bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cataract-prone variants of γD-crystallin populate a conformation with a partially unfolded N-terminal domain under native conditions
Authors: Volz Sara , Malone Jadyn R. , Guseman Alex J. , Gronenborn Angela M. , Marqusee Susan 
Published: June 2024

AbstractHuman γD-crystallin, a monomeric protein abundant in the eye lens nucleus, must remain stably folded for an individual’s entire lifetime to avoid aggregation and protein deposition-associated cataract formation. γD-crystallin contains two homologous domains, an N-terminal domain (NTD) and a C-terminal domain (CTD), which interact via a hydrophobic interface. A number of familial mutations in the gamma crystallin gene are linked to congenital early-onset cataract, most of which result in amino acid changes in the NTD. Several of these, such as V75D and W42R, are known to populate intermediates that, under partially denaturing conditions, possess a natively folded CTD and a completely unfolded NTD, with studies on W42R showing further evidence for a minor population of an intermediate under native conditions. We employed hydrogen-deuterium exchange mass spectrometry (HDX-MS) to probe the structural and energetic features of variants of γD-crystallin under both native and partially denaturing conditions. For V75D and W42R, we identify a species under native conditions that retains partial structure in the NTD and is structurally and energetically distinct from the intermediate populated under partially denaturing conditions. Residues at the NTD-CTD interface play crucial roles in stabilizing this intermediate, and disruption of interface contacts either by amino acid substitution or partial denaturation permits direct observation of two intermediates at the same time. The newly identified intermediate exposes hydrophobic amino acids that are buried in both the folded full-length protein and in the protein’s stable isolated domains. Such non-native exposure of a hydrophobic patch may play an important role in cataract formation.Significance StatementHuman γD-crystallin, which plays a structural role in the eye lens, is a long-lived protein that must remain folded for an individual’s entire lifetime to avoid aggregation and protein deposition - associated cataract formation. By using hydrogen-deuterium exchange mass spectrometry, we demonstrate that two cataract-associated variants of γD-crystallin populate an intermediate with partial structure along the interface between its two domains under native conditions. In these intermediates, hydrophobic amino acids that are normally buried in the N-terminal domain’s native folded structure become exposed, possibly leading to aggregation and cataract formation. Our findings illustrate the importance of studying a protein’s energy landscapes under conditions that are close to physiological.
Self-growth suppression inBradyrhizobium diazoefficiensis caused by a diffusible antagonist
Authors: Sandhu Armaan Kaur , Fischer Brady R. , Subramanian Senthil , Hoppe Adam D. , Brözel Volker S. 
Published: June 2024

AbstractMicrobes in soil navigate interactions by recognizing kin, forming social groups, exhibiting antagonistic behavior, and engaging in competitive kin rivalry. Here, we investigated a novel phenomenon of self-growth suppression (sibling rivalry) observed inBradyrhizobium diazoefficiensUSDA 110. Swimming colonies of USDA 110 developed a distinct demarcation line and inter-colony zone when inoculated adjacent to each other. In addition to self, USDA 110 suppressed growth of otherBradyrhizobiumstrains and several other soil bacteria. We demonstrated that the phenomenon of sibling rivalry is due to growth suppression but not cell death. The cells in the inter-colony zone were culturable but have reduced respiratory activity, ATP levels and motility. The observed growth suppression was due to the presence of a diffusible effector compound. This effector was labile, preventing extraction, and identification, but it is unlikely a protein or a strong acid or base. This counterintuitive phenomenon of self-growth suppression suggests a strategic adaptation for conserving energy and resources in competitive soil environments.Bradyrhizobium’sutilization of antagonism including self-growth suppression likely provides a competitive advantage for long-term success in soil ecosystems.
Enhanced Treatment Efficiency of Holmium:YAG Laser Lithotripsy by Using PEDOT:PSS Nanofluid
Authors: Fan Qingsong , Chen Junqin , Anees Faisal , Dominguez Judith , Chen Ting-Hsuan , Payne Christine , Zhong Pei , Hsu Po-Chun 
Published: June 2024

