bluuebunny/crossref_metadata_2025_split huggingface dataset:
Severe perinatal hydrops fetalis in genome edited pigs with a biallelic five base pair deletion of the Marfan syndrome gene, FBN1
Authors: Tsang Hiu-Gwen , Lillico Simon , Proudfoot Christopher , McCulloch Mary E. B. , Markby Greg , Trejo-Reveles Violeta , Corcoran Brendan M. , Whitelaw C. Bruce A. , MacRae Vicky E. , Summers Kim M. 
Published: July 2020

AbstractThis paper describes a genome editing project using CRISPR-Cas9. The objective was to create a large animal model of human Marfan syndrome by targeting the FBN1 gene of the pig, Sus scrofa, using a single guide and non-homologous end joining which was expected to create short insertion or deletion mutations at the 5’ end of the gene. The editing successfully created a five base pair deletion in exon 2 of FBN1, which was homozygous in two animals. However, the phenotype of these piglets was unexpected, since they showed none of the signs consistent with Marfan syndrome but both suffered extreme hydrops fetalis with a large amount of fluid located under the skin and in the abdomen. One of the edited piglets was stillborn and the other was euthanised at birth on welfare grounds. It is likely that this result was due to unanticipated on- or off-target mutations, possibly in the GLDN gene 3 megabases away from FBN1. This result provides more evidence for unexpected outcomes of CRISPR- Cas9 gene editing and supports the proposal that all genome edited individuals should be subjected to strategies to track the CRISPR footprint, such as whole genome sequencing, before being used for further experimentation or in clinical applications.
Fibroblast fusion to the muscle fiber regulates myotendinous junction formation
Authors: Yaseen-Badarneh Wesal , Kraft-Sheleg Ortal , Zaffryar-Eilot Shelly , Melamed Shay , Sun Chengyi , Millay Douglas P. , Hasson Peleg 
Published: July 2020

SummaryVertebrate muscles and tendons are derived from distinct embryonic origins yet they must interact in order to facilitate muscle contraction and body movements. How robust muscle tendon junctions (MTJs) form to be able to withstand contraction forces is still not understood. Using techniques at a single cell resolution we reexamined the classical view of distinct identities for the tissues composing the musculoskeletal system. We identified fibroblasts that have switched on a myogenic program and demonstrate these dual identity cells fuse into the developing muscle fibers along the MTJs facilitating the introduction of fibroblast-specific transcripts into the elongating myofibers. We suggest this mechanism resulting in a hybrid muscle fiber, primarily along the fiber tips, enables a smooth transition from muscle fiber characteristics towards tendon features essential for forming robust MTJs. We propose that dual characteristics of junctional cells could be a common mechanism for generating stable interactions between tissues throughout the musculoskeletal system.
Cell biological studies of ethanologenic bacteriumZymomonas mobilis
Authors: Fuchino Katsuya , Chan Helena , Hwang Ling Chin , Bruheim Per 
Published: July 2020

AbstractAlphaproteobacteriumZymomonas mobilisexhibits extreme ethanologenic physiology, making this species a promising biofuel producer. Numerous studies have investigated its biology relevant to industrial applications and mostly at the population level. However, the organization of single cells in this industrially important, polyploid species has been largely uncharacterized.In the present study, we characterized basic cellular behaviour ofZ. mobilisstrain Zm6 at a single cell level. We observed that growingZ. mobiliscells often divided at non mid-cell position, which contributed to variant cell size at birth. Yet, the cell size variance was regulated by a modulation of cell cycle span, mediated by a correlation of bacterial tubulin homologue FtsZ-ring accumulation with cell growth. TheZ. mobilisculture also exhibited heterogeneous cellular DNA contents among individual cells, which might have been caused by asynchronous replication of chromosome that was not coordinated to cell growth. Furthermore, slightly angled divisions might have rendered temporary curvatures of attachedZ. mobiliscells. Overall, the presented study uncovered a novel bacterial cell organization inZ. mobilis, the metabolism of which is not favoured for biosynthesis to build biomass.ImportanceWith increasing environmental concerns about the exhausting use of fossil fuels, a development of sustainable biofuel production platform has been attracting significant public attention. EthanologenicZ. mobilisspecies are endowed with an efficient ethanol-fermentation capacity that surpass, in several aspects, that of the baker’s yeastSaccharomyces cerevisiae, the most used microorganism for ethanol productions. For a development ofZ. mobilisculture-based biorefinery, an investigation of its uncharacterized cell biology is important, because bacterial cellular organization and metabolism are closely associated with each other in a single cell compartment.In addition, the current work highlights that polyploid bacteriumZ. mobilisexhibits a distinctive mode of bacterial cell organization, reflecting its unique metabolism that do not prioritize incorporation of nutrients to cell growth. Thus, another significance of presented work is to advance our general understanding in the diversity of bacterial cell architecture.
SLALOM: A Simple and Rapid Method for Enzymatic Synthesis of CRISPR-Cas9 sgRNA Libraries
Authors: Yates Joshua D , Russell Robert C , Yost H Joseph , Hill Jonathon T 
Published: July 2020

