bluuebunny/crossref_metadata_2025_split huggingface dataset:
CRISPR-based gene drives generate super-Mendelian inheritance in the disease vectorCulex quinquefasciatus
Authors: Harvey-Samuel Tim , Feng Xuechun , Okamoto Emily M. , Purusothaman Deepak-Kumar , Leftwich Philip T. , Alphey Luke , Gantz Valentino M. 
Published: June 2023

ABSTRACTCulexmosquitoes pose a significant public health threat as vectors for a variety of diseases including West Nile virus and lymphatic filariasis, and transmit pathogens threatening livestock, companion animals, and endangered birds. Rampant insecticide resistance makes controlling these mosquitoes challenging and necessitates the development of new control strategies. Gene drive technologies have made significant progress in other mosquito species, although similar advances have been lagging inCulex. Here we test the first CRISPR-based homing gene drive forCulex quinquefasciatus, demonstrating the possibility of using this technology to controlCulexmosquitoes. Our results show that the inheritance of two split-gene-drive transgenes, targeting different loci, are biased in the presence of a Cas9-expressing transgene although with modest efficiencies. Our findings extend the list of disease vectors where engineered homing gene drives have been demonstrated to includeCulexalongsideAnophelesandAedes, and pave the way for future development of these technologies to controlCulexmosquitoes.
Consideration of sex as a biological variable in diabetes research across twenty years
Authors: Cherian Celena , Reeves Hayley , De Silva Duneesha , Tsao Serena , Marshall Katie E. , Rideout Elizabeth J. 
Published: June 2023

ABSTRACTSex differences exist in the risk of developing both type 1 and type 2 diabetes, and in the risk of developing diabetes-associated complications. Sex differences in glucose homeostasis, islet and β cell biology, and peripheral insulin sensitivity have also been reported in multiple animals. To determine the degree to which biological sex has been addressed in published literature related to diabetes and insulin biology, we developed a scoring system to assess the inclusion of biological sex in papers related to these topics. We scored manuscripts published inDiabetes, published by the American Diabetes Association, as this journal focuses on diabetes and diabetes-related research. We scored papers published across three years within a 20-year period (1999, 2009, 2019), a timeframe that spans the introduction of funding agency and journal policies to improve the consideration of biological sex as a variable. Our analysis shows fewer than 15% of papers used sex-based analysis in even one figure across all study years, a trend that was reproduced across journal-defined categories of diabetes research (e.g., islet studies, signal transduction). Single-sex studies accounted for approximately 40% of all manuscripts, of which >87% used male subjects only. While we observed a modest increase in the overall inclusion of sex as a biological variable during our study period, our results highlight significant opportunities to improve consideration of sex as a biological variable in diabetes research. In particular, we show that journal policies represent one way to promote better consideration of biological sex as a variable. In the long term, improved practices will reveal sex-specific mechanisms underlying diabetes risk and complications, generating insights to support the development of sex-informed prevention and treatment strategies.
Gut microbiota dysbiosis observed in tuberculosis patients resolves partially with anti-tuberculosis therapy
Authors: Sahu Sukanya , Kaushik Sandeep R. , Chaudhary Shweta , Mahapatra Amit kumar , Kappa Rukuwe , Kapfo Wetesho , Saha Sourav , Das Ranjit , Das Anjan , Khamo Vinotsole , Nanda Ranjan Kumar 
Published: June 2023

