bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbial Community Dynamics Provide Evidence for Hypoxia During a Coral Reef Mortality Event
Authors: Doyle Shawn M. , Self Miabel J. , Hayes Joseph , Shamberger Kathryn E.F. , Correa Adrienne M.S. , Davies Sarah W. , Santiago-Vázquez Lory Z. , Sylvan Jason B. 
Published: February 2022

ABSTRACTIn July 2016, a severe coral reef invertebrate mortality event occurred approximately 200km southeast of Galveston, Texas at the East Flower Garden Bank wherein upwards of 80% of corals in a 0.06 km2 area died. Based on surveys of dead corals and other invertebrates shortly after this mortality event, responders hypothesized that localized hypoxia was the most likely direct cause. However, no dissolved oxygen data were available to test this hypothesis because oxygen is not continuously monitored within the Flower Garden Banks sanctuary. Here we quantify microbial plankton community diversity based on four cruises over two years at the Flower Garden Banks, including a cruise just 5-8 days after the mortality event was first observed. In contrast with observations collected during baseline conditions, microbial plankton communities in the thermocline were differentially enriched with taxa known to be active and abundant in oxygen minimum zones or that have known adaptations to oxygen limitation shortly after the mortality event (e.g. SAR324, Thioglobaceae, Nitrosopelagicus, and Thermoplasmata MGII). Unexpectedly, these enrichments were not localized to the East Bank, but were instead prevalent across the entire study area, suggesting there was a widespread depletion of dissolved oxygen concentrations in the thermocline around the time of the mortality event. Hydrographic analysis revealed the southern East Bank coral reef (where the localized mortality event occurred) was uniquely within the thermocline at this time. Our results demonstrate how temporal monitoring of microbial communities can be a useful tool to address questions related to past environmental events.IMPORTANCEIn the northwestern Gulf of Mexico in July 2016, upwards of 80% of corals in a small area of the East Flower Garden Bank coral reef suddenly died without warning. Oxygen depletion is believed to have been the cause. However, there was considerable uncertainty as no oxygen data is available from the time of the event. Microbes are sensitive to changes in oxygen and can be used as bioindicators of oxygen loss. In this study, we analyze microbial communities in water samples collected over several years at the Flower Garden Banks, including shortly after the mortality event. Our findings indicate that compared to normal conditions, oxygen depletion was widespread in the deep-water layer during the mortality event. Hydrographic analysis of water masses further revealed some of this low oxygen water likely upwelled onto the coral reef.
Construction of a constitutively active type III secretion system for heterologous protein secretion
Authors: Liang Julie Ming , Burdette Lisa Ann , Wong Han Teng , Tullman-Ercek Danielle 
Published: February 2022

AbstractProteins comprise a multibillion-dollar industry in enzymes and therapeutics, but bacterial protein production can be costly and inefficient. Proteins of interest (POIs) must be extracted from lysed cells, purified, and resolubilized. The Salmonella pathogenicity island 1 type III secretion system (T3SS) is a protein secretion complex in Salmonella that has been engineered to secrete heterologous proteins and addresses the problems associated with bacterial protein production. However, the current best practices method of T3SS pathway activation for secretion is not ideal for industrial scaleup. Previously, the T3SS was activated by plasmid-based overexpression of the T3SS transcriptional regulator, hilA, which requires the addition of a small molecule inducer to the culture media and adds significant cost to the production media. Plasmid-based expression is also subject to instability in large-scale fermentation. Here, we show that we can constitutively activate the T3SS by modulating the upstream transcriptional regulator, hilD, either through knocking out hilE, a repressor of HilD, or by adding transcriptional fusions to hilD. Finally, we combine the two most promising genomic modifications to build a constitutively active T3SS capable of secreting a range of heterologous proteins at titers comparable to those reported with synthetic induction of hilA. These improvements further our goal of making an industrially competitive protein production strain that reduces the challenges associated with plasmid induction and maintenance.ImportanceProteins are used in our everyday lives as therapeutics (insulin), industrial enzymes (laundry detergent), and bio-based materials (spider silk). Current industrial protein production in bacteria is costly because it requires purification of the target protein from the other proteins inside the cell. We solve this problem by engineering the Salmonella pathogenicity island 1 type III secretion system (T3SS) to export the target protein into the cell growth media. This makes the protein purification process more efficient and cheaper. However, this system currently requires an expensive inducer reagent to activate it which significantly increases the cost of the production media. We show here the creation of a constitutively active T3SS, meaning the T3SS pathway is always on. In doing so, we successfully created a Salmonella strain that eliminates the need for the inducer reagent and exports proteins at levels comparable to the inducer-activated system, ultimately reducing the cost of T3SS protein production.
Rapid genome surveillance of SARS-CoV-2 and study of risk factors using shipping container laboratories and portable DNA sequencing technology
Authors: Bilooei Sara Farahi , Jovicevic Dejana , Iranzadeh Arash , Thomas Anthony , Muscat Ivan , Mpofu Cynthia , Steiner Helene , Meany Thomas 
Published: February 2022

