bluuebunny/crossref_metadata_2025_split huggingface dataset:
Taxonomic assessment of two wild house mouse subspecies using whole-genome sequencing
Authors: Lawal Raman Akinyanju , Mathis Verity L. , Barter Mary E. , Charette Jeremy R. , Garretson Alexis , Dumont Beth L. 
Published: June 2022

AbstractHouse mice (Mus musculus) are comprised of three primary subspecies. A large number of secondary subspecies have also been suggested on the basis of divergent morphology and molecular variation at limited numbers of markers. While the phylogenetic relationships among the primary M. musculus subspecies are well-defined, the relationships among the secondary subspecies, and their relationships to primary subspecies, remain poorly understood. Here, we integrate de novo genome sequencing of museum-stored specimens of house mice from one secondary subspecies (M. m. bactrianus) and publicly available genome sequences of house mice previously characterized as M. m. helgolandicus, with whole-genome sequences from diverse representatives of the three primary house mouse subspecies. We show that mice assigned to the secondary M. m. bactrianus and M. m. helgolandicus subspecies are not genetically differentiated from the contemporary M. m. castaneus and M. m. domesticus, respectively. Overall, our work suggests that the M. m. bactrianus and M. m. helgolandicus subspecies are not well-justified taxonomic entities, emphasizing the importance of leveraging whole-genome sequence data to inform subspecies designations. Additionally, our investigation has established experimental procedures for generating whole-genome sequences from air-dried museum specimens and provides key genomic resources to inform future genomic investigations of wild mouse diversity.
Testing the Growth Rate and Temperature Compensation Hypotheses in Marine Bacterioplankton
Authors: Givati Shira , Yang Xingyu , Sher Daniel , Rahav Eyal 
Published: June 2022

SummaryTwo different hypotheses have been raised as to how temperature affects resource allocation in microorganisms. The translation-compensation hypothesis (TCH) predicts that the increase in enzymatic efficiency with temperature results in fewer required ribosomes per cell and lower RNA:protein ratio. In contrast, the growth rate hypothesis (GRH) predicts that increasing growth rate with temperature requires more ribosomes and hence a higher cellular RNA:protein. We tested these two hypotheses in lab cultures ofProchlorococcusandAlteromonasas well as over an annual cycle in the Eastern Mediterranean Sea. The RNA:protein ofAlteromonasmostly decreased with temperature in accordance with the TCH, while that ofProchlorococcusincreased with temperature, as predicted by the GRH. No support was found for either hypotheses in surface waters from the Eastern Mediterranean, whereas the fraction of phosphorus in RNA was positively correlated with per-cell bacterial production in the deep chlorophyll maximum, supporting the GRH in this niche. A considerable part of the cellular phosphorus was not allocated to RNA, DNA, phospholipids or polyphosphate, raising the question which cellular molecules contain these P reserves. While macromolecular quotas differed significantly between laboratory cultures and field samples, these were connected through a power law, suggesting common rules of resource allocation.Originality-Significance statementWe investigated whether the translation-compensation hypothesis (TCH) or growth rate hypothesis (GRH) affect the macromolecular composition and phosphorus allocation in both lab cultures ofProchlorococcusandAlteromonasas well as in seawater with natural microbial communities. Our results highlight that the TCH and GRH may each be applicable to different organisms (autotroph or heterotroph), physiological states or environmental conditions. Testing the applicability of theoretical models such as the TCH and GRH in lab cultures and field samples is an important step toward mechanistic models of bacterial physiology. This is especially important to our understanding of how bacterioplankton allocate resources in response to changes in environmental conditions such as temperature and nutrient stress, which are likely to expand due to the predicted global changes.
Genomic regions insertion and deletion in Monkeypox virus causing multi-country outbreak-2022
Authors: Desingu Perumal Arumugam , Nagarajan K. 
Published: June 2022

