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At least 649 records · Page 36Linked to original sources

Molecular evolution of freshwater snail intermediate hosts within the Bulinus forskalii group.

Freshwater snails of the Bulinus forskalii group are one of four Bulinus species complexes responsible for the transmission of schistosomes in Africa and adjacent regions. The species status of these conchologically variable and widely distributed planorbids remains unclear, and parasite compatibility varies considerably amongst the eleven taxa defined, making unambiguous identification and differentiation important prerequisites for determining their distributions and evolutionary relationships. Random Amplified Polymorphic DNA (RAPD) analyses were used to investigate relationships between taxa, with particular emphasis on Central and West African representatives. RAPD-derived phylogenies were compared with those from other independent molecular markers, including partial sequences of mitochondrial cytochrome oxidase subunit I (COI) gene, and the nuclear ribosomal RNA internal transcribed spacer 1 region (ITS1). The phylogenetic reconstructions from the three approaches were essentially congruent, in that all methods of analysis gave unstable tree topologies or largely unresolved branches. There were large sequence divergence estimates between species, with few characters useful for determining relationships between species and limited within species differentiation. Nuclear and mtDNA sequence data from Central and East African representatives of the pan-African B. forskalii showed little evidence of geographical structuring. Despite the unresolved structure within the phylogenies, specimens from the same species clustered together indicating that all methods were capable of differentiating taxa but could not establish the inter-specific relationships with confidence. The limited genetic variation displayed by B. forskalii, and the evolution and speciose nature of the group, are discussed in the context of the increasingly arid climate of the late Miocene and early Pliocene of Africa.

Africa↗

Comparative mapping of human alphoid satellite DNA repeat sequences in the great apes.

Heterochromatic regions of chromosomes contain highly repetitive, tandemly arranged DNA sequences that undergo very rapid variation compared to unique DNA sequences that are predominantly conserved. In this study the chromosomal basis of speciation has been looked at in terms of repeat sequences. We have hybridized twenty-one chromosome-specific human alphoid satellite DNA probes to metaphase spreads of the chimpanzee (Pan troglodytes), gorilla (Gorilla gorilla), and orangutan (Pongo pygmaeus) to investigate the evolutionary relationship of heterochromatic regions among such hominoid species. The majority of the probes did not hybridize to their corresponding equivalent chromosome but presented hybridization signals on non-corresponding chromosomes. Such observations suggest that rapid changes may have occurred in the ancestral alphoid satellite DNA sequence, resulting in divergence among the great ape species.

Animals↗

Atypical mutational properties of human chromosome 21 suggested by comparative genome-scale analyses.

Mutation of genetic material is a necessary component of evolutionary change. There is evidence for both intragenome and intergenome heterogeneity in terms of mutation frequencies. Reported comparisons of DNA sequence differences between human and chimpanzee (Pan troglodytes) suggest that human chromosome 21 may exhibit mutational hypervariability relative to the other autosomes. In the present study, further evidence is provided for such hypervariability based on large-scale analyses of amino acid composition of (translated) human genes and pseudogenes. A comparison of the variation in the above cases (i.e., DNA sequence differences and amino acid composition differences) yields similar ratios (1.2-1.4) for chromosome 21 relative to the other autosomes, e.g., human chromosome 22 - an autosome that is more typical in this respect and is of similar size to 21. Human chromosome 21 is also presented in this study as being atypical in terms of reported associations between mutation rates and GC content or CpG dinucleotides. In terms of GC distribution patterns, a comparison of NT_011512 and NT_011520 contigs revealed a lower heterogeneity for human chromosome 21 relative to 22. Possible hypermutability of chromosome 21 is further discussed in the context of GC patterns, reported long interspersed nuclear element content (LINE1s), and the implications of these parameters for chromatin structure.

Amino Acids↗

Establishing the relationship between complement activation and stimulation of phagocyte oxidative metabolism in hemodialyzed patients: a randomized prospective study.

