bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct regulation of cell cycle regulatory gene expression by NtrX to promote Sinorhizobium meliloti cell division
Authors: Xing Shenghui , Zhang Lanya , An Fang , Huang Leqi , Yang Xinwei , Zeng Shuang , Li Ningning , Zheng Wenjia , Ouenzar Khadidja , Yu Liangliang , Luo Li 
Published: November 2021

ABSTRACTCell division of the alfalfa symbiont, Sinorhizobium meliloti, is regulated by the CtrA signaling network. The gene expression of regulatory proteins in the network is affected by nutrient signaling. In this study, we found that NtrX, one of the regulators of nitrogen metabolic response, can directly regulate the expression of several regulatory genes from the CtrA signaling network. Three sets of S. meliloti ntrX mutants, including the plasmid insertion strain, the depletion strain and the substitution of the 53rd aspartate (ntrXD53E) from a plasmid in the wild-type strain (Sm1021), showed similar cell division defects, such as slow growth, abnormal morphology of partial cells and delayed DNA synthesis. Transcript quantitative evaluation indicated that the transcription of genes such as ctrA and gcrA was up-regulated, while the transcription of genes such as dnaA and ftsZl was down-regulated in the insertion mutant and the strain of Sm1021 expressing ntrXD53E. Correspondingly, inducible transcription of ntrX activates the expression of dnaA and ftsZ1, but represses ctrA and gcrA in the depletion strain. The expression levels of CtrA and GcrA were confirmed by western blotting, which were consistent with the transcription data. The transcriptional regulation of these genes requires phosphorylation of the conserved 53rd aspartate in the NtrX protein. The NtrX protein binds directly to the promoter regions of ctrA, gcrA, dnaA and ftsZ1 by recognizing the characteristic sequence CAAN2-5TTG Our findings reveal that NtrX is a novel transcriptional regulator of the CtrA signaling pathway genes, and positively affects bacterial cell division, associated with nitrogen metabolism.IMPORTANCESinorhizobium meliloti infects the host alfalfa and induces formation of nitrogen-fixing nodules. Proliferation of rhizobia in plant tissues and cells is strictly controlled in the early stage of symbiotic interactions. However, the control mechanism is not very clear. Cell division of S. meliloti in the free-living state is regulated by the CtrA signaling network, but molecular mechanisms by which the CtrA system is associated with environmental nutrient signals (e.g., ammonia nitrogen) need to be further explored. This study demonstrates that NtrX, a regulator of nitrogen metabolism, required for symbiotic nodulation and nitrogen fixation by S. meliloti 1021, can act as a transcriptional regulator of the CtrA signaling system. It may link nitrogen signaling to cell cycle regulation in Rhizobium species.
Antenna modification leads to enhanced nitrogenase activity in a high light tolerant cyanobacterium
Authors: Bandyopadhyay Anindita , Ye Zi , Benedikty Zuzana , Trtilek Martin , Pakrasi Himadri B. 
Published: November 2021

AbstractBiological nitrogen fixation is an energy intensive process that contributes significantly towards supporting life on this planet. Among nitrogen-fixing organisms, cyanobacteria remain unrivaled in their ability to fuel the energetically expensive nitrogenase reaction with photosynthetically harnessed solar energy. In heterocystous cyanobacteria light-driven, photosystem I (PSI)-mediated ATP synthesis plays a key role in propelling the nitrogenase reaction. Efficient light transfer to the photosystems rely on phycobilisomes (PBS), the major antenna protein complexes. PBS undergo degradation as a natural response to nitrogen starvation. Upon nitrogen availability, these proteins are resynthesized back to normal levels in vegetative cells, but their occurrence and function in heterocysts remains inconclusive. Anabaena 33047 is a heterocystous cyanobacterium that thrives under high light, harbors higher amounts of PBS in its heterocysts and fixes nitrogen at higher rates compared to other heterocystous cyanobacteria. To assess the relationship between PBS in heterocysts and nitrogenase function, we engineered a strain that retains high amounts of the antenna proteins in its heterocysts. Intriguingly, under high light intensities the engineered strain exhibited unusually high rates of nitrogenase activity compared to the wild type. Spectroscopic analysis revealed altered PSI kinetics in the mutant, with increased cyclic electron flow around PSI, a route that contributes to ATP generation and nitrogenase activity in heterocysts. Retaining higher levels of PBS in heterocysts appears to be an effective strategy to enhance nitrogenase function in cyanobacteria that are equipped with the machinery to operate under high light intensities.ImportanceThe function of phycobilisomes, the large antenna protein complexes in heterocysts has long been debated. This study provides direct evidence of the involvement of these proteins in supporting nitrogenase activity in Anabaena 33047, a heterocystous cyanobacterium that has affinity for very high light intensities. This strain was previously known to be recalcitrant to genetic manipulation and hence despite its many appealing traits, remained largely unexplored. We developed a genetic modification system for this strain and generated a ΔnblA mutant that exhibited resistance to phycobilisome degradation upon nitrogen starvation. Physiological characterization of the strain indicated that PBS degradation is not essential for acclimation to nitrogen deficiency and retention of PBS is advantageous for nitrogenase function.
Comparative genomics on cultivated and uncultivated, freshwater and marine Candidatus Manganitrophaceae species implies their worldwide reach in manganese chemolithoautotrophy
Authors: Yu Hang , Chadwick Grayson L. , Lingappa Usha F. , Leadbetter Jared R. 
Published: November 2021

