Mottle: Accurate pairwise substitution distance at high divergence through the exploitation of short-read mappers and gradient descent

Current tools for estimating the substitution distance between two related sequences struggle to remain accurate at a high divergence. Difficulties at distant homologies, such as false seeding and over-alignment, create a high barrier for the development of a stable estimator. This is especially true for viral genomes, which carry a high rate of mutation, small size, and sparse taxonomy. Developing an accurate substitution distance measure would help to elucidate the relationship between highly divergent sequences, interrogate their evolutionary history, and better facilitate the discovery of new viral genomes. To tackle these problems, we propose an approach that uses short-read mappers to create whole-genome maps, and gradient descent to isolate the homologous fraction and calculate the final distance value. We implement this approach as Mottle. With the use of simulated and biological sequences, Mottle was able to remain stable to 0.66–0.96 substitutions per base pair and identify viral outgroup genomes with 95% accuracy at the family-order level. Our results indicate that Mottle performs as well as existing programs in identifying taxonomic relationships, with more accurate numerical estimation of genomic distance over greater divergences. By contrast, one limitation is a reduced numerical accuracy at low divergences, and on genomes where insertions and deletions are uncommon, when compared to alternative approaches. We propose that Mottle may therefore be of particular interest in the study of viruses, viral relationships, and notably for viral discovery platforms, helping in benchmarking of homology search tools and defining the limits of taxonomic classification methods. The code for Mottle is available at https://github.com/tphoward/Mottle_Repo

Mental health in UK Biobank - development, implementation and results from an online questionnaire completed by 157 366 participants: a reanalysis

Background UK Biobank is a well-characterised cohort of over 500 000 participants including genetics, environmental data and imaging. An online mental health questionnaire was designed for UK Biobank participants to expand its potential. Aims Describe the development, implementation and results of this questionnaire. Method An expert working group designed the questionnaire, using established measures where possible, and consulting a patient group. Operational criteria were agreed for defining likely disorder and risk states, including lifetime depression, mania/hypomania, generalised anxiety disorder, unusual experiences and self-harm, and current post-traumatic stress and hazardous/harmful alcohol use. Results A total of 157 366 completed online questionnaires were available by August 2017. Participants were aged 45–82 (53% were ≥65 years) and 57% women. Comparison of self-reported diagnosed mental disorder with a contemporary study shows a similar prevalence, despite respondents being of higher average socioeconomic status. Lifetime depression was a common finding, with 24% (37 434) of participants meeting criteria and current hazardous/harmful alcohol use criteria were met by 21% (32 602), whereas other criteria were met by less than 8% of the participants. There was extensive comorbidity among the syndromes. Mental disorders were associated with a high neuroticism score, adverse life events and long-term illness; addiction and bipolar affective disorder in particular were associated with measures of deprivation. Conclusions The UK Biobank questionnaire represents a very large mental health survey in itself, and the results presented here show high face validity, although caution is needed because of selection bias. Built into UK Biobank, these data intersect with other health data to offer unparalleled potential for crosscutting biomedical research involving mental health

