Identities and distributions of the co-invading ectomycorrhizal fungal symbionts of exotic pines in the Hawaiian Islands

Pine species have become invasive throughout the globe and threaten to replace native biota. The threat of pine invasion is particularly pressing in parts of the tropics where there are no native pines. The factors that govern pine invasion are not often well understood. However, key to pine survival is an obligate and mutualistic interaction with ectomycorrhizal fungi. Thus for pines to successfully invade new habitats compatible ectomycorrhizal fungi must already be present, or be co-introduced. The purpose of this study was to examine the community structure of non-native ectomycorrhizal fungi associated with pine invasions in the Hawaiian Islands. To accomplish this we executed a field and greenhouse study and used a molecular ecology approach to identify the fungi associating with invasive pines in Hawai‘i. We show that: (1) ectomycorrhizal fungal species richness in non-native pine plantations is far less than what is found in pine’s native range, (2) there was a significant decrease in average ectomycorrhizal fungal species richness as distance from pine plantations increased and, (3) Suillus species were the dominant fungi colonizing pines outside plantations. The keystone ectomycorrhizal fungal taxa responsible for pine establishment in Hawai‘i are within genera commonly associated with pine invasions throughout the globe. We surmise that these fungi share functional traits such as the ability for long-distance dispersal from plantations and host tree colonization via spore that lead to their success when introduced to new habitats

Gepotidacin for the Treatment of Uncomplicated Urogenital Gonorrhea: A Phase 2, Randomized, Dose-Ranging, Single-Oral Dose Evaluation

Background: In this phase 2 study, we evaluated the efficacy and safety of oral gepotidacin, a novel triazaacenaphthylene bacterial type II topoisomerase inhibitor, for the treatment of uncomplicated urogenital gonorrhea. Methods: Adult participants with suspected urogenital gonorrhea were enrolled and completed baseline (day 1) and test-of-cure (days 4-8) visits. Pretreatment and posttreatment urogenital swabs were collected for Neisseria gonorrhoeae (NG) culture and susceptibility testing. Pharyngeal and rectal swab specimens were collected if there were known exposures. Participants were stratified by gender and randomized 1:1 to receive a 1500-mg or 3000-mg single oral dose of gepotidacin. Results: The microbiologically evaluable population consisted of 69 participants, with NG isolated from 69 (100%) urogenital, 2 (3%) pharyngeal, and 3 (4%) rectal specimens. Microbiological eradication of NG was achieved by 97%, 95%, and 96% of participants (lower 1-sided exact 95% confidence interval bound, 85.1%, 84.7%, and 89.1%, respectively) for the 1500-mg, 3000-mg, and combined dose groups, respectively. Microbiological cure was achieved in 66/69 (96%) urogenital infections. All 3 failures were NG isolates that demonstrated the highest observed gepotidacin minimum inhibitory concentration of 1 µg/mL and a common gene mutation. At the pharyngeal and rectal sites, 1/2 and 3/3 NG isolates, respectively, demonstrated microbiological cure. There were no treatment-limiting adverse events for either dose. Conclusions: This study demonstrated that single, oral doses of gepotidacin were ≥95% effective for bacterial eradication of NG in adult participants with uncomplicated urogenital gonorrhea

Using rapid point-of-care tests to inform antibiotic choice to mitigate drug resistance in gonorrhoea

Background: The first cases of extensively drug resistant gonorrhoea were recorded in the United Kingdom in 2018. There is a public health need for strategies on how to deploy existing and novel antibiotics to minimise the risk of resistance development. As rapid point-of-care tests (POCTs) to predict susceptibility are coming to clinical use, coupling the introduction of an antibiotic with diagnostics that can slow resistance emergence may offer a novel paradigm for maximising antibiotic benefits. Gepotidacin is a novel antibiotic with known resistance and resistance-predisposing mutations. In particular, a mutation that confers resistance to ciprofloxacin acts as the ‘stepping-stone’ mutation to gepotidacin resistance. Aim: To investigate how POCTs detecting Neisseria gonorrhoeae resistance mutations for ciprofloxacin and gepotidacin can be used to minimise the risk of resistance development to gepotidacin. Methods: We use individual-based stochastic simulations to formally investigate the aim. Results: The level of testing needed to reduce the risk of resistance development depends on the mutation rate under treatment and the prevalence of stepping-stone mutations. A POCT is most effective if the mutation rate under antibiotic treatment is no more than two orders of magnitude above the mutation rate without treatment and the prevalence of stepping-stone mutations is 1–13%. Conclusion: Mutation frequencies and rates should be considered when estimating the POCT usage required to reduce the risk of resistance development in a given population. Molecular POCTs for resistance mutations and stepping-stone mutations to resistance are likely to become important tools in antibiotic stewardship

