bluuebunny/crossref_metadata_2025_split huggingface dataset:
Condensin II mediates efficient chromatid resolution and resistance to genotoxic stress in Arabidopsis
Authors: Vladejić Jovanka , Prochazkova Klara , Tomaštíková Eva Dvořák , de Cock Zynke , Zwyrtková Jana , Kaduchová Kateřina , Pavlíková Markéta , Pecinka Ales 
Published: January 2025

ABSTRACTGenome functions are regulated by the means of chromatin and 3D chromosome organization. Dynamic condensation and relaxation of chromosomes during cell cycle is largely controlled by the Condensin complexes. We mapped mutants in Condensin II subunitsSMC2A,CAP-D3andCAP-H2as hypersensitive to DNA-protein crosslink (DPC) inducer zebularine. This suggested that Condensin II complex is required for resistance to genotoxic stress in Arabidopsis and prompted us to explore the underlying phenotypes. We show that the Condensin II role in resistance to zebularine is independent of the DNA damage response signaling by SOG1 and the homology-directed repair pathway. Furthermore, we found that Arabidopsis Condensin II mutants have incompletely condensed mitotic chromosomes and show abnormal chromatin connections during anaphase. Based on the structural and temporal analyses, we propose that the connections represent catenated chromatids. The chromosome connections were more frequent when the Condensin II mutants were treated by zebularine or TOP2 crosslinker and inhibitor ICRF-187. Altogether, we demonstrate that the proper large-scale chromatin organization by Condensin II is important for resistance to DNA damage response-inducing agents in Arabidopsis.
Assessing the impact of yield plasticity on hybrid performance in maize
Authors: Davis Jensina M. , Coffey Lisa M. , Turkus Jonathan , López-Corona Lina , Linders Kyle , Ullagaddi Chidanand , Santra Dipak K. , Schnable Patrick S. , Schnable James C. 
Published: January 2025

ABSTRACTImproving crop resilience in the face of increasingly extreme and unpredictable weather and reduced access to agricultural inputs such as nitrogen fertilizer and water will require an improved understanding of phenotypic plasticity in crops. To understand the roles of different component traits in determining overall plasticity for grain yield, we generated data from a panel of 122 maize (Zea mays) hybrids grown in replicated field trials in 34 environments spanning 700 miles (1126 km) of the U.S. Corn Belt. We observed that the levels of genetic versus environmental control and the relationships between mean parent release year, overall performance, and linear plasticity were trait-dependent across the 18 agronomic and yield components studied. Importantly and unexpectedly, we observed no clear tradeoff between linear plasticity and mean performance and found only rare examples where genotype-by-environment interactions would alter selection decisions based on the environments tested in our dataset. Furthermore, we showed that overall plasticity was repeatable and appears to be under considerable genetic control but that plasticity in response to nitrogen fertilization was not, which may help explain the limited success in breeding for nitrogen use efficiency. Together, these findings improve our understanding of phenotypic plasticity, with implications for maize breeding.
Impact of infusion conditions and anesthesia on CSF tracer dynamics in mouse brain
Authors: Zhu Yuran , Zhu Junqing , Ni Chenxin , Chen Anbang , Li Longshun , Gao Yue , Shoffstall Andrew J. , Yu Xin 
Published: January 2025

