bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isolation of a Bacillus safensis from mine tailings in Peru, genomic characterization and characterization of its cyanide-degrading enzyme CynD
Authors: Arevalo Santiago Justo , Sifuentes Daniela Zapata , Portocarrero Andrea Cuba , Reategui Michella Brescia , Pimentel Claudia Monge , Martins Layla Farage , Pierry Paulo Marques , Piroupo Carlos Morais , Santa Cruz Alcides Guerra , Aguilar Mauro Quiñones , Farah Chuck Shaker , Setubal João Carlos , da Silva Aline Maria 
Published: November 2021

ABSTRACTCyanide is widely used in industry as a potent lixiviant due to its capacity to tightly bind metals. This property imparts cyanide enormous toxicity to all known organisms. Thus, industries that utilize this compound must reduce its concentration in recycled or waste waters. Physical, chemical, and biological treatments have been used for cyanide remediation; however, none of them meet all the desired characteristics: efficiency, low cost and low environmental impact. A better understanding of metabolic pathways and biochemistry of enzymes involved in cyanide degradation is a necessary step to improve cyanide bioremediation efficacy to satisfy the industry requirements. Here, we used several approaches to explore this topic. We have isolated three cyanide-degrading Bacillus strains from water in contact with mine tailings from Lima, Peru, and classified them as Bacillus safensis PER-URP-08, Bacillus licheniformis PER-URP-12, and Bacillus subtilis PER-URP-17 based on 16S rRNA gene sequencing and core genome analyses. Additionally, core genome analyses of 132 publicly available genomes of Bacillus pumilus group including B. safensis and B. altitudinis allowed us to reclassify some strains and identify two strains that did not match with any known species of the Bacillus pumilus group. We searched for possible routes of cyanide-degradation in the genomes of these three strains and identified putative B. licheniformis PER-URP-12 and B. subtilis PER-URP-17 rhodaneses and B. safensis PER-URP-08 cyanide dihydratase (CynD) sequences possibly involved cyanide degradation. We identified characteristic C-terminal residues that differentiate CynD from B. pumilus and B. safensis, and showed that, differently from CynD from B. pumilus C1, recombinant CynD from the Bacillus safensis PER-URP-08 strain remains active up to pH 9 and presents a distinct oligomerization pattern at pH 8 and 9. Moreover, transcripts of B. safensis PER-URP-08 CynD (CynDPER-URP-08) are strongly induced in the presence of cyanide. Our results warrant further investigation of B. safensis PER-URP-08 and CynDPER-URP-08 as potential tools for cyanide-bioremediation.
RNA Profiling of Neuropathic Pain-Associated Human DRGs Reveal Sex-differences in Neuro-immune Interactions Promoting Pain
Authors: Ray Pradipta R. , Shiers Stephanie , Tavares-Ferreira Diana , Sankaranarayanan Ishwarya , Uhelski Megan L. , Li Yan , North Robert Y. , Tatsui Claudio , Dussor Gregory , Burton Michael D. , Dougherty Patrick M. , Price Theodore J. 
Published: November 2021

AbstractNeuropathic pain is a leading cause of high impact pain, is often disabling and is poorly managed by current therapeutics. Here we focused on a unique group of neuropathic pain patients undergoing thoracic vertebrectomy where the DRG is removed as part of the surgery allowing for molecular characterization and identification of mechanistic drivers of neuropathic pain independently of preclinical models. Our goal was to quantify whole transcriptome RNA abundances using RNA-seq in pain-associated human DRGs from these patients, allowing comprehensive identification of molecular changes in these samples by contrasting them with non-pain associated DRGs. We sequenced 70 human DRGs, including over 50 having mRNA libraries with neuronal mRNA. Our expression analysis revealed profound sex differences in differentially expressed genes including increase ofIL1B,TNF,CXCL14, andOSMin male and includingCCL1,CCL21,PENKandTLR3in female DRGs associated with neuropathic pain. Co-expression modules revealed enrichment in members of JUN-FOS signaling in males, and centromere protein coding genes in females. Neuro-immune signaling pathways revealed distinct cytokine signaling pathways associated with neuropathic pain in males (OSM, LIF, SOCS1) and females (CCL1, CCL19, CCL21). We validated cellular expression profiles of a subset of these findings using RNAscopein situhybridization. Our findings give direct support for sex differences in underlying mechanisms of neuropathic pain in patient populations.
Identification of bacteria by poly-aromatic hydrocarbons biosensors
Authors: Shlosberg Yaniv , Farber Yair , Hasson Salah , Bulatov Valery , Schechter Israel 
Published: November 2021

