bluuebunny/crossref_metadata_2025_split huggingface dataset:
A spring-loaded and leakage-tolerant synthetic gene switch for in-vitro detection of DNA and RNA
Authors: Gupta Krishna , Krieg Elisha 
Published: February 2024

ABSTRACTNucleic acid tests (NATs) are essential for biomedical diagnostics. Traditional NATs, often complex and expensive, have prompted the exploration of Toehold-Mediated Strand Displacement (TMSD) circuits as an economical alternative. However, the wide application of TMSD-based reactions is limited by ‘leakage’—the spurious activation of the reaction leading to high background signals and false positives. Here we introduce a new TMSD cascade that recognizes a custom nucleic acid input and generates an amplified output. The system is based on a pair of thermodynamically spring-loaded DNA modules. The binding of a predefined nucleic acid target triggers an intermolecular reaction that activates a T7 promoter, leading to the perpetual transcription of a fluorescent aptamer that can be detected by a smartphone camera. The system is designed to permit the selective depletion of leakage byproducts to achieve high sensitivity and zero-background signal in the absence of the correct trigger. Using Zika virus (ZIKV)- and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-derived nucleic acid sequences, we show that the assay generates a reliable target-specific readout. Native RNA can be directly detected under isothermal conditions, without requiring reverse transcription, with a sensitivity as low as 200 attomole. The modularity of the assay allows easy re-programming for the detection of other targets by exchanging a single sequence domain. This work provides a low-complexity and high-fidelity synthetic biology tool for point-of-care diagnostics and for the construction of more complex biomolecular computations.
Ultraviolet attenuates centromere-mediated meiotic genome stability and alters gametophytic ploidy consistency in flowering plants
Authors: Fu Huiqi , Zhong Jiaqi , Zhao Jiayi , Huo Li , Wang Chong , Ma Dexuan , Pan Wenjing , Sun Limin , Ren Ziming , Fan Tianyi , Wang Ze , Wang Wenyi , Lei Xiaoning , Yu Guanghui , Li Jing , Zhu Yan , Geelen Danny , Liu Bing 
Published: February 2024

AbstractUltraviolet (UV) radiation influences development and genome stability in organisms; however, its impacts on meiosis, a special cell division essential for the delivery of genetic information over generations in eukaryotes, remain not yet elucidated. In this study, we demonstrate that UV attenuates the centromere-mediated meiotic chromosome stability and induces unreduced gametes inArabidopsis thaliana. We show that UV reduces crossover (CO) rate but does not interfere with meiotic chromosome integrity. Functional centromere-specific histone 3 (CENH3) is required for the obligate CO formation, and plays a role in protection of homolog synapsis and sister-chromatid cohesion under UV stress. Moreover, UV specifically alters the orientation and organization of spindles and phragmoplasts at meiosis II, resulting in meiotic restitution and unreduced gametes. Further, we determine that UV-induced meiotic restitution does not rely on the UV Resistance Locus8-mediated UV perception and the Tapetal Development and Function1- and Aborted Microspores-dependent tapetum development, but occurs possibly via impacted JASON function and downregulated Parallel Spindle1. This study sheds light on the impacts of UV on meiotic genome stability and gametophytic ploidy consistency, which thus may influence genome evolution in flowering plants.
Proteolytic Cleavage of the ENaC γ Subunit – Impact Upon Na+and K+Handling
Authors: Ray Evan C. , Nickerson Andrew , Sheng Shaohu , Carrisoza-Gaytan Rolando , Lam Tracey , Marciszyn Allison , Zhang Lei , Jordahl Alexa , Bi Chunming , Winfrey Aaliyah , Kou Zhaohui , Gingras Sebastien , Kirabo Annet , Satlin Lisa M. , Kleyman Thomas R. 
Published: February 2024

