bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbial community structure in hadal sediments: high similarity along trench axes and strong changes along redox gradients
Authors: Schauberger Clemens , Glud Ronnie N , Hausmann Bela , Trouche Blandine , Maignien Lois , Poulain Julie , Wincker Patrick , Arnaud-Haond Sophie , Wenzhöfer Frank , Thamdrup Bo 
Published: June 2021

Abstract
Hadal trench sediments are hotspots of biogeochemical activity in the deep sea, but the biogeochemical and ecological factors that shape benthic hadal microbial communities remain unknown. Here, we sampled ten hadal sites from two trench regions with a vertical resolution of down to 1 cm. We sequenced 16S rRNA gene amplicons using universal and archaea-specific primer sets and compared the results to biogeochemical parameters. Despite bathymetric and depositional heterogeneity we found a high similarity of microbial communities within each of the two trench axes, while composition at the phylum level varied strongly with sediment depth in conjunction with the redox stratification into oxic, nitrogenous, and ferruginous zones. As a result, communities of a given sediment horizon were more similar to each other across a distance of hundreds of kilometers within each trench, than to those of adjacent horizons from the same sites separated only by centimeters. Total organic carbon content statistically only explained a small part of the variation within and between trenches, and did not explain the community differences observed between the hadal and adjacent shallower sites. Anaerobic taxa increased in abundance at the top of the ferruginous zone, seeded by organisms deposited at the sediment surface and surviving burial through the upper redox zones. While an influence of other potential factors such as geographic isolation, hydrostatic pressure, and non-steady state depositional regimes could not be discerned, redox stratification and diagenesis appear to be the main selective forces that structure community composition in hadal sediments.
RIP3 impedes transcription factor EB to suppress autophagic degradation in septic acute kidney injury
Authors: Li Ruizhao , Zhao Xingchen , Zhang Shu , Dong Wei , Zhang Li , Chen Yuanhan , Li Zhilian , Yang Huan , Huang Ying , Xie Zhiyong , Wang Weidong , Li Chunling , Ye Zhiming , Dong Zheng , Liang Xinling 
Published: June 2021

AbstractAutophagy is an important renal-protective mechanism in septic acute kidney injury (AKI). Receptor interacting protein kinase 3 (RIP3) has been implicated in the renal tubular injury and renal dysfunction during septic AKI. Here we investigated the role and mechanism of RIP3 on autophagy in septic AKI. We showed an activation of RIP3, accompanied by an accumulation of the autophagosome marker LC3II and the autophagic substrate p62, in the kidneys of lipopolysaccharide (LPS)-induced septic AKI mice and LPS-treated cultured renal proximal tubular epithelial cells (PTECs). The lysosome inhibitor did not further increase the levels of LCII or p62 in LPS-treated PTECs. Moreover, inhibition of RIP3 attenuated the aberrant accumulation of LC3II and p62 under LPS treatment in vivo and in vitro. By utilizing mCherry-GFP-LC3 autophagy reporter mice in vivo and PTECs overexpression mRFP-GFP-LC3 in vitro, we observed that inhibition of RIP3 restored the formation of autolysosomes and eliminated the accumulated autophagosomes under LPS treatment. These results indicated that RIP3 impaired autophagic degradation, contributing to the accumulation of autophagosomes. Mechanistically, the nuclear translocation of transcription factor EB (TFEB), a master regulator of the lysosome and autophagy pathway, was inhibited in LPS-induced mice and LPS-treated PTECs. Inhibition of RIP3 restored the nuclear translocation of TFEB in vivo and in vitro. Co-immunoprecipitation further showed an interaction of RIP3 and TFEB in LPS-treated PTECs. Also, the expression of LAMP1 and cathepsin B, two potential target genes of TFEB involved in lysosome function, were decreased under LPS treatment in vivo and in vitro, and this decrease was rescued by inhibiting RIP3. Finally, overexpression of TFEB restored the autophagic degradation in LPS-treated PTECs. Together, the present study has identified a pivotal role of RIP3 in suppressing autophagic degradation through impeding the TFEB-lysosome pathway in septic AKI, providing potential therapeutic targets for the prevention and treatment of septic AKI.
Structural basis for SARS-CoV-2 envelope protein recognition of human cell junction protein PALS1
Authors: Chai Jin , Cai Yuanheng , Pang Changxu , Wang Liguo , McSweeney Sean , Shanklin John , Liu Qun 
Published: June 2021

