bluuebunny/crossref_metadata_2025 huggingface dataset:
Heat stress-induced heat shock protein 70 (HSP70) expressions among vulnerable populations in urban and rural areas Klang Valley, Malaysia
Authors: Muhamad Siti Nurfahirah , Akim Abdah Md , Lim Fang Lee , Mohd Shabri Nur Shabrina Azreen , How Vivien
Published: December 2023

As climate change raises global temperatures, there remains a notable gap in understanding the body’s mechanism of the heat stress defense exhibited by Heat Shock Protein (HSP) within the populations. This study aims to evaluate the expression of heat shock protein 70 (HSP70) in vulnerable populations living in urban and rural areas in response to heat exposure. A comparative cross-sectional study involved 54 urban and 54 rural participants from Klang Valley, Malaysia. This study comprises four methods: Part I involves conducting face-to-face interviews questionnaire; Part II involves monitoring indoor heat exposure and classifying thermal stress using the Universal Thermal Climate Index (UTCI); Part III involves using the reverse-transcription quantitative polymerase chain reaction (RT-qPCR) and Part IV involves using the HSP70 High Sensitivity Enzyme-linked Immunosorbent Assay (ELISA). The findings revealed that urban areas have a higher heat level, classified as strong UTCI thermal stress (32.1°C), whereas rural areas have moderate UTCI thermal stress (31.0°C). In response to heat stress, the urban vulnerable populations exhibited higher HSP70 gene expression (0.167 ± 0.86) compared to the rural (0.154 ± 0.28). A significant difference (p<0.001) in HSP70 protein expression was observed in the plasma of urban compared to rural vulnerable populations. There was a strong association between UTCI heat exposure level and the expression of the HSP70 gene and protein in both vulnerable population groups (p<0.001). Although susceptible to vulnerabilities, the populations demonstrated HSP70 expressions in response to varying levels of heat exposure as a coping mechanism at the cellular level.
Neural Activity Shaping in Visual Prostheses with Deep Learning
Authors: Castro Domingos , Grayden David B. , Meffin Hamish , Spencer Martin
Published: December 2023

Objective

The visual perception provided by retinal prostheses is poor and limited to images constructed of phosphenes generated by the electrodes. One limiting factor has been the conventional strategy used to encode the target image into a stimulation pattern. Under this strategy, if the electrode density is high, the current spread of neighbouring unipolar stimuli overlaps, leading to blurred images. Simultaneous multipolar stimulation guided by the measured neural responses can attenuate excessive spread of excitation and allows for a more precise electrical input to the retina. However, it is far from trivial to predict what multipolar stimulus pattern will elicit the desired retinal response for a given target image. Here, we propose to solve this problem using an Artificial Neural Network (ANN) that could be trained with data acquired from the implant itself.

Approach

Our method consists of two ANNs trained sequentially. The Measurement Predictor Network (MPN) is trained on data from the implant and is used to predict how the retina responds to multipolar stimulation by learning the forward model. The Stimulus Generator Network (STG) is trained on a large dataset of natural images and uses the trained MPN to determine efficient multipolar stimulus patterns by learning the inverse model. We validate our methodin silicousing a realistic model of retinal response to multipolar stimulation.

Main Results

We show that the simulated retinal activations elicited with our ANN-based approach are considerably sharper when compared with the conventional method used in existing devices. The SGN finds multipolar stimulation patterns that are tuned to a specific retina, thus providing patient-specific stimuli. Also, due to its small computational cost, the SGN can output stimulation patterns at a very high rate.

Significance

Our novel protocol opens the door to personalized multipolar retinal stimulation, which may improve the visual experience and quality of life of retinal prosthesis users.
Identification of a short, single site matriglycan that maintains neuromuscular function in the mouse
Authors: Yang Tiandi , Chandel Ishita , Gonzales Miguel , Okuma Hidehiko , Prouty Sally J. , Zarei Sanam , Joseph Soumya , Garringer Keith W. , Ocampo Landa Saul , Yonekawa Takahiro , Walimbe Ameya S. , Venzke David P. , Anderson Mary E. , Hord Jeffery M. , Campbell Kevin P.
Published: December 2023

Matriglycan (−1,3-β-glucuronic acid-1,3-α-xylose-) is a polysaccharide that is synthesized on α-dystroglycan, where it functions as a high-affinity glycan receptor for extracellular proteins, such as laminin, perlecan and agrin, thus anchoring the plasma membrane to the extracellular matrix. This biological activity is closely associated with the size of matriglycan. Using high-resolution mass spectrometry and site-specific mutant mice, we show for the first time that matriglycan on the T317/T319 and T379 sites of α-dystroglycan are not identical. T379-linked matriglycan is shorter than the previously characterized T317/T319-linked matriglycan, although it maintains its laminin binding capacity. Transgenic mice with only the shorter T379-linked matriglycan exhibited mild embryonic lethality, but those that survived were healthy. The shorter T379-linked matriglycan exists in multiple tissues and maintains neuromuscular function in adult mice. In addition, the genetic transfer of α-dystroglycan carrying just the short matriglycan restored grip strength and protected skeletal muscle from eccentric contraction-induced damage in muscle-specific dystroglycan knock-out mice. Due to the effects that matriglycan imparts on the extracellular proteome and its ability to modulate cell-matrix interactions, our work suggests that differential regulation of matriglycan length in various tissues optimizes the extracellular environment for unique cell types.
Physiological constraints limiting the growth ofDrosophilalarvae
Authors: Schönborn Jürgen , Akhtar Irfan , Droste Andrea , Wesemann Stephanie , Beller Mathias
Published: December 2023

