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Species distributed across heterogeneous environments often evolve locally adapted ecotypes, but understanding of the genetic mechanisms involved in their formation and maintenance in the face of gene flow is incomplete. In Burkina Faso, the major African malaria mosquitoAnopheles funestuscomprises two strictly sympatric and morphologically indistinguishable yet karyotypically differentiated forms reported to differ in ecology and behavior. However, knowledge of the genetic basis and environmental determinants ofAn. funestusdiversification was impeded by lack of modern genomic resources. Here, we applied deep whole-genome sequencing and analysis to test the hypothesis that these two forms are ecotypes differentially adapted to breeding in natural swamps versus irrigated rice fields. We demonstrate genome-wide differentiation despite extensive microsympatry, synchronicity, and ongoing hybridization. Demographic inference supports a split only ~1,300 years ago, closely following the massive expansion of domesticated African rice cultivation ~1,850 years ago. Regions of highest divergence, concentrated in chromosomal inversions, were under selection during lineage splitting, consistent with local adaptation. The origin of nearly all variation implicated in adaptation, including chromosomal inversions, substantially predates the ecotype split, suggesting that rapid adaptation was fueled mainly by standing genetic variation. Sharp inversion frequency differences likely facilitated adaptive divergence between ecotypes, both by suppressing recombination between opposing chromosomal orientations of the two ecotypes, and by maximizing recombination within the structurally monomorphic rice ecotype. Our results align with growing evidence from diverse taxa that rapid ecological diversification can arise from evolutionarily old structural genetic variants that modify genetic recombination.Significance StatementLocal adaptation to heterogeneous environments is pervasive, but its underlying genetic basis is incompletely understood. Within a major African malaria vector,An. funestus, are two chromosomally differentiated groups that are co-localized, morphologically indistinguishable, and reported to differ both in ecology and behavior relevant to malaria transmission and control. Progress in understanding the genetic basis and environmental determinants of vector diversification was impeded by the lack of modern genomic resources. Here we perform deep whole-genome sequencing on individuals from these groups, establishing that they are differentiated genome-wide in a manner consistent with recent ecotype formation associated with the exploitation of a new anthropogenic larval habitat. Such rapid malaria vector diversification was facilitated by standing genetic variation, including evolutionarily old chromosomal rearrangements.

Publisher Copyright: © 2020 The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. Identification of partial sweeps, which include both hard and soft sweeps that have not currently reached fixation, provides crucial information about ongoing evolutionary responses. To this end, we introduce partialS/HIC, a deep learning method to discover selective sweeps from population genomic data. partialS/HIC uses a convolutional neural network for image processing, which is trained with a large suite of summary statistics derived from coalescent simulations incorporating population-specific history, to distinguish between completed versus partial sweeps, hard versus soft sweeps, and regions directly affected by selection versus those merely linked to nearby selective sweeps. We perform several simulation experiments under various demographic scenarios to demonstrate partialS/HIC's performance, which exhibits excellent resolution for detecting partial sweeps. We also apply our classifier to whole genomes from eight mosquito populations sampled across sub-Saharan Africa by the Anopheles gambiae 1000 Genomes Consortium, elucidating both continent-wide patterns as well as sweeps unique to specific geographic regions. These populations have experienced intense insecticide exposure over the past two decades, and we observe a strong overrepresentation of sweeps at insecticide resistance loci. Our analysis thus provides a list of candidate adaptive loci that may be relevant to mosquito control efforts. More broadly, our supervised machine learning approach introduces a method to distinguish between completed and partial sweeps, as well as between hard and soft sweeps, under a variety of demographic scenarios. As whole-genome data rapidly accumulate for a greater diversity of organisms, partialS/HIC addresses an increasing demand for useful selection scan tools that can track in-progress evolutionary dynamics. publishersversion published

Enterohemorrhagic Escherichia coli O157:H7 is an enteric pathogen responsible for bloody diarrhea, hemolytic uremic syndrome, and in severe cases, even death. The study of O157:H7 is difficult due to the high specificity of the bacteria for the human intestine, along with our lack of sufficiently complex human cell culture models. The recent development of human intestinal enteroids derived from intestinal crypt multipotent stem cells has allowed us to construct two-dimensional differentiated epithelial monolayers grown in transwells that mimic the human intestine. Unlike previous studies, saline was added to the apical surface, while maintaining culture media in the basolateral well. The monolayers continued to grow and differentiate with apical saline. Apical infection with O157:H7 or commensal E. coli resulted in robust bacterial growth from 10(5) to over 10(8) over 24 h. Despite this robust bacterial growth, commensal E. coli neither adhered to nor damaged the epithelial barrier over 30 h. However, O157:H7 was almost fully adhered (>90%) by 18 h with epithelial damage observed by 30 h. O157:H7 contains the locus of enterocyte effacement (LEE) pathogenicity island responsible for attachment and damage to the intestinal epithelium. Previous studies report the ability of nutrients such as biotin, d-serine, and L-fucose to downregulate LEE gene expression. O157:H7 treated with biotin or L-fucose, but not d-serine displayed both decreased attachment and reduced epithelial damage over 36 h. These data illustrate enteroid monolayers can serve as a suitable model for the study of O157:H7 pathogenesis, and identification of potential therapeutics. IMPORTANCE O157:H7 is difficult to study due to its high specificity for the human intestine and the lack of sufficiently complex human cell culture models. The recent development of human intestinal enteroids derived from intestinal crypt multipotent stem cells has allowed us to construct two-dimensional differentiated epithelial monolayers grown in transwells that mimic the human intestine. Our data illustrates enteroid monolayers can serve as a suitable model for the study of O157:H7 pathogenesis, and allow for identification of potential therapeutics.

