bluuebunny/crossref_metadata_2025_split huggingface dataset:
Markovian State Models uncover Casein Kinase 1 dynamics that govern circadian period
Authors: Ricci Clarisse Gravina , Philpott Jonathan M. , Torgrimson Megan R. , Freeberg Alfred M. , Narasimamurthy Rajesh , Pécora de Barros Emilia , Amaro Rommie , Virshup David M. , McCammon J. Andrew , Partch Carrie L. 
Published: January 2025

AbstractCircadian rhythms in mammals are tightly regulated through phosphorylation of Period (PER) proteins by Casein Kinase 1 (CK1, subtypes δ and ε). CK1 acts on at least two different regions of PER with opposing effects: phosphorylation of phosphodegron (pD) regions leads to PER degradation, while phosphorylation of the Familial Advanced Sleep Phase (FASP) region leads to PER stabilization. To investigate how substrate selectivity is encoded by the conformational dynamics of CK1, we performed a large set of independent molecular dynamics (MD) simulations of wildtype CK1 and thetaumutant (R178C) that biases kinase activity toward a pD. We used Markovian State Models (MSMs) to integrate the simulations into a single model of the conformational landscape of CK1 and used Gaussian accelerated molecular dynamics (GaMD) to build the first molecular model of CK1 and the unphosphorylated FASP motif. Together, these findings provide a mechanistic view of CK1, establishing how the activation loop acts as a key molecular switch to control substrate selectivity. We show that thetaumutant favors an alternative conformation of the activation loop and significantly accelerates the dynamics of CK1. This reshapes the binding cleft in a way that impairs FASP binding and would ultimately lead to PER destabilization and shorter circadian periods. Finally, we identified an allosteric pocket that could be targeted to bias this molecular switch. Our integrated approach offers a detailed model of CK1’s conformational landscape and its relevance to normal, mutant, and druggable circadian timekeeping.Statement of SignificanceDisruption of circadian rhythms alters the temporal orchestration of vital cellular processes and increases the propensity for sleep disorders, metabolic disease, and cancer. Circadian rhythms are generated by a vast gene expression program controlled at the cellular level by a molecular clock comprised of dedicated clock proteins. Amongst the essential protein characters is Casein kinase 1 (CK1), which acts on multiple clock protein substrates. A delicate balance of CK1 activity on these substrates is crucial for proper circadian timekeeping, highlighting CK1 as a promising drug target to tune clock timing. This work aims to identify the conformational landscape of CK1 that underlies its substrate specificity and provide molecular insight for pharmacologic development that could modulate CK1 function for those suffering from clock-related syndromes.
Hydrodynamic Circulation, Ecological Drift, and Homogeneous Selection Shape Microbial Communities and Biogeochemical Cycling in Lake Ontario
Authors: Pendleton Augustus , Schmidt Marian L. 
Published: January 2025

AbstractMicrobial communities are vital to the ecology of the Laurentian Great Lakes, yet the influence of point sources, community assembly processes, and hydrodynamic circulation on their abundance and structure remains poorly understood. To address this, we analyzed 16S rDNA gene sequencing, flow cytometry, and water quality data from Lake Ontario during May and September of 2023. Communities were grouped into three depth-month categories: Shallow May, Shallow September, and Deep. Deep communities were dominated by drift, with some dispersal limitation, while shallow communities were shaped by homogenizing selection, especially in September, with contributions from drift. Actinobacteria were associated with homogenizing selection, Alphaproteobacteria with drift, and Bacteroidia in May and Chloroflexi in September with dispersal limitation. Upwellings altered microbial abundance and composition, modifying nitrogen cycling gene abundance. These findings provide insights into the ecological implications for Great Lakes health and conservation, emphasizing how upwelling events create unique microbial communities within the lake.
Female fibroblast activation is estrogen-mediated in sex-specific 3D-bioprinted pulmonary artery adventitia models
Authors: Mueller Mikala C. , Blomberg Rachel , Tanneberger Alicia E. , Davis-Hall Duncan , Neeves Keith B. , Magin Chelsea M. 
Published: January 2025