The phenotype of organisms is the result of complex interactions between physiology, developmental conditions, and intra-organismic processes, such as metabolism and genetic adaptation. Organisms pursue various developmental strategies that depend on factors such as available resources. How organisms regulate and control critical developmental principles is not fully understood. In this study, we investigated the dynamic development ofDrosophila melanogasterlarvae throughin vitroandin silicoexperiments. First, we enhanced the larval metabolic network FlySilico and its parameters using growth and metabolite measurements. Subsequently, we established a dynamic flux balance analysis approach and incorporated spatial physiological information from the larval gut to improve the prediction results. We successfully predicted larval growth on different media and developmental critical processes, such as the emergence of larval metamorphosis. This expands the ability to investigate and understand the process of the larval critical weight and, furthermore, the influence of critical developmental processes of multicellular organisms on metabolism. Thus, we present an approach to understand the development, metabolism, and the role of physiology in the development of multicellular organisms.

Graphical Abstract
Tactile Adaptation to Orientation Produces a Robust Tilt Aftereffect and Exhibits Crossmodal Transfer When Tested in Vision
Authors: Wang Guandong , Alais David
Published: December 2023

Orientation processing is one of the most fundamental functions in both visual and somatosensory perception. Converging findings suggest that orientation processing in both modalities is closely linked: somatosensory neurons share a similar orientation organisation as visual neurons, and the visual cortex has been found to be heavily involved in tactile orientation perception. The tilt aftereffect (TAE) is a demonstration of orientation adaptation and is used widely in behavioural experiments to investigate orientation mechanisms in vision. By testing the classic TAE paradigm in both tactile and crossmodal orientation tasks between vision and touch we were able to show that tactile perception of orientation shows a very robust TAE, similar to its visual counterpart. We further show that orientation adaptation in touch transfers to produce a TAE when tested in vision, but not vice versa. We also observed a similar asymmetricity in the intramodal serial dependence effect within the test sequence. These findings provide concrete evidence that vision and touch engage a similar orientation processing mechanism, but the asymmetry in the crossmodal transfer of TAE and serial dependence provides more insights into the underlying mechanism of this link.
Galectin-3-binding protein inhibits extracellular heparan 6-O-endosulfatse Sulf-2
Authors: Panigrahi Aswini , Benicky Julius , Aljuhani Reem , Mukherjee Pritha , Nováková Zora , Bařinka Cyril , Goldman Radoslav
Published: December 2023

Human extracellular 6-O-endosulfatases Sulf-1 and Sulf-2 are the only enzymes that post-synthetically alter the 6-Osulfation of heparan sulfate proteoglycans (HSPG), which regulates interactions of HSPG with many proteins. Oncogenicity of Sulf-2 in different cancers has been documented and we have shown that Sulf-2 is associated with poor survival outcomes in head and neck squamous cell carcinoma (HNSCC). In spite of its importance, limited information is available on direct protein-protein interactions of the Sulf-2 protein in the tumor microenvironment. In this study, we used monoclonal antibody (mAb) affinity purification and mass spectrometry to identify galectin-3-binding protein (LG3BP) as a highly specific binding partner of Sulf-2 in the secretome of HNSCC cell lines. We validated their direct interactionin vitrousing recombinant proteins and have shown that the chondroitin sulfate (CS) covalently bound to the Sulf-2 influences the binding to LG3BP. We confirmed importance of the CS chain for the interaction by generating a mutant Sulf-2 protein that lacks the CS. Importantly, we have shown that the LG3BP inhibits Sulf-2 activityin vitroin a concentration dependent manner. As a consequence, the addition of LG3BP to a spheroid cell culture inhibited invasion of the HNSCC cells into Matrigel. Thus, Sulf-2 interaction with LG3BP has functional relevance, and may regulate physiological activity of the Sulf-2 enzyme as well as its activity in the tumor microenvironment.
Mind the gap: A systematic review and meta-analysis of how social memory is studied
Authors: Cum Meghan , Pérez Jocelyn Santiago , Wangia Erika , Lopez Naeliz , Wright Elizabeth S. , Iwata Ryo L. , Li Albert , Chambers Amelia R. , Padilla-Coreano Nancy
Published: December 2023

Social recognition is crucial for survival in social species, and necessary for group living, selective reproduction, pair bonding, and dominance hierarchies. Mice and rats are the most commonly used animal models in social memory research, however current paradigms do not account for the complex social dynamics they exhibit in the wild. To assess the range of social memories being studied, we conducted a systematic analysis of neuroscience articles testing the social memory of mice and rats published within the past two decades and analyzed their methods. Our results show that despite these rodent’s rich social memory capabilities, the majority of social recognition papers explore short-term memories and short-term familiarity levels with minimal exposure between subject and familiar stimuli – a narrow type of social memory. We have identified several key areas currently understudied or underrepresented: kin relationships, mates, social ranks, sex variabilities, and the effects of aging. Additionally, reporting on social stimulus variables such as housing history, strain, and age, is limited, which may impede reproducibility. Overall, our data highlight large gaps in the diversity of social memories studied and the effects social variables have on social memory mechanisms.
Single-cell transcriptomic profiling of the neonatal oviduct and uterus reveals new insights into upper Müllerian duct regionalization
Authors: Jia Shuai , Zhao Fei
Published: December 2023

