bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alternative end-joining results in smaller deletions in heterochromatin relative to euchromatin
Authors: Miller Jacob M. , Prange Sydney , Ji Huanding , Rau Alesandra R. , Khodaverdian Varandt Y. , Li Xiao , Patel Avi , Butova Nadejda , Lutter Avery , Chung Helen , Merigliano Chiara , Rawal Chetan C. , Hanscom Terrence , McVey Mitch , Chiolo Irene 
Published: March 2023

ABSTRACTPericentromeric heterochromatin is highly enriched for repetitive sequences prone to aberrant recombination. Previous studies showed that homologous recombination (HR) repair is uniquely regulated in this domain to enable ‘safe’ repair while preventing aberrant recombination. InDrosophilacells, DNA double-strand breaks (DSBs) relocalize to the nuclear periphery through nuclear actin-driven directed motions before recruiting the strand invasion protein Rad51 and completing HR repair. End-joining (EJ) repair also occurs with high frequency in heterochromatin of fly tissues, but how alternative EJ (alt-EJ) pathways operate in heterochromatin remains largely uncharacterized. Here, we induce DSBs in single euchromatic and heterochromatic sites using a new system that combines the DR-whitereporter and I-SceI expression in spermatogonia of flies. Using this approach, we detect higher frequency of HR repair in heterochromatin, relative to euchromatin. Further, sequencing of mutagenic repair junctions reveals the preferential use of different EJ pathways across distinct euchromatic and heterochromatic sites. Interestingly, synthesis-dependent microhomology-mediated end joining (SD-MMEJ) appears differentially regulated in the two domains, with a preferential use of motifs close to the cut site in heterochromatin relative to euchromatin, resulting in smaller deletions. Together, these studies establish a new approach to study repair outcomes in fly tissues, and support the conclusion that heterochromatin uses more HR and less mutagenic EJ repair relative to euchromatin.
A redox-regulated, heterodimeric NADH:cinnamate reductase inVibrio ruber
Authors: Bertsova Yulia V. , Serebryakova Marina V. , Anashkin Victor A. , Baykov Alexander A. , Bogachev Alexander V. 
Published: March 2023

AbstractGenes of putative reductases of α,β-unsaturated carboxylic acids are abundant among anaerobic and facultatively anaerobic microorganisms, yet substrate specificity has been experimentally verified for few encoded proteins. Here, we co-produced inEscherichia colione such protein of the marine bacteriumVibrio ruber(GenBank SJN56021; annotated as urocanate reductase) withVibrio choleraeflavin transferase. The isolated protein (named Crd) is a heterodimer of the SJN56021-encoded subunit CrdB (NADH:flavin, FAD binding 2, andFMN binddomains) and an additional subunit CrdA (SJN56019, a singleNADH:flavindomain) that interact via theirNADH:flavindomains (Alphafold2 prediction). Each domain contains a flavin group (three FMNs and one FAD in total), one of the FMN groups being linked covalently by the flavin transferase. Crd readily reduces cinnamate,p-coumarate, caffeate, and ferulate under anaerobic conditions with NADH or methyl viologen as the electron donor, is moderately active against acrylate and practically inactive against urocanate. The reduction reactions started by NADH demonstrated a time lag of several minutes, suggesting a redox regulation of Crd activity. The oxidized enzyme is inactive, which apparently prevents production of reactive oxygen species under aerobic conditions. Our findings identify Crd as a regulated NADH-dependent cinnamate reductase, apparently protectingV. ruberfrom cinnamate poisoning.Abbreviated SummaryThe genome of the marine bacteriumVibrio ruberencodes a heterodimeric NADH-dependent cinnamate reductase, apparently protectingV. ruberfrom poisoning by cinnamate and its derivatives. The reductase contains four flavin groups, one being linked covalently, and appears to be redox-regulated. Oxidized enzyme is inactive, which apparently prevents production of reactive oxygen species under aerobic conditions.
Brain areas for reversible symbolic reference, a potential singularity of the human brain
Authors: van Kerkoerle Timo , Pape Louise , Ekramnia Milad , Feng Xiaoxia , Tasserie Jordy , Dupont Morgan , Li Xiaolian , Jarraya Bechir , Vanduffel Wim , Dehaene Stanislas , Dehaene-Lambertz Ghislaine 
Published: March 2023