Single electron yields from semileptonic charm and bottom hadron decays in Au plus Au collisions at root s(NN)=200 GeV

The PHENIX Collaboration at the Relativistic Heavy Ion Collider has measured open heavy flavor production in minimum bias Au + Au collisions at root s(NN) = 200 GeV via the yields of electrons from semileptonic decays of charm and bottom hadrons. Previous heavy flavor electron measurements indicated substantial modification in the momentum distribution of the parent heavy quarks owing to the quark-gluon plasma created in these collisions. For the first time, using the PHENIX silicon vertex detector to measure precision displaced tracking, the relative contributions from charm and bottom hadrons to these electrons as a function of transverse momentum are measured in Au + Au collisions. We compare the fraction of electrons from bottom hadrons to previously published results extracted from electron-hadron correlations in p + p collisions at root s(NN) = 200 GeV and find the fractions to be similar within the large uncertainties on both measurements for p(T) \u3e 4 GeV/c. We use the bottom electron fractions in Au + Au and p + p along with the previously measured heavy flavor electron R-AA to calculate the R-AA for electrons from charm and bottom hadron decays separately. We find that electrons from bottom hadron decays are less suppressed than those from charm for the region 3 \u3c p(T) \u3c 4 GeV/c

Measurement of parity-violating spin asymmetries in W-+/- production at midrapidity in longitudinally polarized p plus p collisions

We present midrapidity measurements from the PHENIX experiment of large parity-violating single-spin asymmetries of high transverse momentum electrons and positrons from W-+/-/Z decays, produced in longitudinally polarized p + p collisions at center of mass energies of root s = 500 and 510 GeV. These asymmetries allow direct access to the antiquark polarized parton distribution functions due to the parity-violating nature of the W-boson coupling to quarks and antiquarks. The results presented are based on data collected in 2011, 2012, and 2013 with an integrated luminosity of 240 pb(-1), which exceeds previous PHENIX published results by a factor of more than 27. These high Q(2) data probe the parton structure of the proton at W mass scale and provide an important addition to our understanding of the antiquark parton helicity distribution functions at an intermediate Bjorken x value of roughly M-W / root s = 0.16

Eight common genetic variants associated with serum dheas levels suggest a key role in ageing mechanisms

Dehydroepiandrosterone sulphate (DHEAS) is the most abundant circulating steroid secreted by adrenal glands-yet its function is unknown. Its serum concentration declines significantly with increasing age, which has led to speculation that a relative DHEAS deficiency may contribute to the development of common age-related diseases or diminished longevity. We conducted a meta-analysis of genome-wide association data with 14,846 individuals and identified eight independent common SNPs associated with serum DHEAS concentrations. Genes at or near the identified loci include ZKSCAN5 (rs11761528; p = 3.15×10-36), SULT2A1 (rs2637125; p = 2.61×10-19), ARPC1A (rs740160; p = 1.56×10-16), TRIM4 (rs17277546; p = 4.50×10-11), BMF (rs7181230; p = 5.44×10-11), HHEX (rs2497306; p = 4.64×10-9), BCL2L11 (rs6738028; p = 1.72×10-8), and CYP2C9 (rs2185570; p = 2.29×10-8). These genes are associated with type 2 diabetes, lymphoma, actin filament assembly, drug and xenobiotic metabolism, and zinc finger proteins. Several SNPs were associated with changes in gene expression levels, and the related genes are connected to biological pathways linking DHEAS with ageing. This study provides much needed insight into the function of DHEAS

New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk.

Levels of circulating glucose are tightly regulated. To identify new loci influencing glycemic traits, we performed meta-analyses of 21 genome-wide association studies informative for fasting glucose, fasting insulin and indices of beta-cell function (HOMA-B) and insulin resistance (HOMA-IR) in up to 46,186 nondiabetic participants. Follow-up of 25 loci in up to 76,558 additional subjects identified 16 loci associated with fasting glucose and HOMA-B and two loci associated with fasting insulin and HOMA-IR. These include nine loci newly associated with fasting glucose (in or near ADCY5, MADD, ADRA2A, CRY2, FADS1, GLIS3, SLC2A2, PROX1 and C2CD4B) and one influencing fasting insulin and HOMA-IR (near IGF1). We also demonstrated association of ADCY5, PROX1, GCK, GCKR and DGKB-TMEM195 with type 2 diabetes. Within these loci, likely biological candidate genes influence signal transduction, cell proliferation, development, glucose-sensing and circadian regulation. Our results demonstrate that genetic studies of glycemic traits can identify type 2 diabetes risk loci, as well as loci containing gene variants that are associated with a modest elevation in glucose levels but are not associated with overt diabetes