AbstractIn this paper we report on genome sequencing of 154 SARS-CoV-2 samples between June and July 2021 (Summer outbreak) in the Bailiwick of Jersey, a UK channel island. We have analysed extensive data collected on 598,155 RT-qPCR tests that identified 8,950 positive cases as part of public health surveillance from September 2020 to August 2021. Our study implemented an amplicon-based sequencing approach using the Oxford Nanopore Technology (ONT) portable device. This revealed the emergence of twelve AY sublineages and were clustered into the Delta sub-clades 21I and 21J. This was integrated alongside an existing RT-qPCR diagnostic laboratory to provide a sample-to-sequence turnaround time of approximately 30 hours with significant scope for optimisation. Owing to the geographic remoteness of the island from large scale sequencing infrastructure, this presents an opportunity to provide policy makers with near real-time sequencing findings. Our analysis suggests that age and sex remained a substantial risk factor for mortality. We observe viral loads are higher in advanced ages and unvaccinated individuals. The median age of SARS-CoV-2 positive individuals was higher during winter than the summer outbreak, and the contact tracing program showed that younger individuals stayed positive for longer.
Predictors of longitudinal cognitive ageing from age 70 to 82 including APOE e4 status, early-life and lifestyle factors
Authors: Corley Janie , Conte Federica , Harris Sarah E. , Taylor Adele M. , Redmond Paul , Russ Tom C. , Deary Ian J. , Cox Simon R. 
Published: February 2022

AbstractDiscovering why some people’s cognitive abilities decline more than others is a key challenge for cognitive ageing research. The most effective strategy may be to address multiple risk factors from across the life-course simultaneously in relation to robust longitudinal cognitive data. We conducted a 12-year follow-up of 1091 (at age 70) men and women from the longitudinal Lothian Birth Cohort 1936 study. Comprehensive repeated cognitive measures of visuospatial ability, processing speed, memory, verbal ability, and a general cognitive factor, were collected over five assessments (age 70, 73, 76, 79, and 82 years) and analysed using multivariate latent growth curve modelling. Fifteen life-course variables were used to predict variation in cognitive ability levels at age 70 and cognitive slopes from age 70 to 82. Only APOE e4 carrier status was found to be reliably informative of general- and domain-specific cognitive decline, despite there being many life-course correlates of cognitive level at age 70. APOE e4 carriers had significantly steeper slopes across all three fluid cognitive domains compared with non-carriers, especially for memory (β = −0.234, P< 0.001) and general cognitive function (β = −0.246, P<0.001), denoting a widening gap in cognitive functioning with increasing age. Our findings suggest that when many other candidate predictors of cognitive ageing slope are entered en masse, their unique contributions account for relatively small proportions of variance, beyond variation in APOE e4 status. We conclude that APOE e4 status is important for identifying those at greater risk for accelerated cognitive ageing, even among ostensibly healthy individuals.
Deficiency of the RNA-binding protein Cth2 extends yeast replicative lifespan by alleviating its repressive effects on mitochondrial function
Authors: Patnaik Praveen K. , Beaupere Carine , Barlit Hanna , Romero Antonia María , Tsuchiya Mitsuhiro , Muir Michael , Martínez-Pastor María Teresa , Puig Sergi , Kaeberlein Matt , Labunskyy Vyacheslav M. 
Published: February 2022

