bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aurantimonas marina sp. nov., isolated from deep-sea sediment
Authors: Song Lei , Liu Hongcan , Sun Qinglei , Dong Xiuzhu , Zhou Yuguang 
Published: August 2021

A novel bacterial strain, designated SW136T, was isolated from a deep-sea sediment sample collected from the South China Sea. Cells were Gram-stain-negative, aerobic, catalase-positive and oxidase-positive. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SW136T represented a novel member of the genus

Aurantimonas

, forming a distinct cluster with ‘

Aurantimonas litoralis

’,

Aurantimonas coralicida

and

Aurantimonas manganoxydans

(98.2, 98.1 and 97.9% sequence similarity, respectively). The predominant cellular fatty acid of strain SW136T was C18 : 1
ω7c. Strain SW136T contained ubiquinone-10 as the dominant respiratory quinone, and diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids. The genomic DNA G+C content was 64.3 mol%. The average nucleotide identity and digital DNA–DNA hybridization values of strain SW136T with

A. coralicida

CGMCC 1.12222T and

A. manganoxydans

CGMCC 1.12225T were 78.8 and 78.6 % and 21.5 and 25.5 %, respectively. On the basis of phylogenetic inference and phenotypic characteristics, we propose that strain SW136T represents a novel species of the genus

Aurantimonas

, with the name Aurantimonas marina sp. nov. The type strain is SW136T (=CGMCC 1.17725T=KCTC 82366T).
THE EFFECT OF BARICITINIB USAGE ON THE CLINICAL AND BIOCHEMICAL PROFILES OF COVID-19 PATIENTS- A RETROSPECTIVE OBSERVATIONAL STUDY
Authors: Amarnath Anoop , Das Ananya , Mutya Venakata Sai Shashank , Ibrahim Irfan 
Published: August 2021

ABSTRACTIntroductionCoronaviruses typically cause influenza like illness which progresses to ARDS along with other systemic manifestations. India is experiencing its second wave with a huge surge in the number of cases exponentially causing huge impact on health care infrastructure and the demand supply chain. As a result several new modalities have been used, one of which is the use of remdesivir and baricitinib . Hence this study is aimed at finding out the clinical and biochemical profile of the patients who have received the combinationMaterials and MethodsAll the patients who have received the combination meeting the inclusion and exclusion criteria have been included in the study. A total of 31 participants were included and their records were retrospectively analyzed.ResultsThere was a significant reduction in the oxygen requirement, CRP and IL-6 levels with p values<0.05. However, in the non-survivors group, there was no statistically significant reduction. Serial monitoring of NLR ratio showed increase towards the fifth day, especially in the non-survivor group it was as high as 41.24. The mortality rate was found to be 10% and the cause being secondary sepsis in all of them.ConclusionThe ACTT-2 trail has proved the efficacy of the use of the remdesivir and baricitinib combination with mortality benefit. In our study we found similar results which was well co-related with clinical and biochemical parameters like CRP and IL-6 especially in people with co-morbidites.
Emergence of SARS-CoV-2 variant B.1.575.2 containing the E484K mutation in the spike protein in Pamplona (Spain) May-June 2021
Authors: Trobajo-Sanmartín Camino , Miqueleiz Ana , Portillo María Eugenia , Fernández-Huerta Miguel , Navascués Ana , Sara Pilar Sola , Moreno Paula López , Ordoñez Gonzalo R , Castilla Jesús , Ezpeleta Carmen 
Published: August 2021