A Link Between Methylglyoxal and Heart Failure During HIV-1 Infection

Early-onset heart failure (HF) continues to be a major cause of morbidity and mortality in people living with human immunodeficiency virus type one (HIV-1) infection (PLWH), yet the molecular causes for this remain poorly understood. Herein NOD.Cg- PrkdcscidIl2rgtm1Wjl/SzJ humanized mice (Hu-mice), plasma from PLWH, and autopsied cardiac tissues from deceased HIV seropositive individuals were used to assess if there is a link between the glycolysis byproduct methylglyoxal (MG) and HF in the setting of HIV-1 infection. At five weeks post HIV infection, Hu-mice developed grade III-IV diastolic dysfunction (DD) with an associated two-fold increase in plasma MG. At sixteen-seventeen weeks post infection, cardiac ejection fraction and fractional shortening also declined by 26 and 35%, and plasma MG increased to four-fold higher than uninfected controls. Histopathological and biochemical analyses of cardiac tissues from Hu-mice 17 weeks post-infection affirmed MG increase with a concomitant decrease in expression of the MG-degrading enzyme glyoxalase-1 (Glo1). The endothelial cell marker CD31 was found to be lower, and coronary microvascular leakage and myocardial fibrosis were prominent. Increasing expression of Glo1 in Hu-mice five weeks post-infection using a single dose of an engineered AAV2/9 (1.7 × 1012 virion particles/kg), attenuated the increases in plasma and cardiac MG levels. Increasing Glo1 also blunted microvascular leakage, fibrosis, and HF seen at sixteen weeks post-infection, without changes in plasma viral loads. In plasma fromvirally suppressed PLWH,MG was also 3.7-fold higher. In autopsied cardiac tissues from seropositive, HIV individuals with low viral log, MG was 4.2-fold higher and Glo1 was 50% lower compared to uninfected controls. These data show for the first time a causal link between accumulation of MG and HF in the setting of HIV infection

Exo-π-bonding to an ortho-carborane hypercarbon atom: systematic icosahedral cage distortions reflected in the structures of the fluoro-, hydroxy- and amino-carboranes, 1-X-2-Ph-1,2-C2B10H10 (X = F, OH or NH2) and related anions

The structures of derivatives of phenyl-ortho-carborane bearing on the second cage hypercarbon atom a pi-donor substituent (F, OH, O-, NH2, NH- and CH2-) were investigated by NMR, X-ray crystallography and computational studies. The molecular structures of these compounds, notably their cage C1-C2 distances and the orientations of their pi-donor substituents (OH, NH2, NH- and CH2-) show remarkable and systematic variations with the degree of exo pi-bonding, which varies as expected with the pi-donor characteristics of the substituent

Regional and temporal variability of melts during a Cordilleran magma pulse: Age and chemical evolution of the Jurassic arc, eastern Mojave Desert, California

Intrusive rock sequences in the central and eastern Mojave Desert segment of the Jurassic Cordilleran arc of the western United States record regional and temporal variations in magmas generated during the second prominent pulse of Mesozoic continental arc magmatism. U/Pb zircon ages provide temporal control for describing variations in rock and zircon geochemistry that reflect differences in magma source components. These source signatures are discernible through mixing and fractionation processes associated with magma ascent and emplacement. The oldest well-dated Jurassic rocks defining initiation of the Jurassic pulse are a 183 Ma monzodiorite and a 181 Ma ignimbrite. Early to Middle Jurassic intrusive rocks comprising the main stage of magmatism include two high-K calc-alkalic groups: to the north, the deformed 183–172 Ma Fort Irwin sequence and contemporaneous rocks in the Granite and Clipper Mountains, and to the south, the 167–164 Ma Bullion sequence. A Late Jurassic suite of shoshonitic, alkali-calcic intrusive rocks, the Bristol Mountains sequence, ranges in age from 164 to 161 Ma and was emplaced as the pulse began to wane. Whole-rock and zircon trace-element geochemistry defines a compositionally coherent Jurassic arc with regional and secular variations in melt compositions. The arc evolved through the magma pulse by progressively greater input of old cratonic crust and lithospheric mantle into the arc magma system, synchronous with progressive regional crustal thickening

Phosphine-alkene ligand-mediated alkyl-alkyl and alkyl-halide elimination processes from palladium(II)

N-Diphenylphosphino-7-aza-benzobicyclo[2.2.1]hept-2-ene (2) behaves as a chelating phosphine–alkene ligand for Pd0 and PdII, promoting direct alkyl–alkyl and indirect alkyl–halide reductive elimination reactions due to the stabilisation of the resulting bis(phosphine–alkene)Pd0 complex

SPIRITS 16tn in NGC 3556: A heavily obscured and low-luminosity supernova at 8.8 Mpc

