bluuebunny/crossref_metadata_2025_split huggingface dataset:
Low-Rank Full Matrix Factorization for dropout imputation in single cell RNA-seq and benchmarking with imputation algorithms for downstream applications
Authors: Huang Jinghan , Chow Anson C.M. , Tang Nelson L.S. , Yam Sheung Chi Phillip 
Published: October 2024

AbstractBackgroundWhile single cell RNA sequencing becomes a powerful technology, the presence of the large number of zero counts represents a challenge for both wet-lab processing and data analysis. Imputation of these dropouts can now be performed by three categories of algorithms: Model or smoothing, Matrix theory or Deep learning. However, two fundamental questions remain unsettled: (1) whether imputation should be performed; (2) which imputation algorithm to use with various downstream applications. Notably, imputation is not commonly used in real scRNA-seq applications because of their uncertain benefits, concerns about false inferences in downstream applications, and the lack of in-depth benchmark.MethodsHere, we performed two tasks. First, we developed an algorithm using adaptive low-rank full matrix factorization (afMF) based on a previous limited implementation confined to using low rank matrix decomposition (ALRA). Second, to evaluate the impact of various imputation algorithms on downstream analyses, a new benchmark framework incorporating commonly used downstream applications was developed. This benchmark framework put emphasis on real datasets which had ground truth or matched bulk data such that algorithm performance was compared to more convinced data rather than less realistic simulated parameters.ResultsOur results indicated that afMF and ALRA (matrix based) provided good imputation and outperformed raw log-normalization in various downstream applications. afMF outperformed ALRA in several evaluations (cell-level differential expression analysis, GSEA, classification, biomarker prediction, clustering, SC-bulk profiling similarity). Besides, afMF ranked among the top levels in automatic cell type annotation, trajectory inference by DPT, and AUCell & SCENIC. Both showed acceptable scalability, while afMF had longer running time. MAGIC (smoothing based) and AutoClass (deep learning based) also performed well but may produce false positives. In contrast, more complicated methods (other deep learning or model based) were prone to overfitting and data distortion. We also found that certain downstream algorithms are not compatible with imputation, including trajectory inference with Slingshot and cell-cell communication. Prior imputation either showed no improvement or generated false positive findings with these downstream applications.ConclusionsWe hope this in-depth evaluation and the algorithm developed in this study can enhance the selection of appropriate imputation algorithm for specific scRNA-seq downstream analyses.The algorithm and the benchmark framework are available at GitHub:https://github.com/GO3295/SCImputation
Mobility of Four Structural Regions Drives Isoform-Specific Properties of Plant LPOR
Authors: Gabruk Michał , Łuszczyński Mateusz , Szafran Katarzyna , Ogrodzińska Wiktoria , Rubenstein Brenda M. , da Silva Gabriel Monteiro 
Published: October 2024

AbstractLight-dependent protochlorophyllide oxidoreductase (LPOR) is a photocatalytic enzyme in the chlorophyll (Chl) biosynthetic pathway that underwent duplications in angiosperms, resulting in the emergence of multiple isoforms across various plant species. The physiological roles of these LPOR homologs remained unclear, so we selected six plant species with different number of isoforms of the enzyme and characterized their properties in vitro.Our findings revealed that these isoforms vary in their affinity for the reaction product, chlorophyllide (Chlide), as well as for NADPH under lipid-free conditions and in reaction mixtures supplemented with plant lipids. Additionally, we observed differences in their oligomerization behavior.Our experimental approach generated a dataset comprising several hundred pairs of spectra, recorded before and after reaction-triggering illumination. This data was used to analyze the correlation between fluorescence emission maxima before and after photoconversion. The analysis showed that some isoforms rapidly release Chlide after the reaction, while others retain the pigment in the binding pocket, especially at high NADPH concentrations. These results suggest that LPOR isoforms differ in their rates of Chlide release and complex disassembly, potentially influencing the overall rate of the Chl biosynthetic pathway, even in mature leaves.We further analyzed the flexibility of these isoforms using AlphaFold2 predictions, identifying four regions of the enzyme that are particularly mobile. Two of these regions are involved in pigment binding, while the other two play a role in oligomerization. Based on these findings, we propose a model of conformational changes that drive the formation of LPOR oligomers.
Deciphering molecular determinants of GPCR-G protein receptor interactions by complementary integrative structural biology methods
Authors: Castel Jérôme , Botzanowski Thomas , Brooks Ieva , Frechard Alexandre , Bey Gilbert , Schroeter Marine , Del Nero Elise , Debaene François , Ciesielski Fabrice , Zeyer Denis , Cianferani Sarah , Morales Renaud 
Published: October 2024

