bluuebunny/crossref_metadata_2025_split huggingface dataset:
Near 100% genome editing efficiency with a one-step all RNA prime editing system in a human reporter iPSC line
Authors: Wettschurack Kyle , Skarnes William C. , Pellegrino Enrica , Robinson Morgan , Yang Yang 
Published: January 2025

AbstractCRISPR/Cas9 nucleases offer powerful tools for genome editing but can cause unintended mutations at the target site due to the creation of double-stranded DNA breaks. Prime editing (PE) is arguably a safer technology as it relies on the creation of single-strand DNA nicks and avoids possible indels. Despite its precision, current PE systems are limited by relatively low editing efficiency in non-immortalized cells. Here, we optimized prime editing in human induced pluripotent stem cells (hiPSCs) using a fluorescence-based assay to achieve near-complete editing of a BFP transgene. Using an all-RNA approach, precise prime editing of a single nucleotide variant was observed in >95% of cells with minimal unintended edits at the target site.
Intrinsic functional connectivity delineates transmodal language functions
Authors: Salvo J.J. , Anderson N.L. , Braga R.M. 
Published: January 2025

AbstractCommunication involves the translation of sensory information (e.g., heard words) into abstract concepts according to abstract rules (e.g., the meaning of those words). Accordingly, using language involves an interplay betweenunimodalbrain areas that process sensory information andtransmodalareas that respond to linguistic input regardless of the input modality (e.g., reading sentences vs. listening to speech). Previous work has shown that intrinsic functional connectivity (iFC), when performed within individuals, can delineate a distributed language network that overlaps in detail with regions activated by a reading task. The network was widely distributed across multiple brain regions, recapitulating an organization that is characteristic of association cortex, and which suggests that the distributed language network serves transmodal, not unimodal, functions. Here, we tested whether the distributed language network encapsulates transmodal functions by assessing its degree of overlap with two language tasks, one auditory (i.e., listening to speech) and one visual (i.e., reading sentences). The results show that the distributed language network aligns well with regions activated by both tasks, supporting a transmodal function. Further, the boundaries of the distributed language network along the lateral temporal cortex serve as a good proxy for the division between transmodal language and auditory functions: presentation of sounds (i.e., filtered, incomprehensible speech) evoked activity that was largely outside of the distributed language network but closely followed the network boundaries. These findings support that individualized iFC estimates can delineate the division between sensory-linked and abstract linguistic functions. We conclude that within-individual iFC may be viable for language mapping in individuals with aphasia who cannot perform language tasks in the scanner.
Molecular epidemiology ofAscaris lumbricoidesfollowing multiple rounds of community-wide treatment: who infects whom?
Authors: Landeryou Toby , Maddren Rosie , Hearn Jack , Belachew Mahlet , Rayment Gomez Santiago , Liyew Ewnetu Firdawek , Forbes Kathryn , Mengistu Birhan , Lawton Scott , Eze Jude , Tasew Geremew , Angulo Ufaysa , Anderson Roy 
Published: January 2025

AbstractControl and elimination of the parasiteAscaris lumbricoidesrelies on mass administration using a limited number of anti-helminthics. Whilst these programs have reduced the infection intensity and prevalence within many endemic regions transmission is poorly understood, with reinfection commonly occurring following cessation of treatment. Here, we utilise genomic data to understand parasite transmission within and between households in a community and the genomic impact of repeated MDA. We sequenced 54 whole-genomes from individuals in a longitudinal cohort epidemiological study of transmission and drug treatment extending over 6 years. We found that fine-scale population structure exists in spatially distinct clusters of infected individuals with reinfection occurring within or between geographically close households. This observation helps inform the policy of future control in low prevalence settings suggesting more targeted treatment of infection hotspots We found evidence of positive selection acting on members of gene families previously implicated in reduced drug efficacy but detect no high frequency of impactful variants. As efforts to eliminateA. lumbricoidesintensify, our study provides a foundation for genomic surveillance to help identify both who infects whom and the impact of repeated drug treatment.
Short activation domains control chromatin association of transcription factors
Authors: Fan Vinson B , Darzacq Xavier , Staller Max V 
Published: January 2025