Current stochastic rupture modeling techniques do not consider the influence of first order fault zone characteristics. One such key characteristic is fault slip deficit or inter-seismic locking wh...

To evaluate outcomes of free flaps in low- versus high-risk American Society of Anesthesiologists (ASA) classes utilizing a standardized perioperative clinical pathway.Case series with chart review.Single tertiary care academic institution.Data were collected from 301 patients who underwent 305 free flap reconstructions for head and neck defects from January 2012 to March 2016 by a single surgeon (M.M.). A standardized perioperative clinical pathway was utilized for all patients, aimed at abbreviating hospital stay and minimizing intensive care unit stay. Data included ASA classification, comorbidities, length of hospitalization, intensive care unit stay, 30-day mortality/readmission, discharge disposition, flap survival, and postoperative complications. Low-risk ASA classes were defined as 1 and 2 (n = 53) and high risk as 3 and 4 (n = 248).Total medical complication rates (The ASA classification system is a validated tool in determining perioperative risk. We found that minor medical complications and discharge to a rehabilitation/nursing facility were increased in the high-risk ASA classes; otherwise, there were no statistical differences between the groups. These findings suggest that the ASA classification may be helpful for preoperative discharge planning and counseling but should not be used for patient selection or to assess candidacy for the procedure.

Objective Venous insufficiency occurs in radial forearm free flaps (RFFFs) when either the deep venous system (DVS) or superficial venous system (SVS) is used as the venous outlet. We report our experience using the antecubital perforating vein (APV) in a single-vessel anastomosis to the median-cubital or cephalic vein to drain both systems. Study Design Retrospective review. Setting Single, academic, tertiary care center. Methods Data were collected from 72 patients who underwent RFFF from October 2009 to January 2017. In all cases, DVS and SVS were dissected, and an APV single-vessel anastomosis was attempted. Results Anatomical variations precluded single-vessel anastomosis in 11 (15.3%) cases. In 61 (84.7%) cases, single-vessel anastomosis produced unobstructed drainage for DVS and SVS without intrinsic venous insufficiency. Venous thrombosis and total loss occurred in 2 (3.3%) and 1 (1.6%) patients, respectively. Proximal dissection of the cephalic vein addressed a vessel-depleted neck in 3 cases. Conclusion The antecubital perforating vein is present and functional in most patients, allowing for single anastomosis techniques for RFFF. Antecubital perforators capture DVS and SVS outflow through a single, extended venous pedicle, eliminating the risk of venous insufficiency and need for vein grafts.

Knowledge of species ages and their distribution enhance our understanding of processes that create and maintain species diversity at both local and regional levels. The largest family of freshwater mussels (Unionidae), reach their highest species diversity in drainages of the southeastern united states. By sequencing multiple loci from mussel species distributed throughout the drainages in this region, we attempt to uncover historical patterns of divergence and determine the role of vicariance events on the species formation in mussels and extend our hypothesis to freshwater animals in general. We analyzed 346 sequences from five genera encompassing 37 species. Species were sampled across 12 distinct drainages ending either in the Atlantic Ocean or the Gulf of Mexico. Overall the topologies of the different genera returned phylogenetic trees that were congruent with geographically contiguous drainages. The most common pattern was the grouping between the Atlantic slope and gulf coast drainages, however the Tennessee drainage was often the exception to this pattern grouping with the Atlantic slope. Most mussel species find a most recent common ancestor within a drainage before finding an ancestor between drainages. This supports the hypothesis of allopatric divergence followed by later burst of speciation within a drainage. Our estimated divergence times for the Atlantic-Gulf split agree with other studies estimating vicariance in fish species of the Atlantic and gulf coast.

