bluuebunny/crossref_metadata_2025 huggingface dataset:
Accounting for heterogeneity due to environmental sources in meta-analysis of genome-wide association studies
Authors: Wang Siru , Ojewunmi Oyesola O. , Kamiza Abram , Ramsay Michele , Morris Andrew P , Chikowore Tinashe , Fatumo Segun , Asimit Jennifer L
Published: May 2024

Meta-analysis of genome-wide association studies (GWAS) across diverse populations offers power gains to identify loci associated with complex traits and diseases. Often heterogeneity in effect sizes across populations will be correlated with genetic ancestry and environmental exposures (e.g. lifestyle factors). We present an environment-adjusted meta-regression model (env-MR-MEGA) to detect genetic associations by adjusting for and quantifying environmental and ancestral heterogeneity between populations. In simulations, env-MR-MEGA had similar or greater association power than MR-MEGA, with notable gains when the environmental factor had a greater correlation with the trait than ancestry. In our analysis of low-density lipoprotein cholesterol in ∼19,000 individuals across twelve sex-stratified GWAS from Africa, adjusting for sex, BMI, and urban status, we identified additional heterogeneity beyond ancestral effects for nine variants. Env-MR-MEGA provides an approach to account for environmental effects using summary-level data, making it a useful tool for meta-analyses without the need to share individual-level data.
Disruptors of sestrin-MAPK interactions rejuvenate T cells and expand TCR specificity
Authors: Lanna Alessio , D’Ambra Clara , Rinaldi Federica , Chocarro Luisa , Delpero Manuel , Capitani Melania , Karin Michael
Published: May 2024

Whereas treatments that reactivate exhausted T cells are available, strategies to rejuvenate terminally differentiated senescent lymphocytes are yet to be developed. Senescent T cells, with short telomeres and inactive telomerase, are different from exhausted cells, and may form due to defective telomere transfer reactions upon contact with antigen presenting cells (APCs). Senescent T cells are characterized by presence of sestrin-MAPK kinase activation complexes (sMACs), large immune-inhibitory protein assemblies of sestrins bound to a stress/energy sensing kinase (AMPK) and three functional effector kinases (ERK, JNK and p38 MAPKs). Here we described first in class Disruptors of the Sestrin-MAPK immune-inhibitory Complex (DOS), which target sMAC to ubiquitin-dependent proteasomal degradation, resulting in long-term sestrin transcriptional inhibition, increased T cell fitness, and generation of long-lived stem like memory features. Strikingly, the DOS generated stem T cells presentde novoantigen-specific T-cell receptor DNA rearrangements that precede their future expansion. Although largely senescent at the point of treatment, the DOS regenerated T cells, with stem features and new TCRs, initiated immune-protective rejuvenation-dependent responses to new challenges, with or without vaccination. Therefore, it is possible to generate new T cell clones from formerly senescent cells and expand immune specificity.

Highlights

DOS are the first sestrin-MAPK binding disruptors

DOS rejuvenate T cells (DOS-juvenation)

DOS-juvenated T cells protect old mice from lethal infections, with or without vaccination

DOS-juvenated T cells exist as stem-like cells that undergo antigen-specific TCR revisions
SlimVar: rapidin vivosingle-molecule tracking of chromatin regulators in plants
Authors: Payne-Dwyer Alex L. , Jang Geng-Jen , Dean Caroline , Leake Mark C.
Published: May 2024

Epigenetic regulation maintains gene expression patterns over many rounds of cell division in higher organisms. However, visualization of factors regulating epigenetic switchesin vivois limited by the challenge of imaging cells deep in living tissue, with molecular sensitivity and rapid sampling. We report an easy-to-implement method called Variable-angle Slimfield microscopy (SlimVar), which by simple modification of an inverted optical microscope, enables single-molecule tracking of fluorescent reporters inArabidopsis thaliana. Using SlimVar, we imaged stepwise photobleaching of chromatin-protein assemblies in individual nuclei, 30 µm deep in root tips through multiple cell layers. We find that two homologous proteins key to the epigenetic switch atFLOWERING LOCUS C(FLC) —cold-induced VERNALIZATION INSENSITIVE3 (VIN3) and constitutively expressed VERNALIZATION 5 (VRN5)—exhibit dynamic nuclear assemblies duringFLCsilencing. Upon cold exposure, these assemblies increase in stoichiometry by up to 100% to a median of ∼20 molecules. Larger VRN5 assemblies preferentially co-localize with anFLC lacOtransgenic reporter during prolonged cold, persisting after return to warm conditions. Our findings support a hybrid model of epigenetic memory in which nucleation of histone trimethylation is assisted by dynamic protein assemblies over extended durations. SlimVar therefore has potential to offer molecular insights into proteins expressed at physiological levels in a range of tissues.
Association of Body Index with Fecal Microbiome in Children Cohorts with Ethnic-Geographic Factor Interaction: Accurately Using a Bayesian Zero-inflated Negative Binomial Regression Model
Authors: Huang Jian , Lu Yanzhuan , Tian Fengwei , Ni Yongqing
Published: May 2024

