Wild-type and bln 1 testis, respectively, stained with AXO49 antibodies (blue), which recognize polyglycylated β2tub present in axonemal microtubules, and phalloidin (red). Polyglycylation occurs prior to individualization ( Bressac et al. 1995 ). Axonemes of elongated cysts from wild-type flies stain with AXO49 (C), while those from bln 1 males do not (E). (F–I) EMs of cysts of different developmental stages from wild-type (F and G) and bln 1 (H) testis. (F) Wild-type cyst prior to individualization. Note the structures of the major and minor mitochondrial derivatives, in particular the fact that the major mitochondrial derivative is increased in size and is electron dense. (G) Wild-type cyst following individualization. (H) Representative example of the most mature cysts found in bln 1 testis. Note the dramatically increased cell size and the lack of differentiation of the major and mitochondrial derivatives, as compared to wild-type." | "CC BY" | "no" | "2022-01-13 00:06:56" | "PLoS Biol. 2004 Jan 15; 2(1):e15" |
"PMC300883" | "14737191" | 6 | "pbio.0020015.g006" |  | "Figure 6
driceless Males Lack Active Drice Staining and Show Defects in Individualization (A) Testis from driceless male stained with active DRICE. Active DRICE staining is eliminated. (B) Elongated cysts from driceless male. AXO49 staining (blue) outlines the location of three cystic bulges. Individualization complexes (arrows) are marked with phalloidin (red). (C) Example of a cyst from a driceless male in which individualization has proceeded normally. (D) Example of a cyst from a driceless male in which individualization has failed to occur. (E) Boxed area in (D) shown at higher magnification. A region in which individualization has failed is outlined with a dashed line." | "CC BY" | "no" | "2022-01-13 00:06:56" | "PLoS Biol. 2004 Jan 15; 2(1):e15" |
"PMC300883" | "14737191" | 7 | "pbio.0020015.g007" |  | "Figure 7 Active DRICE Is Eliminated from the Cytoplasm of Wild-Type Spermatids Following Passage of the Individualization Complex, but Not from Spermatids in Which Caspase Activity Has Been Inhibited (A) Cystic bulge from a wild-type cyst stained with active DRICE (red). The cystic bulge (arrowhead) is moving to the left. Active DRICE staining is absent in areas of the spermatid bundle that the individualization complex has passed through and in which excess cytoplasm has been eliminated (arrow). (B) Cystic bulge from a β2tub-p35 cyst. The cystic bulge (arrowhead) is decreased in size, and active DRICE is present in areas of the spermatid bundle through which the individualization complex has moved (arrows). These observations suggest caspase inhibition results in at least a partial failure to eliminate excess cytoplasm, but that this is not necessarily associated with lack of movement of the individualization complex." | "CC BY" | "no" | "2022-01-13 00:06:56" | "PLoS Biol. 2004 Jan 15; 2(1):e15" |
"PMC300884" | "0" | 1 | "pbio.0020017.g001" |  | "The active site of JAMM" | "CC BY" | "no" | "2022-01-13 00:06:50" | "PLoS Biol. 2004 Jan 24; 2(1):e17" |
"PMC300885" | "0" | 1 | "pbio.0020018.g001" |  | "Regulatory relations among transcription modules" | "CC BY" | "no" | "2022-01-13 00:06:56" | "PLoS Biol. 2004 Jan 15; 2(1):e18" |
"PMC300886" | "0" | 1 | "pbio.0020034.g001" |  | "Developing spermatids in a normal Drosophila testis" | "CC BY" | "no" | "2022-01-13 00:06:56" | "PLoS Biol. 2004 Jan 15; 2(1):e34" |
"PMC314462" | "14737181" | 1 | "pbio.0020001.g001" |  | "Figure 1 Relative Increase in Scientific Publications in the Americas This figure shows the relative increase in publication in the Americas measured as the proportional change (%) in the number of SCI publications compared with the number of publications in 1990 ( RICYT 2002 )." | "CC BY" | "no" | "2022-01-13 00:06:56" | "PLoS Biol. 2004 Jan 20; 2(1):e1" |