ABSTRACTCRISPR-Cas9 sgRNA libraries have transformed functional genetic screening and have enabled innovative CRISPR-based methods, such as the visualization of chromatin dynamics in living cells. These libraries have the potential to be applied to a vast number of biological systems and aid in the development of new technologies, but their synthesis is hindered by the cost, time requirements, and technical difficulty of current sgRNA library generation methods. Here, we describe SLALOM—a rapid enzymatic method for generating robust, variant-matched sgRNA libraries from any source of DNA in under 3 hours. This method utilizes a custom sgRNA scaffold sequence and a novel method for detaching oligonucleotides from solid supports using a strand displacing polymerase. Using this method, we have constructed libraries targeting theE. coligenome and the transcriptome of developing zebrafish hearts, demonstrating its potential to expand the reach of CRISPR technology and facilitate methods requiring custom sgRNA libraries.
Incident psychopharmacological treatment and psychiatric hospital contact in individuals with newly developed type 2 diabetes
Authors: Rohde Christopher , Schmitz Norbert , Thomsen Reimar W. , Østergaard Søren D. 
Published: July 2020

AbstractObjectiveTo investigate the association between newly developed type 2 diabetes (T2D) and incident psychopharmacological treatment and psychiatric hospital contact.MethodsWe identified all individuals from the Central- and Northern Denmark Regions with newly developed T2D (defined by the first HbA1c measurement >6.5%) from 2000-2016 and up to five age and sex matched individuals without T2D (controls). Those having received psychopharmacological treatment or having had a psychiatric hospital contact in the five years prior to the onset of T2D were excluded. For this cohort, we first assessed the incidence of psychopharmacological treatment and psychiatric hospital contact among individuals with T2D and controls, respectively. Secondly, we compared the incidence of psychopharmacological/psychiatric hospital contact among individuals with T2D to propensity score matched controls. Finally, we assessed which baseline (T2D onset) characteristics that were associated with subsequent psychopharmacological treatment and psychiatric hospital contact.ResultsWe identified 56,640 individuals with newly developed T2D and 315,694 controls. A total of 8.3% of the individuals with T2D initiated psychopharmacological treatment within the 2 years following onset compared to 4.6% among the age and sex matched controls. Individuals with T2D were at increased risk of initiating psychopharmacological treatment compared to the propensity score matched controls (HR=1.51, 95% CI=1.43-1.59), whereas their risk of psychiatric hospital contact was not increased to the same extent (HR=1.14, 95% CI=0.98-1.32). Older age, somatic comorbidity, and being divorced/widowed was associated with both psychopharmacological treatment and psychiatric hospital contact following T2D.ConclusionIndividuals with T2D are at elevated risk of requiring psychopharmacological treatment.Significant outcomes8.3% of the individuals with T2D initiated psychopharmacological treatment within the 2 years following onset compared to 4.6% among the age and sex matched controlsIndividuals with newly developed T2D were at increased risk of initiating psychopharmacological treatment and of having psychiatric hospital contact compared to propensity score matched controls.Risk factors for psychopharmacological treatment/psychiatric hospital contact following development of T2D include older age, somatic comorbidity and being divorced or widowed.LimitationsIdentification of T2D (a HbA1c level >6.5%) itself might lead to the identification of mental illness and thereby psychopharmacological treatment initiation/psychiatric hospital contact.A proportion of the individuals with T2D will likely have initiated treatment with an antidepressant due to neuropathic pain developed as a complication to T2D
Mode and dynamics of vanA-type vancomycin-resistance dissemination in Dutch hospitals
Authors: Arredondo-Alonso Sergio , Top Janetta , Corander Jukka , Willems Rob J L , Schürch Anita C 
Published: July 2020

