bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence of mango postharvest Stem-end rot disease in Cote d’Ivoire and identification of fungal pathogens associated
Authors: Yeo Yéfoungnigui S. , Kone Yassogui , Dembele Dio D. , Amari Elisee L D G , Rey Jean-Yves , Del Ponte Emerson M. , Fernandez Diana , Kone Daouda 
Published: August 2023

AbstractThe Stem-end rot (SER) postharvest disease of mango (Mangifera indicaL.) fruits is a significant economic threat to mango production. If suitable conditions are not maintained, it can lead to losses of up to 100 %. Despite its importance, very little information is known about this disease in Côte d’Ivoire. This research aimed determining the incidence and severity of SER in mango orchards, assess how preharvest climate parameters affect the disease and determine the pathogenic fungi associated with SER. Therefore, mango SER was evaluated on 1500 mango fruits collected from 15 orchards.in Boundiali, Ferkéssédougou, Korhogo, Odienné, and Sinématiali departments. Mango SER incidence ranged from 10 % to 30 %, while severity ranged from 5 % to 20 %. No significant differences in these parameters were observed between the different departments (P>0.05). The study also revealed a low correlation between SER disease incidence and mean air temperature (r=0.36) and minimum air temperature (r=0.26) data, indicating that preharvest weather conditions may have a marginal impact on mango SER disease intensity in the postharvest phase. Pathogenic fungi associated with SER were isolated and identified using morphological characteristics and multilocus sequence analysis of the rDNA internal transcribed spacer (ITS) region and the translation elongation factor 1-alpha (tef1-α). We identified various fungal species associated with mango SER disease, withLasiodiplodiaspecies (74%) being the most prevalent (includingLasiodiplodia theobromae, L. euphorbicola, andL. caatinguensis), followed byColletotrichum gloeosporioides,Curvularia pseudobrachyspora,Diaporthe endophyticaandFusarium mangiferae. However, onlyLasiodiplodiaspecies andDiaporthe endophyticainduced SER symptoms. This study was the first ever evaluation of mango SER disease and associated fungal pathogens identification in Côte d’Ivoire. This result will assist researchers in developing a control method for mango SER.
Declines in ice cover induce light limitation in freshwater diatoms
Authors: Zepernick Brittany N. , Chase Emily E. , Denison Elizabeth R. , Gilbert Naomi E. , Martin Robbie M. , Truchon Alexander R. , Frenken Thijs , Cody William R. , Chaffin Justin D. , Bullerjahn George S. , McKay R. Michael L. , Wilhelm Steven W. 
Published: August 2023

AbstractThe rediscovery of diatom blooms embedded within and beneath Lake Erie ice cover (2007-2012) ignited an intense interest in psychrophilic adaptations and winter limnology. Subsequent studies determined ice plays a vital role in winter diatom ecophysiology, as diatoms partition to the underside of ice thereby fixing their location within the photic zone. Yet, climate change has led to widespread ice decline across the Great Lakes, with Lake Erie presenting a nearly ice-free state in several recent winters. It has been hypothesized the resultant turbid, isothermal water column will induce light limitation amongst winter diatoms, serving as a detrimental competitive disadvantage. Here, we conducted a physiochemical and metatranscriptomic survey of the winter Lake Erie water column (2019-2020) that spanned spatial, temporal, and climatic gradients to investigate this hypothesis. We determined ice-free conditions decreased diatom bloom magnitude and altered diatom community composition. Diatoms increased the expression of various photosynthetic genes and iron transporters, suggesting they are attempting to increase their quantity of photosystems and light-harvesting components (a well-defined indicator of light limitation). Notably, we identified two gene families which serve to increase diatom fitness in the turbid ice-free water column: proton-pumping rhodopsins (a second means of light-driven energy acquisition) and fasciclins (a means to “raft” together to increase buoyancy and co-locate to the surface to optimize light acquisition). With large-scale climatic changes already underway, our observations provide insight into how diatoms respond to the dynamic ice conditions of today and shed light on how they will fare in a climatically altered tomorrow.
The genomes and epigenomes of aquatic plants (Lemnaceae) promote triploid hybridization and clonal reproduction
Authors: Ernst Evan , Abramson Bradley , Acosta Kenneth , Hoang Phuong T.N. , Mateo-Elizalde Cristian , Schubert Veit , Pasaribu Buntora , Hartwick Nolan , Colt Kelly , Aylward Anthony , Lee Seung Cho , Ramu Umamaheswari , Birchler James A. , Schubert Ingo , Lam Eric , Michael Todd P. , Martienssen Robert A. 
Published: August 2023