"PMC314462" | "14737181" | 2 | "pbio.0020001.g002" |  | "Figure 2 Number of SCI Publications per Million Dollars This figure shows the number of SCI publications per million dollars that are invested in research and development in the Americas ( RICYT 2002 )." | "CC BY" | "no" | "2022-01-13 00:06:56" | "PLoS Biol. 2004 Jan 20; 2(1):e1" |
"PMC314463" | "14737183" | 1 | "pbio.0020003.g001" |  | "Figure 1 Dorsoventral Skin Characteristics (A) Skin slices from animals of different age and genotype demonstrate similar patterns of hair-length variation along the dorsoventral axis (scale bar = 1 cm). (B) Enlarged area from (A), demonstrating the transition in hair length and color in a t / a t mice (scale bar = 0.375 cm). (C) Proportional hair length for (A) plotted as a function of relative position along the dorsoventral axis. (D) Hair length plotted as a function of absolute position along the dorsoventral axis for 8-wk-old BA strain mice. (E) Proportion of zigzag hairs (± SEM) differs slightly between dorsum and ventrum of inbred mice ( p < 0.0001, χ 2 test, n = 1,958, 1,477, 1,579, 1,502). (F) Differences in dorsal and ventral skin development at P4.5 (scale bar = 1 mm, upper; 200 μm, lower). (G) Differences in hair melanin content and DOPA staining for dorsum (d), flank (f), and ventrum (v) in a e / a e and a t / a t mice. The upper panel also demonstrates a cream-colored appearance of the a t / a t ventrum. The middle panel shows representative awls (scale bar = 100 μm). The lower panel shows DOPA-stained dermis (scale bar = 200 μm)." | "CC BY" | "no" | "2022-01-13 00:06:50" | "PLoS Biol. 2004 Jan 20; 2(1):e3" |
"PMC314463" | "14737183" | 2 | "pbio.0020003.g002" |  | "Figure 2 The de H Pigmentation Phenotype (A) 10-wk-old de H /de H and nonmutant animals on a a t background. A thin stripe of yellow hair normally separates the dorsal black hairs from the ventral cream hairs. In de H , the yellow stripe is extended dorsally, and the boundary between the yellow and the black hairs is fuzzier. (B) Skin slices taken from 1.5-mo-old de H /de H and nonmutant littermates (scale bar = 0.5 cm). (C) Proportion of total skin area as determined by observation of pelts taken from the interlimb region. The proportion occupied by the yellow lateral compartment (± SEM) differs between mutant and nonmutant littermate flanks ( p < 0.0005, paired t -test, n = 6 pairs). There is also (data not shown) a small increase in the proportion of total skin area occupied by the ventral cream-colored compartment, 47.9 % in mutant compared to 37.8% in nonmutant ( p < 0.005, paired t -test, n = 6 pairs). (D) On an a e /a e background, the extent of dorsal skin pigmentation is reduced in de H /de H neonates (P3.5). (E) Hair length in a representative pair of 1.5-mo-old de H /de H and nonmutant littermates, averaged over three skin slices at different rostrocaudal levels, and plotted as a function of the absolute distance from middorsum or the percentage of total slice length." | "CC BY" | "no" | "2022-01-13 00:06:50" | "PLoS Biol. 2004 Jan 20; 2(1):e3" |
"PMC314463" | "14737183" | 3 | "pbio.0020003.g003" |  | "Figure 3 Molecular Genetics of de H and Tbx15
(A) Genetic and physical map, as described in the text. Markers M1 to M3 are SSCP markers generated from a BAC contig of the region; marker M4 is STS 16.MMHAP32FLF1 and was also used as an SSCP marker. M2 and M3, which flank the Tbx15 and M6pr-ps on the UCSC genome browser map and lie 634 kb apart, were nonrecombinant with de H in 2340 meioses. (B) The de H mutation is a deletion that starts in Tbx15 intron 1 and ends in the M6pr-ps . (C) Sequence of deletion breakpoints. (D) Diagram of Tbx15 LacZ allele constructed by gene targeting. As described in the text, this allele is predicted to give rise to a protein truncated after approximately 154 codons and is lacking critical residues of the T box. Heterozygotes for the targeted allele exhibit normal size, morphology, and hair-color patterns, but homozygotes and Tbx15 LacZ / de H compound heterozygotes are identical to de H homozygotes." | "CC BY" | "no" | "2022-01-13 00:06:50" | "PLoS Biol. 2004 Jan 20; 2(1):e3" |
