bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Rab-Kinesin12-Fused kinase module couples vesicle delivery and phragmoplast remodelling during cytokinesis inArabidopsis
Authors: Elliott Liam , Kalde Monika , Yamada Moé , Hála Michal , Smertenko Andrei , Rozier Frédérique , Evry James , Irani Niloufer , Jaillais Yvon , Hussey Patrick J , Žárský Viktor , Moore Ian , Kirchhelle Charlotte 
Published: October 2024

AbstractCytokinesis is a key process in the development of multicellular organisms, through both formative and proliferative divisions. In land plants, successful cytokinesis requires precise targeting of Golgi-derived vesicles to the future division plane by the phragmoplast, a cytoskeletal structure that undergoes continuous remodelling. Endomembrane trafficking and phragmoplast remodelling are tightly coupled, indicating the existence of active crosstalk. However, although many molecular regulators of membrane trafficking and cytoskeletal organisation are known, it remains poorly understood how these processes are co-ordinated. Here, we describe a regulatory module consisting of the membrane-associated GTPase RAB-A2a, cytoskeleton-associated Class II Kinesin-12s, and the Fused kinase orthologue TIO. We provide evidence that the interaction between these molecules at the midzone is essential for cytokinesis inArabidopsisthrough simultaneously targeting vesicles to the midzone and coupling phragmoplast remodelling to vesicle delivery.
Evolution and theft: loss of state transitions in Bryopsidales macroalgae and photosynthetic sea slugs
Authors: Havurinne Vesa , Rivoallan Axelle , Mattila Heta , Tyystjärvi Esa , Cartaxana Paulo , Cruz Sónia 
Published: October 2024

AbstractGreen macroalgae within the order Bryopsidales lack the fundamental photoprotective mechanisms of green algae, the xanthophyll cycle and energy-dependent dissipation of excess light. Here, by measuring chlorophyll fluorescence at 77K after specific light treatments, we show that Bryopsidales algae also lack state transitions, another ubiquitous photoprotection mechanism present in other green algae. Certain Sacoglossa sea slugs can feed on Ulvophyceae algae, including some Bryopsidales, and steal chloroplasts –kleptoplasts– that remain functional inside the animal cells for months without the support of the algal nucleus. Our data reveal that the state transition capacity is not retained in the kleptoplasts of the sea slugs, and we provide evidence that the loss is caused by structural changes during their incorporation by the animals. This enforced chloroplast sphericity was observed in all studied kleptoplastic associations, and we propose that it is a fundamental property supporting long-term retention of kleptoplasts in photosynthetic sea slugs.
Investigating Honey Bee Pollen Foraging Patterns Across a Season Using DNA Metabarcoding
Authors: Larsen Sydney N. , Steffen Joshua G. , Briggs Heather M. 
Published: October 2024

AbstractThe western honey bee, orApis mellifera, is a vital pollinator, essential for both ecosystems and agriculture worldwide. As human influences on these bees become more pronounced, understanding their pollen foraging behavior is increasingly important. Pollen provides crucial nutrients forA. melliferasuch as protein and lipids that are necessary for hive health and prosperity. Pollen DNA metabarcoding allows for the longitudinal analysis of the floral sources of corbicular (bee-collected) pollen. In this study we employ the use of metabarcoding and Oxford Nanopore Sequencing technology to analyze the floral composition of pollen samples collected on a weekly basis from two closely related hives. In total, we identified 74 distinct plant taxa (at the genus level) between the two hives. Although both hives had equivalent values of taxonomic richness and diversity, the majority of taxa identified were unique to the individual hives. This indicates a large degree of variation in pollen foraging despite the hives’ relative proximity. In addition to this interhive analysis, we also analyzed changes in pollen origin of a single hive across the course of five months. We identified 59 distinct plant taxa within samples from this hive whose presence and relative abundance differ drastically on a weekly basis with no taxa being present in all samples across the observed time period. In addition, even though there was a median of 8 to 9 taxa detected in each sample, each sample was composed primarily of 1 to 2 taxa indicating a degree of foraging preference that changes on a regular basis. Further quantitative and qualitative comparisons completed in this study demonstrate the degree of variation in pollen foraging patterns both throughout the season and between hives.
Identification and Targeting of Regulators of SARS-CoV-2-Host Interactions in the Airway Epithelium
Authors: Dirvin Brooke , Noh Heeju , Tomassoni Lorenzo , Cao Danting , Zhou Yizhuo , Ke Xiangyi , Qian Jun , Jangra Sonia , Schotsaert Michael , García-Sastre Adolfo , Karan Charles , Califano Andrea , Cardoso Wellington V. 
Published: October 2024