SummaryThe Lemnaceae (duckweeds) are the world’s smallest but fastest growing flowering plants. Prolific clonal propagation facilitates continuous micro-cropping for plant-based protein and starch production, and holds tremendous promise for sequestration of atmospheric CO2. Here, we present chromosomal assemblies, annotations, and phylogenomic analysis ofLemnagenomes that uncover candidate genes responsible for the metabolic and developmental traits of the family, such as anatomical reduction, adaxial stomata, lack of stomatal closure, and carbon sequestration via crystalline calcium oxalate. Lemnaceae have selectively lost genes required for RNA interference, including Argonaute genes required for reproductive isolation (the triploid block) and haploid gamete formation. Triploid hybrids arise commonly amongLemna, and we have found mutations in highly-conserved meiotic crossover genes that could support polyploid meiosis. Syntenic comparisons withWolffiaandSpirodelareveal that diversification of these genera coincided with the “Azolla event” in the mid-Eocene, during which aquatic macrophytes reduced high atmospheric CO2levels to those of the current ice age.Facile regeneration of transgenic fronds from tissue culture, aided by reduced epigenetic silencing, makesLemnaa powerful biotechnological platform, as exemplified by recent engineering of high-oilLemnathat outperforms oil seed crops.
Improving rigor and reproducibility in western blot experiments with the blotRig analysis software
Authors: Omondi Cleopa , Chou Austin , Fond Kenneth A. , Morioka Kazuhito , Joseph Nadine R. , Sacramento Jeffrey A. , Iorio Emma , Torres-Espin Abel , Radabaugh Hannah L. , Davis Jacob A. , Gumbel Jason H. , Russell Huie J. , Ferguson Adam R. 
Published: August 2023

AbstractWestern blot is a popular biomolecular analysis method for measuring the relative quantities of independent proteins in complex biological samples. However, variability in quantitative western blot data analysis poses a challenge in designing reproducible experiments. The lack of rigorous quantitative approaches in current western blot statistical methodology may result in irreproducible inferences. Here we describe best practices for the design and analysis of western blot experiments, with examples and demonstrations of how different analytical approaches can lead to widely varying outcomes. To facilitate best practices, we have developed the blotRig tool for designing and analyzing western blot experiments to improve their rigor and reproducibility. The blotRig application includes functions for counterbalancing experimental design by lane position, batch management across gels, and analytics with covariates and random effects.
Targeting the dependence on PIK3C3-mTORC1 signaling in dormancy-prone breast cancer cells blunts metastasis initiation
Authors: Elkholi Islam E. , Robert Amélie , Malouf Camille , Kuasne Hellen , Drapela Stanislav , Macleod Graham , Hébert Steven , Pacis Alain , Calderon Virginie , Kleinman Claudia L. , Gomes Ana P. , Aguirre-Ghiso Julio A. , Park Morag , Angers Stéphane , Côté Jean-François 
Published: August 2023

AbstractHalting breast cancer metastatic relapses following primary tumor removal and the clinical dormant phase, remains challenging, due to a lack of specific vulnerabilities to target during dormancy. To address this, we conducted genome-wide CRISPR screens on two breast cancer cell lines with distinct dormancy properties: 4T1 (short-term dormancy) and 4T07 (prolonged dormancy). We discovered that loss of class-III PI3K, Pik3c3, revealed a unique vulnerability in 4T07 cells. Surprisingly, dormancy-prone 4T07 cells exhibited higher mTORC1 activity than 4T1 cells, due to lysosome-dependent signaling occurring at the cell periphery. Pharmacological inhibition of Pik3c3 counteracted this phenotype in 4T07 cells, and selectively reduced metastasis burden only in the 4T07 dormancy-prone model. This mechanism was also detected in human breast cancer cell lines in addition to a breast cancer patient-derived xenograft supporting that it may be relevant in humans. Our findings suggest dormant cancer cell-initiated metastasis may be prevented in patients carrying tumor cells that display PIK3C3-peripheral lysosomal signaling to mTORC1.Statement of SignificanceWe reveal that dormancy-prone breast cancer cells depend on the class III PI3K to mediate a constant peripheral lysosomal positioning and mTORC1 hyperactivity. Targeting this pathway might blunt breast cancer metastasis.
PxBLAT: An efficient python binding library for BLAT
Authors: Li Yangyang , Yang Rendong 
Published: August 2023