The exponential growth of High-Throughput Sequencing (HTS) data on the microbial communities presents researchers with an unparalleled opportunity to delve deeper into the association of microorganisms with host phenotype. However, this growth also poses a challenge, as microbial data is complex, sparse, discrete, and prone to zero-inflation. Moreover, current methods for integrating microbiome data and other covariates are severely lacking. Hence, we propose a Bayesian zero-inflated negative binomial (ZINB) regression model that is capable of identifying differentially abundant taxa with distinct phenotypes and quantifying the effects of covariates on these taxa. Our model exhibits excellent performance when tested on simulated data. Upon successfully applying our model to a real multi-ethnic cohort study, we discovered that the prevailing understanding of microbial count data from previous research was overly dogmatic, because only a subset of taxa demonstrated zero inflation in real data. Moreover, we have discovered that dispersion parameters significantly influence the accuracy of model results, and increasing sample size can alleviate this issue. In all, we have presented an innovative integrative Bayesian regression model and a comprehensive pipeline for conducting a multi-ethnic cohort study of children, which facilitates bacterial differential abundance analysis and quantification of microbiome-covariate effects. This approach can be applied to general microbiome studies.

IMPORTANCE

Microbiome are closely associated with physical indicators of the body, such as height, weight, age and BMI, which can be used as measures of human health. How to accurately identify which taxa in the microbiome are closely related to indicators of physical development is valuable as microbial markers of local child growth. Complex biological systems can be effectively modeled with ZINB model which is a Bayesian Generalized Linear Model. However, the potential of the ZINB model in the microbiome field has not yet been fully utilized in practice. Microbial count data are more complex than other scenarios, and our model captures this complexity. Our study is the first to discuss the effects of zero inflation and the degree of overdispersion in microbiome data on the results of model solutions. Finally, our work successfully applied it to a real multi-ethnic cohort study.
Interactive effects of temperature and salinity on metabolism and activity of the copepodTigriopus californicus
Authors: Terry Caroline E. , Liebzeit Josie A. , Purvis Ella M. , Dowd W. Wesley
Published: May 2024

In natural environments two or more abiotic parameters often vary simultaneously, and interactions between covarying parameters frequently result in unpredictable, non-additive biological responses. To better understand the mechanisms and consequences of interactions between multiple stressors it is important to study their effects on both survival and performance. The splashpool copepodTigriopus californicustolerates extremely variable abiotic conditions and exhibits a non-additive, antagonistic interaction resulting in higher survival when simultaneously exposed to high salinity and acute heat stress. Here, we investigatedT. californicus’response in activity and oxygen consumption under simultaneous manipulation of salinity and temperature to identify if this interaction also arises in these sublethal measures of performance. Oxygen consumption and activity rates decreased with increasing assay salinity. Oxygen consumption also sharply increased in response to acute transfer to lower salinities, an effect that was absent upon transfer to higher salinities. Elevated temperature led to reduced rates of activity overall, resulting in no discernible impact of increased temperature on routine metabolic rates. This suggests that swimming activity has a non-negligible effect on copepod’s metabolic rates and must be accounted for in metabolic studies. Temperature also interacted with assay salinity to affect activity and with acclimation salinity to affect routine metabolic rates upon acute salinity transfer, implying that the sublethal impacts of these co-varying factors are also not predictable from experiments that study them in isolation.

Summary Statement

Temperature and salinity interact to affect metabolic rate in the copepodTigriopus californicus, but the stressors’ individual effects and their interaction are complicated by concurrent changes in activity.
T-follicular helper cells are epigenetically poised to transdifferentiate into T-regulatory type-1 cells
Authors: Garnica Josep , Sole Patricia , Yamanouchi Jun , Moro Joel , Mondal Debajyoti , Fandos Cesar , Serra Pau , Santamaria Pere
Published: May 2024

