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At least 379 records · Page 21Linked to original sources
PubMed1993

Lack of T cell dysfunction and programmed cell death in human immunodeficiency virus type 1-infected chimpanzees correlates with absence of monocytotropic variants.

In asymptomatic human immunodeficiency virus (HIV) infection in humans, disturbed T cell functions such as anergy and programmed cell death, thought to result from inappropriate signaling by antigen-presenting cells due to HIV infection, precede increase in virus load, decline in CD4+ T cell numbers, and subsequent disease progression. Here, in 3 long-term HIV-1-infected asymptomatic chimpanzees, antigen-presenting cell function was intact and T cells had normal proliferative capacity with no evidence of HIV-1-associated programmed cell death. Polymerase chain reaction analysis demonstrated low frequencies of cells harboring proviral DNA. Primary virus isolation from the infected animals demonstrated the absence of monocytotropic HIV-1 variants, in concordance with complete insusceptibility of chimpanzee monocytes for HIV-1 infection. Possibly, because of the incapacity of HIV-1 to infect monocytes, systemic immune dysfunction will not occur, contributing to controlled viral replication and maintenance of the asymptomatic state in HIV-infected chimpanzees.

Amino Acid Sequence↗
PubMed2005

Reduced MIC gene repertoire variation in West African chimpanzees as compared to humans.

The human major histocompatibility complex class I chain-related (MIC) genes are members of a multicopy family showing similarity to the classical HLA-A, HLA-B, and HLA-C genes. Only the MICA and MICB genes produce functional transcripts. In chimpanzees, however, only one MIC gene is expressed, showing an intermediate character, resulting from a deletion fusing the MICA and MICB gene segments together. The present population study illustrates that all chimpanzee haplotypes sampled possess the hybrid MICA/B gene. In contrast to the human situation this gene displays reduced allelic variation. The observed repertoire reduction of the chimpanzee MICA/B gene is in conformity with the severe repertoire condensation documented for Patr-B locus lineages, probably due to the close proximity of both genes.

Alleles↗
PubMed2007

Chimpanzee, orangutan, mouse, and human cell cycle promoters exempt CCAAT boxes and CHR elements from interspecies differences.

Mechanisms regulating the cell division cycle are well conserved among all eukaryotes. Consistently many proteins regulating the cell cycle are functionally interchangeable between many organisms. Cell division control is regulated on different levels of which the transcriptional level appears to be particularly important for controlling synthesis of many cell cycle proteins. We had earlier described transcription factor-binding sites essential for regulating genes important for the transition from the G(2) phase to mitosis. A tandem repressor site named cell cycle-dependent element (CDE) and cell cycle genes homology region (CHR) are responsible for the correct expression during the cell cycle. Another feature of these G(2)/M-specific promoters is the activation through 2 or 3 CCAAT boxes binding the transcription factor nuclear factor-Y (NF-Y). These major activating sites have to be spaced 32 or 33 bp apart to be fully functional. We were interested in looking at the evolutionary changes in regulatory elements and overall promoter structure of 3 well-characterized cell cycle genes. Here, we compare the DNA sequences and functional features of the cdc25C, cyclin B1, and cyclin B2 promoters from humans, mouse, chimpanzee, and orangutan. We find numerous differences in the nucleotide sequence between mouse and primate promoters. However, CHR and CCAAT boxes stand out in that they are perfectly conserved in all promoters tested. The CDE site contains nucleotide exchanges between mouse and primate promoters. Comparing sequences and functions of chimpanzee, orangutan, and human promoters, we observe a complete conservation in nucleotide sequence of the regulatory elements. Functional assays of the cyclin B1, cyclin B2, and cdc25C promoters yield moderate variations in activity and thereby a good conservation of function. Although we find nucleotide differences in cell cycle promoters between orangutan and humans of about 5%, there are never changes in any of the CCAAT boxes or CDE/CHR sites in the cyclin B1, cyclin B2, and cdc25C promoters. Furthermore, we describe the influence of the tumor suppressor p53 and the transcriptional activator NF-Y on regulation of the newly cloned primate promoters.

