bluuebunny/crossref_metadata_2025_split huggingface dataset:
The novel conserved NAD+-binding micropeptide SGHRT regulates mitochondrial function and metabolism in human cardiomyocytes
Authors: Do Vinh Dang , Tulsian Nikhil Kumar , Tan Warren KY , Li Zhe , Cheng Liyi , Autio Matias I. , Tan Wilson LW , Tiang Zenia , Perrin Arnaud , Ching Jianhong , Lee Mayin , Bonne Isabelle , Ramachandra Chrishan , Lim Choon Kiat , Hausenloy Derek J , Drum Chester Lee , Richards A. Mark , Anand Ganesh S. , Foo Roger SY 
Published: October 2021

AbstractsNicotinamide adenine dinucleotide (NAD) is a critical metabolite and coenzyme for multiple metabolic pathways and cellular processes (1-4). In this study, we identified Singheart, SGHRT as a nuclear genome-encoded NAD+-binding mitochondrial micropeptide. SGHRT, present in both monomeric and dimeric forms, binds directly to NAD, but not NADH or flavin adenine dinucleotide (FAD). Localized to the inner mitochondrial membrane and mitochondrial matrix, SGHRT interacts with the mitochondrial enzymes Succinate-CoA Ligase and Succinate Dehydrogenase.SGHRTdeletion in human embryonic stem cell derived cardiomyocytes disrupted mitochondria morphology, decreased total NAD and ATP abundance, and resulted in defective TCA cycle metabolism, the electron transport chain and in Ox-Phos processes. These results comprise the first report of an NAD+-binding micropeptide, SGHRT, required for mitochondrial function and metabolism.
The establishment of multiple knockout mutants of Colletotrichum orbiculare by CRISPR/Cas9 and Cre/loxP systems
Authors: Yamada Kohji , Yamamoto Toya , Uwasa Kanon , Osakabe Keishi , Takano Yoshitaka 
Published: October 2021

AbstractPhytopathogenic fungi belonging to the Colletotrichum genus cause devastating damage for many plant species. Among them, Colletotrichum orbiculare is employed as a model fungus to analyze molecular aspects of plant-fungus interactions. Although gene disruption via homologous recombination (HR) was established for C. orbiculare, this approach is laborious due to its low efficiency. Here we developed methods to efficiently generate multiple knockout mutants of C. orbiculare. We first found that CRISPR/Cas9 system massively promoted gene-targeting efficiency. By transiently introducing a CRISPR/Cas9 vector, more than 90 % of obtained transformants were knockout mutants. Furthermore, we optimized a self-excision Cre/loxP marker recycling system for C. orbiculare because limited availability of desired selective markers hampers sequential gene disruption. In this system, integrated selective marker is removable from the genome via Cre recombinase driven by a xylose-inducible promoter, enabling reuse of the same selective marker for the next transformation. Using our CRISPR/Cas9 and Cre/loxP systems, we attempted to identify functional sugar transporters in C. orbiculare. Multiple disruptions of putative quinate transporter genes restrict fungal growth on media containing quinate as a sole carbon source, confirming their functionality as quinate transporters. Our analyses revealed that quinate acquisition is dispensable during fungal infection because this mutant displayed normal virulence to host plants. In addition, we successfully built mutations of 17 cellobiose transporter genes in a strain. From the data of knockout mutants established in this study, we inferred that repetitive rounds of gene disruption using CRISPR/Cas9 and Cre/loxP systems do not cause negative effects for fungal virulence and growth. Therefore, these systems will be powerful tools to perform systematic gene targeting approach for C. orbiculare.
Sperm and northern bottlenose whale interactions with deep-water trawlers in the western North Atlantic
Authors: Oyarbide Usua , Feyrer Laura , Gordon Jonathan 
Published: October 2021