AbstractThe emergence of symbolic thinking has been proposed as a dominant cognitive criterion to distinguish humans from other primates during hominization. Although the proper definition of a symbol has been the subject of much debate, one of its simplest features is bidirectional attachment: the content is accessible from the symbol, and vice versa. Behavioural observations scattered over the past four decades suggest that this criterion might not be met in non-human primates, as they fail to generalise an association learned in one temporal order (A to B) to the reverse order (B to A). Here, we designed an implicit fMRI test to investigate the neural mechanisms of arbitrary audio-visual and visual-visual pairing in monkeys and humans and probe their spontaneous reversibility. After learning a unidirectional association, humans showed surprise signals when this learned association was violated. Crucially, this effect occurred spontaneously in both learned and reversed directions, within an extended network of high-level brain areas, including, but also going beyond, the language network. In monkeys, by contrast, violations of association effects occurred solely in the learned direction and were largely confined to sensory areas. We propose that a human-specific brain network may have evolved the capacity for reversible symbolic reference.
ProteinVAE: Variational AutoEncoder for Translational Protein Design
Authors: Lyu Suyue , Sowlati-Hashjin Shahin , Garton Michael 
Published: March 2023

AbstractThere have recently been rapid advances in deep learning models for protein design. To demonstrate proof-of-concept, these advancements have focused on small proteins with lots of data for training. This means that they are often not suitable for generating proteins with the most potential for high clinical impact –due to the additional challenges of sparse data and large size many therapeutically relevant proteins have. One major application that fits this category is gene therapy delivery. Viral vectors such as Adenoviruses and AAVs are a common delivery vehicle for gene therapy. However, environmental exposure means that most people exhibit potent pre-existing immune responses to many serotypes. This response, primarily driven by neutralizing antibodies, also precludes repeated administration with the same serotype. Rare serotypes, serotypes targeting other species, and capsid engineering, have all been deployed in the service of reducing neutralization by pre-existing antibodies. However, progress has been very limited using conventional methods and a new approach is urgently needed. To address this, we developed a variational autoencoder that can generate synthetic viral vector serotypes without epitopes for pre-existing neutralizing antibodies. A compact generative computational model was constructed, with only 12.4 million parameters that could be efficiently trained on the limited natural sequences (e.g., 711 natural Adenovirus hexon sequences with average length of 938 amino acids). In contrast to the current state-of-the-art, the model was able to generate high-quality Adenovirus hexon sequences that were folded with high confidence by Alphafold2 to produce structures essentially identical to natural hexon structures. Molecular dynamics simulations confirmed that the structures are stable and protein–protein interfaces are intact. Local secondary structure and local mobility is also comparable with natural serotype behavior. Our model could be used to generate a broad range of synthetic adenovirus serotype sequences without epitopes for pre-existing neutralizing antibodies in the human population. It could be used more broadly to generate different types of viral vector, and any large, therapeutically valuable proteins, where available data is sparse.
Chromatin binding by HORMAD proteins regulates meiotic recombination initiation
Authors: Milano Carolyn R. , Ur Sarah N. , Gu Yajie , Tromer Eelco C. , Zhang Jessie , Hochwagen Andreas , Corbett Kevin D. 
Published: March 2023