Animals↗
PubMed1995

Microsatellite allele frequencies in humans and chimpanzees, with implications for constraints on allele size.

The distributions of allele sizes at eight simple-sequence repeat (SSR) or microsatellite loci in chimpanzees are found and compared with the distributions previously obtained from several human populations. At several loci, the differences in average allele size between chimpanzees and humans are sufficiently small that there might be a constraint on the evolution of average allele size. Furthermore, a model that allows for a bias in the mutation process shows that for some loci a weak bias can account for the observations. Several alleles at one of the loci (Mfd 59) were sequenced. Differences between alleles of different lengths were found to be more complex than previously assumed. An 8-base-pair deletion was present in the nonvariable region of the chimpanzee locus. This locus contains a previously unrecognized repeated region, which is imperfect in humans and perfect in chimpanzees. The apparently greater opportunity for mutation conferred by the two perfect repeat regions in chimpanzees is reflected in the higher variance in repeat number at Mfd 59 in chimpanzees than in humans. These data indicate that interspecific differences in allele length are not always attributable to simple changes in the number of repeats.

Alleles↗
PubMed1994

Detection of DNA sequence variation via deliberate heteroduplex formation from genomic DNAs amplified en masse in "population tubes".

We have developed the population tube (poptube) system for sensitive detection and large-scale sampling of DNA sequence variation in several human populations of wide geographic distribution. In this methodology, genomic DNAs from five individuals in a population are PCR amplified en masse to maximize deliberately the chances of forming heteroduplexes among allelic variants. Interpopulation mixing is performed in a separate set of tubes containing one individual from each of five populations as well as a reference chimpanzee sample deliberately chosen to be different from all humans. Mismatches at sites of allelic variation retard the electrophoresis and reduce the stability of heteroduplex molecules. The products are electrophoresed on denaturing gradient gels where detection of heteroduplexes is accomplished readily. Using poptubes, we have discovered a rare variant in an otherwise highly conserved 440-bp segment in the long intron of the glucose-6-phosphate dehydrogenase (G6PD) gene. The polymorphism at this X-chromosome locus could be only detected in males by mixing samples, as homoduplexes for both alleles co-focus on denaturing gradient electrophoresis.

Animals↗
PubMed2006

Estimation of the species-specific mutation rates at the DRB1 locus in humans and chimpanzee.

To estimate the species-specific mutation rates at the DRB1 locus in humans and chimpanzee, we analyzed the nucleotide sequence of a 37.6-kb chimpanzee chromosomal segment containing the entire Patr-DRB1*0701 allele and the flanking nongenic region and we compared it with two corresponding human sequences containing the HLA-DRB1*070101 allele using the sequence of HLA-DRB1*04011 as an outgroup. Because the allelic pair of HLA-DRB1*070101 and Patr-DRB1*0701 shows the lowest number of substitutions between the two species, it appears that these sequences diverged close to the time of the humans-chimpanzee divergence (6 million years ago). Alignment of the nucleotide sequences for HLA-DRB1*070101 and Patr-DRB1*0701 alleles showed that they share a high degree of similarity, suggesting that the studied chromosomal segments with these sequences have not been subjected to recombination since the humans-chimpanzee divergence. Comparison of the flanking 10.6 kb of nongenic sequences revealed an average of 41.5 and 83 single nucleotide substitutions in humans and chimpanzee, respectively. Thus, the species-specific nucleotide substitution rates in the flanking nongenic region were estimated to be 6.53 x 10(-10) and 1.31 x 10(-9) per site per year in humans and chimpanzee, respectively. Unexpectedly, the estimated rate in humans was twofold lower than in chimpanzee (P < 10(-3), Tajima's relative rate test) and lower than the average substitution rate in the human genome. Because the nucleotide substitution rate in nongenic regions free from selection is expected to be equal to the mutation rate, the estimated substitution rate should correspond to the species-specific mutation rate at the DRB1 locus. Our results strongly suggest that the mutation rate at DRB1 locus differs among species.

Alleles↗
PubMed2001

Haplotype variation and linkage disequilibrium in 313 human genes.

