bluuebunny/crossref_metadata_2025_split huggingface dataset:
AlphaFold2 has more to learn about protein energy landscapes
Authors: Chakravarty Devlina , Schafer Joseph W. , Chen Ethan A. , Thole Joseph R. , Porter Lauren L. 
Published: December 2023

AbstractRecent work suggests that AlphaFold2 (AF2)–a deep learning-based model that can accurately infer protein structure from sequence–may discern important features of folded protein energy landscapes, defined by the diversity and frequency of different conformations in the folded state. Here, we test the limits of its predictive power on fold-switching proteins, which assume two structures with regions of distinct secondary and/or tertiary structure. Using several implementations of AF2, including two published enhanced sampling approaches, we generated >280,000 models of 93 fold-switching proteins whose experimentally determined conformations were likely in AF2’s training set. Combining all models, AF2 predicted fold switching with a modest success rate of ∼25%, indicating that it does not readily sample both experimentally characterized conformations of most fold switchers. Further, AF2’s confidence metrics selected against models consistent with experimentally determined fold-switching conformations in favor of inconsistent models. Accordingly, these confidence metrics–though suggested to evaluate protein energetics reliably–did not discriminate between low and high energy states of fold-switching proteins. We then evaluated AF2’s performance on seven fold-switching proteins outside of its training set, generating >159,000 models in total. Fold switching was accurately predicted in one of seven targets with moderate confidence. Further, AF2 demonstrated no ability to predict alternative conformations of two newly discovered targets without homologs in the set of 93 fold switchers. These results indicate that AF2 has more to learn about the underlying energetics of protein ensembles and highlight the need for further developments of methods that readily predict multiple protein conformations.
Loss-of-function mutation in the polyamine transporter geneOsLAT5as a selectable marker for genome editing
Authors: Schenstnyi Kyrylo , Zhang Zhengzhi , Liu Bo , Nakamura Masayoshi , Schepler-Luu Van , Loo Eliza P.I. , Yang Bing , Frommer Wolf B. 
Published: December 2023

AbstractGenome editing by TALENs, CRISPR/Cas, base or prime editing have become routine tools. During stable plant transformation, the gene coding for the editing enzyme, e.g.,Cas9,the guide RNAs (gRNAs), alongside a selectable marker are integrated into the nuclear genome. Identification of successful transformants relies on selectable or screenable markers, typically genes providing resistance to antibiotics or herbicides. Selectable markers use a substantial portion of the T-DNA, hence reducing transfer efficiency by limiting the effective number of TALENs or guide/pegRNAs that can be used in parallel. Moreover, marker genes are frequently subject to gene silencing. Here, we generated loss-of-function mutations in PUT/LAT-type polyamine transporter family genes to confer resistance to the phytotoxin methylviologen (MV) as a method for selection. As a proof of concept, CRISPR/Cas9 vectors with gRNAs were constructed to target three close homologsOsLAT1,OsLAT5, andOsLAT7. We show that loss ofOsLAT5(also known asOsPUT3orOsPAR1) function was sufficient to confer resistance to MV in rice seeds, seedlings and calli, validating the editing approach ofOsLAT5to obtain a selectable marker. We discuss the potential of incorporating a gRNA cassette (forOsLAT5) as a selectable marker and a reporter for successful genome editing for optimizing editing protocols.
Short-term effects of “Yijinjing Wohu Pushi” posture-voice therapy on speech in Parkinson’s disease after STN-DBS
Authors: Sun Xin , Yang Mei , Yan Jin , Wang Linbin , Sun Yuxin , Wang Yong , Yan Shiqing , Li Dianyou , Niu Chuanxin M. 
Published: December 2023