AbstractCommercial fisheries have increased in all the world’s oceans with diverse unintended impacts on marine ecosystems. As a result of resource overlap, interactions between cetaceans and fisheries are a common occurrence and, in many cases, these give rise to significant conservation issues. Research on the distribution and types of such interactions is important for efficient management. In this study, we describe the behaviors of two whale species: sperm whales (Physeter macrocephalus) and northern bottlenose whales (Hyperoodon ampullatus), interacting with benthic trawlers fishing off the eastern Grand Banks of the western North Atlantic in 2007. Whale interactions were only observed when vessels were targeting Greenland halibut (Reinnhardtius hippoglossoides) in deep-water fishing areas and were most common during net hauling. Sperm whales and northern bottlenose whales appeared to engage in feeding behavior close to the surface during hauling, especially during the latter stages, suggesting they targeted fish escapees rather than discards. Using photo-identification methods, seven individual sperm whales were identified with multiple resights of six individuals being recorded over an almost two month period. The maximum distance between two resights was 234 km, suggesting individual sperm whales were repeatedly targeting and even following fishing vessels over multiple days and between fishing areas. By contrast, there were no photographic resights of individual northern bottlenose whales within this study, or with substantial photo-identification catalogues from other adjacent high density areas, suggesting that individuals of this species may be less likely to follow vessels or move between areas. This study documents the earliest confirmed records of northern bottlenose whales in this remote region. These interactions and high encounter rates may indicate that adjacent populations are recovering from the previous century of commercial whaling. Our study provides new insights and details on whale-fisheries interactions, which can inform future research and help managers understand the real and perceived impacts on fisheries and whales.
Limited adaptive evolution ofStaphylococcus aureusduring transition from colonization to invasive infection
Authors: Räz Anna K. , Andreoni Federica , Boumasmoud Mathilde , Bergada-Pijuan Judith , Schweizer Tiziano A. , Shambat Srikanth Mairpady , Hasse Barbara , Zinkernagel Annelies S. , Brugger Silvio D. 
Published: October 2021

AbstractStaphylococcus aureuscarriage is a risk factor for invasive infections. Unique genetic elements favoring the transition from colonizing to invasive phenotype have not yet been identified and phenotypic traits are understudied. We therefore assessed pheno- and genotypic profiles of elevenS. aureusisolate pairs sampled from colonized patients simultaneously suffering from invasiveS. aureusinfections. Ten out of 11 isolate pairs presented the samespaand MLST suggesting colonization as origin for the invasive infection. Systematic analysis of colonizing and invasive isolate pairs showed similar adherence, hemolysis and reproductive fitness properties, minimal genetic differences, identical antibiotic tolerance and bacterial virulence inGalleria mellonella. Our results provide insights into the similar phenotype associated with limited adaptive genetic evolution between the colonizing and invasive isolates. Disruption of the physical barriers mucosa or skin were identified in the majority of patients further emphasizing colonization as a major risk factor for invasive disease.ImportanceS. aureusis a major pathogen of humans causing a wide range of disease. The failure to develop a vaccine and antibiotic warrant the exploration of novel treatment strategies. Asymptomatic colonization of the human nasal passages is a major risk factor for invasive disease and decolonization procedures have shown efficacy in preventing invasive infections. However, the transition ofS. aureusfrom a benign colonizer of the nasal passages to a major pathogen is not well understood and host as well as bacterial properties have been discussed as being relevant for this behavioral change. We conducted a thorough investigation of patient-derived strain pairs reflecting colonizing and invasive isolates in a given patient. Although we identified limited genetic adaptation in certain strains as well as slight differences in adherence capacity of colonizing and invasive isolates, our work suggests that barrier breaches are a key event in the disease continuum ofS. aureus.
Behavioral and slice electrophysiological assessment of DREADD ligand, deschloroclozapine (DCZ) in rats
Authors: Nentwig Todd B. , Obray J. Daniel , Vaughan Dylan T. , Chandler L. Judson 
Published: October 2021