Significance Introgressive hybridization is prevalent in recent and rapid animal radiations, and emerging evidence suggests that it leads to the sharing of genetic variation that can facilitate adaptation to new environments and generate novel phenotypes. Here we study a recent and rapid radiation of African mosquitoes in which only one species, An. funestus, is a primary human malaria vector with a continent-wide geographic distribution. We trace the evolutionary history of the group and demonstrate introgression events between multiple species, the most recent of which involved substantial gene flow into An. funestus that preceded its range expansion across tropical Africa. Our findings point to introgression as an underappreciated factor contributing to the acquisition of high malaria vectorial capacity., Advances in genomics have led to an appreciation that introgression is common, but its evolutionary consequences are poorly understood. In recent species radiations the sharing of genetic variation across porous species boundaries can facilitate adaptation to new environments and generate novel phenotypes, which may contribute to further diversification. Most Anopheles mosquito species that are of major importance as human malaria vectors have evolved within recent and rapid radiations of largely nonvector species. Here, we focus on one of the most medically important yet understudied anopheline radiations, the Afrotropical Anopheles funestus complex (AFC), to investigate the role of introgression in its diversification and the possible link between introgression and vector potential. The AFC comprises at least seven morphologically similar species, yet only An. funestus sensu stricto is a highly efficient malaria vector with a pan-African distribution. Based on de novo genome assemblies and additional whole-genome resequencing, we use phylogenomic and population genomic analyses to establish species relationships. We show that extensive interspecific gene flow involving multiple species pairs has shaped the evolutionary history of the AFC since its diversification. The most recent introgression event involved a massive and asymmetrical movement of genes from a distantly related AFC lineage into An. funestus, an event that predated and plausibly facilitated its subsequent dramatic geographic range expansion across most of tropical Africa. We propose that introgression may be a common mechanism facilitating adaptation to new environments and enhancing vectorial capacity in Anopheles mosquitoes.

Background Understanding local Anopheles species compositions and bionomic traits are vital for an effective malaria vector intervention strategy. Though eight malaria vectors, including species complexes, have been documented across the island of Sulawesi, Indonesia, a comprehensive survey linking morphological and molecular species identification has not been conducted in this global hotspot of biodiversity. Results Eighteen distinct species of Anopheles were molecularly identified in a 1 km2 area in Karama village, West Mamuju Province, Sulawesi. Known species included An. aconitus, An. karwari, An. peditaeniatus, An. vagus, An. barbirostris, An. tessellatus, An. nigerrimus, An. crawfordi, An. maculatus, An. flavirostris and An. kochi. Of the 18 distinct sequence groups identified through both ribosomal DNA internal transcribed spacer region 2, and mitochondrial DNA cytochrome c oxidase subunit 1 loci, 8 could not be identified to species through comparison to published sequences. The comparison of morphological and molecular identities determined that interpretations of local species compositions for primary and expected species in Karama (An. barbirostris and An. vagus) had the highest rate of accuracy (92.1% and 87.6%, respectively) when compared to molecular analysis. However, the remaining distinct sequences molecularly identified to species were identified correctly by morphological methods less frequently, from 0 to 83%. Conclusions Karama, Indonesia has a high diversity of Anopheles spp. The unexpected high number of Anopheles species in a small area points to possible complex transmission dynamics and limitations with vector control based on possible varying behaviors and interactions with both humans and interventions. Morphological identification of Anopheles spp. in this study was more accurate for primary and expected species than secondary or unexpected species. Finally, the inability to identify seven sequence groups to species with consensus sequences implies that future studies employing sequencing are required to clarify species compositions in the Nigerrimus Subgroup, among others, as well as their distribution and vector status. Use of molecular methods in conjunction with morphological investigations for analysis of species composition, population dynamics and bionomic characteristics is directly implicated in understanding drivers of malaria transmission, intervention effectiveness, and the pursuit of malaria elimination.

Background: Anopheles funestus is one of the three most consequential and widespread vectors of human malaria in tropical Africa. However, the lack of a high-quality reference genome has hindered the association of phenotypic traits with their genetic basis in this important mosquito. Findings: Here we present a new high-quality An. funestus reference genome (AfunF3) assembled using 240x coverage of long-read single-molecule sequencing for contigging, combined with 100x coverage of short-read Hi-C data for chromosome scaffolding. The assembled contigs total 446 Mbp of sequence and contain substantial duplication due to alternative alleles present in the sequenced pool of mosquitos from the FUMOZ colony. Using alignment and depth-of-coverage information, these contigs were deduplicated to a 211 Mbp primary assembly, which is closer to the expected haploid genome size of 250 Mbp. This primary assembly consists of 1,053 contigs organized into 3 chromosome-scale scaffolds with an N50 contig size of 632 kbp and an N50 scaffold size of 93.811 Mbp, representing a 100-fold improvement in continuity versus the current reference assembly, AfunF1. Conclusion: This highly contiguous and complete An. funestus reference genome assembly will serve as an improved basis for future studies of genomic variation and organization in this important disease vector.

HIV-infected infants develop broadly neutralizing plasma responses with more rapid kinetics than adults, suggesting the ontogeny of infant responses could better inform a path to achievable vaccine targets. Here we reconstruct the developmental lineage of BF520.1, an infant-derived HIV-specific broadly neutralizing antibody (bnAb), using computational methods developed specifically for this purpose. We find that the BF520.1 inferred naive precursor binds HIV Env. We also show that heterologous cross-clade neutralizing activity evolved in the infant within six months of infection and that, ultimately, only 2% SHM is needed to achieve the full breadth of the mature antibody. Mutagenesis and structural analyses reveal that, for this infant bnAb, substitutions in the kappa chain were critical for activity, particularly in CDRL1. Overall, the developmental pathway of this infant antibody includes features distinct from adult antibodies, including several that may be amenable to better vaccine responses., Development of broadly neutralizing antibodies (bnAb) against HIV-1 in infected adults is a multi-step process unachievable by current vaccine approaches. Here the authors reconstruct the ontogeny of an infant bnAb, which develops in fewer steps, and identify its unique features that may shorten the path to HIV vaccines.