AbstractHypokinetic dysarthria in Parkinson’s Disease (HD-PD) deteriorates patients’ quality of life by impeding communication and social engagement. Existing treatments like levodopa drugs and deep brain stimulation (DBS) can improve motor symptoms but fall short in addressing speech-related impairments; effective speech therapies tend not to mandate the posture, which potentially hinders vocal performance. Here we first proposed a therapeutic protocol that specified a lunging-and-clawing posture (Wohu Pushi method from Yijinjing) during vocalization training. The protocol aimed to ensure that PD patients could accomplish the training even with moderate motor impairments. A total of 20 HD-PD patients with implanted stimulators in subthalamic nuclei (STN-DBS) participated in one session of training, either following our posture-voice therapy (PVT) or the conventional voice therapy (CVT). Results indicated that the maximum phonation time was significantly elongated in PVT(3.85±2.81s) but not in CVT(0.46 ± 2.24s), and the formant-distance was significantly increased in PVT(95.80 ± 112.71Hz) compare to CVT(-47.10 ± 84.28Hz). Our results indicated that by demanding appropriate amount of postural maintenance during vocalization, it might facilitate the recovery of speech-related functions. This study warranted larger-scale clinical trials to understand the impact, limitation, and optimization of posture-voice therapy for HD-PD.
HIPTox – Hazard Identification Platform to Assess the Health Impacts from Indoor and Outdoor Air Pollutant Exposures, through Mechanistic Toxicology: A single-centre double-blind human exposure trial protocol
Authors: Faherty Thomas , Badri Huda , Hu Dawei , Voliotis Aristeidis , Pope Franics D. , Mudway Ian , Smith Jacky , McFiggans Gordon 
Published: December 2023

AbstractOver the past decade, our understanding of the impact of air pollution on short- and long-term population health has advanced considerably, focusing on adverse effects on cardiovascular and respiratory systems. There is, however, increasing evidence that air pollution exposures affect cognitive function, particularly in susceptible groups. Our study seeks to assess and hazard rank the cognitive effects of prevalent indoor and outdoor pollutants through a single-center investigation on the cognitive functioning of healthy human volunteers aged 50 and above, with a familial predisposition to dementia. Participants will all undertake five sequential controlled exposures. The sources of the air pollution exposures are wood smoke, diesel exhaust, cleaning products, and cooking emissions, with clean air serving as the control. Pre- and post-exposure spirometry, nasal lavage, blood sampling, and cognitive assessments will be performed. Repeated testing pre- and post-exposure to controlled levels of pollutants will allow for the identification of acute changes in functioning as well as the detection of peripheral markers of neuroinflammation and neuronal toxicity. This comprehensive approach enables the identification of the most hazardous components in indoor and outdoor air pollutants and further understanding of the pathways contributing to neurodegenerative diseases. The results of this project have the potential to facilitate greater refinement in policy, emphasizing health-relevant pollutants and providing details to aid mitigation against pollutant-associated health risks.
Prevalence and determinants of evidence of silicosis and impaired lung function, among small scale tanzanite miners and the peri-mining community in northern Tanzania
Authors: Mbuya Alexander W. , Mboya Innocent B. , Semvua Hadija H. , Mamuya Simon H. , Howlett Patrick J. , Msuya Sia E. 
Published: December 2023

AbstractAmong mining communities in Tanzania, the limited data available suggests the prevalence of silicosis, obstructive lung diseases (OLD) and restrictive lung disease (RLD) to be around 1.6%, 1.9% and 8.8% respectively. Our study therefore aimed to determine the prevalence and factors associated with evidence of silicosis and ILF among tanzanite mining community in northern Tanzania.We conducted a cross-sectional study, involving 330 randomly selected miners and 330 conveniently selected non-mine workers from the peri-mining community (PMC) in Mererani mines, northern Tanzania. Evidence of silicosis was defined based on study participants’ history of exposure to mining dust and digital chest radiological findings with reference to the 2011 ILO classification of pneumoconiosis. Impaired lung function was determined by spirometry using American Thoracic Society (ATS)/European Respiratory Society (ERS) recommended system 3. Association between evidence of silicosis/impaired lung function and presumed risk factors were determined using binary logistic regression analyses. The study found that 99/330 (30.0%) of miners had evidence of silicosis, of whom 97.0% had accelerated silicosis. Among miners and community members, 75 (11.4%) had ILF, of whom 30 (4.5%) had COPD, 9 (1.4%) had asthma, 29 (4.4%) had restrictive lung disease and 7 (1.1%) had mixed pattern of both obstructive and restrictive lung disease. We found that having a daily income of more than USD 4.3 was associated with lower odds of silicosis (aOR 0.57, 95% CI 0.37-0.89, p<0.05) while ILF was associated with being a miner (aOR 2.06, CI=1.38-3.07, p<0.001).We found a concerningly high prevalence of evidence of silicosis despite short durations of exposure among small scale tanzanite miners. Immediate dust control measures including deployment of wet drilling, wearing of personal protective equipment (PPE) and regular monitoring of dust exposure need to be enforced by the OSHA (Tanzania).
The AMsh glia ofC. elegansmodulates the duration of touch-induced escape responses
Authors: Awe Temitope , Akinosho Aalimah , Niha Shifat , Kelly Laura , Adams Jessica , Stein Wolfgang , Vidal-Gadea Andrés 
Published: December 2023

