bluuebunny/crossref_metadata_2025_split huggingface dataset:
Versatile and Portable Cas12a-mediated Detection of Antibiotic Resistance Markers
Authors: Vargas-Reyes Maryhory , Alcántara Roberto , Alfonsi Soraya , Peñaranda Katherin , Petrelli Dezemona , Spurio Roberto , Pajuelo Monica J. , Milon Pohl 
Published: November 2024

AbstractAntimicrobial resistance (AMR) is a global public health problem particularly accentuated in low-and middle-income countries, largely due to a lack of access to sanitation and hygiene, lack of awareness and knowledge, and the inadequacy of molecular laboratories for timely and accurate surveillance programs. This study introduces a versatile molecular detection toolbox (C12a) for antibiotic resistance gene markers using CRISPR/Cas12a coupled to PCR. Our toolbox can detect less than 3×10-7ng of DNA (100 attoMolar) or 102CFU/mL. High concordance was observed when comparing the C12a toolbox with sequenced genomes and antibiotic susceptibility tests for theblaCTX-M-15andfloRantibiotic resistance genes (ARGs), which confer resistance to cefotaxime and other β- lactams, and amphenicols, respectively. C12aINT, designed to detect the Integrase 1 gene, confirmed a high prevalence of the integrase/integron system inE. colicontaining multiple ARGs. The C12a toolbox was tested across a wide range of laboratory infrastructure including a portable setup. When combined with lateral flow assays (LFA), C12a exhibited competitive performance, making it a promising solution for on-site ARG detection. Altogether, this work presents a collection of molecular tools (primers, crRNAs, probes) and validated assays for rapid, versatile, and portable detection of antibiotic resistance markers, highlighting the C12a toolbox potential for applications in surveillance and ARG identification in clinical and environmental settings.
Microstructural Brain Changes in Buerger’s Disease and Smokers: A Case-Control Study Using Diffusion Tensor Imaging
Authors: Asadollahi Shahir Ali Asghar , Gharib Mohammad Hadi , Shahali Ramsheh Maryam , Zahedpasha Reza , Razman Asma , Omidi Abdollah , Kharazm Pezhman , Ghaderi Amir , Ghorbani Somayeh , Hashemian Shervin-sadat 
Published: November 2024

AbstractAimThromboangiitis Obliterans (TAO), or Buerger’s disease, affects peripheral vessels and is linked to smoking. This Diffusion tensor imaging tractography (DTI) study examines brain function changes in TAO patients compared to healthy smokers and non-smokers, aiming to reveal neurological implications beyond the known peripheral effects.MethodsThe case-control study involved 50 participants aged 27-56 in northeast Iran, including TAO patients, healthy smokers, and non-smoking controls. MRI scans with DTI were conducted to assess 21 brain tracts for fractional anisotropy (FA) and apparent diffusion coefficient (ADC).ResultsSignificant differences in brain tract integrity were observed among the groups. TAO patients showed lower FA values in the minor forceps compared to healthy smokers, while smokers had higher FA values than non-smoking controls. ADC values were notably higher in TAO patients across several tracts, including corticospinal tracts, fornix tracts, arcuate fasciculus, and inferior longitudinal fasciculus, compared to both healthy smokers and controls.ConclusionThe study highlights distinct brain tract alterations in TAO patients and suggests potential neurological consequences associated with the disease and smoking habits. DTI proves valuable in understanding microstructural brain changes and could serve as a diagnostic tool for evaluating smoking-related neurologic complications, providing insights into TAO’s impact beyond peripheral vessels.Key PointsAdvanced MRI techniques, particularly DTI, reveal significant differences in fractional anisotropy (FA) and apparent diffusion coefficient (ADC) in the brains of individuals with Buerger’s disease and smokers.Notable ADC variations in corticospinal and fornix tracts are observed between Buerger’s patients, smokers, and non-smokers.FA values in the superior longitudinal fasciculus and the minor and major forceps significantly differ among Buerger’s patients, smokers, and controls, highlighting microstructural brain alterations.
Highway paving dramatically increased dengue transmission in the Amazon
Authors: Singleton Alyson L. , Lescano Andres G. , MacDonald Andrew J. , Mandle Lisa , Sipin Terrell J. , Martel Kevin S. , Munayco César V. , Carrera Esteban D. R. , Choque Gustavo A. , Bautista Ana S. M. , Luby Stephen P. , Mordecai Erin A. 
Published: November 2024