The human disease lymphatic filariasis causes the debilitating effects of elephantiasis and hydrocele. Lymphatic filariasis currently affects the lives of 90 million people in 52 countries. There are three nematodes that cause lymphatic filariasis,Brugia malayi, B. timori, andWuchereria bancrofti, but 90% of all cases of lymphatic filariasis are caused solely byW. bancrofti. Here we use population genomics to identify the geographic origin ofW. bancroftiand reconstruct its spread. Previous genomic sequencing efforts have suffered from difficulties in obtaining Wb DNA. We used selective whole genome amplification to enrichW. bancroftiDNA from infected blood samples and were able to analyze 47 whole genomes ofW. bancroftifrom endemic locations in Haiti, Mali, Kenya, and Papua New Guinea. Our results are consistent with a Southeast Asia or East Asia origin forW. bancroftispread around the globe by infecting migrating populations of humans. Austronesians probably introducedW. ban-croftito Madagascar where later migrations moved it to continental Africa. From Africa,W. bancroftispread to the New World during the transatlantic slave trade. The greater genetic diversity ofW. bancroftipopulations from Haiti are also consistent with genetic admixture from multiple source populations. Genome scans for locally adapted haplotypes identified genes associated with human immune suppression and insecticide sensitivity. Locally adapted haplotypes may provide a foundation to understand the distribution ofW. bancrofticompared to that of other filarial nematodes and how populations may differ in response to eradication efforts.

Neurostimulation demonstrates success as a medical treatment for patients suffering from neurodegenerative diseases and psychiatric disorders. Despite promising clinical results, the cellular-level processes by which they achieve these favorable outcomes are not completely understood. Specifically, the neuronal mechanisms by which neurostimulation impacts ion channel gating and transmembrane ionic flux are unknown. To help elucidate these mechanisms, we have developed a novel mathematical model that integrates the Poisson-Nernst-Planck system of PDEs and Hodgkin-Huxley based ODEs to model the effects of this neurotherapy on transmembrane voltage, ion channel gating, and ionic mobility. Using a biologically-inspired domain, in silico simulations are used to assess the impact of TES and DBS on neuronal electrodynamics. Results show that an instantaneous polarization of the membrane’s resting potential occurs in a location specific manner, where the type and degree of polarization depends on the position on the membrane. This polarization in turn leads ion channel gating and transmembrane ionic flux to change in a site specific fashion. In addition, results show differences in polarization, membrane voltage, and transmembrane ion mobility resulting from highly distinct forms of neurostimulation, namely tran-scranial electrical stimulation and deep brain stimulation.

The distribution of neutral hydrogen in the intergalactic medium (IGM) is currently explored at low-z by means of UV spectroscopy of quasars. We propose an alternative approach based on UV colours of quasars as observed from GALEX surveys. We built a NUV-selected sample of 9033 quasars with (FUV-NUV) colours. The imprint of HI absorption in the observed colours is suggested qualitatively by their distribution as a function of quasar redshift. Because broad band fluxes lack spectral resolution and are sensitive to a large range of N_HI a Monte Carlo simulation of IGM opacity is required for quantitative analysis. It was performed with absorbers randomly distributed along redshift and column density distributions, assumed to be a broken power law with index beta1 (10^15 < N_HI, Accepted for publication in A&A; 11 pages, 12 figures

Background Adolescents and young adults with HIV are a unique population given the distinct psychosocial challenges of their age-group coupled with having a stigmatizing disease. In 2018, approximately 1.6 million adolescents were living with HIV worldwide, with the highest HIV prevalence found in Eswatini. As this group struggles more than any other age-group with medication adherence, novel interventions that are peer-inclusive and empowering should be explored to support their treatment. Methods We piloted a theater camp to determine the impact of fostering creative expression amongst adolescents and young adults enrolled at our HIV clinic in Mbabane, Eswatini. A two-week camp was conducted in collaboration with a non-profit organization of professional teachers, actors, and musicians. We emphasized enrollment of patients struggling with medication adherence, teen mothers, and those on second-line antiretroviral treatment. Twenty individuals (ages 12-23) participated in self-expression activities, story development, and a final play performed for the community. To assess impact, we compared viral loads pre- and post- camp as well as surveyed participants on effect of participation on areas such as personal stigma, sense of community, and confidence. Results Of those who participated, 25% showed a substantial decrease and 10% a substantial increase in viral load after the camp (>0.1 log10 change). Those who completed the survey (n=18) felt the camp helped them with confidence (13/18), teamwork (13/18), and friendships (11/18). Quotes from participants reinforced this growing sense of community, confidence, and decreased personal stigma. One wrote “theater camp helped me know that I can do a lot of things in life to achieve my future goals although I am HIV positive” and another stated “it made me not feel sorry for being an HIV positive person.” Conclusion Our pilot program demonstrates creative arts programming has beneficial psychosocial effects, aids in community building, and potentially enhances the effectiveness of medical treatment. Further programs and studies should continue to investigate creative arts as an avenue for treatment support, self-expression, and community building among vulnerable populations such as adolescents and young adults with HIV. Disclosures All Authors: No reported disclosures