The upper Müllerian duct (MD) is patterned and specified into two morphologically and functionally distinct organs, the oviduct and uterus. It is known that this regionalization process is instructed by inductive signals from the adjacent mesenchyme. However, the interaction landscape between epithelium and mesenchyme during upper MD development remains largely unknown. Here, we performed single-cell transcriptomic profiling of mouse neonatal oviducts and uteri at the initiation of MD epithelial differentiation (postnatal day 3). We identified major cell types including epithelium, mesenchyme, pericytes, mesothelium, endothelium, and immune cells in both organs with established markers. Moreover, we uncovered region-specific epithelial and mesenchymal subpopulations and then deduced region-specific ligand-receptor pairs mediating mesenchymal-epithelial interactions along the craniocaudal axis. Unexpectedly, we discovered a mesenchymal subpopulation marked by neurofilaments with specific localizations at the mesometrial pole of both the neonatal oviduct and uterus. Lastly, we analyzed and revealed organ-specific signature genes of pericytes and mesothelial cells. Taken together, our study enriches our knowledge of upper Müllerian duct development, and provides a manageable list of potential genes, pathways, and region-specific cell subtypes for future functional studies.
Activation of Store-Operated Calcium Entry and Mitochondrial Respiration by Enterovirus 71 Is Essential for Efficient Virus Replication
Authors: Hsu Bang-Yan , Tsai Ya-Hui , Weng Ta-Chou , Kung Szu-Hao
Published: December 2023

Enterovirus (EV) infections disrupt cellular calcium (Ca2+) homeostasis. The EV protein 2B is localized to the endoplasmic reticulum (ER) and causes depletion of ER Ca2+stores. This depletion coincides with a substantial increase in cytosolic Ca2+levels driven by extracellular Ca2+influx. However, the precise mechanism underlying this influx remains elusive. In the present study, we demonstrated that EV71 infections induce store-operated Ca2+entry (SOCE) by activating the Ca2+sensor stromal interaction molecule 1 (STIM1), which subsequently interacts with Orai1, a plasma membrane (PM) Ca2+channel. This finding was supported by confocal imaging, which revealed that STIM1, typically localized in the ER, becomes active and colocalizes with Orai1 at the PM in EV71-infected cells. Pharmacological inhibition of the STIM1–Orai1 interaction and knockdown of either STIM1 or Orai1 significantly reduced virus-induced cytosolic Ca2+levels and viral replication. Global transcriptome analysis revealed that differentially expressed genes are primarily associated with the mitochondrial electron transport chain (ETC) upon SOCE activation, contributing to enhanced ATP generation and oxygen consumption. This increase in mitochondrial Ca2+levels is correlated with the mid-stage of virus infection. Furthermore, we demonstrated that high levels of mitochondrial Ca2+influx led to apoptotic cell death favoring viral release at the late stage of virus infection. Finally, SOCE-dependent EV replication was observed in a mouse intestinal organoid culture, a more physiologically relevant cell system. Our results provide valuable insights into the mechanism through which EV infections induce SOCE-mediated spatial and temporal control of Ca2+signaling, substantially affecting the virus life cycle.

IMPORTANCE

Host cell Ca2+signals play crucial roles in various steps of virus life cycles, including entry, replication, and exit. EV requires increased cytosolic Ca2+levels for efficient replication, but the precise mechanisms underlying the association between Ca2+levels and EV replication remain elusive. Using EV71 as a model virus, we demonstrated that EV71 infection elevated cytosolic Ca2+levels through store-operated Ca2+entry activation and progressive Ca2+mobilization to mitochondria. This led to the upregulation of electron transport chain activity, which is essential for efficient virus replication and apoptotic cell death, facilitating viral release during the mid and late stages of the infectious cycle, respectively. These findings substantially enhance the understanding of how EVs co-opt host cell mechanisms to promote their own life cycle. STIM1 and Orai1 may be novel targets for broad-spectrum host-directed therapeutics against EVs and other viruses that employ similar replication mechanisms.
SpottedPy quantifies relationships between spatial transcriptomic hotspots and uncovers new environmental cues of epithelial-mesenchymal plasticity in cancer
Authors: Withnell Eloise , Secrier Maria
Published: December 2023

Spatial transcriptomics is revolutionising the exploration of intratissue heterogeneity in cancer, yet capturing cellular niches and their spatial relationships remains challenging. We introduce SpottedPy, a Python package designed to identify tumour hotspots and map spatial interactions within the cancer ecosystem. Using SpottedPy, we examine epithelial-mesenchymal plasticity in breast cancer and highlight stable niches associated with angiogenic and hypoxic regions, shielded by CAFs and macrophages. Hybrid and mesenchymal hotspot distribution followed transformation gradients reflecting progressive immunosuppression. Our method offers flexibility to explore spatial relationships at different scales, from immediate neighbours to broader tissue modules, providing new insights into tumour microenvironment dynamics.
Metagenomic Detection and Genetic Characterization of Human Sapovirus among Children in Nigeria
Authors: Uwem George Etop , Temitope Faleye O. C. , Lander De Coninck , Sheriff Agbaje Tunde , Ijeoma Ifeorah Maryjoy , Bernard Onoja Anyebe , Elijah Oni Igbekele , Oluseyi Olayinka Adebowale , Toluwani Ajileye Goodnews , Arthur Oragwa Obinna , Toluwanimi Akinleye Emmanuel , Bolutife Popoola Olubukola , Oluwadamilola Osasona Gideon , Olaitan Olayinka Titilola , Oluwadamilola George Adefunke , Ahmed Muhammad Iluoreh , Isaac Komolafe , Adekunle Adeniji Johnson , Jelle Matthijnssens , Olubusuyi Adewumi Moses
Published: December 2023