AbstractThe COVID-19 pandemic, caused by the SARS-CoV-2 virus, has created global health and economic emergencies. SARS-CoV-2 viruses promote their own spread and virulence by hijacking human proteins, which occurs through viral protein recognition of human targets. To understand the structural basis for SARS-CoV-2 viral-host protein recognition, here we use cryo-electron microscopy (cryo-EM) to determine a complex structure of the human cell junction protein PALS1 and SARS-CoV-2 viral envelope (E) protein. Our reported structure shows that the E protein C-terminal DLLV motif recognizes a pocket formed exclusively by hydrophobic residues from the PDZ and SH3 domains of PALS1. Our structural analysis provides an explanation for the observation that the viral E protein recruits PALS1 from lung epithelial cell junctions. In addition, our structure provides novel targets for peptide- and small-molecule inhibitors that could block the PALS1-E interactions to reduce E-mediated virulence.
Designing an irreversible metabolic switch for scalable induction of microbial chemical production
Authors: Mannan Ahmad A. , Bates Declan G. 
Published: June 2021

AbstractBacteria can be harnessed to synthesise high-value chemicals. A promising strategy for increasing productivity uses inducible control systems to switch metabolism from growth to chemical synthesis once a large population of cell factories are generated. However, use of expensive chemical inducers limits scalability of this approach for biotechnological applications. Switching using cheap nutrients is an appealing alternative, but their tightly regulated uptake and consumption again limits scalability. Here, using mathematical models of fatty acid uptake in E. coli as an exemplary case study, we unravel how the cell’s native regulation and program of induction can be engineered to minimise inducer usage. We show that integrating positive feedback loops into the circuitry creates an irreversible metabolic switch, which, requiring only temporary induction, drastically reduces inducer usage. Our proposed switch should be widely applicable, irrespective of the product of interest, and brings closer the realization of scalable and sustainable microbial chemical production.
A molecular pathology, neurobiology, biochemical, genetic and neuroimaging study of progressive apraxia of speech
Authors: Josephs Keith A. , Duffy Joseph R. , Clark Heather M. , Utianski Rene L. , Strand Edythe A. , Machulda Mary M. , Botha Hugo , Martin Peter R. , Pham Nha Trang Thu , Stierwalt Julie , Ali Farwa , Buciuc Marina , Baker Matthew , Fernandez De Castro Cristhoper H. , Spychalla Anthony J. , Schwarz Christopher G. , Reid Robert I. , Senjem Matthew L. , Jack Clifford R. , Lowe Val J. , Bigio Eileen H. , Reichard Ross R. , Polley Eric. J. , Ertekin-Taner Nilufer , Rademakers Rosa , DeTure Michael A. , Ross Owen A. , Dickson Dennis W. , Whitwell Jennifer L. 
Published: June 2021

AbstractProgressive apraxia of speech is a neurodegenerative syndrome affecting spoken communication. Molecular pathology, biochemistry, genetics, and longitudinal imaging were investigated in 32 autopsy-confirmed patients with progressive apraxia of speech who were followed over 10 years. Corticobasal degeneration and progressive supranuclear palsy (4R-tauopathies) were the most common underlying pathologies. Perceptually distinct speech characteristics, combined with age-at-onset, predicted specific 4R-tauopathy; phonetic subtype and younger age predicted corticobasal degeneration, and prosodic subtype and older age predicted progressive supranuclear palsy. Phonetic and prosodic subtypes showed differing relationships within the cortico-striato-pallido-nigro-luysial network. Biochemical analysis revealed no distinct differences in aggregated 4R-tau while tau H1 haplotype frequency (69%) was lower compared to 1000+ autopsy-confirmed 4R-tauopathies. Corticobasal degeneration patients had faster rates of decline, greater cortical degeneration, and shorter illness duration than progressive supranuclear palsy. These findings help define the pathobiology of progressive apraxia of speech and may have consequences for development of 4R-tau targeting treatment.
Room temperature electrically pumped topological insulator lasers
Authors: Choi Jae-Hyuck , Hayenga William E. , Liu Yuzhou G. N. , Parto Midya , Bahari Babak , Christodoulides Demetrios N. , Khajavikhan Mercedeh 
Published: June 2021

AbstractTopological insulator lasers (TILs) are a recently introduced family of lasing arrays in which phase locking is achieved through synthetic gauge fields. These single frequency light source arrays operate in the spatially extended edge modes of topologically non-trivial optical lattices. Because of the inherent robustness of topological modes against perturbations and defects, such topological insulator lasers tend to demonstrate higher slope efficiencies as compared to their topologically trivial counterparts. So far, magnetic and non-magnetic optically pumped topological laser arrays as well as electrically pumped TILs that are operating at cryogenic temperatures have been demonstrated. Here we present the first room temperature and electrically pumped topological insulator laser. This laser array, using a structure that mimics the quantum spin Hall effect for photons, generates light at telecom wavelengths and exhibits single frequency emission. Our work is expected to lead to further developments in laser science and technology, while opening up new possibilities in topological photonics.
Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing
Authors: Yuen Zaka Wing-Sze , Srivastava Akanksha , Daniel Runa , McNevin Dennis , Jack Cameron , Eyras Eduardo 
Published: June 2021

