A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes

Analyses of 55 individual and 31 concatenated protein data sets encoded in Reclinomonas americana and Marchantia polymorpha mitochondrial genomes revealed that current methods for constructing phylogenetic trees are insufficiently sensitive (or artifact-insensitive) to ascertain the sister of mitochondria among the current sample of eight alpha-proteobacterial genomes using mitochondrially-encoded proteins. However, Rhodospirillum rubrum came as close to mitochondria as any alpha-proteobacterium investigated. This prompted a search for methods to directly compare eukaryotic genomes to their prokaryotic counterparts to investigate the origin of the mitochondrion and its host from the standpoint of nuclear genes. We examined pairwise amino acid sequence identity in comparisons of 6,214 nuclear protein-coding genes from Saccharomyces cerevisiae to 177,117 proteins encoded in sequenced genomes from 45 eubacteria and 15 archaebacteria. The results reveal that approximately 75% of yeast genes having homologues among the present prokaryotic sample share greater amino acid sequence identity to eubacterial than to archaebacterial homologues. At high stringency comparisons, only the eubacterial component of the yeast genome is detectable. Our findings indicate that at the levels of overall amino acid sequence identity and gene content, yeast shares a sister-group relationship with eubacteria, not with archaebacteria, in contrast to the current phylogenetic paradigm based on ribosomal RNA. Among eubacteria and archaebacteria, proteobacterial and methanogen genomes, respectively, shared more similarity with the yeast genome than other prokaryotic genomes surveyed

Facile synthesis and defect optimization of 2D-layered MoS2 on TiO2 heterostructure for industrial effluent, wastewater treatments

Supplementary information is available for this paper at https://doi.org/10.1038/s41598-020-78268-4.Copyright © The Author(s) 2020. Current research is paying much attention to heterojunction nanostructures. Owing to its versatile characteristics such as stimulating morphology, affluent surface-oxygen-vacancies and chemical compositions for enhanced generation of reactive oxygen species. Herein, we report the hydrothermally synthesized TiO2@MoS2 heterojunction nanostructure for the effective production of photoinduced charge carriers to enhance the photocatalytic capability. XRD analysis illustrated the crystalline size of CTAB capped TiO2, MoS2@TiO2 and L-Cysteine capped MoS2@TiO2 as 12.6, 11.7 and 10.2 nm, respectively. The bandgap of the samples analyzed by UV–Visible spectroscopy are 3.57, 3.66 and 3.94 eV. PL spectra of anatase phase titania shows the peaks present at and above 400 nm are ascribed to the defects in the crystalline structure in the form of oxygen vacancies. HRTEM reveals the existence of hexagonal layered MoS2 formation on the spherical shaped TiO2 nanoparticles at the interface. X-ray photoelectron spectroscopy recommends the chemical interactions between MoS2 and TiO2, specifically, oxygen vacancies. In addition, the electrochemical impedance spectroscopy studies observed that L-MT sample performed low charge transfer resistance (336.7 Ω cm2) that promotes the migration of electrons and interfacial charge separation. The photocatalytic performance is evaluated by quantifying the rate of Congo red dye degradation under visible light irradiation, and the decomposition efficiency was found to be 97%. The electron trapping recombination and plausible photocatalytic mechanism are also explored, and the reported work could be an excellent complement for industrial wastewater treatment.MHRD-SPARC; UKIERI; DST-SERB; RUSA 2.0; COMPETE agency, PT2020; EU-EC/MSCA-COFUND-2015-FP Nano TRAIN for Growth II; INSPIRE Faculty Scheme; SERB-EMRhttps://doi.org/10.1038/s41598-020-78268-

A Quick Mind with Letters Can Be a Slow Mind with Natural Scenes: Individual Differences in Attentional Selection

Background Most people show a remarkable deficit in reporting the second of two targets (T2) when presented 200–500 ms after the first (T1), reflecting an ‘attentional blink’ (AB). However, there are large individual differences in the magnitude of the effect, with some people, referred to as ‘non-blinkers’, showing no such attentional restrictions. Methodology/Principal Findings Here we replicate these individual differences in a task requiring identification of two letters amongst digits, and show that the observed differences in T2 performance cannot be attributed to individual differences in T1 performance. In a second experiment, the generality of the non-blinkers' superior performance was tested using a task containing novel pictures rather than alphanumeric stimuli. A substantial AB was obtained in non-blinkers that was equivalent to that of ‘blinkers’. Conclusion/Significance The results suggest that non-blinkers employ an efficient target selection strategy that relies on well-learned alphabetic and numeric category sets.University of Groningen. Research School Behavioural and Cognitive Neuroscience

The sulfur pathway and diagnosis of sulfate depletion in grapevine

Sulfur is an essential nutrient to all plant species. Plants assimilate sulfur in a well-described pathway, which has been taken up by roots. Regulatory mech- anism has been the subject of many research papers. However, recent studies highlighted differences between crop plants and the model plant Arabidopsis thaliana. Our work focuses on the identification of genes involved in the sulfur metabolism in the Vitis vinifera genome, and their response to sulfur deficiency and other abiotic stress endured by grapevine in the field, namely water stress. Here, we describe the identification and brief characterization of the first assimilation enzymes involved in the sulfur pathway, the enzyme responsible for sulfur activa- tion, ATP sulfurylase (ATPS), and the two enzymes that reduce sulfate to sulfide, Adenosine 50-phosphosulate reductase (APR) and Sulfite reductase (SiR). A reduc- tion was observed in the number of ATPS and APR isoforms identified in V. vinifera genome when compared to A. thaliana or Glycine max genomes. Two ATPS isoforms were present in the Vitis genome, of which only ATPS1 transcript was detected in the tested tissues, and one APR isoform, suggesting an absence of redundancy in the role of both enzymes. ATPS1, APR and SiR transcript level was up-regulated in response to 2 days exposure to sulfur deficiency in V. vinifera cell cultures, which was completely reversed by the addition of GSH to the culture medium. Apparently, oxidative stress triggered GSH has a pivotal role in the regulation of ATPS1, APR and SiR transcription level, since their up-regulation was observed in mRNA from field grapevine berries under water stress, which is known to induce oxidative stress.info:eu-repo/semantics/publishedVersio