Variation within genes has important implications for all biological traits. We identified 3899 single nucleotide polymorphisms (SNPs) that were present within 313 genes from 82 unrelated individuals of diverse ancestry, and we organized the SNPs into 4304 different haplotypes. Each gene had several variable SNPs and haplotypes that were present in all populations, as well as a number that were population-specific. Pairs of SNPs exhibited variability in the degree of linkage disequilibrium that was a function of their location within a gene, distance from each other, population distribution, and population frequency. Haplotypes generally had more information content (heterozygosity) than did individual SNPs. Our analysis of the pattern of variation strongly supports the recent expansion of the human population.

Alleles↗
PubMed1998

Rapid, transient changes at the env locus of plasma human immunodeficiency virus type 1 populations during the emergence of protease inhibitor resistance.

Plasma human immunodeficiency virus type 1 (HIV-1) populations were genetically analyzed at their most variable locus, the envelope gene, during the rapid emergence of resistance to protease inhibitor monotherapy. Plasma virus populations remained genetically constant prior to drug treatment and during the 1 to 2 weeks following initiation of therapy, while viremia fell 10- to 100-fold. Concomitant with rapid plasma viremia rebounds associated with the emergence of drug-resistant virus, marked alterations were then detected at the env locus. Plasma population changes lasted only a few weeks before the reappearance of the pretreatment envelope variants. The emergence of resistance to single protease inhibitors was therefore associated with major but transient changes at a nonselected locus. Selection for resistance to single protease inhibitors thus appears to be more complex than the continued replication of a large, random, and therefore genetically representative sampling of the pretreatment plasma population. The possibility that drug-privileged anatomical sites containing distinct envelope variants and/or a small effective HIV-1 population size account for these results is discussed.

Drug Resistance, Microbial↗
PubMed2000

Genetic perspectives on human origins and differentiation.

This is a review of genetic evidence about the ancient demography of the ancestors of our species and about the genesis of worldwide human diversity. The issue of whether or not a population size bottleneck occurred among our ancestors is under debate among geneticists as well as among anthropologists. The bottleneck, if it occurred, would confirm the Garden of Eden (GOE) model of the origin of modern humans. The competing model, multiregional evolution (MRE), posits that the number of human ancestors has been large, occupying much of the temperate Old World for the last two million years. While several classes of genetic marker seem to contain a strong signal of demographic recovery from a small number of ancestors, other nuclear loci show no such signal. The pattern at these loci is compatible with the existence of widespread balancing selection in humans. The study of human diversity at (putatively) neutral genetic marker loci has been hampered since the beginning by ascertainment bias since they were discovered in Europeans. The high levels of polymorphism at microsatellite loci means that they are free of this bias. Microsatellites exhibit a clear almost linear diversity gradient away from Africa, so that New World populations are approximately 15% less diverse than African populations. This pattern is not compatible with a model of a single large population expansion and colonization of most of the Earth by our ancestors but suggests, instead, gradual loss of diversity in successive colonization bottlenecks as our species grew and spread.

Animals↗
PubMed2000

Phylogenetic variation and polymorphism at the toll-like receptor 4 locus (TLR4).

BACKGROUND: Differences in responses to bacterial surface lipopolysaccharides (LPSs) are apparent between and within mammalian species. It has been shown in mice that resistance to LPS is caused by defects in the Toll-like receptor 4 gene (Tlr4), the product of which is thought to bind LPS and mediate LPS signal transduction in immune system cells. RESULTS: We have sequenced the Toll-like receptor 4 gene of humans (TLR4; 19.0 kilobases, kb) and mice (Tlr4; 91.7 kb), as well as the coding region and splice junctions of Tlr4 from 35 mouse (Mus musculus) strains, from the chimpanzee and from the baboon. No other discernible genes or regions of interspecies conservation lies close to Tlr4 and, in both humans and mice, flanking sequences and introns are rich in repeats of retroviral origin. Interstrain analyses reveal that Tlr4 is a polymorphic protein and that the extracellular domain is far more variable than the cytoplasmic domain, both among strains and among species. The cytoplasmic domain of the Tlr4 protein is highly variable at the carboxy-terminal end. CONCLUSIONS: We suggest that selective evolutionary pressure exerted by microbes expressing structurally distinguishable LPS molecules has produced the high level of variability in the Tlr4 extracellular domain. The highly variable carboxy-terminal region of the cytoplasmic domain is likely to determine the magnitude of the response to LPS within a species.