ABSTRACTAlthough the impact of SARS-CoV-2 in the lung has been extensively studied, the molecular regulators and targets of the host-cell programs hijacked by the virus in distinct human airway epithelial cell populations remain poorly understood. This is in part ascribed to the use of nonprimary cell systems, overreliance on single-cell gene expression profiling that does not ultimately reflect protein activity, and bias toward the downstream effects rather than their mechanistic determinants. Here we address these issues by network-based analysis of single cell transcriptomic profiles of pathophysiologically relevant human adult basal, ciliated and secretory cells to identify master regulator (MR) protein modules controlling their SARS-CoV-2-mediated reprogramming. This uncovered chromatin remodeling, endosomal sorting, ubiquitin pathways, as well as proviral factors identified by CRISPR analyses as components of the host response collectively or selectively activated in these cells. Large-scale perturbation assays, using a clinically relevant drug library, identified 11 drugs able to invert the entire MR signature activated by SARS-CoV-2 in these cell types. Leveraging MR analysis and perturbational profiles of human primary cells represents a novel mechanism-based approach and resource that can be directly generalized to interrogate signatures of other airway conditions for drug prioritization.
hu.MAP3.0: Atlas of human protein complexes by integration of > 25,000 proteomic experiments
Authors: Fischer Samantha N. , Claussen Erin R. , Kourtis Savvas , Sdelci Sara , Orchard Sandra , Hermjakob Henning , Kustatscher Georg , Drew Kevin 
Published: October 2024

AbstractMacromolecular protein complexes carry out most functions in the cell including essential functions required for cell survival. Unfortunately, we lack the subunit composition for all human protein complexes. To address this gap we integrated >25,000 mass spectrometry experiments using a machine learning approach to identify > 15,000 human protein complexes. We show our map of protein complexes is highly accurate and more comprehensive than previous maps, placing ∼75% of human proteins into their physical contexts. We globally characterize our complexes using protein co-variation data (ProteomeHD.2) and identify co-varying complexes suggesting common functional associations. Our map also generates testable functional hypotheses for 472 uncharacterized proteins which we support using AlphaFold modeling.Additionally, we use AlphaFold modeling to identify 511 mutually exclusive protein pairs in hu.MAP3.0 complexes suggesting complexes serve different functional roles depending on their subunit composition. We identify expression as the primary way cells and organisms relieve the conflict of mutually exclusive subunits. Finally, we import our complexes to EMBL-EBI’s Complex Portal (https://www.ebi.ac.uk/complexportal/home) as well as provide complexes through our hu.MAP3.0 web interface (https://humap3.proteincomplexes.org/). We expect our resource to be highly impactful to the broader research community.
Rapid onset fibrotic remodeling and ventricular dysfunction induced by phenylephrine involve targeted reprogramming of myocyte and fibroblast transcriptomes
Authors: Kimball Todd H. , Gromova Tatiana , Gehred Natalie D. , Chapski Douglas J. , Wang Ke , Vaseghi Marmar , Fischer Matthew A. , Lefer David J. , Vondriska Thomas M. 
Published: October 2024

AbstractCatecholamine dysregulation is a common feature of multiple acute and chronic cardiac conditions, including heart failure. To investigate the role of altered α-adrenergic stimulation on cardiac function, we developed a short-term exposure model, administering phenylephrine subcutaneously to mice for one week. Compared to vehicle-injected controls, phenylephrine-treated animals exhibited increased ejection fraction, decreased chamber size, diastolic dysfunction and ventricular hypertrophy in the absence of hypertension. Remarkably, these animals developed extensive fibrotic remodeling of the tissue that plateaued at 24 hours and myocyte hypertrophy localized to regions of fibrotic deposition after 3 days of treatment. Transcriptome analyses of purified myocyte and fibroblast populations from these hearts revealed an unexpected role for myocytes in the production of extracellular matrix. Comparison with other models of cardiac stress, including pressure overload hypertrophy and cytokine activation of fibroblasts, identified stimulus-specific transcriptional circuits associated with cardiac pathology. Given the rapid, robust fibrotic response that preceded myocyte hypertrophy, intercellular communication analyses were conducted to investigate fibroblast to myocyte signaling, identifying potential crosstalk between these cells. These studies thoroughly describe and phenotypically characterize a new model of short-term catecholamine stress and provide an atlas of transcriptional remodeling in myocytes and fibroblasts.Graphical Abstract
Pan-Prediction of MHC-II Restricted Epitopes Across Species via an Alphafold-based Quantification Scheme
Authors: Wang Suqiu , Kong Lingming , Hu Dongmei , Zheng Liangzhen , Fei Caiyi , Du Liubao , Tang Ziche , Wang Sheng , Xu Shi , Yang Hanchun , Zhang Nianzhi 
Published: October 2024