Transverse energy production and charged-particle multiplicity at midrapidity in various systems from root s(NN)=7.7 to 200 GeV

Measurements of midrapidity charged-particle multiplicity distributions, dN(ch)/d eta, and midrapidity transverse-energy distributions, dE(T)/d eta, are presented for a variety of collision systems and energies. Included are distributions for Au + Au collisions at root s(NN) = 200, 130, 62.4, 39, 27, 19.6, 14.5, and 7.7 GeV, Cu + Cu collisions at root s(NN) = 200 and 62.4 GeV, Cu + Au collisions at root s(NN) = 200 GeV, U + U collisions at root s(NN) = 193 GeV, d + Au collisions at root s(NN) = 200 GeV, He-3 + Au collisions at root s(NN) = 200 GeV, and p + p collisions at root s(NN) = 200 GeV. Centrality-dependent distributions at midrapidity are presented in terms of the number of nucleon participants, N-part, and the number of constituent quark participants, N-qp. For all A + A collisions down to root s(NN) = 7.7 GeV, it is observed that the midrapidity data are better described by scaling with N-qp than scaling with N-part. Also presented are estimates of the Bjorken energy density, epsilon(BJ), and the ratio of dE(T)/d eta to dN(ch)/d eta, the latter of which is seen to be constant as a function of centrality for all systems

Hundreds of variants clustered in genomic loci and biological pathways affect human height

Most common human traits and diseases have a polygenic pattern of inheritance: DNA sequence variants at many genetic loci influence the phenotype. Genome-wide association (GWA) studies have identified more than 600 variants associated with human traits, but these typically explain small fractions of phenotypic variation, raising questions about the use of further studies. Here, using 183,727 individuals, we show that hundreds of genetic variants, in at least 180 loci, influence adult height, a highly heritable and classic polygenic trait. The large number of loci reveals patterns with important implications for genetic studies of common human diseases and traits. First, the 180 loci are not random, but instead are enriched for genes that are connected in biological pathways (P = 0.016) and that underlie skeletal growth defects (P < 0.001). Second, the likely causal gene is often located near the most strongly associated variant: in 13 of 21 loci containing a known skeletal growth gene, that gene was closest to the associated variant. Third, at least 19 loci have multiple independently associated variants, suggesting that allelic heterogeneity is a frequent feature of polygenic traits, that comprehensive explorations of already-discovered loci should discover additional variants and that an appreciable fraction of associated loci may have been identified. Fourth, associated variants are enriched for likely functional effects on genes, being over-represented among variants that alter amino-acid structure of proteins and expression levels of nearby genes. Our data explain approximately 10% of the phenotypic variation in height, and we estimate that unidentified common variants of similar effect sizes would increase this figure to approximately 16% of phenotypic variation (approximately 20% of heritable variation). Although additional approaches are needed to dissect the genetic architecture of polygenic human traits fully, our findings indicate that GWA studies can identify large numbers of loci that implicate biologically relevant genes and pathways.

Molecular Adaptations for Sensing and Securing Prey and Insight into Amniote Genome Diversity from the Garter Snake Genome

Colubridae represents the most phenotypically diverse and speciose family of snakes, yet no well-assembled and annotated genome exists for this lineage. Here, we report and analyze the genome of the garter snake, Thamnophis sirtalis, a colubrid snake that is an important model species for research in evolutionary biology, physiology, genomics, behavior, and the evolution of toxin resistance. Using the garter snake genome, we show how snakes have evolved numerous adaptations for sensing and securing prey, and identify features of snake genome structure that provide insight into the evolution of amniote genomes. Analyses of the garter snake and other squamate reptile genomes highlight shifts in repeat element abundance and expansion within snakes, uncover evidence of genes under positive selection, and provide revised neutral substitution rate estimates for squamates. Our identification of Z and W sex chromosome-specific scaffolds provides evidence for multiple origins of sex chromosome systems in snakes and demonstrates the value of this genome for studying sex chromosome evolution. Analysis of gene duplication and loss in visual and olfactory gene families supports a dim-light ancestral condition in snakes and indicates that olfactory receptor repertoires underwent an expansion early in snake evolution. Additionally, we provide some of the first links between secreted venom proteins, the genes that encode them, and their evolutionary origins in a rear-fanged colubrid snake, together with new genomic insight into the coevolutionary arms race between garter snakes and highly toxic newt prey that led to toxin resistance in garter snakes