AbstractPulmonary arterial hypertension (PAH) impacts male and female patients in different ways. Female patients exhibit a greater susceptibility to disease (4:1 female-to-male ratio) but live longer after diagnosis than male patients. This complex sexual dimorphism is known as the estrogen paradox. Prior studies suggest that estrogen signaling may be pathologic in the pulmonary vasculature and protective in the heart, yet the mechanisms underlying these sex-differences in PAH remain unclear. PAH is a form of a pulmonary vascular disease that results in scarring of the small blood vessels, leading to impaired blood flow and increased blood pressure. Over time, this increase in blood pressure causes damage to the heart. Many previous studies of PAH relied on male cells or cells of undisclosed origin forin vitromodeling. Here we present a dynamic, 3D-bioprinted model that incorporates cells and circulating sex hormones from female patients to specifically study how female patients respond to changes in microenvironmental stiffness and sex hormone signaling. Poly(ethylene glycol)-alpha methacrylate (PEGαMA)-based hydrogels containing female human pulmonary artery adventitia fibroblasts (hPAAFs) from idiopathic PAH (IPAH) or control donors were 3D bioprinted to mimic pulmonary artery adventitia. These biomaterials were initially soft, like healthy blood vessels, and then stiffened using light to mimic vessel scarring in PAH. These 3D-bioprinted models showed that stiffening the microenvironment around female IPAH hPAAFs led to hPAAF activation. On both the protein and gene-expression levels, cellular activation markers significantly increased in stiffened samples and were highest in IPAH patient-derived cells. Treatment with a selective estrogen receptor modulator reduced expression hPAAF activation markers, demonstrating that hPAAF activation is a one pathologic response mediated by estrogen signaling in the vasculature, validating that drugs currently in clinical trials could be evaluated in sex-specific 3D-bioprinted pulmonary artery adventitia models.
Neoplastic immune mimicry potentiates breast tumor progression
Authors: Berens Eric B. , Khou Sokchea , Huang Elaine , Hoffman Amber , Johnson Briana , Kirchberger Nell , Sivagnanam Shamilene , Calistri Nicholas L. , Derrick Daniel , Liby Tiera A. , McLean Ian C. , Alanizi Aryn A. , Ozmen Furkan , Ozmen Tugba Y. , Mills Gordon B. , Hwang E. Shelley , Schedin Pepper J. , Gonzalez Hugo , Werb Zena , Heiser Laura M. , Coussens Lisa M. 
Published: January 2025

AbstractDedifferentiation programs are commonly enacted during breast cancer progression to enhance tumor cell fitness. Increased cellular plasticity within the neoplastic compartment of tumors correlates with disease aggressiveness, often culminating in greater resistance to cytotoxic therapies or augmented metastatic potential. Here we report that subpopulations of dedifferentiated neoplastic breast epithelial cells express canonical leukocyte cell surface receptor proteins and have thus named this cellular program “immune mimicry.” We document neoplastic cells engaging in immune mimicry within public human breast tumor single-cell RNA-seq datasets, histopathological breast tumor specimens, breast cancer cell lines, as well as in murine transgenic and cell line-derived mammary cancer models. Immune-mimicked neoplastic cells harbor hallmarks of dedifferentiation and are enriched in treatment-resistant and high-grade breast tumors. We corroborated these observations in aggressive breast cancer cell lines where anti-proliferative cytotoxic chemotherapies drove epithelial cells toward immune mimicry. Moreover, in subsequent proof-of-concept studies, we demonstrate that expression of the CD69 leukocyte activation protein by neoplastic cells confers a proliferative advantage that facilitates early tumor growth and therefore conclude that neoplastic breast epithelial cells upregulating leukocyte surface receptors potentiate malignancy. Moving forward, neoplastic immune mimicry should be evaluated for prognostic utility in breast cancer to determine stratification potential for patients with increased risks of tumor recurrence, metastasis, and therapeutic resistance.One Sentence SummaryNeoplastic breast epithelial cells express surface receptors canonically attributed to leukocytes and are associated with therapy resistance and aggressive tumor behavior.
Identification of regions required for allelic specificity at the cell wall remodeling allorecognition checkpoint inNeurospora crassa
Authors: Rico-Ramirez Adriana M. , Glass N. Louise 
Published: January 2025