AbstractHolmium: yttrium-aluminum-garnet (Ho:YAG) laser lithotripsy has been considered the gold standard for treating urinary stones, a disease with increasing prevalence in the US in recent years. While various efforts have been made to enhance the stone ablation efficiency of Ho:YAG laser, these have primarily focused on adjusting laser source settings such as pulse energy and frequency. In this study, we introduced a novel strategy to improve the ablation efficiency of the Ho:YAG laser by incorporating nanoparticles into the fluid surrounding the stone with strong near-infrared light absorption. Experimental results of stone damage revealed an 82% increase in photothermal ablation efficiency when using a “dusting” mode of laser lithotripsy in 0.03 wt.% PEDOT:PSS solution in direct contact. The enhanced NIR absorbance of the fluid was found to promote vapor tunnel formation, facilitating increased laser energy transmission to the stone surface, and to enhance stone absorbance due to trapped fluid inside, leading to greater laser energy absorption for photothermal ablation. Furthermore, cytotoxicity tests on PEDOT:PSS solution demonstrated minimal toxicity when carefully controlling concentration and application duration. This modification of fluid absorbance for efficiency improvement presents a versatile approach compatible with previously reported laser setting modulation methods, showcasing significant potential for enhancing Ho:YAG laser lithotripsy.
Biomolecular Condensation of Trypsin Prevents Autolysis and Promotes Ca2+-Mediated Activation of Esterase Activity
Authors: Patel Chinmaya Kumar , Mukherjee Tushar Kanti 
Published: June 2024

AbstractThe presence of Ca2+ions is known to facilitates the biocatalytic activity of trypsin-like serine proteases via structural stabilization against thermal denaturation and autolysis. Herein, we report a new and hidden regulatory role of Ca2+in the catalytic pathways of trypsin and α-chymotrypsin under physiological conditions. We discovered that macromolecular crowding promotes spontaneous homotypic condensation of native trypsin via liquid-liquid phase separation to yield membraneless condensates/droplets in a broad range of concentrations, pH, and temperature. These condensates are stabilized by multivalent hydrophobic interactions between short patches of hydrophobic residues. Importantly, no liquid-to-solid-like phase transition has been observed over a period of 14 days, indicating the structural intrigrity of phase-separated trypsin within the droplets. Structural insights revealed minimal conformational perturbation of trypsin upon phase separation. Interestingly, we found that Ca2+binding in the calcium binding loop reversibly regulates the biomolecular condensation of trypsin and α-chymotrypsin. While Ca2+-bound trypsin are ineffective to undergo LLPS to form condensate, its removal facilitates condensation under similar experimental conditions. More importantly, we show that biomolecular condensation effectively prevents autolysis of trypsin at physiological conditions and preserve its native-like esterase activity over a period of 14 days, whereas free trypsin loses 86% of its initial activity. In addition, it has been found that phase-separated trypsin responds to Ca2+-dependent activation of its esterase activity even after 14 days of storage while free trypsin failed to do so. Our findings indicate that biomolecular condensates of trypsin and trypsin-like serine proteases act as storage media to prevent autolysis and premature activation, and at the same time preserve their native-like active conformations. The present study highlights an important physiological aspect of biomolecular condensates of trypsin-like serine proteases by which cells can spatio-temporally regulate their biocatalytic efficacy via Ca2+-signalling.
Anaesthesia and delirium: a Mendelian randomization study
Authors: Li YanHui , Sun Yingwei , Zhou Chuanyang , Tan Lei 
Published: June 2024

