Latency, Expression and Splicing During Infection With HIV

Over 35 million people are living with human immunodeficiency virus (HIV-1). The mechanisms causing integrated provirus to become latent, the diversity of spliced viral transcripts and the cellular response to infection are not fully characterized and hinder the eradication of HIV-1. We applied high-throughput sequencing to investigate the effects of host chromatin on proviral latency and variation of expression and splicing in both the host and virus during infection. To evaluate the link between host chromatin and proviral latency, we compared genomic and epigenetic features to HIV-1 integration site data for latent and active provirus from five cell culture models. Latency was associated with chromosomal position within individual models. However, no shared mechanisms of latency were observed between cell culture models. These differences suggest that cell culture models may not completely reflect latency in patients. We carried out two studies to explore mRNA populations during HIV infection. Single-molecule amplification and sequencing revealed that the clinical isolate HIV89.6 produces at least 109 different spliced mRNAs. Viral message populations differed between cell types, between human donors and longitudinally during infection. We then sequenced mRNA from control and HIV89.6-infected primary human T cells. Over 17 percent of cellular genes showed altered activity associated with infection. These gene expression patterns differed from HIV infection in cell lines but paralleled infections in primary cells. Infection with HIV89.6 increased intron retention in cellular genes and abundance of RNA from human endogenous retroviruses. We also quantified the frequency and location of chimeric HIV-host RNAs. These two studies together provided a detailed accounting of both HIV89.6 and host expression and alternative splicing. A more cost-effective method of detecting viral load would aid patients with poor access to healthcare. We developed improved methods for assaying HIV-1 RNA using loop-mediated isothermal amplification based on primers targeting regions of the HIV-1 genome conserved across subtypes. Combined with lab-on-a-chip technology, these techniques allow quantitative measurements of viral load in a point-of-care device targeted to resource-limited settings. This work disclosed novel HIV-host interactions and developed techniques and knowledge that will aid in the study and management of HIV-1 infection

The Change of Alveolar Bone Thickness on Mandibular Central Incisors of Skeletal Class II Patients After Orthodontic Treatment Using Cone-Beam Computed Tomography.

Objective: To test the null hypothesis that orthodontic tooth movement does not create dehiscences and the sagittal width dimension of alveolar bone is maintained. Materials and Methods: In 60 skeletal class II patients, CBCT images at pre- (T1) and post-orthodontic treatment (T2) were obtained and the presence of dehiscences was recorded. Based on the presence of dehiscences at T1 and T2, the patients were divided into four groups. The alveolar bone thickness at the level of 2 (CEJ2), 5 (CEJ5), 10 (CEJ10), and 15 (CEJ15) mm from the cementoenamel junction (CEJ) was measured on CBCT images in cross section along the long axis on the central incisors. CBCT-synthesized lateral cephalometric images were analyzed. Statistical analysis and the Pearson correlation analyses were utilized at a pResults: CBCT imaging showed that 27.1% of the mandibular central incisors had dehiscences at T1. With pre-existing dehiscence, the incidence of dehiscence increased to 50% at T2. Patients that developed dehiscences after orthodontic treatment showed the highest percentage of alveolar bone loss (-23.7% at CEJ2, -19.9% at CEJ5 at T2). In the group where patients developed dehiscences after orthodontic treatment, there was statistically significant mean increase of L1-NB (3.1mm) and IMPA (9.8°) (pConclusions: When camouflaging skeletal Class II patients, the limits of mandibular anterior incisor forward movement might be less than previously thought. In order to prevent the development of inadvertent dehiscences during the orthodontic treatment, careful diagnosis with CBCT images is recommended. Furthermore, when excessive protrusion and/or proclination is planned, additional treatment modalities such as orthognathic surgery, tooth extraction, and partial corticotomy with bone grafting should be considered