AbstractHuman health is consistently threatened by different species of pathogenic bacteria. To fight the spread of diseases, it is important to develop rapid methods for bacterial identification. Over the years, different kinds of biosensors were developed for this cause. Another environmental risk are poly-aromatic hydrocarbons (PAHs) that may be emitted from industrial facilities and pollute environmental water and soil. One of the methods for their purification is conducted by the addition of bacteria that can degrade the PAHs, while the bacteria itself can be filtrated at the end of the process. Although many studies reported monitoring of the PAHs degradation by fluorescence, not much attention was dedicated to studying the influence of the PAHs on the intrinsic fluorescence of the degrading bacteria. In this work, we apply synchronous fluorescence (SF) measurements to study the ability of the 5 PAHs: 9-Antracene carboxylic acid (9ACA), Pyrene, Perylene, Pentacene, and Chrysene to interact with bacteria and change its fluorescence spectra. We show that upon incubation of each PAH with the bacterium E.coli only the 2 PAHs 9ACA and Perylene cause an intensity decrease in the emission at λ = 300 – 375 nm, which derives from the emission of Tyrosine and Tryptophane (TT). Also, we show that upon incubation of 9ACA and Perylene with 5 different pathogenic bacteria, the intensity increase or decrease in the TT emission is unique to each bacterial species. Based on this observation, we suggest that the PAHs 9ACA and Perylene can be utilized as biosensors for bacterial identification.
Genome assembly of Danaus chrysippus and comparison with the Monarch Danaus plexippus
Authors: Singh Kumar Saurabh , De-Kayne Rishi , Omufwoko Kennedy Saitoti , Martins Dino J. , Bass Chris , ffrench-Constant Richard , Martin Simon H. 
Published: November 2021

AbstractMilkweed butterflies in the genus Danaus are studied in a diverse range of research fields including the neurobiology of migration, biochemistry of plant detoxification, host-parasite interactions, evolution of sex chromosomes, and speciation. We have assembled a nearly chromosomal genome for Danaus chrysippus (known as the African Monarch, African Queen, and Plain Tiger) using long read sequencing data. This species is of particular interest for the study of genome structural change and its consequences for evolution. Comparison with the genome of the North American Monarch Danaus plexippus reveals generally strong synteny, but highlights three inversion differences. The three chromosomes involved were previously found to carry peaks of intra-specific differentiation in D. chrysippus in Africa, suggesting that these inversions may be polymorphic and associated with local adaptation. The D. chrysippus genome is over 40% larger than that of D. plexippus, and nearly all of the additional ∼100 Megabases of DNA comprises repeats. Future comparative genomic studies within this genus will shed light on the evolution of genome architecture.
MECP2pedia: A Comprehensive Transcriptome Portal for MECP2 Disease Research
Authors: Trostle Alexander J. , Li Lucian , Kim Seon-Young , Wang Jiasheng , Al-Ouran Rami , Yalamanchili Hari Krishna , Liu Zhandong , Wan Ying-Wooi 
Published: November 2021

SummaryMutations in MeCP2 result in a crippling neurological disease, but we lack a lucid picture of MeCP2s molecular role. Focusing on individual transcriptomic studies yields inconsistent differentially expressed genes. We have aggregated and homogeneously processed modern public MeCP2 transcriptome data, which we present in a web portal. With this big data, we discovered a commonly perturbed core set of genes that transcends the limitations of any individual study. We then found distinct consistently up and downregulated subsets within these genes. We observe enrichment for this mouse core in other species MeCP2 models and see overlap between this core and ASD models. Analysis of signal to noise finds that many studies lack enough biological replicates. By integrating and examining transcriptomic data at scale, we have generated a valuable resource and insight on MeCP2 function.
Natural selection shapes the population dynamics of birds and mammals
Authors: Witting Lars 
Published: November 2021