The present prospective study was conducted in order to establish the relationship between complement activation and stimulation of phagocyte oxidative metabolism observed in long-term hemodialysis (HD) patients during the early phase of dialysis with cellulosic membranes. Two groups of 10 randomized (HD) patients treated with cellulosic (Cuprophan, CUP) or synthetic polyacrilonitrile (PAN AN-69) membranes were studied. Leukocyte counts, C3a antigen plasma concentration and whole blood basal and stimulated chemiluminescence (CL) production were determined in blood samples drawn from the fistula before dialysis (T0) and from both the afferent and efferent lines of the dialyser at 15 min (T15) and at the end (Tend) of the dialysis session. This study confirms that, coincident with the nadir of leukopenia observed at T15, dialysis with CUP but not PAN membranes induces a marked rise in C3a antigen levels and profound alterations in whole blood CL production consisting of a dramatic increase in basal CL and a significant loss in CL response capacity to stimulating agents. It further demonstrates that a direct relationship exists between the variations in C3a antigen plasma levels and whole blood CL production observed in the CUP group of patients from T0 to T15 (delta 15) of dialysis. This relationship is characterized by a positive correlation between delta 15 C3a and delta 15 basal CL levels in afferent and efferent lines, and a negative correlation between delta 15 C3a and delta 15 CL response capacity values in the efferent but not afferent line. In contrast, no significant correlation with the type of dialysis membrane could be demonstrated between the variations in polymorphonuclear neutrophil counts and C3a antigen levels.(ABSTRACT TRUNCATED AT 250 WORDS)

Acrylic Resins↗

The sequential sampling of Psorophora columbiae larvae in rice fields.

Sequential sampling plans were developed for larval populations of Psorophora columbiae developing in rice fields during the growth of rice for a 2nd crop in southwestern Louisiana. Two types of plans were developed: 1) sequential counting plans to estimate the true mean of a population with a prespecified coefficient of variation and 2) sequential decision plans to assist in deciding whether the mean larval count/dip lies outside preselected upper or lower levels. The procedure by which the plans were developed consisted of: 1) conventional larval sampling by dipping along rice field levees that divided each field into pans; 2) counting the number of 2nd through 4th instar larvae observed in two dips taken at each sampling location; and 3) determination of the appropriate statistical parameters from which probability curves, number of samples required, and cumulative larval totals for specific sampling plans could be derived. Both sequential sampling plans are based upon distributions attendant to naturally occurring populations.

Agriculture↗

Evolution of an intronic microsatellite polymorphism in Toll-like receptor 2 among primates.

Nonhuman primates express varying responses to Mycobacterium tuberculosis: New World monkeys appear to be resistant to tuberculosis (TB) while Old World monkeys seem to be particularly susceptible. The aim of this study was to elucidate the presence of the regulatory guanine-thymine (GT) repeat polymorphisms in intron 2 of Toll-like receptor 2 (TLR2) associated with the development of TB in humans and to determine any variations in these microsatellite polymorphisms in primates. We sequenced the region encompassing the regulatory GT repeat microsatellites in intron 2 of TLR2 in 12 different nonhuman primates using polymerase chain reaction amplification, TA cloning, and automatic sequencing. The nonhuman primates included for this study were as follows: chimpanzee (Pan troglodytes), bonobo (Pan paniscus), gorilla (Gorilla gorilla), orangutan (Pongo pygmaeus), Celebes ape (Macaca nigra), rhesus monkey (Macaca mulatta), pigtail macaque (Macaca nemestrina), patas monkey (Erythrocebus patas), spider monkey (Ateles geoffroyi), Woolly monkey (Lagothrix lagotricha), tamarin (Saguinus labiatus), and ring-tailed lemur (Lemur catta). Nucleotide sequences encompassing the regulatory GT repeat region are similar across species and are completely conserved in great apes. However, Old World monkeys lack GT repeats altogether, while New World monkeys and ring-tailed lemurs have much more complex structures around the position of the repeats. In conclusion, the genetic structures encompassing the regulatory GT repeats in intron 2 of human TLR2 are similar among nonhuman primates. The sequence is most conserved in New World monkeys and less in Old World monkeys.

Animals↗

Relationship of bone utilization and biomechanical competence in hominoid mandibles.

This investigation explores regional variation in bone mass in the mandibles of large-bodied hominoids with respect to the masticatory biomechanical environment. Cortical area, subperiosteal area, mandibular length, maximum and minimum area moments of inertia are sampled at 7 sections along the mandibular corpus in 20 specimens each of Homo sapiens, Pan troglodytes, Pongo pygmaeus and Gorilla gorilla. The null hypothesis is that bone is utilized similarly among species, between sexes and among corpus locations in terms of economy of bone deployment (relative to subperiosteal area) and efficiency in producing structural stiffness (relative to cross-sectional moments of inertia). The alternative hypothesis is that dietary toughness and the scaling of muscular force recruitment produces an unfavourable stress environment in the mandible such that larger species (Gorilla and Pongo) use relatively more cortical bone than Pan and Homo. Three-way factorial analysis of variance (with species, sex and location as main effects) indicates significant interaction of species and location for all indices of bone economy and efficiency. Sex is significant as a main effect or interacting with location in all indices of cortical area. While allometric effects are not readily discernible in these data, the null hypothesis of a common pattern of bone utilization is decisively rejected. Human mandibles use relatively more cortical bone than those of great apes, particularly in anterior regions of the corpus. Among the apes, orangutans use very little cortical bone to achieve mechanical stiffness.