We present the discovery by the SPitzer InfraRed Intensive Transients Survey (SPIRITS) of a likely supernova (SN) in NGC 3556 at only 8.8 Mpc, which, despite its proximity, was not detected by optical searches. A luminous infrared (IR) transient at $M_{[4.5]} = -16.7$ mag (Vega), SPIRITS 16tn is coincident with a dust lane in the inclined, star-forming disk of the host. Using IR, optical, and radio observations, we attempt to determine the nature of this event. We estimate $A_V \approx$ 8 - 9 mag of extinction, placing it among the three most highly obscured IR-discovered SNe to date. The [4.5] light curve declined at a rate of 0.013 mag day$^{-1}$, and the $[3.6] - [4.5]$ color grew redder from 0.7 to $\gtrsim$ 1.0 mag by 184.7 days post discovery. Optical/IR spectroscopy shows a red continuum, but no clearly discernible features, preventing a definitive spectroscopic classification. Deep radio observations constrain the radio luminosity of SPIRITS 16tn to $L_{\nu} \lesssim 10^{24}$ erg s$^{-1}$ Hz$^{-1}$ between 3 - 15 GHz, excluding many varieties of radio core-collapse SNe. A type Ia SN is ruled out by the observed red IR color, and lack of features normally attributed to Fe-peak elements in the optical and IR spectra. SPIRITS 16tn was fainter at [4.5] than typical stripped-envelope SNe by $\approx$ 1 mag. Comparison of the spectral energy distribution to SNe II suggests SPIRITS 16tn was both highly obscured, and intrinsically dim, possibly akin to the low-luminosity SN 2005cs. We infer the presence of an IR dust echo powered by a peak luminosity of the transient of $5 \times 10^{40}$ erg s$^{-1} < L_{\mathrm{peak}} < 4\times10^{43}$ erg s$^{-1}$, consistent with the observed range for SNe II. This discovery illustrates the power of IR surveys to overcome the compounding effects of visible extinction and optically sub-luminous events in completing the inventory of nearby SNe.Comment: 25 pages, 10 figures, submitted to Ap

Metabolic drift in the aging brain.

Brain function is highly dependent upon controlled energy metabolism whose loss heralds cognitive impairments. This is particularly notable in the aged individuals and in age-related neurodegenerative diseases. However, how metabolic homeostasis is disrupted in the aging brain is still poorly understood. Here we performed global, metabolomic and proteomic analyses across different anatomical regions of mouse brain at different stages of its adult lifespan. Interestingly, while severe proteomic imbalance was absent, global-untargeted metabolomics revealed an energymetabolic drift or significant imbalance in core metabolite levels in aged mouse brains. Metabolic imbalance was characterized by compromised cellular energy status (NAD decline, increased AMP/ATP, purine/pyrimidine accumulation) and significantly altered oxidative phosphorylation and nucleotide biosynthesis and degradation. The central energy metabolic drift suggests a failure of the cellular machinery to restore metabostasis (metabolite homeostasis) in the aged brain and therefore an inability to respond properly to external stimuli, likely driving the alterations in signaling activity and thus in neuronal function and communication

Myasthenia gravis-like syndrome induced by expression of interferon gamma in the neuromuscular junction.

Abnormal humoral responses toward motor end plate constituents in muscle induce myasthenia gravis (MG). To study the etiology of this disease, and whether it could be induced by host defense molecules, we examined the consequences of interferon (IFN) gamma production within the neuromuscular junction of transgenic mice. The transgenic mice exhibited gradually increasing muscular weakness, flaccid paralysis, and functional disruption of the neuromuscular junction that was reversed after administration of an inhibitor of acetylcholinesterase, features which are strikingly similar to human MG. Furthermore, histological examination revealed infiltration of mononuclear cells and autoantibody deposition at motor end plates. Immunoprecipitation analysis indicated that a previously unidentified 87-kD target antigen was recognized by sera from transgenic mice and also by sera from the majority of human MG patients studied. These results suggest that expression of IFN-gamma at motor end plates provokes an autoimmune humoral response, similar to human MG, thus linking the expression of this factor with development of this disease