Using a metagenomic sequencing approach on stool samples from children with Acute Flaccid Paralysis (AFP), we describe the genetic diversity of Sapoviruses (SaVs) in children in Nigeria. We identified six near-complete genome sequences and two partial genome sequences. Multiple SaV genogroups and genotypes were detected, including GII (GII.4 and GII.8), GIV (GIV.1) and GI (GI.2 and GI.7). Sequence identity and phylogenetic analysis showed that the Nigerian SaVs were related to previously documented gastroenteritis outbreaks associated strains from China and Japan. Minor variations in the functional motifs of the nonstructural proteins NS3 and NS5 were confirmed in the Nigerian strains. To adequately understand the effect of such amino acid changes, a better understanding of the biological function of these proteins is vital. The identification of distinct SaVs reinforces the need for robust surveillance in acute gastroenteritis (AGE) and non-AGE cohorts to better understand SaVs genotype diversity, evolution, and its role in disease burden in Nigeria.
Persistence of an infectious form of SARS-CoV-2 post protease inhibitor treatment of permissive cells in vitro
Authors: Nair Manoj S. , Luck Maria I. , Huang Yaoxing , Sabo Yosef , Ho David D.
Published: December 2023

Reports have described SARS-CoV-2 rebound in COVID-19 patients treated with nirmatrelvir, a 3CL protease inhibitor. The cause remains a mystery, although drug resistance, re-infection, and lack of adequate immune responses have been excluded. We now present virologic findings that provide a clue to the cause of viral rebound, which occurs in ∼20% of the treated cases. The persistence of an intermediary form of infectious SARS-CoV-2 was experimentally documented in vitro after treatment with nirmatrelvir or another 3CL protease inhibitor, but not with a polymerase inhibitor, remdesivir. This infectious intermediate decayed slowly with a half-life of ∼1 day, suggesting that its persistence could outlive the treatment course to re-ignited SARS-CoV-2 infection as the drug is eliminated. Additional studies are needed to define the nature of this viral intermediate, but our findings point to a particular direction for future investigation and offer a specific treatment recommendation that should be tested clinically.
Profiling cellular heterogeneity and fructose transporter expression in the rat nephron by integrating single-cell and microdissected tubule segment transcriptomes
Authors: Zhang Ronghao , Jadhav Darshan Aatmaram , Kramer Benjamin , Gonzalez-Vicente Agustin ,   the Kidney Precision Medicine Project
Published: December 2023

Single-cell RNA sequencing (scRNAseq) is a crucial tool in kidney research. These technologies cluster cells according to transcriptome similarity, irrespective of the anatomical location and ordering within the nephron. Thus, a cluster transcriptome may obscure heterogeneity of the cell population within a nephron segment. Elevated dietary fructose leads to salt-sensitive hypertension, in part by fructose reabsorption in the proximal tubule (PT). However, organization of the four known fructose transporters in apical PTs (SGLT4, SGLT5, GLUT5 and NaGLT1) remains poorly understood. We hypothesized that cells within each subsegment of the proximal tubule exhibit complex, heterogenous fructose transporter expression patterns. To test this hypothesis we analyzed rat and kidney transcriptomes and proteomes from publicly available scRNAseq and tubule microdissection databases. We found that microdissected PT-S1 segments consist of 81±12% cells with scRNAseq-derived transcriptional characteristics of S1, whereas PT-S2 express a mixture of 18±9% S1, 58±8% S2, and 19±5% S3 transcripts, and PT-S3 consists of 75±9% S3 transcripts. The expression of all four fructose transporters was detectable in all three PT segments, but key fructose transporters SGLT5 and GLUT5 progressively increased from S1 to S3, and both were significantly upregulated in S3 vs. S1/S2 (Slc5a10: 1.9 log2FC, p<1×10-299; Scl2a5: 1.4 log2FC, p<4×10-105). A similar distribution was found in human kidneys. These data suggest that S3 is the primary site of fructose reabsorption in both humans and rats. Finally, because of the multiple scRNAseq transcriptional phenotypes found in each segment our findings also imply that anatomic labels applied to scRNAseq clusters may be misleading.
Computational detection of antigen specific B cell receptors following immunization
Authors: Abbate Maria Francesca , Dupic Thomas , Vigne Emmanuelle , Shahsavarian Melody A. , Walczak Aleksandra M. , Mora Thierry
Published: December 2023

