bluuebunny/crossref_metadata_2025_split huggingface dataset:
In vivo CRISPR screening identifies RNF20/40 as epigenetic regulators of cardiomyocyte maturation
Authors: VanDusen Nathan J. , Lee Julianna Y. , Gu Weiliang , Sethi Isha , Zheng Yanjiang , King Justin S. , Zhou Ping-Zhu , Suo Shengbao , Guo Yuxuan , Ma Qing , Yuan Guo-Cheng , Pu William T. 
Published: October 2019

ABSTRACTBetween birth and adulthood cardiomyocytes (CMs) undergo dramatic changes in size, ultrastructure, metabolism, and gene expression, in a process collectively referred to as CM maturation. The transcriptional network that coordinates CM maturation is poorly understood, creating a bottleneck for cardiac regenerative medicine. Forward genetic screens are a powerful, unbiased method to gain novel insights into transcriptional networks, yet this approach has rarely been used in vivo in mammals because of high resource demands. Here we utilized somatic mutagenesis to perform the first reported in vivo CRISPR genetic screen within a mammalian heart. We discovered and validated several novel transcriptional regulators of CM maturation. Among them were RNF20 and RNF40, which form a complex that monoubiquitinates H2B on lysine 120. Mechanistic studies indicated that this epigenetic mark controls dynamic changes in gene expression required for CM maturation. These insights into CM maturation will inform efforts in cardiac regenerative medicine. More broadly, our approach will enable unbiased forward genetics across mammalian organ systems.
Accurate and Complete Genomes from Metagenomes
Authors: Chen Lin-Xing , Anantharaman Karthik , Shaiber Alon , Eren A. Murat , Banfield Jillian F. 
Published: October 2019

AbstractGenomes are an integral component of the biological information about an organism and, logically, the more complete the genome, the more informative it is. Historically, bacterial and archaeal genomes were reconstructed from pure (monoclonal) cultures and the first reported sequences were manually curated to completion. However, the bottleneck imposed by the requirement for isolates precluded genomic insights for the vast majority of microbial life. Shotgun sequencing of microbial communities, referred to initially as community genomics and subsequently as genome-resolved metagenomics, can circumvent this limitation by obtaining metagenome-assembled genomes (MAGs), but gaps, local assembly errors, chimeras and contamination by fragments from other genomes limit the value of these genomes. Here, we discuss genome curation to improve and in some cases achieve complete (circularized, no gaps) MAGs (CMAGs). To date, few CMAGs have been generated, although notably some are from very complex systems such as soil and sediment. Through analysis of ~7000 published complete bacterial isolate genomes, we verify the value of cumulative GC skew in combination with other metrics to establish bacterial genome sequence accuracy. Interestingly, analysis of cumulative GC skew identified potential mis-assemblies in some reference genomes of isolated bacteria and the repeat sequences that likely gave rise to them. We discuss methods that could be implemented in bioinformatic approaches for curation to ensure that metabolic and evolutionary analyses can be based on very high-quality genomes.
DHHC20 palmitoyl-transferase reshapes the membrane to foster catalysis
Authors: Stix R. , Song J. , Banerjee A. , Faraldo-Gómez J.D. 
Published: October 2019

