bluuebunny/crossref_metadata_2025_split huggingface dataset:
An engineered chromatin protein with enhanced preferential binding of H3K27me3 over H3K9me3
Authors: Franklin Kierra A. , Priode J. Harrison , Steppe Paige , Haynes Karmella A. 
Published: October 2024

ABSTRACTThe human genome is organized within the nucleus as chromatin, which is largely comprised of histone proteins that assemble on DNA into nucleosome complexes. Histone post-translational modifications (PTMs) are dynamic chromatin features that signal distinct gene expression states and modulate important cellular functions like cell differentiation. Histone binding domains (HBDs) from chromatin reader-effector proteins are being used as new tools to target and track histone PTMs in living cells. HBDs bind histones through multi-contact interactions that may confer more specificity than antibodies, but are hard to study because of their weaker affinityin vitro. To explore the large HBD design space, we developed the “Cell-Free Histone-Binding Immunoassay” (CHIA) where interactions between cell-free-expressed HBD proteins and immobilized biotinylated histone peptides are measured in an ELISA-style assay. We showed that the number of functional CBX8 polycomb chromodomains (PCD) in a fusion protein scales with H3K27me3 binding. We tackled the challenge of engineering a high affinity HBD that distinguishes H3 A-A-R-K27me3-S from a similar region on the same histone, T-A-R-K9me3-S. Previously reported K33E and Q9D CBX7 PCD variants bound with high affinity to H3K27me3, and bound as strongly with H3K9me3. In contrast, the K33E substitution enhanced CBX8 PCD binding to K27me3 with minimal K9me3 binding. To determine if the CBX8 hydrophobic clasp (V10 and L49) supports K27me3 specificity we tested hydrophobic substitutions, and observed increased affinity and strong specificity for H3K27me3. These results will enable more robust sensing of H3K27me3 for applications such as histone PTM-detection, and cell engineering.
Seasonal contact and migration structure mass epidemics and inform outbreak preparedness in bottlenose dolphins
Authors: Collier Melissa , Urian Kim , Theisen Sarah , Jacoby Ann-Marie , Wilkin Sarah , Patterson Eric M. , Wallen Megan M. , Colizza Vittoria , Mann Janet , Bansal Shweta 
Published: October 2024

AbstractInfectious respiratory diseases have detrimental impacts across wildlife taxa, particularly in marine species. Despite this vulnerability, we lack information on the complex spatial and contact structures of marine populations which reduces our ability to understand disease spread and our preparedness for epidemic response. We leveraged a collated dataset to establish the first data-driven epidemiological model on a cetacean species, the Tamanend’s bottlenose dolphin (Tursiops erebennus), whose populations are periodically impacted by deadly respiratory disease in the northwest Atlantic. We found their spatial distribution and contact is heterogeneous along the coastline and varies by ecotype, which explains differences in infection burdens observed in past outbreaks. We also determined that outbreaks beginning in northern parts of their habitat during migratory seasons have the highest epidemic risk and that dolphins in North Carolina estuaries would be the best sentinels for disease surveillance. Our mathematical model provides a generalizable, non-invasive tool that takes advantage of routinely collected marine mammal data to mechanistically understand disease transmission and inform disease surveillance tactics for marine sentinels. Our findings highlight the heterogeneities that play a crucial role in shaping the impacts of infectious diseases in wildlife, and how a data-driven understanding of these mechanisms can enhance epidemic preparedness.
Convergent transcriptomic and genomic adaptation in xeric rodents
Authors: Domitille Chalopin , Carine Rey , Jeremy Ganofsky , Juliana Blin , Pascale Chevret , Marion Mouginot , Bastien Boussau , Sophie Pantalacci , Marie Sémon 
Published: October 2024