Chronic antigenic stimulation can trigger the formation of IL-10-producing T-regulatory type 1 (TR1) cellsin vivo. We have recently shown that T follicular helper (TFH) cells are precursors of TR1 cells and that the TFH-to-TR1 cell transdifferentiation process is characterized by the progressive loss and acquisition of opposing transcription factor gene expression programs that evolve through at least one transitional cell stage. Here, we use a broad range of bulk and single-cell transcriptional and epigenetic tools to investigate the epigenetic underpinnings of this process. At the single cell level, the TFH-to-TR1 cell transition is accompanied by both, downregulation of TFH cell-specific gene expression due to loss of chromatin accessibility, and upregulation of TR1 cell-specific genes linked to chromatin regions that remain accessible throughout the transdifferentiation process, with minimal generation of new open chromatin regions. By interrogating the epigenetic status of accessible TR1 genes on purified TFH and conventional T cells, we find that most of these genes, includingIl10, are already poised for expression at the TFH cell stage. Whereas these genes are closed and hypermethylated in Tconv cells, they are accessible, hypomethylated and enriched for H3K27ac-marked and hypomethylated active enhancers in TFH cells. These enhancers are enriched for binding sites for the TFH and TR1-associated transcription factors TOX-2, IRF4 and c-MAF. Together, these data suggest that the TR1 gene expression program is genetically imprinted at the TFH cell stage.
Fabrication of mRNA encapsulated Lipid nanoparticles usingState-of-the-artSMART-MaGIC Technology and transfectionin vitro
Authors: Heshmati Niloofar , Chakka Jaidev , Zhang Yu , Maniruzzaman Mohammed
Published: May 2024

The messenger ribose nucleic acid (mRNA)in lieuof Corona virus of 2019 (COVID-19) vaccines were effectively delivered through Lipid nanoparticles (LNP) which were proved effective carriers for clinical applications. In the present work, mRNA (erythropoietin (EPO)) encapsulated LNPs were prepared using a next generation state-of-the-art patented Sprayed Multi Absorbed-droplet Reposing Technology (SMART) coupled with Multi-channeled and Guided Inner-Controlling printheads (MaGIC) technologies. The LNP-mRNA were synthesized at different N/P ratios and the particles were characterized for particle size & zeta potential (Zetasizer), encapsulation or complexation (gel retardation assay) and transfection (Fluorescence microscopy) in MG63 sarcoma cellsin vitro. The results showed a narrow distribution of mRNA-lipid particles of 200 nm when fabricated with SMART alone and then the size was reduced to approximately 50 nm with the combination of SMART-MaGIC technologies. The gel retardation assay showed that the N/P>1 showed strong encapsulation of mRNA with lipid. Thein vitroresults showed the toxicity profile of the lipids where N/P ratio of 5 is the optimized with >50% cell viability. The functional LNP-mRNA were prepared and analyzed with SMART-MaGIC technologies which could be a potential new fabrication method of mRNA loaded LNPs.

Highlights

The particle size was reduced to around 50 nm with implementation of SMART-MaGIC.

The loading efficiency is 100%.

The functionality of the mRNA is unaffected during the preparation process.

The transfection facilitated transient expression of the proteinin vitro.

The EPO mRNA is more effective than EPO protein to reduce chemo-toxic effectsin vitro.
Sensitivity to visual features in inattentional blindness
Authors: Nartker Makaela , Firestone Chaz , Egeth Howard , Phillips Ian
Published: May 2024

The relation between attention, perception and awareness is among the most fundamental problems in the science of the mind. One of the most striking and well-known phenomena bearing on this question isinattentional blindness(IB; Neisser & Becklen, 1975; Mack & Rock, 1998; Most et al., 2001, 2005). In IB, naïve observers fail to report clearly visible stimuli when their attention is otherwise engaged—famously even missing a gorilla parading before their eyes (Simons & Chabris, 1999). This phenomenon and the research programs it has motivated carry tremendous theoretical significance, both as crucial evidence that awareness requires attention (Cohen et al., 2012; Prinz, 2012; Noah & Mangun, 2020) and as a key tool in seeking the neural correlates of consciousness (Rees et al., 1999; Pitts et al., 2014; Hutchinson, 2019). However, these and other implications critically rest on a notoriously biased measure: asking participants whether they noticed anything unusual (and interpreting negative answers as reflecting a complete lack of perception). Here, in the largest ever set of IB studies, we show that, as a group, inattentionally blind participants can successfully report the location, color and shape of the stimuli they deny noticing. This residual visual sensitivity shows that perceptual information remains accessible in IB. We further show that subjective reports in IB are conservative, by introducing absent trials where no IB stimulus is presented; this approach allows us to show for the first time that observers collectively show a systematic bias to report not noticing in IB—essentially ‘playing it safe’ in reporting their sensitivity. This pair of results is consistent with an alternative hypothesis about IB, namely that inattentionally blind subjects retain some degree of awareness of the stimuli they fail to report. Overall, these data provide the strongest evidence to date of significant residual visual sensitivity in IB. They also challenge the use of inattentional blindness to argue that awareness requires attention.
Sympathetic neuron derived NPY protects from obesity by sustaining the mural progenitors of thermogenic adipocytes
Authors: Zhu Yitao , Yao Lu , Gallo-Ferraz Ana Luisa , Bombassaro Bruna , Simoes Marcela R. , Abe Ichitaro , Chen Jing , Sarker Gitalee , Ciccarelli Alessandro , Lee Carl , Martinez-Sanchez Noelia , Dustin Michael , Anderson Kurt , Zhan Cheng , Horvath Tamas , Velloso Licio A. , Kajimura Shingo , Domingos Ana I.
Published: May 2024