B cell receptors (BCRs) play a crucial role in recognizing and fighting foreign antigens. High-throughput sequencing enables in-depth sampling of the BCRs repertoire after immunization. However, only a minor fraction of BCRs actively participate in any given infection. To what extent can we accurately identify antigen-specific sequences directly from BCRs repertoires? We present a computational method grounded on sequence similarity, aimed at identifying statistically significant responsive BCRs. This method leverages well-known characteristics of affinity maturation and expected diversity. We validate its effectiveness using longitudinally sampled human immune repertoire data following influenza vaccination and Sars-CoV-2 infections. We show that different lineages converge to the same responding CDR3, demonstrating convergent selection within an individual. The outcomes of this method hold promise for application in vaccine development, personalized medicine, and antibody-derived therapeutics.
AlphaFold2 structures template ligand discovery
Authors: Lyu Jiankun , Kapolka Nicholas , Gumpper Ryan , Alon Assaf , Wang Liang , Jain Manish K. , Barros-Álvarez Ximena , Sakamoto Kensuke , Kim Yoojoong , DiBerto Jeffrey , Kim Kuglae , Tummino Tia A. , Huang Sijie , Irwin John J. , Tarkhanova Olga O. , Moroz Yurii , Skiniotis Georgios , Kruse Andrew C. , Shoichet Brian K. , Roth Bryan L.
Published: December 2023

AlphaFold2 (AF2) and RosettaFold have greatly expanded the number of structures available for structure-based ligand discovery, even though retrospective studies have cast doubt on their direct usefulness for that goal. Here, we tested unrefined AF2 modelsprospectively, comparing experimental hit-rates and affinities from large library docking against AF2 models vs the same screens targeting experimental structures of the same receptors. Inretrospectivedocking screens against the σ2and the 5-HT2A receptors, the AF2 structures struggled to recapitulate ligands that we had previously found docking against the receptors’ experimental structures, consistent with published results.Prospectivelarge library docking against the AF2 models, however, yielded similar hit rates for both receptors versus docking against experimentally-derived structures; hundreds of molecules were prioritized and tested against each model and each structure of each receptor. The success of the AF2 models was achieved despite differences in orthosteric pocket residue conformations for both targets versus the experimental structures. Intriguingly, against the 5-HT2A receptor the most potent, subtype-selective agonists were discovered via docking against the AF2 model, not the experimental structure. To understand this from a molecular perspective, a cryoEM structure was determined for one of the more potent and selective ligands to emerge from docking against the AF2 model of the 5-HT2A receptor. Our findings suggest that AF2 models may sample conformations that are relevant for ligand discovery, much extending the domain of applicability of structure-based ligand discovery.
Engineered Skin Microbiome Reduces Mosquito Attraction to Mice
Authors: Liu Feng , Coutinho-Abreu Iliano V. , Raban Robyn , Nguyen Tam Thuy Dan , Dimas Alejandra R. , Merriman Joseph A. , Akbari Omar S.
Published: December 2023

The skin microbiome plays a pivotal role in the production of attractive cues detected by mosquitoes. Here we leveraged recent advances in genetic engineering to significantly reduce the production of L-(+)-lactic acid as a strategy to reduce mosquito attraction to the highly prominent skin commensalsStaphylococcus epidermidisandCorynebacterium amycolatum. Engraftment of these engineered bacteria onto the skin of mice reduced mosquito attraction and feeding for up to 11 uninterrupted days, which is considerably longer than the several hours of protection conferred by the leading chemical repellent DEET. Taken together, our findings demonstrate engineering the skin microbiome to reduce attractive volatiles represents an innovative untapped strategy to reduce vector attraction, preventing bites, and pathogen transmission setting the stage for new classes of long-lasting microbiome-based repellent products.

One-Sentence Summary

Modified microbes make skin less attractive to mosquitoes
STOPGAP, an open-source package for template matching, subtomogram alignment, and classification
Authors: Wan William , Khavnekar Sagar , Wagner Jonathan
Published: December 2023

Cryo-electron tomography (cryo-ET) enables molecular-resolution 3D imaging of complex biological specimens such as viral particles, cellular sections, and in some cases, whole cells. This enables the structural characterization of molecules in their near-native environments, without the need for purification or separation, thereby preserving biological information such as conformational states and spatial relationships between different molecular species. Subtomogram averaging is an image processing workflow that allows users to leverage cryo-ET data to identify and localize target molecules, determine high-resolution structures of repeating molecular species, and classifying different conformational states. Here we describe STOPGAP, an open-source package for subtomogram averaging designed to provide users with fine control over each of these steps. In providing detailed descriptions of the image processing algorithms that STOPGAP uses, we intend for this manuscript to also serve as a technical resource to users as well as further community-driven software development.
CD4+T cells are homeostatic regulators duringMtbreinfection
Authors: Bromley Joshua D. , Ganchua Sharie Keanne C. , Nyquist Sarah K. , Maiello Pauline , Chao Michael , Borish H. Jacob , Rodgers Mark , Tomko Jaime , Kracinovsky Kara , Mugahid Douaa , Nguyen Son , Wang Dennis , Rosenberg Jacob M. , Klein Edwin C. , Gideon Hannah P. , Floyd-O’Sullivan Roisin , Berger Bonnie , Scanga Charles A , Lin Philana Ling , Fortune Sarah M. , Shalek Alex K. , Flynn JoAnne L.
Published: December 2023