AbstractCysteine palmitoylation, a form of S-acylation, is a key post-translational modification in cellular signaling. This type of reversible lipidation is catalyzed by a family of integral membrane proteins known as DHHC acyltransferases. The first step in the S-acylation process is the recognition of free acyl-CoA from the lipid bilayer. The DHHC enzyme then becomes auto-acylated, at a site defined by a conserved Asp-His-His-Cys motif. This reaction entails ionization of the catalytic Cys. Intriguingly, in known DHHC structures this catalytic Cys appears to be exposed to the hydrophobic interior of the lipid membrane, which would be highly unfavorable for a negatively charged nucleophile, thus hindering auto-acylation. Here, we use biochemical and computational methods to reconcile these seemingly contradicting facts. First, we experimentally demonstrate that human DHHC20 is active when reconstituted in POPC nanodiscs. Microsecond-long all-atom molecular dynamics simulations are then calculated for hDHHC20 and for different acyl-CoA forms, also in POPC. Strikingly, we observe that hDHHC20 induces a drastic deformation in the membrane, particularly on the cytoplasmic side where auto-acylation occurs. As a result, the catalytic Cys becomes hydrated and optimally positioned to encounter the cleavage site in acyl-CoA. In summary, we hypothesize that DHHC enzymes locally reshape the membrane to foster a morphology that is specifically adapted for acyl-CoA recognition and auto-acylation.Significance StatementPalmitoylation, the most common form of S-acylation and the only reversible type of protein lipidation, is ubiquitous in eukaryotic cells. In humans, for example, it has been estimated that as much as ∼10% of the proteome becomes palmitoylated, i.e. thousands of proteins. Accordingly, protein palmitoylation touches every important aspect of human physiology, both in health and disease. Despite its biological and biomedical importance, little is known about the molecular mechanism of the enzymes that catalyze this post-translational modification, known as DHHC acyltransferases. Here, we leverage the recently-determined atomic-resolution structure of human DHHC20 to gain novel insights into the mechanism of this class of enzymes, using both experimental and computational approaches.
Antibody feedback limits the expansion of cognate memory B cells but drives the diversification of vaccine-induced antibody responses
Authors: McNamara Hayley A. , Idris Azza H. , Sutton Henry J. , Flynn Barbara J. , Cai Yeping , Wiehe Kevin , Lyke Kirsten E. , Chatterjee Deepyan , KC Natasha , Chakravarty Sumana , Sim B. Kim Lee , Hoffman Stephen L. , Bonsignori Mattia , Seder Robert A. , Cockburn Ian A. 
Published: October 2019

AbstractGenerating sufficient antibody to block infection is a key challenge for vaccines against malaria. Here we show that antibody titres to a key target, the repeat region of thePlasmodium falciparumcircumsporozoite protein (PfCSP), plateaued after two immunizations in a clinical trial of the radiation-attenuated sporozoite vaccine. To understand the mechanisms limiting vaccine responsiveness, we developed Ig-knockin mice with elevated numbers ofPfCSP-binding B cells. We determined that recall responses were inhibited by antibody feedback via epitope masking of the immunodominantPfCSP repeat region. Importantly, the amount of antibody that prevents boosting is below the amount of antibody required for protection. Finally, while antibody feedback limited responses to thePfCSP-repeat region in vaccinated volunteers, potentially protective subdominant responses to C-terminal regions did expand with subsequent boosts. These data suggest that antibody feedback drives the diversification of immune responses and that vaccination for malaria will require the targeting of multiple antigens.
The tip of the VgrG spike is essential to functional type VI secretion assembly in Acinetobacter baumannii
Authors: Lopez Juvenal , Ly Pek Man , Feldman Mario F. 
Published: October 2019

AbstractThe type VI secretion system (T6SS) is a critical weapon in bacterial warfare between Gram-negative bacteria. Although invaluable for niche establishment, this machine represents an energetic burden to its host bacterium. Acinetobacter baumannii is an opportunistic pathogen that poses a serious threat to public health due to its high rates of multidrug resistance. In some A. baumannii strains, the T6SS is transcriptionally downregulated by large multidrug-resistance plasmids. Other strains, such as the clinical isolate AbCAN2, express T6SS-related genes but lack T6SS activity under laboratory conditions, despite not harboring these plasmids. This suggests that alternative mechanisms exist to repress the T6SS. Here, we employed a transposon mutagenesis approach in AbCAN2 to identify novel T6SS repressors. Our screen revealed that the T6SS of this strain is inhibited by a homolog of VgrG, an essential structural component of all T6SSs reported to date. We named this protein inhibitory VgrG (VgrGi). Biochemical and in silico analyses demonstrated that the unprecedented inhibitory capability of VgrGi is due to a single amino acid mutation in the widely conserved C-terminal domain of unknown function DUF2345. We also show that unlike in other bacteria, the C-terminus of VgrG is essential for functional T6SS assembly in A. baumannii. Our study provides insight into the architectural requirements underlying functional assembly of the T6SS of A. baumannii. We propose that T6SS-inactivating point mutations are beneficial to the host bacterium, as they eliminate the energy cost associated with maintaining a functional T6SS, which appears to be unnecessary for A. baumannii virulence.ImportanceDespite the clinical relevance of A. baumannii, little is known about its fundamental biology. Here, we show that a single amino acid mutation in VgrG, a critical T6SS structural protein, abrogates T6SS function. Given that this mutation was found in a clinical isolate, we propose that the T6SS of A. baumannii is likely not involved in virulence, an idea supported by multiple genomic analyses showing that the majority of clinical A. baumannii strains lack proteins essential to the T6SS. We also show that, unlike in other species, the C-terminus of VgrG is a unique architectural requirement for functional T6SS assembly in A. baumannii, suggesting that over evolutionary time, bacteria have developed changes to their T6SS architecture, leading to specialized systems.
Area requirements to safeguard Earth’s marine species
Authors: Jones Kendall R. , Klein Carissa , Grantham Hedley S. , Possingham Hugh P. , Halpern Benjamin S. , Burgess Neil D. , Butchart Stuart H.M. , Robinson John G. , Kingston Naomi , Watson James E.M. 
Published: October 2019