ABSTRACTThe ENaC gamma subunit is essential for homeostasis of Na+, K+, and body fluid. Dual subunit cleavage before and after a short inhibitory tract allows dissociation of this tract, increasing channel open probability (PO),in vitro. Cleavage proximal to the tract occurs at a furin recognition sequence (143RKRR146in mouse). Loss of furin-mediated cleavage preventsin vitroactivation of the channel by proteolysis at distal sites. We hypothesized that143RKRR146mutation to143QQQQ146(Q4) in 129/Sv mice would reduce ENaC PO, impair flow-stimulated flux of Na+(JNa) and K+(JK) in perfused collecting ducts, reduce colonic amiloride-sensitive short circuit current (ISC), and impair Na+, K+, and body fluid homeostasis. Immunoblot ofQ4/Q4mouse kidney lysates confirmed loss of a band consistent in size with the furin-cleaved proteolytic fragment. However,Q4/Q4male mice on a low Na+diet did not exhibit altered ENaC POor flow-induced JNa, though flow-induced JKmodestly decreased. Colonic amiloride-sensitive ISCinQ4/Q4mice was not altered.Q4/Q4males, but not females, exhibited mildly impaired fluid volume conservation when challenged with a low Na+diet. Blood Na+and K+were unchanged on a regular, low Na+, or high K+diet. These findings suggest that biochemical evidence of gamma subunit cleavage should not be used in isolation to evaluate ENaC activity. Further, factors independent of gamma subunit cleavage modulate channel POand the influence of ENaC on Na+, K+, and fluid volume homeostasis in 129/Sv mice,in vivo.
Discovering genotype-phenotype relationships with machine learning and the Visual Physiology Opsin Database (VPOD)
Authors: Frazer Seth A. , Baghbanzadeh Mahdi , Rahnavard Ali , Crandall Keith A. , Oakley Todd H. 
Published: February 2024

AbstractBackgroundPredicting phenotypes from genetic variation is foundational for fields as diverse as bioengineering and global change biology, highlighting the importance of efficient methods to predict gene functions. Linking genetic changes to phenotypic changes has been a goal of decades of experimental work, especially for some model gene families including light-sensitive opsin proteins. Opsins can be expressed in vitro to measure light absorption parameters, including λmax - the wavelength of maximum absorbance - which strongly affects organismal phenotypes like color vision. Despite extensive research on opsins, the data remain dispersed, uncompiled, and often challenging to access, thereby precluding systematic and comprehensive analyses of the intricate relationships between genotype and phenotype.ResultsHere, we report a newly compiled database of all heterologously expressed opsin genes with λmaxphenotypes called the Visual Physiology Opsin Database (VPOD).VPOD_1.0contains 864 unique opsin genotypes and corresponding λmaxphenotypes collected across all animals from 73 separate publications. We useVPODdata anddeepBreaksto show regression-based machine learning (ML) models often reliably predict λmax, account for non-additive effects of mutations on function, and identify functionally critical amino acid sites.ConclusionThe ability to reliably predict functions from gene sequences alone using ML will allow robust exploration of molecular-evolutionary patterns governing phenotype, will inform functional and evolutionary connections to an organism’s ecological niche, and may be used more broadly forde-novoprotein design. Together, our database, phenotype predictions, and model comparisons lay the groundwork for future research applicable to families of genes with quantifiable and comparable phenotypes.Key PointsWe introduce the Visual Physiology Opsin Database (VPOD_1.0), which includes 864 unique animal opsin genotypes and corresponding λmaxphenotypes from 73 separate publications.We demonstrate that regression-based ML models can reliably predict λmax from gene sequence alone, predict non-additive effects of mutations on function, and identify functionally critical amino acid sites.We provide an approach that lays the groundwork for future robust exploration of molecular-evolutionary patterns governing phenotype, with potential broader applications to any family of genes with quantifiable and comparable phenotypes.
Cell-free expression and biochemical characterization of polysaccharide-synthesizing glycosyltransferases
Authors: Jayachandran Dharanidaran , Parvate Amar D. , Brookreson Jory T. , Evans James E. , Chundawat Shishir P.S. 
Published: February 2024

