bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbial community of recently discovered Auka vent field sheds light on vent biogeography and evolutionary history of thermophily
Authors: Speth Daan R. , Yu Feiqiao B. , Connon Stephanie A. , Lim Sujung , Magyar John S. , Peña Manet E. , Quake Stephen R. , Orphan Victoria J. 
Published: August 2021

AbstractHydrothermal vents have been key to our understanding of the limits of life, and the metabolic and phylogenetic diversity of thermophilic organisms. Here we used environmental metagenomics combined with analysis of physico-chemical data and 16S rRNA amplicons to characterize the diversity, temperature optima, and biogeographic distribution of sediment-hosted microorganisms at the recently discovered Auka vents in the Gulf of California, the deepest known hydrothermal vent field in the Pacific Ocean. We recovered 325 metagenome assembled genomes (MAGs) representing 54 phyla, over 1/3 of the currently known phylum diversity, showing the microbial community in Auka hydrothermal sediments is highly diverse. Large scale 16S rRNA amplicon screening of 227 sediment samples across the vent field indicates that the MAGs are largely representative of the microbial community. Metabolic reconstruction of a vent-specific, deeply branching clade within the Desulfobacterota (Tharpobacteria) suggests these organisms metabolize sulfur using novel octaheme cytochrome-c proteins related to hydroxylamine oxidoreductase. Community-wide comparison of the average nucleotide identity of the Auka MAGs with MAGs from the Guaymas Basin vent field, found 400 km to the Northwest, revealed a remarkable 20% species-level overlap between vent sites, suggestive of long-distance species transfer and sediment colonization. An adapted version of a recently developed model for predicting optimal growth temperature to the Auka and Guaymas MAGs indicates several of these uncultured microorganisms could grow at temperatures exceeding the currently known upper limit of life. Extending this analysis to reference data shows that thermophily is a trait that has evolved frequently among Bacteria and Archaea. Combined, our results show that Auka vent field offers new perspectives on our understanding of hydrothermal vent microbiology.
Myth-busting the provider-user relationship for digital sequence information
Authors: Scholz Amber Hartman , Lange Matthias , Habekost Pia , Oldham Paul , Cancio Ibon , Cochrane Guy , Freitag Jens 
Published: August 2021

AbstractThe United Nations Convention on Biological Diversity (CBD) formally recognized the sovereign rights of nations over their biological diversity. Implicit within the treaty is the idea that mega-biodiverse countries will provide genetic resources and grant access to them and scientists in high-income countries will use these resources and share back benefits. However, little research has been conducted on how this framework is reflected in real-life scientific practice. Currently, parties to the CBD) are debating whether or not digital sequence information (DSI) should be regulated under a new benefit-sharing framework. At this critical time point in the upcoming international negotiations, we test the fundamental hypothesis of provision and use by looking at the global patterns of access and use in scientific publications. Our data reject the provider-user relationship and suggest far more complex information flow for digital sequence information. Therefore, any new policy decisions on digital sequence information should be aware of the high level of use of DSI across low- and middle-income countries and seek to preserve open access to this crucial common good.
Nutrient limitation magnifies fitness costs of antimalarial drug resistance mutations
Authors: Nair Shalini , Li Xue , Arya Grace A. , McDew-White Marina , Ferrari Marco , Anderson Tim 
Published: August 2021