AbstractWith eco-evolutionary processes explaining a wide range of ecological dynamics, I analyse for natural selection effects in the population dynamics of birds and mammals. By fitting single-species age-structured population dynamic models to 3,369 and 483 timeseries of 900 and 208 species of birds and mammals, I estimate that selection-based models are 780 (se:1.3) to 150,000 (se:2) times more probable than models with no selection. AIC model-selection includes natural selection in 79% to 92% of the accepted models, explaining 80% of the population dynamics variance, with median selection regulation being 1.2 (se:0.11) times stronger than density regulation. The estimated dynamics is damped to stable cyclic with median population periods around seven and eight generations for stable cycles. The estimated cycles follow from selected life history changes that solve several population cycle enigmas, highlighting the population dynamic implications of a natural selection that predicts also the life histories and abundancies of animals.
A predictive framework for sustainable youth skills development
Authors: Telukdarie Arnesh , Munsamy Megashnee , Mohlala Popopo Jonas , Monnapula Lesego Lydia , Viswanathan Radhakrishnan 
Published: November 2021

PurposeThe purpose of this research is to investigate sustainable strategies for skills development that is specific to the youth of South Africa. International and South African data are statistically analysed and quantified to provide inputs for the systems dynamics (SD)-based predictive skills model. The skills model simulates the impact of barriers and drivers on youth skills development towards identification of focus areas for improvement.Design/methodology/approachThe research adopts a mixed-methods approach. The study begins with an explorative literature study on skills development, with the findings applied in developing (1) South African specific research instruments for small, medium and micro enterprises (SMMEs) and skills programme grant recipients and (2) a conceptual framework of the SD predictive skills model. The responses to the South African specific instruments are analysed via confirmatory factor analysis (CFA), which quantifies the input coefficients to the system dynamics model. To quantify the global inputs for the SD model, an in-depth literature review of the global skills development initiatives is conducted. The SD model output on skills, for the South African inputs, is comparatively evaluated against global inputs.FindingsThe paper details the results of the literature analysis, instrument analyses, CFA and SD model. The instrument results rank experience, skills and interactions with experts and work-based learning as most important. South African and global learners identify networking as the primary medium for identifying training and employment opportunities. South African and global learners also identify qualifications and work-based experience as key to finding employment. The quantified results of the SA and global analysis are used as inputs in the SD model to deliver a forecasting tool. The SD model finds that the global data provide for better development of the skills base than the South African inputs. The key focus areas identified for improvement in South Africa include networking, work-based experience and a reduction in administrative requirements.Originality/valueThe research's originality resides in the ability to predict the impact of drivers and barriers on skills development. This research sought to transform qualitative global and South African inputs into a consolidated, predictive systems-based model. The SD model can be adopted as an indicator of drivers and barriers focused towards the optimisation of skills development.
Temperature sensitivity of Antarctic soil‐humic substance degradation by cold‐adapted bacteria
Authors: Kim Dockyu , Park Ha Ju , Kim Mincheol , Lee Seulah , Hong Soon Gyu , Kim Eungbin , Lee Hyoungseok 
Published: November 2021

SummaryHeteropolymer humic substances (HS) are the largest constituents of soil organic matter and are key components that affect plant and microbial growth in maritime Antarctic tundra. We investigated HS decomposition in Antarctic tundra soils from distinct sites by incubating samples at 5°C or 8°C (within a natural soil thawing temperature range of −3.8°C to 9.6°C) for 90 days (average Antarctic summer period). This continuous 3‐month artificial incubation maintained a higher total soil temperature than that in natural conditions. The long‐term warming effects rapidly decreased HS content during the initial incubation, with no significant difference between 5°C and 8°C. In the presence of Antarctic tundra soil heterogeneity, the relative abundance of Proteobacteria (one of the major bacterial phyla in cold soil environments) increased during HS decomposition, which was more significant at 8°C than at 5°C. Contrasting this, the relative abundance of Actinobacteria (another major group) did not exhibit any significant variation. This microcosm study indicates that higher temperatures or prolonged thawing periods affect the relative abundance of cold‐adapted bacterial communities, thereby promoting the rate of microbial HS decomposition. The resulting increase in HS‐derived small metabolites will possibly accelerate warming‐induced changes in the Antarctic tundra ecosystem.
Lithic cyanobacterial communities in the polyextreme Sahara Desert: implications for the search for the limits of life
Authors: Mehda Smail , Muñoz‐Martín M. Ángeles , Oustani Mabrouka , Hamdi‐Aïssa Baelhadj , Perona Elvira , Mateo Pilar 
Published: November 2021