ABSTRACTMany physiological processes are dependent on G protein-coupled receptors (GPCRs), the biggest family of human membrane proteins and a significant class of therapeutic targets. Once activated by external stimuli, GPCRs use G proteins and arrestins as transducers to generate second messengers and trigger downstream signaling, leading to diverse signaling profiles. The G protein-coupled bile acid receptor 1 (GPBAR1, also known as Takeda G protein-coupled receptor 5, TGR5) is a class A bile acid membrane receptor that regulates energy homeostasis and glucose and lipid metabolism. GPBAR1/G protein interactions are implicated in the prevention of diabetes and the reduction of inflammatory responses, making GPBAR1 a potential therapeutic target for metabolic disorders. Here, we present an integrated structural biology approach combining hydrogen/deuterium exchange mass spectrometry (HDX-MS) and cryo-electron microscopy (cryo-EM) to identify the molecular determinants of GPBAR1 conformational dynamics upon G protein binding. Thanks to extensive optimization of both HDX-MS and cryo-EM workflows, we achieved over 99% sequence coverage along with a 2.5-Å resolution structure, both of which are state-of-the-art and solely obtained for complete GPCR complexes. Altogether, our results provide information on the under-investigated GPBAR1 binding mode to its cognate G protein, pinpointing the synergic and powerful combination of higher (cryo-EM) and lower (HDX-MS) resolution structural biology techniques to dissect GPCR/G protein binding characteristics.Short statementThis work highlights the utility of integrating cryo-EM and HDX-MS for studying large multiprotein complexes such as GPCR/G protein complexes. Cryo-EM offers high-resolution structural details, while HDX-MS reveals the dynamic conformational changes during assembly, providing a comprehensive structural view of difficult-to-study membrane protein systems.
ConvNTC: Convolutional neural tensor completion for predicting the disease-related miRNA pairs and cell-related drug pairs
Authors: Liu Pei , Liang Xiao , Li Yue , Luo Jiawei 
Published: October 2024

AbstractSystematic investigation of high-order molecular interactions can deepen our understanding of the mechanisms underlying biological systems. However, effectively capturing both multilinear and nonlinear relationships to accurately identify the complex triplet relationships remains a challenge. In this paper, we present a novelConvolutinalNeuralTensorCompletion (ConvNTC) to model triplet network connections. ConvNTC consists of a multilinear module and nonlinear module. The former is a tensor decomposition approach that integrates multiple constraints to learn the tensor factor embeddings. The latter contains three components: an embedding generator to produce position-specific index embeddings for each tensor entry in addition to the factor embeddings, a convolutional encoder to perform nonlinear feature mapping while preserving the tensor’s rank-one property, and a Kolmogorov-Arnold Network (KAN) based predictor to effectively capture high-dimensional relationships aligned with the intrinsic structure of real-world data. We demonstrate ConvNTC on two triplet prediction tasks of the disease-related miRNA pairs and cell-related drug pairs, respectively. Comprehensive experiments against ten state-of-the-art methods demonstrate the superiority of ConvNTC in terms of triplet imputation. ConvNTC reveals promising prognostic values of the miRNA-miRNA interactions on breast cancer and detects synergistic drug combinations in cancer cell lines. The source code is available athttps://github.com/Liangyushi/ConvNTC.
Birds migrate longitudinally in response to the resultant Asian monsoons of the Qinghai-Tibet Plateau uplift
Authors: Zhang Wenyuan , Gu Zhongru , Chen Yangkang , Zhang Ran , Zhan Xiangjiang 
Published: October 2024