AbstractPolysaccharides are a major class of natural polymers found abundantly across all major life forms and play a critical role as structural, metabolic, or functional components in biomolecular processes. Some polysaccharides like cellulose and hyaluronan are synthesized by membrane-bound family-2 glycosyltransferases (GTs). Despite the fact that the GT-2 family has the maximum number of deposited sequences, the biochemistry of GT-2 family enzymes is still poorly understood due to difficulties associated with GT membrane protein expression, purification, and reconstitution in lipid carriers. Here, we chosePopulus tremula x tremuloidescellulose synthase 8 (PttCesA8) andStreptococcus equisimilishyaluronan synthase (SeHas) as putative family-2-GTs to be expressed in a wheat-germ-based cell-free expression (CFE) system as proteoliposomes. The cell-free products were obtained as reconstituted liposomes directly from CFE reactions at high yields and short processing times compared to other approaches. GT enzymes expression was confirmed using SDS-PAGE and immunoblotting, and the integration of GTs in lipid layers was observed using cryogenic electron microscopy. Both GTs tested were catalytically active when incubated with their respective substrates and cofactors. The Michalis-Menten kinetic constants, Kmfor PttCesA8, was 295.8 µM, and SeHas was 321.51 µM (toward UDP N-Acetyl Glucosamine) and 207.88 µM (toward UDP Glucuronic Acid), respectively. UDP was found to actively inhibit both these GTs with apparent inhibition constants of 10.08 µM and 24.38 µM. Mutation of specific conserved residues in structure-deficit SeHas confirmed the importance of lysine-139, glutamine-248, and threonine-283 residues in hyaluronan biosynthesis. In summary, wheat-germ-based CFE can be used to express functionally active and liposome-reconstituted family-2 GTs at high yields with relative ease to enable classical enzymology assays and will also enable more detailed structural studies in the near future.
Memory-boundk-mer selection for large and evolutionary diverse reference libraries
Authors: Şapcı Ali Osman Berk , Mirarab Siavash 
Published: February 2024

ABSTRACTUsingk-mers to find sequence matches is increasingly used in many bioinformatic applications, including metagenomic sequence classification. The accuracy of these down-stream applications relies on the density of the reference databases, which, luckily, are rapidly growing. While the increased density provides hope for dramatic improvements in accuracy, scalability is a concern. Referencek-mers are kept in the memory during the query time, and saving allk-mers of these ever-expanding databases is fast becoming impractical. Several strategies for subsampling have been proposed, including minimizers and finding taxon-specifick-mers. However, we contend that these strategies are inadequate, especially when reference sets are taxonomically imbalanced, as are most microbial libraries. In this paper, we explore approaches for selecting a fixed-size subset ofk-mers present in an ultra-large dataset to include in a library such that the classification of reads suffers the least. Our experiments demonstrate the limitations of existing approaches, especially for novel and poorly sampled groups. We propose a library construction algorithm called KRANK (K-mer RANKer) that combines several components, including a hierarchical selection strategy with adaptive size restrictions and an equitable coverage strategy. We implement KRANK in highly optimized code and combine it with the locality-sensitive-hashing classifier CONSULT-II to build a taxonomic classification and profiling method. On several benchmarks, KRANKk-mer selection dramatically reduces memory consumption with minimal loss in classification accuracy. We show in extensive analyses based on CAMI benchmarks that KRANK outperformsk-mer-based alternatives in terms of taxonomic profiling and comes close to the best marker-based methods in terms of accuracy.
Postdoctoral Scholar Recruitment and Hiring Practices in STEM: A Pilot Study
Authors: Heirwegh Meagan , Rees Douglas C. , Malcom-Piqueux Lindsey 
Published: February 2024

AbstractDespite the importance of the postdoctoral position in the training of scientists for independent research careers, few studies have addressed recruiting and hiring of postdocs. We conducted a pilot study on postdoctoral hiring in the Division of Chemistry and Chemical Engineering at the California Institute of Technology to serve as a starting point to better understand postdoctoral recruiting and hiring processes. From this survey of both postdocs and faculty, together with the available literature, the picture emerges that the postdoc hiring process is more decentralized than either faculty hiring or graduate admissions. Postdoc positions are often filled through a passive process where the initial expression of interest from a prospective postdoc is through a “cold-call” contact to a prospective advisor. Individual faculty members are often responsible for developing and implementing their own outreach and recruitment plans and deciding who to hire into a postdoc position. The overall opacity of the processes and practices by which postdocs are identified, recruited, and hired make it difficult to pinpoint where interventions could be effective to ensure equitable hiring practices. Implementation of such practices is critical to training a diverse postdoc population and subsequently of the future STEM faculty recruited from this group.
Pathogen and pest risks to vegetatively propagated crops in humanitarian contexts: Toward a national plant health risk analysis for Cameroon and Ethiopia
Authors: Mouafo-Tchinda Romaric A. , Etherton Berea A. , Plex Sulá Aaron I. , Andrade-Piedra Jorge , Ogero Kwame , Omondi Bonaventure A. , McEwan Margaret A. , Tene Tayo Paul M. , Harahagazwe Dieudonné , Cherinet Mihiretu , Gebeyehu Setegn , Sperling Louise , Garrett Karen A. 
Published: February 2024