SummaryDrug resistance mutations tend to disrupt key physiological processes, and therefore carry a fitness cost. The size of these fitness costs is a central determinant of the rate of spread of these mutations in natural populations so are important to quantify. Head-to-head competition assays provide a standard approach to measuring differential fitness, and have been used extensively for malaria parasites. These assays typically use standardized culture media, containing RPMI 1640, which has a 1.4 to 5.5-fold (mean: 2.6-fold) higher concentration of amino acids than human blood. In this rich media we predict that fitness costs will be underestimated because resource competition is weak. We tested this prediction using an artemisinin sensitive parasite edited to contain kelch-C580Y or R561H mutations conferring resistance to artemisinin or synonymous control mutations. We examined the impact of these single amino acid mutations on fitness, using replicated head-to head competition experiments conducted in media containing (i) normal RPMI, (ii) modified RPMI with reduced amino acid concentration, (iii) RPMI containing only isoleucine, or (iv) 3-fold diluted RPMI. We found a significant 1.3 to 1.4-fold increase in fitness costs measured in modified and isoleucine-only media relative to normal media, while fitness costs were 2.5-fold higher in diluted media. We conclude that fitness costs are strongly affected by media composition and will be significantly underestimated in normal RPMI. Elevated fitness costs in nature will limit spread of ART-resistance but will also promote evolution of compensatory mutations that restore fitness, and can be exploited to maximize selection in laboratory experiments.
Mitotic Spindle Positioning (MISP) is an actin bundler that selectively stabilizes the rootlets of epithelial microvilli
Authors: Angelo Morales E. , Arnaiz Cayetana , Krystofiak Evan S. , Zanic Marija , Tyska Matthew J. 
Published: August 2021

ABSTRACTMicrovilli are conserved actin-based surface protrusions that have been repurposed throughout evolution to fulfill diverse cell functions. In the case of transporting epithelia, microvilli are supported by a core of actin filaments bundled in parallel by villin, fimbrin, and espin. Remarkably, microvilli biogenesis persists in mice lacking all three of these factors, suggesting the existence of unknown bundlers. We identified Mitotic Spindle Positioning (MISP) as an actin binding factor that localizes specifically to the rootlet end of the microvillus. MISP promotes rootlet elongation in cells, and purified MISP exhibits potent filament bundling activity in vitro. MISP-bundled filaments also recruit fimbrin, which further elongates and stabilizes bundles. MISP confinement to the rootlet is enforced by ezrin, which prevents decoration of the membrane-wrapped distal end of the core bundle. These discoveries reveal how epithelial cells optimize apical membrane surface area and offer insight on the remarkable robustness of microvilli biogenesis.
Model-guided engineering of DNA sequences with predictable site-specific recombination rates
Authors: Zhang Qiuge , Azarin Samira M. , Sarkar Casim A. 
Published: August 2021

AbstractSite-specific recombination (SSR) is an important tool in genome editing and gene circuit design. However, its applications are limited by the inability to simply and predictably tune SSR reaction rates across orders of magnitude. Facile rate manipulation can in principle be achieved by modifying the nucleotide sequence of the DNA substrate of the recombinase, but the design principles for rationally doing so have not been elucidated. To enable predictable tuning of SSR reaction kinetics via DNA sequence, we developed an integrated experimental and computational method to parse individual nucleotide contributions to the overall reaction rate, which we used to analyze and engineer the DNA attachment sequence attP for the inversion reaction mediated by the serine recombinase Bxb1. A quantitative PCR method was developed to measure the Bxb1 reaction rate in vitro. Then, attP sequence libraries were designed, selected, and sequenced to inform a machine-learning model, which revealed that the Bxb1 reaction rate can be accurately represented assuming independent contributions of nucleotides at key positions. Next, we used the model to predict the performance of DNA site variants in reaction rate assays both in vitro and in Escherichia coli, with flipping rates ranging from 0.01- to 10-fold that of the wild-type attP sequence. Finally, we demonstrate that attP variants with predictable DNA recombination rates can be used in concert to achieve kinetic control in gene circuit design by coordinating the coexpression of two proteins in both their relative proportion and their total amount. Our high-throughput, data-driven method for rationally tuning SSR reaction rates through DNA sequence modification enhances our understanding of recombinase function and expands the synthetic biology toolbox.Graphical abstract
Microbiome assembly predictably shapes diversity across a range of disturbance frequencies
Authors: Santillan Ezequiel , Wuertz Stefan 
Published: August 2021