AbstractTranscription factors regulate gene expression with DNA-binding domains (DBDs) and activation domains. It is generally assumed that DBDs are solely responsible for interacting with DNA and chromatin. Here, we used single-molecule tracking of transcription factors in living cells to find that short activation domains can control the fraction of molecules bound to chromatin. Activation domains with high bound fractions also have longer residence times on chromatin. Mutations in activation domains that increase activity of a transcriptional reporter increase the fraction of molecules bound to chromatin. Reciprocally, mutations that decrease reporter activity decrease fraction bound. These effects were consistent across three activation domains and three DBD classes. Taken together, these results suggest that activation domains play a major role in tethering transcription factors to chromatin, challenging the traditional view that the DBD is solely responsible for binding chromatin.
Stress-driven emergence of heritable non-genetic drug resistance
Authors: Xie Jinglin L. , Yin Sifei , Yang Theodore S. , Chandrasekher Kiran , Hanson Luke , Kim Sang Hu , Esqueda Lucas , Hogan Catherine A. , Banaei Niaz , Round June L. , Ost Kyla S. , Berman Judith , Jarosz Daniel F. 
Published: January 2025

AbstractDrug resistance is the chief cause of treatment failure for therapies targeting chronic and infectious diseases. Whether the emergence of resistance is accelerated by environmental exposure to low levels of therapeutics remains controversial. Here, we report a non-genetic mechanism of stress adaptation that promotes heritable resistance to the widely used antifungal drug fluconazole. In the human fungal pathogenCandida albicans,transient exposure to subtherapeutic fluconazole doses induces a protective response that we term para-resistance. Like conventional resistance mechanisms, para-resistance is heritable. However, it does not arise from genetic mutations and can revert spontaneously. Systematic analyses of para-resistant isolates suggest that its key regulators include the stress-activated MAP kinase Hog1, the histone deacetylase subunit Snt1, the chromatin regulator Rap1, and the Sko1 transcriptional factor. Notably, molecules that disrupt biomolecular condensation and prion propagation – crucial for the inheritance of protein assemblies – block the induction of para-resistance, whereas inhibiting histone deacetylases facilitates its induction. We find that para-resistance is common in clinical isolates and, remarkably, passage through the mammalian gut triggers its acquisition, compromising fluconazole’s therapeutic efficacy. Our work defines a pervasive, prion-like epigenetic mechanism of stress adaptation and highlights potential strategies to mitigate the rapid emergence of drug resistance.
Discovery ofNANOGenhancers and their essential roles in self-renewal and differentiation in human embryonic stem cells
Authors: Yan Jielin , Luo Renhe , Rosen Bess P. , Liu Dingyu , Wong Wilfred , Leslie Christina S. , Huangfu Danwei 
Published: January 2025

AbstractHuman embryonic stem cells (hESCs) are notable for their ability to self-renew and to differentiate into all tissue types in the body.NANOGis a core regulator of hESC identity, and dynamic control of its expression is crucial to maintain the balance between self-renewal and differentiation. Transcriptional regulation depends on enhancers, butNANOGenhancers in hESCs are not well characterized. Here we report twoNANOGenhancers discovered from a CRISPR interference screen in hESCs. Deletion of a single copy of either enhancer significantly reducedNANOGexpression, compromising self-renewal and increasing differentiation propensity. Interestingly, these twoNANOGenhancers are involved in a tandem duplication event found in certain primates including humans but not in mice. However, the duplicated counterparts do not regulateNANOGexpression. This work expands our knowledge of functional enhancers in hESCs, and highlights the sensitivity of the hESC state to the dosage of core regulators and their enhancers.
Human shape perception spontaneously discovers the biological origin of novel, but natural, stimuli
Authors: Dehn Kira I. , Maiello Guido , Hartmann Frieder T. , Morgenstern Yaniv , Hawkins Sara Joy , Offner Thomas , Walter Joshua , Hassenklöver Thomas , Manzini Ivan , Fleming Roland W. 
Published: January 2025