Adult↗

Metabolic response to feeding in the Chinese striped-necked turtle, Ocadia sinensis.

We measured oxygen consumption in juvenile Chinese striped-necked turtles (Ocadia sinensis) after they ingested food, either as a single meal or as double meals, to examine the influence of meal type and feeding frequency on specific dynamic action (SDA). Temporal variation in oxygen consumption after feeding was evident in the ingesting turtles but not in the unfed control turtles. In the single-meal experiment, the peak metabolic rate and the integrated SDA response (the whole energetic cost for the processes of digestion) both did not differ between turtles ingesting mealworms and shrimps when the influence of variation in ingested energy was removed, and the time to reach peak metabolic rate was not affected by meal type and the amount of food ingested. Turtles in the double-meal experiment ingested more energy and hence had a prolonged duration of SDA response than did those in the single-meal experiment, but the integrated SDA response did not differ between both experimental treatments when the influence of variation in ingested energy was removed. Our results show that meal type and feeding frequency have important consequences on the SDA response of juvenile O. sinensis. As the integrated SDA response remained remarkably constant either between turtles ingesting different food or between turtles ingesting the same food but at different frequencies when the influence of variation in ingested energy was removed, we therefore conclude that the energetic cost associated with ingestion is primarily determined by energy content of food ingested in juvenile O. sinensis.

Animal Nutritional Physiological Phenomena↗

No association between the promoter variants of tumor necrosis factor alpha (TNF-alpha) and schizophrenia in Chinese Han population.

An increasing amount of evidence suggests that the pathophysiology of schizophrenia is associated with activation of the immune system. Four studies have established an association of -308G/A polymorphism of tumor necrosis factor alpha (TNF-alpha), a cytokine involved in inflammatory processes, with schizophrenia [Mol. Psychiatry 6 (2001) 79; Mol. Psychiatry 8 (2003) 718; Schizophr. Res. 65 (2003) 19; Biol. Psychiatry 54 (2003) 1205]. In the present study, however, no significant positive association has been found between any individual SNP or haplotype constituted of the five promoter polymorphisms (-1031T/C, -863C/A, -857C/T, -308G/A and -238G/A) in the human TNF-alpha gene and schizophrenia (314 Chinese Han schizophrenic patients and 340 healthy control). A meta-analysis we did in this work, which is based on previous nine studies plus our own unpublished data including a total of 2399 schizophrenic patients (sporadic cases 2099, familial cases >505) and more than 3261 controls, failed to show significant difference of -308G/A distribution between patients and controls in both the whole sample and the pooled Asian sample. By contraries, the significant results in the pooled Caucasian sample imply an ethnic heterogeneity in -308G/A variation in the TNF-alpha gene in schizophrenia.

Adult↗

Alternative splicing of transcripts for the alpha 3 chain of mouse collagen VI: identification of an abundant isoform lacking domains N7-N10 in mouse and human.

Three distinct alpha chains form the collagen VI monomer, the alpha 3(VI) chain being much larger than the alpha 1(VI) and alpha 2(VI) chains. The alpha 3(VI) chain has 10 von Willebrand Factor type A domains of approximately 200 amino acids at the N-terminus (N1-N10) compared with only one such domain in the alpha 1(VI) and alpha 2(VI) chains. Domains N10, N9, N7 and N3 of the alpha 3(VI) chain are subject to alternative splicing in chick and/or human tissues, indicating the possibility of isoforms that have different functions depending on which N-terminal domains are included or excluded. In this study we have PCR amplified and sequenced mouse alpha 3(VI) cDNA encoding the N2-N10 domains. By reverse transcription-PCR using oligonucleotides spanning different regions of the cDNA we have undertaken a comprehensive analysis of alternative splicing of the alpha 3(VI) mRNA in embryonic and adult mouse tissues. We demonstrate that domains N10, N9 and N7 are also subject to alternative splicing in mouse tissues and in addition identify an abundant novel variant transcript that lacks all four N-terminal domains (N7-N10) in mouse tissues and human cells. We also identify less abundant transcripts that lack a large part of the N3 domain, and transcripts lacking the entire N5 domain. Using specific RNase protection assays we show that the shorter transcripts containing domains (N8+N7+N6), (N8+N6) and N6 are present at higher levels than transcripts containing the N10 and/or N9 domains, with tissue-specific variation in the levels of variant transcripts. These studies demonstrate a larger range of collagen VI protein variants than previously described.