AbstractBackgroundDelirium is a frequent complication in hospitalized older adults post-surgery associated with adverse outcomes. Although anaesthesia is traditionally linked to increased delirium risk, the causal relationship remains uncertain.MethodsWe conducted Mendelian randomization (MR) analyses using genome-wide association studies (GWAS) summary statistics to explore the causal effects of different anaesthesia types (general, regional, and local) on delirium risk. We employed the weighted median, MR-Egger, and MR-PRESSO methods for estimation and conducted sensitivity analyses to address pleiotropy and heterogeneity.ResultsGenetically determined anaesthesia types showed no significant causal effect on delirium risk. Sensitivity analyses confirmed the robustness of these findings, with no evidence of horizontal pleiotropy or significant heterogeneity.ConclusionsMendelian randomization provides strong evidence against a causal link between genetically determined anaesthesia and increased delirium risk.
Knockdown of PAK1IP1 can induce CASP-3-dependent pyroptosis to inhibit the progression of hepatocellular carcinoma
Authors: Lu Xiaoliang , Chen Jie , Lu Zefa , Zang Hong 
Published: June 2024

AbstractBackgroundHepatocellular carcinoma (HCC), is a prevalent and fatal malignancy originating from hepatic cells with a consistently rising incidence in recent decades. In this study, we aim to identify potential prognostic biomarkers and reveal new mechanism in HCC.MethodsHCC-related datasets (GSE45267 and GSE49515) and TCGA information were downloaded for DEGs, and the common DEGs were WGCNA, protein-protein interaction network (PPI), risk model, expression, survival and prognostic nomogram to determine the key gene related to HCC. Further, the key gene was analyzed by clinical feature analysis, immunoassay and cell experiments to investigate its exact role in HCC.ResultsBased on the above comprehensive analysis, we targeted the key gene PAK1-interacting protein 1(PAK1IP1) with a good prognostic value in HCC. PAK1IP1 was remarkably increased in tumor samples than normal samples, which might be related to immune cell infiltration in liver cancer. It was up-regulated in HCC cells, and its knockdown could suppress HCC proliferation and migration. Besides, ELISA and flow cytometry showed that PAK1IP1 could regulate Lipopolysaccharide (LPS)-induced pyroptosis of HCC cells. Knocking down PAK1IP1 could induce CASP-3-dependent pyroptosis in HCC cells to suppress the development of HCC.ConclusionTo sum up, PAK1IP1 was identified as a promising prognostic biomarker, and knockdown of PAK1IP1 can induce CASP-3-dependent pyroptosis to suppress HCC development, which sheds new light on HCC tumorigenesis.
Mechanosensory representation of wing deformations
Authors: Yarger Alexandra M. , Maeda Masateru , Siwanowicz Igor , Kajiyama Haruhiro , Walker Simon M. , Bomphrey Richard J. , Lin Huai-Ti 
Published: June 2024

AbstractEfficient representation of structural deformations is crucial for monitoring the instantaneous state of biological structures. Insects’ ability to encode wing deformations during flight demonstrates a general morphological computing principle applicable across sensory systems in nature as well as engineered systems. To characterize how relevant features are encoded, we measured and modelled displacement and strain across dragonfly wing surfaces in tethered and free flight. Functional interpretations were supported by neuroanatomical maps, and ablation and perturbation experiments. We find that signal redundancy is reduced by non-random sensor distributions and that morphology limits the stimulus space such that sensory systems can monitor natural states with few sensors. Deviations from the natural states are detected by a flexible population of additional sensors with many distinguishable activation patterns.
Testing the reality gap with kilobots performing two ant-inspired foraging behaviours
Authors: Ellis Niamh , Caravaggio Alexander , Kelly Jonathan , Young Ian , Manfredini Fabio , Giannaccini Maria Elena 
Published: June 2024