Animals↗
PubMed2026

A pan-cancer multi-omic SuperLearner for regulated cell death survival topologies.

INTRODUCTION: Regulated cell death (RCD) pathways influence tumor progression and immune modulation. We previously constructed a signature database mapping 25 RCD forms across seven multi-omic layers and 33 tumor types (CancerRCDShiny). Despite their ability to identify risk populations, translating these signatures into personalized clinical workflows requires a shift from cohort stratification to individualized risk mapping by modeling patient risk (survival topologies) to capture the non-linear dynamics of RCD signatures. METHODS: We engineered a pan-cancer multi-omic SuperLearner pipeline across 33 cancer types. Phase I performed zero-leakage harmonization and groupwise imputation to prevent cross-cohort amalgamation. Phase II deployed Elastic Net-regularized Cox regression as a CANARY diagnostic to map proportional hazards failures. Strata with a 35% missingness barrier entered Phase III, deploying a Quadripartite ensemble: Random Survival Forests, XGBoost, Survival-Boruta, and Multi-Task Logistic Regression, fused within an Elastic Net Multi-View Meta-Learner (MVL), with post-hoc TreeSHAP and LIME interpretability. RESULTS: The CANARY diagnostic demonstrated the structural invalidity of pan-cancer geometric proportional hazards. Across 96 admissible strata, Phase III executed algorithmic displacement: continuous multi-omic topologies suppressed static genomic mutations and copy number variations (85.7% vs. 0.0% apex retention). The MVL stabilized predictions against extreme variance; LIME surrogate validations (R 2&#x202f;<&#x202f;0.10) confirmed the systematic failure of linear interpretative proxies. N-dimensional TreeSHAP interaction mapping exposed synergistic and antagonistic rescue trajectories defining individualized Survival Topologies, which were invisible to additive models. The architecture was deployed as CancerRCDPredictor, a digital molecular tumor board with integrated LLM capabilities. The MVL SuperLearner achieved a median C-index of 0.749 (IQR: 0.722-0.836) across 96 modelable strata, with 95% bootstrap confidence intervals confirming precision (median width: 0.052) and permutation significance in 93.8% of strata (p&#x202f;<&#x202f;0.001). External CPTAC validation across ten cancer types demonstrated significant cross-cohort generalizability in clear cell renal carcinoma (KIRC; C-index 0.675, p&#x202f;=&#x202f;0.017) and modest performance across the remaining adequately powered cancers (median 0.582), underscoring the need for larger multi-institutional validation cohorts. CONCLUSION: This pan-cancer multi-omic SuperLearner bypasses linear topological failures, advancing beyond generalized stratification to establish a deterministically mapped architecture for predicting RCD-related survival topologies. Through the CancerRCDPredictor interface, multi-omic insights translate into individualized survival topology exploration, providing a foundation for future precision oncology validation.

SuperLearner↗
PubMed2004

Inter- and intra-specific variation in the ontogeny of the hominoid facial skeleton: testing assumptions of ontogenetic variability.

In this paper we use geometric morphometric techniques to test two assumptions that are commonly made about variations in facial ontogeny: closely related species, or members of the same species, will share a common early post-natal ontogeny; and closely related species, or members of the same species, will share a common ontogenetic scaling trajectory. To test these assumptions we use four species of hominines: Homo sapiens, Gorilla gorilla, Pan troglodytes and Pan paniscus. The first assumption is falsified, both inter- and intra-specifically, using discriminant analysis with crossvalidation of subadults prior to the onset of the eruption of the permanent dentition. The second assumption only holds true for inter-specific comparisons of ontogenetic scaling trajectories, while assumptions of variation in intra-specific scaling trajectories are falsified with these data.