AbstractDespite global policy commitments to preserve Earth’s marine biodiversity, many species are in a state of decline. Using data on 22,885 marine species, we identify 8.5 million km2 of priority areas that complement existing areas of conservation and biodiversity importance. New conservation priorities are found in over half (56%) of all coastal nations, with key priority regions in the northwest Pacific Ocean and Atlantic Ocean. We identify where different conservation actions, ranging from marine protected areas to broader policy approaches, may best overcome anthropogenic threats to these areas. This analysis shows 26-41% of the ocean (depending on targets used for species representation) needs to be effectively conserved through a combination of site-based actions and wider policy responses to achieve global conservation and sustainable development agendas.One Sentence SummaryAt least 26% of the ocean needs a combination of site-based conservation and wider policy responses to achieve global conservation goals.
Clustered Functional Domains for Curves and Corners in Cortical Area V4
Authors: Jiang Rundong , Andolina Ian M. , Li Ming , Tang Shiming 
Published: October 2019

AbstractThe ventral visual pathway is crucially involved in integrating low-level visual features into complex representations for objects and scenes. At an intermediate stage of the ventral visual pathway, V4 plays a crucial role in supporting this transformation. Many V4 neurons are selective for shape segments like curves and corners, however it remains unclear whether these neurons are organized into clustered functional domains, a structural motif common across other visual cortices. Using two-photon calcium imaging in awake macaques, we confirmed and localized cortical domains selective for curves or corners in V4. Single-cell resolution imaging confirmed that curve or corner selective neurons were spatially clustered into such domains. When tested with hexagonal-segment stimuli, we find that stimulus smoothness is the cardinal difference between curve and corner selectivity in V4. Combining cortical population responses with single neuron analysis, our results reveal that curves and corners are encoded by neurons clustered into functional domains in V4. This functionally-specific population architecture bridges the gap between the early and late cortices of the ventral pathway and may serve to facilitate complex object recognition.
Evaluation of Commercially Available Exosomal Isolation Kits from Human Plasma
Authors: Sun Yuzhe , Zhen Hefu , Guo Mei , Ye Jingyu , Liu Zhili , Zhang Xiuqing , Yang Yan , Nie Chao 
Published: October 2019

AbstractExosomes are cell-derived lipid bilayer particles which are abundant in biological fluids. Exosome is an emerging source of biomarkers to diagnose various human diseases. Sequencing based exosomal studies could provide a comprehensive view of exosomal RNA and protein. To extracted these inclusions, exosomes should be isolated from the plasma first. Several exosome isolation methods were introduced since the discover of exosome. To promote the clinical application of exosomal inclusions, different isolation methods should be compared. We isolated exosomes from human plasma by using user-friendly and commercially available kits, SBI ExoQuick and QIAGEN exoRNeasy. Subsequently, small RNA sequencing was performed with two groups of isolated exosome samples and one group of plasma samples. No fundamental differences of exRNA yield between SC and EQ were found. In RNA profile analysis, the small RNA aligned reads, miRNA pattern, sample clustering varied as a result of methodological differences. Small RNA isolated by ExoQuick presented better data quality and RNA profile than exoRNeasy. This study compared sRNA sequencing data generated from two exosome isolation kits, it provides a reference for future small RNA studies and biomarker prediction in human plasma exosome.
Harm to others acts as a cingulate dependent negative reinforcer in rat
Authors: Hernandez-Lallement Julen , Attah Augustine Triumph , Gazzola Valeria , Keysers Christian 
Published: October 2019