ABSTRACTRepeated adaptations rely in part on convergent genetic changes. The extent of convergent changes at the genomic scale is debated and may depend on the interplay between different factors. Rodents have repeatedly adapted to life in arid conditions, notably with altered renal morphology and physiology. This occurred at different time periods, allowing us to test the importance of time in convergent genomic evolution. We analyzed kidney transcriptomes from 34 species to quantify and characterize convergent evolution at the level of gene expression, tissue composition, and coding sequences. We found that several genes showed convergent expression changes, some of which also carried convergent changes in their coding sequence. We then subdivided these data to test the influence of evolutionary history. First, within the subfamily Murinae, we found more convergent gene expression, reflecting convergent changes in cell proportions. Second, we compared data for recent (within genera) and ancient (between genera) adaptations, and observed more convergent changes in the latter. Our study shows that adaptation to xeric environments in rodents involves repeated changes in tissue composition, gene expression and coding sequences, and that the degree of convergent evolution increases with both the age of the adaptations and species relatedness.
Genome-widein vivodynamics of cohesin-mediated loop extrusion and its role in transcription activation
Authors: Popay Tessa M. , Pant Ami , Munting Femke , Black Morgan E. , Haghani Nicholas , Dixon Jesse R. 
Published: October 2024

AbstractThe organization of the genome in three-dimensional space is highly dynamic, yet how these dynamics are regulated and the role they play in genome function is poorly understood. Here, we utilized acute depletion of NIPBL to characterize the role of cohesin-mediated loop extrusionin vivo. Using this approach, we found that many chromatin loops are rapidly diminished upon loss of NIBPL, consistent with recent single locus imaging studies showing that chromatin loops are transient. However, we also identified cohesin-dependent chromatin loops that are associated with distinct chromatin states and may be “long-lived”, given that they require NIPBL for their establishment upon mitotic exit, but are persistent when NIPBL is depleted from interphase cells. In addition to the reformation of 3D genome structures, mitotic exit coincides with widespread transcriptional activation. We found that NIPBL is essential for establishing the expression of lineage-defining genes during the M-G1 transition but has diminished impact on the steady-state maintenance of their expression. At genes sensitive to its depletion, NIPBL supports a unique local genome organization defined by greater spatial proximity to nearby super-enhancers and weaker transcription start site insulation of genomic contacts. Overall, we show that NIPBL-mediated loop extrusion is critical to genome organization and transcription regulationin vivo.
Reference-free variant calling with local graph construction with ska lo (SKA)
Authors: Derelle Romain , Madon Kieran , Hellewell Joel , Rodríguez-Bouza Víctor , Arinaminpathy Nimalan , Lalvani Ajit , Croucher Nicholas J. , Harris Simon R. , Lees John A. , Chindelevitch Leonid 
Published: October 2024

AbstractThe study of genomic variants is increasingly important for public health surveillance of pathogens. Traditional variant calling methods from whole-genome sequencing data rely on reference-based alignment, which can introduce biases and require significant computational resources. Alignment-free and reference-free approaches offer an alternative by leveraging k-mer-based methods, but existing implementations often suffer from sensitivity limitations, particularly in high mutation density genomic regions. Here, we present ska lo, a graph-based algorithm that aims to identify variants between pathogen whole-genome sequencing data by traversing a coloured De Bruijn graph and building variant groups (ie, sets of variant combinations). Through in-silico benchmarking and real-world dataset analyses, we demonstrate that ska lo achieves high sensitivity in SNP calls while also enabling the detection of insertions and deletions, as well as SNP positioning on a reference genome for recombination analyses. These findings highlight ska lo as a simple, fast and effective tool for pathogen genomic epidemiology, extending the range of reference-free variant calling approaches. ska lo is freely available as part of the SKA program (https://github.com/bacpop/ska.rust).
Cryo-EM structures of G4-stalled CMG reveal inchworm mechanism of DNA translocation
Authors: Batra Sahil , Allwein Benjamin , Kumar Charanya , Devbhandari Sujan , Bruning Jan-Gert , Bahng Soon , Lee Chong , Marians Kenneth J. , Hite Richard K. , Remus Dirk 
Published: October 2024