"PMC314463" | "14737183" | 4 | "pbio.0020003.g004" |  | "Figure 4 Developmental Expression of Tbx15
(A) At E12.5, transverse sections at different levels show expression in head mesenchyme (a and b); myotome, occipital, and periocular mesenchyme (b); palatal shelf, cervical sclerotome, and nasal cartilage (c); maxillary and mandibular processes (d); limbs (e); and myotome and lateral mesenchyme (e and f) (scale bars = 500 μm). (B) Transverse sections through the flank at different times show expression in lateral mesenchyme (E11.5), expanding dorsally at E12.5, and both ventrally and dorsally at E13.5, detectable in loose mesenchyme underlying the dermis and the abdominal and subcutaneous muscles (scale bar = 500 μm). At P3.5, Tbx15 is expressed in the entire dermis and is most strongly expressed in dermal sheaths (scale bar = 200 μm)." | "CC BY" | "no" | "2022-01-13 00:06:50" | "PLoS Biol. 2004 Jan 20; 2(1):e3" |
"PMC314463" | "14737183" | 5 | "pbio.0020003.g005" |  | "Figure 5 Embryonic Expression of Tbx15 Compared to Agouti in a t / a t Mice (A and C) Tbx15 . (B and D) Agouti . At E12.5, expression of Tbx15 in dorsal skin is approximately complementary to that of Agouti in ventral skin. At E14.5, the levels of expression for both genes are lower, but Tbx15 expression has expanded ventrally and overlaps extensively with that of Agouti . In all four panels, arrows mark the approximate ventral limit of Tbx15 and the approximate dorsal limit of Agouti (scale bars = 500 μm)." | "CC BY" | "no" | "2022-01-13 00:06:50" | "PLoS Biol. 2004 Jan 20; 2(1):e3" |
"PMC314463" | "14737183" | 6 | "pbio.0020003.g006" |  | "Figure 6 Effect of de H on Agouti Expression Comparable sections from a t /a t ; de H / de H and a t /a t ; +/+ littermates. (A) At E14.5, de H / de H embryos have a smaller body cavity and loose skin within which Agouti expression appears to be shifted dorsally, as marked by arrows (scale bars = 500 μm). (B) At P4.5, Agouti expression in both dorsal and ventral skin is similar in de H / de H compared to nonmutant, but in the midflank region, there is increased Agouti expression in de H / de H , especially in the upper dermis (scale bars = 200 μm). Sections shown are representative of two mutant and two nonmutant samples examined at each time." | "CC BY" | "no" | "2022-01-13 00:06:50" | "PLoS Biol. 2004 Jan 20; 2(1):e3" |
"PMC314463" | "14737183" | 7 | "pbio.0020003.g007" |  | "Figure 7 Embryonic Establishment of Dorsoventral Skin Patterning Pieces of skin from dorsal, flank, and ventral regions of a t /a E12.5 embryos were transplanted into the testes of congenic animals as described in the text. Hair color of the grafts was examined 3 wk later. Grafts of ventral embryonic skin ( n = 3) produced yellow hairs, dorsal embryonic skin ( n = 4) produced black hairs, and flank embryonic skin produced mostly (13 out of 15) black and yellow hairs in distinct regions as shown. In parallel, in situ hybridization studies revealed that the embryonic flank contains the boundary of expression between Agouti and Tbx15 (scale bars = 1 mm for hairs and 200 μm for in situ hybridization results)." | "CC BY" | "no" | "2022-01-13 00:06:50" | "PLoS Biol. 2004 Jan 20; 2(1):e3" |