AbstractHuman mobility drives the spread of many infectious diseases, yet the health impacts of changes in mobility due to new infrastructure development are poorly understood and currently not accounted for in impact assessments. We take a novel quasi-experimental approach to identifying the link between mobility and infectious disease, leveraging historical road upgrades as a proxy for regional human mobility changes. We analyzed how highway paving altered transmission of dengue—a high-burden mosquito-borne disease—via changes in human movement in the Madre de Dios region of Peru. The paving of the Interoceanic Highway through a formerly isolated region of the Amazon in 2009 provided a unique opportunity to quantify the causal impact of road paving on disease transmission. To uncover this relationship, we compared dengue incidence data from healthcare facilities in Madre de Dios near to versus far from the newly paved highway before and after paving, while controlling for observable and unobservable confounding variables (a difference-in-differences causal inference approach). We found that the paving of the highway caused at least an additional 9,826 (95% CI: 8,562–10,684) dengue cases since paving, accounting for 45.2% (95% CI: 39.4%–49.2%) of all dengue cases recorded in the region post highway paving (2009–2022). Our findings demonstrate the impact that infrastructure can have on dengue transmission, likely via its effects on human mobility. As a result, we advocate for future road construction plans in tropical regions to account for potential increases in dengue transmission during impact assessments.Significance statementLarge-scale infrastructure projects are critical for meeting global development goals, but they can also have unintended consequences for local human and environmental health. More evidence attributing human health effects to infrastructure projects is needed to understand how to mitigate these negative health impacts. Our study contributes to this body of knowledge, attributing nearly half of recent dengue cases in Madre de Dios, Peru to the paving of the Interoceanic Highway through the region in 2009. Our results demonstrate the impact that highway construction can have on human health and call for future infrastructure projects through tropical forests to consider infectious disease outcomes in their impact assessments.
Precision-cut lung slices in air-liquid interface (PCLS-ALI): A novelex-vivomodel for the study of Pulmonary Aspergillosis
Authors: Gonzales-Huerta LE , Williams TJ , Aljohani R , Robertson BD , Evans CA , Armstrong-James DPH 
Published: November 2024

ABSTRACTPulmonary Aspergillosis is a respiratory infection with a high mortality rate, which affects patients with immunosuppression or structural lung defects. Antifungal treatment options are few and many have narrow therapeutic margins and potentially serious side effects. In recent years, there are growing numbers of reports of antifungal resistance. Thus, there is an urgent need for effective models to study fungal pathogenesis and test antifungal therapies in the respiratory system. Here, we present a novelex-vivomodel using precision-cut lung slices in an air-liquid interface platform to evaluate lung tissue responses to fungal infection and antifungal treatment. Readouts assessed were lactate dehydrogenase for tissue damage, release of inflammatory cytokines (TNF-α, IL-1β, CXCL1), and histology for confirmation of hyphal invasion. Overall, the PCLS-ALI model is a promising approach for understanding lung tissue responses to fungal infections, which fulfils the reduction and refinement components of the 3Rs guiding principles for ethical use of experimental animals.
TEAD-targeting small molecules induce a cofactor switch to regulate the Hippo pathway
Authors: Guarnaccia Alissa D. , Hagenbeek Thijs J. , Lee Wendy , Kljavin Noelyn , Choi Meena , Ulas Gözde , Kameswaran Vasumathi , Le Daniel , Paul Sayantanee , Vaidya Samir , Zbieg Jason R. , Crawford James J. , Daniel Bence , Dey Anwesha , Lill Jennie R. 
Published: November 2024

SUMMARYTEAD proteins are the main transcriptional effectors of the Hippo signaling pathway and a pharmacological target in oncology. Most TEAD-targeting small molecules act by disrupting interaction with the oncogenic transcriptional activators YAP and TAZ. Here, we describe an alternative mechanism for TEAD lipid pocket binding molecules. We report that select sulfonamide-containing compounds promote TEAD interaction with the transcriptional repressor VGLL4 to induce a small molecule-mediated cofactor switch from YAP to VGLL4. Chemically induced VGLL4–TEAD complexes counteract YAP activity at chromatin to repress pro-growth gene networks, including genes involved in cellular proliferation and mechanosignaling. VGLL4 is required for an anti-proliferative response to these select compounds, and genetic deletion of VGLL4 causes resistance to these moleculesin vitroandin vivo. Our data reveal a category of molecules that facilitate the repressive VGLL4–TEAD interaction and open up new understandings for curbing the oncogenic activity of Hippo pathway deregulation.
Standard-flow targeted proteomics for quantification of enzymes in glucosinolate biosynthetic pathways
Authors: Vik Daniel 
Published: November 2024

