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101.
Taina T. Immonen Jessica M. Conway Ethan O. Romero-Severson Alan S. Perelson Thomas Leitner 《PLoS computational biology》2015,11(12)
HIV-1 is subject to immune pressure exerted by the host, giving variants that escape the immune response an advantage. Virus released from activated latent cells competes against variants that have continually evolved and adapted to host immune pressure. Nevertheless, there is increasing evidence that virus displaying a signal of latency survives in patient plasma despite having reduced fitness due to long-term immune memory. We investigated the survival of virus with latent envelope genomic fragments by simulating within-host HIV-1 sequence evolution and the cycling of viral lineages in and out of the latent reservoir. Our model incorporates a detailed mutation process including nucleotide substitution, recombination, latent reservoir dynamics, diversifying selection pressure driven by the immune response, and purifying selection pressure asserted by deleterious mutations. We evaluated the ability of our model to capture sequence evolution in vivo by comparing our simulated sequences to HIV-1 envelope sequence data from 16 HIV-infected untreated patients. Empirical sequence divergence and diversity measures were qualitatively and quantitatively similar to those of our simulated HIV-1 populations, suggesting that our model invokes realistic trends of HIV-1 genetic evolution. Moreover, reconstructed phylogenies of simulated and patient HIV-1 populations showed similar topological structures. Our simulation results suggest that recombination is a key mechanism facilitating the persistence of virus with latent envelope genomic fragments in the productively infected cell population. Recombination increased the survival probability of latent virus forms approximately 13-fold. Prevalence of virus with latent fragments in productively infected cells was observed in only 2% of simulations when we ignored recombination, while the proportion increased to 27% of simulations when we allowed recombination. We also found that the selection pressures exerted by different fitness landscapes influenced the shape of phylogenies, diversity trends, and survival of virus with latent genomic fragments. Our model predicts that the persistence of latent genomic fragments from multiple different ancestral origins increases sequence diversity in plasma for reasonable fitness landscapes. 相似文献
102.
Hoane JS Carruthers VB Striepen B Morrison DP Entzeroth R Howe DK 《International journal for parasitology》2003,33(7):671-679
Sarcocystis neurona, an apicomplexan parasite, is the primary causative agent of equine protozoal myeloencephalitis. Like other members of the Apicomplexa, S. neurona zoites possess secretory organelles that contain proteins necessary for host cell invasion and intracellular survival. From a collection of S. neurona expressed sequence tags, we identified a sequence encoding a putative microneme protein based on similarity to Toxoplasma gondii MIC10 (TgMIC10). Pairwise sequence alignments of SnMIC10 to TgMIC10 and NcMIC10 from Neospora caninum revealed approximately 33% identity to both orthologues. The open reading frame of the S. neurona gene encodes a 255 amino acid protein with a predicted 39-residue signal peptide. Like TgMIC10 and NcMIC10, SnMIC10 is predicted to be hydrophilic, highly alpha-helical in structure, and devoid of identifiable adhesive domains. Antibodies raised against recombinant SnMIC10 recognised a protein band with an apparent molecular weight of 24 kDa in Western blots of S. neurona merozoites, consistent with the size predicted for SnMIC10. In vitro secretion assays demonstrated that this protein is secreted by extracellular merozoites in a temperature-dependent manner. Indirect immunofluorescence analysis of SnMIC10 showed a polar labelling pattern, which is consistent with the apical position of the micronemes, and immunoelectron microscopy provided definitive localisation of the protein to these secretory organelles. Further analysis of SnMIC10 in intracellular parasites revealed that expression of this protein is temporally regulated during endopolygeny, supporting the view that micronemes are only needed during host cell invasion. Collectively, the data indicate that SnMIC10 is a microneme protein that is part of the excreted/secreted antigen fraction of S. neurona. Identification and characterisation of additional S. neurona microneme antigens and comparisons to orthologues in other Apicomplexa could provide further insight into the functions that these proteins serve during invasion of host cells. 相似文献
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Fledgling Bachman’s Sparrows in a longleaf pine ecosystem: survival,movements, and habitat selection