Adolescent↗
PubMed1996

Values of blood coagulating factors vary with ambient temperature: the Cardiovascular Disease Risk Factor Two-Township Study in Taiwan.

Seasonal influence on mortality from cardiovascular and cerebrovascular diseases is well documented. Understanding the seasonal variations in cardiovascular risk factors can shed light on this phenomenon. Elevation of coagulation factors during cold weather may in part explain the higher mortality from myocardial infarction and stroke in winter. The Cardiovascular Disease Risk Factors Community Study (CVDFACTS) included subjects belonging to 2 cohorts located in northern and southern Taiwan. This study included 2877 subjects aged 18 and above whose blood levels were examined for various coagulating factors. Besides measuring conventional cardiovascular risk factors including: blood pressure, body mass index and total cholesterol, values for blood fibrinogen, factor VII activity, factor VIII activity, plasminogen, antithrombin III, prothrombin time and activated partial thromboplastin time were determined for all subjects. Of these hemostatic parameters, levels of all, except prothrombin time, were statistically different between days with mean temperature > 20 degrees C and days with temperature < or = 20 degrees C (P < 0.01). In cold weather, a greater tendency to clot in circulatory system was demonstrated in this study, indicating seasonal variations may be demonstrated in this subtropical region.

Adult↗
PubMed1995

The cell surface antigen and DNA content distribution of lymph nodes with reactive hyperplasia.

Few studies have comprehensively examined the expression and distribution of cell surface antigens and DNA content in non-neoplastic, reactive lymph nodes. We have performed a flow cytometric immunophenotypic and DNA content analysis of 64 lymph nodes from 62 patients (23 male; 39 female; ages 21 months to 80 years) with typical reactive lymphoid hyperplasia as assessed by histology. CD45, a pan-leukocyte marker, was detected on virtually all cells (99 +/- 4%). All pan-T-cell-associated antigens studied were expressed within a narrow range of average values (54 - 64%), and no loss of individual T-cell antigens was observed in any case. Intercase variation of fluorescence intensity for each antigen was minimal. The mean CD4:CD8 ratio was 3.9 +/- 2.6, with only one case (HIV+) showing a marked CD4:CD8 inversion (0.4). The number of cells coexpressing CD4 and CD8 was very low (3 +/- 3%), consistent with the mature phenotypic nature of the majority of T lymphocytes. B-cells, as defined by CD19 and CD20 antibodies, accounted for 36 +/- 16% and 43 +/- 18% of cells analyzed, respectively, and, like the pan-T-cell antigens, displayed minimal intercase variability in antigen expression. Cells coexpressing CD20 and CD5 were noted, although their frequency could not be calculated accurately. IgD- and IgM-bearing cells were both generally well-defined populations: 24 +/- 10% and 31 +/- 14%, respectively. On the other hand, IgG- and IgA-bearing cells displayed broad fluorescence intensity, precluding an exact calculation of their frequencies.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗
PubMed2005

Testosterone and energetics in wild chimpanzees (Pan troglodytes schweinfurthii).

Ovarian function in female hominoids is sensitive to both energy flux and energy balance, resulting in a reduced probability of conception during periods when a successful reproductive outcome is less likely. However, the extent to which energetic factors constrain gonadal function in male hominoids is not clear. We examined the effects of both acute and chronic variation in energy availability on urinary testosterone (T) levels in adult male chimpanzees. Acute changes in energy availability, which were assayed by means of observational data on feeding behavior, did not result in decreased T production for 11 individuals at Kibale National Park, Uganda. Chronic energy shortages, on the other hand, may be associated with lower T levels in this population. Adult males in Kibale (n=11), who maintain suboptimal access to energy, exhibit significantly lower urinary T levels than males in captivity (n=11), who are more sedentary and better fed. These results suggest that data on hormonal function in captive chimpanzees should be interpreted with caution because individuals may produce T at levels well above those that are typical in the wild. They also suggest that short-term variations in T levels in male hominoids are more likely to be explained by social factors than by energetic ones.

Animals↗