AbstractPredicting MHC-II restricted epitopes across species used to be challenging, but Alphafold (AF) may provide a structure-based pan-prediction solution. In this study, we established the new tool AF-pred with a clear standard for quantitative prediction results. Compared to the sequence-based tools heavily trained with human ligandome, AF-pred does not show advantage in predicting the binding patterns of human HLA-II but has far better performance in predicting binding patterns of other animals’ MHC-II. Using recently resolved bat MHC-II structures, we analyzed AF-pred’s prediction capability, logic and limitation. In addition, we also explored the impact of AF algorithm iterations on the prediction of MHC-II restricted epitopes. The results demonstrated that AF-pred is capable of cross-species prediction of MHC-II restricted epitopes and is conducive to the development of novel veterinary vaccines.
Rare variants and survival of patients with idiopathic pulmonary fibrosis
Authors: Alonso-Gonzalez Aitana , Jáspez David , Lorenzo-Salazar José M. , Ma Shwu-Fan , Strickland Emma , Mychaleckyj Josyf , Kim John S. , Huang Yong , Adegunsoye Ayodeji , Oldham Justin M. , Steward Iain , Molyneaux Philip L. , Maher Toby M. , Wain Louise V. , Allen Richard J. , Jenkins R. Gisli , Kropski Jonathan A. , Yaspan Brian , Blackwell Timothy S. , Zhang David , Garcia Christine Kim , Martinez Fernando J. , Noth Imre , Flores Carlos 
Published: October 2024

ABSTRACTBackgroundThe clinical course of idiopathic pulmonary fibrosis (IPF) is highly variable and unpredictable, with multiple genetic variants influencing IPF outcomes. Notably, rare pathogenic variants in telomere-related genes are associated with poorer clinical outcomes in these patients. Here we assessed whether rare qualifying variants (QVs) in monogenic adult-onset pulmonary fibrosis (PF) genes are associated with IPF survival. Using polygenic risk scores (PRS), we also evaluated the influence of common IPF risk variants in individuals carrying these QVs.MethodsWe identified QVs in telomere and non-telomere genes linked to monogenic PF forms using whole-genome sequences (WGS) from 888 Pulmonary Fibrosis Foundation Patient Registry (PFFPR) individuals. We also derived a PRS for IPF (PRS-IPF) from 19 previously published common sentinel IPF variants. Using regression models, we then examined the mutual relationships of QVs and PRS-IPF and their association with survival. Validation of results was sought in WGS from an independent IPF study (PROFILE, n=472), and results from the two cohorts were meta-analyzed.ResultsCarriers of QVs in monogenic adult-onset PF genes, representing nearly 1 out of 6 IPF patients, were associated with lower PRS-IPF (Odds Ratio [OR]: 1.79; 95% Confidence Interval [CI]: 1.15-2.81; p=0.010) and shorter survival (Hazard Ratio [HR]: 1.53; 95% CI: 1.12-2.10; p=7.3×10-3). Notably, carriers of pathogenic variants at telomere genes showed the strongest association with survival (HR: 1.76; 95% CI: 1.13-2.76; p=0.013). The meta-analysis of the results showed a consistent direction of effect across both cohorts.ConclusionsWe revealed the opposite effects of QVs and PRS-IPF on IPF survival. Thus, a distinct IPF molecular subtype might be defined by QVs in monogenic adult-onset PF genes. Assessing the carrier status for QVs and modelling PRS-IPF promises to further contribute to predicting disease progression among IPF patients.
Long-term clinical and patient reported outcomes of an enhanced monofocal intraocular lens
Authors: Latz Catharina , Licht Annika , Ponto Katharina A. , Menzel-Severing Johannes , Piñero David P. , Mirshahi Alireza 
Published: October 2024