AbstractDNA methylation plays a fundamental role in the control of gene expression and genome integrity. Although there are multiple tools that enable its detection from Nanopore sequencing, their accuracy remains largely unknown. Here, we present a systematic benchmarking of tools for the detection of CpG methylation from Nanopore sequencing using individual reads, control mixtures of methylated and unmethylated reads, and bisulfite sequencing. We found that tools have a tradeoff between false positives and false negatives and present a high dispersion with respect to the expected methylation frequency values. We described various strategies to improve the accuracy of these tools, including a consensus approach, METEORE (https://github.com/comprna/METEORE), based on the combination of the predictions from two or more tools that shows improved accuracy over individual tools. Snakemake pipelines are also provided for reproducibility and to enable the systematic application of our analyses to other datasets.
Heteromeric HSFA2/HSFA3 complexes drive transcriptional memory after heat stress in Arabidopsis
Authors: Friedrich Thomas , Oberkofler Vicky , Trindade Inês , Altmann Simone , Brzezinka Krzysztof , Lämke Jörn , Gorka Michal , Kappel Christian , Sokolowska Ewelina , Skirycz Aleksandra , Graf Alexander , Bäurle Isabel 
Published: June 2021

AbstractAdaptive plasticity in stress responses is a key element of plant survival strategies. For instance, moderate heat stress (HS) primes a plant to acquire thermotolerance, which allows subsequent survival of more severe HS conditions. Acquired thermotolerance is actively maintained over several days (HS memory) and involves the sustained induction of memory-related genes. Here we show that FORGETTER3/ HEAT SHOCK TRANSCRIPTION FACTOR A3 (FGT3/HSFA3) is specifically required for physiological HS memory and maintaining high memory-gene expression during the days following a HS exposure. HSFA3 mediates HS memory by direct transcriptional activation of memory-related genes after return to normal growth temperatures. HSFA3 binds HSFA2, and in vivo both proteins form heteromeric complexes with additional HSFs. Our results indicate that only complexes containing both HSFA2 and HSFA3 efficiently promote transcriptional memory by positively influencing histone H3 lysine 4 (H3K4) hyper-methylation. In summary, our work defines the major HSF complex controlling transcriptional memory and elucidates the in vivo dynamics of HSF complexes during somatic stress memory.
Large variation in anti-SARS-CoV-2 antibody prevalence among essential workers in Geneva, Switzerland
Authors: Stringhini Silvia , Zaballa María-Eugenia , Pullen Nick , de Mestral Carlos , Perez-Saez Javier , Dumont Roxane , Picazio Attilio , Pennacchio Francesco , Dibner Yaron , Yerly Sabine , Baysson Helene , Vuilleumier Nicolas , Balavoine Jean-François , Bachmann Delphine , Trono Didier , Pittet Didier , Chappuis François , Kherad Omar , Kaiser Laurent , Azman Andrew S. ,   SEROCoV-WORK + Study Group, Alber Victoria , Arm-Vernez Isabelle , Bachmann Delphine , Bachmann Donatien , Baggio Stéphanie , Monteiro Gil Barbosa , Baysson Hélène , Bleich Patrick , Boissel Isabelle , Collombet Prune , Courvoisier Delphine , Couson Philippine , Davidovic Alioucha , Deiri Clement , Del Rio Divina , de Mestral Carlos , De Ridder David , D’ippolito Paola , Duc Joséphine , Eckerle Isabella , El Merjani Nacira , Ferniot Gwennaelle , Flahault Antonie , Francioli Natalie , Frangville Marion , Garande Carine , Gétaz Laurent , Giraldo Pamela , Golaz Fanny , Guérin Julie , Haboury Ludivine , Harnal Séverine , Javet Victoria , Kaiser Laurent , Laboulais Amélie , Lamour Gaëlle , Lefebvre Xavier , Lescuyer Pierre , Loizeau Andrea Jutta , Lombard Fanny-Blanche , Lorthe Elsa , Martinez Chantal , Massiha Kourosh , Metral-Boffod Ludovic , Meyer Benjamin , Mostaguir Khaled , Nehme Mayssam , Noël Natacha , Oederlin Nicolas , Petrovic Dusan , Piumatti Giovanni , Portier Jane , Poulain Géraldine , Pugin Caroline , Rakotomiaramanana Barinjaka , Randrianandrasana Zo Francia , Richard Aude , Richard Viviane , Rodriguez-Velazquez Sabina , Salzmann-Bellard Lilas , Thorens Leonard , Torroni Simon , Vidonne David , Violot Guillemette , Waldmann Zoé , Will Manon , Wisniak Ania , Guessous Idris 
Published: June 2021