AbstractCameroon and Ethiopia face humanitarian crises that disrupt the production of key food security crops like banana and plantain, cassava, potato, and sweetpotato. In this study, we address seed degeneration in these crops, the reduction in planting material quality due to the accumulation of pathogens and pests. We consider the context of humanitarian crises, with the goal of developing an ongoing ‘national plant health risk analysis’, in this case to inform decisions about mitigating seed degeneration. We analyzed cropland density maps and applied network centrality metrics to identify locations that are candidates for disease and pest management and surveillance in Cameroon and Ethiopia. We used expert knowledge elicitation and global trade data to map pathogen and pest movement risks and characterize trade of crop-specific commodities and planting materials. We identified specific locations that may be important for pathogen and pest spread in in Cameroon and Ethiopia, given their roles in the cropland network, and the reported presence of pathogens and pests. This national plant health risk analysis can inform regional and national surveillance and management strategies and provide a baseline for more in-depth studies in Cameroon and Ethiopia. We discuss strategies for ongoing improvement of a national plant health risk analysis, to inform decision-making in the humanitarian sector for designing on-the-ground actions to avoid unintentional spread of pathogens and pests during agricultural recovery interventions.
A Specialized Centrosome-Proteasome Axis Mediates Proteostasis and Influences Cardiac Stress through Txlnb
Authors: McLendon Jared M. , Zhang Xiaoming , Stein Colleen S. , Baehr Leslie M. , Bodine Sue C. , Boudreau Ryan L. 
Published: February 2024

AbstractBackgroundCentrosomes localize to perinuclear foci where they serve multifunctional roles, arranging the microtubule organizing center (MTOC) and anchoring ubiquitin-proteasome system (UPS) machinery. In mature cardiomyocytes, centrosomal proteins redistribute into a specialized perinuclear cage-like structure, and a potential centrosome-UPS interface has not been studied. Taxilin-beta (Txlnb), a cardiomyocyte-enriched protein, belongs to a family of centrosome adapter proteins implicated in protein quality control. We hypothesize that Txlnb plays a key role in centrosomal-proteasomal crosstalk in cardiomyocytes.MethodsIntegrative bioinformatics assessed centrosomal gene dysregulation in failing hearts. Txlnb gain/loss-of-function studies were conducted in cultured cardiomyocytes and mice. Txlnb’s role in cardiac proteotoxicity and hypertrophy was examined using CryAB-R120G mice and transverse aortic constriction (TAC), respectively. Molecular modeling investigated Txlnb structure/function.ResultsHuman failing hearts show consistent dysregulation of many centrosome-associated genes, alongside UPS-related genes. Txlnb emerged as a candidate regulator of cardiomyocyte proteostasis that localizes to the perinuclear centrosomal compartment. Txlnb’s interactome strongly supports its involvement in cytoskeletal, microtubule, and UPS processes, particularly centrosome-related functions. Overexpressing Txlnb in cardiomyocytes reduced ubiquitinated protein accumulation and enhanced proteasome activity during hypertrophy. Txlnb-knockout (KO) mouse hearts exhibit proteasomal insufficiency and altered cardiac growth, evidenced by ubiquitinated protein accumulation, decreased 26Sβ5 proteasome activity, and lower mass with age. In Cryab-R120G mice, Txlnb loss worsened heart failure, causing lower ejection fractions. After TAC, Txlnb-KO mice also showed reduced ejection fraction, increased heart mass, and elevated ubiquitinated protein accumulation. Investigations into the molecular mechanisms revealed that Txlnb-KO did not affect proteasomal subunit expression but led to the upregulation of Txlna and several centrosomal proteins (Cep63, Ofd1, and Tubg) suggesting altered centrosomal dynamics. Structural predictions support Txlnb’s role as a specialized centrosomal-adapter protein bridging centrosomes with proteasomes, confirmed by microtubule-dependent perinuclear localization.ConclusionsTogether, these data provide initial evidence connecting Txlnb to cardiac proteostasis, hinting at the potential importance of functional bridging between specialized centrosomes and UPS in cardiomyocytes.
A Curated Cell Life Imaging Dataset of Immune-enriched Pancreatic Cancer Organoids with Pre-trained AI Models
Authors: Kulkarni Ajinkya , Ferreira Nathalia , Scodellaro Riccardo , Alves Frauke 
Published: February 2024

