HIV-1 and its envelope glycoprotein down-regulate chemotactic ligand receptors and chemotactic function of peripheral blood monocytes

Peripheral blood monocytes from AIDS patients exhibit defective migratory responses to chemotactic stimuli in vitro and to inflammatory sites in vivo. In studies presented here, normal monocytes were infected with the HIV-1/HTLV-IIIBa-L isolate in vitro and evaluated for chemotactic responsiveness. Within 2 days after viral exposure, but before evidence of virus production in the monocytes, chemotactic activity was significantly impaired. Decreased chemotactic activity was associated with modulation of receptors for the chemotactic ligands, C5a and FMLP, on the monocyte cell surface. In addition to HIV-1, monocytes treated with purified HIV-1 envelope glycoprotein gp120 demonstrated a comparable modulation of chemotactic ligand receptors and migratory function. In addition, the HIV-1 or HIV-1 gp120-treated monocytes were induced to undergo differentiation as monitored by HLA-DR expression. Immunoprecipitation of the gp120 with a specific antibody reversed its effects on monocyte chemotaxis and HLA-DR expression. Taken together, these data indicate that the initial interaction of HIV-1 with the monocyte is not passive, but that the binding of HIV-1 and/or HIV-1 gp120 to the CD4R on monocytes transduces a signal leading to transient monocyte activation.     

Temperature- and size-dependent growth and movement of the North Pacific giant octopus (Enteroctopus dofleini) in the Bering Sea

Octopus growth and movement occurs during all life stages and have implications for survival, food web dynamics and reproduction. From 2009 to 2011, 1714 North Pacific giant octopus (Enteroctopus dofleini) were tagged and recaptured in the eastern Bering Sea with visible implant elastomers to better understand the ecology of this data-poor species. Over this period, 246 of the tagged individuals were recaptured. In autumn, when temperatures were warmest, E. dofleini had higher growth rates and moved more than in the colder winter months. For both short- and long-term recaptures, small octopus grew faster than large octopus. Movement of octopus over short- and long-term periods was low for very small and very large octopus and high for median-sized octopus, which is likely to be a function of maturity status and reproductive activities. Approximately 80% of recaptures moved less than 2?km from the initial tagging location for time periods up to a year, suggesting long-term site fidelity. As temperature and size may be tightly linked to growth and movement rates for E. dofleini in the eastern Bering Sea, predicted climate warming will likely alter ecological processes for the species and impact their distribution.     

Improving model construction of profile HMMs for remote homology detection through structural alignment

Background  

Remote homology detection is a challenging problem in Bioinformatics. Arguably, profile Hidden Markov Models (pHMMs) are one of the most successful approaches in addressing this important problem. pHMM packages present a relatively small computational cost, and perform particularly well at recognizing remote homologies. This raises the question of whether structural alignments could impact the performance of pHMMs trained from proteins in the Twilight Zone, as structural alignments are often more accurate than sequence alignments at identifying motifs and functional residues. Next, we assess the impact of using structural alignments in pHMM performance.     

Modulation of the immune response by anaphylatoxin in the microenvironment of the interacting cells

It was shown that the anaphylatoxins C3a and C5a can modulate in vitro immunological reactivities. C3a suppresses both the in vitro polyclonal antibody response and the specific antibody response to sheep red blood cells (SRBC) of both mouse spleen cells and human peripheral blood cells. The target cell in the mouse for C3a appears to be an Lyt-1+2- suppressor-inducer cell and macrophages appear not to be required. In contrast to C3a, C5a enhances in vitro responses of mice. Both the response to SRBC and the mixed lymphocyte reaction are enhanced by C5a. This enhancement appears to be through an Ia- macrophage that contains receptors for C5a. It appears that enhancement may be brought about by interleukin 1, which is released when Ia- macrophages are pulsed with C5a. It is suggested that these anaphylatoxins, when present in high concentrations in the microenvironment of the interacting cells of the immune system, play a dynamic role in the regulation of the immune response. Peptide fragments cleaved from the Fc portion of antibody, complexed with antigen in this microenvironment, may have a similar regulating role.     