AbstractWe introduce PxBLAT, a Python library designed to enhance usability and efficiency in interacting with the BLAST-like alignment tool (BLAT). PxBLAT provides an intuitive Application Programming Interface (API) design, allowing the incorporation of its functionality directly into Python-based bioinformatics workflows. Moreover, PxBLAT’s design philosophy emphasizes ease of use, memory efficiency, and the elimination of intermediary files and unnecessary system calls, thereby enhancing computational speed and user experience. Benchmark tests reveal its superior performance across various datasets, illustrating its capacity to maintain correctness. PxBLAT supports Python (version 3.9+), and pre-compiled packages are released via PyPI (https://pypi.org/project/pxblat/) and Bioconda (https://anaconda.org/bioconda/pxblat). The source code and executable are freely available for academic, nonprofit, and personal use. Its documentation is available on ReadTheDocs (https://pxblat.readthedocs.io/en/latest/).
Single-cell analysis characterizes PLK1 as a catalyst of an immunosuppressive tumor microenvironment in LUAD
Authors: Kong Yifan , Li Chaohao , Liu Jinpeng , Zhang Min , Allison Derek B. , Hassan Faisal , He Daheng , Wang Xinyi , Mao Fengyi , Zhang Qiongsi , Zhang Yanquan , Li Zhiguo , Wu Sai , Wang Chi , Liu Xiaoqi 
Published: August 2023

AbstractPLK1 (Polo-like kinase 1) plays a critical role in the progression of lung adenocarcinoma (LUAD). Recent studies have unveiled that targeting PLK1 improves the efficacy of immunotherapy, highlighting its important role in the regulation of tumor immunity. Nevertheless, our understanding of the intricate interplay between PLK1 and the tumor microenvironment (TME) remains incomplete. Here, using genetically engineered mouse model and single-cell RNA-seq analysis, we report that PLK1 promotes an immunosuppressive TME in LUAD, characterized with enhanced M2 polarization of tumor associated macrophages (TAM) and dampened antigen presentation process. Mechanistically, elevated PLK1 coincides with increased secretion of CXCL2 cytokine, which promotes M2 polarization of TAM and diminishes expression of class II major histocompatibility complex (MHC-II) in professional antigen-presenting cells. Furthermore, PLK1 negatively regulates MHC-II expression in cancer cells, which has been shown to be associated with compromised tumor immunity and unfavorable patient outcomes. Taken together, our results reveal PLK1 as a novel modulator of TME in LUAD and provide possible therapeutic interventions.
Phylogeny and divergence time estimation of Io moths and relatives (Lepidoptera: Saturniidae:Automeris)
Authors: Skojec Chelsea , Earl Chandra , Couch Christian D. , Masonick Paul , Kawahara Akito Y. 
Published: August 2023

AbstractThe saturniid moth genusAutomerisincludes 145 described species. Their geographic distribution ranges from the eastern half of North America to as far south as Peru.Automeris moths are cryptically colored, with forewings that resemble dead leaves, and conspicuously colored, elaborate eyespots hidden on their hindwings. Despite their charismatic nature, the evolutionary history and relationships withinAutomerisand between closely related genera, remain poorly understood. In this study, we present the most comprehensive phylogeny ofAutomeristo date, including 80 of the 145 described species. We also incorporate two morphologically similar hemileucine genera,PseudautomerisandLeucanella, as well as a morphologically distinct genus,Molippa. We obtained DNA data from both dry-pinned and ethanol-stored museum specimens and conducted Anchored Hybrid Enrichment (AHE) sequencing to reconstruct a high-quality dataset for phylogenetic analysis. The resulting phylogeny supportsAutomerisas a paraphyletic genus, withLeucanellaandPseudautomerisnested within, with the most recent common ancestor dating back to 21 mya. This study lays the foundation for future research on various aspects ofAutomerisbiology, including anti-predator defense mechanisms, ecological adaptations, geographical distribution patterns, and potential drivers of speciation.
Quantitative Receptor Model for Responses That Are Left- or Right-Shifted Versus Occupancy (Are More or Less Concentration Sensitive): The SABRE Approach
Authors: Buchwald Peter 
Published: August 2023