AbstractDiversity is frequently linked to the functional stability of ecological communities. However, its association with assembly mechanisms remains largely unknown, particularly under fluctuating disturbances. Here, we subjected complex bacterial communities in bioreactor microcosms to different frequencies of organic loading shocks, tracking temporal dynamics in their assembly, structure and function. Null modelling revealed a stronger role of stochasticity at intermediate disturbance frequencies, preceding the formation of a peak in α-diversity. Communities at extreme ends of the disturbance range had the lowest α-diversity and highest within-treatment similarity in terms of β-diversity, with stronger deterministic assembly. Stochasticity prevailed during the initial successional stages, coinciding with better specialized function (nitrogen removal). In contrast, general functions (carbon removal and microbial aggregate settleability) benefited from stronger deterministic processes. We showed that changes in assembly processes predictably precede changes in diversity under a gradient of disturbance frequencies, advancing our understanding of the mechanisms behind disturbance-diversity-function relationships.
Adipose triglyceride lipase promotes prostaglandin-dependent actin remodeling by regulating substrate release from lipid droplets
Authors: Giedt Michelle S. , Thomalla Jonathon M. , Johnson Matthew R. , Lai Zon Weng , Tootle Tina L. , Welte Michael A. 
Published: August 2021

AbstractA key factor controlling oocyte quality and fertility is lipids. Even though lipid droplets (LDs) are crucial regulators of lipid metabolism, their roles in fertility are poorly understood. During Drosophila oogenesis, LD accumulation in nurse cells coincides with dynamic actin remodeling necessary for late-stage follicle morphogenesis and fertility. Loss of the LD-associated Adipose Triglyceride Lipase (ATGL) disrupts both actin bundle formation and cortical actin integrity, an unusual phenotype also seen when Pxt, the enzyme responsible for prostaglandin (PG) synthesis, is missing. Dominant genetic interactions and PG treatment of follicles in vitro reveal that ATGL and Pxt act in the same pathway to regulate actin remodeling, with ATGL upstream of Pxt. Further, lipidomic analysis detects arachidonic acid (AA) containing triglycerides in ovaries. Because AA is the substrate for Pxt, we propose that ATGL releases AA from LDs to drive PG synthesis necessary for follicle development. We also find that exogenous AA is toxic to follicles in vitro, and LDs modulate this toxicity. This leads to the model that LDs both sequester AA to limit toxicity, and release AA via ATGL to drive PG production. We speculate that the same pathways are conserved across organisms to regulate oocyte development and promote fertility.
Multi-plasmid clash in a bacterial community: plasmid viability depends on the ecological setting of hosts
Authors: Given Cindy , Penttinen Reetta , Jalasvuori Matti 
Published: August 2021

AbstractPlasmids are genetic elements that disperse horizontally between different strains and species of bacteria and a major factor in the dissemination of virulence factors and antibiotic resistance. Understanding the ecology of plasmids has a notable anthropocentric value and therefore the interactions between bacterial hosts and individual plasmids have been studied in detail. However, bacterial systems often carry multiple genetically distinct plasmids, but dynamics of these multiplasmid “clashes” has remained unstudied. Here, we set to investigate the survival of 11 mobilizable or conjugative plasmids in five different ecological settings. The key incentive was to determine whether plasmid dynamics are reproducible and whether there are trade-offs in plasmid fitness that stem from the ecological situation of their initial hosts. Growth rates and maximum population densities increased in all communities and treatments over the 42-day evolution experiment although plasmid contents at the end varied notably. We show that large multiresistance conferring plasmids are unfit when the community also contains smaller plasmids with fewer resistance genes. This suggests that restraining the use to few antibiotics can make bacterial communities sensitive to others. The hosts also appear to react to the presence of multiple genetically different plasmids by enhancing fimbriae production instead of alleviating costs of individual plasmids. In general, the survivors of the here-studied multi-plasmid clash are significantly affected by the presence or absence of antibiotic selection and plasmid-free hosts of varying fitness. Therefore, these trade-offs in different settings can explain for example why some resistance plasmids have an advantage during a rapid proliferation of antibiotic sensitive pathogen whereas others dominate in alternative situations.
Completion of neural crest cell production and emigration is regulated by retinoic acid-dependent inhibition of BMP signaling
Authors: Rekler Dina , Kalcheim Chaya 
Published: August 2021