AbstractDNA G-quadruplexes (G4s) are non-B-form DNA secondary structures that threaten genome stability by impeding DNA replication. To elucidate how G4s induce replication fork arrest, we have characterized fork collisions with preformed G4s in the parental DNA using fully reconstituted yeast and human replisomes. We demonstrate that a single G4 in the leading strand template is sufficient to stall replisomes by blocking the CMG helicase. An ensemble of high-resolution cryo-EM structures of stalled yeast and human CMG complexes reveals that the G4 is fully folded and lodged inside the CMG central channel. The stalled CMG is conformationally constrained and arrests in the transition between translocation states. Unexpectedly, our analysis suggests that CMG employs an unprecedented inchworm mechanism to translocate on DNA. These findings illuminate the eukaryotic replication fork mechanism under both normal and perturbed conditions.
Autophosphorylation of the oncogenic protein TEL-ABL confers resistance to the allosteric ABL inhibitor asciminib
Authors: Muratcioglu Serena , Eide Christopher A. , Gorday Kent , Sumpena Emily , Zuo Wenqi , Groves Jay T. , Druker Brian J. , Kuriyan John 
Published: October 2024

AbstractChromosomal translocations that fuse the ABL1 gene to BCR and TEL cause human leukemias. Oligomerization and the loss of an inhibitory myristoylation modification lead to unregulated kinase activity of the BCR-ABL and TEL-ABL fusion proteins. ATP-competitive ABL inhibitors, such as imatinib and ponatinib, are effective against both fusion proteins. We discovered that asciminib, an allosteric inhibitor of BCR-ABL that binds to the myristoyl binding site in the ABL kinase domain, is >2000-fold less potent against TEL-ABL than BCR-ABL in cell-growth assays. This is surprising because the ABL components of the two fusion proteins, including the asciminib binding sites, have identical sequence. We deleted a short helical segment in the ABL kinase domain that closes over asciminib when it is bound. This deletion results in asciminib resistance in BCR-ABL, but has no effect on TEL-ABL, suggesting that the native autoinhibitory mechanism that asciminib engages in BCR-ABL is disrupted in TEL-ABL. We show, using mammalian cell expression and single-molecule microscopy, that BCR-ABL is mainly dimeric while TEL-ABL forms higher-order oligomers. Oligomerization can promote trans-autophosphorylation of ABL, and we find that a regulatory phosphorylation site in the SH3 domain of ABL (Tyr 89) is highly phosphorylated in TEL-ABL. This phosphorylation is expected to disassemble the autoinhibited conformation of ABL, thereby preventing asciminib binding. We show that TEL-ABL is intrinsically susceptible to inhibition by asciminib, but that increased phosphorylation results in resistance. Our results demonstrate that different ABL fusion proteins can have dramatically different responses to allosteric inhibitors due to differential phosphorylation.One Sentence SummaryWhen TEL-ABL is phosphorylated, it is insensitive to asciminib. However, when TEL-ABL is dephosphorylated by a phosphatase, asciminib sensitivity is restored.
Soil depth determines the microbial communities inSorghum bicolorfields
Authors: Murray Emily R. , Minich Jeremiah J. , Saxton Jocelyn , de Gracia Marie , Eck Nathaniel , Allsing Nicholas , Kitony Justine , Patel-Jhawar Kavi , Allen Eric E. , Michael Todd P. , Shakoor Nadia 
Published: October 2024

AbstractSorghum bicolor, an important global crop, adapted to thrive in hotter and drier conditions than maize or rice, has deep roots that interact with a unique and stratified soil microbiome that plays a crucial role in plant health, growth, and carbon storage. Microbiome studies on agricultural soils, particularly fields growingS. bicolor, have been mostly limited to surface soils (<30 cm). Here we investigated the abiotic factors of soil properties, field location, depth, and the biotic factors of sorghum type across 38 genotypes on the soil microbiome. Utilizing 16S rRNA gene amplicon sequencing, our analysis reveals significant changes in microbial composition and decreasing diversity at increasing soil depths withinS. bicolorregardless of genotype or fields. Notably, specific microbial families, such as Thermogemmatisporaceae and an unclassified family within the ABS-6 order, were enriched in deeper soil layers beyond 30 cm. Additionally, microbial richness and diversity declined with depth, reaching a minimum at the 60 - 90 cm layer, with layers beyond 90 cm increasing in alpha diversity. These findings highlight the importance of soil depth in agricultural soil microbiome studies.
Tunable Low-Rate Genomic Recombination with Cre-lox inE. coli: A Versatile Tool for Synthetic Biology and Environmental Sensing
Authors: Garabello Elisa , Yoon Hyun , Reid Matthew C. , Giometto Andrea 
Published: October 2024