AbstractDesigner Receptors Exclusively Activated by Designer Drugs (DREADDs) have become a premier neuroscience research tool in the past decade for their utility in providing reversible manipulations of cellular activity following experimenter-controlled delivery of a DREADD-specific ligand. However, the commonly used DREADD ligand, clozapine-N-oxide (CNO), has metabolic and off-target effects that may confound experimental results and interpretations. Moreover, CNO has relatively poor affinity for DREADD receptors, which necessitates high doses for systemic administration applications. New DREADD ligands aim to reduce metabolic and potential off-target effects while maintaining strong efficacy for the designer receptors. Recently a novel DREADD ligand, deschloroclozapine (DCZ), was shown to induce chemogenetic-mediated cellular and behavioral effects in mice and monkeys without detectable side effects. While promising, further testing of DCZ across species and experimental paradigms is warranted. The goal of the present study was to examine the effectiveness of systemic DCZ for DREADD-based chemogenetic manipulations in behavioral and slice electrophysiological applications in rats. We demonstrate that a relatively low dose of DCZ (0.1 mg/kg) supports excitatory DREADD-mediated cFos induction, DREADD-mediated inhibition of a central amygdala-dependent behavior, and DREADD-mediated inhibition of neuronal activity in a slice electrophysiology preparation. In addition, we show that this dose of DCZ does not alter gross locomotor activity or induce a place preference/aversion in control rats without DREADD expression. Together, our findings support the use of systemic DCZ for DREADD-based manipulations in rats, and provide evidence that DCZ is a superior alternative to CNO.
Optimized Multicolour Immunofluorescence Panel for Cattle B Cell Phenotyping by an 8-Colour, 10-Parameter Panel
Authors: Roos Eduard O. , Placido Marie Bonnet-Di , Mwangi William N , Moffat Katy , Fry Lindsay , Waters Ryan , Hammond John A. 
Published: October 2021

AbstractThis 8-colour, 10-parameter panel has been optimised to distinguish between functionally distinct subsets of cattle B cells in both fresh and cryopreserved peripheral blood mononuclear cells (PBMCs). Existing characterised antibodies against cell surface molecules (immunoglobulin light chain (S-Ig(L)), CD20, CD21, CD40, CD71 and CD138) enabled the discrimination of 24 unique populations within the B cell population. This allows the identification of five putative functionally distinct B cell subsets critical to infection and vaccination responses; 1) naïve B cells (BNaïve), 2) regulatory B cells (BReg), 3) memory B cells (BMem), 4) plasmablasts (PB) and 5) plasma cells (PC). Although CD3 and CD8α can be included as an additional dump channel, it does not significantly improve the panel’s ability to separate “Classical” B cells. This panel will promote better characterisation and tracking of B cell responses in cattle as well as other bovid species as the reagents are likely to cross react.
Multi-omic analysis of the Arabidopsis clock activator mutantrve 4 6 8reveals connections to carbohydrate metabolism and proteasome regulation
Authors: Scandola S , Mehta D , Li Q , Rodriguez M , Castillo B , Uhrig RG 
Published: October 2021

ABSTRACTPlants are able to sense changes in their light environments, such as the onset of day and night, as well as anticipate these changes in order to adapt and survive. Central to this ability is the plant circadian clock, a molecular circuit that precisely orchestrates plant cell processes over the course of a day. REVEILLE proteins (RVEs) are recently discovered members of the plant circadian circuitry that activate the evening complex and PRR genes to maintain regular circadian oscillation. The RVE 8 protein and its two homologs, RVE 4 and 6, have been shown to limit the length of the circadian period, withrve 4 6 8triple-knockout plants possessing an elongated period along with increased leaf surface area, biomass, cell size and delayed flowering relative to wild-type Col-0 plants. Here, using a multi-omics approach consisting of phenomics, transcriptomics, proteomics, and metabolomics we draw novel connections between RVE8-like proteins and a number of core plant cell processes. In particular, we reveal that loss of RVE8-like proteins results in altered carbohydrate, organic acid and lipid metabolism, including a starch excess phenotype at dawn. We further demonstrate thatrve 4 6 8plants have lower levels of 20S proteasome subunits and possess significantly reduced proteasome activity, potentially explaining the increase in cell-size observed in RVE8-like mutants. Overall, this robust, multi-omic dataset, provides substantial new insights into the far reaching impact RVE8-like proteins have on the diel plant cell environment.
Multi-omics analysis reveals cross-organism interactions in coral holobiont
Authors: Maruyama Toru , Ito Michihiro , Wakaoji Satoshi , Okubo Yusuke , Ide Keigo , Nishikawa Yohei , Fujimura Hiroyuki , Suda Shoichiro , Nakano Yoshikatsu , Satoh Noriyuki , Shinzato Chuya , Yura Kei , Takeyama Haruko 
Published: October 2021