AbstractTracer imaging has been instrumental in mapping the brain’s solute transport pathways facilitated by cerebrospinal fluid (CSF) flow. However, the impact of tracer infusion parameters on CSF flow remains incompletely understood. This study evaluated the influence of infusion location, rate, and anesthetic regimens on tracer transport using dynamic contrast-enhanced MRI with Gd-DTPA as a CSF tracer. Infusion rate effects were assessed by administering Gd-DTPA into the cisterna magna (ICM) at two rates under isoflurane anesthesia. Anesthetic effects were evaluated by comparing transport patterns between isoflurane and ketamine/xylazine (K/X) anesthesia at the slower rate. Gd-DTPA transport was also examined after lateral ventricle (ICV) infusion, the primary site of CSF production. The results demonstrate that, besides anesthesia, both the location and rate of infusion substantially affected solute transport within the brain. ICV infusion led to rapid, extensive transport into deep brain regions, while slower ICM infusion resulted in more pronounced transport to dorsal brain regions. Cross-correlation and hierarchical clustering analyses of region-specific Gd-DTPA signal time courses revealed that ICM infusion facilitated transport along periarterial spaces, while ICV infusion favored transport across the ventricular-parenchymal interface. These findings underscore the importance of experimental conditions in influencing tracer kinetics and spatial distribution in the brain.
Genomic connectivity and adaptation signals of the freshwater spongeEphydatia muelleriacross its distribution
Authors: Cassidy Robert , de la Cruz Laura , Mitsi Konstantina , Galià-Camps Carles , Benítez-López Ana , Gracia-Sancha Carlota , Lorente-Sorolla Jose , Álvarez Almudena , Mozo Rocío , Kolomyjec Stephen , Nichols Scott , Manconi Renata , Pereira Raquel , Evans Karen , Itskovitch Valeria , Horton April L. , Leys Sally P. , Taboada Sergio , Riesgo Ana 
Published: January 2025

1.AbstractFreshwater sponges fulfill critical ecological functions, including maintaining water quality, regulating nutrient dynamics, offering habitats for diverse taxa, and serving as a vital food source for various species. However, their patterns of dispersal and genetic connectivity remain inadequately understood, posing significant challenges to effective conservation assessments. We examined genetic connectivity and genetic adaptation to local environmental conditions inEphydatia muelleriacross its geographic range using ddRADseq-derived SNPs from 106 individuals collected from 11 localities spanning North America, Europe, and Asia. Analysis of 3,182 neutral SNPs revealed low connectivity and strong genetic structure among regions within two main genetic clusters of North America and Eurasia, while 115 SNPs identified to be under selection showed considerable evidence for differentiated, polygenic adaptation to light and temperature conditions across sampled locations, as well as selection on gene regulatory processes. These findings align with the “monopolization hypothesis”, suggesting that historical climatic and geological conditions of the Last Glacial Maximum, including habitat expansion, contraction, and natural barriers, have contributed more to the current genetic structure ofE. muelleripopulations than contemporary gene flow, which is restricted by monopolistic habitat colonization by this species. Our results provide novel support for ecological theory on dispersal in aquatic invertebrates, as well as insights into the plasticity ofE. muelleriin the face of varying environmental conditions that are fundamentally important for freshwater ecosystem conservation.
High-frequencyWus2-integrated transformation toolkit enhancesCas9editing efficiency and expands capability withSpRYin sorghum
Authors: Shen Jianqiang , Aregawi Kiflom , Anwar Sultana , Miller Tamara , Lemaux Peggy G. 
Published: January 2025

AbstractSorghum bicolorL. (Moench) ranks as the fifth most important crop globally, serving diverse purposes such as forage, food, feed, and fuel. Its natural tolerance to various environmental stresses makes it a valuable resource for addressing climate resilience. Harnessing such genetic resources for crop improvement requires highly efficient genetic transformation and genome editing tools. However, sorghum has historically been recalcitrant to genetic transformation, and publicly available engineering tools remain limited. In this study, we report a high-efficiency engineering toolkit, including shuttle and binary vectors, optimized for genome editing viaAgrobacterium-mediated transformation. Using this toolkit, we successfully introduced CRISPR/Cas9-based editing machinery to target thephytoene desaturase(PDS) gene, achieving editing efficiencies up to 95.7% with monocistronic gRNA expression cassettes. To further expand the genome editing repertoire, we employed a protospacer adjacent motif (PAM)-flexibleCas9variant,SpRY(ZmSpRYi), and achieved comparable editing efficiencies. Using our toolkit increases the potential for advanced editing tools to be used in engineering genetic variation of agronomically important quantitative traits. It also paves the way for deploying advanced genome editors, such as prime editors and base editors, to manipulate genetic and genomic resources. These advances provide a robust approach for advancing research in sorghum and other cereals, offering new opportunities for sustainable crop improvement.
The paradoxical impact of drought on West Nile virus risk: insights from long-term ecological data
Authors: Sambado Samantha , Sipin Terrell J , Rennie Zoe , Larsen Ashley , Cunningham James , Quandt Amy , Sousa Dan , MacDonald Andrew J 
Published: January 2025