ABSTRACTA variety of synthetic biology applications, from environmental sensing to bioproduction, would benefit from the ability to induce genomic alterations at low, tunable rates. Site-specific recombinases can be used to perform a variety of targeted DNA modifications such as excisions, inversions, and integrations. Their specificity and efficiency are offset by leaky expression and challenges in engineering a dynamic range of recombination rates. Here, we developed a tightly regulated, titratable Cre recombinase system that is tailored to achieve low recombination rates inEscherichia coli. As a proof-of-concept application of this design, we developed a whole-cell recombination-based arsenic biosensor, with detection sensitivity comparable to traditional wet chemical methods. Furthermore, our biosensor allows decoupling exposure from measurement, which could benefit assays in more complex, realistic settings. This system enables targeted genetic recombination events at experimentally tunable rates with application in ecological, environmental and cell physiology research, and beyond.Abstract Figure
Advancing Adoptive Cell Therapy: Optimized Expansion of Adaptive NK Cells for Solid Tumors
Authors: Almazán Nerea Martín , Román Sara , Sun Yizhe , Bräutigam Lars , Pantalone Mattia Russel , Stragliotto Giuseppe , Gultekin Okan , Saheli Sahar , Lehti Kaisa , Nauclér Cecilia Söderberg , Sarhan Dhifaf 
Published: October 2024

ABSTRACTBackgroundImmune therapies are emerging as a critical component of cancer treatment, capable of delivering durable and potentially curative responses. While CAR-T cell therapy has proven effective for hematological malignancies, it faces challenges in treating solid tumors due to tumor antigen heterogeneity, an immunosuppressive tumor microenvironment, and physical barriers hindering CAR-T cell infiltration. NK cells, particularly adaptive NK (aNK) cells, offer a promising alternative due to their ability to recognize and kill tumor cells without prior sensitization and their resistance to immunosuppressive environments.PurposeThe study investigates the role of cytokines, specifically IL-21 and IL-15, in enhancing aNK cell expansion and activation using peripheral blood mononuclear cells (PBMCs) from healthy donors and tumor-infiltrating lymphocytes (TILs) from glioblastoma (GBM) patients.MethodsBuffy coats and GBM TILs were collected from Karolinska Hospital. NK cells were isolated and expanded in vitro with IL-15 and IL-21 cytokines and feeder cells (K562 and K562E). Furthermore, tumor lysate was added in the cultures to boost memory responses in aNK cells. NK cell functionality, cytotoxicity, and phenotyping was assessed using flow cytometry and statistical analysis (t-test and two-way ANOVA) used to validate the results. Further animal model was used to validate the cytotoxicity capacities of these cells against GBM tumors using a zebrafish model.ResultsIL-21 drives the expansion of aNK better than IL-15 controls, data shown in PBMCs and TILs derived from GBM patients and IPLA OVCA patients. Additionally, the use of tumor lysate as a booster for restimulation further amplifies the cytotoxic capacity of aNK cells against autologous tumors. The zebrafish model validates this method, by decreasing the tumor size in zebrafish animals after 3 days of injection.ConclusionThe results demonstrate that IL-21 is essential for the specific expansion of aNK cells, enhancing their aggressiveness towards tumor cells. Additionally, tumor lysate significantly increases the cytotoxic efficacy of aNK cells upon restimulation with the same tumor cells. These findings suggest that IL-21 plays a crucial role in the specific expansion and activation of aNK cells, enhancing their aggressiveness towards tumor cells.By optimizing the expansion protocol, this method aims to advance the clinical application of aNK cells in immunotherapies for solid tumors, offering a potential solution to the limitations faced by current CAR-T therapies.
Coordinate post-transcriptional regulation by microRNAs and RNA binding proteins is critical for early embryonic cell fate decisions
Authors: Sangokoya Carolyn , Blelloch Robert 
Published: October 2024