AbstractAllorecognition is the ability of organisms/cells to differentiate self from non-self. In the fungusNeurospora crassa, allorecognition systems serve as checkpoints to restrict germling/hyphal fusion between genetically incompatible strains. Thecellwallremodeling (cwr) checkpoint functions after chemotrophic interactions and is triggered upon cell/hyphal contact, regulating cell wall dissolution and subsequent cell fusion. Thecwrregion consists of two linked loci,cwr-1andcwr-2, that are under severe linkage disequilibrium. Phylogenetic analysis of wildN. crassapopulations showed thatcwr-1/cwr-2alleles fall into six different haplogroups (HGs). Strains containing deletions ofcwr-1andcwr-2will fuse with previously HG incompatible cells, indicatingcwrnegatively regulates cell fusion. CWR-1 encodes a polysaccharide monooxygenase (PMO) domain that oxidatively degrades chitin; the PMO domain is sufficient to cause fusion arrest and confers allelic specificity by interactingin transwith CWR-2, a predicted transmembrane protein. However, the catalytic activity of CWR-1 is not required for triggering a block in cell fusion. The L2 and LC regions of the CWR-1 PMO domain show high levels of structural variability between different HGs. CWR-1 chimeras containing a LC region from a different HG were sufficient to trigger a cell fusion block, but not quite at wild type levels, suggesting that the complete PMO structure is necessary for allorecognition. Modeling of the transmembrane protein CWR-2 revealed allelic variability in the two major extracellular domains (ED2/ED4). Chimeras of CWR-2 with swapped ED2 or ED4 or ED2/ED4 domains from differentcwr-2haplogroups also altered allelic specificity.SummaryAllorecognition or nonself recognition enables fungi to distinguish genetically different individuals, thereby regulating cooperation to form mycelial networks. This study focused on the cell wall remodeling checkpoint (cwr), where genetic differences in two genes,cwr-1andcwr-2, triggers allorecognition. Upon cell contact, CWR-1 in one cell functionsin transwith CWR-2 in a second cell to confer a block in cell fusion. Chimeric proteins were created and tested to pinpoint domains involved in allelic specificity. For CWR-1, the L2 and LC domains are critical, while for CWR-2, the ED2 and ED4 domains have an important role in regulating cell fusion.Graphical Abstract
Enantioselective Protein Affinity Selection Mass Spectrometry (EAS-MS)
Authors: Wang Xiaoyun , Sun Jianxian , Ahmad Shabbir , Yang Diwen , Li Fengling , Chan U Hang , Zeng Hong , Simoben Conrad V. , Houliston Scott , Dong Aiping , Bolotokova Albina , Gibson Elisa , Kutera Maria , Ghiabi Pegah , Kondratov Ivan , Matviyuk Tetiana , Chuprina Alexander , Mavridi Danai , Lenz Christopher , Joerger Andreas C. , Brown Benjamin D. , Heath Richard B. , Yue Wyatt W. , Robbie Lucy K. , Beyett Tyler S. , Müller Susanne , Knapp Stefan , Harding Rachel , Schapira Matthieu , Brown Peter J. , Santhakumar Vijayaratnam , Ackloo Suzanne , Arrowsmith Cheryl H. , Edwards Aled M. , Peng Hui , Halabelian Levon 
Published: January 2025

ABSTRACTWe report an enantioselective protein affinity selection mass spectrometry screening approach (EAS-MS) that enables the detection of weak binders, informs about selectivity, and generates orthogonal confirmation of binding. After method development with control proteins, we screened 31 human proteins against a designed library of 8,210 chiral compounds. 16 binders to 12 targets, including many proteins predicted to be “challenging to ligand”, were discovered and confirmed in orthogonal assays. 7 binders to 6 targets bound in an enantioselective manner, withKDs ranging from 3 to 20 µM. Binders for four targets (DDB1, WDR91, WDR55, and HAT1) were selected for in-depth characterization using X-ray crystallography. In all four cases, the mechanism for enantioselective selectivity was readily explained. EAS-MS can be used to identify and characterize selective and weakly-binding ligands for novel protein targets with unprecedented throughput and sensitivity.
Comparative genomic analysis of a novel heat-tolerant and euryhaline strain of unicellular marine cyanobacteriumCyanobacteriumsp. DS4 from a high-temperature lagoon
Authors: Chen Ching-Nen Nathan , Lin Keng-Min , Lin Yu-Chen , Chang Hsin-Ying , Yong Tze Ching , Chiu Yi-Fang , Kuo Chih-Horng , Chu Hsiu-An 
Published: January 2025