SummaryThe hyperarid Sahara Desert presents extreme and persistent dry conditions with a limited number of hours during which the moisture availability, temperature and light allow phototrophic growth. Some cyanobacteria can live in these hostile conditions by seeking refuge under (hypolithic) or inside (endolithic) rocks, by colonizing porous spaces (cryptoendoliths) or fissures in stones (chasmoendoliths).Chroococcidiopsisspp. have been reported as the dominant or even the only phototrophs in these hot desert lithic communities. However, the results of this study reveal the high diversity of and variability in cyanobacteria among the sampled habitats in the Sahara Desert. The chasmoendolithic samples presented high coccoid cyanobacteria abundances, although the dominant cyanobacteria were distinct among different locations. A high predominance of a newly described cyanobacterium,Pseudoacaryochloris sahariense, was found in hard, compact, and more opaque stones with cryptoendolithic colonization. On the other hand, the hypolithic samples were dominated by filamentous, non‐heterocystous cyanobacteria. Thermophysiological bioassays confirmed desiccation and extreme temperature tolerance as drivers in the cyanobacterial community composition of these lithic niches. The results of the present study provide key factors for understanding life strategies under polyextreme environmental conditions. The isolated strains, especially the newly described cyanobacteriumP. sahariense, might represent suitable microorganisms in astrobiology studies aimed at investigating the limits of life.
Controlling pathogenic risks of water treatment biotechnologies at the source by genetic editing means
Authors: Wu Jie , Liu Dong‐Feng , Li Hui‐Hui , Min Di , Liu Jia‐Qi , Xu Peng , Li Wen‐Wei , Yu Han‐Qing , Zhu Yong‐Guan 
Published: November 2021

SummaryAntimicrobial‐resistant pathogens in the environment and wastewater treatment systems, many of which are also important pollutant degraders and are difficult to control by traditional disinfection approaches, have become an unprecedented treat to ecological security and human health. Here, we propose the adoption of genetic editing techniques as a highly targeted, efficient and simple tool to control the risks of environmental pathogens at the source. An ‘all‐in‐one’ plasmid system was constructed in Aeromonas hydrophila to accurately identify and selectively inactivate multiple key virulence factor genes and antibiotic resistance genes via base editing, enabling significantly suppressed bacterial virulence and resistance without impairing their normal phenotype and pollutant‐degradation functions. Its safe application for bioaugmented treatment of synthetic textile wastewater was also demonstrated. This genetic‐editing technique may offer a promising solution to control the health risks of environmental microorganisms via targeted gene inactivation, thereby facilitating safer application of water treatment biotechnologies.
Predicting the Divestment of Prior Acquisitions
Authors: Amiri Sina , King David R. , DeMarie Samuel , Brown James R. 
Published: November 2021

AbstractWe evaluate whether, in addition to seeking higher stock performance from acquisitions, firm managers also seek predictable stock performance. Building on prior research, we argue that higher volatility in a firm's stock performance following an acquisition is associated with divestment of a prior acquisition. Survival analysis of a longitudinal, panel dataset of 738 matched US acquisitions with 9,973 firm‐year observations shows that higher volatility in an acquiring firm's stock performance, following an acquisition, significantly predicts divestment of a prior acquisition. This effect is independent and stronger than the effect of the mean stock performance of an acquiring firm following an acquisition. We also find moderating effects for acquisition relatedness and acquiring firm stock performance after an acquisition. When an acquired unit is related to the parent firm's operations, it will be more likely to be divested if subsequent stock performance displays higher volatility. Still, higher overall stock performance makes a parent firm less likely to divest an acquired unit, suggesting that larger mean returns override concerns about higher stock performance volatility during corporate restructuring.
A More Miserable Life than Living in the Jungle: A Japanese ‘Comfort Woman’ Story
Authors: Tsukamoto Sachiyo 
Published: November 2021

