Single Amino Acid Substitution in Homogentisate Dioxygenase Affects Melanin Production in Bacillus thuringiensis

Bacillus thuringiensis formulation losing its activity under field conditions due to UV radiation and photoprotection of B. thuringiensis based on melanin has attracted the attention of researchers for many years. Here, a single amino acid substitution (G272E) in homogentisate 1,2-dioxygenase was found to be responsible for pigment overproduction in B. thuringiensis BMB181, a derivative of BMB171. Disrupting the gene encoding homogentisate dioxygenase in BMB171 induced the accumulation of the homogentisic acid and provoked an increased pigment formation. To gain insights into homogentisate 1,2-dioxygenase in B. thuringiensis, we constructed a total of 14 mutations with a single amino acid substitution, and six of the mutant proteins were found to affect the melanin production when substituted by alanine. This study provides a new way to construct pigment-overproducing strains by impairing the homogentisate dioxygenase with a single mutation in B. thuringiensis, and the findings will facilitate a better understanding of this enzyme

Epigenome-Wide Histone Acetylation Changes in Peripheral Blood Mononuclear Cells in Patients with Type 2 Diabetes and Atherosclerotic Disease

There is emerging evidence of an association between epigenetic modifications, glycemic control and atherosclerosis risk. In this study, we mapped genome-wide epigenetic changes in patients with type 2 diabetes (T2D) and advanced atherosclerotic disease. We performed chromatin immunoprecipitation sequencing (ChIP-seq) using a histone 3 lysine 9 acetylation (H3K9ac) mark in peripheral blood mononuclear cells from patients with atherosclerosis with T2D (n = 8) or without T2D (ND, n = 10). We mapped epigenome changes and identified 23,394 and 13,133 peaks in ND and T2D individuals, respectively. Out of all the peaks, 753 domains near the transcription start site (TSS) were unique to T2D. We found that T2D in atherosclerosis leads to an H3K9ac increase in 118, and loss in 63 genomic regions. Furthermore, we discovered an association between the genomic locations of significant H3K9ac changes with genetic variants identified in previous T2D GWAS. The transcription factor 7-like 2 (TCF7L2) rs7903146, together with several human leukocyte antigen (HLA) variants, were among the domains with the most dramatic changes of H3K9ac enrichments. Pathway analysis revealed multiple activated pathways involved in immunity, including type 1 diabetes. Our results present novel evidence on the interaction between genetics and epigenetics, as well as epigenetic changes related to immunity in patients with T2D and advanced atherosclerotic disease.Peer reviewe

Averting biodiversity collapse in tropical forest protected areas

The rapid disruption of tropical forests probably imperils global biodiversity more than any other contemporary phenomenon¹⁻³. With deforestation advancing quickly, protected areas are increasingly becoming final refuges for threatened species and natural ecosystem processes. However, many protected areas in the tropics are themselves vulnerable to human encroachment and other environmental stresses⁴⁻⁹. As pressures mount, it is vital to know whether existing reserves can sustain their biodiversity. A critical constraint in addressing this question has been that data describing a broad array of biodiversity groups have been unavailable for a sufficiently large and representative sample of reserves. Here we present a uniquely comprehensive data set on changes over the past 20 to 30 years in 31 functional groups of species and 21 potential drivers of environmental change, for 60 protected areas stratified across the world’s major tropical regions. Our analysis reveals great variation in reserve ‘health’: about half of all reserves have been effective or performed passably, but the rest are experiencing an erosion of biodiversity that is often alarmingly widespread taxonomically and functionally. Habitat disruption, hunting and forest-product exploitation were the strongest predictors of declining reserve health. Crucially, environmental changes immediately outside reserves seemed nearly as important as those inside in determining their ecological fate, with changes inside reserves strongly mirroring those occurring around them. These findings suggest that tropical protected areas are often intimately linked ecologically to their surrounding habitats, and that a failure to stem broad-scale loss and degradation of such habitats could sharply increase the likelihood of serious biodiversity declines.Keywords: Ecology, Environmental scienc