ABSTRACTMosquito-borne diseases are deeply embedded within ecological communities, with environmental changes – particularly climate change – shaping their dynamics. Increasingly intesense droughts across the globe have profound implications for the transmission of these diseases, as drought conditions can alter mosquito breeding habitats, host-seeking behaviors, and mosquito-host contact rates. To quantify the effect of drought on disease transmission, we use West Nile virus (WNV) as a model system and leverage a robust mosquito and virus dataset consisting of over 500,000 trap nights collected from 2010-2023, spanning a historic drought period followed by atmospheric rivers. We pair this surveillance dataset with a novel modeling approach that incorporates monthly changes in bird host community competence, along with drought conditions, to estimate the effect of drought severity on WNV risk using panel regression models. Our results show that while drought decreases mosquito abundances, it paradoxically increases WNV infection rates. This counterintuitive pattern likely stems from reduced water availability, which concentrates mosquitos and pathogen-amplifying bird hosts around limited water sources, thereby increasing disease transmission risk. However, the magnitude of the effect depends critically on mosquito species, suggesting species-specific behavioral traits are key to understanding the effect of drought on mosquito-borne disease risk across real landscapes.
Transcriptome responses of twoHalophila stipulaceaseagrass populations from pristine and impacted habitats, to single and combined thermal and excess nutrient stressors, reveal local adaptive features and core stress-response genes
Authors: Nguyen Hung Manh , Yaakov Beery , Beca-Carretero Pedro , Procaccini Gabriele , Wang Guannan , Dassanayake Maheshi , Winters Gidon , Barak Simon 
Published: January 2025

AbstractIn their natural habitats, seagrasses face multiple abiotic stressors, which can often occur simultaneously. However, most studies investigating the effects of environmental stressors on seagrasses have focused on growth and physiological responses to single stressors. Here, we examined the transcriptome responses of the tropical seagrassHalophila stipulaceacollected from a northern Gulf of Aqaba pristine site (South Beach - SB) and an anthropogenically-impacted site (Tur Yam - TY), grown in a mesocosm, and exposed to ecologically-relevant, single and combined, thermal and excess nutrient stressors. The combined thermal and nutrient stressor elicited greater transcriptome reprogramming than the single stressors in both populations and induced the expression of a combination-specific set of genes involved in abiotic and biotic stress responses. Furthermore, thermal stress exerted a more dominant influence than excess nutrient stress upon the transcriptome response to the combined stress. Transcriptomes of plants from the impacted TY site displayed reduced plasticity, the presence of genes exhibiting a “stress-ready” mode of expression under all stresses, and increased resilience (recovery to control transcriptomes). We also identified core stress-response genes that could be leveraged as early indicators of stress in the field. Overall, our data suggest that environmental conditions in seagrass habitats can drive local molecular adaptation, and that the response of seagrasses to combined stressors associated with climate change and coastal anthropogenic stressors cannot be predicted from the response to single stressors.
Mathematical Characterization of Drug-Induced Persistence in Cancer
Authors: Park Ji Tae , Levine Herbert 
Published: January 2025

AbstractWe introduce a general phenomenological framework for understanding how phenotypic plasticity gives rise to drug persisters. These persisters, often quiescent but sometimes which again return to cycling, survive in the presence of treatment and eventually can lead to mutants with true resistance. Our framework builds on recent experimental observations regarding variations between and among single-cell clones and the possible role of the drug itself in enhancing the survival strategy. Predictions of our approach include the existence of an optimum drug concentration as well as an optimum drug holiday schedule to minimize the persistence-based threat.
Exploring genetic diversity in the species-rich genusLiolaemus: The interplay among isolation by distance, body size, and environmental variability
Authors: Ruiz-Monachesi M. R. , Cruz F. B. , Martínez J. J. 
Published: January 2025