AbstractThe meiotic chromosome axis coordinates chromosome organization and interhomolog recombination in meiotic prophase and is essential for fertility. InS. cerevisiae, the HORMAD protein Hop1 mediates enrichment of axis proteins at nucleosome-rich genomic islands through a central chromatin-binding region (CBR). Here, we use cryoelectron microscopy to show that the Hop1 CBR directly recognizes bent nucleosomal DNA through a composite interface in its PHD and winged helix-turn-helix domains. Targeted disruption of the Hop1 CBR-nucleosome interface causes loss of axis proteins from nucleosome-rich islands, reduces meiotic DNA double-strand breaks (DSBs), and leads to defects in chromosome synapsis. Synthetic effects with the disassemblase Pch2 suggest that nucleosome binding delays a conformational switch in Hop1 from a DSB-promoting, Pch2-inaccessible state to a DSB-inactive, Pch2-accessible state to regulate the extent of meiotic DSB formation. Phylogenetic analyses of meiotic HORMADs reveal an ancient origin of this domain, suggesting that these mechanisms are broadly conserved.
Performance of ChatGPT on the MCAT: The Road to Personalized and Equitable Premedical Learning
Authors: Bommineni Vikas L , Bhagwagar Sanaea , Balcarcel Daniel , Davatzikos Christos , Boyer Donald 
Published: March 2023

ABSTRACTDespite an increasingly diverse population, an unmet demand for undergraduates from underrepresented racial and ethnic minority (URM) backgrounds exists in the field of medicine as a result of financial hurdles and insufficient educational support faced by URM students in the premedical journey. With the capacity to provide highly individualized and accessible no- or low-cost dynamic instruction, large language models (LLMs) and their chatbot derivatives are posed to change this dynamic and subsequently help shape a more diverse future physician workforce. While studies have established the passing performance and insightful explanations of one of the most accurate LLM-powered chatbots to date—Chat Generative Pre-trained Transformer (ChatGPT)—on standardized exams such as medical licensing exams, the role of ChatGPT in premedical education remains unknown. We evaluated the performance of ChatGPT on the Medical College Admission Test (MCAT), a standardized 230-question multiple choice exam that assesses a broad range of competencies in the natural, physical, social, and behavioral sciences as well as critical analysis and reasoning. Depending on its visual item response strategy, ChatGPT performed at or above the median performance of 276,779 student test takers on the MCAT. Additionally, ChatGPT-generated answers demonstrated both a high level of agreement with the official answer key as well as insight into its explanations. Based on these promising results, we anticipate two primary applications of ChatGPT and future LLM iterations in premedical education: firstly, such models could provide free or low-cost access to personalized and insightful explanations of MCAT competency-related questions to help students from all socioeconomic and URM backgrounds. Secondly, these models could be used to generate additional test questions by test-makers or for targeted preparation by pre-medical students. These applications of ChatGPT in premedical education could be an invaluable, innovative path forward to increase diversity and improve equity among premedical students.
Digitally Diagnosing Multiple Developmental Delays using Crowdsourcing fused with Machine Learning: A Research Protocol
Authors: Washington Peter 
Published: March 2023

AbstractBackgroundRoughly 17% percent of minors in the United States aged 3 through 17 years have a diagnosis of one or more developmental or psychiatric conditions, with the true prevalence likely being higher due to underdiagnosis in rural areas and for minority populations. Unfortunately, timely diagnostic services are inaccessible to a large portion of the United States and global population due to cost, distance, and clinician availability. Digital phenotyping tools have the potential to shorten the time-to-diagnosis and to bring diagnostic services to more people by enabling accessible evaluations. While automated machine learning (ML) approaches for detection of pediatric psychiatry conditions have garnered increased research attention in recent years, existing approaches use a limited set of social features for the prediction task and focus on a single binary prediction.ObjectiveI propose the development of a gamified web system for data collection followed by a fusion of novel crowdsourcing algorithms with machine learning behavioral feature extraction approaches to simultaneously predict diagnoses of Autism Spectrum Disorder (ASD) and Attention-Deficit/Hyperactivity Disorder (ADHD) in a precise and specific manner.MethodsThe proposed pipeline will consist of: (1) a gamified web applications to curate videos of social interactions adaptively based on needs of the diagnostic system, (2) behavioral feature extraction techniques consisting of automated ML methods and novel crowdsourcing algorithms, and (3) development of ML models which classify several conditions simultaneously and which adaptively request additional information based on uncertainties about the data.ConclusionsThe prospective for high reward stems from the possibility of creating the first AI-powered tool which can identify complex social behaviors well enough to distinguish conditions with nuanced differentiators such as ASD and ADHD.
Zfp106 binds to G-quadruplex RNAs and inhibits RAN translation and formation of RNA foci caused by G4C2 repeats
Authors: Celona Barbara , Wu Haifan , Dang Bobo , Kratochvil Huong T. , DeGrado William F. , Black Brian L. 
Published: March 2023