AbstractProduction and emigration of neural crest cells is a transient process followed by the emergence of the definitive roof plate. The mechanisms regulating the end of neural crest ontogeny are poorly understood. Whereas early crest development is stimulated by mesoderm-derived retinoic acid, we report that the end of the neural crest period is regulated by retinoic acid synthesized in the dorsal neural tube. Inhibition of retinoic acid signaling in the neural tube prevents the normal upregulation of BMP inhibitors in the nascent roof plate and prolongs the period of BMP responsiveness which otherwise ceases close to roof plate establishment. Consequently, neural crest production and emigration are extended well into the roof plate stage. In turn, extending the activity of neural crest-specific genes inhibits the onset of retinoic acid synthesis in roof plate suggesting a mutual repressive interaction between neural crest and roof plate traits. Although several roof plate-specific genes are normally expressed in the absence of retinoic acid signaling, roof plate and crest markers are co-expressed in single cells and this domain also contains dorsal interneurons. Hence, the cellular and molecular architecture of the roof plate is compromised. Collectively, our results demonstrate that neural tube-derived retinoic acid, via inhibition of BMP signaling, is an essential factor responsible for the end of neural crest generation and the proper segregation of dorsal neural lineages.
Macaques preferentially attend to intermediately surprising information
Authors: Wu Shengyi , Blanchard Tommy , Meschke Emily , Aslin Richard N. , Hayden Benjamin Y. , Kidd Celeste 
Published: August 2021

AbstractNormative learning theories dictate that we should preferentially attend to informative sources, but only up to the point that our limited learning systems can process their content. Humans, including infants, show this predicted strategic deployment of attention. Here we demonstrate that rhesus monkeys, much like humans, attend to events of moderate surprisingness over both more and less surprising events. They do this in the absence of any specific goal or contingent reward, indicating that the behavioral pattern is spontaneous. We suggest this U-shaped attentional preference represents an evolutionarily preserved strategy for guiding intelligent organisms toward material that is maximally useful for learning.
Unique features of magic spot metabolism in Clostridioides difficile
Authors: Poudel Asia , Pokhrel Astha , Oludiran Adenrele , Coronado Estevan J. , Alleyne Kwincy , Gilfus Marrett M. , Gurung Raj K. , Adhikari Surya B. , Purcell Erin B. 
Published: August 2021

AbstractThe ‘magic spot’ alarmones (pp)pGpp, previously implicated in Clostridioides difficile antibiotic survival, are synthesized by CdRSH and CdRelQ. These enzymes are transcriptionally activated by diverse environmental stresses, but both exclusively synthesize pGpp rather than ppGpp as has previously been reported. While direct synthesis of pGpp from a GMP substrate and (p)ppGpp hydrolysis into pGpp by NUDIX hydrolases have previously been reported, there is no precedent for a bacterium synthesizing pGpp exclusively. Hydrolysis of the 5’ phosphate or pyrophosphate from GDP or GTP substrates is necessary for activity by the clostridial enzymes, neither of which can utilize GMP as a substrate. Both enzymes are remarkably insensitive to the size of their metal ion cofactor, tolerating a broad array of metals that do not allow activity in (pp)pGpp synthetases from other organisms. It is clear that while C. difficile utilizes magic spot signaling, its mechanisms of alarmone synthesis are not directly homologous to those in more completely characterized organisms.
Vaccinia virus-based vaccines confer protective immunity against SARS-CoV-2 virus in Syrian hamsters
Authors: Kulkarni Rakesh , Chen Wen-Ching , Lee Ying , Kao Chi-Fei , Hu Shiu-Lok , Ma Hsiu-Hua , Jan Jia-Tsrong , Liao Chun-Che , Liang Jian-Jong , Ko Hui-Ying , Sun Cheng-Pu , Lin Yin-Shoiou , Wang Yu-Chiuan , Wei Sung-Chan , Lin Yi-Ling , Ma Che , Chao Yu-Chan , Chou Yu-Chi , Chang Wen 
Published: August 2021