ABSTRACTObjectiveMycobacterium tuberculosis(Mtb) primarily affects the lungs with involvement of other organs causing tuberculosis (TB) in humans. Since the lung-gut axis is bidirectional, and the gut microbiota contributes to metabolic and immune homeostasis, we looked at the gut microbiota and metabolites of TB patients and controls, and whether the perturbations, if any, resolve with anti-tuberculosis treatment.MethodsIn this multicentric case-control study, a total of 107 fecal samples belonging to drug naïve active tuberculosis (ATB) patients and controls (non-tuberculosis: NTB and healthy), were collected from two clinical sites in India. A group of drug-naïve ATB patients (n=10) from one site was followed-up and monitored at 2, 4, 6, and 8 months of their anti-tuberculosis treatment. The fecal microbiome and metabolome of these study participants were characterized by 300 bp pair end sequencing of the V3-V4 region of 16S rRNA gene and gas chromatography-time of flight-mass spectrometry (GC-TOF-MS) respectively to identify disease and treatment-specific variations, if any.ResultsDrug naïveATB and NTB patients showed a significant reduction of gut microbial diversity with respect to age matched healthy controls in both the clinical sites. ATB patient’s had underrepresentation of gut commensals such asFaecalibacterium prausnitzii, Prevotella copriDSM 18205,Coprococcus catus,and overrepresentation ofClostridium difficileATCC 9689 = DSM 1296. Longitudinally followed-up ATB patients showed elimination ofAlkalihalobacilluswith treatment initiation, whereas harmful taxa such asStenotrophomonasandKlebsiella pneumoniaeappeared in treatment-completed subjects. Interestingly, the fecal metabolites also showed group-specific differences, clustering ATB patients away from the controls irrespective of the study sites. Consistently, fecal 2-piperidinone abundance was higher in ATB patients compared to healthy controls. The fecal metabolome of longitudinally followed-up ATB patients showed a gradual shift towards healthy during the course of treatment completion.ConclusionGut microbial dysbiosis observed in tuberculosis patients at case presentation is partially resolved with 6 months of treatment completion and also reflected in their metabolite level. The observed microbial and metabolite imbalance in these ATB patients could explain disease pathology which needs further exploration to exploit their translational potential for therapeutics development.
High-fat diet-induced obesity increases susceptibility to endogenous and ethyl carbamate-induced somatic mutagenesis
Authors: Lichtler Rebecca , Wilson Mark J. , Wickliffe Jeffrey K. 
Published: June 2023

AbstractObesity and dietary fat consumption are associated with increased risk for certain cancers. We conducted a set of experiments designed to investigate both the inherent mutagenicity of high-fat diet (HFD) and the effect of HFD exposure on sensitivity to ethyl carbamate, a known mutagen. Greater body mass in females was associated with higher frequency of Pig-a mutant erythrocytes and HFD-induced obese female mice exhibited increased sensitivity to ethyl carbamate-induced mutagenesis compared to control mice. Together, these findings indicate that HFD exposure induces both endogenously generated changes related to mutagenesis and interacts with the mutagenic effects of ethyl carbamate.
Transgene-Free Ex Utero Derivation of A Human Post-Implantation Embryo Model Solely from Genetically Unmodified Naïve PSCs
Authors: Oldak Bernardo , Wildschutz Emilie , Bondarenko Vladyslav , Aguilera-Castrejon Alejandro , Zhao Cheng , Tarazi Shadi , Comar Mehmet-Yunus , Ashouokhi Shahd , Lokshtanov Dmitry , Roncato Francesco , Viukov Sergey , Ariel Eitan , Rose Max , Livnat Nir , Shani Tom , Joubran Carine , Cohen Roni , Addadi Yoseph , Kedmi Merav , Keren-Shaul Hadas , Petropoulos Sophie , Lanner Fredrik , Novershtern Noa , Hanna Jacob H. 
Published: June 2023

AbstractOur ability to study early human post-implantation development remains highly limited due to the ethical and technical challenges associated with intrauterine development of the human embryo after implantation. Despite the great progress made on human gastruloids, axioloids and in vitro cultured blastoids, such elegant models do not constitute an integrated Stem cell-derived Embryo Models (SEMs) that includes all the key extra-embryonic tissues of the early post-implantation human conceptus (e.g., hypoblast, yolk-sac, trophoblasts, amnion, and extraembryonic mesoderm), and thus, do not recapitulate post-implantation epiblast development within the context of these extra-embryonic compartments. Mouse naïve pluripotent stem cells (PSCs) have recently been shown to give rise to embryonic and extra-embryonic stem cells capable of self-assembling into post-gastrulation mouse SEMs, while bypassing the blastocyst-like stage, and eventually initiating organogenesisex utero. Here, we implement critical adaptations to extend these finding to humans, while using only genetically unmodified human naïve PSCs, thus circumventing the need for ectopic expression of lineage promoting transgenes. Such integrated human SEMs recapitulate the organization of all known compartments of early post-implantation stage human embryos, including epiblast, hypoblast, extra-embryonic mesoderm, and trophoblast surrounding the latter layers. The organized human SEMs recapitulate key hallmarks of post-implantation stage embryogenesis up to 13-14 days post-fertilization (dpf, Carnegie stage 6a), such as bilaminar disk formation, epiblast lumenogenesis, amniogenesis, anterior-posterior symmetry breaking, PGC specification, primary and secondary yolk sac formation, and extra-embryonic mesoderm expansion that defines a chorionic cavity and a connective stalk. This new platform constitutes a tractable stem cell-based model for experimentally interrogating previously inaccessible windows of human peri- and early post-implantation development.
Cyclophosphamide induces the loss of taste bud innervation in mice
Authors: Wood Ryan M. , Vasquez Erin L. , Kuri Eduardo Gutierrez , Connelly Kevin , Humayun Saima , Macpherson Lindsey J. 
Published: June 2023