AbstractIron dyshomeostasis contributes to aging, but little information is available about the molecular mechanisms. Here, we provide evidence that, in Saccharomyces cerevisiae, aging is associated with altered expression of genes involved in iron homeostasis. We further demonstrate that defects in the conserved mRNA-binding protein Cth2, which controls stability and translation of mRNAs encoding iron-containing proteins, increase lifespan by alleviating its repressive effects on mitochondrial function. Mutation of the conserved cysteine residue in Cth2 that inhibits its RNA-binding activity is sufficient to confer longevity, whereas Cth2 gain-of-function shortens replicative lifespan. Consistent with its function in RNA degradation, we demonstrate that Cth2 deficiency relieves Cth2-mediated post-transcriptional repression of nuclear-encoded components of the electron transport chain. Our findings uncover a major role of the RNA-binding protein Cth2 in the regulation of lifespan and suggest that modulation of iron starvation signaling can serve as a target for potential aging interventions.
Association Mapping Across a Multitude of Traits Collected in Diverse Environments Identifies Pleiotropic Loci in Maize
Authors: Mural Ravi V. , Sun Guangchao , Grzybowski Marcin , Tross Michael C. , Jin Hongyu , Smith Christine , Newton Linsey , Andorf Carson M. , Woodhouse Margaret R. , Thompson Addie M. , Sigmon Brandi , Schnable James C. 
Published: February 2022

ABSTRACTClassical genetic studies have identified many cases of pleiotropy where mutations in individual genes alter many different phenotypes. Quantitative genetic studies of natural genetic variants frequently examine one or a few traits, limiting their potential to identify pleiotropic effects of natural genetic variants. Widely adopted community association panels have been employed by plant genetics communities to study the genetic basis of naturally occurring phenotypic variation in a wide range of traits. High-density genetic marker data – 18M markers – from two partially overlapping maize association panels comprising 1,014 unique genotypes grown in field trials across at least seven US states and scored for 162 distinct trait datasets enabled the identification of of 2,154 suggestive marker-trait associations and 697 confident associations in the maize genome using a resampling-based genome-wide association strategy. The precision of individual marker-trait associations was estimated to be three genes based a reference set of genes with known phenotypes. Examples were observed of both genetic loci associated with variation in diverse traits (e.g. above-ground and below-ground traits), as well as individual loci associated with the same or similar traits across diverse environments. Many significant signals are located near genes whose functions were previously entirely unknown or estimated purely via functional data on homologs. This study demonstrates the potential of mining community association panel data using new higher density genetic marker sets combined with resampling-based genome-wide association tests to develop testable hypotheses about gene functions, identify potential pleiotropic effects of natural genetic variants, and study genotype by environment interaction.
A TREX1 model reveals double-strand DNA preference and inter-protomer regulation
Authors: Hemphill Wayne O. , Hollis Thomas , Salsbury Freddie R. , Perrino Fred W. 
Published: February 2022

AbstractThe TREX1 3’ → 5’ exonuclease degrades DNAin vivoto prevent chronic immune activation through the cGAS-STING pathway. TREX1 degrades ss- and dsDNA containing a free 3’-hydroxyl, but the precise nature of immune-activating DNA remains an open question. The TREX1 homodimer structure is critical for exonuclease activity with amino acids from one protomer acting across the dimer interface contributing to catalysis in the opposing protomer. The unique TREX1 obligate homodimer structure suggests an intricate connection between the TREX1 protomers that has yet to be explained. We used biochemical assays, molecular dynamics simulations, and kinetic modeling to determine relative TREX1 affinities for ss- and dsDNA and to interrogate inter-protomer communication within the TREX1 homodimer. These new findings indicate that TREX1 is a semi-processive exonuclease with at least a 20-fold greater affinity for dsDNA than for ssDNA. Furthermore, we find extensively correlated dynamics between TREX1 protomers revealing newly identified substrate interactions in the TREX1 enzyme. These data indicate that TREX1 has evolved as a semi-processive exonuclease with a likelyin vivofunction to degrade dsDNA, where the TREX1 homodimer structure facilitates a mechanism for efficient binding and catabolism of dsDNA. These studies identify previously unrecognized regions of the TREX1 enzyme involved in DNA interactions, and our findings contribute to an emerging model of TREX1 exonuclease activity.
Horizontal gene transfer increases microbiome stability
Authors: Coyte K. Z. , Stevenson C. , Knight C. G. , Harrison E. , Hall J. P. J. , Brockhurst M. A. 
Published: February 2022