AbstractInsights gained from quantitative proteomics studies show that the relationship between transcript and protein abundance is not generally linear. Quantitative measurement of both proteins and transcripts is required to reveal their actual relationship. Whereas quantitative analysis of transcripts is widely established, there is a need for easily accessible protein level technologies. Mass spectrometry-based proteomics is a promising solution, provided that it can be made accessible to a broader user group than it currently is. Developments in proteomics methodology show that relatively simple instrumentation allows for targeted proteomics which provides a reliable and accessible technology platform for protein quantification. I here describe the successful implementation of standard-flow targeted proteomics and its use to quantify 12 enzymes in the glucosinolate biosynthetic pathways in Arabidopsis thaliana. Enabled by targeted proteomics, I analyzed a series of transcription factor mutants and found that transcript and protein generally correlated well under these unchallenged conditions. When I treated wild-type plants with the phytohormone methyl-jasmonate, I observed uncoupling of metabolite, transcript and protein levels, suggesting post-transcriptional and/or -translational in addition to transcriptional regulation.
The genome assembly of the westslope cutthroat trout,Oncorhynchus lewisi, reveals interspecific chromosomal rearrangements with the rainbow trout
Authors: Flores Anne-Marie , Christensen Kris A. , Godin Theresa , Palti Yniv , Campbell Matthew R. , Waldbieser Geoffrey C. , Simpson Sheron A. , Scheffler Brian E. , Smith Seth R. , Whiteley Andrew R. , Kovach Ryan P. , Luikart Gordon , Boyer Matthew C. , Kardos Marty , Relyea Scott , Wells Craig , Koop Ben F. 
Published: November 2024

AbstractCutthroat trout (Oncorhynchus clarkii) are popular among anglers throughout their native range along the West Coast and interior of North America. As they colonized the interior of North America, cutthroat trout diverged into several genetically distinct groups. Many of these groups are now threatened by habitat destruction, hybridization with rainbow trout (O. mykiss), and competition from introduced species. These groups were previously classified as subspecies, but recent research suggests they may represent distinct species. In this study, we produced a chromosomal-level genome assembly and a genetic map for one of the species in the cutthroat trout species complex, the westslope cutthroat trout (O. lewisi—formerlyO. clarki lewisi). We also constructed haplotype-resolved assemblies from a westslope cutthroat-rainbow trout F1 hybrid. We used the new genome assemblies to identify major interspecific chromosomal rearrangements between the two sister species, including fusions, fissions, and inversions. These genome assemblies and chromosome data provide valuable insights regarding genetic variation within cutthroat trout and in hybrids between rainbow and cutthroat trout.Article SummaryWestslope cutthroat trout inhabit bodies of water in several states and provinces near the Rocky Mountains and are well-known among anglers. In this study, we produced the first publicly available genome assemblies and a high-density genetic map for this species. These are research tools that allow detailed genetic analyses, including identifying differences among the genomes of related species. These comparisons allow researchers to understand the evolution of these species better and may provide insight into why successful interbreeding is possible among cutthroat and rainbow trout.
Identification of the MRTFA/SRF pathway as a critical regulator of quiescence in cancer
Authors: Panesso-Gómez Santiago , Cole Alexander J. , Wield Alyssa , Anyaeche Vivian I. , Shah Jaynish , Jiang Qi , Ebai Tonge , Sharrow Allison C. , Tseng George , Yoon Euisik , Brown Daniel D. , Clark Amanda M. , Larsen Scott D , Eder Ian , Gau David , Roy Partha , Dahl Kris N. , Tran Lam , Jiang Hui , McAuliffe Priscilla F , Lee Adrian V , Buckanovich Ronald J. 
Published: November 2024