AbstractMany common chemotherapeutics produce disruptions in the sense of taste which can lead to loss of appetite, nutritional imbalance, and reduced quality of life, especially if taste loss persists after treatment ends. Cyclophosphamide (CYP), an alkylating chemotherapeutic agent, affects taste sensitivity through its cytotoxic effects on mature taster receptor cells (TRCs) and on taste progenitor cell populations, retarding the capacity to replace TRCs. Mechanistic studies have focused primarily on taste cells, however, taste signaling requires communication between TRCs and the gustatory nerve fibers which innervate them. Here, we evaluate the effect of CYP on the peripheral gustatory nerve fibers that innervate the taste bud. Following histological analysis of tongue tissues, we find that CYP reduces innervation within the fungiform and circumvallate taste buds within 4-8 days after administration. To better understand the dynamics of the denervation process, we used 2-photon intravital imaging to observe the peripheral gustatory neuron arbors within individual fungiform taste buds before and after CYP treatment. We find that gustatory fibers retract from the taste bud proper but are maintained within the central papilla core. These data indicate that, in addition to TRCs, gustatory nerve fibers are also affected by CYP treatment. Because the connectivity between TRCs and gustatory neurons must be re-established for proper function, gustatory fibers should continue to be included in future studies to understand the mechanisms leading to chemotherapy-induced persistent taste loss.
Specific genomic targeting of the RNF12/RLIM E3 ubiquitin ligase selectively programmes developmental transcription
Authors: Espejo-Serrano Carmen , Aitken Catriona , Tan Beatrice F. , May Danielle G. , Chrisopulos Rachel J. , Roux Kyle J. , Mackintosh Samuel G. , Gribnau Joost , Bustos Francisco , Gontan Cristina , Findlay Greg M. 
Published: June 2023

SummaryThe E3 ubiquitin ligase RNF12/RLIM controls developmental gene expression and is mutated in the X-linked intellectual disability disorder Tonne-Kalscheuer syndrome (TOKAS). However, the mechanisms by which RNF12 E3 ubiquitin ligase activity controls specific gene expression signatures are not known. Here, we show that chromatin forms a regulatory platform for RNF12 substrate ubiquitylation and transcriptional patterning. RNF12 is recruited to specific genomic regions via a distinct consensus sequence motif, which enables targeting to key transcription factor substrate REX1. Mechanistically, RNF12 chromatin recruitment is largely REX1 independent, but is achieved via the conserved basic region (BR) adjacent to the RING domain. This region is critical for REX1 ubiquitylation on chromatin and downstream RNF12-dependent gene regulation. Furthermore, we find that RNF12 N-terminal sequences suppress chromatin recruitment and substrate ubiquitylation, uncovering a previously unappreciated autoinhibitory mechanism that governs genome targeting. Taken together, our results provide insight into mechanisms by which selective substrate targeting of an E3 ubiquitin ligase enables specific programming of gene expression.
Cell morphology best predicts tumorigenicity and metastasisin vivoacross multiple TNBC cell lines of different metastatic potential
Authors: Conner Sydney , Guarin Justinne R. , Le Thanh T. , Fatherree Jackson , Kelley Charlotte , Payne Samantha , Salhany Ken , McGinn Rachel , Henrich Emily , Yui Anna , Parker Savannah , Srinivasan Deepti , Bloomer Hanan , Borges Hannah , Oudin Madeleine J. 
Published: June 2023