AbstractHumans excel at categorizing objects by shape. This facility involves identifying shape features that objects have in common with other members of their class and relies—at least in part—on semantic/cognitive constructs. For example, plants sprout branches, fish grow fins, shoes are molded to our feet. Can humans parse shapes according to the processes that give shapes their key characteristics, even when such processes are hidden? To answer this, we investigated how humans perceive the shape of cells from the olfactory system ofXenopus laevistadpoles. These objects are novel to most humans yet occur in nature and cluster into classes following their underlying biological function. We reconstructed 3D cell models through 3D-microscopy and photogrammetry, then conducted psychophysical experiments. Human participants performed two tasks: they arranged 3D-printed cell models by similarity and rated them along eight visual dimensions. Participants were highly consistent in their arrangements and ratings and spontaneously grouped stimuli to reflect the cell classes, unwittingly revealing the underlying processes shaping these forms. Our findings thus demonstrate that human perceptual organization mechanisms spontaneously parse the biological systematicities of never-before-seen, natural shapes. Integrating such human perceptual strategies into automated systems may enhance morphology-based analysis in biology and medicine.
Breaking Barriers in Crosslinking Mass Spectrometry: Enhanced Throughput and Sensitivity with the Orbitrap Astral Mass Analyzer
Authors: Müller Fränze , Stejskal Karel , Mechtler Karl 
Published: January 2025

AbstractThe advancement of crosslinking mass spectrometry (CLMS) has significantly enhanced the ability to study protein-protein interactions and complex biological systems. This study evaluates the performance of the Orbitrap Astral and Eclipse mass spectrometers in CLMS workflows, focusing on the identification of low-abundance crosslinked peptides. The comparison employed consistent liquid chromatography setups and experimental conditions, using Cas9 crosslinked with PhoX and DSSO as quality control samples. Results demonstrated that the Astral analyzer outperformed the Eclipse, achieving over 40% more unique residue pairs (URP) due to its superior sensitivity and dynamic range, attributed to its multi-reflection time-of-flight analyzer and nearly lossless ion transmission. Additionally, the study revealed that single higher-energy collisional dissociation (HCD) fragmentation methods significantly outperformed stepped HCD methods on the Astral, while the Eclipse maintained similar performance across both approaches. Gradient optimization experiments further highlighted the impact of separation times on crosslink identifications, with longer gradients yielding higher identification rates. Collectively, this work underscores the importance of instrumentation choice, fragmentation strategies, and method optimization in maximizing CLMS performance for protein interaction studies.
Preferences for tongue swab-versus sputum-based testing in the context of TB care: a Best-Worst Scaling exercise in Vietnam and Zambia
Authors: del Mar Castro Maria , Le Hien , Muzazu Seke , Pham Nam , Trinh Trang , Nyirenda Herbert , Shabalu Patricia , West Nora , Phan Ha , Cattamanchi Adithya , Denkinger Claudia M. , Muyoyeta Monde , Kerkhoff Andrew D. 
Published: January 2025

AbstractBackgroundThe development of non-sputum-based tests is an urgent priority to increase access to tuberculosis (TB) diagnostic testing. Understanding preferences of people undergoing testing is critical for designing tests and strategies aligned with their needs.MethodsWe conducted a survey and Best-Worst Scaling (BWS) exercise to determine relative preferences for tongue swab-vs. sputum-based testing among people (≥13 years) with presumptive TB at primary health centers in Vietnam and Zambia. The BWS assessed sixteen TB test features, including accuracy, sample type, turnaround time, cost, and service aspects. We analyzed preferences using Hierarchical Bayes modeling and identified distinct preference groups using Latent Class Multinomial Logit analyses (LCA).ResultsAmong 409 participants enrolled, 356 (87%) met quality criteria for analysis. When asked directly, most participants preferred providing tongue swabs over sputum (58% vs 29%, p<0.001; 13% no preference). In the BWS exercise, tongue swab was also preferred over sputum (mean rescaled preference weight [MPW] 6.4 [95%CI: 5.9-6.8] vs. 5.0 [95%CI: 4.6-5.4]). However, support and counseling (MPW=14.0), sensitivity (MPW=12.3), specificity (MPW=10.2), and provider attitude (MPW=7.4) were the most important features overall. Less important features included facility opening hours (MPW=3.4) and the influence of trusted sources on testing decisions (MPW=2.2). LCA identified five distinct preference groups, but support and counseling were universally valued. Participants in Groups 2 (27.3%; n=97) and 3 (17.1%; n=61) valued tongue swabs over many other features. Group 5 participants (11%; n=39) strongly valued sputum-based testing.ConclusionsParticipants in Vietnam and Zambia preferred tongue swab-based TB testing over sputum. However, sample type was less important than test accuracy and other TB care features affecting the testing experience.
Investigating Neural Processing of Color in Normal and Impaired Vision
Authors: Rina Andriani 
Published: January 2025