Neuropeptide Y (NPY) is secreted by sympathetic nerves1,2, but its direct impact on thermogenic adipocytes is unknown. Here we uncover the mechanism by which peripheral NPY protects from obesity. Our imaging of cleared murine brown and white adipose tissue (BAT and WAT) established that NPY+sympathetic axons are only a minority that mostly maps to the peri-vasculature; our analysis of single-cell RNA-sequencing datasets identifies mural cells as the main NPY-responsive cells in adipose tissues. We show that NPY sustains mural cells, which are known to be a source of beige cells in both BAT and WAT3–5and that NPY facilitates the differentiation to thermogenic adipocytes. We found that diet-induced-obesity leads to neuropathy of NPY+axons and concomitant depletion of the mural cell pool of beige fat progenitors. This defect is replicated in conditional knockout (cKO) mice with NPY specifically abrogated from sympathetic neurons. These cKO mice have whitened BAT with reduced thermogenic ability and lower energy expenditure even before the onset of obesity; they develop adult-onset obesity on a regular chow diet and are more susceptible to diet induced obesity without increasing food consumption. Our results indicate that, relative to central NPY, peripheral NPY produced by the sympathetic nerves has the opposite effect on body weight homeostasis by sustaining the proliferation of the mural cell progenitors of thermogenic adipocytes.
Generating Synthetic Single Cell Data from Bulk RNA-seq Using a Pretrained Variational Autoencoder
Authors: Cho Hyun Jae , Xie Eric , Zhang Aidong , Bekiranov Stefan
Published: May 2024

Single cell RNA sequencing (scRNA-seq) is a powerful approach which generates genome-wide gene expression profiles at single cell resolution. Among its many applications, it enables determination of the transcriptional states of distinct cell types in complex tissues, thereby allowing the precise cell type and set of genes driving a disease to be identified. However, scRNA-seq remains costly, and there are extremely limited samples generated in even the most extensive human disease studies. In sharp contrast, there is a wealth of publicly available bulk RNA-seq data, in which single cell and cell type information are effectively averaged. To further leverage this wealth of RNA-seq data, methods have been developed to infer the fraction of cell types from bulk RNA-seq data using single cell data to train models. Additionally, generative AI models have been developed to generate more of an existing scRNA-seq dataset. In this study, we develop an innovative framework that takes full advantage of powerful generative AI approaches and existing scRNA-seq data to generate representative scRNA-seq data from bulk RNA-seq. Our bulk to single cell variational autoencoder-based model, termedbulk2sc, is trained to deconvolve pseudo-bulk RNA-seq datasets back into their constituent single-cell transcriptomes by learning the specific distributions and proportions related to each cell type. We assess the performance of bulk2sc by comparing synthetically generated scRNA-seq to actual scRNA-seq data. Application of bulk2sc to large-scale bulk RNA-seq human disease datasets could yield single cell level insights into disease processes and suggest targeted scRNA-seq experiments.
Multivariate Analysis of the Impact of Demographic and Clinical Factors on Cardiovascular Health
Authors: Benfallah Youssef , Guo Wanru , Sarfraz Shoaib , Yang Yanyu
Published: May 2024

Background

This study investigates the influence of demographic and clinical factors on cardiovascular health using a multivariate analysis approach. We analyzed data from one of the largest heart-related disease datasets, merging variables such as age, sex, chest pain type, to determine their association with resting blood pressure, cholesterol, and maximum heart rate.

Methods

Two-means comparison is used to investigate the effect of heart disease with response variables, One-way and two-way MANOVA are used to study the relationship between chest pain type, as well as sex and heart disease on the response variables, respectively. Profile analysis and MANCOVA were also conducted to determine a final model.

Results

Our findings indicate significant effects of heart disease on resting blood pressure, cholesterol and maximum heart rate. Chest pain type also has a significant effect on maximum heart rate achieved, but not blood pressure and cholesterol. There are also notable interactions between sex and heart disease status on all response variables. Finally, we formulized a multivariate regression model with age, sex, chest pain type, heart disease, and the interaction between heart disease and sex as predictors.