AbstractChemolithoautotrophic manganese oxidation has long been theorized, but only recently demonstrated in a bacterial co-culture. The majority member of the co-culture, Candidatus Manganitrophus noduliformans, is a distinct but not yet isolated lineage in the phylum Nitrospirota (Nitrospirae). Here, we established two additional MnCO3-oxidizing cultures using inocula from Santa Barbara (USA) and Boetsap (South Africa). Both cultures were dominated by strains of a new species, designated Candidatus Manganitrophus morganii. The next abundant members differed in the available cultures, suggesting that while Ca. Manganitrophus species have not been isolated in pure culture, they may not require a specific syntrophic relationship with another species. Phylogeny of cultivated Ca. Manganitrophus and related metagenome-assembled genomes revealed a coherent taxonomic family, Candidatus Manganitrophaceae, from both freshwater and marine environments and distributed globally. Comparative genomic analyses support this family being Mn(II)-oxidizing chemolithoautotrophs. Among the 895 shared genes were a subset of those hypothesized for Mn(II) oxidation (Cyc2 and PCC_1) and oxygen reduction (TO_1 and TO_2) that could facilitate Mn(II) lithotrophy. An unusual, plausibly reverse Complex 1 containing 2 additional pumping subunits was also shared by the family, as were genes for the reverse TCA carbon fixation cycle, which could enable Mn(II) autotrophy. All members of the family lacked genes for nitrification found in Nitrospira species. The results suggest that Ca. Manganitrophaceae share a core set of candidate genes for the newly discovered manganese dependent chemolithoautotrophic lifestyle, and likely have a broad, global distribution.ImportanceManganese (Mn) is an abundant redox-active metal that cycled in many of Earth’s biomes. While diverse bacteria and archaea have been demonstrated to respire Mn(III/IV), only recently have bacteria been implicated in Mn(II) oxidation dependent growth. Here, two new Mn(II)-oxidizing enrichment cultures originated from two continents and hemispheres were examined. By comparing the community composition of the enrichments and performing phylogenomic analysis on the abundant Nitrospirota therein, new insights are gleaned on cell interactions, taxonomy, and machineries that may underlie Mn(II)-based lithotrophy and autotrophy.
Impact of SARS-CoV-2 Vaccines on Covid-19 Incidence and Mortality in the United States
Authors: Fang Fang , Clemens John David , Zhang Zuo-Feng , Brewer Timothy F. 
Published: November 2021