AbstractLimited data exist on SARS-CoV-2 infection rates across sectors and occupations, hindering our ability to make rational policy, including vaccination prioritization, to protect workers and limit SARS-CoV-2 spread. Here, we present results from our SEROCoV-WORK + study, a serosurvey of workers recruited after the first wave of the COVID-19 pandemic in Geneva, Switzerland. We tested workers (May 18—September 18, 2020) from 16 sectors and 32 occupations for anti-SARS-CoV-2 IgG antibodies. Of 10,513 participants, 1026 (9.8%) tested positive. The seropositivity rate ranged from 4.2% in the media sector to 14.3% in the nursing home sector. We found considerable within-sector variability: nursing home (0%–31.4%), homecare (3.9%–12.6%), healthcare (0%–23.5%), public administration (2.6%–24.6%), and public security (0%–16.7%). Seropositivity rates also varied across occupations, from 15.0% among kitchen staff and 14.4% among nurses, to 5.4% among domestic care workers and 2.8% among journalists. Our findings show that seropositivity rates varied widely across sectors, between facilities within sectors, and across occupations, reflecting a higher exposure in certain sectors and occupations.
Sugar phosphate activation of the stress sensor eIF2B
Authors: Hao Qi , Heo Jin-Mi , Nocek Boguslaw P. , Hicks Kevin G. , Stoll Vincent S. , Remarcik Clint , Hackett Sean , LeBon Lauren , Jain Rinku , Eaton Dan , Rutter Jared , Wong Yao Liang , Sidrauski Carmela 
Published: June 2021

AbstractThe multi-subunit translation initiation factor eIF2B is a control node for protein synthesis. eIF2B activity is canonically modulated through stress-responsive phosphorylation of its substrate eIF2. The eIF2B regulatory subcomplex is evolutionarily related to sugar-metabolizing enzymes, but the biological relevance of this relationship was unknown. To identify natural ligands that might regulate eIF2B, we conduct unbiased binding- and activity-based screens followed by structural studies. We find that sugar phosphates occupy the ancestral catalytic site in the eIF2Bα subunit, promote eIF2B holoenzyme formation and enhance enzymatic activity towards eIF2. A mutant in the eIF2Bα ligand pocket that causes Vanishing White Matter disease fails to engage and is not stimulated by sugar phosphates. These data underscore the importance of allosteric metabolite modulation for proper eIF2B function. We propose that eIF2B evolved to couple nutrient status via sugar phosphate sensing with the rate of protein synthesis, one of the most energetically costly cellular processes.
When band convergence is not beneficial for thermoelectrics
Authors: Park Junsoo , Dylla Maxwell , Xia Yi , Wood Max , Snyder G. Jeffrey , Jain Anubhav 
Published: June 2021

AbstractBand convergence is considered a clear benefit to thermoelectric performance because it increases the charge carrier concentration for a given Fermi level, which typically enhances charge conductivity while preserving the Seebeck coefficient. However, this advantage hinges on the assumption that interband scattering of carriers is weak or insignificant. With first-principles treatment of electron-phonon scattering in the CaMg2Sb2-CaZn2Sb2 Zintl system and full Heusler Sr2SbAu, we demonstrate that the benefit of band convergence can be intrinsically negated by interband scattering depending on the manner in which bands converge. In the Zintl alloy, band convergence does not improve weighted mobility or the density-of-states effective mass. We trace the underlying reason to the fact that the bands converge at a one k-point, which induces strong interband scattering of both the deformation-potential and the polar-optical kinds. The case contrasts with band convergence at distant k-points (as in the full Heusler), which better preserves the single-band scattering behavior thereby successfully leading to improved performance. Therefore, we suggest that band convergence as thermoelectric design principle is best suited to cases in which it occurs at distant k-points.
Exposure to screens and children’s language development in the EDEN mother–child cohort
Authors: Martinot Pauline , Bernard Jonathan Y. , Peyre Hugo , De Agostini Maria , Forhan Anne , Charles Marie-Aline , Plancoulaine Sabine , Heude Barbara 
Published: June 2021