Conclusion

These findings can inform physicians on possible treatment strategies in cardiovascular diseases.
Signatures of social pain empathy: general and process-specific brain-wide representations of social exclusion and separation
Authors: Zhang Xiaodong , Qing Peng , Liu Qi , Liu Can , Liu Lei , Gan Xianyang , Fu Kun , Lan Chunmei , Zhou Xinqi , Kendrick Keith M. , Becker Benjamin , Zhao Weihua
Published: May 2024

Empathy can be elicited by physiological pain, as well as in social contexts. Although physiological and different social contexts induce a strong subjective experience of empathy, the general and context-specific neural representations remain elusive. Here, we combine fMRI with multivariate pattern analysis to establish neurofunctional models for pain empathy triggered by social exclusion and separation. Our findings revealed both overlapping and distinct neural representations for social exclusion and separation empathy across cortical and subcortical regions. This study established an evolutionary model that traces the progression from social pain to physiological pain empathy. In conclusion, this study establishes neural decoding models for pain empathy evoked by social exclusion and social separation, revealing their neural foundations and interconnectedness of empathy induced by social and physiological stimuli. These findings deepen our understanding of the neurobiological mechanisms underlying social pain empathy and provide robust neuromarkers to precisely evaluate empathy across physiological and social domains.
Systemic migrations in enucleated cells
Authors: De la Fuente Ildefonso M. , Carrasco-Pujante Jose , Camino-Pontes Borja , Fedetz Maria , Bringas Carlos , Pérez-Samartín Alberto , Pérez-Yarza Gorka , López José I. , Cortes Jesus M , Malaina Iker
Published: May 2024

Directional locomotion is a fundamental characteristic of many cells with great relevance in essential physiological and human pathological processes. For decades, research efforts have focused on studying specific individual processes and their corresponding biomolecular components involved in cellular locomotion movements. However, the notion that migratory displacements are functionally integrated and regulated at the systemic level has never been recognized. Recently, we have shown that locomotion movements correspond to an emergent systemic behavior which depends on a complex integrated self-organized system carefully regulated at a global cellular level. Here, to study the forces driving the locomotion movement of the cell, and to corroborate the thesis on the systemic character of the cellular migratory responses we have carried out an extensive study of locomotion movements with enucleated cells (cytoplasts) belonging toAmoeba proteus. The migratory behavior of both enucleated and non-enucleated cells has been individually studied in four different scenarios: in absence of stimuli, under a galvanotactic field, in chemotactic gradient, and under very complex conditions such as simultaneous galvanotactic and chemotactic stimuli. All these experimental displacement trajectories, obtained on flat two-dimensional surfaces, have been analyzed using advanced non-linear quantitative approaches. Our results show that both non-enucleated amoebas and cytoplasts display the same complex kind of dynamic structure in their migratory trajectories. The locomotion displacements of enucleated cells are regulated by complex self-organized integrative dynamics, modulated at a global-systemic level which seems to depend on the cooperative interaction of most, if not all, molecular components of cells.
CONSTITUTIVE OPENING OF THE Kv7.2 PORE ACTIVATION GATE CAUSESKCNQ2-DEVELOPMENTAL ENCEPHALOPATHY
Authors: Nappi Mario , Alberini Giulio , Berselli Alessandro , Roscioni Agnese , Soldovieri Maria Virginia , Barrese Vincenzo , Weckhuysen Sarah , Chiu Ting-Gee Annie , Scheffer Ingrid E. , Benfenati Fabio , Maragliano Luca , Miceli Francesco , Taglialatela Maurizio
Published: May 2024

Pathogenic variants inKCNQ2encoding for Kv7.2 voltage-gated potassium channel subunits cause developmental encephalopathies (KCNQ2-encephalopathies), both with and without epilepsy. We herein describe the clinical,in vitroandin silicofeatures of two encephalopathy-causing variants (A317T, L318V) in Kv7.2 affecting two consecutive residues in the S6activation gate undergoing large structural rearrangements during pore opening. Currents through these mutant channels displayed increased density, hyperpolarizing shifts in activation gating, and insensitivity to phosphatidylinositol 4,5-bisphosphate (PIP2), a critical regulator of Kv7 channel function; all these features are consistent with a strong gain-of-function effect. An increase in single-channel open probability, with no change in membrane abundance or single-channel conductance, was responsible for the observed gain-of-function effects. All-atoms Molecular Dynamics simulations revealed that the mutations widened the inner pore gate and stabilized a constitutively open channel configuration in the closed state, with minimal effects on the open conformation. Thus, a PIP2-independent stabilization of the inner pore gate open configuration is a novel molecular pathogenetic mechanism forKCNQ2-developmental encephalopathies.
A Sap Peptide Conserved across Flowering Plants Positively Regulates Lignin Biosynthesis, Biomass and Immunity
Authors: Chen Chang-Hung , Liou Pin-Chien , Hsu Yi-Fan , Wang I-Fan , Kuo Chun-Yu , Huang Kuan-Hao , Yu Jhong-He , Chen Chin-Wen , Wu Chia-Chen , Lin Da-Gin , Li Cheng-Bin , Tu Yuan-Kai , Hsu Chuan-Chih , Su Jung-Chen , Xia Kai , Tsai Isheng Jason , Lin Ying-Chung Jimmy , Chen Ying-Lan
Published: May 2024