AbstractRobotics looks to nature for inspiration to perform effectively in unstructured environments and can be used as a platform to test biological hypotheses. Social animals often share information about food source locations: one example is tandem running in ants, where a leader guides a naive recruit to a known profitable food site. This is extremely advantageous as it allows the sharing of important information among colony members, but it also has costs, such as waiting time inside the nest when no leaders are around, and a reduced walking speed for the tandem couple compared to individual ants. Whether and when these costs outweigh the benefits is not well understood as it is challenging to observe complex social behaviours in nature. We developed two kilobot-based approaches to compare tandem running and lone scout foraging, where an ant searches for food without any previous knowledge of its location: one approach based on real-life experiments and one on computer simulations. We investigated the role that the size of the search arena played in the effectiveness of foraging. Tandem pairs were faster for all three arena sizes; however, this result was reversed in the simulations. These results highlight the inconsistencies between simulation and real-life kilobot experiments, previously reported for other systems and known as reality gap. Further testing is needed to inform on whether robotic applications should utilise agents with the same roles and capabilities for search, detection and repair-type tasks as simulations, or whether instead the two approaches should be treated separately.
stVCR: Reconstructing spatio-temporal dynamics of cell development using optimal transport
Authors: Peng Qiangwei , Zhou Peijie , Li Tiejun 
Published: June 2024

AbstractTime-series spatial transcriptome data with single-cell resolution provide an opportunity to study cell differentiation, growth and migration in physical space over time. Due to the destructive nature of sequencing, simultaneous reconstruction of cell differentiation, growth and migration trajectories remains challenging, especially migration in physical space, as the coordinates obtained at different temporal snapshots are not in the same coordinate system. To realize this potential, we developed stVCR, which is an optimal transport algorithm with dynamical form, unbalanced setting and invariance to rigid body transformations. stVCR extends the previous algorithm, which only reconstructs differentiation trajectories and population growth, to end-to-end simultaneously reconstruct cell differentiation, growth, migration in physical space and align spatial coordinates of multiple snapshots. In addition, stVCR allows the study of the interaction between gene expression and spatial migration and the effect of gene expression and spatial migration on growth. We verified the effectiveness of stVCR on simulated data and axolotl brain regeneration data.
Consciousness in Non-REM-parasomnia episodes
Authors: Siclari Francesca 
Published: June 2024

AbstractSleepwalking and related parasomnias are thought to result from incomplete awakenings out of Non rapid eye movement (Non-REM) sleep. Non-REM parasomnia behaviors have been described as unconscious and automatic, or related to vivid, dream-like conscious experiences. Similarly, some observations have suggested that patients are unresponsive during episodes, while others that they can interact with their surroundings. To better grasp and characterize the full spectrum of consciousness and environmental disconnection associated with behavioral episodes, 35 adult patients with Non-REM sleep parasomnias were interviewed in-depth about their experiences. The level of consciousness during parasomnia episodes was reported to be variable both within and between individuals, ranging from minimal or absent consciousness and largely automatic behaviors (frequently/always present in 36% of patients) to preserved conscious experiences characterized by delusional thinking of varying degrees of specificity (65%), often about impending danger, variably formed, uni- or multisensory hallucinations (53%), impaired insight (77%), negative emotions (75%) and variable, but often pronounced amnesia (30%). Patients described their experiences as a dream scene during which they felt awake (‘awake dreaming’). Surroundings were either realistically perceived, misinterpreted (in the form of perceptual illusions or misidentifications of people) or entirely hallucinated as a function of the prevailing delusion. These observations suggest that the level of consciousness and sensory disconnection in Non-REM parasomnias is variable and graded. In their full-fledged expression, Non-REM parasomnia experiences feature several core features of dreams. They therefore represent a valuable model for the study of consciousness, sleep-related sensory disconnection and dreaming.
Integrating diverse statistical methods to analyse stage-discriminatory cell interactions in colorectal neoplasia
Authors: Bull Joshua A. , Mulholland Eoghan J. , Moore Joshua W. , Bosque Jesús J. , Stolz Bernadette J. , Boen Joseph , Eggington Holly R. , Belnoue-Davis Hayley L. , Jones Helen , Gatenbee Chandler D. , Anderson Alexander R. A. , Easton Alistair , Todd Peter , Cunningham Christopher , Taylor Stephen , Byrne Helen M. , Leedham Simon 
Published: June 2024