AbstractIntraspecific genetic variation enhances the specieś capacity to endure diverse environments. Such variation may drive genetic divergence among populations, often manifesting as isolation by distance (IBD). Here, we investigated how ecological, environmental, life-history, morphological, and phylogenetic factors, shape IBD and genetic diversity (π) inLiolaemuslizards. Further we explored differences related to reproductive modes and taxonomic groups. Using data from GenBank, we examined two mitochondrial genes: Cytb (86 species) and 12S rRNA (37 species). We integrated geographic information for each species to evaluate genetic differentiation concerning spatial distribution. We calculated the IBD slope (βIBD), Manteĺsr, and π for each gene, then tested for an association between βIBDand π. Phylogenetic multiple linear regression revealed that IBD, in the case of Cytb, was present in 56.16% of species and was negatively associated with snout-vent length (SVL). At the same time βIBD-Cytbwas positively linked to geographic range size. Additionally, π of Cytb gene declined with increasing temperature range variability and body size. In contrast, for 12S rRNA, IBD was present in 42.42% of species but showed no relation with SVL; instead, phylogenetic history played a more substantial role in determining π-12S rRNA. Remarkably, only Cytb showed a positive association between β and π. These results underscore different evolutionary patterns across the two genes and suggest that both, isolation by distance, alongside thermal heterogeneity, shape genetic diversity within particular reproductive modes and phylogenetic contexts inLiolaemus.
Cis-regulatory Mutations Drive Tissue-specific Subfunctionalization of sRNA loci Regulating Soybean Seed Color During Domestication
Authors: Vodkin Lila O. , Jones Sarah I. , Cho Young B. 
Published: January 2025

ABSTRACTGene duplication and structural rearrangements have played a pivotal role in plant genome evolution, enabling functional divergence and the development of novel traits. In soybeans (Glycine max), theIlocus, which regulates seed color through tissue-specific subfunctionalization of sRNA loci, offers an example of these mechanisms. Using long-read sequencing, we investigated structural variations underlying four major alleles (I, ii, ik,andi) at theIlocus. Our study revealed that large-scale rearrangements, including duplications, inversions, and deletions, within a 180-kb CHS repeat-rich region drive allele-specific RNA silencing through small interfering RNAs (siRNAs). The dominantIallele contains a cis-regulatory region of DnaJ upstream of CHS genes, while theiiandikalleles feature subtilisin- and P450-driven siRNA loci, respectively. The recessiveiallele lacks siRNA production due to deletions or inversions disrupting CHS gene clusters. Phenotypic analyses and RNA-seq confirmed allele-specific, tissue-dependent expression of siRNAs correlating with seed coat pigmentation patterns. This study highlights the evolutionary role of repeat-rich regions in generating regulatory innovations and phenotypic diversity. Our findings underscore the importance of structural rearrangements in domestication traits and demonstrate the power of long-read sequencing for resolving complex genomic regions, advancing both evolutionary biology and crop improvement.SIGNIFICANCE□Naturally occurring mutations in the soybean seed coat have revealed the evolution of sRNA genes and their subfunctionalization, resulting in tissue-specific gene expression.□Non-homologous recombination of repetitive sequences drives cis-regulatory region rearrangements, leading to the subfunctionalization of sRNA loci that regulates one of domestication traits.
Robustness of a Bistable Biomolecular Positive Feedback Circuit to Global Parametric Perturbations
Authors: Chorasiya G. , Prakash R. , Sen S. 
Published: January 2025