Saving endangered whales at no cost

Author Posting. © Elsevier B.V., 2007. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Current Biology 17 (2007): R10-R11, doi:10.1016/j.cub.2006.11.045.The North Atlantic right whale is one of the most critically endangered marine species. Drastic overexploitation has driven this large, slow-swimming baleen whale to virtual extinction in Europe, while a small remnant population of ~350 individuals remains on the U.S. and Canadian east coast. Although this species has been protected for 70 years, recovery has been slight and extinction is still looming because of accidental mortality from shipstrikes and fishing gear (Figure 1A,B). Seventy five percent of appropriately photographed whales show evidence of entanglement, predominantly with lobster fishing gear, and this percentage has increased from 52% in the 1980s. At the same time, the U.S. lobster fishery is severely overexploited (the inshore fishing mortalities in the two main U.S. regions are 0.69 and 0.84, while 0.2 achieves maximum yield per recruit). We argue here that this endangered whale species can be protected from entanglement mortality, and the fishery can benefit simultaneously, by a large reduction of lobster traps used; a classic win–win situation.This work was supported by the Lenfest Foundation and NSERC

Heightened resistance to host type 1 interferons characterizes HIV-1 at transmission and after antiretroviral therapy interruption

Type 1 interferons (IFN-I) are potent innate antiviral effectors that constrain HIV-1 transmission. However, harnessing these cytokines for HIV-1 cure strategies has been hampered by an incomplete understanding of their antiviral activities at later stages of infection. Here, we characterized the IFN-I sensitivity of 500 clonally derived HIV-1 isolates from the plasma and CD4+ T cells of 26 individuals sampled longitudinally after transmission or after antiretroviral therapy (ART) and analytical treatment interruption. We determined the concentration of IFNα2 and IFNβ that reduced viral replication in vitro by 50% (IC50) and found consistent changes in the sensitivity of HIV-1 to IFN-I inhibition both across individuals and over time. Resistance of HIV-1 isolates to IFN-I was uniformly high during acute infection, decreased in all individuals in the first year after infection, was reacquired concomitant with CD4+ T cell loss, and remained elevated in individuals with accelerated disease. HIV-1 isolates obtained by viral outgrowth during suppressive ART were relatively IFN-I sensitive, resembling viruses circulating just before ART initiation. However, viruses that rebounded after treatment interruption displayed the highest degree of IFNα2 and IFNβ resistance observed at any time during the infection course. These findings indicate a dynamic interplay between host innate responses and the evolving HIV-1 quasispecies, with the relative contribution of IFN-I to HIV-1 control affected by both ART and analytical treatment interruption. Although elevated at transmission, host innate pressures are the highest during viral rebound, limiting the viruses that successfully become reactivated from latency to those that are IFN-I resistant

Allometry and Ecology of the Bilaterian Gut Microbiome.

Classical ecology provides principles for construction and function of biological communities, but to what extent these apply to the animal-associated microbiota is just beginning to be assessed. Here, we investigated the influence of several well-known ecological principles on animal-associated microbiota by characterizing gut microbial specimens from bilaterally symmetrical animals (Bilateria) ranging from flies to whales. A rigorously vetted sample set containing 265 specimens from 64 species was assembled. Bacterial lineages were characterized by 16S rRNA gene sequencing. Previously published samples were also compared, allowing analysis of over 1,098 samples in total. A restricted number of bacterial phyla was found to account for the great majority of gut colonists. Gut microbial composition was associated with host phylogeny and diet. We identified numerous gut bacterial 16S rRNA gene sequences that diverged deeply from previously studied taxa, identifying opportunities to discover new bacterial types. The number of bacterial lineages per gut sample was positively associated with animal mass, paralleling known species-area relationships from island biogeography and implicating body size as a determinant of community stability and niche complexity. Samples from larger animals harbored greater numbers of anaerobic communities, specifying a mechanism for generating more-complex microbial environments. Predictions for species/abundance relationships from models of neutral colonization did not match the data set, pointing to alternative mechanisms such as selection of specific colonists by environmental niche. Taken together, the data suggest that niche complexity increases with gut size and that niche selection forces dominate gut community construction.IMPORTANCEThe intestinal microbiome of animals is essential for health, contributing to digestion of foods, proper immune development, inhibition of pathogen colonization, and catabolism of xenobiotic compounds. How these communities assemble and persist is just beginning to be investigated. Here we interrogated a set of gut samples from a wide range of animals to investigate the roles of selection and random processes in microbial community construction. We show that the numbers of bacterial species increased with the weight of host organisms, paralleling findings from studies of island biogeography. Communities in larger organisms tended to be more anaerobic, suggesting one mechanism for niche diversification. Nonselective processes enable specific predictions for community structure, but our samples did not match the predictions of the neutral model. Thus, these findings highlight the importance of niche selection in community construction and suggest mechanisms of niche diversification