AbstractCOVID-19 in humans is caused by Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) that belongs to the beta family of coronaviruses. SARS-CoV-2 causes severe respiratory illness in 10-15% of infected individuals and mortality in 2-3%. Vaccines are urgently needed to prevent infection and to contain viral spread. Although several mRNA- and adenovirus-based vaccines are highly effective, their dependence on the “cold chain” transportation makes global vaccination a difficult task. In this context, a stable lyophilized vaccine may present certain advantages. Accordingly, establishing additional vaccine platforms remains vital to tackle SARS- CoV-2 and any future variants that may arise. Vaccinia virus (VACV) has been used to eradicate smallpox disease, and several attenuated viral strains with enhanced safety for human applications have been developed. We have generated two candidate SARS-CoV-2 vaccines based on two vaccinia viral strains, MVA and v-NY, that express full-length SARS-CoV-2 spike protein. Whereas MVA is growth-restricted in mammalian cells, the v-NY strain is replication-competent. We demonstrate that both candidate recombinant vaccines induce high titers of neutralizing antibodies in C57BL/6 mice vaccinated according to prime-boost regimens. Furthermore, our vaccination regimens generated TH1-biased immune responses in mice. Most importantly, prime-boost vaccination of a Syrian hamster infection model with MVA-S and v-NY-S protected the hamsters against SARS-CoV-2 infection, supporting that these two vaccines are promising candidates for future development. Finally, our vaccination regimens generated neutralizing antibodies that partially cross-neutralized SARS-CoV-2 variants of concern.
Portrayals of autism and social awareness: a scoping review
Authors: Fontes Rosa , Pino-Juste Margarita 
Published: August 2021

Purpose
The purpose of this paper is to look at recent trends in scientific literature on the portrayal of autism in published and broadcast media and social awareness of the subject.

Design/methodology/approach
A bibliometric analysis of content of such publications was performed.

Findings
Results show that portrayals of autism from books, newspapers, news broadcasts, films and TV series are being scrutinized. Research focuses on the social categories of resulting stereotypes, the quality of such depictions, the benefits and downsides, stigmatization of individuals (with autism) and how society responds to these portrayals.

Originality/value
It is important to understand if media portrayals of autism are creating a realistic and constructive awareness of autism in society.
Knowledge-oriented leadership towards organizational performance: symmetrical and asymmetrical approach
Authors: Farooq Sahibzada Umar , Xu Yan , Afshan Gul , Khalid Roshi 
Published: August 2021

PurposeThe purpose of this paper is to investigate the associations among knowledge-oriented leadership (KOL), knowledge worker satisfaction (KWS), knowledge worker productivity (KWP) and organizational performance (OP). The study hypothesizes that the explicit mixtures, i.e. KOL, KWS and KWP can improve OP.Design/methodology/approachThe study sample was composed of 248 academicians and management staff of higher educational institutes (HEIs). The relations were tested through Smart PLS 3.2.9. The fuzzy-set qualitative comparative analysis (fsQCA) method was also used for examining configurational paths.FindingsThe study found a substantial direct influence of KOL on OP. The findings revealed that KOL significantly affects KWS, and KWS enhances KWP, which ultimately improves the OP of HEIs. Grounded on the fsQCA, the outcomes exposed configurational trails to the enhanced OP.Originality/valueThere is scarce of studies that determine the connection of KOL, KWS, KWP and OP. This is one of the preliminary studies that examine the association of KOL, KWS, KWP and OP in HEIs. From a procedural viewpoint, the research subsidizes by merging symmetric and asymmetric tools to further understand structural issues. The use of fsQCA discloses numerous paths to improve OP and renders asymmetric relations. fsQCA also aids to comprehend the relations that might not be directly understandable via symmetric means.