ABSTRACTBackgroundCyanobacteria have diversified through their long evolutionary history and occupy a wide range of environments on Earth. To advance our understanding of their adaption mechanisms in extreme environments, we performed stress tolerance characterizations, whole genome sequencing, and comparative genomic analyses of a novel heat-tolerant and euryhaline strain of the unicellular cyanobacteriumCyanobacteriumsp. Dongsha4 (DS4). This strain was isolated from a lagoon on Dongsha Island in the South China Sea, a habitat with fluctuations in temperature, salinity, light intensity, and nutrient supply.ResultsDS4 cells can tolerate long-term high-temperature up to 50 ℃ and salinity from 0 to 6.6 %, which is similar to the results previously obtained forCyanobacterium aponinum. In contrast, most mesophilic cyanobacteria cannot survive under these extreme conditions. Based on the 16S rRNA gene phylogeny, DS4 is most closely related toCyanobacteriumsp. NBRC 102756 isolated from Iwojima Island, Japan, andCyanobacteriumsp. MCCB114 isolated from Vypeen Island, India. For comparison with strains that have genomic information available, DS4 is most similar toCyanobacterium aponinumstrain PCC 10605 (PCC10605), sharing 81.7% of the genomic segments and 92.9% average nucleotide identity (ANI). Gene content comparisons identified multiple distinct features of DS4. Unlike related strains, DS4 possesses the genes necessary for nitrogen fixation. Other notable genes include those involved in photosynthesis, central metabolisms, cyanobacterial starch metabolisms, stress tolerances, and biosynthesis of novel secondary metabolites.ConclusionsThese findings promote our understanding of the physiology, ecology, evolution, and stress tolerance mechanisms of cyanobacteria. The information is valuable for future functional studies and biotechnology applications of heat-tolerant and euryhaline marine cyanobacteria.
International Corneal and Ocular Surface Disease Dataset for Electronic Health Records
Authors: Ting Darren S. J. , Kaye Stephen B. , Rauz Saaeha ,   the International Corneal and Ocular Surface Disease (C&OSD) Dataset Development Working Group
Published: January 2025

ABSTRACTBackground/AimsTo provide a comprehensive and internationally standardised Cornea and Ocular Surface Disease (C&OSD) dataset for use in electronic health records (EHRs).MethodsThis was an international consensus study conducted through roundtable discussions involving 35 international experts specialising in the field of C&OSD. The Royal College of Ophthalmologists dataset guidelines were used to articulate initial C&OSD data elements template by curating data elements from validated published datasets obtained through scientific literature searches, and accessing existing international patient clinical and reported outcome recording instruments and registries. These included data elements recommended by the Dry Eye Workshop II, International Meibomian Gland Dysfunction Workshop, Ocular Surface Disease Activity and Damage Indices, the Cicatrising Conjunctivitis Assessment Tool, Limbal Stem Cell Deficiency Clinical and Confocal Grading, Chronic Ocular Manifestations in Patients with Stevens–Johnson Syndrome, and the UK Transplant Registry. Data elements pooled into an independent operational data model.ResultsA comprehensive generic dataset (common to all ophthalmology datasets) and C&OSD specific dataset was developed. Within the C&OSD dataset, several gateway disease datasets, such as atopic or allergic eye diseases, meibomian gland dysfunction, cicatrising conjunctivitis, chemical injury, dry eye, limbal stem cell deficiency, microbial or infectious keratitis, corneal erosion syndrome, and keratoconus, were established to streamline data entry for clinical audit and research purposes.ConclusionA comprehensive C&OSD dataset is provided which can be used by both generalist and specialist ophthalmologists. Adoption of the full dataset by EHR providers will lead to better interoperability and patient care and facilitate international research collaboration.
Genetically Defined Organoid Models Reveal Mechanisms Driving Squamous Cell Neoplastic Evolution and Identify Potential Therapeutic Vulnerabilities
Authors: Zhao Hua , Park Young Min , Zheng Yueyuan , Mao Qiong , Collet Casey , Hu Boyan , Zhou Tianming , Lin Luda , Wong Stephanie , Pan Yuhao , Monreal Anette Vistoro , Sinha Uttam K. , Sedghizadeh Parish , Soragni Alice , Lin De-Chen 
Published: January 2025