AbstractPurposeTo evaluate long-term clinical and patient-reported outcomes (PROMs) following the implantation of an enhanced monofocal intraocular lens (IOL).MethodsThis ambispective non-comparative single-centre study involved 41 patients (ages 48-84) who underwent bilateral cataract surgery with the Tecnis Eyhance IOL (model ICB00, Johnson & Johnson Vision). Distance and intermediate visual acuities, refraction, and PROMs were assessed 18 months or more after surgery. Spectacle independence was evaluated using the PRSIQ questionnaire, with patients self-reporting on visual quality, difficulties in performing specific tasks and perception of photic phenomena at distance and intermediate vision.ResultsAt 18 months or later, 100.0%, 73.2%, 100% and 79.5% of patients achieved a binocular uncorrected distance, uncorrected intermediate, corrected distance, and distance-corrected intermediate visual acuity of 0.20 logMAR or better, respectively. Less than 10% of patients reported photic phenomena. Mean visual quality scores were 1.68±0.72 for distance and 2.05±0.92 for intermediate vision (1=very good to 6=very poor). The dashboard was clearly visible while driving for 95.1% of patients, while 45.0% could perform screen work without glasses; an additional 40.0% could do so with enlarged fonts. Complete spectacle independence was reported by 87.8% for distance vision, and 53.7% for intermediate vision. At least moderately satisfied were 90.2% with distance vision, 87.8% with intermediate vision, and 51.2% with near vision.ConclusionsThe enhanced monofocal IOL ICB00 provides good long-term distance and intermediate visual quality, leading to considerable spectacle independence and patient satisfaction. Most patients required near vision correction.
Probabilistic Multiple Sequence Alignment using Spatial Transformations
Authors: García López Sebastián , Hauberg Søren , Boomsma Wouter 
Published: October 2024

AbstractMultiple Sequence Alignment (MSA) has long been a prominent and critical tool in bioinformatics and computational biology. Its importance lies in its ability to provide valuable insights into the relationships between sequences and the evolutionary pressure leading to amino acid preferences at particular sites in a protein. Despite the recent advances in protein language models, MSAs remain critical in many applications, e.g. for state-of-the-art prediction of 3D structure and protein variant effects. Sequence alignment is typically considered a deterministic preprocessing step, leading to a single static MSA. Especially for low-similarity sequences, parts of an alignment will be subject to substantial uncertainty, which is disregarded when processing a static MSA. Earlier, HMM-based approaches handled this uncertainty by considering the full posterior ensemble over alignments. In this paper, we explore whether a similar approach is feasible within a modern deep learning approach, where we move beyond the Markovian restrictions of earlier models. In particular, we consider whether we can learn the alignment process as distribution over spatial transformations, in combination with a deep latent variable model of protein sequences. A proof-of-concept implementation of this work is available athttps://github.com/deltadedirac/Explicit_Disentanglement_Molecules.
A global resource constrained model to predict metabolic flux dynamics in fluctuating environments
Authors: Yuan Huili , Bai Yang , Fu Xiongfei 
Published: October 2024

SummaryEnvironmental changes often induce global variations on bacterial gene expression, frequently accompanied by alterations in growth rates. Integrating non-metabolic cellular processes, such as gene expression and macromolecule synthesis, with metabolic modeling remains a significant challenge in systems biology due to the lack of mechanistic representation of gene regulation. Here, we introduce a novel constraint-based modeling framework called dynamic Constrained Allocation Flux Balance Analysis (dCAFBA), which comprehensively integrates metabolism, cellular resource allocation, and gene regulation. We employ a quasi-steady-state assumption, positing that reaction fluxes achieve balance at each time step, adapting more rapidly than protein synthesis and growth dilution. This approach enables the prediction of reaction flux dynamics and protein allocation necessary to achieve cellular objectives, such as optimizing growth during various growth shifts (including carbon, amino acid, and transcriptional signal), without detailing molecular gene regulations. Our model offers a new method for interpreting proteome allocation and cellular metabolism in complex and transient environments, providing mechanistic insights valuable for metabolic engineering.
Characteristics of Vitelline Warbler songs and calls
Authors: Cummings Wyatt J. , Goodman David D. L. , Layne Craig D. , Singer Katherine I. , Whitney Thomas M. 
Published: October 2024