Wuchereria bancrofti is a parasitic nematode and the primary cause of lymphatic filariasis--a disease specific to humans. W. bancrofti currently infects over 90 million people throughout the tropics and has been acknowledged by the world health organization as a vulnerable parasite. Current research has focused primarily on the clinical manifestations of disease and little is known about the evolutionary history of W. bancrofti. To improve upon knowledge of the evolutionary history of W. bancrofti, we whole genome sequenced 13 W. bancrofti larvae. We circumvent many of the difficulties of multiple infections by sampling larvae directly from mosquitoes that were experimentally inoculated with infected blood. To begin, we used whole genome data to reconstruct the historical population size. Our results support a history of fluctuating population sizes that can be correlated with human migration and fluctuating mosquito abundances. Next, we reconstructed the putative pedigree of W. bancrofti worms within an infection using the kinship coefficient. We deduced that there are full-sib and half-sib relationships residing within the same larval cohort. Through combined analysis of the mitochondrial and nuclear genomes we concluded that this is likely a results of polyandrous mating, the first time reported for W. bancrofti. Lastly, we scanned the genomes for signatures of natural selection. Annotation of putative selected regions identified proteins that may have aided in a parasitic life style or may have evolved to protect against current drug treatments. We discuss our results in the greater context of understanding the biology of an animal with a unique life history and ecology.

The temperature and concentration dependences of 207Pb NMR chemical shifts of Pb(NO3)2 in D2O are reported. The results are analyzed in terms of exchange between a solvated lead ion and the Pb(NO3)+ contact-ion pair. Predictions of the chemical shift difference between the aquated ion and contact-ion pair are carried out for the gas-phase entities and for the solvated species with a DFT calculation. Previously reported data on 207Pb NMR chemical shifts of Pb(NO3)2 in H2O are reevaluated. From the analysis, the enthalpy of dissociation of the contact-ion pair is found to be–42.3±1.0 kJ/mol.

Background People aged 85 years and older are the fastest growing age group worldwide. This study assessed respiratory health, prevalence of respiratory disease and use of spirometry in respiratory diagnosis in a population-based cohort of 85 year olds to better understand respiratory health and disease in this sector of society. Methods A single year birth-cohort of 85 year olds participated in a respiratory assessment at their home or residential institution including self-reporting of symptoms and measurement of spirometry. General practice medical records were reviewed for respiratory diagnoses and treatments. Findings In the 845 participants, a substantial burden of respiratory disease was seen with a prevalence of COPD in medical records of 16.6% (n=140). A large proportion of the cohort had environmental exposures through past or current smoking (64.2%, n=539) and occupational risk factors (33.6%, n=269). Spirometry meeting reliability criteria was performed in 87% (n=737) of participants. In the subgroup with a diagnosis of COPD (n=123), only 75.6% (n=93) satisfied Global Initiative in Obstructive Lung Disease (GOLD) criteria for airflow obstruction, and in a healthy subgroup without respiratory symptoms or diagnoses (n=151), 44.4% (n=67) reached GOLD criteria for airflow obstruction and 43.3% (n=29) National Institute of Health and Care Excellence criteria for at least moderate COPD. Interpretation Spirometry can be successfully performed in the very old, aged 85 years, and may help identify respiratory diseases such as COPD. However interpretation in this age group using current definitions of COPD based on spirometry indices may be difficult and lead to overdiagnosis in a healthy group with transient symptoms.

Simple Summary Chromosomal inversions occur when a segment of DNA breaks in two places, rotates 180 degrees, and reattaches. Inversions can protect sets of genetic variants, including those adapted to local conditions, from being split up in the random shuffling that occurs when genetic information is transmitted from one generation to the next. For this reason, inversions can play a role in local adaptation and range expansion. Like many malaria mosquitoes, Anopheles funestus, which plays a major role in transmitting malaria in sub-Saharan Africa, carries several common chromosomal inversions. Three of these inversions have been implicated in traits such as indoor resting behavior, which affects their rate of contact with both humans and insecticide-based interventions. Inversions therefore have relevance for malaria epidemiology and control. Inversions are traditionally identified by examining chromosomes under a microscope, but this method is difficult and time-consuming, and only applicable to a subset of female adult mosquitoes. To overcome this limitation, we developed high-throughput DNA-based diagnostic methods to predict the presence of inversions. The availability of these methods will allow scientists to more easily identify inversions in larger samples of mosquitoes, from all life stages and both sexes, which will help us determine how inversions are affecting malaria transmission. Abstract Polymorphic chromosomal inversions have been implicated in local adaptation. In anopheline mosquitoes, inversions also contribute to epidemiologically relevant phenotypes such as resting behavior. Progress in understanding these phenotypes and their mechanistic basis has been hindered because the only available method for inversion genotyping relies on traditional cytogenetic karyotyping, a rate-limiting and technically difficult approach that is possible only for the fraction of the adult female population at the correct gonotrophic stage. Here, we focus on an understudied malaria vector of major importance in sub-Saharan Africa, Anopheles funestus. We ascertain and validate tag single nucleotide polymorphisms (SNPs) using high throughput molecular assays that allow rapid inversion genotyping of the three most common An. funestus inversions at scale, overcoming the cytogenetic karyotyping barrier. These same inversions are the only available markers for distinguishing two An. funestus ecotypes that differ in indoor resting behavior, Folonzo and Kiribina. Our new inversion genotyping tools will facilitate studies of ecotypic differentiation in An. funestus and provide a means to improve our understanding of the roles of Folonzo and Kiribina in malaria transmission.