AbstractBackgroundEnterococcus faecium is a commensal of the gastrointestinal tract of animals and humans but also a causative agent of hospital-acquired infections. Resistance against glycopeptides and especially to vancomycin, a first-line antibiotic to treat infections with multidrug-resistant Gram-positive pathogens, has motivated the inclusion of E. faecium in the WHO global priority list. Vancomycin resistance can be conferred by the vanA gene cluster on the transposon Tn1546, which is frequently present in plasmids. The vanA gene cluster can be disseminated clonally but also horizontally either by plasmid dissemination or Tn1546 transposition between different genomic locations. Here, we reconstructed all nested genetic elements (clone, plasmid, transposon) to study how the dissemination of vanA-type vancomycin resistance occurred in Dutch hospitals (2012-2015).MethodsWe performed a retrospective study of the genomic epidemiology of 309 vancomycin-resistant E. faecium (VRE) isolates across 32 Dutch hospitals (2012-2015). Genomic information regarding clonality and Tn1546 characterisation was extracted using hierBAPS sequence clusters (SC) and TETyper, respectively. Plasmids were predicted using gplas in combination with a network approach based on shared k-mer content. This allowed determining all nested genomic elements (clone, plasmid and transposon) involved in the dissemination of the vanA gene cluster. Next, we conducted an “all vs. all” pairwise comparison between isolates sharinga potential epidemiological link to elucidate whether clonal, plasmid or Tn1546 spread accounted for the dissemination of vanA resistance.ResultsThe 309 VRE isolates belonged to 18 different SCs of which SC13 (n = 102, 33%), SC17 (n = 52, 16.8%) and SC18 (n = 42, 13.6%) were predominant. We identified seven different plasmid types bearing the vanA gene cluster, four of which were highly similar (identity ∼99%, coverage∼84%) to previously described complete plasmid sequences. We estimated that clonal dissemination contributed most (∼45%) to the spread of vancomycin-resistance in Dutch hospitals, followed by Tn1546 mobilisation (∼12%) and plasmid dissemination (∼6%).ConclusionsThe dissemination of the vanA gene cluster in Dutch hospitals between 2012 and 2015 was dominated by clonal spread. However, we also identified outbreak settings with high frequencies of Tn1546 transposition and/or plasmid dissemination in which the spread of resistance was mainly driven by horizontal gene transfer (HGT). This study demonstrates the feasibility of distinguishing between modes of dissemination with short-read data and provides one of the first quantitative assessments to estimate the relative contribution of nested genomic elements in the dissemination of vanA-type vancomycin resistance cluster.
Overcoming data gaps in life course epidemiology by matching across cohorts
Authors: Kezios Katrina L. , Zimmerman Scott , Rudolph Kara , Calonico Sebastian , Al-Hazzouri Adina Zeki , Glymour M. Maria 
Published: July 2020