AbstractOnce considered mere structural support cells in the nervous system, glia have recently been demonstrated to play pivotal roles in sensorimotor processing and to directly respond to sensory stimuli. However, their response properties and contributions to sensory-induced behaviors remain little understood. InCaenorhabditis elegans, the amphid sheath glia (AMsh) directly respond to aversive odorants and mechanical stimuli, but their precise transduction machinery and their behavioral relevance remain unclear.We investigated the role of AMsh in mechanosensation and their impact on escape behaviors inC. elegans. We found that nose touch stimuli in immobilized animals induced a slow calcium wave in AMsh, which coincided with the termination of escape reversal behaviors. Genetic ablation of AMsh resulted in prolonged reversal durations in response to nose touch, but not to harsh anterior touch, highlighting the specificity of AMsh’s role in distinct escape behaviors.Mechanotransduction in AMsh requires the α-tubulin MEC-12 and the ion channels ITR-1 and OSM-9, indicating a unique mechanosensory pathway that is distinct from the neighboring ASH neurons. We find that GABAergic signaling mediated by the GABA-A receptor orthologs LGC-37/8 and UNC-49 play a crucial role in modulating the duration of nose touch-induced reversals.We conclude that in addition to aversive odorant detection, AMsh mediate mechanosensation, play a pivotal role in terminating escape responses to nose touch, and provide a mechanism to maintain high sensitivity to polymodal sensory stimuli.SignificancePolymodal nociceptive sensory neurons have the challenge of multitasking across sensory modalities. They must respond to dangerous stimuli of one modality, but also adapt to repeated nonthreatening stimuli without compromising sensitivity to harmful stimuli from different modalities. Here we show that a pair of glia in the nematodeC. elegansmodulate the duration of nose-touch induced escape responses. We identify several molecules involved in the transduction of mechanical stimuli in these cells and show that they use the signaling molecule GABA to modulate neural function. We propose a mechanism through which these glia might function to maintain this polysensory neuron responsive to dangerous stimuli across different modalities.
SurfDock is a Surface-Informed Diffusion Generative Model for Reliable and Accurate Protein-ligand Complex Prediction
Authors: Cao Duanhua , Chen Mingan , Zhang Runze , Yu Jie , Jiang Xinyu , Fan Zhehuan , Zhang Wei , Zheng Mingyue 
Published: December 2023

ABSTRACTIn the field of structure-based drug design, accurately predicting the binding conformation of ligands to proteins is a long-standing objective. Despite recent advances in deep learning yielding various methods for predicting protein-ligand complex structures, these AI-driven approaches frequently fall short of traditional docking methods in practice and often yield structures that lack physical and chemical plausibility. To overcome these limitations, we present SurfDock, an advanced geometric diffusion network, distinguished by its ability to integrate multiple protein representations including protein sequence, three-dimensional structural graphs, and surface-level details into its equivariant architecture. SurfDock employs a generative diffusion model on a non-Euclidean manifold, enabling precise optimization of molecular translations, rotations, and torsions for reliable binding poses generation. Complemented by a mixture density network for scoring using the same comprehensive representation, SurfDock achieves significantly improved docking success rates over all existing methods, excelling in both accuracy and adherence to physical constraints. Equipped with post-docking energy minimization as an optional feature, the plausibility of generated poses is further enhanced. Importantly, SurfDock demonstrates excellent generalizability to unseen proteins and extensibility to virtual screening tasks with state-of-the-art performance. We consider it a transformative contribution that could serve as an invaluable asset in structure-based drug design.
Fine-tuning protein language models boosts predictions across diverse tasks
Authors: Schmirler Robert , Heinzinger Michael , Rost Burkhard 
Published: December 2023