Abstract/SummaryPost-transcriptional control by RNA binding proteins (RBPs) and microRNAs play central roles in mRNA stability and translation (1). However, little is known about how RBPs and microRNAs coordinate in developmental time to regulate cell fate. Here, we show that coordinate RBP and microRNA control of a single transcript, Profilin 2 (Pfn2), is essential for differentiation of embryonic stem cells (ESCs) into the primary germ layer lineages. The Pfn2 3’untranslated region has a binding site for Iron Regulatory Proteins and a nearby binding site for ESC enriched microRNAs (2,3). Deletion of this microRNA site leads to increased PFN2 and reduced FGF signaling during pluripotency transition prior to germ layer formation (4). In contrast, deletion of the iron response element leads to decreased PFN2 and a Wnt signaling defect, reduced nuclear beta-catenin, and a subsequent block in mesendodermal lineages during early germ layer formation. The choreographed microRNA-IRE axis of control on the Pfn2 transcript is essential for two key signal transduction steps during ESC differentiation.
Machine learning sparse reaction-diffusion models from stochastic dynamics and spatiotemporal patterns
Authors: Abubaker-Sharif Bedri , Devreotes Peter N. , Iglesias Pablo A. 
Published: October 2024

AbstractIn recent years, live-cell imaging has generated detailed spatiotemporal datasets of biochemical networks within cells. These networks often exhibit characteristics of spatially-distributed excitable systems, with propagating waves of signaling activity that govern processes such as cell migration, division, and other essential physiological functions. Traditionally, these reaction-diffusion systems have been modeled using stochastic partial differential equations incorporating spatial Langevin-type dynamics. Although these knowledge-based models have provided valuable insights, they are typically not directly inferred from experimental data. In this study, we introduce and apply two data-driven methodologies for learning the structure and parameters of spatial Langevin equation (SLE) models: 1) Kramers-Moyal regression, an adaptation of an established approach to fit microscale stochastic dynamics, and 2) wave features optimization, a novel approach to match macroscale spatiotemporal patterns. Unlike black-box neural network models that predict system behavior but provide no mechanistic insight, this approach estimates nonlinear model equations that directly relate to system structure and dynamics. As a proof-of-concept, we focus on simulation datasets derived from two stochastic reaction-diffusion models: one based on the FitzHugh-Nagumo equations (FHN model) and another on a biochemically adapted version of the FHN equations (FR model). Our results demonstrate that optimizing stochastic dynamics and wave patterns enables the accurate estimation of SLE model structure and parameters directly from 1D and 2D spatial data. With sparsity enforcement, we also identify novel sparse reaction-diffusion models for excitable systems. We show that this approach effectively approximates system behavior even when working with datasets similar to experimental conditions, with low temporal resolution and unobserved molecular components. By leveraging machine learning techniques for robust estimation of excitable reaction-diffusion models from spatiotemporal data, this work enhances our ability to model and understand the complex systems that regulate cell behavior.
Red sandstone surface microbiota: functional convergence despite taxonomic divergence under dispersal limitation and hetero selection
Authors: Wang Bowen , Zhu Chengshuai , Wang Xin , Yang Tianyu , Zhang Bingjian , Hu Yulan 
Published: October 2024

AbstractUnderstanding the role of microbiota on stone surfaces is essential for developing effective grottoes conservation strategies. However, ecological feature of microbial communities on stone surfaces remains underexplored. In this study, we explored diversity, ecological feature, and functional profiles of microbial communities on the red sandstone surface of the Leshan Giant Buddha from microbial ecology perspective. The results show that Proteobacteria, Actinobacteria, and Cyanobacteria are the dominant prokaryotic phyla, and Ascomycota is the most dominant eukaryotic phylum. Interestingly, despite taxonomic divergence, the functional profiles of different types of the microbial communities remain convergent across all samples. As indicated by the ecological modelling, the interplay of dispersal limitation and hetero selection might have contributed to such species divergence, while selective pressure from the harsh environment on the stone surface promoted functional convergence. The assembly of visually distinct microbial communities is linked to a narrower ecological niche, higher proportion of habitat specialists, elevated complexity, and increased resilience of the prokaryotic network to disturbances. Microbial-mediated ammonium assimilation and nitrogen mineralization might be the two prominent processes that contribute to stone biodeterioration. This study deepens our understanding of microbial community assembly mechanism on stone cultural heritage surfaces and functional potentials, which provides microbial ecological insights for the conservation of these cultural treasures.