AbstractLifecourse epidemiology is hampered by the absence of studies with exposures and outcomes measured at different life stages. We describe when the effect of an exposure (A) on an outcome (Y) in a target population is identifiable in a combined (“synthetic”) cohort created by pooling an early-life cohort including exposure measures with a late-life cohort including outcome measures. We enumerate the causal assumptions needed for unbiased effect estimation in the synthetic cohort and illustrate by simulating target populations under four causal models. From each population, we drew hypothetical early- and late-life cohorts and created a synthetic cohort by matching individuals from the two cohorts based on mediators and/or confounders. We compared bias when estimating the effect of A on Y in the synthetic cohort, varying which matching variables were available, the match ratio, and the distance matching criterion. When the set of matching variables includes all variables d-connecting exposure and outcome (i.e., variables blocking all back and front door pathways), the synthetic cohort yields unbiased effect estimates. Methods based on merging cohorts provide opportunities to hasten the evaluation of early- and mid-life determinants of late life health, but rely on available measures of both confounders and mediators.
Irradiance modulates thermal niche in a previously undescribed low-light and cold-adapted nano-diatom
Authors: Kling Joshua D. , Kelly Kyla J. , Pei Sophia , Rynearson Tatiana A. , Hutchins David A. 
Published: July 2020

AbstractDiatoms have well-recognized roles in fixing and exporting carbon and supplying energy to marine ecosystems, but only recently have we begun to explore the diversity and importance of nano- and pico-diatoms. Here we describe a small (~5 μm) diatom from the genusChaetocerosIsolated from a wintertime temperate estuary (2° C, Narragansett Bay, RI), with a unique obligate specialization for low-light environments (< 120 μmol photons m-2sec-1). This diatom exhibits a striking interaction between irradiance and thermal responses whereby as temperatures increase, so does its susceptibility to light stress. Historical 18S rRNA amplicon data from our study site show this isolate was abundant throughout a six-year period, and its presence strongly correlates with winter and early spring months when light and temperature are low. Two ASVs matching this isolate had a circumpolar distribution in Tara Polar Ocean Circle samples, indicating its unusual light and temperature requirements are adaptations to life in a cold, dark environment. We expect this isolate’s low light, psychrophilic niche to shrink as future warming-induced stratification increases both light and temperature levels experienced by high latitude marine phytoplankton.
Dynamic multi-OMICs of glioblastoma reveal sensitivity to neddylation inhibition dependent on nuclear PTEN and DNA replication pathways: Nuclear PTEN mediates MLN4924 sensitivity in GBM
Authors: Ferdosi S R. , Taylor B , Lee M , Tang N , Peng S , Bybee R , Reid G , Hartman L , Garcia-Mansfield K , Sharma R , Pirrotte P , Ma Jianhui , Parisian Alison D , Furnari F , Dhruv HD , Berens ME 
Published: July 2020

Withdrawal StatementThe authors have withdrawn their manuscript because the reported synergy of TOP2A inhibitors plus MLN4924 proved to be untrue (not reproducible). Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author (mberens@tgen.org).
Neural representation of abstract task structure during generalization
Authors: Vaidya Avinash R. , Jones Henry M. , Castillo Johanny , Badre David 
Published: July 2020

AbstractCognitive models in psychology and neuroscience widely assume that the human brain maintains an abstract representation of tasks. This assumption is fundamental to theories explaining how we learn quickly, think creatively, and act flexibly. However, neural evidence for a verifiably generative abstract task representation has been lacking. Here, we report an experimental paradigm that requires forming such a representation to act adaptively in novel conditions without feedback. Using functional magnetic resonance imaging, we observed that abstract task structure was represented within left mid-lateral prefrontal cortex, bilateral precuneus and inferior parietal cortex. These results provide support for the neural instantiation of the long-supposed abstract task representation in a setting where we can verify its influence. Such a representation can afford massive expansions of behavioral flexibility without additional experience, a vital characteristic of human cognition.
Mycorrhizal symbiosis alleviates plant water deficit within and across plant generations via plasticity
Authors: Puy Javier , Carmona Carlos P. , Hiiesalu Inga , Öpik Maarja , de Bello Francesco , Moora Mari 
Published: July 2020