ABSTRACTUpper aerodigestive squamous cell carcinoma (UASCC) is an aggressive and lethal neoplasm, with its early neoplastic transformation mechanisms remaining poorly understood. Here, we characterize over 25 genetically-defined organoid models derived from murine and human oral/esophageal tissues harboring key driver mutations. Double knockout ofTP53andCDKN2Ainduced morphological dysplasia, hyperproliferation, loss of squamous differentiation, and tumorigenicity, which were further exacerbated by additional driver mutations (e.g.,PIK3CA,NOTCH1,KMT2C). Single-cell analysis revealed an expansion of quiescent basal cells and proliferative squamous cells, alongside a loss of differentiated squamous cells during malignant transformation. A distinct senescence program, regulated by ANXA1, was markedly diminished during early neoplastic evolution. Mechanistically, the ANXA1-SMAD3-p27KIP1pathway was identified as a critical regulator of this senescence program, acting to suppress neoplastic features in organoid models. Lastly, our high-throughput, single-organoid-resolution drug screens unexpectedly revealedPIK3CA-driven organoids exhibited sensitivity to Mitomycin C and Onalespib. This study provides novel mechanistic insights into early neoplastic evolution and underscores the value of genetically-defined organoid models for investigating cancer biology and identifying targeted therapies.
RecAlign: A* recombination-aware sequence to graph mapping
Authors: Bonizzoni Paola , Monti Davide Cesare , Della Vedova Gianluca , Riccardi Brian , Rizzi Raffaella , Siren Jouni 
Published: January 2025

AbstractPangenomics and long reads bring the promise of integrating read mapping with variant calling, since a pangenome encodes a reference genome that incorporates evolutionary or population aspects, while even a single long read can provide a good evidence of different kinds of variants (not only the single nucleotide variants that can be easily observed by short reads). This promise needs to be fulfilled by the development of new read mapping approaches that are tailored for that purpose. This paper focuses on integrating recombination events, that are key in bacteria, into read mapping. A first approach in that direction [ACBC+24] provides an exact dynamic programming algorithm that is too slow to manage multiple recombinations or long reads. We present a novel A* algorithm for recombination-aware sequence-to-graph mapping that significantly reduces running time by incorporating haplotype information and an efficient heuristic function. Our tool,RecAlign, demonstrates up to a two-order magnitude improvement in time and space complexity over [ACBC+24] and efficiently handles multiple recombinations.
Draft genome sequences of four lactic acid bacteria from fermented chicken meat unveil biosynthetic gene clusters for antimicrobial compounds
Authors: Alam Mahabub , Hassan Tamanna , Nizami Tanvir Ahmad , Akter Lipi , Rakib Tofazzal Md 
Published: January 2025

AbstractLactic acid bacteria play a crucial role in fermented food production and serve as important sources of antimicrobial peptides. This study reports four lactic acid bacteria strains, isolated from fermented chicken meat, which harbor biosynthetic gene clusters encoding antimicrobial compounds. These strains are classified within the generaPediococcusandLactiplantibacillus.
Multifunctional bending magnet beamline with a capillary optic for X-ray fluorescence studies of metals in tissue sections
Authors: Roter Benjamin , Crawford Andrew M. , Jin Qiaoling , Glowacki Arthur T. , Lai Barry , Marin Fabricio S. , Maxey Evan , Shi Xianbo , Culotta Valeria C. , Wildeman Asia S. , Patel Naisargi K. , O’halloran Thomas V. , Jacobsen Chris 
Published: January 2025

AbstractScanning fluorescence X-ray microscopy lets one non-destructively and quantitatively map the distribution of most biologically-important metals in cells and tissues. For studies on large-scale tissues and organs, a spatial resolution of several micrometers is often sufficient; in this case, bending magnets at synchrotron light sources provide abundant X-ray flux. We describe here the use of bending magnet beamline 8-BM-B at the Advanced Photon Source (APS) with two distinct microscopy stations: a pre-existing one with Kirkpatrick-Baez (KB) mirror optics for slightly higher throughput and the ability to accommodate samples tens of centimeters across, and a new prototype station with an axially-symmetric, single-bounce, capillary optic with slightly less flux, but slightly higher fluence (which affects achievable resolution at low metal concentration) and higher spatial resolution. The KB station providesδres= 10.5 µm spatial resolution at a per-pixel exposure time oftdwell= 100 ms and a fluence per time of 5.8× 107photons /(µm2·s), while the prototype capillary station providesδres= 6.3 µm attdwell= 50 ms and a fluence per time of 6.1× 107photons (µm2·s). We used image power spectral density to estimate the achieved spatial resolutionδresfrom individually acquired images, withδresdepending-on the optic, the fluorescence signal strength of the sample being imaged, and the method used to process raw fluorescence spectral data.