ABSTRACTTumor organoids are three-dimensional in vitro models which can recapitulate the complex mutational landscape and tissue architecture observed in cancer patients, providing a realistic tumor microenvironment for testing novel therapies, including immunotherapies. A significant challenge in organoid research in oncology lies in developing efficient and reliable methods for segmenting organoid images, quantifying organoid growth, regression and response to treatments, as well as predicting the behavior of organoid systems. Up to now, a curated dataset of organoids co-cultured with immune cells is not available. To address this gap, we present a new public dataset, comprising both phase-contrast images of murine and patient-derived tumor organoids of one of the deadliest cancer types, the Pancreatic Ductal Adenocarcinoma, co-cultured with immune cells, and state-of-the-art algorithms for object detection and segmentation. Our dataset,OrganoIDNetData, encompassing 190 images with 33906 organoids, can be a potential common benchmark for different organoids segmentation protocols, moving beyond the current practice of training and testing these algorithms on isolated datasets.
Development and Validation of the Participation Questionnaire for Preschoolers with Autism Spectrum Disorder: A Focus on Structural Validity, Internal Consistency, and Construct Validity
Authors: Nakamura Takuto , Nagayama Hirofumi , Sasada Satoshi 
Published: February 2024

ABSTRACTAimTo develop and validate the Participation Questionnaire for Preschoolers (PQP), a new disease-specific participation measurement tool for children with autism spectrum disorder (ASD)MethodsIn this cross-sectional study, questionnaires were distributed to caregivers of children through child development facilities and medical institutions. The sample comprised 180 children with ASD and 100 children with developmental disabilities without ASD. Additional participants with ASD were recruited through users of a developmental support website. Following item reduction based on the data from children with ASD, exploratory factor analysis was conducted, and Cronbach’s alpha coefficients were calculated. Correlations between PQP scores and age, symptom severity, sensory processing, and family functioning were evaluated to examine the construct validity. PQP scores for children with ASD were then compared with those for children with developmental disabilities.ResultsIn total, 412 participants completed the questionnaire. Item reduction analysis led to the exclusion of seven items, revealing four factors. The PQP demonstrated high internal consistency and good construct validity, with observation of score differences based on the presence or absence of an ASD diagnosis.ConclusionThe PQP appears to be an effective tool for children with ASD. However, further research is required to assess its longitudinal properties.
Liquid Biopsy for Detection of Pancreaticobiliary Cancers in Suspected Patients by Functional Enrichment and Immunofluorescent Profiling of Circulating Tumor Cells and their Clusters
Authors: Gaya Andrew , Rohatgi Nitesh , Limaye Sewanti , Shreenivas Aditya , Ajami Ramin , Akolkar Dadasaheb , Datta Vineet , Srinivasan Ajay , Patil Darshana 
Published: February 2024

ABSTRACTBackgroundCirculating tumor cells (CTCs) have historically been used for prognostication in oncology. We evaluate performance of liquid biopsy CTC assay as a diagnostic tool in suspected pancreaticobiliary cancers. The assay utilises functional enrichment of CTCs followed by immunofluorescent profiling of organ specific markers.MethodsMulticentric case control study was followed by a prospective observational study. Adult patients undergoing tissue sampling for suspected pancreaticobiliary cancer were included in the studies. Blood samples for TruBlood® CTC assay were drawn before tissue sampling. Patients with a prior cancer treatment or cancer history were excluded. CTCs and their clusters were harvested by a unique functional enrichment method which is label-free, size independent and non-mechanical. The CTCs then underwent immunofluorescent profiling for CA19.9, Maspin, EpCAM, CK and CD45, blinded to the tissue histopathological diagnosis. TruBlood® malignant or non-malignant predictions were compared with tissue diagnoses to establish the sensitivity and specificity.ResultsThe case-control study evaluated 360 participants including 188 cases diagnosed with pancreaticobiliary cancer and 172 healthy individuals. A subsequent prospective observational study included 88 individuals with suspicion of pancreaticobiliary malignancy. The test had 95.9% overall sensitivity (95% CI: 86.0% - 99.5%) and 92.3% specificity (95% CI: 79.13% to 98.38%) to differentiate pancreaticobiliary cancers (PBC) (n = 49) from benign PB conditions (n = 39).ConclusionsThe high accuracy of the CTC based TruBlood test demonstrates its potential clinical application as a diagnostic tool to assist effective detection of pancreaticobiliary cancers when tissue sampling is unviable or inconclusive. A confirmational prospective interventional studiy in patients with suspicion of pancreaticobiliary malignancy including those with unavailability of tissue diagnosis is warranted.