ABSTRACTThis article analyses the recollection of a Japanese ‘comfort women’ survivor published in 1975. By applying the analytical concept of gender and trauma, this study draws on the ‘politics of integrity’ theorised by Aurora Levins Morales (1998) as well as the theory of ‘coherence of the self’ proposed by Charlotte Linde (1993). The social, political and psychological analysis of her life story reveals the complexity of the politics of integrity in telling a story of trauma. It concludes how strongly her silent voice of trauma required societal acknowledgement of her sense of self to regain human integrity and dignity.
There is no association between combined oral hormonal contraceptives and depression: a Swedish register‐based cohort study
Authors: Lundin C , Wikman A , Lampa E , Bixo M , Gemzell‐Danielsson K , Wikman P , Ljung R , Sundström Poromaa I 
Published: November 2021

ObjectiveTo investigate whether users of hormonal contraceptives (HCs) are at increased risk of depression compared with non‐users.DesignRegister‐based cohort study.SettingSweden.SampleWomen aged 15–25 years between 2010 and 2017 with no prior antidepressant treatment, psychiatric diagnose or contraindication for HCs (n = 739 585).MethodsWomen with a prescription of HC were identified via the Swedish Prescribed Drug Register (SPDR). Relative risks (RRs) for first depression diagnosis in current HC‐users compared with non‐users were modelled by Poisson regression. Adjustments included age, medical indication for HC‐use and parental history of mental disorders, among others.Main outcome measuresDepression, captured by a redeemed prescription of antidepressant treatment, or a first depression diagnosis in the SPDR and the National Patient Register.ResultsCompared with non‐users, women on combined oral contraceptives (COCs) and oral progestogen‐only products had lower or no increased risk of depression, relative risk (RR) 0.89 (95% CI 0.87–0.91) and 1.03 (95% CI 0.99–1.06) after adjustments, respectively. Age‐stratified analyses demonstrated that COC use in adolescents conferred no increase in risk (RR 0.96, 95% CI 0.93–0.98), whereas use of progestogen‐only pills (RR 1.13, 95% CI 1.07–1.19), contraceptive patch/vaginal ring (RR 1.43, 95% CI 1.30–1.58), implant (RR 1.38, 95% CI 1.30–1.45) or a levonorgestrel intrauterine device (RR 1.59, 95% CI 1.46–1.73) were associated with increased risks.ConclusionsThis study did not find any association between use of COCs, which is the dominating HC in first time users, and depression. Non‐oral products were associated with increased risks. Residual confounding must be addressed in the interpretation of the results.Tweetable abstractThere is no association between combined hormonal contraceptives and depression.
Humoral response to BNT162b2 mRNA COVID‐19 vaccine in peritoneal and hemodialysis patients: A comparative study
Authors: Duarte Rui , Roldão Marisa , Figueiredo Cátia , Luz Ivan , Ferrer Francisco , Gonçalves Hernâni , Sofia Flora , Lopes Karina 
Published: November 2021

AbstractIntroductionMaintenance dialysis patients (MDP) are at higher risk of exposure with increased mortality from COVID‐19 with generalized immunization becoming the cornerstone in prevention. This study aims to compare humoral response between hemodialysis (HD) and peritoneal dialysis (PD) patients.Materials and MethodsObservational prospective study following HD and PD programs from a Portuguese Center receiving BNT162b2 vaccine. Specific anti‐Spike IgG quantification to compare both for absolute value and non‐responders (NR) between modalities and against risk factors.ResultsOf 67 MDP, 42 were HD and 25 PD patients. PD developed higher antibody titers after both first (median 5.44 vs. 0.99 AU/ml, p < 0.01) and second dose (median 170.43 vs. 65.81 AU/ml; p < 0.01). HD associated with NR after the first dose (p < 0.01).ConclusionThis study demonstrated improved humoral immunogenicity with BNT162b2 in PD compared to HD patients. These differences are attributed to comorbidity burden and age differences, rather than dialysis modality.