AbstractPrediction methods inputting embeddings from protein Language Models (pLMs) have reached or even surpassed state-of-the-art (SOTA) performance on many protein prediction tasks. In natural language processing (NLP) fine-tuning large Language Models (LLMs) has become thede factostandard. In contrast, most pLM-based protein predictions do not back-propagate to the pLM. Here, we compared the fine-tuning of three SOTA pLMs (ESM2, ProtT5, Ankh) on eight different tasks. Two results stood out. Firstly, task-specific supervised fine-tuning almost always improved downstream predictions. Secondly, parameter-efficient fine-tuning could reach similar improvements consuming substantially fewer resources at up to 4.5-fold acceleration of training over fine-tuning full models. Our results suggested to always try fine-tuning, in particular for problems with small datasets, such as for fitness landscape predictions of a single protein. For ease of adaptability, we provided easy-to-use notebooks to fine-tune all models used during this work for per-protein (pooling) and per-residue prediction tasks athttps://github.com/RSchmirler/data-repo_plm-finetune-eval.
Chandipura Virus forms cytoplasmic inclusion bodies through phase separation and proviral association of cellular protein Kinase R and stress granules protein TIA-1
Authors: Sarkar Sharmistha , Ganguly Surajit , Ganguly Nirmal K. , Sarkar Debi. P. , Sharma Nishi Raj 
Published: December 2023

AbstractNegative-strand RNA viruses form cytoplasmic inclusion bodies (IBs) representing virus replication foci through phase separation or bio-molecular condensation of viral and cellular proteins, as a hallmark of their infection. Alternatively, mammalian cells form stalled-mRNA containing antiviral stress granules (SGs), as a consequence of phosphorylation of eukaryotic initiation factor 2α (eIF2α) through condensation of several RNA-binding proteins including TIA-1. Whether and how Chandipura virus (CHPV), an emerging human pathogen causing influenza-like illness, coma and death; forms IBs and evades antiviral SGs, remains unknown. By confocal imaging on CHPV-infected Vero-E6 cells, we found that CHPV infection doesn’t induce formation of distinct canonical SGs. Instead, CHPV proteins condense and co-localize together with SG-proteins to form heterogeneous IBs, which ensued independent of the activation of eIF2α and eIF2α Kinase, Protein Kinase R (PKR). Interestingly, siRNA-mediated depletion of PKR or TIA-1 significantly decreased viral transcription and virion production. Moreover, CHPV infection also caused condensation and recruitment of PKR to IBs. Compared to SGs, IBs exhibited significant rapidity in disassembly dynamics. Altogether, our study demonstrates that CHPV-replication co-optimizing with SG-proteins and revealing unprecedented proviral role of TIA-1/PKR, may have implication in understanding the mechanisms regulating CHPV-IB formation, and designing antiviral therapeutic.ImportanceCHPV is an emerging tropical pathogen reported to cause acute influenza-like-illness and encephalitis in children with very high mortality rate of ∼70%. Lack of a vaccines and an effective therapy against CHPV makes it a potent pathogen for causing an epidemic in tropical parts of globe. Given these forewarnings, it is of paramount importance that CHPV biology must be understood comprehensively. Targeting of host factors offers several advantages over targeting the viral components due to in general higher mutation rate in viral genome. In this study, we aimed at understanding the role of those cellular RNA binding proteins in CHPV replication, which form SGs. Our study helps understand participation of cellular factors in CHPV replication and could help develop effective therapeutics against the virus.
The Horizontal Ladder Test (HLT) protocol: A novel, optimized, and reliable means of assessing motor coordination inSus scrofa domesticus
Authors: Liu Xiaobo , Gutierrez Ana G. , Vega Arlette , Willms Joshua O. , Driskill Jackson , Panthagani Praneetha , Sanchez Jordan , Aguilera Monica , Backus Brittany , Bailoo Jeremy D. , Bergeson Susan E. 
Published: December 2023