AbstractCorals create an ecosystem, called a holobiont, with intracellular algae (zooxanthellae) and resident bacteria. Zooxanthellae and some bacteria play major roles in the physiological properties of the coral host. However, because of the difficulties in experimental verification of cross-organism interactions, the mechanisms underpinning these interactions are largely unknown. To address this, we here generated and then analyzed multi-omics datasets for corals, zooxanthellae, and bacteria collected at Okinawa, Japan, from November 2014 to September 2016. Using cross-organism co-expression analysis, we successfully characterized the host–alga relationship in the coral holobiont. Specifically, we observed that the coral host dominates the zooxanthellae. The multi-omics analysis also suggested that infection with coral-associated bacteria Endozoicomonas likely involves coral-like ephrin ligands, triggering an immune response of the coral host. This study highlights the potential of the multi-omics approach to elucidate coral–microbe interactions.
A method for identifying environmental stimuli and genes responsible for genotype-by-environment interactions from a large-scale multi-environment data set
Authors: Onogi Akio , Sekine Daisuke , Kaga Akito , Nakano Satoshi , Yamada Tetsuya , Yu Jianming , Ninomiya Seishi 
Published: October 2021

AbstractIt has not been fully understood in real fields what environment stimuli cause the genotype-by-environment (G × E) interactions, when they occur, and what genes react to them. Large-scale multi-environment data sets are attractive data sources for these purposes because they potentially experienced various environmental conditions. Here we developed a data-driven approach termed Environmental Covariate Search Affecting Genetic Correlations (ECGC) to identify environmental stimuli and genes responsible for the G × E interactions from large-scale multi-environment data sets. ECGC was applied to a soybean (Glycine max) data set that consisted of 25,158 records collected at 52 environments. ECGC illustrated what meteorological factors shaped the G × E interactions in six traits including yield, flowering time, and protein content and when they were involved. For example, it illustrated the relevance of precipitation around sowing dates and hours of sunshine just before maturity to the interactions observed for yield. Moreover, genome-wide association mapping on the sensitivities to the identified stimuli discovered candidate and known genes responsible for the G × E interactions. Our results demonstrate the capability of data-driven approaches to bring novel insights on the G × E interactions observed in fields.Key messageThe proposed method is able to identify environmental stimuli and genes responsible for the G × E interactions observed in multi-environmental trials. The method is based on similarity search between genetic correlation and environmental stimuli among environments.
Italian universities do not recruit according to proficiency in scientific production
Authors: Gallina Pasquale , Porfirio Berardino 
Published: October 2021

AbstractWe analyzed the files regarding recruitment competitions won by 186 professors of selected bibliometric disciplines in Florence between January 2014 and 30 June 2021. An equal number of professors recruited at other Italian universities and of researchers who never attained professorship in Italy were randomly chosen in the same disciplines as each Florentine professor among individuals possessing National Scientific Qualification, a prerequisite for professorship. The H-indexes at the time of qualification (T1), of the Florence call (T2), and the current (T3) time were obtained from Scopus.Non-recruited researchers were more likely (Chi-square test) to show a higher H-index than both Florentine (T1 p=0.0005, T2 p=0.0015, T3 p=0.0095) and non-Florentine professors (T1 p=0.0078, T2 p=0.0245, T3 p=0.0500). Fifty-four non-recruited scientists serve in foreign universities, 100 at national/international research centers. The remaining 32 scientists (25 who keep producing despite precarious employment, and seven who have stopped publishing) were, at any rate, as likely as Florentine (T3 p=0.69) and non-Florentine professors (T3 p=0.14) to show a higher H-index.This study suggests that Italian academia does not recruit professors according to their qualitative/quantitative ability to publish, a detriment to knowledge for the nationwide system and on a global scale.
Regulation of skeletal muscle metabolism and contraction performance via teneurin-latrophilin action
Authors: Reid Andrea L. , Hogg David W. , Dodsworth Thomas L. , Chen Yani , Reid Ross M. , Xu Mei , Husic Mia , Biga Peggy R. , Slee Andrew , Buck Leslie T. , Barsyte-Lovejoy Dalia , Locke Marius , Lovejoy David A. 
Published: October 2021