AbstractBackgroundMetastasis is the leading cause of death in breast cancer patients. For metastasis to occur, tumor cells must invade locally, intravasate, and colonize distant tissues and organs, all steps that require tumor cell migration. The majority of studies on invasion and metastasis rely on human breast cancer cell lines. While it is known that these cells have different properties and abilities for growth and metastasis, thein vitromorphological, proliferative, migratory, and invasive behavior of these cell lines and their correlation toin vivobehavior is poorly understood. Thus, we sought to classify each cell line as poorly or highly metastatic by characterizing tumor growth and metastasis in a murine model of six commonly used human triple-negative breast cancer xenografts, as well as determine which in vitro assays commonly used to study cell motility best predictin vivometastasis.MethodsWe evaluated the liver and lung metastasis of human TNBC cell lines MDA-MB-231, MDA-MB-468, BT549, Hs578T, BT20, and SUM159 in immunocompromised mice. We characterized each cell line’s cell morphology, proliferation, and motility in 2D and 3D to determine the variation in these parameters between cell lines.ResultsWe identified MDA-MB-231, MDA-MB-468, and BT549 cells as highly tumorigenic and metastatic, Hs578T as poorly tumorigenic and metastatic, BT20 as intermediate tumorigenic with poor metastasis to the lungs but highly metastatic to the livers, and SUM159 as intermediate tumorigenic but poorly metastatic to the lungs and livers. We showed that metrics that characterize cell morphology are the most predictive of tumor growth and metastatic potential to the lungs and liver. Further, we found that no singlein vitromotility assay in 2D or 3D significantly correlated with metastasisin vivo.ConclusionsOur results provide an important resource for the TNBC research community, identifying the metastatic potential of 6 commonly used cell lines. Our findings also support the use of cell morphological analysis to investigate the metastatic potential and emphasize the need for multiplein vitromotility metrics using multiple cell lines to represent the heterogeneity of metastasisin vivo.
Structural modeling of cytokine-receptor-JAK2 signaling complexes using AlphaFold Multimer
Authors: Pogozheva Irina D. , Cherepanov Stanislav , Park Sang-Jun , Raghavan Malini , Im Wonpil , Lomize Andrei L. 
Published: June 2023

AbstractHomodimeric class 1 cytokine receptors include the erythropoietin (EPOR), thrombopoietin (TPOR), granulocyte colony-stimulating factor 3 (CSF3R), growth hormone (GHR), and prolactin receptors (PRLR). They are cell-surface single-pass transmembrane (TM) glycoproteins that regulate cell growth, proliferation, and differentiation and induce oncogenesis. An active TM signaling complex consists of a receptor homodimer, one or two ligands bound to the receptor extracellular domains and two molecules of Janus Kinase 2 (JAK2) constitutively associated with the receptor intracellular domains. Although crystal structures of soluble extracellular domains with ligands have been obtained for all the receptors except TPOR, little is known about the structure and dynamics of the complete TM complexes that activate the downstream JAK-STAT signaling pathway. Three-dimensional models of five human receptor complexes with cytokines and JAK2 were generated using AlphaFold Multimer. Given the large size of the complexes (from 3220 to 4074 residues), the modeling required a stepwise assembly from smaller parts with selection and validation of the models through comparisons with published experimental data. The modeling of active and inactive complexes supports a general activation mechanism that involves ligand binding to a monomeric receptor followed by receptor dimerization and rotational movement of the receptor TM α-helices causing proximity, dimerization, and activation of associated JAK2 subunits. The binding mode of two eltrombopag molecules to TM α-helices of the active TPOR dimer was proposed. The models also help elucidating the molecular basis of oncogenic mutations that may involve non-canonical activation route. Models equilibrated in explicit lipids of the plasma membrane are publicly available.
Second-order effects of chemotherapy pharmacodynamics and pharmacokinetics on tumor regression and cachexia
Authors: Pierik Luke , McDonald Patricia , Anderson Alexander R. A. , West Jeffrey 
Published: June 2023

