HIV-1 tropism determination using a phenotypic Env recombinant viral assay highlights overestimation of CXCR4-usage by genotypic prediction algorithms for CRRF01_AE and CRF02_AG

Background: Human Immunodeficiency virus type-1 (HIV) entry into target cells involves binding of the viral envelope (Env) to CD4 and a coreceptor, mainly CCR5 or CXCR4. The only currently licensed HIV entry inhibitor, maraviroc, targets CCR5, and the presence of CXCX4-using strains must be excluded prior to treatment. Co-receptor usage can be assessed by phenotypic assays or through genotypic prediction. Here we compared the performance of a phenotypic Env-Recombinant Viral Assay (RVA) to the two most widely used genotypic prediction algorithms, Geno2Pheno([coreceptor]) and webPSSM. Methods: Co-receptor tropism of samples from 73 subtype B and 219 non-B infections was measured phenotypically using a luciferase-tagged, NL4-3-based, RVA targeting Env. In parallel, tropism was inferred genotypically from the corresponding V3-loop sequences using Geno2Pheno([coreceptor]) (5-20% FPR) and webPSSM-R5X4. For discordant samples, phenotypic outcome was retested using co-receptor antagonists or the validated Trofile (R) Enhanced-Sensitivity-Tropism-Assay. Results: The lower detection limit of the RVA was 2.5% and 5% for X4 and R5 minority variants respectively. A phenotype/genotype result was obtained for 210 samples. Overall, concordance of phenotypic results with Geno2Pheno([coreceptor]) was 85.2% and concordance with webPSSM was 79.5%. For subtype B, concordance with Geno2pheno([coreceptor]) was 94.4% and concordance with webPSSM was 79.6%. High concordance of genotypic tools with phenotypic outcome was seen for subtype C (90% for both tools). Main discordances involved CRF01_AE and CRF02_AG for both algorithms (CRF01_AE: 35.9% discordances with Geno2Pheno([coreceptor]) and 28.2% with webPSSM; CRF02_AG: 20.7% for both algorithms). Genotypic prediction overestimated CXCR4-usage for both CRFs. For webPSSM, 40% discordance was observed for subtype A. Conclusions: Phenotypic assays remain the most accurate for most non-B subtypes and new subtype-specific rules should be developed for non-B subtypes, as research studies more and more draw conclusions from genotypically-inferred tropism, and to avoid unnecessarily precluding patients with limited treatment options from receiving maraviroc or other entry inhibitors

A Defensin-Like Gene Expressed in the Black-Legged Tick, Ixodes scapularis (Acari: Ixodidae)

The black-legged tick Ixodes scapularis linnaeus (Acari: Ixodidae) is an important vector of microbial pathogens. Knowledge of the tick\u27s innate immune response, particularly defensin and other antimicrobial peptides, is important for understanding how microbes survive in this tick. A defensin gene (slnA) from I. scapularis was obtained by reverse transcription-polymerase chain reaction (RT-PCR) using mRNA extracted from tissues of female ticks. RT-PCR indicated the gene was expressed in the midgut, haemocytes, and fat-body, although no evidence of a peptide was found. Sequencing a cloned cDNA fragment revealed a 225 bp open reading frame encoding a 74 amino acid pre-prodefensin, including the putative 38 amino acid mature peptide. Similarity between the defensin amino acid sequences of I. scapularis and Dermacentor variabilis (Say) (Acari: Ixodidae) was 62.2% for the pre-prodefensin region; for the mature defensins from these two species the similarity was 78.9%, with the six cysteine residues being located in the same relative position. PCR amplification and sequencing of chromosomal DNA suggests that slnA, along with vsnA, the defensin gene from D. variabilis, does not contain any introns. This is in contrast to the defensins described for the soft tick, Ornithodoros moubata (sensu Walton) (Acari: Argasidae). The role of defensin in the innate immune response of I. scapularis following microbial invasions is discussed

Rangelands in a fragmented grass‑dominated landscape are vulnerable to tree invasion from roadsides

Roadsides can be vectors for tree invasion within rangelands by bisecting landscapes and facilitating propagule spread to interior habitat. Current invasive tree management in North America’s Great Plains focuses on reducing on-site (i.e., interior habitat) vulnerability through on-site prevention and eradication, but invasive tree management of surrounding areas known to serve as invasion vectors, such as roadsides and public rights-of-ways, is sporadic. We surveyed roadsides for invasive tree propagule sources in a central Great Plains grassland landscape to determine how much of the surrounding landscape is potentially vulnerable to roadside invasion, and by which species, and thereby provide insights into the locations and forms of future landcover change. Invasive tree species were widespread in roadsides. Given modest seed dispersal distances of 100–200 m, our results show that roadsides have potential to serve as major sources of rangeland exposure to tree invasion, compromising up to 44% of rangelands in the study area. Under these dispersal distances, funds spent removing trees on rangeland properties may have little impact on the landscape’s overall vulnerability, due to exposure driven by roadside propagule sources. A key implication from this study is that roadsides, while often neglected from management, represent an important component of integrated management strategies for reducing rangeland vulnerability to tree invasion