AbstractThe genetic diversity and evolutionary origin of the Monkeypox virus (MPXV) that is currently creating a multi-country outbreak-2022 is not fully understood. Here we report that the MPXVs that cause outbreak-2022 (MPXVs-2022) have deletion/insertion of ∼500 to 2000bp nucleotide in multiple genomic regions. Our analyses revealed that MPXVs-2022 are very close to the West African Clade of MPXVs (WA-MPXVs) that caused the Outbreak in Nigeria in 2017-2018. Furthermore, we classified the WA-MPXVs detected before 2017 that could not be transmitted from human-to-human as WA-MPXVs-I and WA-MPXVs detected after 2017 that could be transmitted from human-to-human as WA-MPXVs-II (including MPXVs-2022), and human-to-human transmissible Central African MPXVs (CA-MPXV) remained as a separate clade. Overall our results suggest that although WA-MPXVs-II are almost identical to WA-MPXVs-I throughout the genome and two large genomic insertions (∼500, 2000bp size insertion), they differ from WA-MPXVs-I in 5’-inverted terminal repeat (5’-ITR) (deletion of the last-2000bp-5’-ITR) and 13 proteins that of CA-MPXVs, and the presence of seven unique proteins in WA-MPXVs-II is likely to be a significant cause of outbreak-2022. This study shed light on the genetic diversity and evolutionary origin of MPXVs causing outbreak-2022.
PipeIT2: A tumor-only somatic variant calling workflow for Molecular Diagnostic Ion Torrent sequencing data
Authors: Schnidrig Desiree , Garofoli Andrea , Benjak Andrej , Rätsch Gunnar , Rubin Mark A. ,   SOCIBP consortium, Piscuoglio Salvatore , Ng Charlotte K. Y. 
Published: June 2022

ABSTRACTPrecision oncology relies on the accurate identification of somatic mutations in cancer patients. While the sequencing of the tumoral tissue is frequently part of routine clinical care, the healthy counterparts are rarely sequenced. We previously published PipeIT, a somatic variant calling workflow specific for Ion Torrent sequencing data enclosed in a Singularity container. PipeIT combines user-friendly execution, reproducibility and reliable mutation identification, but relies on matched germline sequencing data to exclude germline variants. Expanding on the original PipeIT, here we describe PipeIT2 to address the clinical need to define somatic mutations in the absence of germline control. We show that PipeIT2 achieves a >95% recall for variants with variant allele fraction >10%, reliably detects driver and actionable mutations and filters out most of the germline mutations and sequencing artifacts. With its performance, reproducibility and ease of execution, PipeIT2 is a valuable addition to molecular diagnostics laboratories.
Leaf specific overexpression of a mitochondrially-targeted glutamine synthetase in tomato increased assimilate export resulting in earlier fruiting and elevated yield
Authors: Vallarino José G. , Shameer Sanu , Zhang Youjun , Ratcliffe R. George , Sweetlove Lee J. , Fernie Alisdair R. 
Published: June 2022

ABSTRACTTo identify potential strategies for increasing the efficiency of tomato leaf metabolism, with a focus on the links between nitrogen/carbon metabolism, we explored a diel Flux Balance Analysis (FBA) model of a source leaf in which the metabolic output was varied up to the theoretically-achievable maximum. We noticed a potentially interesting switch in the use of glutamine synthetase (GS) isoforms –from the chloroplast isoform to the mitochondrial one- for nitrogen assimilation. To further explore this prediction, we characterized transgenic tomato plants over-expressing two tomato GS genes, GS1 and GS2, targeted to mitochondria. Both sets of transgenic plants were characterized as displaying faster growth rate, early flowering and increased fruit yield. In leaves, metabolomic profiling and enzyme activity analysis pointed that GS activity in mitochondrial plays a role in increasing the intracellular synthesis and subsequent export of sugar. Consistent with these changes, higher sucrose concentration in leaf exudates and reduced activities of enzymes involved in leaf starch synthesis were observed. Moreover, mitochondrial GS activity affected chloroplast redox status in a manner that modulated photorespiration and nitrogen metabolism. The combined data reveal the influence of mitochondrial GS activity on both foliar carbon/nitrogen balance and regulation of source-sink metabolism in tomato plants.
Plant-herbivore interactions: experimental demonstration of genetic variability in plant-plant signaling
Authors: Estarague Aurélien , Violle Cyrille , Vile Denis , Hany Anaïs , Martino Thibault , Moulin Pierre , Vasseur François 
Published: June 2022