AbstractSimple one-to three-parameter models routinely used to fit typical dose-response curves and calculate EC50values using the Hill or Clark equation cannot provide the full picture connecting measured response to receptor occupancy, which can be quite complex due to the interplay between partial agonism and (pathway-dependent) signal amplification. The recently introduced SABRE quantitative receptor model is the first one that explicitly includes a parameter for signal amplification (γ) in addition to those for binding affinity (Kd), receptor-activation efficacy (ε), constitutive activity (εR0), and steepness of response (Hill slope,n). It can provide a unified framework to fit complex cases, where fractional response and occupancy do not match, as well as simple ones, where parameters constrained to specific values can be used (e.g.,εR0=0,γ=1, orn=1). Here, it is shown that SABRE can fit not only typical cases where response curves are left-shifted compared to occupancy (κ=Kd/EC50>1) due to signal amplification (γ>1), but also less common ones where they are right-shifted (i.e., less concentration-sensitive;κ=Kd/EC50<1) by modeling them as apparent signal attenuation/loss (γ<1). Illustrations are provided withμ-opioid receptor (MOPr) data from three different experiments with one left- and one right-shifted response (G protein activation andβ-arrestin2 recruitment, respectively; EC50,Gprt<Kd<EC50,βArr). For such cases of diverging pathways with differently shifted responses, partial agonists can cause very weak responses in the less concentration-sensitive pathway without having to be biased ligands due to the combination of low ligand efficacy and signal attenuation/loss – an illustration with SABRE-fitted oliceridine data is included.
Tesofensine, a novel antiobesity drug, silences GABAergic hypothalamic neurons
Authors: Perez Claudia I. , Luis-Islas Jorge , Lopez Axel , Diaz Xarenny , Molina Omar , Arroyo Benjamin , Moreno Mario G. , Lievana Elvi Gil , Fonseca Esmeralda , Castañeda-Hernández Gilberto , Gutierrez Ranier 
Published: August 2023

ABSTRACTObesity is a major global health epidemic that has adverse effects on both the people affected as well as the cost to society. Several anti-obesity drugs that target GLP-1 receptors have recently come to the market. Here we describe the effects of tesofensine, a novel anti-obesity drug that acts as a triple monoamine neurotransmitter reuptake inhibitor. We investigated its effects on weight loss and underlying neuronal mechanisms in mice and rats using various techniques. These include behavioral tasks, DeepLabCut videotaped analysis, electrophysiological ensemble recordings, optogenetic activation, and chemogenetic silencing of GABAergic neurons in the Lateral Hypothalamus (LH). We found that tesofensine induced greater weight loss in obese than lean rats, which was associated with changes in LH ensemble activity. In Vgat-ChR2 and Vgat-IRES-cre transgenic mice, we found for the first time that tesofensine inhibited a subset of LH GABAergic neurons, reducing their ability to promote feeding behavior, and chemogenetically silencing them enhanced tesofensine’s food-suppressing effects. Unlike phentermine, a dopaminergic appetite suppressant, tesofensine causes few, if any, head-weaving stereotypy at therapeutic doses. Most importantly, we found that tesofensine prolonged the weight loss induced by 5-HTP, a serotonin precursor, and blocked the body weight rebound that often occurs after weight loss. Behavioral studies on rats with the tastant sucrose indicated that tesofensine’s appetite suppressant effects are independent of taste aversion and do not directly affect the perception of sweetness or palatability of sucrose. In summary, our data provide new insights into the effects of tesofensine on weight loss and the underlying neuronal mechanisms, suggesting that tesofensine may be an effective treatment for obesity and that it may be a valuable adjunct to other appetite suppressants to prevent body weight rebound.
Social flocking increases in harsh and challenging environments
Authors: Bellefeuille Jessica J. , Ratnayake Ruchitha C. B. , Cornthwaite Emily , Dakin Roslyn 
Published: August 2023