"PMC314463" | "14737183" | 8 | "pbio.0020003.g008" |  | "Figure 8 Comparison of the Dorsoventral a t /a t Pigmentation Boundary to the Lateral Somitic Frontier (A) Dorsoventral slices of skin from at the midtrunk region prepared such that the dorsal midline lies in the center of the slice. Sections were taken at P1.5 (a) or P4.5 (b–e) from a t /a t or R26R /+; Tg.Hoxb6-Cre /+ mice (the latter were stained with X-Gal), as described in Materials and Methods. For purposes of comparison, images were proportionally scaled. The boundary of X-Gal staining marks dermis derived from lateral plate versus dermis derived from mesoderm (the lateral somitic frontier) and lies more dorsal than the a t /a t pigmentation boundary. (B) Quantitation of mean (± SEM) dorsal pigmentation area ( n = 5) and somite-derived dermis area ( n = 3) shows a significant difference ( p < 0.005, t -test). (C) RNA in situ hybridization showing that Tbx15 expression at E11.5 is complementary to En1 expression on the flank (scale bars = 200 μm). The arrow indicates the boundary between the expression domains of the two genes." | "CC BY" | "no" | "2022-01-13 00:06:50" | "PLoS Biol. 2004 Jan 20; 2(1):e3" |
"PMC314463" | "14737183" | 9 | "pbio.0020003.g009" |  | "Figure 9 Model for Acquisition of Dorsoventral Patterning in the Trunk and the Role of Tbx15
(A) A tricolor pigmentation pattern is generated by the combination of distinct mechanisms that affect distribution of Agouti mRNA and histochemical staining for melanocytes; effects of the latter mechanism by itself are evident in a e / a e mice (see Figure 1 ). In a t /a t mice, reduced hair melanocyte activity and high levels of Agouti mRNA in the ventrum lead to a cream color; as melanocyte activity gradually increases towards the dorsum, a lateral stripe is apparent on the flank. The distributions of Agouti mRNA and histochemical staining for melanocytes are both affected by Tbx15 and are externally evident by a widening of the lateral stripe and an increased proportion of total skin occupied by the cream-colored area. (B) The lateral yellow stripe in a t /a t mice lies at the same level as the limb dorsoventral boundary. As described in the text, we propose that distinct dorsoventral compartments in ectoderm of the trunk provide an instructional cue to the mesoderm, leading to expression of Tbx15 in dorsal trunk mesenchyme and acquisition of dorsal dermis character. In the absence of Tbx15 , dorsal mesenchyme assumes ventral characteristics instead." | "CC BY" | "no" | "2022-01-13 00:06:50" | "PLoS Biol. 2004 Jan 20; 2(1):e3" |
"PMC314464" | "14737184" | 1 | "pbio.0020004.g001" |  | "Figure 1 Sequence Analysis of spect cDNA (A) Nucleotide sequence of spect cDNA (top lane) and the deduced amino acid sequence (bottom lane) are shown. The predicted N-terminal signal sequence is underlined. The numbers indicate positions of the nucleotides starting from the 5′ end. The asterisks indicate the termination codon. (B) A comparison of deduced amino acid sequences of P. berghei spect (top) and P. falciparum spect (bottom). Gaps are introduced to obtain optical matching by using GENETIX-MAC software. Asterisks or dots show conserved or similar residues, respectively. The amino acid numbers from the first Met residue are shown on the left of each line." | "CC BY" | "no" | "2022-01-13 00:06:50" | "PLoS Biol. 2004 Jan 20; 2(1):e4" |
"PMC314464" | "14737184" | 2 | "pbio.0020004.g002" |  | "Figure 2 SPECT Is a Microneme Protein Specifically Produced in the Liver-Infective Sporozoite Stage (A) Indirect immunofluorescence microscopy of all four invasive forms of the malarial parasite (indicated over the panel). Parasites were stained with primary antibodies against SPECT, followed by FITC-conjugated secondary antibodies. SPECT was detected only in the salivary gland sporozoite, the liver-infective stage. The corresponding phase-contrast or DAPI-stained image (Phase or DAPI) is shown under each image. Scale bars, 5 μm (B) Western blot analysis of SPECT production in the midgut sporozoite (M) and the salivary gland sporozoite (S). Lysate of 500,000 sporozoites was loaded onto each lane and detected with the same antibody used in (A). SPECT was detected as a single band of 22 kDa (arrowhead) only in the salivary gland sporozoite. (C) Immunoelectron microscopy of sporozoites in the salivary gland. Ultrathin sections of a mosquito salivary gland infected with sporozoites were incubated with the same antibody used in (A) followed by secondary antibodies conjugated with gold particles (15 nm). Particles were localized to micronemes (Mn) but not to rhoptories (Rh). Axial (inset) and vertical images are shown. Scale bars, 0.5 μm." | "CC BY" | "no" | "2022-01-13 00:06:50" | "PLoS Biol. 2004 Jan 20; 2(1):e4" |