Development and validation of a prognostic multivariable model to predict insufficient clinical response to methotrexate in rheumatoid arthritis

Objective The objective was to predict insufficient response to 3 months methotrexate (MTX) in DMARD naïve rheumatoid arthritis patients. Methods A Multivariable logistic regression model of rheumatoid arthritis patients starting MTX was developed in a derivation cohort with 285 patients starting MTX in a clinical multicentre, stratified single-blinded trial, performed in seven secondary care clinics and a tertiary care clinic. The model was validated in a validation cohort with 102 patients starting MTX at a tertiary care clinic. Outcome was insufficient response (disease activity score (DAS)28 >3.2) after 3 months of MTX treatment. Clinical characteristics, lifestyle variables, genetic and metabolic biomarkers were determined at baseline in both cohorts. These variables were dichotomized and used to construct a multivariable prediction model with backward logistic regression analysis. Results The prediction model for insufficient response in the derivation cohort, included: DAS28>5.1, Health Assessment Questionnaire>0.6, current smoking, BMI>25 kg/m2, ABCB1 rs1045642 genotype, ABCC3 rs4793665 genotype, and erythrocyte-folate<750 nmol/L. In the derivation cohort, AUC of ROC curve was 0.80 (95%CI: 0.73–0.86), and 0.80 (95%CI: 0.69–0.91) in the validation cohort. Betas of the prediction model were transformed into total risk score (range 0–8). At cutoff of 4, probability for insufficient response was 44%. Sensitivity was 71%, specificity 72%, with positive and negative predictive value of 72% and 71%. Conclusions A prognostics prediction model for insufficient response to MTX in 2 prospective RA cohorts by combining genetic, metabolic, clinical and lifestyle variables was developed and validated. This model satisfactorily identified RA patients with high risk of insufficient response to MTX

Analysis of copy number variation in men with non-obstructive azoospermia

BACKGROUND: Recent findings demonstrate that single nucleotide variants can cause non-obstructive azoospermia (NOA). In contrast, copy number variants (CNVs) were only analysed in few studies in infertile men. Some have reported a higher prevalence of CNVs in infertile versus fertile men. OBJECTIVES: This study aimed to elucidate if CNVs are associated with NOA. MATERIALS AND METHODS: We performed array-based comparative genomic hybridization (aCGH) in 37 men with meiotic arrest, 194 men with Sertoli cell-only phenotype, and 21 control men. We filtered our data for deletions affecting genes and prioritized the affected genes according to a literature search. Prevalence of CNVs was compared between all groups. Exome data of 2,030 men were screened to detect further genetic variants in prioritized genes. Modelling was performed for the protein encoded by the novel candidate gene TEKT5 and we stained for TEKT5 in human testicular tissue. RESULTS: We determined the cause of infertility in two individuals with homozygous deletions of SYCE1 and in one individual with a heterozygous deletion of SYCE1 combined with a likely pathogenic missense variant on the second allele. We detected heterozygous deletions affecting MLH3, EIF2B2, SLX4, CLPP and TEKT5, in one subject each. CNVs were not detected more frequently in infertile men compared with controls. DISCUSSION: While SYCE1 and MLH3 encode known meiosis-specific proteins, much less is known about the proteins encoded by the other identified candidate genes, warranting further analyses. We were able to identify the cause of infertility in one out of the 231 infertile men by aCGH and in two men by using exome sequencing data. CONCLUSION: As aCGH and exome sequencing are both expensive methods, combining both in a clinical routine is not an effective strategy. Instead, using CNV calling from exome data has recently become more precise, potentially making aCGH dispensable

Axisymmetric compressible boundary layer on a long thin moving cylinder

The steady laminar boundary layer flow on a thin and isothermal moving cylinder in a viscous compressible fluid at rest is studied in this paper. The fluid considered is a model fluid in which ϱ∼ T −1 and μ∼ T ω . The transformed non-similar boundary layer equations are solved numerically using a very efficient numerical method for some values of ω and wall enthalpy g ω parameters. The skin friction coefficient and Nusselt number are calculated for Pr=0.7 and some values of ω and g ωPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/41705/1/707_2005_Article_BF01291848.pd

Опыт использования акустического доплеровского измерителя течений (АDCP) в условиях Черного моря

В статье излагается методика проведения измерений Lowered ADCP и обработки первичной информации. При последующей обработке данных широко использовался опыт МГИ НАНУ с аналогичными акустическими измерителями течений в 80-е гг. В результате обобщен опыт применения Lowered ADCP в условиях Черного моря, даны алгоритмы обработки данных, приведены профили абсолютной скорости течений на ряде станций и показано, что предлагаемый подход дает более адекватную качественную и количественную оценку профиля скорости течения, чем известные методы.The methods of measurements with Lowered ADCP and processing of the initial information are presented. During the following data processing the experience of Marine Hydrophysical Institute of NAS of Ukraine with the similar acoustic currents meters in the 80-ies was widely applied. As a result the experience of Lowered ADCP application under the Black Sea conditions is generalized, the algorithms of data processing are given, the profiles of absolute speed of currents are given on the series of stations. It is shown that the proposed approach provides more adequate qualitative and quantitative estimation of the current velocity profile than the known methods do