ABSTRACTThe uplift of the Qinghai-Tibet Plateau is one of the greatest geological events on Earth, pivotally shaping biogeographic patterns across continents, especially for migratory species that need to overcome topographical barriers to fulfil their annual circle. However, how the uplift influences animal migration strategies remains largely unclear. We compare the current flyways of 50 avian species migrating across the plateau with those reconstructed before the uplift as a counterfactual. We find that the major effect of the plateau uplift is changing avian migratory directions from the latitudinal to the longitudinal. The monsoon system generated by the uplift rather than the high elevationper seshapes those changes. These findings unveil how an important global geological event has influenced biogeographic patterns of migratory birds, yielding testable hypotheses for how observed avian distributions emerge.
Controlled enzyme cargo loading in engineered bacterial microcompartment shells
Authors: Tefft Nicholas M. , Wang Yali , Jussupow Alexander , Feig Michael , TerAvest Michaela A. 
Published: October 2024

AbstractBacterial microcompartments (BMCs) are nanometer-scale organelles with a protein-based shell that serve to co-localize and encapsulate metabolic enzymes. They may provide a range of benefits to improve pathway catalysis, including substrate channeling and selective permeability. Several groups are working toward using BMC shells as a platform for enhancing engineered metabolic pathways. The microcompartment shell ofHaliangium ochraceum(HO) has emerged as a versatile and modular shell system that can be expressed and assembled outside its native host and with non-native cargo. Further, the HO shell has been modified to use the engineered protein conjugation system SpyCatcher-SpyTag for non-native cargo loading. Here, we used a model enzyme, triose phosphate isomerase (Tpi), to study non-native cargo loading into four HO shell variants and begin to understand maximal shell loading levels. We also measured activity of Tpi encapsulated in the HO shell variants and found that activity was determined by the amount of cargo loaded and was not strongly impacted by the predicted permeability of the shell variant to large molecules. All shell variants tested could be used to generate active, Tpi-loaded versions, but the simplest variants assembled most robustly. We propose that the simple variant is the most promising for continued development as a metabolic engineering platform.
Pathogen priming alters host transmission potential and predictors of transmissibility in a wild songbird species
Authors: Leon A.E. , Fleming-Davies A. , Adelman J.S. , Hawley D.M. 
Published: October 2024

AbstractPathogen reinfections occur widely, but the extent to which reinfected hosts contribute to ongoing transmission is often unknown despite its implications for host-pathogen dynamics. House finches (Haemorhous mexicanus) acquire partial protection from initial exposure to the bacterial pathogenMycoplasma gallisepticum(MG), with hosts readily reinfected with homologous or heterologous strains on short timescales. However, the extent to which reinfected hosts contribute to MG transmission has not been tested. We used three pathogen priming treatments– none, intermediate (repeated low-dose priming), or high (single high-dose priming)– to test how prior pathogen priming alters the likelihood of transmission to a cagemate during index bird reinfection with a homologous or heterologous MG strain. Relative to unprimed control hosts, the highest priming level strongly reduced maximum pathogen loads and transmission success of index birds during reinfections. Reinfections with the heterologous strain, previously shown to be more virulent and transmissible than the homologous strain used, resulted in higher pathogen loads within high-primed index birds, and showed higher overall transmission success regardless of host priming treatment. This suggests that inherent differences in strain transmissibility are maintained in primed hosts, leading to the potential for ongoing transmission during reinfections. Finally, among individuals, transmission was most likely from hosts harboring higher within-host pathogen loads, while associations between disease severity and transmission probability were dependent on a given bird’s priming treatment. Overall, our results indicate that reinfections can result in ongoing transmission, particularly where reinfections result from heterologous and highly transmissible strains, with key implications for virulence evolution.ImportanceAs Covid-19 dramatically illustrated, humans and other animals can become infected with the same pathogen multiple times. Because individuals already have defenses against pathogen their immune systems have encountered before, reinfections are typically less severe, and are thought to be less contagious, but this is rarely directly tested. We used a songbird species and two strains of its common bacterial pathogen to study how contagious hosts are when their immune systems have some degree of prior experience with a pathogen. We found that reinfected hosts are not as contagious as initially infected ones. However, the more transmissible of the two strains, which also causes more harm to its hosts, was able to multiply more readily than the other strain within reinfected hosts, and was more contagious in both reinfected and first-infected hosts. This suggests that reinfections might favor more harmful pathogen strains that are better able to overcome immune defenses.
Fluorescent Antibody-Based Detection and Ultrastructural Analysis ofStreptococcus pneumoniaein Human Sputum
Authors: Jop Vidal Ana G. , Francis Meg , Chitanvis Maneesha , Frame Ithiel J. , Sharma Poonam , Vidal Patricio , Lanata Claudio F. , Grijalva Carlos , Daley William , Vidal Jorge E. 
Published: October 2024