AbstractDrug dose response curves are ubiquitous in cancer biology, but these curves are often used to measure differential response in first-order effects: the effectiveness of increasing the cumulative dose delivered. In contrast, second-order effects (the variance of drug dose) are often ignored. Knowledge of second-order effects may improve the design of chemotherapy scheduling protocols, leading to improvements in tumor response without changing the total dose delivered. By considering treatment schedules with identical cumulative dose delivered, we optimize treatment by comparing high variance schedules (e.g. high dose, low dose) with low variance schedules (constant dose). We extend a previous framework used to quantify second-order effects, known as antifragility theory, to investigate the role of drug pharmacokinetics. Using a simple one-compartment model, we find that high variance schedules are effective for a wide range of cumulative dose values. Next, using a mouse-parameterized two-compartment model of 5-fluorouracil, we show that the optimal schedule depends on initial tumor volume. Finally, we illustrate the trade-off between tumor response and lean mass preservation. Mathematical modeling indicates that high variance dose schedules provide a potential path forward in mitigating the risk of chemotherapy-associated cachexia by preserving lean mass without sacrificing tumor response.
Characterization of cotton virus A, a novel and distinct member of the genusCaulimoviruswith endogenous viral elements inGossypiumspp
Authors: West-Ortiz Michael , Stuehler Douglas , Pollock Emma , Wilson Jennifer R. , Preising Stephanie , Larrea-Sarmiento Adriana , Alabi Olufemi , Fuchs Marc , Heck Michelle , Olmedo-Velarde Alejandro 
Published: June 2023

AbstractThe complete genome sequence of cotton virus A, a new virus infecting cotton (Gossypiumspp.), was determined using high-throughput sequencing, PCR and rolling circle amplification. The 7,482-nt genome is a circular dsDNA molecule that codes for six open reading frames similar to other members of theCaulimovirusgenus (familyCaulimoviridae) but presenting key genome organization differences. P3, P5 and P6 are presumed movement, coat, and reverse transcriptase proteins, respectively. P1, P2 and P4 showed no homology to virus proteins. Endogenous viral elements were found inG. hirsutumandG. tomentosum, but not inG. barbadense, G. arboreum,orG. herbaceum.
Evidence of Disrupted-in Schizophrenia 1 (DISC1) as an arsenic binding protein and implications regarding its role as a translational activator
Authors: Watanabe Muneaki , Khu Tung Mei , Warren Grant , Shin Juyoung , Stewart Charles E. , Roche Julien 
Published: June 2023

ABSTRACTDisrupted-in-schizophrenia-1 (DISC1) is a scaffold protein that plays a pivotal role in orchestrating signaling pathways involved in neurodevelopment, neural migration, and synaptogenesis. Among those, it has recently been reported that the role DISC1 in the Akt/mTOR pathway can shift from a global translational repressor to a translational activator in response to oxidative stress induced by arsenic. In this study we are providing evidence that DISC1 can directly bind arsenic via a C-terminal cysteine motif (C-X-C-X-C). A series of fluorescence-based binding assays were conducted with a truncated C-terminal domain construct of DISC1 and a of series of single, double, and triple cysteine mutants. We found that arsenous acid, a trivalent arsenic derivative, specifically binds to the C-terminal cysteine motif of DISC1 with low micromolar affinity. All three cysteines of the motif are required for high-affinity binding. Electron microscopy experiments combined with in silico structural predictions revealed that that the C-terminal of DISC1 forms an elongated tetrameric complex. The cysteine motif is consistently predicted to be located within a loop, fully exposed to solvent, providing a simple molecular framework to explain the high-affinity of DISC1 toward arsenous acid. This study sheds light on a novel functional facet of DISC1 as an arsenic binding protein and highlights its potential role as both a sensor and translational modulator within the Akt/mTOR pathway.
Cryo2StructData: A Large Labeled Cryo-EM Density Map Dataset for AI-based Modeling of Protein Structures
Authors: Giri Nabin , Wang Liguo , Cheng Jianlin 
Published: June 2023

ABSTRACTThe advent of single-particle cryo-electron microscopy (cryo-EM) has brought forth a new era of structural biology, enabling the routine determination of large biological molecules and their complexes at atomic resolution. The high-resolution structures of biological macromolecules and their complexes significantly expedite biomedical research and drug discovery. However, automatically and accurately building atomic models from high-resolution cryo-EM density maps is still time-consuming and challenging when template-based models are unavailable. Artificial intelligence (AI) methods such as deep learning trained on limited amount of labeled cryo-EM density maps generate inaccurate atomic models. To address this issue, we created a dataset called Cryo2StructData consisting of 7,600 preprocessed cryo-EM density maps whose voxels are labelled according to their corresponding known atomic structures for training and testing AI methods to build atomic models from cryo-EM density maps. It is larger and of higher quality than any existing, publicly available dataset. We trained and tested deep learning models on Cryo2StructData to make sure it is ready for the large-scale development of AI methods for building atomic models from cryo-EM density maps.