AbstractPlant-herbivore interactions mediated by plant-plant signaling were documented in different species. Here, we tested if herbivore foraging activity on plants was influenced by plant’s prior contact with a damaged plant and if the effect of such plant-plant signaling was variable across genotypes.We filmed snails during one hour on two plants differing only in a prior contact with a damaged plant or not. We replicated eight times the experiment on 113 natural genotypes of Arabidopsis thaliana. We recorded snails’ first choice, and measured its first duration on a plant, the proportion of time spent on both plants and leaf consumption.On average, snails spent more time on plants that experienced a prior contact with a damaged plant, and consumed them more. However, plant-plant signaling effect on snail behavior was variable across genotypes. Genome-wide association studies revealed that a small number of genetic polymorphisms related to stress coping ability and jasmonate pathway explained this variation.Plant-plant signaling modified the foraging activity of herbivores in A. thaliana. Depending on the plant genotype, plant-plant signaling made undamaged plants more repulsive or attractive to snails. This finding questions the theoretical basement of the evolution of plant-herbivore interactions mediated by plant-plant signaling.HighlightPlant-plant signaling differently affects snail foraging activity depending on genetic variations in A.thaliana. These findings question the theoretical basement of the evolution of plant-herbivore interactions mediated by plant-plant signaling.
Rieske FeS overexpression in tobacco provides increased abundance and activity of Cytochromeb6f
Authors: Heyno Eiri , Ermakova Maria , Lopez-Calcagno Patricia E. , Woodford Russell , Brown Kenny L. , Matthews Jack S. A. , Osmond Barry , Raines Christine A. , Caemmerer Susanne von 
Published: June 2022

AbstractPhotosynthesis is fundamental for plant growth and yield. The Cytochromeb6fcomplex catalyses a rate-limiting step in thylakoid electron transport and therefore represents an important point of regulation of photosynthesis. Here we show that overexpression of a single core subunit of Cytochromeb6f, the Rieske FeS protein, led to up to a 40% increase in the abundance of the complex inNicotiana tabacum(tobacco) and was accompanied by an enhancedin vitroCytochromefactivity, indicating a full functionality of the complex. Analysis of transgenic plants overexpressing Rieske FeS by the light-induced fluorescence transients technique revealed a more oxidised primary quinone acceptor of Photosystem II (QA) and plastoquinone pool and a faster electron transport from the plastoquinone pool to Photosystem I upon changes in irradiance, compared to control plants. A faster establishing of qE, the energy-dependent component of non-photochemical quenching, in transgenic plants suggested a more rapid build-up of the transmembrane proton gradient, also supporting the increasedin vivoCytochromeb6factivity. However, there was no consistent increase in steady-state rates of electron transport or CO2assimilation in plants overexpressing Rieske FeS grown in either laboratory conditions or in field trials, suggesting that thein vivoactivity of the complex was only transiently increased upon changes in irradiance. Our results show that overexpression of Rieske FeS in tobacco enhances abundance of functional Cytochromeb6fand electron transport capacity and may have a potential to increase plant productivity if combined with other traits.One-sentence summaryIncreased abundance of Cytochromeb6fcomplex leads to transient increases in photosynthetic electron transport rate in tobacco.
Efficient Modification and Preparation of Circular DNA for Expression in Cell Culture
Authors: Oliynyk Roman Teo , Church George M. 
Published: June 2022