Resistance to Type 1 Interferons is a Major Determinant of HIV-1 Transmission Fitness

Sexual transmission of HIV-1 is an inefficient process, with only one or few variants of the donor quasispecies establishing the new infection. A critical, and as yet unresolved, question is whether the mucosal bottleneck selects for viruses with increased transmission fitness. Here, we characterized 300 limiting dilution-derived virus isolates from the plasma, and in some instances genital secretions, of eight HIV-1 donor and recipient pairs. Although there were no differences in the amount of virion-associated envelope glycoprotein, recipient isolates were on average threefold more infectious (P = 0.0001), replicated to 1.4-fold higher titers (P = 0.004), were released from infected cells 4.2-fold more efficiently (P < 0.00001), and were significantly more resistant to type I IFNs than the corresponding donor isolates. Remarkably, transmitted viruses exhibited 7.8-fold higher IFNα2 (P < 0.00001) and 39-fold higher IFNβ (P < 0.00001) half-maximal inhibitory concentrations (IC50) than did donor isolates, and their odds of replicating in CD4+ T cells at the highest IFNα2 and IFNβ doses were 35-fold (P < 0.00001) and 250-fold (P < 0.00001) greater, respectively. Interestingly, pretreatment of CD4+ T cells with IFNβ, but not IFNα2, selected donor plasma isolates that exhibited a transmitted virus-like phenotype, and such viruses were also detected in the donor genital tract. These data indicate that transmitted viruses are phenotypically distinct, and that increased IFN resistance represents their most distinguishing property. Thus, the mucosal bottleneck selects for viruses that are able to replicate and spread efficiently in the face of a potent innate immune response

Investigating Behaviour and Population Dynamics of Striped Marlin (Kajikia audax) from the Southwest Pacific Ocean with Satellite Tags

Behaviour and distribution of striped marlin within the southwest Pacific Ocean were investigated using electronic tagging data collected from 2005–2008. A continuous-time correlated random-walk Kalman filter was used to integrate double-tagging data exhibiting variable error structures into movement trajectories composed of regular time-steps. This state-space trajectory integration approach improved longitude and latitude error distributions by 38.5 km and 22.2 km respectively. Using these trajectories as inputs, a behavioural classification model was developed to infer when, and where, ‘transiting’ and ‘area-restricted’ (ARB) pseudo-behavioural states occurred. ARB tended to occur at shallower depths (108±49 m) than did transiting behaviours (127±57 m). A 16 day post-release period of diminished ARB activity suggests that patterns of behaviour were affected by the capture and/or tagging events, implying that tagged animals may exhibit atypical behaviour upon release. The striped marlin in this study dove deeper and spent greater time at ≥200 m depth than those in the central and eastern Pacific Ocean. As marlin reached tropical latitudes (20–21°S) they consistently reversed directions, increased swimming speed and shifted to transiting behaviour. Reversals in the tropics also coincided with increases in swimming depth, including increased time ≥250 m. Our research provides enhanced understanding of the behavioural ecology of striped marlin. This has implications for the effectiveness of spatially explicit population models and we demonstrate the need to consider geographic variation when standardizing CPUE by depth, and provide data to inform natural and recreational fishing mortality parameters