ABSTRACTBackgroundDespite safe and effective vaccines to prevent Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) infections and disease, a substantial minority of the US remains resistant to getting vaccinated. It is imperative to know if expanding vaccination rates could reduce community-wide Coronavirus 2019 (COVID-19) disease, not just among those vaccinated.MethodsNegative binomial models were used to estimate associations between U.S. county-level vaccination rates and county-wide COVID-19 incidence and mortality between April 23rd and September 30th, 2021. A two-week lag and a four-week lag were introduced to assess vaccination rate impact on incidence and mortality, respectively. Stratified analyses were performed for county vaccination rates 40%, and before and after Delta became the dominant variant.FindingsAmong 3,070 counties, each percentage increase in population vaccination rates reduced county-wide COVID-19 incidence by 0·9% (relative risk (RR) 0. 9910 (95% CI: 0·9869, 0·9952)) and mortality by 1·9% (RR 0·9807 (95% CI: 0·9745, 0·9823)). Among counties with vaccination coverage >40%, each percentage increase in vaccination rates reduced COVID-19 disease by 1·5%, RR 0·9850 (95% CI: 0·9793, 0·9952) and mortality by 2·7% (RR 0·9727 (95% CI: 0·9632, 0·9823)). These associations were not observed among counties with <40% vaccination rates. Increasing vaccination rates from 40% to 80% would have reduced COVID-19 cases by 45·4% (RR 0·5458 (95% CI: 0·4335, 0·6873)) and deaths by 67·0% (RR 0·3305 (95% CI: 0·2230, 0·4898)). An estimated 5,989,952 COVID-19 cases could have been prevented and 127,596 lives saved had US population vaccination rates increased from 40% to 80%.InterpretationsIncreasing U.S. SARS-CoV-2 vaccination rates results in population-wide reductions in COVID-19 incidence and mortality. Furthermore, increasing vaccination rates above 40% has protective effects among non-vaccinated persons. Given ongoing vaccine hesitancy in the U.S., increasing vaccination rates could better protect the entire community and potentially reach herd immunity.FundingNational Cancer Institute
Extreme temperatures and mortality in 326 Latin American cities
Authors: Kephart Josiah L. , Sánchez Brisa N. , Moore Jeffrey , Schinasi Leah H. , Bakhtsiyarava Maryia , Ju Yang , Gouveia Nelson , Caiaffa Waleska T , Dronova Iryna , Arunachalam Saravanan , Roux Ana V. Diez , Rodríguez Daniel A. 
Published: November 2021

ABSTRACTBackgroundClimate change and urbanization are rapidly increasing human exposure to extreme ambient temperatures, yet few studies have examined the impact of temperature on mortality across Latin America, where 80% of residents live in urban areas.MethodsWe used distributed lag nonlinear conditional Poisson models to estimate city-specific associations between daily temperatures above (“heat”) and below (“cold”) each city-specific minimum mortality temperature and all-cause mortality, overall and stratified by age and cause of death. We estimated the percentage of total deaths attributable to heat or cold (excess death fraction [EDF]) and the difference in mortality per 1°C higher daily mean temperature above the 95th percentile of observed daily temperature.ResultsWe analyzed data from 326 cities in nine Latin American countries between 2002-2015, representing 15,431,532 deaths from 249 million residents. The EDF of total deaths from heat was 0.67% (95% confidence interval [CI] 0.58%, 0.74%), and from cold was 5.09% (95% CI 4.64%, 5.47%). EDFs from heat and cold were particularly high among individuals aged 65+ years (0.81% [95% CI 0.75%, 0.86%] and 6.82% [95% CI 6.41%, 7.18%], respectively). The relative risk of death per 1°C increase above the city-specific 95th percentile daily temperature was 1.057 (95% CI 1.046, 1.067).ConclusionsIn Latin American cities, a substantial proportion of deaths are attributable to non-optimal ambient temperatures. Older populations are particularly vulnerable. Marginal increases in observed hot temperatures are associated with steep increases in mortality risk. Projected increases in temperature from climate change may have a substantial impact on mortality.SIGNIFICANCE STATEMENTLatin America has a large population at risk of urban heat exposure, yet little is known about the linkages between ambient temperature and health in the region. We analyzed over 15 million deaths in 326 Latin American cities to characterize the relationship between ambient temperature and mortality, overall and by age and cause of death. We found that 5.75% of all deaths are associated with non-optimal temperatures, older individuals are particularly vulnerable, and cardiorespiratory deaths are especially affected. A single degree increase (1°C) in daily temperature was associated with a 5.7% higher mortality among hot days, suggesting that projected increases in temperature from climate change may have a substantial impact on mortality.
The Direct and Indirect Effects of a Global Pandemic on US Fishers and Seafood Workers
Authors: White Easton , Levine Jill , Moeser Amanda , Sorensen Julie 
Published: November 2021