AbstractWith the emergence of new SARS-CoV-2 variants and the acquisition of novel mutations in exiting lineages, the need to implement methods capable of monitoring viral dynamics arises. We report the emergence and spread of a new SARS-CoV-2 variant within B.1.575 lineage containing the E484K mutation in the spike protein (named B.1.575.2) in a region of Northern Spain between May and June 2021. SARS-CoV-2 positive samples with cycle threshold value less than or equal to 30 were selected to screen of presumptive variants using the TaqPath™ COVID-19 RT-PCR kit and TaqMan™ SARS-CoV-2 Mutation Panel. Confirmation of variants was performed by whole genome sequencing. Of the 200 samples belonging to the B.1.575 lineage, 194 (97%) corresponded to the B.1.575.2 sub-lineage, which was related to the presence of the E484K mutation. Of 197 cases registered in GISAID EpiCoV database as lineage B.1.575.2 194 (99.5%) were identified in Pamplona (Spain).This report emphasizes the importance of complementing surveillance of SARS-CoV-2 with sequencing for the rapid control of emerging viral variants.
What has changed in the experiences of people with mental health problems during the COVID-19 pandemic? Findings from follow-up interviews using a coproduced, participatory qualitative approach
Authors: Shah Prisha , Hardy Jackie , Birken Mary , Foye Una , Olive Rachel Rowan , Nyikavaranda Patrick , Dare Ceri , Stefanidou Theodora , Schlief Merle , Pearce Eiluned , Lyons Natasha , Machin Karen , Jeynes Tamar , Chipp Beverley , Chhapia Anjie , Barber Nick , Gillard Steven , Pitman Alexandra , Simpson Alan , Johnson Sonia , Lloyd-Evans Brynmor 
Published: August 2021

AbstractPurposeWe sought to understand how the experiences of people in the UK with pre-existing mental health conditions had developed during the course of the COVID-19 pandemic.MethodsIn September-October 2020 we interviewed adults with mental health conditions pre-dating the pandemic, whom we had previously interviewed three months earlier. Participants had been recruited through online advertising and voluntary sector community organisations. Interviews were conducted by telephone or video-conference by researchers with lived experience of mental health difficulties, and explored changes over time in people’s experience of the pandemic.ResultsWe interviewed 44 people, achieving diversity of demographic characteristics and a range of mental health conditions and service use among our sample. Three overarching themes were derived from interviews. The first theme “Spectrum of adaptation”: to difficulties in access to, or the quality of, statutory mental health services, through developing new personal coping strategies or identifying alternative sources of support. The second theme is “Accumulating pressures”: from pandemic-related anxieties and sustained disruption to social contact and support, and to mental health treatment. The third theme “Feeling overlooked”: A sense of people with pre-existing mental health conditions being overlooked during the pandemic by policy-makers at all levels. The latter was compounded for people from ethnic minority communities or with physical health problems.ConclusionOur study highlights the need to support marginalised groups who are at risk of increased inequalities, and to maintain crucial mental and physical healthcare and social care for people with existing mental health conditions, notwithstanding challenges of the pandemic.
Functional connectome mediates the association between sleep disturbance and mental health in preadolescence
Authors: Yang Fan Nils , Liu Tina Tong , Wang Ze 
Published: August 2021

AbstractBackgroundSleep disturbance is known to be associated with various mental disorders and typically precedes the onset of mental disorders in youth. Given the increasingly acknowledged bi-directional influence between sleep disturbance and mental disorders, we addressed the possibility of a shared neural mechanism that underlies sleep disturbance and mental disorders in preadolescents.MethodsWe analyzed a dataset of 9350 9-10 year-old children, among whom 8845 had one-year follow-up data, from the Adolescent Brain and Cognitive Development (ABCD) Study. Linear mixed-effects models, mediation analysis, and longitudinal mediation analysis were used.ResultsOut of 338 unique connectivities, the effect of total sleep disturbance (TSP, from Sleep Disturbance Scale) and total problems (TP, from Child Behavior Checklist) converged in the default mode network (DMN) and its anti-correlated dorsal attention network (DAN). Within- and between-network connectivities (DMN-DAN, DMN-DMN, DAN-DAN) mediated the relationship between baseline TSD and TP at one-year follow-up and the relationship between baseline TP and TSD at one-year follow-up. Moreover, the identified network connectivities (DMN-DAN, DAN-DAN) also correlated with the total cognitive composite score from the NIH toolbox.ConclusionsThe pathway model in which sleep disturbance and mental problems affect each other through two anticorrelated brain networks (DMN and DAN) suggests a common neural mechanism between sleep disturbance and mental disorders. A less segregated DMN and DAN is also associated with negative outcomes on mental well-being, sleep disturbance, and cognition. These findings have important implications for the design of prevention and neurofeedback intervention for mental disorders and sleep problems.HighlightsThe impact of sleep disturbance and mental disorders on functional connectivity converged in default mode and dorsal attention networks.The relationship between sleep disturbance and mental disorders was mediated via a shared brain network mechanismSleep disturbance and mental disorders at baseline can each predict the other one year later through the identified network connectivitiesA less segregated default mode and dorsal attention networks was correlated with poorer cognitive performance.
Safety Assessment of Broadband Laser Exposure in µOCT
Authors: Spicer Graham L. C. , Child Benjamin , Gardecki Joseph A. , Kumar Aditya , Wartak Andreas , Gregg Abigail , Leung Hui Min , Tearney Guillermo J. 
Published: August 2021