Immunological priming – either in the context of prior infection or vaccination – elicits protective responses against subsequentMycobacterium tuberculosis(Mtb) infection. However, the changes that occur in the lung cellular milieu post-primaryMtbinfection and their contributions to protection upon reinfection remain poorly understood. Here, using clinical and microbiological endpoints in a non-human primate reinfection model, we demonstrate that priorMtbinfection elicits a long-lasting protective response against subsequentMtbexposure and that the depletion of CD4+T cells prior toMtbrechallenge significantly abrogates this protection. Leveraging microbiologic, PET-CT, flow cytometric, and single-cell RNA-seq data from primary infection, reinfection, and reinfection-CD4+T cell depleted granulomas, we identify differential cellular and microbial features of control. The data collectively demonstrate that the presence of CD4+T cells in the setting of reinfection results in a reduced inflammatory lung milieu characterized by reprogrammed CD8+T cell activity, reduced neutrophilia, and blunted type-1 immune signaling among myeloid cells, mitigatingMtbdisease severity. These results open avenues for developing vaccines and therapeutics that not only target CD4+and CD8+T cells, but also modulate innate immune cells to limitMtbdisease.
Leveraging ancestral sequence reconstruction for protein representation learning
Authors: Matthews D. S. , Spence M. A. , Mater A. C. , Nichols J. , Pulsford S. B. , Sandhu M. , Kaczmarski J. A. , Miton C. M. , Tokuriki N. , Jackson C. J.
Published: December 2023

Protein language models (PLMs) convert amino acid sequences into the numerical representations required to train machine learning (ML) models. Many PLMs are large (>600 M parameters) and trained on a broad span of protein sequence space. However, these models have limitations in terms of predictive accuracy and computational cost. Here, we use multiplexed Ancestral Sequence Reconstruction (mASR) to generate small but focused functional protein sequence datasets for PLM training. Compared to large PLMs, this local ancestral sequence embedding (LASE) produces representations 10-fold faster and with higher predictive accuracy. We show that due to the evolutionary nature of the ASR data, LASE produces smoother fitness landscapes in which protein variants that are closer in fitness value become numerically closer in representation space. This work contributes to the implementation of ML-based protein design in real-world settings, where data is sparse and computational resources are limited.
Climate change decreases the likelihood of tropical forest community persistence with a strong mediation of plant-plant network structures
Authors: Luo Zijing , Liu Hanlun , Li Yuanzhi , Wang Weimin , Mayfield Margaret M. , Chu Chengjin
Published: December 2023

Climate change is known to negatively impact tropical forests; yet how climate change impacts tree community persistence at local scales remains less clear. Using data from a long-term tropical forest census plot over 25 years, we constructed plant- plant interaction networks based on tree growth. We then quantified community persistence as feasibility domain of constituent species using recently developed frameworks of structural stability. We found a decrease in structural stability under warming and precipitation changes over time as evidenced by both direct environmental effects and indirect effects via network structure; and indirect effects were stronger than direct effects. Among these structures, facilitation:competition degree ratio and competitive transitivity were most positively related with structural stability. Our study highlights how the lens of plant-plant interaction networks can identify novel details about risk to tropical forest diversity under climate change at local scales. Insights from this work will be helpful for aligning forest management activities with areas under the greatest risk of species loss.
Development and validation of allele specificRLKgene markers for banana bunchy top disease (BBTD) resistance in banana
Authors: Caro Reina Esther S. , Manohar Anand Noel C. , Gardoce Roanne R. , Dela Cueva Fe M. , Gueco Lavernee S. , Manuel Ma. Carmina C. , Lantican Darlon V.
Published: December 2023

As global demand for bananas rises, the threat of banana bunchy top disease (BBTD), caused bybanana bunchy top virus(BBTV), poses a significant constraint to sustainable banana production. To circumvent this, it is critical to fast-track the development of BBTV-resistant banana cultivars. In a dataset of differentially expressed genes between BBTV-resistant and susceptible bananas, sixRLKgenes involved in plant defense against pathogens were exclusively upregulated in the BBTV-resistant wildMusa balbisianacompared to the BBTV-susceptibleMusa acuminatacv. ’Lakatan’. Here, two genic variants ofRLKs, single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSR), were identified in 10 banana accessions representing major genomic groupings. Nine gene-specific markers were developed using three marker systems: SSR, allele-specific PCR, and tetra primer amplification refractory mutation system PCR markers. Six of these were polymorphic and successfully discriminated 117Musagenotypes at the NPGRL-IPBex situgermplasm, with an average polymorphism information content of 0.36 for SNP markers and 0.49 for SSR marker, both of which are moderately informative. These markers facilitated the construction of a dendrogram using the Unweighted Neighbor-Joining (UNJ) method with 1000 bootstrap iterations, identifying four major clades:M. acuminataspp. and otherMusaspp. (I), wildM. balbisiana(BBw) and other accessions with high-proportion of B-genome (II & III), hybrid bananas (triploids and tetraploids) (IV), which revealed the genetic diversity and relationships amongMusaaccessions. Ultimately, this genomic resource will aid in positioning the Philippines as a key player in banana disease resistance breeding towards a food-secure banana industry.
Metabolic scaling in small life forms
Authors: Ritchie Mark E. , Kempes Christopher P.
Published: December 2023