AbstractBackgroundPneumococcal pneumonia continues to be a significant global health burden, affecting both children and adults. Traditional diagnostic methods for sputum analysis remain challenging. The objective of this study was twofold: to develop a rapid and easy-to-perform assay for the identification ofStreptococcus pneumoniae(Spn) directly in sputum specimens using fluorescence microscopy, and to characterize with high-resolution confocal microscopy the ultrastructure of pneumococci residing in human sputum.MethodsWe fluorescently labeled antibodies against the pneumococcal capsule (Spn-FLUO). The specificity and sensitivity of Spn-FLUO for detecting Spn was evaluatedin vitroandin vivousing mouse models of carriage and disease, human nasopharyngeal specimens, and sputum from patients with pneumococcal pneumonia. Spn was confirmed in the specimens using culture and a species-specific qPCR assays. Confocal microscopy and Imaris software analysis were utilized to resolve the ultrastructure of pneumococci in human sputum.ResultsCompared with cultures and qPCR, Spn-FLUO demonstrated high sensitivity (78-96%) in nasopharyngeal samples from mice and humans. The limit of detection (LOD) in nasopharyngeal samples was ≥1.6×10⁴ GenEq/ml. The specificity in human nasopharyngeal specimens was 100%. In lung specimens from mice infected with pneumococci, Spn-FLUO reached 100% sensitivity with a LOD of ≥1.39×10⁴ GenEq/ml. In human sputum, the sensitivity for detecting Spn was 92.7% with a LOD of 3.6×10³ GenEq/ml. Ultrastructural studies revealed that pneumococci are expectorated as large aggregates with a median size of 1336 µm².ConclusionsSpn-FLUO is a rapid and sensitive assay for detecting Spn in human sputum within 30 min. The study highlights that most pneumococci form aggregates in human sputum.
Syzygium cumini(L.) Skeels has Thermostable and Selective Anti-Bacillus anthracisActivity
Authors: Kaur Rajinder , Singh Ashish Kumar , Maurya Indresh Kumar , Singh Samer 
Published: October 2024

ABSTRACTIntroductionGastrointestinal (GI) anthrax caused byBacillus anthracisremains a neglected disease in many parts of the Americas, Asia, and Africa. The symptoms include dysentery, stomachache, bloating of the stomach, vomiting, fever, chills,etc.Current study evaluated several edible plants traditionally indicated for GI disease/symptoms in the Indian subcontinent for their anti-B. anthracisactivity.Materials & MethodsAqueous extracts of plant parts were assessed for anti-B. anthracisactivity using standard antimicrobial susceptibility testing assays. Most promising extracts were evaluated for desirable activity under conditions relevant to their usage, including extremes of temperature, pH, presence of bile salt, impact on gut microflora, and interaction with FDA-approved drugs for anthrax treatment. The bioactive components separated by bioactivity-guided thin-layer-chromatography were subjected to GC-MS characterization.ResultsAqueousSyzygium cumini(L.) Skeels or ‘Jamun’ extract (AJE) was most potent and reduced the viable colony-forming units (CFU) by 6-logs within 2 hours of exposure at ≥1.9%w/v concentration. It displayed both desirable selectivity towards gut microflora and thermostability (>90% and ∼80% of anti-B. anthracisactivity were retained on incubation at 50°C for 20 days and at 95°C for 12h, respectively). AJE and FDA-approved antibiotics for anthrax displayed synergy. GC-MS analysis of AJE identified various previously-identified antimicrobials belonging to categories of alkaloids, flavonoids, phenols,etc.ConclusionAJE has potent and selective anti-B. anthracisactivity with the desired degree of thermotolerance, compatibility with gut microflora, and recommended antibiotics. Further studies exploring the bioactive components in AJE and their potential application in preventing anthrax and anthrax-like diseases may be undertaken.
α-Synuclein Strain Dynamics Correlate with Cognitive Shifts in Parkinson’s Disease
Authors: Gadhave Kundlik , Xu Enquan , Wang Ning , Zhang Xiaodi , Deyell Jacob , Yang Jun , Wang Anthony , Cha Youngjae , Kumbhar Ramhari , Liu Haiqing , Niu Lili , Chen Rong , Zhang Shu , Bakker Catherine C. , Jin Lingtao , Liang Yajie , Ying Mingyao , Dawson Valina L. , Dawson Ted M. , Rosenthal Liana S. , Mao Xiaobo 
Published: October 2024