Codes

<div>This is code linking to a study "Discriminative Prediction of A-To-I RNA Editing Events from DNA Sequence"</div><div>It includes a string kernel support vector machines and a basic shell script to show how to make prediction.</div

In-situ facile synthesis novel N-doped thin graphene layer encapsulated Pd@N/C catalyst for semi-hydrogenation of alkynes

Transition metal-catalyzed semi-hydrogenation of alkynes has become one of the most popular methods for alkene synthesis. Specifically, the noble metal Pd, Rh, and Ru-based heterogeneous catalysts have been widely studied and utilized in both academia and industry. But the supported noble metal catalysts are generally suffering from leaching or aggregation during harsh reaction conditions, which resulting low catalytic reactivity and stability. Herein, we reported the facile synthesis of nitrogen doped graphene encapsulated Pd catalyst and its application in the chemo-selective semi-hydrogenation of alkynes. The graphene layer served as "bulletproof" over the active Pd Nano metal species, which was confirmed by Xray and TEM analysis, enhanced the catalytic stability during the reaction conditions. The optimized prepared Pd@N/C catalyst showed excellent efficiency in semi-hydrogenation of phenylacetylene and other types of alkynes with un-functionalized or functionalized substituents, including the hydrogenation sensitive functional groups (NO2, ester, and halogen). (C) 2021 Elsevier Inc. All rights reserved

Serum Renin Levels Increase With Age in Boys Resulting in Higher Renin Levels in Young Men Compared to Young Women, and Soluble Angiotensin-Converting Enzyme 2 Correlates With Renin and Body Mass Index

Background: Age, sex, and body constitution may affect the shedding of membrane bound angiotensin-converting enzyme 2 (mACE2) and lead to a relative mACE2 deficiency. However, it is unclear if differences, reflected by serum renin levels, exist in the basal renin-angiotensin-system (RAS) between children and adults, boys, and girls as well as young women and young men. Furthermore, it remains to be investigated if renin and soluble ACE2 (sACE2) levels are correlated with body mass index (BMI) in children and young adults. The aim of this observational study was to assess age-and sex differences in serum renin, and the relationship between renin, soluble angiotensin-converting enzyme 2, and body mass index in a prospectively followed population-based cohort of children which were followed into young adulthood. Study Design: We analyzed renin and sACE2 in serum in a prospectively followed population-based cohort at 9.9 (0.6) [mean (SD)] (n = 173), 11.7 (0.6) (n = 156), 14.8 (0.8) (n = 149), 18.8 (0.3) (n = 93), and 23.5 (0.7) (n = 152) years of age. Height (cm) and weight (kg) was measured and body mass index (BMI) was calculated as weight (kg)/height (m)2. Sex-related differences in renin levels were calculated using analysis of covariance, adjusted for age. Correlations were assessed by calculating the correlation coefficient (R2) using a multivariable linear mixed model. Results: Both sexes had low renin levels up to 12 years of age. Thereafter renin levels increased more in boys than in girls. Males from the age of 15 had significantly higher levels than females (p < 0.001). There was a positive linear relationship between renin and sACE2 levels in male and female subjects (p < 0.001), and between sACE2 levels and BMI in males (p < 0.001). Conclusion: Renin levels increase with age, are higher in men than in women since around puberty, and are correlated with sACE2 levels. Furthermore, sACE2 levels are correlated with body mass index in males. These findings indicate that high renin levels in males and females and a high BMI in males may activate pathways which increase the shedding of mACE2, with possible implications for the risk of severe coronavirus disease 2019

Polygenic scores for low lung function and the future risk of adverse health outcomes