AbstractMicro-optical coherence tomography (µOCT) improves the spatial resolution of in vivo OCT imaging by utilizing sophisticated focusing schemes and broadband illumination. This study explores the safety of coronary and trachea tissue exposure to µOCT illumination. © 2021 The Authors
RADseq data reveal a lack of admixture in a mouse lemur contact zone contrary to previous microsatellite results
Authors: Poelstra Jelmer , Montero B. Karina , Lüdemann Jan , Yang Ziheng , Rakotondranary S. Jacques , Hohenlohe Paul , Stetter Nadine , Ganzhorn Jörg U. , Yoder Anne D. 
Published: August 2021

AbstractDespite being one of the most fundamental biological processes, the process of speciation remains poorly understood in many groups of organisms. Mouse lemurs are a species-rich genus of small primates endemic to Madagascar, whose diversity has only recently been uncovered using genetic data and is primarily found among morphologically cryptic, allopatric populations. To assess to what extent described species represent reproductively isolated entities, studies are needed in areas where mouse lemur taxa come into contact. Hybridization has previously been reported in a contact zone between two closely related mouse lemur species (Microcebus murinusandM. griseorufus) based on microsatellite data. Here, we revisit this system using RADseq data for populations in, near, and far from the contact zone, including many of the individuals that had previously been identified as hybrids. Surprisingly, we find no evidence for admixed nuclear ancestry in any of the individuals. Re-analyses of microsatellite data and simulations suggest that previously inferred hybrids were false positives and that the programNewHybridscan be particularly sensitive to erroneously inferring hybrid ancestry. Using coalescent-bases analyses, we also show an overall lack of recent gene flow between the two species, and low levels of ancestral gene flow. Combined with evidence for local syntopic occurrence, these data indicate thatM. murinusandM. griseorufusare reproductively isolated. Finally, we estimate that they diverged less than a million years ago, suggesting that completion of speciation is relatively rapid in mouse lemurs. Future work should focus on the underpinnings of reproductive isolation in this cryptic primate radiation, which are mostly unknown. Our study also provides a cautionary tale for the inference of hybridization with microsatellite data.
Transcriptomic and functional analysis of Aβ1-42 oligomer-stimulated human monocyte-derived microglia-like cells
Authors: Smit Tamar , Ormel Paul R. , Sluijs Jacqueline A. , Hulshof Lianne A. , Middeldorp Jinte , de Witte Lot D. , Hol Elly M. , Donega Vanessa 
Published: August 2021

AbstractDysregulation of microglial function contributes to Alzheimer’s disease (AD) pathogenesis. Several genetic and transcriptome studies have revealed microglia specific genetic risk factors, and changes in microglia expression profiles in AD pathogenesis, viz. the human-Alzheimer’s microglia/myeloid (HAM) profile in AD patients and the disease-associated microglia profile (DAM) in AD mouse models. The transcriptional changes involve genes in immune and inflammatory pathways, and in pathways associated with Aβ clearance. Aβ oligomers have been suggested to be the initial trigger of microglia activation in AD. To study the direct response to Aβ oligomers exposure, we assessed changes in gene expression in an in vitro model for microglia, the human monocyte-derived microglial-like (MDMi) cells. We confirmed the initiation of an inflammatory profile following LPS stimulation, based on increased expression of IL1B, IL6, and TNFα. In contrast, the Aβ1-42 oligomers did not induce an inflammatory profile or a classical HAM or DAM profile. Interestingly, we observed a specific increase in the expression of metallothioneins in the Aβ1-42 oligomer treated MDMi cells. Metallothioneins are involved in metal ion regulation, protection against reactive oxygen species, and have anti-inflammatory properties. In conclusion, our data suggests that Aβ1-42 oligomers may trigger a protective response both in vitro and in vivo.
Increases in multiple resources promote plant invasion
Authors: Zhang Zhijie , Liu Yanjie , Hardrath Angelina , Jin Huifei , van Kleunen Mark 
Published: August 2021