ABSTRACTExpansion of intronic GGGGCC repeats in theC9orf72gene causes amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Transcription of the expanded repeats results in the formation of RNA-containing nuclear foci and altered RNA metabolism. In addition, repeat-associated non-AUG (RAN) translation of the expanded GGGGCC-repeat sequence results in the production of highly toxic dipeptide-repeat (DPR) proteins. GGGGCC-repeat-containing transcripts form G-quadruplexes, which are associated with formation of RNA foci and RAN translation. Zfp106, an RNA-binding protein essential for motor neuron survival in mice, suppresses neurotoxicity in aDrosophilamodel ofC9orf72ALS via a previously unknown mechanism. Here, we show that Zfp106 inhibits formation of RNA foci and significantly reduces RAN translation caused by GGGGCC-repeats in mammalian cells. Further, we show that Zfp106 binds to RNA G-quadruplexes and causes a conformational change in the G-quadruplex structure formed by GGGGCC-repeats. These data suggest that Zfp106 suppresses GGGGCC repeat-mediated cytotoxicity through alteration of the repeat’s G-quadruplex structure.
FBP1 is a nonenzymatic safety valve that curtails AKT activation to prevent insulin hyperresponsiveness
Authors: Gu Li , Zhu Yahui , Watari Kosuke , Lee Maiya , Liu Junlai , Perez Sofia , Thai Melinda , Mayfield Joshua , Zhang Bichen , Rocha Karina Cunha e , Li Fuming , Kim Laura C. , Jones Alexander C. , Wierzbicki Igor H , Liu Xiao , Newton Alexandra C. , Kisseleva Tatiana , Lee Jun Hee , Ying Wei , Gonzalez David J. , Saltiel Alan R. , Simon M. Celeste , Karin Michael 
Published: March 2023

SUMMARYInsulin inhibits gluconeogenesis and stimulates glucose conversion to glycogen and lipids. How these activities are coordinated to prevent hypoglycemia and hepatosteatosis is not clear. Fructose-1,6 bisphosphatase (FBP1) is rate controlling for gluconeogenesis. However, inborn human FBP1 deficiency does not cause hypoglycemia unless accompanied by fasting or starvation, which also trigger paradoxical hepatomegaly, hepatosteatosis, and hyperlipidemia in affected individuals. Hepatocyte FBP1-ablated mice exhibit identical fasting-conditional pathologies along with AKT hyperactivation, whose inhibition reversed hepatomegaly, hepatosteatosis and hyperlipidemia but not hypoglycemia. Surprisingly, fasting-mediated AKT hyperactivation is insulin-dependent. FBP1 prevents insulin hyperresponsiveness, independently of its catalytic activity, by interacting with AKT, PP2A-C and Aldolase-B (ALDOB) to specifically accelerate AKT dephosphorylation. Enhanced by fasting and weakened by elevated insulin, FBP1:AKT:PP2A-C:ALDOB complex formation, which is disrupted by human FBP1 deficiency mutations or a C-terminal FBP1 truncation, prevents insulin-triggered liver pathologies and maintains lipid and glucose homeostasis. Conversely, a complex disrupting peptide reverses diet-induced insulin resistance.
Differential requirements for different subfamilies of the mammalian SWI/SNF chromatin remodeling enzymes in myoblast differentiation
Authors: Padilla-Benavides Teresita , Olea-Flores Monserrat , Sharma Tapan , Syed Sabriya A. , Witwicka Hanna , Zuñiga-Eulogio Miriam D. , Zhang Kexin , Navarro-Tito Napoleon , Imbalzano Anthony N. 
Published: March 2023