Metabolic scaling is one of the most important patterns in biology. Theory explaining the 3/4-power size-scaling of biological metabolic rate does not predict the non-linear scaling observed for smaller life forms. Here we present a new model for cells < 10−8m3that maximizes power from the reaction-displacement dynamics of enzyme-catalyzed reactions. Maximum metabolic rate is achieved through an allocation of cell volume to optimize a ratio of reaction velocity to molecular movement. Small cells < 10−17m3generate power under diffusion by diluting enzyme concentration as cell volume increases. Larger cells require bulk flow of cytoplasm generated by molecular motors. These outcomes predict curves with literature-reported parameters that match the observed scaling of metabolic rates for unicells, and predicts the volume at which Prokaryotes transition to Eukaryotes. We thus reveal multiple size-dependent physical constraints for microbes in a model that extends prior work to provide a parsimonious hypothesis for how metabolism scales across small life.
FGF12 Modulates Cardiomyocyte Hypertrophy by Inhibiting GATA4-ERK1/2 Phosphorylation Through Altered Intracellular Localization
Authors: Zhang Taojun , Yin Kunlun , Yang Fangfang , Li Tianjiao , Wang Shuiyun , Zhou Zhou
Published: December 2023

Background

Hypertrophic cardiomyopathy (HCM) is a heritable pathological condition resulting from mutations in sarcomere-related proteins, leading to severe structural abnormalities without effective treatment options. Although reducedfibroblast growth factor 12(FGF12) expression is observed in HCM patients, its functional role remains unclear.

Methods

Employing immunoprecipitation (IP)-mass spectrometry (MS) and CUT&Tag sequencing, we investigated FGF12-interacting proteins in myocardial samples from healthy volunteers and HCM patients. CRISPR-Cas9 was utilized to explore the function and interaction partners of FGF12 in cardiomyocytes induced from human pluripotent stem cells (hiPSCs-CMs), other cell lines, and mouse models (MYH7R403Qand MYBPC3c.790G>A, transverse aortic constriction (TAC)). During hypertrophy, FGF12 localizes intranuclearly, prompting investigations into its binding to gene promoter regions through CUT&Tag sequencing and dual-luciferase experiments using myocardial tissues from patients. The beating frequency of hiPS-CMs was assessed using the CardioExcyte 96 real-time label-free cardiomyocyte functional analysis system.

Results

FGF12 was found to associate with proteins involved in energy metabolism, predominantly localizing to the perinuclear space under physiological conditions but shifting into the nucleus of hypertrophic cardiomyocytes. Co-IP-MS revealed significant interactions between FGF12 and metabolism-associated proteins, particularly GATA binding protein 4 (GATA4) and mitogen-activated protein kinase 1/3 (MAPK1/3) in the perinuclear space. In a hypertrophic state, FGF12 bound to the GATA4 promoter region, increasing its expression upon nuclear translocation. Bothin vitroandin vivomodels demonstrated that FGF12 interaction with GATA4 inhibited GATA4 and MAPK1/3 phosphorylation, inducing the expression of hypertrophy-associated genes. Overexpression of FGF12-NLS-del (nuclear localization signal deletion) resulted in decreased GATA4 phosphorylation, suggesting inhibition in the perinuclear region.

Conclusions

This study elucidates a pathological mechanism of HCM involving FGF12, where its nuclear localization enhances phosphorylation, GATA4 expression, and activation of the ERK1/2-pGATA4 pathway genes associated with hypertrophy. Beyond advancing our understanding of HCM, these findings propose FGF12 as a potential therapeutic target for HCM, warranting further exploration to potentially alleviate this condition affecting millions of individuals.
Association of poultry vaccination with the interspecies transmission and molecular evolution of H5 subtype avian influenza virus
Authors: Li Bingying , Raghwani Jayna , Hill Sarah C. , François Sarah , Lefrancq Noémie , Liang Yilin , Wang Zengmiao , Dong Lu , Lemey Phillipe , Pybus Oliver G. , Tian Huaiyu
Published: December 2023

The effectiveness of vaccinating poultry in preventing the transmission of highly pathogenic avian influenza viruses (AIVs) has been questioned for years and its impact on wild birds is uncertain1–3. Here we reconstruct movements of H5 subtype AIV lineages among vaccinated poultry, unvaccinated poultry, and wild birds, worldwide from 1996 to 2023. We find that lineage transitions among host types are lagged and that movements from wild birds to unvaccinated poultry were more frequent than those from wild birds to vaccinated poultry. However, we also find that the HA gene of the AIV lineage that circulated predominately among Chinese poultry with high vaccination coverage underwent faster evolution and greater nonsynonymous divergence than other lineages. Further, this Chinese poultry lineage contained more codons inferred to be under positive selection, including at known antigenic sites, and its rates of nonsynonymous divergence and adaptative fixation increased after mass poultry vaccination began. Our results indicate that the epidemiological, ecological and evolutionary consequences of widespread AIV vaccination in poultry may be linked in complex ways, and that much work is needed to better understand how such interventions may affect AIV transmission to, within and from wild birds.
Concerted SUMO-targeted ubiquitin ligase activities of TOPORS and RNF4 are essential for stress management and cell proliferation
Authors: Liu Julio C.Y. , Ackermann Leena , Hoffmann Saskia , Gál Zita , Hendriks Ivo A. , Jain Charu , Morlot Louise , Tatham Michael H. , McLelland Gian-Luca , Hay Ronald T. , Nielsen Michael Lund , Brummelkamp Thijn , Haahr Peter , Mailand Niels
Published: December 2023