"PMC314464" | "14737184" | 3 | "pbio.0020004.g003" |  | "Figure 3 Targeted Disruption of the spect Gene (A) Schematic representation of targeted disruption of the spect gene. The targeting vector (top) containing a selectable marker gene is integrated into the spect gene locus (middle) by double crossover. This recombination event resulted in the disruption of the spect gene and confers pyrimethamine resistance to disruptants (bottom). (B) Genomic Southern blot hybridization of wild-type (WT) and spect (−) populations. Genomic DNA isolated from the respective parasite populations was digested with EcoT22I and hybridized with the probe indicated in (A) by a solid bar. By integration of the targeting construct, the size of detected fragments was decreased from 1.9 kbp to 1.2 kbp. The result is shown for two independently prepared populations, spect (−)1 and spect (−)2. (C) Immunofluorescence microscopy of the wild-type (WT) and spect (−) parasite. Sporozoites were collected from the salivary gland and stained with primary antibody against SPECT followed by FITC-conjugated secondary antibodies. The apical end of each sporozoite is indicated by an arrowhead." | "CC BY" | "no" | "2022-01-13 00:06:50" | "PLoS Biol. 2004 Jan 20; 2(1):e4" |
"PMC314464" | "14737184" | 4 | "pbio.0020004.g004" |  | "Figure 4 Targeted Disruption of spect Results in Reduction of Sporozoite Infectivity to the Liver (A) The salivary gland sporozoites of each parasite population were injected intravenously into five rats. The parasitemia of each rat was checked by a Giemsa-stained blood smear after inoculation on the days indicated. The average parasitemia after inoculation of 30,000 sporozoites was significantly low in disruptant populations, whereas their growth rates in the blood were essentially the same as the wild-type. The numbers of parasites inoculated were as follows: 30,000 spect (−)1 (open circles), 30,000 spect (−)2 (open triangles), 30,000 wild-type (filled circles), and 3,000 wild-type (filled squares). Values shown represent the mean parasitemia (± SEM) of five rats. (B) The salivary gland sporozoites (500,000) of wild-type or spect -disrupted parasites were inoculated intravenously into 3-wk-old rats. After 24 h, the livers were fixed with paraformaldehyde and frozen. The number of EEFs on each cryostat sections was estimated by indirect immunofluorescence analysis using anti-CS antiserum. Values shown represent the mean number of EEFs per square millimeter (± SEM) of at least three rats." | "CC BY" | "no" | "2022-01-13 00:06:50" | "PLoS Biol. 2004 Jan 20; 2(1):e4" |
"PMC314464" | "14737184" | 5 | "pbio.0020004.g005" |  | "Figure 5
spect Disruption Results in Loss of Cell-Passage Activity of the Sporozoite (A) spect disruption does not affect sporozoite ability to infect hepatocytes. (Top panel) Comparison of EEF numbers between disruptants ( spect (−)) and wild-type (WT) parasites. Salivary gland sporozoites were added to HepG2 cells and cultured for 48 h. EEFs formed were counted after immunofluorescence staining with an antiserum against CS protein. (Bottom panels) Representative fluorescence stained images. (B) Sporozoites lacking SPECT cannot traverse HeLa cells. (Top) Comparison of cell-passage activity between disruptants and wild-type parasites. Salivary gland sporozoites were added to HeLa cells and incubated for 1 h with FITC-conjugated dextran (1 mg/ml). Cell-passage activity was estimated by the number of cells wounded by sporozoite passage, which were identified by cytosolic labeling with FITC-conjugated dextran. (Bottom) Representative fluorescence stained images. All data are mean numbers of EEFs or FITC-positive cells in a one-fifth area of an 8-well chamber slide with standard errors for at least three independent experiments." | "CC BY" | "no" | "2022-01-13 00:06:50" | "PLoS Biol. 2004 Jan 20; 2(1):e4" |