AbstractChemoresistance is a major driver of cancer deaths. One understudied mechanism of chemoresistance is quiescence. We used single cell culture to identify, retrieve, and RNA-Seq profile primary quiescent ovarian cancer cells (qOvCa). We found that many qOvCa differentially expressed genes are transcriptional targets of the Myocardin Related Transcription Factor/Serum Response Factor (MRTF/SRF) pathway. We also found that genetic disruption of MRTF-SRF interaction, or an MRTF/SRF inhibitor (CCG257081) impact qOvCa gene expression and induce a quiescent state in cancer cells. Suggesting a broad role for this pathway in quiescence, CCG257081 treatment induced quiescence in breast, lung, colon, pancreatic and ovarian cancer cells. Furthermore, CCG081 (i) maintained a quiescent state in patient derived breast cancer organoids and, (ii) induced tumor growth arrest in ovarian cancer xenografts. Together, these data suggest that MRTF/SRF pathway is a critical regulator of quiescence in cancer and a possible therapeutic target.SignificanceQuiescence is a critical driver of chemoresistance. The MRFT-SRF pathway regulates cancer cell quiescence and inhibiting the MRTF-SRF pathway can prevent the outgrowth of quiescent cancer cells and improve cancer outcomes.
Intravenous gene therapy improves lifespan and clinical outcomes in feline Sandhoff Disease
Authors: Maguire Anne S. , Ta Linh , Gross Amanda L. , Osterhoudt Devin E. , Cannon Jessica S. , Hall Paige I. , Sandey Maninder , Seyfried Thomas N. , Gray-Edwards Heather L. , Sena-Esteves Miguel , Martin Douglas R. 
Published: November 2024

AbstractSandhoff Disease (SD), a fatal neurodegenerative disorder, is caused by the absence of ß-hexosaminidase (Hex) and subsequent accumulation of GM2 ganglioside in lysosomes. Previous studies have led to adeno-associated virus (AAV) gene therapy for children with GM2 gangliosidosis in both expanded access and Phase I/II clinical trials via intracranial and/or cerebrospinal fluid-based delivery. The current study investigated intravenous (IV) gene therapy of SD cats, treated at one month of age with a bicistronic AAV vector. While untreated SD cats lived to 4.3±0.2 months, cats treated with low and high doses lived to 8.3±1.2 and 12.4±2.7 months, respectively. In-life assessments revealed clear clinical benefit of AAV treatment, with the most dramatic improvement seen in the reduction of overt full-body tremors. Cerebrospinal fluid levels of aspartate aminotransferase (AST) and lactate dehydrogenase (LDH) were decreased, indicating a reduction of cell damage within the central nervous system. Magnetic resonance imaging (MRI) and spectroscopy (MRS) acquired on a 7 Tesla scanner indicated that structural pathology and metabolite abnormalities are partially normalized by AAV treatment. Dose-dependent reduction of GM2 ganglioside storage and increases in Hex activity were most substantial in the caudal regions of the brain and in the spinal cord. Immunohistochemistry revealed reduction in neuroinflammatory cell populations and partial correction of myelin deficits. These results support the dose-dependent efficacy of AAV delivered IV for significant restoration of clinical metrics and Hex function in a feline model of SD.One Sentence SummaryIntravenous administration of AAV gene therapy is safe and efficacious in a feline model of Sandhoff disease.
Heat-Triggered Transcriptional Reprogramming in Microspores Disrupts Progression of Pollen Development inBrassica napusL
Authors: Lohani Neeta , Singh Mohan B. , Bhalla Prem L. 
Published: November 2024