Alexander C. Fish Christopher S. DePerno Jessica M. Schillaci Christopher E. Moorman 《Journal of Field Ornithology》2020,91(4):354-366
Fledgling ecology remains understudied for many passerine species, yet information about the fledgling life stage is critical for understanding full-annual life cycles and population recruitment. We examined the survival, habitat selection, and movements of fledgling Bachman’s Sparrows (Peucaea aestivalis) in a longleaf pine-wiregrass (Pinus palustris-Aristida stricta) community managed with frequent prescribed fire. We captured and marked 36 fledglings on the day of fledging and used radio-telemetry to relocate them daily until independence during three breeding seasons (2014–2016). We visually confirmed the status of fledglings as live or dead during daily relocations and determined causes of mortality. We measured vegetation characteristics at fledgling locations and compared them to the characteristics of vegetation at the locations of adult males. We used a Known Fates analysis in Program MARK to estimate fledgling survival, and generalized linear mixed effect models to determine habitat selection. Estimated fledgling survival until independence was 0.31 (SE = 0.08), with most mortality during the first 4 d post-fledging. Fledglings with longer wing chords had higher rates of survival than those with shorter wing chords, possibly due to an increased ability to evade predators. Fledgling movements were restricted primarily to natal territories. Fledgling Bachman’s Sparrows were located in areas with greater woody plant, forb, and grass cover and less bare ground than available in natal territories. Similar to fledglings of other songbirds, understory woody and herbaceous plants appear to provide critical cover for fledgling Bachman’s Sparrows, and maintenance of such cover should receive consideration in management plans for longleaf pine communities. 相似文献
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Jessica R. Benson Jiameng Xu Derek M. Moynes Tamia K. Lapointe Christophe Altier Stephen J. Vanner Alan E. Lomax 《Cell and tissue research》2014,356(2):309-317
Sensitization of dorsal root ganglia (DRG) neurons is an important mechanism underlying the expression of chronic abdominal pain caused by intestinal inflammation. Most studies have focused on changes in the peripheral terminals of DRG neurons in the inflamed intestine but recent evidence suggests that the sprouting of central nerve terminals in the dorsal horn is also important. Therefore, we examine the time course and reversibility of changes in the distribution of immunoreactivity for substance P (SP), a marker of the central terminals of DRG neurons, in the spinal cord during and following dextran sulphate sodium (DSS)-induced colitis in mice. Acute and chronic treatment with DSS significantly increased SP immunoreactivity in thoracic and lumbosacral spinal cord segments. This increase developed over several weeks and was evident in both the superficial laminae of the dorsal horn and in lamina X. These increases persisted for 5 weeks following cessation of both the acute and chronic models. The increase in SP immunoreactivity was not observed in segments of the cervical spinal cord, which were not innervated by the axons of colonic afferent neurons. DRG neurons dissociated following acute DSS-colitis exhibited increased neurite sprouting compared with neurons dissociated from control mice. These data suggest significant colitis-induced enhancements in neuropeptide expression in DRG neuron central terminals. Such neurotransmitter plasticity persists beyond the period of active inflammation and might contribute to a sustained increase in nociceptive signaling following the resolution of inflammation. 相似文献
108.
Jessica M. Rothman Colin A. Chapman Peter J. Van Soest 《International journal of primatology》2012,33(3):542-566
An important goal of primatology is to identify the ecological factors that affect primate abundance, diversity, demography, and social behavior. Understanding the nutritional needs of primates is central to understanding primate ecology because adequate nutrition is a prerequisite for successful reproduction. Here, we review nutritional methods and provide practical guidelines to measure nutrient intake by primates in field settings. We begin with an assessment of how to estimate food intake by primates using behavioral observations. We then describe how to collect, prepare, and preserve food samples. Finally, we suggest appropriate nutritional assays for estimating diet nutritional quality and point to the merits and limitations of each. We hope this review will inspire primatologists to use nutritional ecology to answer many unresolved questions in primatology. 相似文献
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Mita Das Marjan Boerma Jessica R. Goree Elise G. Lavoie Michel Fausther Igor B. Gubrij Amanda K. Pangle Larry G. Johnson Jonathan A. Dranoff 《PloS one》2014,9(4)