AbstractThe United States’ seafood industry experienced major shifts in consumer demand and COVID-19 social-distancing restrictions starting in March 2020, when the early stages of the pandemic were unfolding. However, the specific effects on workers across seafood value chains are less well known. According to the US Centers for Disease Control and Protection (CDC), fishers and seafood workers face an increased risk of workplace exposure to COVID-19 given the close proximity to others in processing facilities and on fishing vessels, long work hours, and communal housing, living, and transportation arrangements associated with seasonal employment. To explore this hypothesis, and given a lack of data on the sector, we reviewed news articles, scientific articles, and white papers to identify the various effects of COVID-19 on US seafood workers and to track COVID-19 cases and outbreaks. Here, we show that most COVID-19 cases among seafood workers were reported during the summer of 2020 and during the beginning of 2021 with outbreaks primarily occurring in seafood processing. COVID-19 cases were documented throughout coastal areas, with Alaska experiencing the largest number of cases and outbreaks. Based on news reports, seafood workers were about twice as likely to contract COVID-19 as workers in other parts of the overall US food system. By examining news articles and scientific literature, we also documented several indirect effects of the pandemic. Social-distancing restrictions limited crew size and number of workers on processing lines, resulting in longer work hours and more physical and mental taxation. Economic consequences of the pandemic were reportedly a primary concern for fishers and aquaculture businesses, including changes in markets, supply, and demand, in addition to revenue loss, price fluctuations, supply chain issues, and labor shortages. Fewer outlets interviewed workers in seafood processing; however, concerns about workplace safety, contracting COVID-19, access to medical services, vaccination, and paid sick leave were all noted. We also highlight several inequities in COVID-19 responses within the seafood sector, both along racial and gender lines. Peer-reviewed studies and news coverage all point to diverse direct and indirect effects of the COVID-19 pandemic on workers across seafood value chains. The summary of these effects can serve as a foundation for future work on infection control and occupational outreach to workers in the seafood sector.
The sequences of 150,119 genomes in the UK biobank
Authors: Halldorsson Bjarni V. , Eggertsson Hannes P. , Moore Kristjan H.S. , Hauswedell Hannes , Eiriksson Ogmundur , Ulfarsson Magnus O. , Palsson Gunnar , Hardarson Marteinn T. , Oddsson Asmundur , Jensson Brynjar O. , Kristmundsdottir Snaedis , Sigurpalsdottir Brynja D. , Stefansson Olafur A. , Beyter Doruk , Holley Guillaume , Tragante Vinicius , Gylfason Arnaldur , Olason Pall I. , Zink Florian , Asgeirsdottir Margret , Sverrisson Sverrir T. , Sigurdsson Brynjar , Gudjonsson Sigurjon A. , Sigurdsson Gunnar T. , Halldorsson Gisli H. , Sveinbjornsson Gardar , Norland Kristjan , Styrkarsdottir Unnur , Magnusdottir Droplaug N. , Snorradottir Steinunn , Kristinsson Kari , Sobech Emilia , Jonsson Helgi , Geirsson Arni J. , Olafsson Isleifur , Jonsson Palmi , Pedersen Ole Birger , Erikstrup Christian , Brunak Søren , Ostrowski Sisse Rye ,   DBDS Genetic Consortium, Thorleifsson Gudmar , Jonsson Frosti , Melsted Pall , Jonsdottir Ingileif , Rafnar Thorunn , Holm Hilma , Stefansson Hreinn , Saemundsdottir Jona , Gudbjartsson Daniel F. , Magnusson Olafur T. , Masson Gisli , Thorsteinsdottir Unnur , Helgason Agnar , Jonsson Hakon , Sulem Patrick , Stefansson Kari 
Published: November 2021

AbstractWe describe the analysis of whole genome sequences (WGS) of 150,119 individuals from the UK biobank (UKB). This constitutes a set of high quality variants, including 585,040,410 SNPs, representing 7.0% of all possible human SNPs, and 58,707,036 indels. The large set of variants allows us to characterize selection based on sequence variation within a population through a Depletion Rank (DR) score for windows along the genome. DR analysis shows that coding exons represent a small fraction of regions in the genome subject to strong sequence conservation. We define three cohorts within the UKB, a large British Irish cohort (XBI) and smaller African (XAF) and South Asian (XSA) cohorts. A haplotype reference panel is provided that allows reliable imputation of most variants carried by three or more sequenced individuals. We identified 895,055 structural variants and 2,536,688 microsatellites, groups of variants typically excluded from large scale WGS studies. Using this formidable new resource, we provide several examples of trait associations for rare variants with large effects not found previously through studies based on exome sequencing and/or imputation.
Reversible regulation of Cas12a activities by AcrVA5-mediated acetylation and CobB-mediated deacetylation
Authors: Kang Xiaoman , Yin Lei , Zhuang Songkuan , Hu Tianshuai , Wu Zhile , Zhao Guoping , Chen Yijian , Xu Yong , Wang Jin 
Published: November 2021