AbstractDNA plasmids are an essential tool for delivery and expression of RNAs and proteins in cell culture experiments. The preparation of plasmids typically involves a laborious process of bacterial cloning, validation, and purification. While the expression plasmids can be designed and ordered from the contract manufacturers, the cost may be prohibitive when a large number of plasmids is required. We have developed an efficient fully synthetic method and protocol that enables the production of circularized DNA containing expression elements ready for transfection in as little as 3 hours, thereby eliminating the bacterial cloning steps. The protocol describes how to take a linear double-stranded DNA fragment and efficiently circularize and purify this DNA fragment with minimal hands-on time. As proof of the principle, we applied Circular Vector expressing engineered prime editing guide RNA (epegRNA) in cell culture, and demonstrated matching and even exceeding performance of this method as compared to guides expressed by plasmids. The method is not limited to gene editing and its speed of preparation, low cost, and ease of use will make it a useful tool in a variety of applications requiring the expression of short RNAs and proteins.
The immunodominant protein P116 extracts cholesterol and other essential lipids
Authors: Sprankel Lasse , Vizarraga David , Martín Jesús , Manger Sina , Meier-Credo Jakob , Marcos Marina , Julve Josep , Rotllan Noemi , Scheffer Margot P. , Escolà-Gil Joan Carles , Langer Julian D. , Piñol Jaume , Fita Ignacio , Frangakis Achilleas S. 
Published: June 2022

AbstractMany human pathogens need to extract lipids from their environment for survival and proliferation. How this is accomplished on a molecular level is largely unknown1. Here, we report a comprehensive structural and functional analysis of the previously uncharacterized protein P116 (MPN_213) from Mycoplasma pneumoniae, a human pathogen responsible for approximately 30% of community-acquired human pneumonia2. Single-particle cryo-electron microscopy of P116 at 3.3 Å resolution reveals a homodimer with a core domain presenting a previously unseen fold. This fold creates a large cavity of ∼18,000 Å3 with a hydrophobic internal surface that is accessible to solvent. Within the cavity ligands with a length of 10-19 Å and a width of 4 Å could be observed. These ligands were identified as the essential lipids phosphatidylcholine, sphingomyelin and cholesterol using mass spectrometry. When the cavity is emptied, the protein undergoes an extensive conformational change that can no longer accommodate lipids. When emptied P116 is incubated with high-density lipoproteins (HDLs) a net transfer of cholesterol is demonstrated by a radioactivity experiment and cryo-electron microscopy resolves a complex between P116 and HDL. Taken together, our results reveal the mechanism by which P116 extracts essential lipids from the host environment and possibly then delivers them into the membrane by a wringing movement. This mechanism may be precedential for other cholesterol-auxotrophic bacteria.
Deep Learning for Rare Disease: A Scoping Review
Authors: Lee Junghwan , Liu Cong , Kim Junyoung , Chen Zhehuan , Sun Yingcheng , Rogers James R. , Chung Wendy K. , Weng Chunhua 
Published: June 2022

AbstractAlthough individually rare, collectively more than 7,000 rare diseases affect about 10% of patients. Each of the rare diseases impacts the quality of life for patients and their families, and incurs significant societal costs. The low prevalence of each rare disease causes formidable challenges in accurately diagnosing and caring for these patients and engaging participants in research to advance treatments. Deep learning has advanced many scientific fields and has been applied to many healthcare tasks. This study reviewed the current uses of deep learning to advance rare disease research. Among the 332 reviewed articles, we found that deep learning has been actively used for rare neoplastic diseases (250/332), followed by rare genetic diseases (170/332) and rare neurological diseases (127/332). Convolutional neural networks (307/332) were the most frequently used deep learning architecture, presumably because image data were the most commonly available data type in rare disease research. Diagnosis is the main focus of rare disease research using deep learning (263/332). We summarized the challenges and future research directions for leveraging deep learning to advance rare disease research.
Missing Americans: Early Death in the United States, 1933-2021
Authors: Bor Jacob , Stokes Andrew C. , Raifman Julia , Venkataramani Atheendar , Bassett Mary T. , Himmelstein David , Woolhandler Steffie 
Published: June 2022