SummaryEmpathy, the ability to share another individual’s emotional state and/or experience, has been suggested to be a source of prosocial motivation by making actions that harm others aversive. The neural underpinnings and evolution of such harm aversion remain poorly understood. Here, we characterize an animal model of harm aversion in which a rat can choose between two levers providing equal amounts of food, but one additionally delivering a footshock to a neighboring rat. We find that independently of sex and familiarity, rats reduce their usage of the preferred lever when it causes harm to a conspecific, displaying an individually varying degree of harm aversion. Prior experience with pain increases this effect. In additional experiments, we show that rats reduce the usage of the harm-inducing lever when it delivers twice, but not thrice the number of pellets than the non-preferred lever, setting boundaries on the magnitude of harm aversion. Finally, we show that pharmacological deactivation of the anterior cingulate cortex, a region we have shown to be essential for emotional contagion, reduces harm aversion, while leaving behavioral flexibility unaffected. This model of harm aversion might help shed light onto the neural basis of psychiatric disorders characterized by reduced harm aversion, including psychopathy and conduct disorders with reduced empathy, and provide an assay for the development of pharmacological treatments of such disorders.
How long is long enough? Decreasing on plant extract lethal effects, over time, affectingAedes aegyptilarval mortality
Authors: Cozzer Gilberto Dinis , de Souza Rezende Renan , Lutinski Junir Antônio , Junior Walter Antônio Roman , Busato Maria Assunta , Dal Magro Jacir , Albeny-Simões Daniel 
Published: October 2019

AbstractThe mosquitoAedes aegyptihas overcome all kinds of human being mosquito control attempts over the last century. Strategies for vector population control resorts to the use of synthetic insecticides, which can lead to problems of intoxication in humans and environmental contamination. We evaluated the effects ofBacillus thuringiensisvar.israelensis(Bti),Ilex paraguariensis(mate-herb) andIlex theezans(caúna-herb) extracts againstA. aegyptilarvae mortality. The bioassays were conducted under controlled laboratory conditions of temperature (27±3°C) and photoperiod (12h). HydroalcoholicI. theezansleaves extract displayed better residual effect compared toI. paraguariensisfruit aqueous extract. Variation in larval mortality was also observed in the exposure periods (low after a few weeks). Low mortality after a few weeks may mean increased the food for mosquito in a oppose effect over time. The residual effect ofBtiwas observed during the 56 days of the study duration (100% of mortality). The strongest residual effect ofI. theezanswas probably due to the presence of chemical on its leaves, such coumarins, hemolytic saponins and cyanogenic glucosides, absent inI. paraguariensis. On the other hand, alternative methods to vector control present risks in a long term scale by reversal of larvicide effect into food resource. Our results contributed to the prospection of natural insecticides and open the possibility for subsequent studies of the use of plant extracts in field situations in a short time scale.
Downregulation of a satiety signal from peripheral fat bodies improves visual attention while reducing sleep need inDrosophila
Authors: Ertekin Deniz , Kirszenblat Leonie , Faville Richard , van Swinderen Bruno 
Published: October 2019

AbstractSleep is vital for survival. Yet, under environmentally challenging conditions such as starvation, animals suppress their need for sleep. Interestingly, starvation-induced sleep loss does not evoke a subsequent sleep rebound. Little is known about how starvation-induced sleep deprivation differs from other types of sleep loss, or why some sleep functions become dispensable during starvation. Here we demonstrate that downregulation of unpaired-2 (upd2, theDrosophilaortholog of leptin), is sufficient to mimic a starved-like state in flies. We use this ‘genetically starved’ state to investigate the consequences of a starvation signal on visual attention and sleep in otherwise well-fed flies, thereby sidestepping the negative side-effects of undernourishment. We find that knockdown ofupd2in the fat body is sufficient to suppress sleep while also increasing selective visual attention and promoting night-time feeding. Further, we show that this peripheral signal is integrated in the fly brain via insulin-expressing cells. Together, these findings identify a role for peripheral tissue-to-brain interactions in the simultaneous regulation of sleep and attention, to potentially promote adaptive behaviors necessary for survival in hungry animals.Author SummarySleep is important for maintaining both physiological (e.g., metabolic, immunological, and developmental) and cognitive processes, such as selective attention. Under nutritionally impoverished conditions, animals suppress sleep and increase foraging to locate food. Yet it is currently unknown how an animal is able to maintain well-tuned cognitive processes, despite being sleep deprived. Here we investigate this question by studying flies that have been genetically engineered to lack a satiety signal, and find that signaling from fat bodies in the periphery to insulin-expressing cells in the brain simultaneously regulates sleep need and attention-like processes.
Expressional artifact caused by a co-injection markerrol-6inC. elegans
Authors: Jin HoYong , Emmons Scott W. , Kim Byunghyuk 
Published: October 2019