"PMC314464" | "14737184" | 6 | "pbio.0020004.g006" |  | "Figure 6 Restoration of spect (−) Sporozoite Infectivity in Kupffer Cell-Depleted Rats (A) Liposome-encapsulated Cl 2 MDP (filled points) or PBS (open) was injected intravenously into rats. After 48 h, 30,000 sporozoites of spect (−)1 (circles), spect (−)2 (triangles), or wild-type (squares) populations were inoculated intravenously. Parasitemia of each rat was checked by Giemsa-stained blood smears after inoculation on the days indicated. Values shown represent the mean parasitemia (± SEM) of five rats. (B) Salivary gland sporozoites (500,000) of each parasite population were inoculated intravenously into Kupffer cell-depleted rats. After 24 h, the livers were fixed with paraformaldehyde and frozen. The number of EEFs on each cryostat section was estimated by indirect immunofluorescence analysis using anti-CS antiserum. Values shown represent the mean number of EEFs per square millimeter (± SEM) of at least three rats." | "CC BY" | "no" | "2022-01-13 00:06:50" | "PLoS Biol. 2004 Jan 20; 2(1):e4" |
"PMC314464" | "14737184" | 7 | "pbio.0020004.g007" |  | "Figure 7 Schematic Representation of Sporozoite Migration to and Infection of Hepatocytes (Left) Sporozoites migrate to the space of Disse through the Kupffer cells. [1] The sporozoite (Sp) in the circulatory system is sequestered to the sinusoidal endothelial cell (EC) by specific recognition of the cell surface or glycosaminoglycans extending from the hepatocytes (He) through fenestration. [2] The sporozoite begins to glide on the epithelial cell surface. [3] Encountering a Kupffer cell (KC), the sporozoite ruptures the plasma membrane, passes through the cell, and enters into the space of Disse. Thus, the sporozoite gains access to hepatocytes. This step requires SPECT. [4] The sporozoite infects a hepatocyte with formation of a vacuole and develops into EEF in the hepatocyte. (Right) An alternative route to the hepatocyte. A small number of sporozoites, which find gaps in the sinusoidal layer while gliding, migrate to hepatocytes directly through the openings without need for cell passage and infect the hepatocytes. Likewise, in Kupffer cell-depleted rats, both wild-type and spect (−) sporozoites can enter hepatocytes through numerous gaps present between the sinusoidal endothelial cells." | "CC BY" | "no" | "2022-01-13 00:06:50" | "PLoS Biol. 2004 Jan 20; 2(1):e4" |
"PMC314465" | "14737185" | 1 | "pbio.0020005.g001" |  | "Figure 1 Results of the Pilot Study in Human and Mouse The percentage of OR genes from each family is given for the entire repertoire (filled bars) and a sample of 100 genes amplified using PC1 and PC2 degenerate primers (open bars). (A) OR genes in human. (B) OR genes in mouse. None of the differences between the full repertoires and the samples are significant at the 5% level. Only full-length OR genes (larger than 850 bp) were considered." | "CC BY" | "no" | "2022-01-13 00:06:50" | "PLoS Biol. 2004 Jan 20; 2(1):e5" |