SummaryHIV-infected infants develop broadly neutralizing plasma responses with more rapid kinetics than adults, suggesting the ontogeny of infant responses could better inform a path to achievable vaccine targets. We developed computational methods to reconstruct the developmental lineage of BF520.1, the first example of a HIV-specific broadly neutralizing antibody (bnAb) from an infant. The BF520.1 inferred naïve precursor binds HIV Env and a bnAb evolved within six months of infection and required only 3% mutation. Mutagenesis and structural analyses revealed that for this infant bnAb, substitutions in the kappa chain were critical for activity, particularly in CDRL1. Overall, the developmental pathway of this infant antibody includes features distinct from adult antibodies, including several that may be amenable to better vaccine responses.

Background Understanding population genetic structure in the malaria vector Anopheles gambiae (s.s.) is crucial to inform genetic control and manage insecticide resistance. Unfortunately, species characteristics such as high nucleotide diversity, large effective population size, recent range expansion, and high dispersal ability complicate the inference of genetic structure across its range in sub-Saharan Africa. The ocean, along with the Great Rift Valley, is one of the few recognized barriers to gene flow in this species, but the effect of inland lakes, which could be useful sites for initial testing of genetic control strategies, is relatively understudied. Here we examine Lake Victoria as a barrier between the Ugandan mainland and the Ssese Islands, which lie up to 60 km offshore. We use mitochondrial DNA (mtDNA) from populations sampled in 2002, 2012 and 2015, and perform Bayesian cluster analysis on mtDNA combined with microsatellite data previously generated from the same 2002 mosquito DNA samples. Results Hierarchical analysis of molecular variance and Bayesian clustering support significant differentiation between the mainland and lacustrine islands. In an mtDNA haplotype network constructed from this and previous data, haplotypes are shared even between localities separated by the Rift Valley, a result that more likely reflects retention of shared ancestral polymorphism than contemporary gene flow. Conclusions The relative genetic isolation of An. gambiae on the Ssese Islands, their small size, level terrain and ease of access from the mainland, the relative simplicity of the vectorial system, and the prevalence of malaria, are all attributes that recommend these islands as possible sites for the testing of genetic control strategies.

Background We conducted a placebo-controlled trial of azithromycin therapy in bronchiolitis obliterans syndrome (BOS) post lung transplantation. Methods We compared azithromycin (250 mg alternate days, 12 weeks) with placebo. Primary outcome was FEV1 change at 12 weeks. Results 48 patients were randomised; (25 azithromycin, 23 placebo). It was established, post randomisation that two did not have BOS. 46 patients were analysed as intention to treat (ITT) with 33 ‘Completers’. ITT analysis included placebo patients treated with open-label azithromycin after study withdrawal. Outcome The ITT analysis (n=46, 177 observations) estimated mean difference in FEV1 between treatments (azithromycin minus placebo) was 0.035 L, with a 95% CI of −0.112 L to 0.182 L (p=0.6). Five withdrawals, who were identified at the end of the study as having been randomised to placebo (four with rapid loss in FEV1, one withdrawn consent) had received rescue open-label azithromycin, with improvement in subsequent FEV1 at 12 weeks. Study Completers showed an estimated mean difference in FEV1 between treatment groups (azithromycin minus placebo) of 0.278 L, with 95% CI for the mean difference: 0.170 L to 0.386 L (p=