5' Untranslated Regions↗

Phenotypic and genotypic diversity of Streptococcus sanguis in infants.

Streptococcus sanguis comprises a heterogeneous group of oral streptococci indigenous to the oral cavity of humans. A total of 289 isolates from an infant population (n=37) were tentatively identified as S. sanguis on the basis of the distinctive colony morphology as shown on MM10-sucrose non-selective medium. These isolates were divided into four biovars of S. sanguis as determined by an extended panel of biochemical attributes. Chromosomal DNA was extracted from each isolate, and an AP-PCR fingerprint profile was obtained to allow study of the diversity within and among the infants. In this study, all four biovars of S. sanguis were detected in the infants. A wide genotypic diversity of S. sanguis was observed among these isolates; on average, each infant harbored 2.7 unique amplitypes as shown by the AP-PCR fingerprints. To explore the phylogenic relationship among these S. sanguis isolates, 20 strains representing the four biovars were selected at random for sequencing of their 16S rDNA and 16S-23S rDNA intergenic spacer chromosomal loci. Two major sequence patterns were identified within the 16S rDNA sequences. A phylogenic analysis showed that members from each of the four biovars of S. sanguis bore close relationship with the type-strain ATCC 10556 sequence, and that all of the isolates representing the four biovars could be clustered into two main phylotypes. The biovars were distributed throughout the phylotypes, indicating no correlation between the genetic and phenotypic groupings.

Bacterial Typing Techniques↗

A low rate of simultaneous double-nucleotide mutations in primates.

The occurrence of double-nucleotide (doublet) mutations is contrary to the normal assumption that point mutations affect single nucleotides. Here we develop a new method for estimating the doublet mutation rate and apply it to more than a megabase of human-chimpanzee-baboon genomic DNA alignments and more than a million human single-nucleotide polymorphisms. The new method accounts for the effect of regional variation in evolutionary rates, which may be a confounding factor in previous estimates of the doublet mutation rate. Furthermore we determine sequence context effects by using sequence comparisons over a variety of lineage lengths. This approach yields a new estimate of the doublet mutation rate of 0.3% of the singleton rate, indicating that doublet mutations are far rarer than previously thought. Our results suggest that doublet mutations are unlikely to have caused the correlation between synonymous and nonsynonymous substitution rates in mammals, and also show that regional variation and sequence context effects play an important role in primate DNA sequence evolution.

Animals↗

Ergonomic exposure assessment: an application of the PATH systematic observation method to retail workers. Postures, Activities, Tools and Handling.

This study examined biomechanical stressor variables (physical work exposures) in relation to job title, gender, and back-belt status in 134 retail store workers. The principal concerns were to quantitatively describe physical work exposures and to determine the degrees to which these quantitative variables correlated with job title and with the use of back belts. An additional objective was to assess the inter-rater reliability of the observation method. The systematic observation method employed was based on a modification of the PATH (Postures, Activities, Tools, and Handling) measurement method. Chi-square analysis indicated that the frequencies of bent or twisted postures followed the pattern of unloaders > stockers > department managers. For weight handled per lift, lower, or carry, the pattern was unloaders > department managers > stockers. The mean lifting frequencies per hour were 35.9 for department managers, 48.8 for stockers, and 137.4 for unloaders. Back-belt-wearing percentages were higher for unloaders (63%) compared with stockers (48%) and department managers (25%). Back-belt-wearing workers had higher levels of biomechanical stressor variables, including arm position, twisting, weight handled, and number of lifts per hour. Kappa statistics ranged from 0.5 to 0.63, a level of adequate or good reliability beyond chance. The method employed in this study is applicable in studies that require only fairly crude distinctions among biomechanical stressor variables. Nevertheless, this level of distinction may be sufficient when implementing intervention studies and control strategies for many material-handling-intensive jobs.

Back Injuries↗

Comparison of in vivo plasma and peripheral blood mononuclear cell HIV-1 quasi-species to short-term tissue culture isolates: an analysis of tat and C2-V3 env regions.