AbstractGrouping with others can provide enhanced information about resources and threats. A key hypothesis in social evolution proposes that individuals can benefit from social information in environments where it is challenging to meet energetic needs. Here, we test this hypothesis by examining the environmental drivers of conspecific flocking behaviour in a large archive of citizen science observations of two common North American birds, the dark-eyed junco (Junco hyemalis) and black-capped chickadee (Poecile atricapillus). To quantify flocking behaviour, we apply the index of dispersion,D, as a metric of clumpiness in each species’ spatiotemporal distribution. We show that juncos in winter are nearly always more clustered than a random expectation, whereas chickadees span a range from uniform to socially clustered distributions. In both species, the degree of social clustering strongly increases with abundance. We identify several key environmental variables that explain the extent of conspecific flocking in both species. Flocks are more socially clustered at higher latitudes, higher elevations, closer to midwinter, and at temperatures that are colder than average given the location and time of year. Together, these findings support the hypothesis that sociality is a key strategy for coping with harsh environments.HIGHLIGHTSGrouping with others can be an important source of information about resourcesWe analyzed how flocking behaviour changes throughout winter in two bird speciesWe used the index of dispersion to quantify social clustering at a broad scaleIn both species, social clustering increases in response to climate challenges
Lactate activates the mitochondrial electron transport chain independent of its metabolism
Authors: Cai Xin , Ng Charles C. , Jones Olivia , Fung Tak Shun , Ryu Keunwoo , Li Dayi , Thompson Craig B. 
Published: August 2023

SUMMARYLactate has long been considered a cellular waste product. However, we found that as extracellular lactate accumulates, it also enters the mitochondrial matrix and stimulates mitochondrial electron transport chain (ETC) activity. The resulting increase in mitochondrial ATP synthesis suppresses glycolysis and increases the utilization of pyruvate and/or alternative respiratory substrates. The ability of lactate to increase oxidative phosphorylation does not depend on its metabolism. Both L- and D-lactate are effective at enhancing ETC activity and suppressing glycolysis. Furthermore, the selective induction of mitochondrial oxidative phosphorylation by unmetabolized D-lactate reversibly suppressed aerobic glycolysis in both cancer cell lines and proliferating primary cells in an ATP-dependent manner and enabled cell growth on respiratory-dependent bioenergetic substrates. In primary T cells, D-lactate enhanced cell proliferation and effector function. Together, these findings demonstrate that lactate is a critical regulator of the ability of mitochondrial oxidative phosphorylation to suppress glucose fermentation.
Heterogeneous presynaptic receptive fields contribute to directional tuning in starburst amacrine cells
Authors: Gaynes John A. , Budoff Samuel A. , Grybko Michael J. , Poleg-Polsky Alon 
Published: August 2023

AbstractThe processing of visual information by retinal starburst amacrine cells (SACs) involves transforming excitatory input from bipolar cells (BCs) into directional calcium output. While previous studies have suggested that an asymmetry in the kinetic properties of bipolar cells along the soma-dendritic axes of the postsynaptic cell could enhance directional tuning at the level of individual branches, it remains unclear whether biologically relevant presynaptic kinetics contribute to direction selectivity when visual stimulation engages the entire dendritic tree. To address this question, we built multicompartmental models of the bipolar–SAC circuit and trained them to boost directional tuning. We report that despite significant dendritic crosstalk and dissimilar directional preferences along the dendrites that occur during whole-cell stimulation, the rules that guide BC kinetics leading to optimal directional selectivity are similar to the single-dendrite condition. To correlate model predictions to empirical findings, we utilized two-photon glutamate imaging to study the dynamics of bipolar release onto ON- and OFF- starburst dendrites in the murine retina. We reveal diverse presynaptic dynamics in response to motion in both BC populations; algorithms trained on the experimental data suggested that the differences in the temporal release kinetics are likely to correspond to heterogeneous receptive field (RF) properties among the different BC types, including the spatial extent of the center and surround components. In addition, we demonstrate that circuit architecture composed of presynaptic units with experimentally recorded dynamics could enhance directional drive but not to levels that replicate empirical findings, suggesting other DS mechanisms are required to explain SAC function. Our study provides new insights into the complex mechanisms underlying direction selectivity in retinal processing and highlights the potential contribution of presynaptic kinetics to the computation of visual information by starburst amacrine cells.