Signaling peptides act as hormones to deliver short- or long-distance intercellular signals to govern complex developmental processes. Identifying endogenous signaling peptides is challenging due to their low abundance and the unknown cleavage sites required for release from precursor proteins, not to mention the investigation of their evolutionary roles across species. Consequently, very few peptides were evolutionarily characterizedin vivo, especially long-distance signaling peptides. Here we present current largest peptidomic datasets from six species (maize, camphor tree, tomato, rose gum, soybean and poplar), totaling 12,242 peptides, selected from all representative evolutionary clades of angiosperms, including monocots, magnoliids, rosid eudicots, and asterid eudicots. A sap peptide was found to be identical across all six species and named as ASAP (angiospermsappeptide), emerging as the most conserved peptide family discovered thus far. ASAP rapidly induces a series of protein phosphorylation involved in a signaling cascade previously reported to regulate lignin biosynthesis, plant growth and plant immunity. Functional assays on ASAP activity demonstrated its capability on the induction of monolignol biosynthesis and lignin deposition. High-throughput phenomic analyses showed that ASAP significantly increased plant above- and below-ground biomass. In addition, ASAP treatment enhanced plant immunity and reduced the number of galls and egg masses against nematode invasion. This study provides insights into the conservation and functional significance of plant long-distance mobile signaling peptides, offering potential applications in crop improvement and disease management strategies.
Novel cell-to-cell interactions revealed by cryotomography of a DPANN coculture system
Authors: Johnson Matthew D , Shepherd Doulin C , Sakai Hiroyuki D. , Mudaliyar Manasi , Pandurangan Arun Prasad , Short Francesca L , Veith Paul D. , Scott Nichollas E , Kurosawa Norio , Ghosal Debnath
Published: May 2024

DPANN is a widespread and highly diverse group of archaea characterised by their small size, reduced genome, limited metabolic pathways, and symbiotic existence. Known DPANN species are predominantly obligate ectosymbionts that depend on their host for their survival and proliferation. Despite the recent expansion in this clade, the structural and molecular details of host recognition, host-DPANN intercellular communication, and host adaptation in response to DPANN attachment remain unknown. Here, we used electron cryotomography (cryo-ET) to reveal that theCandidatusMicrarchaeota (ARM-1) interacts with its host,Metallosphaera javensisthrough intercellular proteinaceous nanotubes. These tubes (∼4.5 nm wide) originate in the host, extend all the way to the DPANN cytoplasm and act like tunnels for intercellular exchange. Combining cryo-ET and sub-tomogram averaging, we revealed thein situarchitectures of host and DPANN S-layers and the structures of the nanotubes in their primed and extended states, providing mechanistic insights into substrate exchange. Additionally, we performed comparative proteomics and genomic analyses to identify host proteomic changes in response to the DPANN attachment. Our results showed striking alterations in host-proteome during symbiosis and upregulation/downregulation of key cellular pathways. Collectively, these results provided unprecedented insights into the structural basis of host-DPANN communication and deepen our understanding of the host ectosymbiotic relationships.
The novel role of Kallistatin in linking metabolic syndromes and cognitive memory deterioration by inducing amyloid-β plaques accumulation and tau protein hyperphosphorylation
Authors: Qi Weiwei , Long Yanlan , Li Ziming , Zhao Zhen , Shi Jinhui , Xie Wanting , Wang Laijian , Tan Yandan , Zhou Ti , Jiang Ping , Jiang Bin , Yang Xia , Gao Guoquan
Published: May 2024