AbstractMammalian SWI/SNF (mSWI/SNF) complexes are ATP-dependent chromatin remodeling enzymes that are critical for normal cellular functions and that are mis-regulated in ∼20% of human cancers. These enzymes exhibit significant diversity in the composition of individual enzyme complexes. mSWI/SNF enzymes are classified into three general sub-families based on the presence or absence of specific subunit proteins. The three sub-families are called BAF (BRM or BRG1-associated factors), ncBAF (non-canonical BAF), and PBAF (Polybromo-associated BAF). The biological roles for the different subfamilies of mSWI/SNF enzymes are poorly described. We knocked down (KD) the expression of genes encoding subunit proteins unique to each of the three subfamilies,Baf250A, Brd9, andBaf180, which mark the BAF, ncBAF, and PBAF sub-families, respectively, and examined the requirement for each in myoblast differentiation. We found that BAF250A and the BAF complex was required to drive lineage-specific gene expression during myoblast differentiation. KD ofBaf250Areduced the expression of the lineage determinantMyogeninand other differentiation markers, due to decreased binding of BAF250A to myogenic gene promoters. KD ofBrd9delayed myoblast differentiation. However, RNA-seq analysis revealed that while theBaf250A-dependent gene expression profile included genes involved in myogenesis, theBrd9-dependent gene expression profile did not. Moreover, no-colocalization of Baf250A and Brd9 was observed in differentiating cells, suggesting independent mechanisms of action for BAF and ncBAF complexes in myogenesis. The PBAF complex was dispensable for myoblast differentiation. The results distinguish between the roles of the mSWI/SNF enzyme subfamilies during myoblast differentiation.
Transcription factor interactions explain the context-dependent activity of CRX binding sites
Authors: Loell Kaiser J. , Friedman Ryan Z. , Myers Connie A. , Corbo Joseph C. , Cohen Barak A. , White Michael A. 
Published: March 2023

AbstractThe effects of transcription factor binding sites (TFBSs) on the activity of acis-regulatory element (CRE) depend on the local sequence context. In rod photoreceptors, binding sites for the transcription factor (TF) Cone-rod homeobox (CRX) occur in both enhancers and silencers, but the sequence context that determines whether CRX binding sites contribute to activation or repression of transcription is not understood. To investigate the context-dependent activity of CRX sites, we fit neural network-based models to the activities of synthetic CREs composed of photoreceptor TFBSs. The models revealed that CRX binding sites consistently make positive, independent contributions to CRE activity, while negative homotypic interactions between sites cause CREs composed of multiple CRX sites to function as silencers. The effects of negative homotypic interactions can be overcome by the presence of other TFBSs that either interact cooperatively with CRX sites or make independent positive contributions to activity. The context-dependent activity of CRX sites is thus determined by the balance between positive heterotypic interactions, independent contributions of TFBSs, and negative homotypic interactions. Our findings explain observed patterns of activity among genomic CRX-bound enhancers and silencers, and suggest that enhancers may require diverse TFBSs to overcome negative homotypic interactions between TFBSs.
Rapid generation ofC. eleganssingle copy transgenes combining RMCE and drug selection
Authors: Nonet Michael L. 
Published: March 2023

AbstractI outline a streamlined method to create single copy large genomic insert transgenes using Recombination-Mediated Cassette Exchange (RMCE) that relies solely on drug selection yielding a homozygous fluorescent protein (FP) marked transgene in 3 generations (8 days) at high efficiency (>1 insertion per 2 injected P0 animals). Landing sites for this approach are available on four chromosomes in several configurations which yield lines marked in distinct cell types. An array of vectors permit creating transgenes using a variety of selection methods (HygR, NeoR, PuroR, unc-119(+)) that yield lines expressing different colored FP tagged lines (BFP, GFP, mNG, andScarlet). Although these transgenes retain a plasmid backbone and a selection marker, the inclusion of these sequences typically does not alter the expression of several cell specific promoters tested. However, in certain orientations promoters exhibits crosstalk with adjacent transcription units. In cases where crosstalk is problematic, theloxP-flanked fluorescent marker, plasmid backbone andhygRgene can be excised by crossing through germline Cre expressing lines also created using this technique. Finally, genetic and molecular reagents designed to facilitate customization of both targeting vectors and landing sites are also described. Together, the rRMCE toolbox provides a platform for developing further innovative uses of RMCE to create complex genetically engineered tools.