Use of Postmortem Human Dura Mater and Scalp for Deriving Human Fibroblast Cultures

Fibroblasts can be collected from deceased individuals, grown in culture, reprogrammed into induced pluripotent stem cells (iPSCs), and then differentiated into a multitude of cell types, including neurons. Past studies have generated iPSCs from somatic cell biopsies from either animal or human subjects. Previously, fibroblasts have only been successfully cultured from postmortem human skin in two studies. Here we present data on fibroblast cell cultures generated from 146 scalp and/or 53 dura mater samples from 146 postmortem human brain donors. In our overall sample, the odds of successful dural culture was almost two-fold compared with scalp (OR = 1.95, 95% CI: [1.01, 3.9], p = 0.047). Using a paired design within subjects for whom both tissues were available for culture (n = 53), the odds of success for culture in dura was 16-fold as compared to scalp (OR = 16.0, 95% CI: [2.1–120.6], p = 0.0007). Unattended death, tissue donation source, longer postmortem interval (PMI), and higher body mass index (BMI) were associated with unsuccessful culture in scalp (all p<0.05), but not in dura. While scalp cells proliferated more and grew more rapidly than dura cells [F (1, 46) = 12.94, p<0.008], both tissues could be generated and maintained as fibroblast cell lines. Using a random sample of four cases, we found that both postmortem scalp and dura could be successfully reprogrammed into iPSC lines. Our study demonstrates that postmortem dura mater, and to a lesser extent, scalp, are viable sources of living fibroblasts for culture that can be used to generate iPSCs. These tissues may be accessible through existing brain tissue collections, which is critical for studying disorders such as neuropsychiatric diseases.     

Sex‐biased transcriptome divergence along a latitudinal gradient

Sex‐dependent gene expression is likely an important genomic mechanism that allows sex‐specific adaptation to environmental changes. Among Drosophila species, sex‐biased genes display remarkably consistent evolutionary patterns; male‐biased genes evolve faster than unbiased genes in both coding sequence and expression level, suggesting sex differences in selection through time. However, comparatively little is known of the evolutionary process shaping sex‐biased expression within species. Latitudinal clines offer an opportunity to examine how changes in key ecological parameters also influence sex‐specific selection and the evolution of sex‐biased gene expression. We assayed male and female gene expression in Drosophila serrata along a latitudinal gradient in eastern Australia spanning most of its endemic distribution. Analysis of 11 631 genes across eight populations revealed strong sex differences in the frequency, mode and strength of divergence. Divergence was far stronger in males than females and while latitudinal clines were evident in both sexes, male divergence was often population specific, suggesting responses to localized selection pressures that do not covary predictably with latitude. While divergence was enriched for male‐biased genes, there was no overrepresentation of X‐linked genes in males. By contrast, X‐linked divergence was elevated in females, especially for female‐biased genes. Many genes that diverged in D. serrata have homologs also showing latitudinal divergence in Drosophila simulans and Drosophila melanogaster on other continents, likely indicating parallel adaptation in these distantly related species. Our results suggest that sex differences in selection play an important role in shaping the evolution of gene expression over macro‐ and micro‐ecological spatial scales.     

Breed and other effects on reproductive traits and breeding soundness categorization in young beef bulls in Florida

Yearling, grass-fed, beef bulls at the USDA Subtropical Agricultural Research Station, Brooksville, Florida, were assessed for physical and semen traits in January, April, July and October of 1991 (Trial 1) and 1992 (Trial 2). Bulls were given a breeding soundness evaluation (BSE) using revised semen and scrotal circumference (SC) criteria. In Trial 1, the bulls consisted of Angus (n = 15), Brahman (n = 14), Hereford (n = 15) and Senepol (n = 14). In Trial 2, the breeds were Angus (n = 15), Brahman (n = 16), Romosinuano (n = 13) and Nellore x Brahman (n = 9). Trial bulls generally showed delayed growth compared with grain-fed bulls in temperate environments. Breed influenced semen traits (percentage sperm motility, normal spermatozoa and those with primary abnormalities) in both trials. Temperate Bos taurus breeds (Angus, Hereford) were generally superior to Bos indicus breeds (Brahman, Nellore x Brahman). Tropically-adapted Bos taurus breeds (Senepol, Romosinuano) were intermediate for those traits tested. In general, tropically-adapted Bos taurus breeds were more similar in reproductive development to temperate Bos taurus than to Bos indicus breeds. Breed by test period interactions occurred and were mainly influenced by delayed sexual maturity of Bos indicus bulls. Qualitative semen traits increased with bull age, particularly from 12 to 18 mo. Scrotal circumference development was slower in the Bos indicus breeds. Bulls of satisfactory BSE status at 18.1 to 22 mo of age were 73.9% in Trial 1 and 58.5% in Trial 2. Brahman bulls had the least satisfactory BSE scores in both years (Trial 1, 44.4%; Trial 2, 22.2%). Most bulls failed to achieve satisfactory BSE status due to a small SC relative to age (Trial 1, 66%; Trial 2, 72%). The most efficacious use of the BSE was > or = 15 mo in Bos taurus bulls and > 18 mo for Bos indicus bulls. Although the BSE has proven to be useful for the assessment of young, pasture-raised bulls in semi-tropical environments, use of SC thresholds linked more with growth traits than with calendar age would improve comparisons of relative reproductive development in such bulls, particularly those of Bos indicus derivation.