Accumulation of amyloid β (Aβ) peptides and hyperphosphorylated tau proteins in the hippocampus triggers cognitive memory decline in Alzheimer’s disease (AD). The incidence and mortality of sporadic AD were tightly associated with diabetes and hyperlipidemia, while the exact linked molecular is uncertain. Here, we reported that serum Kallistatin concentrations were meaningfully higher in AD patients, with a higher concentration of fasting blood glucose and triglyceride. In addition, the constructed Kallistatin-transgenic (KAL-TG) mice defined its cognitive memory impairment phenotype and lower LTP in hippocampal CA1 neurons accompanied by increased Aβ deposition and tau phosphorylation. Mechanistically, Kallistatin could directly bind to the Notch1 receptor and thereby upregulate BACE1 expression by inhibiting PPARγ signaling, resulting in Aβ cleavage and production. Besides, Kallistatin could promote the phosphorylation of tau by activating GSK-3β. Fenofibrate, a hypolipidemic drug, could alleviate cognitive memory impairment by down-regulating Aβ and tau phosphorylation of KAL-TG mice. Collectively, our data clarified a novel mechanism for Aβ accumulation and tau protein hyperphosphorylation regulation by Kallistatin, which might play a crucial role in linking metabolic syndromes and cognitive memory deterioration, and suggested that fenofibrate might have the potential for treating metabolism-related AD.

Highlights

Kallistatin-transgenic(KAL-TG) mice defined its cognitive memory impairment phenotype accompanied by increased Aβ deposition and tau phosphorylation.

Kallistatin could directly bind to the Notch1 receptor and thereby upregulate BACE1 expression by inhibiting PPARγ signaling.

Fenofibrate could alleviate cognitive memory impairment and down-regulate the serum Kallistatin level.
Accurate Conformation Sampling via Protein Structural Diffusion
Authors: Fan Jiahao , Li Ziyao , Alcaide Eric , Ke Guolin , Huang Huaqing , Weinan E
Published: May 2024

Accurately sampling of protein conformations is pivotal for advances in biology and medicine. Although there have been tremendous progress in protein structure prediction in recent years due to deep learning, models that can predict the different stable conformations of proteins with high accuracy and structural validity are still lacking. Here, we introduce UFConf, a cutting-edge approach designed for robust sampling of diverse protein conformations based solely on amino acid sequences. This method transforms AlphaFold2 into a diffusion model by implementing a conformation-based diffusion process and adapting the architecture to process diffused inputs effectively. To counteract the inherent conformational bias in the Protein Data Bank, we developed a novel hierarchical reweighting protocol based on structural clustering. Our evaluations demonstrate that UFConf out-performs existing methods in terms of successful sampling and structural validity. The comparisons with long time molecular dynamics show that UFConf can overcome the energy barrier existing in molecular dynamics simulations and perform more efficient sampling. Furthermore, We showcase UFConf’s utility in drug discovery through its application in neural protein-ligand docking. In a blind test, it accurately predicted a novel protein-ligand complex, underscoring its potential to impact real-world biological research. Additionally, we present other modes of sampling using UFConf, including partial sampling with fixed motif, langevin dynamics and structural interpolation.
rpfFis not required forX. translucenspv. undulosa pathogenesis
Authors: Heiden Nathaniel , Butchacas Jules , Klass Taylor , Cohen Stephen P. , Roman-Reyna Veronica , Merfa Marcus V. , Valero David Guillermo E. , Vargas-Garcia Christian , Olmos Cristian , Vélez-Negrón Yesenia , Lewandowski Monica M. , Jacobs Jonathan M.
Published: May 2024

Bacterial cells self-coordinate via a mechanism called quorum sensing. InXanthomonasspecies the generpfFencodes the quorum sensing autoinducer synthase.Xanthomonasspecies are divided into two main phylogenetic groups called Clade I and Clade II. Therpfquorum sensing system has been well studied in multiple Clade IIXanthomonasspecies and deletion ofrpfFresulted in a major loss of virulence on susceptible hosts. However, the only Clade IXanthomonasspecies in which therpfFsystem was previously studied was in the sugarcane pathogenX. albilineans. InX. albilineanstherpfcluster plays a relatively small role in pathogenesis.Xanthomonas translucenspv. undulosa (Xtu) is a Clade IXanthomonasspecies that causes bacterial leaf streak (BLS) and black chaff of wheat and barley and has increased as a concern in recent decades. Neither major resistance nor chemical treatments are available to prevent disease caused by Xtu. Interference withrpfbacterial quorum sensing systems has demonstrated some success in other systems. It was unknown whether BLS caused by Xtu could be prevented via quorum sensing interference. We found that Xtu encodes anrpfFhomolog and we created anrpfFknockout mutant to study the role of therpfsystem in Xtu. We found that therpfFmutant was unaffected in its pathogenesis as it caused BLS symptoms and multiplied within wheat plants to the same levels as the wildtype strain. The XturpfFmutant grew normally in lag and log phasesin vitro, however it exhibited a shorter stationary phase and an early death phase in plant-derived media. The importance of RpfF in Xtu’s life cycle is unknown, though it appears to carry out a role in population stability. Our research determined thatrpfFis not a major Xtu pathogenicity factor. Therefore, we do not recommend the targeting of therpfquorum sensing system as a preventative treatment for BLS of wheat.
Projections from thalamic nucleus reuniens to medial septum enable extinction of remote fear memory
Authors: Tomaszewski Kamil F. , Ziółkowska Magdalena , Łukasiewicz Kacper , Cały Anna , Sotoudeh Narges , Puchalska Monika , Salamian Ahmad , Radwanska Kasia
Published: May 2024