AbstractThe Vitelline Warbler (Setophaga vitellina) is an understudied species endemic to a few small islands in the western Caribbean. Little is known beyond its phylogenetic relationship to other New World warblers. We used island-wide surveys and bioacoustic recordings to investigate the distribution, vocalizations, and ecology ofS. vitellinaacross a significant portion of the species’ range on Little Cayman Island. We recorded 417 songs from 91 individuals and analyzed the length, frequency, and shape of various song components. We observed and characterized high variation in the composition and character of songs. We also describe the call of the species, document an association with gumbo limbo (Bursera simaruba) trees, and report interactions with other bird species. Improved knowledge of Vitelline Warblers has value for evaluating conservation threats to an island endemic and for understanding the evolution of vocalization behavior in Neotropical songbirds.
Abnormalities of the liver have big impacts on orthotopic liver transplantation
Authors: Chen Yongfeng , Li Wenzhong , Chen Guoyong , Zhou Shaotang 
Published: October 2024

AbstractBackgroundOrthotopic rat liver transplantation (OLT) is widely used in basic research; normal liver anatomy and structures are attributable to its success while its deformities complicate to have a negative on OLT.MethodsFor tolerance induction project, we performed OLT from Lewis to Brown Norway (BN) rat as chronic rejection model and encountered two anatomical deformities of recipient rats: of 47 liver transplantations, accessory liver lobe occurred to 4 cases and bifurcations of liver outflow to 5 cases in BN rats.ResultsFor the accessory liver lobe, we discontinued OLT for one case with a big accessory liver lobe; two rats died from pneumothorax upon separation; and succeed in one case with the small lobe. For two vein outflows of the liver, we succeeded in OLT due to its reconstruction in one case but the recipient died one week later, and succeeded in 1 case after one small orifice was sutured, we failed in 3 cases due to thrombosis following OLT. For 38 rats with normal livers, only 4 rats failed to survive LT. There were significant differences in OLT success (p<0.01)ConclusionLiver abnormal anatomy has negative impact on OLT, giving a clue to that pre-transplant comprehensive screening is significant and beneficial clinically.
Ligand-Receptor Interactions for Cell-Cell Communication Analysis in Rat, Chicken, Pig, and Monkey Single-Cell and Spatial Transcriptomics
Authors: Chen Sheng , Peng Yan , Zhang Xiaoling , Jiang Ting , Fang Binbin , Zhang Pengyue , Li Yanze , Ren Yonghong , Sun Yimin 
Published: October 2024

AbstractCell-cell communication is a frequently used analysis approach in single cell RNA and spatial transcriptomics, and many tools like CellPhoneDB, CellChat and stLearn have been developed. Ligand-receptor interactions are the core of cell-cell communication analysis. Since receptor-ligand and even protein-protein interactions were focus on humans and mice research, curated human and mouse receptor-ligand databases have been established, cell-cell interactions for these two species single-cell RNA sequencing data can be directly analyzed. However, for rats, chickens, pigs, monkeys, and other species, cell-cell interaction analysis is often implemented through orthologous gene mapping, due to the lack of curated ligand-receptor interaction databases for these species.We collected cell-cell interaction data mainly from KEGG for rats, chickens, pigs, and monkeys, and extended the data from Reactome and IntAct. Then, by using CellChatV2 with our collected rat ligand-receptor interactions and CellChatV2’s own mouse data, respectively, we analyzed 10x Genomics rat public scRNA data, and found that 70 significantly ligand-receptor interactions from the mouse analysis result were also significantly in rats. We also obtained some chicken, pig, and monkey scRNA data from published literature, and analyzed cell-cell interactions using our collected ligand-receptor interactions for these species, and it was proved that our data is reliable and useful. Lastly, we have transformed the ligand-receptor interactions for rat, chicken, pig, and monkey species into the CellChatDB format, which enables swift and straightforward analysis of cell-cell communication in single-cell and spatial data of these four species.All the ligand-receptor interaction datasets for rats, chickens, pigs, and monkeys, as well as the program codes, are available athttps://github.com/qingchen36/ligand-receptor. Using our program, one can rapidly obtain receptor-ligand interaction data for other species.