AbstractThis study examines cortical responses to chromatic and luminance stimuli in individuals with normal trichromatic vision, Daltonism, and achromatopsia. Functional magnetic resonance imaging (fMRI) data were collected using stimuli modeled after Wade et al. (2008) to evaluate the differential activation of visual cortical areas. In normal trichromats, hV4 demonstrated the highest chromatic sensitivity, while ventral areas showed stronger responses to color compared to dorsal regions. In Daltonic and achromatopsia participants, cortical activation was observed under combined chromatic and luminance conditions; however, no significant color-specific activity was detected, even in hV4.This work establishes a baseline for understanding cortical responses in color vision deficiencies and preceded gene therapy studies in the same achromatopsia patients (Fischer et al., 2020; Seitz et al., 2022). These findings contribute to ongoing research into neural plasticity and targeted therapeutic interventions.
Molecular analyses of individual variation in honey bee sociability
Authors: Traniello Ian M. , Avalos Arian , Gachomba Michael J. M. , Gernat Tim , Chen Zhenqing , Cash-Ahmed Amy C. , Hamilton Adam R. , Cook Jennifer L. , Robinson Gene E. 
Published: January 2025

AbstractIndividual variation in sociability is a central feature of every society. This includes honey bees, with some individuals well-connected and sociable, and others at the periphery of their colony’s social network. However, the genetic and molecular bases of sociability are poorly understood. Trophallaxis – a behavior involving sharing liquid with nutritional and signaling properties - comprises a social interaction and a proxy for sociability in honey bee colonies: more sociable bees engage in more trophallaxis. Here we identify genetic and molecular mechanisms of trophallaxis-based sociability by combining genome sequencing, brain transcriptomics, and automated behavioral tracking. A genome-wide association study (GWAS) identified 18 single-nucleotide polymorphisms (SNPs) associated with variation in sociability. Several SNPs were localized to genes previously associated with sociability in other species, including in the context of human autism, suggesting shared molecular mechanisms of sociability. Variation in sociability also was linked to differential brain gene expression, particularly genes associated with neural signaling and development. Using comparative genomic and transcriptomic approaches, we also detected evidence for divergent mechanisms underpinning sociability across species, including those related to reward sensitivity and encounter probability. These results highlight both potential evolutionary conservation of the molecular roots of sociability and points of divergence.
Critical Scaling of Novelty in the Cortex
Authors: Ribeiro Tiago L. , Vakili Ali , Gifford Bridgette , Siddiqui Raiyyan , Sinfuego Vincent , Pajevic Sinisa , Plenz Dietmar 
Published: January 2025

AbstractThe ability to detect unanticipated, novel events and rapidly relay this information across neural networks is fundamental to brain function, enabling the selection of appropriate behavioral responses. Here, we examine the transmission of holographically triggered action potentials in primary visual cortex of quietly resting mice, focusing on the dynamics of communication from pyramidal neurons. We demonstrate that these novel action potentials, which are uncorrelated with preceding activity, exert a disproportionally large influence on neighboring neurons. Their influence scales robustly to an exponent between 0.2 and 0.3 relative to their number. Remarkably, even a small number of novel action potentials can engage a majority of the local network, achieving high decoding accuracy of the perturbation origin in the face of high trial-by-trial variability and ongoing activity characterized by scale-invariant, parabolic neuronal avalanches. This heightened susceptibility to small, local perturbations aligns with the behavior of complex systems exhibiting critical dynamics. Our findings reveal that scaling underpins the efficient communication of unanticipated action potentials, suggesting it is a fundamental mechanism for detecting and processing novel events in the brain. These results provide new insights into the neural basis of novelty detection and highlight the importance of critical dynamics in cortical network function.
The cytosolic cysteinyl-tRNA synthetase is capable of regulating ATF4 translation independent of eIF2α phosphorylation state
Authors: Xu Acer E. , Weissman Jonathan S. 
Published: January 2025