AbstractInvasion by alien plants is frequently attributed to increased resource availabilities. Still, our understanding is mainly based on effects of single resources despite the fact that plants rely on multiple resources. How multiple resources affect success of alien plants remains largely unexplored. Here, with two common garden experiments, one in China and one in Germany, we tested whether nutrient and light availabilities affected the competitive outcomes between alien and native plants. We found that under low resource availabilities or with addition of only one type of resource aliens were not more competitive than natives. However, with a joint increase of nutrients and light intensity, aliens outcompeted natives. Our finding indicates that addition of multiple resources could greatly reduce the number of limiting factors (i.e. niche dimensionality), and that this favors the dominance of alien species. It also indicates that habitats experiencing multiple global changes might be more vulnerable to plant invasion.
SUMOylation of Jun fine-tunes the Drosophila gut immune response
Authors: Soory Amarendranath , Ratnaparkhi Girish 
Published: August 2021

ABSTRACTPost-translational modification by the small ubiquitin-like modifier, SUMO can modulate the activity of its conjugated proteins. The transcriptional regulator Jun, a member of the AP-1, complex is one such SUMO target. We find that Jra, the Drosophila Jun ortholog, is a regulator of the Pseudomonas entomophila induced gut immune gene regulatory network, modulating the expression of a few thousand genes, as measured by quantitative RNA sequencing. Decrease in Jra in gut enterocytes is protective, suggesting that reduction of Jra signaling favors the host over the pathogen. In Jra, lysines 29 and 190 are SUMO conjugation targets, with the JraK29R+K190R double mutant being SUMO conjugation resistant (SCR). Interestingly, a JraSCR fly line, generated by CRISPR/Cas9 based genome editing, is more sensitive to infection, with adults showing a weakened host response and increased proliferation of Pseudomonas. Transcriptome analysis of the guts of JraSCR and JraWT flies suggests that lack of SUMOylation of Jra significantly changes core elements of the immune gene regulatory network, that include antimicrobial agents, secreted ligands, feedback regulators, and transcription factors. SUMOylation attenuates Jra activity, with the master immune regulator Relish being an important transcriptional target. Our study implicates Jra as a major immune regulator, with dynamic SUMO conjugation/deconjugation modulating the kinetics of the gut transcriptional immune response.
Sphingosine 1-Phosphate Mediates Adiponectin Receptor Signaling Essential For Lipid Homeostasis And Embryogenesis
Authors: Ruiz Mario , Devkota Ranjan , Panagaki Dimitra , Bergh Per-Olof , Kaper Delaney , Henricsson Marcus , Nik Ali , Petkevicius Kasparas , Höög Johanna L. , Bohlooly-Y Mohammad , Carlsson Peter , Borén Jan , Pilon Marc 
Published: August 2021

AbstractCells and organisms require proper membrane composition to function and develop. Phospholipids are the major component of membranes and are primarily acquired through the diet. Given great variability in diet composition, cells must be able to deploy mechanisms that correct deviations from optimal membrane composition and properties. Here, using lipidomics and unbiased proteomics, we found that the embryonic lethality in mice lacking the fluidity regulators Adiponectin Receptors 1 and 2 (AdipoR1/2) is associated with aberrant high saturation of the membrane phospholipids. Using mouse embryonic fibroblasts (MEFs) derived from AdipoR1/2-KO embryos, human cell lines and the model organismC. eleganswe found that, mechanistically, AdipoR1/2-derived sphingosine 1-phosphate (S1P) signals in parallel through S1PR3-SREBP1 and PPARγ to sustain the expression of the fatty acid desaturase SCD and maintain membrane properties. Thus, our work identifies an evolutionary conserved pathway by which cells and organism achieve membrane homeostasis and adapt to a variable environment.
Heterochromatin rewiring and domain disruption-mediated chromatin compaction during erythropoiesis
Authors: Li Dong , Wu Fan , Zhou Shuo , Huang Xiao-Jun , Lee Hsiang-Ying 
Published: August 2021