AbstractThe clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR associated (Cas) system protects bacteria and archaea from the invasion of foreign genetic elements. To cope with the host CRISPR systems, phages have evolved many strategies, including the anti-CRISPR (Acr) proteins, to inactivate the Cas nucleases. Recently, it has been reported that the type V-A Cas12a effector can be acetylated and inactivated by AcrVA5, which is a GNAT-family acetyltransferase. However, it is unclear whether the host has any coping strategies to reactivate the defense system. Here we show that the AcrVA5-acetylated Cas12a can be deacetylated by bacterial deacetylase CobB, reactivating Cas12a for both in vitro cleavage of target DNA sequences and in vivo protection of the host from invasion of foreign nucleic acids. Therefore, this study not only shows the reversible regulation of Cas12a activities by post-translational modification but also reveals CobB as a secondary safeguard to bacterial CRISPR defense systems. In addition, we demonstrate that AcrVA5 is a wide-spectrum acetyltransferase, acetylating a large number of target proteins besides Cas12a, and the AcrVA5-acetylated targets can also be deacetylated by CobB.
Identification of diverse viruses associated with grasshoppers unveils phylogenetic congruence between hosts and viruses
Authors: Xu Yao , Jiang Jingyi , Lin Xiaoju , Shi Wangpeng , Cao Chuan 
Published: November 2021

AbstractLocusts and grasshoppers are one of the most dangerous agricultural pests. Environmentally benign microbial pesticides are increasingly desirable for controlling locust outbreaks in fragile ecosystems. Here we use metagenomic sequencing to profile the rich viral communities in 34 grasshopper species and report 322 viruses, including 202 novel species. Most of the identified viruses are related to other insect viruses and some are targeted by antiviral RNAi pathway, indicating they infect grasshoppers. Some plant/fungi/vertebrate associated viruses are also abundant in our samples. Our analysis of relationships between host and virus phylogenies suggests that the composition of viromes is closely allied with host evolution, and there is significant phylogenetic relatedness between grasshoppers and viruses from Lispiviridae, Partitiviridae, Orthomyxoviridae, Virgaviridae and Flaviviridae. Overall, this study is a thorough exploration of viruses in grasshoppers and provide an essential evolutionary and ecological context for host-virus interaction in Acridoidea.Author SummaryLocusts are the most destructive migratory pest in the world and continue to cause massive damages that endanger food security and threaten millions of people in 21st century. While chemical pesticides are still heavily relied on, biological pesticides developed from natural pathogens offer a reliable, less harmful alternative for controlling locust outbreaks in fragile ecosystems. Unfortunately, little is known about natural pathogens infecting this pest. In this study, we profile the viral communities in 34 grasshopper species include some major swarming species. While we identified as many as 202 novel viral species associated with grasshoppers, some of them are of potential to be developed as biocontrol agents. Our analysis of relatedness of phylogenies of grasshoppers and associated viruses helps to shed light on the eco-evolutionary interactions between insects and viruses. This work provides a valuable dataset of both academic and applied interest.
Stimulation of immunity-linked genes by membrane disruption is linked to Golgi function and the ARF-1 GTPase
Authors: Fanelli Matthew J. , Welsh Christofer M. , Lui Dominique S. , Smulan Lorissa J. , Walker Amy K. 
Published: November 2021

AbstractImmunity-linked genes (ILGs) are activated by pathogens but also may respond to imbalances in lipids. Why pathogen attack and metabolic changes both impact ILG activation is unclear. We find that ILGs are activated when membrane phosphatidylcholine ratios change in secretory organelles inC. elegans. RNAi targeting of the ADP-ribosylation factor ARF-1, which disrupts the Golgi, also activates ILG expression, suggesting that activation of this membrane stress response could occur outside the ER. Our data argue that ILG upregulation is a coordinated response to changes in trafficking resulting from intrinsic cues (changes in membrane lipids) or extrinsic stimulation (increased secretion during immune response). Indeed, a focused RNAi screen of ILGs uncovered defects in secretion of two GFP reporters as well as accumulation of a pathogen-responsive CUB-domain fusion protein. These results also suggests that genes shared between the classical pathogen responses and lipid stress may act to counteract stress on secretory function.TeaserPathogen response genes are also activated by lipid imbalances, which we suggest occurs because both processes put stress on the secretory pathway.