"PMC314465" | "14737185" | 2 | "pbio.0020005.g002" |  | "Figure 2 The Proportion of OR Pseudogenes in 20 Species Primate species are color-coded according to family. The arrow points to the howler monkey. Datapoints (from left to right) are for apes (green): human ( Homo sapiens ), chimpanzee ( Pan troglodytes ), gorilla ( Gorilla gorilla ), orangutan ( Pongo pygmaeus ), gibbon ( Hylobates syndactylus ); for OWMs (blue): Guinea baboon ( Papio papio ), rhesus macaque ( Macaca mulatta ), silver langur ( Trachypithecus auratus ), mona ( Cercopithecus mona ), agile mangabey ( Cercocebus agilis ), black-and-white colobus ( Colobus guereza ); for NWMs (red): brown capuchin monkey ( Cebus apella ), southern owl monkey ( Aotus azarai ), spider monkey ( Ateles fusciceps ), black howler monkey ( Alouatta caraya ), squirrel monkey ( Saimiri sciureus ), wooly monkey ( Lagothrix lagotricha ), common marmoset ( Callithrix jacchus ); for one prosimian primate (brown): crowed lemur ( Eulemur mongoz ); and for the mouse ( Mus musculus ) (grey)." | "CC BY" | "no" | "2022-01-13 00:06:50" | "PLoS Biol. 2004 Jan 20; 2(1):e5" |
"PMC314465" | "14737185" | 3 | "pbio.0020005.g003" |  | "Figure 3 Phylogenetic Tree of Primates Schematic phylogenetic tree of the primate species used in the current study. Phylogenetic relationships between species are based on Harada et al. (1995 ), Page et al. (1999 ), and Surridge et al. (2003 ). Arrows indicate on which lineages the acquisition of full trichromatic color vision occurred ( Goodman et al. 1998 ; Jacobs and Deegan 2001 ). The red color highlights lineages with a high proportion of OR pseudogenes." | "CC BY" | "no" | "2022-01-13 00:06:50" | "PLoS Biol. 2004 Jan 20; 2(1):e5" |
"PMC314466" | "14737186" | 1 | "pbio.0020006.g001" |  | "Figure 1 DOCK2, ELMO1, and Rac Are Abundant Nef-Associated Proteins in T Cells (A) Schematic representation of epitope-tagged HIV-1 Nef (NA7-hf). The structured regions of Nef are boxed and the disordered regions, as determined by X-ray crystallography and NMR studies, are shown by a thin line. The locations of the N-terminal myristoyl moiety, prolines P72 and P75 in the PP-II helix, arginine R106, leucines L164 and L165 (LL164), and the C-terminal HA-FLAG epitopes are indicated. (B) DOCK2, ELMO1, and Rac2 specifically copurify with HIV-1 Nef from Jurkat T cells. Jurkat T cells (1.8 ×10 10 ) stably expressing NA7-hf (lane 3) or control Jurkat cells (lane 2) were subjected to the two-step immunopurification procedure described in the text (see Materials and Methods ). Polypeptides present in purified immune complexes were resolved by SDS-PAGE and analyzed by LC/MS/MS. We identified 58 DOCK2-specific peptides covering 869 out of 1830 total amino acid residues (47.5% coverage, expectation value 6.0 × 10 –130 ), 10 ELMO1-specific peptides covering 122 out of 727 total amino acid residues (16.8% coverage, expectation value 1.0 × 10 −10 ), and three Rac-specific (two of which were Rac2-specific) peptides covering 26 out of 192 total amino acid residues (13.5% coverage, expectation value 4.6 × 10 −4 ). Bands corresponding to DOCK2, ELMO1, Rac2 and their predicted molecular weights, NA7-hf Nef, and the FLAG peptide used for elution are indicated." | "CC BY" | "no" | "2022-01-13 00:06:50" | "PLoS Biol. 2004 Jan 20; 2(1):e6" |
"PMC314466" | "14737186" | 2 | "pbio.0020006.g002" |  | "Figure 2 Lentiviral Nef Binds the DOCK2–ELMO1–Rac Complex (A) HIV-1 Nef binds the DOCK2–ELMO1–Rac2 complex. His-DOCK2, Myc-ELMO1, and Myc-Rac2 alone (lanes 1, 3, and 5) or together with NA7-hf Nef (lanes 2, 4, and 6) were transiently expressed in HEK 293 cells as indicated. DOCK2 was precipitated from extracts (lanes 1 and 2) with Ni–NTA resin (lanes 3 and 4). Nef–DOCK2 was then precipitated with anti-FLAG affinity gel (lanes 5 and 6), and the epitope-tagged proteins were detected by immunoblotting and visualized by enhanced chemiluminescence. (B) Rac1 associates with HIV-1 Nef. Nef and associated proteins were isolated from extracts of HEK 293 cells transiently expressing DOCK2, ELMO1, and Rac1 either alone (lanes 1 and 4), with NA7-hf (lanes 2 and 5), or with a Nef variant containing a disrupted myristoylation signal (lanes 3 