AbstractRising temperatures due to climate change pose significant threats to global food security, particularly by impacting crop fertility and yield. Despite the known susceptibility of male reproductive development to heat stress, the specific adaptive mechanisms and critical regulatory genes involved in the stage-specific heat stress response in crops are still not well understood. This study examines the impact of acute heat stress on pollen development in Brassica napus (Canola), an essential oilseed crop, with a focus on the uninucleate microspore stage. We demonstrate that a brief exposure to 40°C during the uninucleate microspore stage results in loss of cellular polarity, failed asymmetric cell division, loss of cytoplasm, and pollen abortion, leading to a significant decline in pollen viability. Transcriptome analysis reveals the complexity of heat-induced transcriptional reprogramming in microspores, identifying 8.1% (6,245) of the expressed genes as responsive to high temperature, with a higher degree of downregulation. Fourteen differentially expressed transcription factors (TFs) belonging to diverse TF families were identified in heat-stressed microspores, with overrepresented target genes. The differential regulation of cell cycle control genes in heat-stressed microspores supports our microscopic observations and details the transcriptional reprogramming underlying the failure of heat-stressed microspores to undergo the first and second pollen mitotic divisions (PMI and PMII), resulting in aberrant pollen development inB. napus. Heat stress disrupts key biological pathways such as transcription, mRNA processing, translational control, protein homeostasis, autophagy, phytohormone signaling, and reactive oxygen species (ROS) homeostasis. Heat stress alters the intricate network of multiple signaling pathways, potentially disrupting the regulatory pathways underlying pollen development, with evident crosstalk underscoring the complexity of the heat stress response in pollen development. These findings underscore the critical vulnerability of the microspore stage to heat stress in Canola. Understanding the identified heat-responsive genes and regulatory networks provides valuable insights for breeding climate-resilient Canola varieties, thereby contributing to global food security amidst changing climatic conditions.HighlightsAcute heat stress during microspore stage inBrassica napusdisrupts pollen development.Heat stress induces complex transcriptional reprogramming in microspores, with higher degree of downregulation.Transcriptional control, RNA processing, coordination of protein homeostasis and translational control is altered in heat-stressed microsporesMisregulation of cell cycle control genes supports the loss of cellular polarity and failure to undergo asymmetric cell division in heat stressed microspores.
Interferon Epsilon Protects Epithelial Barriers from Viral Infection through Autocrine Intracellular Signaling
Authors: Casazza Rebecca L. , Skavicus Samantha , Hare David , Cooley Kaila A. , Heaton Nicholas S. , Coyne Carolyn B. 
Published: November 2024

AbstractAntiviral defenses at mucosal barriers are essential for preventing viral entry and systemic infection. Interferon epsilon (IFNε), a unique type I interferon not induced by infection, is constitutively expressed in the female reproductive tract (FRT), where it provides broad antiviral protection and fluctuates with hormone status. The role of IFNε outside the FRT remains unclear, although it is expressed in the intestinal epithelium. We generated an IFNε knockout mouse (Ifnε-/-) and confirmed its antiviral activity in the FRT. Using single-cell RNA sequencing of the cycling mouse FRT, we show thatIfnεexpression is restricted to specific epithelial cells, is not hormonally regulated, and induces basal interferon-stimulated genes in an autocrine manner. scRNASeq of WT andIfnε-/-uteruses showed that loss ofIfnεreduced basal ISG levels inIfnε-expressing epithelial cells without impacting other cell types. Consistent with this, IFNε was retained intracellularly in primary human FRT cells. scRNASeq of human stem cell-derived enteroids and tissue revealed that multiple GI epithelial cells express high basal IFNε levels, andIfnε-/-mice are more susceptible to enteric viral infection. Our findings reveal that IFNε is an intracellular IFN that provides mucosal immunity across various epithelial tissues, extending its protective functions beyond the FRT.
GWAC: A machine learning method to identify functional variants in data-constrained species
Authors: Sharo Andrew G. 
Published: November 2024

AbstractAs environments change, the ability of species to adapt depends on the functional variation they harbor. Identifying these functional variants is an important challenge in conservation genetics. Due to the limited data available for most species of conservation interest, genome-wide selection scans that link specific genetic variants with a phenotype are not feasible. However, functional variants may still be identified by considering predicted consequence, evolutionary conservation, and other sequence-based features. We developed Genome-Wide vAriant Classification (GWAC), a supervised machine learning framework to prioritize genome-wide variants by functional impact. GWAC requires only features that can be generated from an annotated genome. We evaluate GWAC by first using a set of human data constrained to match what may be available for threatened species. We find that GWAC weights features more heavily that are known to be predictive of functional variation and prioritizes both single nucleotide variants and indels, consistent with mutational constraint found in population genetics studies. GWAC performs nearly as well as CADD, a leading genome-wide predictor in humans that uses substantially more features and data that are typically available only for model organisms. While it is not possible to empirically evaluate GWAC on a species for which no functional variants are known, we find that a version of GWAC generated for the greater prairie chicken (Tympanuchus cupido pinnatus) weights features similarly to our human version. We compare the results of using a species-specific variant impact predictor against lifting-over variants from a closely related model organism and find that the species-specific approach retains functional variants that are lost during lift-over. We anticipate GWAC could be used to estimate conservation metrics such as genetic load and adaptive capacity, while also enabling researchers to identify individual variants responsible for adaptive phenotypes.