AbstractGenes encoding resistance to stressors, such as antibiotics or environmental pollutants, are widespread across microbiomes, often encoded on mobile genetic elements. Yet despite their prevalence, the impact of resistance genes and their mobility upon the dynamics of microbial communities remains largely unknown. Here we develop eco-evolutionary theory to explore how resistance genes alter the stability of diverse microbiomes. We show that adding resistance genes to a microbiome typically increases its overall stability, particularly for mobile resistance genes with high transfer rates that efficiently spread resistance throughout the community. However, the impact of resistance genes upon the stability of individual taxa varies depending upon the mobility of the resistance gene and the network of ecological interactions within the community. Non-mobile resistance genes can benefit susceptible taxa in cooperative communities, yet damage those in competitive communities. Moreover, whilst the transfer of mobile resistance genes generally increases the stability of previously susceptible recipient taxa to perturbation, it can, counterintuitively, decrease the stability of the originally resistant donor species. We confirmed these theoretical predictions experimentally using competitive soil microcosm communities. Here the stability of a susceptible microbial community to perturbation was increased by adding mobile resistance genes encoded on conjugative plasmids but was decreased when these same genes were encoded on the chromosome. Together these findings highlight the importance of horizontal gene transfer in driving the eco-evolutionary dynamics of diverse microbiomes.
The lipid raft-associated protein stomatin is required for accumulation of dectin-1 in the phagosomal membrane and for full activity of macrophages against Aspergillus fumigatus
Authors: Goldmann Marie , Schmidt Franziska , Cseresnyés Zoltán , Orasch Thomas , Jahreis Susanne , Hartung Susann , Figge Marc Thilo , von Lilienfeld-Toal Marie , Heinekamp Thorsten , Brakhage Axel A. 
Published: February 2022

AbstractAlveolar macrophages are among the first cells to come into contact with inhaled fungal conidia of the human pathogenic fungus Aspergillus fumigatus. In lung alveoli, they contribute to phagocytosis and elimination of conidia. As a counter defense, conidia contain a grey-green pigment allowing them to survive in phagosomes of macrophages for some time. Previously, we showed that this conidial pigment interferes with the formation of flotillin-dependent lipid-rafts in the phagosomal membrane thereby preventing the formation of functional phagolysosomes. In this study, the role of the lipid raft-associated protein stomatin in macrophages during antifungal defense was investigated. To determine the function of this integral membrane protein, a stomatin-deficient macrophage cell line was generated by CRISPR/Cas9 gene editing. Immunofluorescence and flow cytometry revealed that stomatin contributes to the phagocytosis of conidia and is important for recruitment of both the β-glucan receptor dectin-1 and the vATPase to the membrane of phagosomes. In the stomatin knockout cell line, fusion of phagosomes and lysosomes was reduced when infected with pigmentless pksP conidia. Thus, our data suggest that stomatin is involved in maturation of phagosomes via fostering fusion of phagosomes with lysosomes.
Ex Vivo Herpes Simplex Virus Reactivation Involves a DLK-Dependent Wave of Lytic Gene Expression that is Independent of Histone Demethylase Activity and Viral Genome Synthesis
Authors: Whitford Abigail L. , Clinton Corinne A. , Kennedy E.B. Lane , Dochnal Sara A. , Suzich Jon B. , Cliffe Anna R. 
Published: February 2022

AbstractHerpes Simplex virus-1 (HSV-1) maintains a lifelong latent infection in neurons and periodically reactivates, resulting in the production of infectious virus. The exact cellular pathways that induce reactivation are not understood. In primary neuronal models of HSV latency, the cellular protein Dual Leucine Zipper kinase (DLK) has been found to initiate a wave of viral gene expression known as Phase I. Phase I occurs independently of both viral DNA replication and the activities of histone demethylase enzymes required to remove repressive heterochromatin modifications associated with the viral genome. Here we investigated whether Phase-I like gene expression occurs in ganglia reactivated from infected mice. Using the combined trigger of explant-induced axotomy and inhibition of PI3K signaling, we found that HSV lytic gene expression was induced rapidly from both sensory and sympathetic neurons.Ex vivoreactivation involved a wave of viral late gene expression that occurred independently of viral genome synthesis and histone demethylase activity, and preceded the detection of infectious virus. Importantly, we found that DLK was required for the initial induction of lytic gene expression. These data confirm the essential role of DLK in inducing HSV-1 gene expression from the heterochromatin associated genome and further demonstrate that HSV-1 gene expression during reactivation occurs via mechanisms that are distinct from lytic replication.
Reduced polymerase pausing compensates for increased chromatin accessibility in the aging liver
Authors: Bozukova Mihaela , Grbavac Dora , Nikopoulou Chrysa , Tessarz Peter 
Published: February 2022