and 6). Nef and associated proteins were detected in anti-FLAG immunoprecipitates (lanes 1–3) and in extracts (lanes 4–6) by immunoblotting. (C) The interaction with DOCK2, ELMO1, and Rac2 is a conserved function of lentiviral Nef proteins. The ability of selected hf-tagged HIV-1 (lanes 1–3 and 5) and SIV mac239 (lane 4) Nef proteins to bind DOCK2, ELMO1, and Rac2 was determined as described in the legend to (B) above. The protein band in (C) indicated by the asterisk is the heavy chain of anti-FLAG mAb." | "CC BY" | "no" | "2022-01-13 00:06:50" | "PLoS Biol. 2004 Jan 20; 2(1):e6" |
"PMC314466" | "14737186" | 3 | "pbio.0020006.g003" |  | "Figure 3 Nef Activates Rac in Resting CD4 + T Lymphocytes (A) HIV-1 Nef activates Rac in Jurkat T cells. Jurkat T cells (lane 1) were transduced with a control empty vector (FUGW; lane 2) or the same vector expressing HIV-1 NA7 Nef (FUGWCNA7; lane 3). Rac GTP was precipitated from cell extracts with recombinant PAK1 PBD–GST. PBD–GST bound Rac GTP (top), total Rac present in extracts (middle), and Nef (bottom) were detected by immunoblotting. (B) Flow cytometric analysis of Gag and CD4 expression in resting CD4 + T lymphocytes transduced with HIV-1 derived vectors in the presence of IL-7. Percentages of cells productively infected with nef -deleted H-Δ vector (boxed area in middle panel) or with HIV-1 NA7 nef containing H-NA7 vector (right panel) are shown. Results obtained with uninfected control CD4 + T cells cultured in the presence of IL-7 are also shown (left panel). (C) HIV-1 Nef specifically activates Rac in resting primary CD4 + T lymphocytes. Rac GTP and CDC42 GTP were precipitated with PAK1 PBD–GST from extracts prepared from CD4 + T lymphocytes transduced with HIV-1 derived vectors, shown in (B), and analyzed as described in (A)." | "CC BY" | "no" | "2022-01-13 00:06:50" | "PLoS Biol. 2004 Jan 20; 2(1):e6" |
"PMC314466" | "14737186" | 4 | "pbio.0020006.g004" |  | "Figure 4 ELMO1 and DOCK2 Mediate Rac Activation by HIV-1 Nef (A) ELMO1 is required for Rac activation by Nef in NS1 cells. Rac GTP and total Rac in the extracts prepared from ELMO1-deficient NS1 cells (lanes 1 and 2) and ELMO1-expressing NS1 cells (lanes 3 and 4) following transduction with a lentiviral vector expressing HIV-1 Nef (lanes 2 and 4) or a control empty vector (lanes 1 and 3) were visualized as described in the legend to Figure 3 . (B) Nef activates Rac through DOCK2 and ELMO1 in HEK 293 cells. Rac GTP and total Rac in the extracts prepared from HEK 293 cells coexpressing the indicated proteins were visualized as described above." | "CC BY" | "no" | "2022-01-13 00:06:50" | "PLoS Biol. 2004 Jan 20; 2(1):e6" |
"PMC314466" | "14737186" | 5 | "pbio.0020006.g005" |  | "Figure 5 Nef Potentiates Rac Activation through Association with DOCK2–ELMO1 (A and B) Myristoylation signal, P72,P75, and R106 in Nef are required for Rac activation. Rac GTP and total Rac in the extracts prepared from Jurkat T cells transduced with lentiviral vectors expressing no Nef (−) or the indicated Nef proteins (A) and HEK 293 cells transiently coexpressing the indicated Nef mutants together with DOCK2, ELMO1, and Rac2 (B) were visualized as described in the legend to Figure 3 and quantified by direct imaging of chemiluminescent signals. The fraction of total Rac present in the extracts that was PBD–GST bound is shown in the histograms. Data in the histogram shown in (B) are averages of three independent experiments and error bars represent two standard deviations. (C) Myristoylation signal, P72,P75, and R106 in Nef are required for association with DOCK2, ELMO1, and Rac2. The ability of selected Nef mutants to associate with DOCK2, ELMO1, and Rac2 was determined as described in Figure 2 ." | "CC BY" | "no" | "2022-01-13 00:06:50" | "PLoS Biol. 2004 Jan 20; 2(1):e6" |
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