Abstractα-Synuclein (α-syn) strains can serve as discriminators between Parkinson’s disease (PD) from other α-synucleinopathies. The relationship between α-syn strain dynamics and clinical performance as patients transition from normal cognition (NC) to cognitive impairment (CI) is not known. Here, we show that the biophysical properties and neurotoxicity of α-syn strains change as PD cognitive status transitions from NC to mild cognitive impairment (PD-MCI) and dementia (PD-D). Both cross-sectional and longitudinal analyses reveal distinct α-syn strains in PD patients correlating to their level of cognitive impairment. This study presents evidence that individuals with PD have different α-syn strains that change in accordance with their cognitive status and highlights the potential of α-syn strain dynamics to guide future diagnosis, management, and stratification of PD patients.One Sentence SummaryDistinct features of α-syn strains change with cognitive decline in Parkinson’s disease.
Comparative proteomics of biofilm development inPseudoalteromonas tunicatadiscovers a distinct family of Ca2+-dependent adhesins
Authors: Ali Sura , Stavropoulos Alexander , Jenkins Benjamin , Graves Sadie , Che Geoffrey , Cheng Jiujun , Tan Huagang , Wei Xin , Egan Suhelen , Neufeld Josh D. , Eckhard Ulrich , Charles Trevor C. , Doxey Andrew C. 
Published: October 2024

ABSTRACTThe marine bacterium,Pseudoalteromonas tunicata, is a useful model for studying mechanisms of biofilm development due to its ability to colonize and form biofilms on a variety of marine and eukaryotic host-associated surfaces. However, the pathways responsible forP. tunicatabiofilm formation are still incompletely understood, in part due to a lack of functional information for a large proportion of its proteome. Here, we used comparative shotgun proteomics to examineP. tunicatabiofilm development throughout the planktonic phase to three stages of biofilm development at 24, 48, and 72 h. Proteomic analysis identified 232 proteins that were up-regulated during different stages of biofilm development, including many hypothetical proteins as well as proteins known to be important forP. tunicatabiofilm development such as the autocidal enzyme AlpP, violacein proteins, S-layer protein SLR4, and various pili proteins. We further investigated the top identified biofilm-associated protein (Bap), a previously uncharacterized 1600 amino acid protein (EAR30327), which we designated as “BapP”. Based on AlphaFold modeling and genomic context analysis, we predicted BapP as a distinct Ca2+-dependent biofilm adhesin. Consistent with this prediction, a ΔbapPknockout mutant was defective in forming both pellicle and surface-associated biofilms, which was rescued by re-insertion ofbapPinto the genome. Similar to mechanisms of RTX adhesins, BapP-mediated biofilm formation was influenced by Ca2+levels, and BapP is likely exported by a type 1 secretion system. Ultimately, our work not only provides a useful proteomic dataset for studying biofilm development in an ecologically relevant organism, but it also adds to our knowledge of bacterial adhesin diversity, emphasizing Bap-like proteins as widespread determinants of biofilm formation in bacteria.