ABSTRACTRegulation of gene expression is tightly linked to the organization of the mammalian genome. With age, chromatin alterations occur on all levels of genome organization, accompanied by changes in the gene expression profile. However, little is known about the changes on the level of transcriptional regulation with age. Here, we used a multi-omic approach and integrated ATAC-, RNA- and NET-seq to identify age-related changes in the chromatin landscape of murine liver and to investigate how these are linked to transcriptional regulation. We provide the first systematic inventory of the connection between aging, chromatin accessibility and transcriptional regulation in a whole tissue. We observe that aging in murine liver is accompanied by an increase in chromatin accessibility at promoter regions of protein-coding genes. Yet, although promoter accessibility is a requirement for transcription, the increased accessibility does not result in enhanced transcriptional output. Instead, aging is accompanied by a decrease of promoter-proximal pausing of RNA polymerase II (Pol II). We propose that these changes in transcriptional regulation are due to a reduced stability of the pausing complex and may represent a mechanism to compensate for the age-related increase in chromatin accessibility in order to prevent aberrant transcription.
Rif-Correct, a software tool for bacterial mRNA half-life estimation
Authors: Aretakis James R. , Schrader Jared M. 
Published: February 2022

AbstractBackgroundGenome-wide measurement of bacterial mRNA lifetimes using the antibiotic rifampicin has provided new insights into the control of bacterial mRNA decay. However, for long polycistronic mRNAs, the estimation of mRNA half-life can be confounded with transcriptional runoff caused by rifampicin’s inhibition of initiating RNA polymerases, and not elongating RNA polymerases.ResultsWe present the Rif-correct software package, a free open-source tool that uses transcriptome models of transcript architecture to allow for more accurate mRNA half-life estimates that account for the transcriptional runoff. Rif-correct is implemented as a customizable python script that allows for users to control all the analysis parameters to achieve improved mRNA half-life estimates.ConclusionsRif-correct is the first free open-source computational analysis pipeline for Rif-seq dataset mRNA half-life estimation. It is simple to run, fast, and easy to run with a detailed instruction manual and example datasets.
Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole
Authors: Zhao Jierui , Bui Mai Thu , Ma Juncai , Künzl Fabian , De La Concepcion Juan Carlos , Chen Yixuan , Petsangouraki Sofia , Mohseni Azadeh , Leon Marta Garcia , Gomez Marta Salas , Giannini Caterina , Gwennogan Dubois , Kobylinska Roksolana , Clavel Marion , Schellmann Swen , Jaillais Yvon , Friml Jiri , Kang Byung-Ho , Dagdas Yasin 
Published: February 2022

AbstractAutophagosomes are double-membraned vesicles that traffic harmful or unwanted cellular macromolecules to the vacuole for recycling. Although autophagosome biogenesis has been extensively studied, mechanisms of autophagosome maturation, i.e., delivery and fusion with the vacuole, remain largely unknown in plants. Here, we have identified an autophagy adaptor, CFS1, that directly interacts with the autophagosome marker ATG8 and localizes on both membranes of the autophagosome. Autophagosomes form normally in Arabidopsis thaliana cfs1 mutants, but their delivery to the vacuole is disrupted. CFS1’s function is evolutionarily conserved in plants as it also localizes to the autophagosomes and plays a role in autophagic flux in the liverwort Marchantia polymorpha. CFS1 regulates autophagic flux by connecting autophagosomes with the ESCRT-I component VPS23, leading to the formation of amphisomes. Disrupting the VPS23-CFS1 interaction affects autophagic flux and renders plants sensitive to starvation stress. Altogether, our results reveal a deeply conserved mechanism of vacuolar delivery in plants that is mediated by amphisomes.