ABSTRACTPigs can be an important model for preclinical biological research, including neurological diseases such as Alcohol Use Disorder. Such research often involves longitudinal assessment of changes in motor coordination as the disease or disorder progresses. Current motor coordination tests in pigs are derived from behavioral assessments in rodents and lack critical aspects of face and construct validity. While such tests may permit for the comparison of experimental results to rodents, a lack of validation studies of such tests in the pig itself may preclude the drawing of meaningful conclusions. Here, we present a novel, optimized, and reliable horizontal ladder test (HLT) test protocol for evaluating motor coordination in pigs and an initial validation of its construct validity using voluntary alcohol consumption as an experimental manipulation.Abstract Figure
Differential gene expression underpinning production of distinct sperm morphs in the wax mothGalleria mellonella
Authors: Moth Emma , Messer Fiona , Chaudhary Saurabh , White-Cooper Helen 
Published: December 2023

AbstractMale Lepidoptera makes two distinct sperm types; each ejaculate contains both eupyrene sperm, which can fertilise the egg, and apyrene sperm, which are not fertilisation competent. These sperm have distinct morphologies, unique functions, and different proteomes. Their production is highly regulated, however very few genes with specific roles in production of one or other morph have been described. We present the first comparative transcriptomics study of precursors of eupyrene and apyrene sperm to identify genes potentially implicated in regulating or enacting the distinct differentiation programmes. Differentially expressed genes included genes with potential roles in transcriptional regulation, cell cycle and sperm morphology. We identified gene duplications generating paralogues with functions restricted to one or other morph. However phylogenetic analysis also revealed evolutionary flexibility in expression patterns of duplicated genes between different Lepidopteran species. Improved understanding of Lepidopteran reproduction will be vital in targeting prevalent pests in agriculture, and on the flip side, ensuring the fertility and thus survival of pollinator populations in response to environmental stress.
Impairments in the early consolidation of spatial memories via group II mGluR agonism in the mammillary bodies
Authors: Milczarek Michal M. , Perry James C. , Amin Eman , Haniffa Salma , Hathaway Thomas , Vann Seralynne D. 
Published: December 2023

AbstractmGluR2 receptors are widely expressed in limbic brain regions associated with memory, including the hippocampal formation, retrosplenial and frontal cortices, as well as subcortical regions including the mammillary bodies. mGluR2/3 agonists have been proposed as potential therapeutics for neurological and psychiatric disorders, however, there is still little known about the role of these receptors in cognitive processes, including memory consolidation. To address this, we assessed the effect of the mGluR2/3 agonist, eglumetad, on spatial memory consolidation in both mice and rats. Using the novel place preference paradigm, we found that post-sample injections of eglumetad impaired subsequent spatial discrimination when tested 6 hours later. Using the immediate early gene c-fosas a marker of neural activity, we showed that eglumetad injections reduced activity in a network of limbic brain regions including the hippocampus and mammillary bodies. To determine whether the systemic effects could be replicated with more targeted manipulations, we performed post-sample infusions of the mGluR2/3 agonist 2R,4R-APDC into the mammillary bodies. This impaired novelty discrimination on a place preference task and an object-in-place task, again highlighting the role of mGluR2/3 transmission in memory consolidation and demonstrating the crucial involvement of the mammillary bodies in post-encoding processing of spatial information.
Class-specific sensing of HIV-1 antigens by the B cell antigen receptor depends on the CH1 domain
Authors: Ortiz Yaneth , Anasti Kara , Pane Advaiti K. , Cronin Ken , Alam S. Munir , Reth Michael 
Published: December 2023

SUMMARYHow different classes of the B cell antigen receptor (BCR) sense viral antigens used in vaccination protocols is poorly understood. Here we study antigen binding and sensing of Ramos B cells expressing BCRs of either the IgM or IgG1 class with a specificity for the CD4-binding-site of the envelope (Env) protein of the human immune deficiency virus-1 (HIV-1). We find that, in spite of their identical antigen binding site, the two BCR classes differ drastically from each other in that the IgM-BCR and IgG1-BCR bind preferentially to monovalent and polyvalent antigens, respectively. By generating an IgM/IgG1 chimeric BCR we found that the class-specific antigen-sensing behavior can be transferred with the CH1γ domain from the IgG1-BCR to the IgM-BCR. Our results indicate that the class-switching process not only results in the production of antibody classes with different effector functions but also alters the antigen sensing of secondary B lymphocytes. These findings suggest that antigen valency in existing vaccination protocols should be modified and altered between primary versus secondary (booster) immunization.