Wuchereria bancrofti (Wb) is the most widely distributed of the three nematodes known to cause lymphatic filariasis (LF), the other two being Brugia malayi and Brugia timori. Current tools available to monitor LF are limited to diagnostic tests targeting DNA repeats, filarial antigens, and anti-filarial antibodies. While these tools are useful for detection and surveillance, elimination programs have yet to take full advantage of molecular typing for inferring infection history, strain fingerprinting, and evolution. To date, molecular typing approaches have included whole mitochondrial genomes, genotyping, targeted sequencing, and random amplified polymorphic DNA (RAPDs). These studies have revealed much about Wb biology. For example, in one study in Papua New Guinea researchers identified 5 major strains that were widespread and many minor strains some of which exhibit geographic stratification. Genome data, while rare, has been utilized to reconstruct evolutionary relationships among taxa of the Onchocercidae (the clade of filarial nematodes) and identify gene synteny. Their phylogeny reveals that speciation from the common ancestor of both B. malayi and Wb occurred around 5-6 millions years ago with shared ancestry to other filarial nematodes as recent as 15 million years ago. These discoveries hold promise for gene discovery and identifying drug targets in species that are more amenable to in vivo experiments. Continued technological developments in whole genome sequencing and data analysis will likely replace many other forms of molecular typing, multiplying the amount of data available on population structure, genetic diversity, and phylogenetics. Once widely available, the addition of population genetic data from genomic studies should hasten the elimination of LF parasites like Wb. Infectious disease control programs have benefited greatly from population genetics data and recently from population genomics data. However, while there is currently a surplus of data for diseases like malaria and HIV, there is a scarcity of this data for filarial nematodes. With the falling cost of genome sequencing, research on filarial nematodes could benefit from the addition of population genetics statistics and phylogenetics especially in dealing with elimination programs. A comprehensive review focusing on population genetics of filarial nematode does not yet exist. Here our goal is to provide a current overview of the molecular epidemiology of W. bancrofti (Wb) the primary causative agent of LF. We begin by reviewing studies utilizing molecular typing techniques with specific focus on genomic and population datasets. Next, we used whole mitochondrial genome data to construct a phylogeny and examine the evolutionary history of the Onchocercidae. Then, we provide a perspective to aid in understanding how population genetic techniques translate to modern epidemiology. Finally, we introduce the concept of genomic epidemiology and provide some examples that will aid in future studies of Wb.

The draft genome assembly of the Wolbachia endosymbiont of Wuchereria bancrofti (wWb) consists of 1060 850 bp in 100 contigs and contains 961 ORFs, with a single copy of the 5S rRNA, 16S rRNA and 23S rRNA and each of the 34 tRNA genes. Phylogenetic core genome analyses show wWb to cluster with other strains in supergroup D of the Wolbachia phylogeny, while being most closely related to the Wolbachia endosymbiont of Brugia malayi strain TRS (wBm). The wWb and wBm genomes share 779 orthologous clusters with wWb having 101 unclustered genes and wBm having 23 unclustered genes. The higher number of unclustered genes in the wWb genome likely reflects the fragmentation of the draft genome., The Wuchereria bancrofti Wolbachia endosymbiont wWb genome provides insight on the Wolbachia core genome from causative agents of lymphatic filariasis and the evolutionary relationship between Wolbachia endosymbionts in supergroup D.

The study of the microbial communities has gained traction in recent years with the advent of next-generation sequencing with, or without, PCR-based amplification of the 16S ribosomal RNA region. Such studies have been applied to topics as diverse as human health and environmental ecology. Fewer studies have investigated taxa outside of bacteria, however. We present here data demonstrating the utility of studying taxa outside of bacteria including algae, diatoms, archaea and fungi. Here, we show how location along the Cuyahoga River as well as a transient rainfall event heavily influence the microbial composition. Our data reveal how individual OTUs vary between samples and how the patterns of OTU abundance can accurately predict sampling location. The clustering of samples reveals that these taxa are all sensitive to water conditions in unique ways and demonstrate that, for our dataset, algae was most distinctive between sample groups, surpassing bacteria. Diversity between sampling sites could allow studies investigating pollution or water quality to identify marker OTUs or patterns of OTU abundance as indicators to assess environmental conditions or the impact of human activity. We also directly compare data derived from primers amplifying distinct taxa and show that taxa besides bacteria are excellent indicators of water condition.

Adolescence is a developmental period characterized by unique behavioral phenotypes (increased novelty seeking, risk taking, sociability and impulsivity) and increased risk for destructive behaviors, impaired decision making and psychiatric illness. Adaptive and maladaptive adolescent traits have been associated with development of the medial prefrontal cortex (mPFC), a brain region that mediates regulatory control of behavior. However, the molecular changes that underlie brain development and behavioral vulnerability have not been fully characterized. Using high-throughput 2D DIGE spot profiling with identification by MALDI-TOF mass spectrometry, we identified 62 spots in the PFC that exhibited age-dependent differences in expression. Identified proteins were associated with diverse cellular functions, including intracellular signaling, synaptic plasticity, cellular organization and metabolism. Separate Western blot analyses confirmed age-related changes in DPYSL2, DNM1, STXBP1 and CFL1 in the mPFC and expanded these findings to the dorsal striatum, nucleus accumbens, motor cortex, amygdala and ventral tegmental area. Ingenuity Pathway Analysis (IPA) identified functional interaction networks enriched with proteins identified in the proteomics screen, linking age-related alterations in protein expression to cellular assembly and development, cell signaling and behavior, and psychiatric illness. These results provide insight into potential molecular components of adolescent cortical development, implicating structural processes that begin during embryonic development as well as plastic adaptations in signaling that may work in concert to bring the cortex, and other brain regions, into maturity.