AbstractPhenotypic plasticity is essential for organisms to adapt to local ecological conditions. It is expected that mutualistic interactions, such as arbuscular mycorrhizal (AM) symbiosis, mediate plant phenotypic plasticity, although it is not clear to what extent this plasticity may be heritable (i.e., transgenerational plasticity).We tested for plant plasticity within- and across-generations in response to AM symbiosis and varying water availability in a full factorial experiment over two generations, using a genetically uniform line of a perennial apomictic herb,Taraxacum brevicorniculatum. We examined changes in phenotype, performance, and AM fungal colonization of the offspring throughout plant development.AM symbiosis and water availability triggered phenotypic changes during the life cycle of plants. Additionally, both triggered adaptive transgenerational effects, especially detectable during the juvenile stage of the offspring. Water deficit and absence of AM fungi caused concordant plant phenotypic modifications towards a “stress-coping phenotype”, both within- and across-generations. AM fungal colonization of offspring was also affected by the parental environment.AM symbiosis can trigger within-generation and transgenerational plasticity in terms of functional traits related to resource-use acquisition and AM fungal colonization. Thus, transgenerational effects of mycorrhizal symbiosis are not limited to plant fitness, but also improve plants’ ability to cope with environmental stress.
A spatially resolved single cell atlas of human gastrulation
Authors: Tyser Richard C.V. , Mahammadov Elmir , Nakanoh Shota , Vallier Ludovic , Scialdone Antonio , Srinivas Shankar 
Published: July 2020

ABSTRACTGastrulation is the fundamental process during the embryogenesis of all multicellular animals through which the basic body plan is first laid down. It is pivotal in generating cellular diversity coordinated with spatial patterning. Gastrulation in humans occurs in the third week following fertilization. Our understanding of this process in humans is extremely limited, and based almost entirely on experimental models. Here, we characterize in a spatially resolved manner the single cell transcriptional profile of an entire gastrulating human embryo approximately 16 to 19 days after fertilization. We used these data to provide the first unequivocal demonstration that human embryonic stem cells represent the early post implantation epiblast. We identified both primordial germ cells and red blood cells, which had never been characterized so early during human development. Comparison with mouse gastrula transcriptomes revealed many commonalities between the human and mouse but also several key differences, particularly in FGF signaling, that we validated experimentally. This unique dataset offers a unique glimpse into a central but generally inaccessible stage of our development, provides new context for interpreting experiments in other model systems and represents a valuable resource for guiding directed differentiation of human cellsin vitro.
Overlapping and non-overlapping roles of the class-I histone deacetylase-1 corepressors, LET-418, SIN-3, and SPR-1 inCaenorhabditis elegansembryonic development
Authors: Kubota Yukihiro , Ohnishi Yuto , Hamasaki Tasuku , Yasui Gen , Ota Natsumi , Kitagawa Hiromu , Esaki Arashi , Fahmi Muhamad , Ito Masahiro 
Published: July 2020

AbstractHistone deacetylases (HDACs) are divided into four classes. Class-I HDAC, HDAC-1 forms three types of complexes, namely the Nucleosome Remodeling Deacetylase complex, the Sin3 complex, and the CoREST complex, with specific corepressor component Mi2/CHD-3, Sin3, and RCOR1 in human, respectively. The functions of these HDAC-1 complexes are regulated by their corepressors, however, their exact mechanistic roles in several biological processes remain unexplored, such as in embryonic development. Here, we report that each of the corepressors, LET-418, SIN-3, and SPR-1, the homologous of Mi2, Sin3, and RCOR1, respectively, were expressed throughoutCaenorhabditis elegansembryonic development and served essential roles in the process. Moreover, genetic analysis suggested that three pathways (i.e., LET-418– SIN-3–SPR-1, SIN-3–SPR-1, and LET-418) participated in embryonic development. Our terminal-phenotype observations of single mutants of each corepressor implied that LET-418, SIN-3, and SPR-1 played similar roles in promoting advancement to the middle and late embryonic stages. Genome-wide comparative-transcriptome analysis indicated that 47.5% and 42.3% of genes were commonly increased and decreased insin-3andspr-1mutants, respectively. These results suggest that among the three pathways studied, the SIN-3–SPR-1 pathway mainly serves to regulate embryonic development. Comparative-Gene Ontology analysis indicated that these three pathways played overlapping and distinct roles in regulatingC. elegansembryonic development.