AbstractDevelopment of mammalian red blood cells involves progressive chromatin compaction and subsequent enucleation in terminal stages of differentiation, but the molecular mechanisms underlying the three-dimensional chromatin reorganization and compaction remains obscure. Here, we systematically analyze the distinct features of higher-order chromatin in purified populations of primary human erythroblasts. Our results reveal that while heterochromatin regions undergo substantial compression, select transcription competent regions with active transcription signature are preferentially maintained to achieve a highly-compacted yet functional chromatin state in terminal erythropoiesis, which is about 20-30% of the nuclear volume compared to that of erythroid progenitors. While the partition of euchromatic and heterochromatic regions (compartment A and B) remain mostly unchanged, H3K9me3 marks relocalize to the nuclear periphery and a significant number of H3K9me3 long-range interactions are formed in the three-dimensional rewiring during terminal erythroid chromatin condensation. Moreover, ∼63% of the topologically associating domain (TAD) boundaries are disrupted, while certain TADs with active chromatin modification are selectively maintained during terminal erythropoiesis. The most well-maintained TADs are enriched for chromatin structural factors CTCF and SMC3, as well as factors and marks of the active transcription state. Finally, we demonstrate that the erythroid master regulator GATA1 involves in safeguarding select essential chromatin domains during terminal erythropoiesis. Our study therefore delineate the molecular characteristics of a development-driven chromatin compaction process, which reveals transcription competence as a key determinant of the select domain maintenance to ensure appropriate gene expression during immense chromatin compaction.
Temperature and nutrients drive eco-phenotypic dynamics in a microbial food web
Authors: Han Ze-Yi , Wieczynski Daniel J. , Yammine Andrea , Gibert Jean P. 
Published: August 2021

ABSTRACTAnthropogenic increases in temperature and nutrient loads will likely impact food web structure and stability. Although their independent effects have been reasonably well studied, their joint effects—particularly on coupled ecological and phenotypic dynamics—remain poorly understood. Here we experimentally manipulated temperature and nutrient levels in microbial food webs and used time-series analysis to quantify the strength of reciprocal effects between ecological and phenotypic dynamics across trophic levels. We found that i) joint –often interactive– effects of temperature and nutrients on ecological dynamics are more common at higher trophic levels, ii) temperature and nutrients interact to shift the relative strength of top-down vs. bottom-up control, and iii) rapid phenotypic change mediates observed ecological responses to changes in temperature and nutrients. Our results uncover how feedbacks between ecological and phenotypic dynamics mediate food web responses to environmental change. This suggests important but previously unknown ways that temperature and nutrients might jointly control the rapid eco-phenotypic feedbacks that determine food web dynamics in a changing world.
A GGDEF domain serves as a spatial on-switch for a phosphodiesterase by direct interaction with a polar landmark protein
Authors: Rick Tim , Kreiling Vanessa , Höing Alexander , Fiedler Svenja , Glatter Timo , Steinchen Wieland , Hochberg Georg , Bähre Heike , Seifert Roland , Bange Gert , Knauer Shirley K. , Graumann Peter L. , Thormann Kai M. 
Published: August 2021

AbstractIn bacteria, the monopolar localization of enzymes and protein complexes can result in a bi-modal distribution of enzyme activity between the dividing cells and heterogeneity of cellular behaviors. In Shewanella putrefaciens, the multidomain hybrid diguanylate cyclase/phosphodiesterase PdeB, which degrades the secondary messenger c-di-GMP, is located at the flagellated cell pole. Here we show how PdeB polar recruitment is mediated by direct interaction between the inactive diguanylate cyclase (GGDEF) domain of PdeB and the C-terminal FimV domain of the polar landmark protein HubP. We demonstrate that this interaction is crucial for full function of PdeB as a phosphodiesterase. Thus, the GGDEF domain serves as a spatially controlled on-switch that effectively restricts PdeBs activity to the flagellated cell pole. We further show that PdeB regulates abundance and activity of at least two crucial surface-interaction factors, the BpfA surface adhesion protein and the MSHA type IV pilus. The heterogeneity in c-di-GMP concentrations that is generated by differences in abundance and temporal polar appearance of PdeB as well as by bi-modal distribution after cell fission orchestrates the population behavior with respect to cell-surface interaction and environmental spreading.SignificancePhenotypic heterogeneity benefits the proliferation of microbial populations in changing environments. Such heterogeneity can be created by recruitment of enzymatic activity to specific cellular compartments, e.g., the cell pole. Here we show how a GGDEF domain of a multidomain phosphodiesterase has adopted the function as a spatial on-switch that is specifically activated upon direct interaction with a polar landmark protein.