Rapid reversion of sequence polymorphisms dominates early human immunodeficiency virus type 1 evolution

The error-prone replication of human immunodeficiency virus type 1 (HIV-1) enables it to continuously evade host CD8+ T-cell responses. The observed transmission, and potential accumulation, of CD8+ T-cell escape mutations in the population may suggest a gradual adaptation of HIV-1 to immune pressures. Recent reports, however, have highlighted the propensity of some escape mutations to revert upon transmission to a new host in order to restore efficient replication capacity. To more specifically address the role of reversions in early HIV-1 evolution, we examined sequence polymorphisms arising across the HIV-1 genome in seven subjects followed longitudinally 1 year from primary infection. As expected, numerous nonsynonymous mutations were associated with described CD8+ T-cell epitopes, supporting a prominent role for cellular immune responses in driving early HIV-1 evolution. Strikingly, however, a substantial proportion of substitutions (42%) reverted toward the clade B consensus sequence, with nearly one-quarter of them located within defined CD8 epitopes not restricted by the contemporary host's HLA. More importantly, these reversions arose significantly faster than forward mutations, with the most rapidly reverting mutations preferentially arising within structurally conserved residues. These data suggest that many transmitted mutations likely incur a fitness cost that is recovered through retrieval of an optimal, or ancestral, form of the virus. The propensity of mutations to revert may limit the accumulation of immune pressure-driven mutations in the population, thus preserving critical CD8+ T-cell epitopes as vaccine targets, and argue against an unremitting adaptation of HIV-1 to host immune pressures.     

Ecomorphological adaptations to bioluminescence in Porichthys notatus

Synopsis The midshipman fish, Porichthys notatus, is a visually active nocturnal predator. It must acquire exogenous sources of luciferin to remain luminescent and feeds on a variety of luminescent prey. Its ecomorphological adaptations for nocturnal predation were examined by observing predation on zooplankton illuminated by dinoflagellates. Its visual sensitivity is well adapted for detection of its own luminescence and its prey's luminescence. P. notatus can detect the luminescence of dinoflagellates and use this indirect light to increase predation on nonluminescent prey. Flash frequency and duration modulated predation rates. The interval between flash onset and strike initiation regulated strike success. High prey concentration decreased predation success due to increased optical and mechanosensory noise. Other ecomorphological adaptations of this predator to its special photic environment include a pigmented digestive tract, duplex retina with the capacity to discriminate emission spectra, contractible pupil, and the potential to counter illuminate. These morphological adaptations combined with an ambush predator style allow effective predation while minimizing exposure risk.     

Bacteria,phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations

Disturbance of the beneficial gut microbial community is a potential collateral effect of antibiotics, which have many uses in animal agriculture (disease treatment or prevention and feed efficiency improvement). Understanding antibiotic effects on bacterial communities at different intestinal locations is essential to realize the full benefits and consequences of in-feed antibiotics. In this study, we defined the lumenal and mucosal bacterial communities from the small intestine (ileum) and large intestine (cecum and colon) plus feces, and characterized the effects of in-feed antibiotics (chlortetracycline, sulfamethazine and penicillin (ASP250)) on these communities. 16S rRNA gene sequence and metagenomic analyses of bacterial membership and functions revealed dramatic differences between small and large intestinal locations, including enrichment of Firmicutes and phage-encoding genes in the ileum. The large intestinal microbiota encoded numerous genes to degrade plant cell wall components, and these genes were lacking in the ileum. The mucosa-associated ileal microbiota harbored greater bacterial diversity than the lumen but similar membership to the mucosa of the large intestine, suggesting that most gut microbes can associate with the mucosa and might serve as an inoculum for the lumen. The collateral effects on the microbiota of antibiotic-fed animals caused divergence from that of control animals, with notable changes being increases in Escherichia coli populations in the ileum, Lachnobacterium spp. in all gut locations, and resistance genes to antibiotics not administered. Characterizing the differential metabolic capacities and response to perturbation at distinct intestinal locations will inform strategies to improve gut health and food safety.     

Redescription and Life History of Contortylenchus brevicomi,a Parasite of the Southern Pine Beetle Dendroctonus frontalis

Larval and adult life stages are described for Contortylenchus brevicomi (Massey) Rühm parasitizing a Mississippi population of Dendroctonus frontalis, the southern pine beetle. Fourth-stage larvae and free-living adult females of this species are identified and described for the first time. The life cycle of C. brevicomi can be reconstructed from this study. The adult female nematode lays eggs in a mature beetle. Larval development progresses within the hemocoel until fourth-stage larvae exit the host. Mating occurs in beetle galleries and only females enter an immature beetle host.     

Lithiation‐Induced Dilation Mapping in a Lithium‐Ion Battery Electrode by 3D X‐Ray Microscopy and Digital Volume Correlation

Recent advances in high‐resolution 3D X‐ray computed tomography (CT) allow detailed, non‐destructive 3D structural mapping of a complete lithium‐ion battery. By repeated 3D image acquisition (time lapse CT imaging) these investigations of material microstructure are extended into the fourth dimension (time) to study structural changes of the device in operando. By digital volume correlation (DVC) of successive 3D images the dimensional changes taking place during charge cycling are quantified at the electrode level and at the Mn₂O₄ particle scale. After battery discharging, the extent of lithiation of the manganese (III/IV) oxide grains in the electrode is found to be a function of the distance from the battery terminal with grains closest to the electrode/current collector interface having the greatest expansion (≈30%) and grains furthest from the current collector and closest to the counter electrode showing negligible dilation. This implies that the discharge is limited by electrical conductivity. This new CT+DVC technique is widely applicable to the 3D exploration of the microstructural degradation processes for a range of energy materials including fuel cells, capacitors, catalysts, and ceramics.     

Increased sequence diversity coverage improves detection of HIV-specific T cell responses

The accurate identification of HIV-specific T cell responses is important for determining the relationship between immune response, viral control, and disease progression. HIV-specific immune responses are usually measured using peptide sets based on consensus sequences, which frequently miss responses to regions where test set and infecting virus differ. In this study, we report the design of a peptide test set with significantly increased coverage of HIV sequence diversity by including alternative amino acids at variable positions during the peptide synthesis step. In an IFN-gamma ELISpot assay, these "toggled" peptides detected HIV-specific CD4(+) and CD8(+) T cell responses of significantly higher breadth and magnitude than matched consensus peptides. The observed increases were explained by a closer match of the toggled peptides to the autologous viral sequence. Toggled peptides therefore afford a cost-effective and significantly more complete view of the host immune response to HIV and are directly applicable to other variable pathogens.