AbstractAchieving robustness to global perturbations where all parameters can change at the same time is challenging because the controller would also face the same disturbance as the plant. For nonlinear positive feedback, an important mechanism for cell fate determination in biomolecular contexts, quantitative aspects of robustness to such perturbations are generally unclear. Here we used mathematical methods of control and dynamical systems, interval analysis, and a benchmark model of a bistable biomolecular positive feedback circuit to address this. We confirmed that such perturbations can change the qualitative behaviour of the system extinguishing bistability. We obtained a quantitative relation between the relative variation in the stable steady state and the unstable steady state in terms of the relative changes in the parameters. We showed how the deviation in the trajectories near the unstable steady state due to global perturbations could diverge almost exponentially, after an initial transient, which could have a significant impact on the bistable switching dynamics. We found that the size of the eigenvalue for the unstable steady state was greater than that for the stable steady state, and proved this for certain parameters using a rigorous numerical construction. We noted a tradeoff between enhancing the parameter space of bistability and the increased sensitivity in the bistable dynamics due to parametric perturbations. We obtained rigorous bounds on the entire transient response for global parametric perturbations. These results provide a quantitative insight into the robustness of a bistable biomolecular positive feedback circuit to global parametric perturbations.
De novoAutogenic Engineered Living Functional Materials
Authors: Hammad Hoda M. , Swarnadeep Seth , Crater Erin R. , Moore Robert B. , Deshmukh Sanket , Manjula-Basavanna Avinash , Duraj-Thatte Anna M. 
Published: January 2025

AbstractAutogenic engineered living materials (ELMs) involvein situproduction and engineering of native extracellular matrix (ECM). However, the existing autogenic ELMs have limited scope and functionalities. Herein, we report a platform forde novoautogenic functional ELMs. By protein mining, we have discovered CsgA-like 33,564 homologs that can find potential utility asde novoECM of protein nanofibers. By employing AlphaFold2 and molecular dynamics simulations, we shed insights into the CsgA-like β-solenoid protein structures and stability. By hackingEscherichia colicurli machinery, we demonstrate the production ofde novoautogenic ELMs from CsgA-like proteins (≤9-times the molecular weight and β-sheet repeat units) of extremophilic non-model bacteria. Additionally, we biomanufacture macroscopic materials with tunable mechanical properties (enhancing storage modulus by 3-times) and programmable functionalities (3D printability, binding to nanoparticles/antibodies). This work showcases a versatile platform to discover, rationally design, and harness the sophisticated functionalities of natural systems for futuristic autogenic ELMs.
Patient Experiences of Treatment Deferral for Evaluation and Monitoring after a Trace Xpert Ultra Result
Authors: Visek Caitlin , Mukiibi James , Nantale Mariam , Nalutaaya Annet , Biché Patrick , Sung Joowhan , Kayondo Francis , Akampurira Joab , Mukiibi Michael , Kiyonga Rogers , Katamba Achilles , Kendall Emily A. 
Published: January 2025

ABSTRACTBackgroundA “trace” result from the Xpert Ultra molecular TB test indicatesMycobacterium tuberculosisDNA detection but may not always signify TB disease. Little is known about the experiences of individuals with trace results who are not immediately treated.MethodsWe enrolled Ugandan adults and adolescents with trace Xpert Ultra sputum results, plus positive and negative controls, from community-screening and clinic settings. After a comprehensive TB evaluation, participants not recommended to start treatment immediately were closely monitored with interval reassessments. Surveys captured participants’ perceptions and preferences related to their uncertain TB status at baseline and during follow-up.ResultsA total of 321 people with trace sputum (PWTS), 236 positive controls, and 279 negative controls were enrolled. A minority of PWTS thought they were highly likely to have or develop TB, and most reported low associated anxiety initially (258/321, 80%) and during follow-up. While about half (172/321, 54%) would have favored treatment at baseline if not in the study, those who remained untreated were less inclined toward treatment at six months. Participants generally preferred sensitive diagnostic tests, even with frequent false positives.ConclusionsDeferring treatment for PWTS, with sufficient testing and monitoring, is acceptable to most patients.