SummarySpatial biology has the potential to unlock information about the disrupted cellular ecosystems that define human disease. Quantitative analysis of spatially-resolved cell interactions allows mapping of tissue self-organisation and assessment of why cells interact differently in physiological and pathological contexts. However, the complexity of mammalian tissues, that occur across a spectrum of length scales, presents significant challenges for spatial analysis, increasing the gap between our capacity to generate and biologically interpret these datasets. Here, we have adapted a range of mathematical tools to develop a suite of spatial descriptors, and deployed them to determine how cell interactions change as colorectal cancer progresses from benign precursors. We demonstrate that combining mathematical analyses permits insightful examination of tissue organisational structures and identifies variable cell-interaction pathways that underpin disease progression. Mathematical tool triangulation can cross-corroborate spatial biology findings, facilitating development of analysis pipelines that are robust to individual method limitations.
A CRISPR homing screen finds a chloroquine resistance transporter-like protein of thePlasmodiumoocyst essential for mosquito transmission of malaria
Authors: Balakrishnan Arjun , Hunziker Mirjam , Tiwary Puja , Pandey Vikash , Drew David , Billker Oliver 
Published: June 2024

SUMMARYGenetic screens with barcodedPlasmoGEM vectors have identified thousands ofPlasmodiumgene functions in haploid blood stages, gametocytes and liver stages. However, the formation of diploid cells by fertilisation has hindered the use of genetic screens to investigate vector-parasite interactions during the mosquito stages of the parasite. In this study, we developed a scalable genetic system that uses barcoded gene targeting vectors equipped with a CRISPR-mediated homing mechanism to generate homozygous loss-of-function mutants to reveal gene functions in the functionally diploid life cycle stages. In this system, a knockout vector additionally expressing a gRNA for its target is integrated into one of the parental alleles and directs Cas9 to the intact allele after fertilisation, leading to its disruption. We find that this homing strategy is 90% effective in the oocyst, resulting in the generation of homozygous genotypes. A pilot screen reveals that PBANKA_0916000 encodes a chloroquine resistance transporter-like protein, CRTL, essential for oocyst growth and sporogony. The data point to an unexpected importance for the transmission of malaria of the poorly understood digestive vacuole of the oocyst that contains hemozoin crystals. The new screening strategy provides a method to discover systematically and at scale the essential malaria transmission genes whose first essential functions are after fertilisation in the bloodmeal, enabling their potential as targets for transmission-blocking interventions to be assessed.
Predicting binding events in very flexible, allosteric, multi-domain proteins
Authors: Basciu Andrea , Athar Mohd , Kurt Han , Neville Christine , Malloci Giuliano , Muredda Fabrizio C. , Bosin Andrea , Ruggerone Paolo , Bonvin Alexandre M. J. J. , Vargiu Attilio V. 
Published: June 2024

AbstractKnowledge of the structures formed by proteins and small molecules is key to understand the molecular principles of chemotherapy and for designing new and more effective drugs. During the early stage of a drug discovery program, it is customary to predict ligand-protein complexesin silico, particularly when screening large compound databases. While virtual screening based on molecular docking is widely used for this purpose, it generally fails in mimicking binding events associated with large conformational changes in the protein, particularly when the latter involve multiple domains. In this work, we describe a new methodology to generate bound-like conformations of very flexible and allosteric proteins bearing multiple binding sites by exploiting only information on the unbound structure and the putative binding sites. The protocol is validated on the paradigm enzyme adenylate kinase, for which we generated a significant fraction of bound-like structures. A fraction of these conformations, employed in ensemble-docking calculations, allowed to find native-like poses of substrates and inhibitors (binding to the active form of the enzyme), as well as catalytically incompetent analogs (binding the inactive form). Our protocol provides a general framework for the generation of bound-like conformations of challenging drug targets that are suitable to host different ligands, demonstrating high sensitivity to the fine chemical details that regulate protein’s activity. We foresee applications in virtual screening, in the prediction of the impact of amino acid mutations on structure and dynamics, and in protein engineering.