AbstractWe assessed how many U.S. deaths would have been averted each year, 1933-2021, if U.S. age-specific mortality rates had equaled those of other wealthy nations. The annual number of excess deaths in the U.S. increased steadily beginning in the late 1970s, reaching 626,353 in 2019. Excess deaths surged during the COVID-19 pandemic. In 2021, there were 1,092,293 “Missing Americans” and 25 million years of life lost due to excess mortality relative to peer nations. In 2021, half of all deaths under 65 years and 91% of the increase in under-65 mortality since 2019 would have been avoided if the U.S. had the mortality rates of its peers. Black and Native Americans made up a disproportionate share of Missing Americans, although the majority were White.One sentence summaryIn 2021, 1.1 million U.S. deaths – including 1 in 2 deaths under age 65 years – would have been averted if the U.S. had the mortality rates of other wealthy nations.
A cytoplasmic chemoreceptor and Reactive Oxygen Species mediate bacterial chemotaxis to copper
Authors: Louis Gwennaëlle , Cherry Pauline , Michaux Catherine , Rahuel-Clermont Sophie , Dieu Marc , Tilquin Françoise , Maertens Laurens , Houdt Rob Van , Renard Patricia , Perpete Eric , Matroule Jean-Yves 
Published: June 2022

AbstractChemotaxis is a widespread strategy used by unicellular and multicellular living organisms to maintain their fitness in stressful environments. We previously showed that bacteria can trigger a negative chemotactic response to a copper (Cu)-rich environment. Cu ions toxicity on bacterial cell physiology has been mainly linked to mismetallation events and ROS production, although the precise role of Cu-generated ROS remains largely debated.Here, we found that the cytoplasmic Cu ions content mirrors variations of the extracellular Cu ions concentration and triggers a dose-dependent oxidative stress, which can be abrogated by superoxide dismutase and catalase overexpression. The inhibition of ROS production in the cytoplasm not only improves bacterial growth but also impedes Cu-chemotaxis, indicating that ROS derived from cytoplasmic Cu ions mediate the control of bacterial chemotaxis to Cu.We also identified the Cu chemoreceptor McpR, which binds Cu ions with low affinity, suggesting a labile interaction. In addition, we demonstrate that the cysteine 75 and histidine 99 within the McpR sensor domain are key residues in Cu chemotaxis and Cu coordination. Finally, we discovered thatin vitroboth Cu(I) and Cu(II) ions modulate McpR conformation in a distinct manner. Overall, our study provides mechanistic insights on a redox-based control of Cu chemotaxis, indicating that the cellular redox status can play a key role in bacterial chemotaxis.
Laboratory strains of Escherichia coli K-12: not such perfect role models after all
Authors: Browning Douglas F. , Hobman Jon L. , Busby Stephen J.W. 
Published: June 2022

AbstractEscherichia coli K-12 was originally isolated 100 years ago and since then, it has become an invaluable model organism and a cornerstone of molecular biology research. However, despite its apparent pedigree, since its initial isolation, E. coli K-12 has been repeatedly cultured, passaged, and mutagenized, resulting in an organism that carries extensive genetic changes. To understand more about the evolution of this important model organism, we have sequenced the genomes of two ancestral K-12 strains, WG1 and EMG2, considered to be the progenitors of many key laboratory strains. Our analysis confirms that these strains still carry genetic elements such as bacteriophage lambda (λ) and the F plasmid, but also indicates that they have undergone extensive lab-based evolution. Thus, scrutinizing the genomes of ancestral E. coli K-12 strains, leads us to question whether E. coli K-12 is a sufficiently robust model organism for 21st century microbiology.DATA SUMMARYAll supporting data are provided within the article or through supplementary data files. Supplementary Figs. S1 to S14 and Supplementary File S1 are available with the online version of this article. All genome sequence data has been deposited in NCBI GenBank under Bioproject ID PRJNA848777. The assembled and annotated genomes of WG1 and EMG2 have been deposited with the accession numbers, CP099590 and CP099591 (WG1) and CP099588 and CP099589 (EMG2).Impact StatementSince its isolation in 1922, Escherichia coli K-12, has become arguably the premier model organism for contemporary science. The adoption of E. coli K-12 by many microbiologists across the globe, means that it has a complex pedigree, and, although many E. coli K-12 strains have been sequenced, little is known about the early versions of K-12, which still carry the F plasmid and bacteriophage λ. To understand more about the lab-based evolution that has shaped this important model organism, we have sequenced two ancestral K-12 strains, WG1 and EMG2, that are considered to be the progenitors of many of the laboratory strains used today.