AbstractStudies in children have reported associations of screen time and background TV on language skills as measured by their parents. However, few large, longitudinal studies have examined language skills assessed by trained psychologists, which is less prone to social desirability. We assessed screen time and exposure to TV during family meals at ages 2, 3 and 5–6 years in 1562 children from the French EDEN cohort. Language skills were evaluated by parents at 2 years (Communicative Development Inventory, CDI) and by trained psychologists at 3 (NEPSY and ELOLA batteries) and 5–6 years (verbal IQ). Cross-sectional and longitudinal associations were assessed by linear regression adjusted for important confounders. Overall, daily screen time was not associated with language scores, except in cross-sectional at age 2 years, where higher CDI scores were observed for intermediate screen time. Exposure to TV during family meals was consistently associated with lower language scores: TV always on (vs never) at age 2 years was associated with lower verbal IQ (− 3.2 [95% IC: − 6.0, − 0.3] points), independent of daily screen time and baseline language score. In conclusion, public health policies should better account for the context of screen watching, not only its amount.
Biophysical and structural studies reveal marginal stability of a crucial hydrocarbon biosynthetic enzyme acyl ACP reductase
Authors: Sharma Ashima , Shakeel Tabinda , Gupta Mayank , Rajacharya Girish H. , Yazdani Syed Shams 
Published: June 2021

AbstractAcyl-ACP reductase (AAR) is one of the two key cyanobacterial enzymes along with aldehyde deformylating oxygenase (ADO) involved in the synthesis of long-chain alkanes, a drop-in biofuel. The enzyme is prone to aggregation when expressed in Escherichia coli, leading to varying alkane levels. The present work attempts to investigate the crucial structural aspects of AAR protein associated with its stability and folding. Characterization by dynamic light scattering experiment and intact mass spectrometry revealed that recombinantly expressed AAR in E. coli existed in multiple-sized protein particles due to diverse lipidation. Interestingly, while thermal- and urea-based denaturation of AAR showed 2-state unfolding transition in circular dichroism and intrinsic fluorescent spectroscopy, the unfolding process of AAR was a 3-state pathway in GdnHCl solution suggesting that the protein milieu plays a significant role in dictating its folding. Apparent standard free energy $$\left( {\Delta {\text{G}}_{{{\text{NU}}}}^{{{\text{H}}_{2} {\text{O}}}} } \right)$$

Δ

G

NU

H
2

O

of ~ 4.5 kcal/mol for the steady-state unfolding of AAR indicated borderline stability of the protein. Based on these evidences, we propose that the marginal stability of AAR are plausible contributing reasons for aggregation propensity and hence the low catalytic activity of the enzyme when expressed in E. coli for biofuel production. Our results show a path for building superior biocatalyst for higher biofuel production.
Bacillus amyloliquefaciens FH-1 significantly affects cucumber seedlings and the rhizosphere bacterial community but not soil
Authors: Wang Jingjing , Xu Song , Yang Rong , Zhao Wei , Zhu Dan , Zhang Xiaoxia , Huang Zhiyong 
Published: June 2021

AbstractPlant growth-promoting bacteria (PGPB) inoculants have been applied worldwide. However, the ecological roles of PGPB under different soil conditions are still not well understood. The present study aimed to explore the ecological roles of Bacillus amyloliquefaciens FH-1 (FH) on cucumber seedlings, rhizosphere soil properties, and the bacterial community in pot experiments. The results showed that FH had significant effects on cucumber seedlings and the rhizosphere bacterial community but not on soil properties. The FH promoted cucumber seedlings growth, reduced the rhizosphere bacterial diversity, increased Proteobacteria, and decreased Acidobacteria. Linear discriminant analysis (LDA) effect size (LEfSe) revealed that FH enriched two taxa (GKS2_174 and Nannocystaceae) and inhibited 18 taxa (mainly Acidobacteria, Actinobacteria, BRC1, Chloroflexi, Plantctomycetes, and Verrucomicrobia). Co-occurrence network analysis demonstrated that FH increased bacteria-bacteria interactions and that Bacillus (genus of FH) had few interactions with the enriched and inhibited taxa. This might indicate that FH does not directly affect the enriched and inhibited taxa. Correlation analysis results displayed that cucumber seedlings’ weight and height/length (except root length) were significantly correlated with the 18 inhibited taxa and the enriched taxa Nannocystaceae. It was speculated that FH might promote cucumber seedling growth by indirectly enriching Nannocystaceae and inhibiting some taxa from Acidobacteria, Actinobacteria, BRC1, Chloroflexi, Plantctomycetes, and Verrucomicrobia.