Comparison of computed tomographic angiography and intraoperative mesenteric portovenography for extrahepatic portosystemic shunts

Objectives Comparison of intra-operative mesenteric portovenography and computed tomographic angiography for the documentation of the portal vasculature in patients with single extrahepatic portosystemic shunts. Methods Retrospective study of patients with extrahepatic portosystemic shunts that underwent preoperative computed tomographic angiography and intra-operative mesenteric portography. Studies were compared for identification of the intra- and extrahepatic portal vasculature. Results Computed tomographic angiography demonstrated all four portal vein tributaries and sub-tributaries. Intra-operative mesenteric portography inconsistently demonstrated the cranial mesenteric vein, the gastroduodenal vein (12 of 49 dogs and 0 of 10 cats), splenic vein (46 of 49 dogs and 8 of 10 cats) and caudal mesenteric vein (3 of 49 dogs and 2 of 10 cats). Computed tomographic angiography showed the intrahepatic portal vein with shunts emanating from the left gastric vein, splenocaval shunts or shunts involving the left colic vein. It showed intrahepatic portal branching in 5 of 12 patients with shunts involving the right gastric vein. Intra-operative mesenteric portography showed the intrahepatic portal vein in 29 of 59 patients but was outperformed by computed tomographic angiography in all cases except those patients with a shunt involving the right gastric vein. Clinical Significance In cases that have undergone diagnostic preoperative computed tomographic angiography there is no indication for diagnostic intra-operative mesenteric portovenography before ligation. In contrast, portovenography performed “after” temporary full ligation of the shunt provides clinical useful information and might be considered an integral investigation during shunt attenuation surgery

HIV outbreaks among people who inject drugs in Europe, North America and Israel

During 2011–16, HIV outbreaks occurred among people who inject drugs (PWID) in Canada (southeastern Saskatchewan), Greece (Athens), Ireland (Dublin), Israel (Tel Aviv), Luxembourg, Romania (Bucharest), Scotland (Glasgow), and USA (Scott County, Indiana). Factors common to many of these outbreaks included community economic problems, homelessness, and changes in drug injection patterns. The outbreaks differed in size (from under 100 to over 1000 newly reported HIV cases among PWID) and in the extent to which combined prevention had been implemented before, during, and after the outbreaks. Countries need to ensure high coverage of HIV prevention services and coverage higher than the current UNAIDS recommendation might be needed in areas in which short acting drugs are injected. In addition, monitoring of PWID with special attention for changing drug use patterns, risk behaviours, and susceptible subgroups (eg, PWID experiencing homelessness) needs to be in place to prevent or rapidly detect and contain new HIV outbreaks

Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle

Background Domestication of the now-extinct wild aurochs, Bos primigenius, gave rise to the two major domestic extant cattle taxa, B. taurus and B. indicus. While previous genetic studies have shed some light on the evolutionary relationships between European aurochs and modern cattle, important questions remain unanswered, including the phylogenetic status of aurochs, whether gene flow from aurochs into early domestic populations occurred, and which genomic regions were subject to selection processes during and after domestication. Here, we address these questions using whole-genome sequencing data generated from an approximately 6,750-year-old British aurochs bone and genome sequence data from 81 additional cattle plus genome-wide single nucleotide polymorphism data from a diverse panel of 1,225 modern animals. Results Phylogenomic analyses place the aurochs as a distinct outgroup to the domestic B. taurus lineage, supporting the predominant Near Eastern origin of European cattle. Conversely, traditional British and Irish breeds share more genetic variants with this aurochs specimen than other European populations, supporting localized gene flow from aurochs into the ancestors of modern British and Irish cattle, perhaps through purposeful restocking by early herders in Britain. Finally, the functions of genes showing evidence for positive selection in B. taurus are enriched for neurobiology, growth, metabolism and immunobiology, suggesting that these biological processes have been important in the domestication of cattle. Conclusions This work provides important new information regarding the origins and functional evolution of modern cattle, revealing that the interface between early European domestic populations and wild aurochs was significantly more complex than previously thought

T–T Neutron Spectrum from Inertial Confinement Implosions

A new technique that uses inertial confinement implosions for measuring low-energy nuclear reactions important to nuclear astrophysics is described. Simultaneous measurements of n–D and n–T elastic scattering at 14.1 MeV using deuterium–tritium gas-filled capsules provide a proof of principle for this technique. Measurements have been made of D(d,p)T (dd) and T(t,2n)[superscript 4]He (tt) reaction yields relative to the D(t,n)[superscript]He (dt) reaction yield for deuterium–tritium mixtures with fT/fD between 0.62 and 0.75 and for a wide range of ion temperatures to test our understanding of the implosion processes. Measurements of the shape of the neutron spectrum from the T(t,2n)[superscript 4]He reaction have been made for each of these target configurations.National Laser User’s Facility (Grant NA0000877)United States. Dept. of Energy (Grant DE-FG52-09NA29553)University of Rochester. Fusion Science Center (Rochester Subaward 415023-G, UR Account 5-24431)University of Rochester. Laboratory for Laser Energetics (Grant 412160-001G)Lawrence Livermore National Laboratory (Grants B580243 and DE-AC52-07NA27344