ABSTRACTIn transgenic research, selection markers have greatly facilitated the generation of transgenic animals. A prerequisite for a suitable selection marker to be used along with a test gene of interest is that the marker should not affect the phenotype of interest in transformed animals. One of the most common selection markers used inC. eleganstransgenic approaches is therol-6co-injection marker, which induces a behavioral roller phenotype due to a cuticle defect but is not known to have other side effects. However, we found that therol-6co-injection marker can cause expression of GFP in the test sequence in a male-specific interneuron called CP09. We found that therol-6gene sequence included in the marker plasmid is responsible for this unwanted expression. Accordingly, the use of therol-6co-injection marker is not recommended when researchers intend to examine precise expression or perform functional studies especially targeting maleC. elegansneurons. Therol-6sequence region we identified can be used to drive a specific expression in CP09 neuron for future research.
Mapping and DNA sequence characterisation of the Rysto locus conferring extreme virus resistance to potato cultivar ‘White Lady’
Authors: Kondrák Mihály , Kopp Andrea , Uri Csilla , Sós-Hegedűs Anita , Csákvári Edina , Schiller Mátyás , Barta Endre , Cernák István , Polgár Zsolt , Taller János , Bánfalvi Zsófia 
Published: October 2019

AbstractVirus resistance genes carried by wild plant species are valuable resources for plant breeding. The Rysto gene, conferring a broad spectrum of durable resistance, originated from Solanum stoloniferum and was introgressed into several commercial potato cultivars, including ‘White Lady’, by classical breeding. Rysto was mapped to chromosome XII in potato, and markers used for marker-assisted selection in breeding programmes were identified. Nevertheless, there was no information on the identity of the Rysto gene. To begin to reveal the identification of Rysto, fine-scale genetic mapping was performed which, in combination with chromosome walking, narrowed down the locus of the gene to approximately 1 Mb. DNA sequence analysis of the locus identified six full-length NBS-LRR-type (short NLR-type) putative resistance genes. Two of them, designated TMV2 and TMV3, were similar to a TMV resistance gene isolated from tobacco and to Y-1, which co-segregates with Ryadg, the extreme virus resistance gene originated from Solanum andigena and localised to chromosome XI. Furthermore, TMV2 of ‘White Lady’ was found to be 95% identical at the genomic sequence level with the recently isolated Rysto gene of the potato cultivar ‘Alicja’. In addition to the markers identified earlier, this work generated five tightly linked new markers which can serve potato breeding efforts for extreme virus resistance.
Ablation of Arf-expressing cells ameliorates cigarette smoke-induced lung dysfunction in mice
Authors: Mikawa Ryuta , Sato Tadashi , Suzuki Yohei , Baskoro Hario , Sugimoto Masataka 
Published: October 2019

AbstractSenescent cells accumulate in tissues during aging or pathological settings. The semi-genetic or pharmacological targeting of senescent cells revealed that cellular senescence underlies many aspects of the aging-associated phenotype and diseases. We previously reported that cellular senescence contributes to aging- and disease-associated pulmonary dysfunction. We herein report that the elimination of Arf-expressing senescent cells ameliorates cigarette smoke-induced lung pathologies in mice. Cigarette smoke induced the expression of Ink4a and Arf in lung tissue with concomitant increases in lung tissue compliance and alveolar airspace. The elimination of Arf-expressing senescent cells prior to cigarette smoke exposure protected against these changes. Furthermore, the administration of cigarette smoke extract lead to pulmonary dysfunction, which was ameliorated by subsequent senescent cell elimination. Collectively, these results suggest that senescent cells are a potential therapeutic target for cigarette smoking-associated lung disease.