Aims Reduced lung function and adverse health outcomes are often observed. This study characterizes genetic susceptibility for reduced lung function and risk of developing a range of adverse health outcomes. Methods We studied 27,438 middle-aged adults from the Malmo Diet and Cancer study (MDCS), followed up to 28.8 years. Trait-specific Polygenic scores (PGS) for forced expiratory volume in 1 s (FEV1) and forced vital capacity (FVC) were constructed for each participant using MDCS genetic data and summary statistics from the latest GWAS of lung function. Linear regression models and cox proportional hazards regression models were used to assess associations between adverse health outcomes and lung function-PGS. Results FEV1-PGS and FVC-PGS were significantly associated with mean sBP at baseline after adjustments (FEV1-PGS Q1 (highest PGS = highest lung function): 140.7mmHg vs. Q4: 141.5mmHg, p-value 0.008). A low FVC-PGS was significantly associated with the risk of future diabetic events after adjustments (Q4 vs. Q1 HR: 1.22 (CI 1.12-1.32), p-trend &lt; 0.001) and had added value to risk prediction models for diabetes. Low FEV1-PGS was significantly associated with future coronary events (Q4 vs. Q1 HR: 1.13 (CI: 1.04-1.22), p-trend 0.008). No significant association was found between PGS and sudden cardiac death, chronic kidney disease or all-cause mortality. Results remained largely unchanged in a subgroup of subjects when further adjusted for apolipoproteins. Conclusion Genetic susceptibility for reduced lung function is associated with higher sBP, increased risk of diabetes and to a lesser extent, future coronary events, suggesting etiological roles of lung function on these outcomes. Using PGS, high-risk groups could be early detected to implement early lifestyle changes to mitigate the risk

PlantLoc: an accurate web server for predicting plant protein subcellular localization by substantiality motif.

Knowledge of subcellular localizations (SCLs) of plant proteins relates to their functions and aids in understanding the regulation of biological processes at the cellular level. We present PlantLoc, a highly accurate and fast webserver for predicting the multi-label SCLs of plant proteins. The PlantLoc server has two innovative characters: building localization motif libraries by a recursive method without alignment and Gene Ontology information; and establishing simple architecture for rapidly and accurately identifying plant protein SCLs without a machine learning algorithm. PlantLoc provides predicted SCLs results, confidence estimates and which is the substantiality motif and where it is located on the sequence. PlantLoc achieved the highest accuracy (overall accuracy of 80.8%) of identification of plant protein SCLs as benchmarked by using a new test dataset compared other plant SCL prediction webservers. The ability of PlantLoc to predict multiple sites was also significantly higher than for any other webserver. The predicted substantiality motifs of queries also have great potential for analysis of relationships with protein functional regions. The PlantLoc server is available at http://cal.tongji.edu.cn/PlantLoc/

Predicting turns in proteins with a unified model.

MOTIVATION: Turns are a critical element of the structure of a protein; turns play a crucial role in loops, folds, and interactions. Current prediction methods are well developed for the prediction of individual turn types, including α-turn, β-turn, and γ-turn, etc. However, for further protein structure and function prediction it is necessary to develop a uniform model that can accurately predict all types of turns simultaneously. RESULTS: In this study, we present a novel approach, TurnP, which offers the ability to investigate all the turns in a protein based on a unified model. The main characteristics of TurnP are: (i) using newly exploited features of structural evolution information (secondary structure and shape string of protein) based on structure homologies, (ii) considering all types of turns in a unified model, and (iii) practical capability of accurate prediction of all turns simultaneously for a query. TurnP utilizes predicted secondary structures and predicted shape strings, both of which have greater accuracy, based on innovative technologies which were both developed by our group. Then, sequence and structural evolution features, which are profile of sequence, profile of secondary structures and profile of shape strings are generated by sequence and structure alignment. When TurnP was validated on a non-redundant dataset (4,107 entries) by five-fold cross-validation, we achieved an accuracy of 88.8% and a sensitivity of 71.8%, which exceeded the most state-of-the-art predictors of certain type of turn. Newly determined sequences, the EVA and CASP9 datasets were used as independent tests and the results we achieved were outstanding for turn predictions and confirmed the good performance of TurnP for practical applications