AbstractSkeletal muscle regulation is responsible for voluntary muscular movement in vertebrates. The genes of two essential proteins, teneurins and latrophilins (LPHN), evolving in ancestors of multicellular animals, form a ligand-receptor pair, and are now shown to be required for skeletal muscle function. Teneurins possess a bioactive peptide, termed the teneurin C-terminal associated peptide (TCAP) that interacts with the LPHNs to regulate skeletal muscle contractility strength and fatigue by an insulin-independent glucose importation mechanism. CRISPR-based knockouts and siRNA-associated knockdowns of LPHN-1 and-3 shows that TCAP stimulates an LPHN-mediated cytosolic Ca2+ signal transduction cascade to increase energy metabolism and enhance skeletal muscle function via increases in type-1 oxidative fiber formation and reduce the fatigue response. Thus, the teneurin/TCAP-LPHN system is presented as a novel mechanism likely to regulate the energy requirements and performance of skeletal muscle.
Female choice can explain the fertilization pattern in oaks
Authors: Schneider Katharina , Staňková Kateřina , Brown Joel S. 
Published: October 2021

AbstractWe extend a two-step lottery model of Craft et al. to test the hypothesis that oak trees pursue a form of within-flower female choice to increase the diversity of fathers. Oak trees produce six ovules per flower while maturing just one acorn. When assuming a random ovule selection - which is a natural assumption in the absence of other hypotheses - observed fertilization patterns in oaks cannot be explained: long-distance fertilization is unusually common, even as nearby oak trees may be absent as pollen donors. Our model demonstrates how producing multiple ovules per flower permits selection for rare, distant fathers. The number of ovules per flower that maximizes paternal diversity increases with the number of trees. We introduce a cost function for ovule production for which six ovules per flower balance these costs with the benefits of diversifying fathers. Using data from two published field studies, 7 of 8 investigated maternal oaks had actual paternal diversity indices (average diversity index of 15.42) that fit the female choice hypothesis (estimated diversity of 14.66) significantly better than assuming a random selection from the six available ovules (estimated diversity of 7.649). A third field study permitted us to compare paternity by distance classes for two maternal trees. Both fit the female choice model better than random ovule selection.
Ultrahigh-Throughput Ambient MS: Direct Analysis at 22 Samples per Second by Infrared Matrix-Assisted Laser Desorption Electrospray Ionization Mass Spectrometry
Authors: Radosevich Andrew J. , Pu Fan , Chang-Yen David , Sawicki James W. , Talaty Nari N. , Elsen Nathaniel L. , Williams Jon D. , Pan Jeffrey Y 
Published: October 2021

AbstractInfrared Matrix-Assisted Laser Desorption Electrospray Ionization (IR-MALDESI) mass spectrometry is an ambient-direct sampling method being developed for high-throughput, label-free, biochemical screening of large-scale compound libraries. Here, we report the development of an ultrahigh-throughput continuous motion IR-MALDESI sampling approach capable of acquiring data at rates up to 22.7 samples per second in a 384-well microtiter plate. At top speed, less than 1% analyte carryover is observed from well-to-well and signal intensity relative standard deviations (RSD) of 11.5% and 20.9% for 3 μM 1-hydroxymidazolam and 12 μM dextrorphan, respectively, are achieved. The ability to perform parallel kinetics studies on 384 samples with ~30s time resolution using an isocitrate dehydrogenase 1 (IDH1) enzyme assay is shown. Finally, we demonstrate the repeatability and throughput of our approach by measuring 115,200 samples from 300 microtiter plate reads consecutively over 5.54 hours with RSDs under 8.14% for each freshly introduced plate. Taken together, these results demonstrate the use of IR-MALDESI at sample acquisition rates that surpass other currently reported direct sampling mass spectrometry approaches used for high throughput compound screening.For Table of Contents Only