Simian foamy viruses (SFV) are complex retroviruses that are ubiquitous in nonhuman primates (NHP) and are zoonotically transmitted to humans, presumably through NHP saliva, by licking, biting, and other behaviors. We have studied SFV in free-ranging rhesus macaques in Bangladesh. It has been previously shown that SFV in immunocompetent animals replicates to detectable levels only in superficial epithelial cells of the oral mucosa, although latent proviruses are found in most, if not all, tissues. In this study, we compare DNA sequences from latent SFV proviruses found in blood cells of 30 Bangladesh rhesus macaques to RNA sequences of transcriptionally active SFV from buccal swabs obtained from the same animals. Viral strains, defined by differences in SFV gag sequences, from buccal mucosal specimens overlapped with those from blood samples in 90% of animals. Thus, latent proviruses in peripheral blood mononuclear cells (PBMC) are, to a great extent, representative of viruses likely to be transmitted to other hosts. The level of SFV RNA in buccal swabs varied greatly between macaques, with increasing amounts of viral RNA in older animals. Evidence of APOBEC3-induced mutations was found in gag sequences derived from the blood and oral mucosa.

Deficiency of mannose-binding lectin (MBL), a serum protein involved in killing and promoting phagocytosis of pathogens, is associated with respiratory infection and disease progression in a number of acute and chronic lung diseases, including cystic fibrosis (CF)- associated bronchiectasis. No such association has been studied in non-CF bronchiectasis (nCF-Br). One hundred and thirty-three adult patients with nCF-Br were studied. Serum MBL levels were measured and deficiency defined using two cut-off levels, i.e. MBL ≤100 ng/ml and ≤600 ng/ml. Parameters of severity included lung function impairment, annual exacerbation and hospital admission rates, breathlessness, and Pseudomonas aeruginosa and Haemophilus influenzae infection rates. The incidence of MBL deficiency using cut-off levels of 100 ng/ml and 600 ng/ml was 10% and 26% respectively, similar to rates seen in the general population. There was no significant difference in mean FEV1% predicted between MBL deficient and sufficient patients at both cut-off levels (≤100 ng/ml: 63.8% vs . 64.6%, P = 0.91; ≤ 600 ng/ml: 66.5% vs . 63.9%, P = 0.56). In addition, exacerbation/hospital admission rates, symptoms of breathlessness and isolation/colonisation rates with P. aeruginosa and H. influenzae were similar in both groups at both cut-off levels. In conclusion, MBL deficiency is not associated with markers of disease severity in patients with nCF-Br.

Sickle cell disease (SCD) is an autosomal recessive inherited hematological disorder characterized by chronic hemolysis and vaso-occlusion, resulting in multiorgan dysfunction and premature death. The only known curative therapy for patients with severe SCD is myeloablative conditioning and allo-SCT from HLA-matched sibling donors. In this state of the art review, we discuss current and future considerations including patient selection/eligibility, intensity of conditioning regimens, allogeneic graft sources, graft manipulation, mixed donor chimerism, organ function and stability and autologous gene correction stem cell strategies. Recent novel approaches to promote mixed donor chimerism have included the use of matched unrelated adult donors, umbilical cord blood donors, haploidentical familial donors and the utilization of nonmyeloablative, such as reduced intensity and reduced toxicity conditioning regimens. Future strategies will include gene therapy and autologous gene correction stem cell designs. Prospects are bright for novel stem and cellular approaches for patients with severe SCD, and we are currently at the end of the beginning for utilizing cellular therapeutics for the curative treatment of this chronic and debilitating condition.

Background: Fatigue is a complex, disabling symptom in non-CF bronchiectasis (nCF-Br). Fatigue can be formally measured using the validated fatigue impact scale (FIS). The relationship between fatigue and clinically important factors such as airflow obstruction, breathlessness or Pseudomonas aeruginosa infection in nCF-Br is unclear. Aim: To measure the correlation between FIS scores and markers of disease severity in nCF-Br. Design: A prospective cohort study. Methods: Patients attending a specialist service were studied. Lung function (FEV1% predicted), Medical Research Council dyspnoea score (MRCD), sputum culture results and FIS were recorded. Patients were categorized according to sputum culture into three subgroups: Pseudomonas ‘colonization’, ‘isolation’ and neither. Results: One hundred and seventeen consecutive patients were included. Average FEV1% predicted was 64% (SD ±28%). Twelve (10%) patients had Pseudomonas aeruginosa isolation; 47 (40%) patients had P. aeruginosa colonization. Fatigue levels were similar in patients with and without colonization (median 38 versus 32, P = 0.155). Significant fatigue (FIS > 40) was similar in all three Pseudomonas subgroups ( P = 0.31, chi-square). Fatigue correlated with MRCD score ( r = 0.57, P

A number of studies now point to the association of patterns of phylogeography with discontinuities in coastal current patterns. If such phylogeographic patterns are indicative of populations that retain local diversity, as has been predicted by recent modelling, such results may be of use in marine reserve planning. Here we show that there is a distributional correlation on the Pacific coast of North America between marine reserve placement and phylogeographic patterns. A number of factors could contribute to this correlation, but its existence suggests the utility of genetic studies in marine conservation planning.