OBJECTIVE: To determine whether the HIV-1 genomes that grow out in vitro from peripheral blood mononuclear cells (PBMC) better represent the in vivo quasi-species present in plasma or PBMC. RESULTS: For one patient (9606), PBMC culture represented more accurately the plasma rather than the in vivo PBMC quasi-species distribution, because a large number of tat-defective proviruses present in PBMC in vivo were not detected in plasma nor in the PBMC cultures. For a second patient (9605), PBMC culture was representative of both in vivo PBMC and plasma tat sequences, but selection of C2-V3 env sequences was observed in PBMC cultures compared with sequences present in both plasma and PBMC in vivo. This selection consisted of the absence in vitro of genomes with certain amino-acid substitutions at or near conserved glycosylation sites of the C2 region at positions 276 and 289. Site 276 has been reported to be important for viral infectivity, and these substitutions may therefore have affected infectivity. In the third patient (10095), selection of both tat and C2-V3 sequences was observed in culture as compared to plasma and PBMC in vivo. In contrast to the first two patients, this third patient contained V3 sequences in vivo that were predicted to impart syncytium induction and enhanced replication capacity. It was these sequences that grew out preferentially in vitro. CONCLUSION: This study suggests that short-term PBMC culture is representative of HIV-1 genomes present in PBMC and plasma in vivo to the degree that they are infectious.

Amino Acid Sequence↗

Voltammetric determination of cadmium(II) using a chemically modified electrode.

An 1-(pyridylazo)-2-naphthol modified glassy carbon electrode has been investigated as sensor for the measurement of trace levels of Cd2+. Cd2+ is deposited on the surface of a PAN modified glassy carbon electrode at -1.10 V (vs. SCE) via forming Cd2+-PAN and subsequent reduction at the electrode. In the following step, Cd-PAN is oxidized, and voltammograms are recorded by scanning the potential in a positive direction. Calibration plots were found to be linear in the range 2 x 10(-8) mol/L to 8 x 10(-7) mol/L. The detection limit was 5 x 10(-10) mol/L, and the coefficient of variation, determined on one single electrode at a concentration of 5 x 10(-7) mol/L, was calculated to be 3.2% (n = 5). Using this new kind of modified electrode, trace levels of Cd(II) in water samples were determined; the average recovery was calculated to be 98.78%.

Cadmium↗

Integrated pan-cancer profiling highlights OSR2 as a prognostic indicator and immune-associated biomarker.

BACKGROUND: Odd-skipped-related 2 (OSR2), encoded by the OSR2 gene, has been reported to function as a checkpoint associated with CD8⁺ T-cell exhaustion in the tumor microenvironment of solid malignancies, suggesting its potential as a therapeutic target to improve immunotherapeutic responses. Nevertheless, the molecular and clinical significance of OSR2 across diverse cancer types has not yet been systematically investigated, and its pan-cancer expression profile, prognostic implications, and associations with tumor immunity remain to be fully elucidated. METHODS: In this study, we integrated datasets from The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression (GTEx) portal, and the Human Protein Atlas to construct a systematic pan-cancer profile of OSR2. The prognostic value of OSR2 was comprehensively assessed using univariate Cox regression, survival analysis, and receiver operating characteristic (ROC) curve analysis. In addition, we performed an in-depth analysis of the relationships between OSR2 and multiple molecular and immunological features, including copy number variation (CNV), DNA methylation, tumor mutational burden (TMB), microsatellite instability (MSI), immune-related gene expression, immune cell infiltration, and drug sensitivity, with the aim of exploring its potential immunological associations with the tumor microenvironment. RESULTS: OSR2 expression was significantly upregulated or downregulated in the majority of tumor tissues relative to normal counterparts and exhibited distinct cancer-type-specific patterns across clinical stages. CNV alterations and aberrant DNA methylation were closely associated with abnormal OSR2 mRNA expression in multiple cancers. Prognostic analyses indicated that OSR2 expression was significantly associated with overall survival, disease-specific survival, disease-free interval, and progression-free interval across multiple cancer types, showing either risk-associated or protective associations in a tumor-context-dependent manner. Furthermore, OSR2 expression showed strong associations with immune cell infiltration, particularly T-cell subsets, and was significantly correlated with the expression of multiple immune checkpoint-related genes across diverse malignancies. OSR2 expression was also closely associated with TMB, MSI, and sensitivity to multiple anticancer agents. CONCLUSION: Taken together, these findings suggest that OSR2 is associated with prognosis and immune-related features across multiple cancer types. OSR2 may be linked to features of the tumor immune microenvironment through its relationships with immune cell infiltration, immune checkpoint gene expression, and genomic instability, and thus may serve as a candidate biomarker for further investigation in cancer immunotherapy.

CD8⁺ T-cell↗