AbstractIn mammalian cells, the integrated stress response (ISR) triggers ATF4 translation under general conditions of cell stress. Mammalian target of rapamycin (mTOR) signaling also triggers ATF4 translation under general pro-growth conditions. While the transcriptomic changes of these two contradictory pathways are have been studied, a full understanding of all pathways capable of increasing ATF4 translation and how these pathways are regulated and interact with each other remains unknown. In a genome-wide CRISPRi screen, we found that loss of CARS is sufficient to activate ATF4 translation independent of canonical ISR signaling. This ATF4 translation does not require eIF2α phosphorylation and does not require MTOR kinase activity. In a genome-wide epistasis CRISPRi screen using a staggered sgRNA infection strategy, we identified METAP2 and OGT as potential downstream factors in this pathway. This represents a novel pathway for activation of ATF4 translation that may enable targeted manipulation of ATF4 for beneficial therapeutic outcomes.
Correlation between DNA double strand breaks and cell death in peripheral blood lymphocytes from breast cancer patients
Authors: Solana-Peña Ángela , Pujol-Canadell Monica , López Juan-Sebastián , Macià Miquel , Martínez Pérez Evelyn , Linares Isabel , Stefanovic Milica , Pérez-Montero Héctor , González-Viguera Javier , Arangüena Peñacoba Marina , Ventura Montse , de Miguel-Garcia Gisela , Guedea Ferran , Erill Nadina , González-Rumayor Victor , Armengol Gemma , Barquinero Joan Francesc 
Published: January 2025

AbstractRadiotherapy is an effective treatment to fight cancer. However, it not only affects cancer cells but also healthy tissues, causing side effects. Different factors can influence the appearance of radiotoxicity, like total dose administered or patient individual characteristics, such as genetic variability. Several biomarkers have been proposed to predict radiotoxicity, especially those based on apoptosis or DNA damage, for example γ-H2AX, which correlates with DNA double strand breaks. Our purpose is to analyze how apoptosis and γ-H2AX correlate to each other and to link these results with selected SNPs associated with apoptosis. Blood samples from 60 breast cancer patients in remission were recruited. After mononucleated cells isolation, samples were irradiated. Then, we assessed induction and kinetics of disappearance of γ-H2AX at different times after 2-Gy irradiation and apoptosis induced 24 and 48 h after 8-Gy irradiation. A negative correlation was observed between basal and residual γ-H2AX and apoptosis at 48 h post-irradiation. This result supports previous studies with cancer patients showing a negative correlation between these two biomarkers. Considering the high variability of radio-induced apoptosis, we performed a genotyping study. Two SNPs located atTP53andFASgenes were associated with apoptosis. Overall, our results indicate that individuals with less efficiency in removing damaged cells, probably due to genetic polymorphisms, presented more basal and residual levels of DNA damage.
C. elegansLET-381/FoxF and DMD-4/DMRT control development of the mesodermal HMC endothelial cell
Authors: Stefanakis Nikolaos , Xi Jasmine , Jiang Jessica , Shaham Shai 
Published: January 2025

ABSTRACTEndothelial cells form the inner layer of blood vessels and play key roles in circulatory system development and function. A variety of endothelial cell types have been described through gene expression and transcriptome studies; nonetheless, the transcriptional programs that specify endothelial cell fate and maintenance are not well understood. To uncover such regulatory programs, we studied theC. elegansHead Mesodermal Cell (HMC), a non-contractile mesodermal cell bearing molecular and functional similarities to vertebrate endothelial cells. Here, we demonstrate that a Forkhead transcription factor, LET-381/FoxF, is required for HMC fate specification and maintenance of HMC gene expression. DMD-4, a Dmrt transcription factor, acts downstream of and in conjunction with LET-381 to mediate HMC fate specification and gene expression maintenance. DMD-4, independently of LET-381, also represses the expression of genes associated with a different, non-HMC, mesodermal fate. Our studies uncover essential roles for FoxF transcriptional regulators in endothelial cell development, and suggest that the identity of FoxF co-functioning target transcription factors promotes specific non-contractile mesodermal fates.