Protein SUMOylation provides a principal driving force for cellular stress responses including DNA-protein crosslink (DPC) repair and arsenic-induced PML body degradation. In genome-scale screens, we identified the human E3 ligase TOPORS as a key effector of SUMO-dependent DPC resolution. We demonstrate that TOPORS promotes DPC repair by functioning as a SUMO-targeted ubiquitin ligase (STUbL) for DPCs, combining ubiquitin ligase activity through its RING domain with poly-SUMO chain binding via a cluster of SUMO-interacting motifs, analogous to the STUbL RNF4. Surprisingly, the STUbL activities of TOPORS and RNF4 are both required for SUMO-dependent DPC repair, PML degradation and other stress responses, making overlapping and distinct contributions to ubiquitin chain formation on SUMOylated targets to enable p97/VCP unfoldase recruitment. Combined loss of TOPORS and RNF4 is synthetic lethal even in unstressed cells, leading to defective clearance of SUMOylated proteins from chromatin accompanied by cell cycle arrest and apoptosis. Together, our findings establish TOPORS as a novel STUbL whose concerted action with RNF4 defines a general mechanistic principle in crucial cellular processes governed by direct SUMO-ubiquitin crosstalk.

Highlights

The RING E3 ligase TOPORS is required for SUMO-dependent DPC repair

TOPORS is a novel SUMO-targeted ubiquitin ligase (STUbL)

TOPORS promotes multiple STUbL-driven processes in conjunction with RNF4

Combined TOPORS and RNF4 loss is synthetic lethal in human cells
Association between electrophysiological phenotypes and Kv2.1 potassium channel expression explained by geometrical analysis
Authors: Reyes-Garibaldi Julio César , Herrera-Valdez Marco Arieli
Published: December 2023

Excitable cells exhibit different electrophysiological profiles while responding to current stimulation in current-clamp experiments. In theory, the differences could be explained by changes in the expression of proteins mediating transmembrane ion transport. Experimental verification by performing systematic, controlled variations in the expression of proteins of the same type (e.g. voltage-dependent, noninactivating Kv2.1 channels) is difficult to achieve in the absence of other changes. However, biophysical models enable this possibility and allows us to assess and characterise the electrophysiological phenotypes associated to different levels of expression of non-inactivating voltage-dependent K-channels of type Kv2.1. To do so, we use a 2-dimensional biophysical model of neuronal membrane potential and study the phase plane geometry and bifurcation structures associated with different levels of Kv2.1 expression with the input current as bifurcation parameter. We find that increasing the expression of Kv2.1 channels reduces the size of the region of the phase plane from which action potentials can be initiated. The changes in expression can also be related to different transitions between rest and repetitive firing in current clamp experiments. For instance, increasing the number of Kv2.1 channels shifts the rheobase current to higher levels, but also expands the dynamic range in which excitatory external current produces repetitive spiking. Our analysis shows that changes in the responses to increasing input currents can be associated to different sequences of fixed point bifurcations. In general, the fixed points are attracting, then repulsive, and later become attracting again as the input current increases, but the bifurcation sequences also include changes in fixed point type, and change qualitatively with the expression of Kv2.1 channels. In the non-repetitive spiking regime with low current stimulation, low expression of Kv2.1 channels yields bifurcation sequences that include transitions between 3 and 1 fixed points, and repetitive firing starts with delays that decrease with increasing current (aggregation). For higher expression of Kv2.1 channels there is only one fixed point that changes in type and attractivity as the input current increases, convergence to rest tends to be oscillatory (resonance), and repetitive spiking starts without noticeable delays. Our models explain how the same neuron is theoretically be capable of including both aggregating and resonant modes of integration for synaptic input, as shown in current clamp experiments.
Increased1H-NMR metabolomics-based health score associates with declined cognitive performance and functional independence in older adults at risk of cardiovascular disease
Authors: Zonneveld Michelle H. , Kuhaili Nour Al , Mooijaart Simon P. , Slagboom P. Eline , Jukema J. Wouter , Noordam Raymond , Trompet Stella
Published: December 2023

Background

The 1-HMR metabolomics-based MetaboHealth score, comprised of 14 serum metabolic markers, associates with disease-specific mortality, but it is unclear whether the score also reflects cognitive changes and functional impairment.

Objectives

Assess the associations between the MetaboHealth score with cognitive and daily functioning, and cognitive and functional decline in older people at increased cardiovascular risk.

Methods

5292 older people free of dementia at baseline with mean age 75.3 years (standard deviation=3.4) from the Prospective Study of Pravastatin in the Elderly (PROSPER). MetaboHealth score was measured at baseline, and cognitive function and functional independence were measured at baseline and every 3 months during up to 2.5-years follow-up. Cognitive function was assessed using the Stroop test (selective attention), the Letter Digit Coding test (LDCT) (processing speed), and the two versions of the Picture Learning test (delayed and immediate; memory). Two tests of functional independence were used: Barthel Index (BI) and instrumental activities at daily living (IADL).

Results

A higher MetaboHealth score was associated with worse cognitive function (in all domains) and with worse functional independence. For example, after full adjustments, a 1-SD higher MetaboHealth score was associated with 9.02 (95%CI 7.29, 10.75) seconds slower performance on the Stroop test and 2.79 (-3.26,-2.21) less digits coded on the LDCT. During follow-up, 1-SD higher MetaboHealth score was associated with an additional decline of 0.53 (0.23,0.83) seconds on the Stroop test and -0.08 (-0.11,-0.06) points on the IADL.

Conclusion

Metabolic disturbance, as reflected by an increased metabolomics-based health score, may mark future cognitive and functional decline.