Aversive experiences lead to the formation of long-lasting memories. Despite the need to better understand how enduring fear memories can be attenuated, the underlying brain circuits remain largely unknown. In this study, employing a combination of genetic manipulations, neuronal circuit mapping, and chemogenetics in mice, we identify a new projection from the thalamic nucleus reuniens (RE) to the medial septum (MS), and show that this circuit is involved in the extinction of remote (30-day old), but not recent (1-day old), fear memories. These findings provide the first functional description of the RE→MS circuit and highlight the significance of the thalamo-septal regions in memory organization as a function of memory age, a phenomenon known as systems consolidation.
Huntingtin loss-of-function contributes to transcriptional deregulation in Huntington’s disease
Authors: Emilia Kozłowska , Agata Ciołak , Grażyna Adamek , Julia Szcześniak , Agnieszka Fiszer
Published: May 2024

Huntington’s disease (HD) is a fatal neurodegenerative disorder that is caused by the expansion of CAG repeats in theHTTgene, which results in a long polyglutamine (polyQ) tract in the huntingtin protein (HTT). In this study, we searched for networks of deregulated RNAs that contribute to initial transcriptional changes in HD neuronal cells and HTT-deficient cells.

We used RNA-seq (including small RNA sequencing) to analyze a set of isogenic, human induced pluripotent stem cell (iPSC)-derived neural stem cells (NSCs); and we observed numerous changes in gene expression and substantial dysregulation of miRNA expression in HD andHTT-knockout (HTT-KO) cell lines. The gene set that was upregulated in both HD andHTT-KO cells was enriched in genes that are associated with DNA binding and regulation of transcription. For both of these models, we confirmed the substantial upregulation of the transcription factors (TFs)TWIST1, SIX1, TBX1, TBX15, MSX2, MEOX2andFOXD1in NSCs and medium spiny neuron (MSN)-like cells. Moreover, we identified miRNAs that were consistently deregulated in HD andHTT-KO NSCs and MSN-like cells, including miR-214, miR-199, and miR-9. We suggest that these miRNAs function in the network that regulatesTWIST1andHTTexpressionviaregulatory feed-forward loop (FFL) in HD. Additionally, we reported that the expression of selected TFs and miRNAs tended to progressively change during the neural differentiation of HD cells, what was not observed inHTT-KO model. Based on comparing the HD andHTT-KO cell lines, we propose that early transcriptional deregulation in HD is largely caused by loss of HTT function.
Isoform-specific N-linked glycosylation of voltage-gated sodium channel alpha-subunits alters beta-subunit binding sites
Authors: Beaudoin Christopher A. , Kohli Manas , Salvage Samantha C. , Liu Hengrui , Arundel Samuel J. , Hamaia Samir W. , Lei Ming , Huang Christopher L.-H. , Jackson Antony P.
Published: May 2024

Voltage-gated sodium channel beta-subunits (Nav1.1-1.9) initiate and propagate action potentials in neurons and myocytes. The Nav beta-subunits (beta1-4) have been shown to modulate beta-subunit properties. Homo-oligomerization of beta-subunits on neighboring or opposing plasma membranes has been suggested to facilitate cis or trans interactions, respectively. The interactions between several Nav channel isoforms and beta-subunits have been determined using cryogenic electron microscopy (cryo-EM). Interestingly, the Nav cryo-EM structures reveal the presence of N-linked glycosylation sites. However, only the first glycan moieties are typically resolved at each site due to the flexibility of mature glycan trees. Thus, existing cryo-EM structures may risk de-emphasizing the structural implications of glycans on the Nav channels. Herein, molecular modelling and all-atom molecular dynamics simulations were applied to investigate the conformational landscape of N-linked glycans on Nav channel surfaces. The simulations revealed that negatively-charged sialic acid residues of two glycan sites may interact with voltage-sensing domains. Notably, two Nav1.5 isoform-specific glycans extensively cover the alpha-subunit region that, in other Nav channel alpha-subunit isoforms, corresponds to the binding site for the beta1- (and likely beta3-) subunit immunoglobulin (Ig) domain. Nav1.8 contains a unique N-linked glycosylation site that likely prevents its interaction with the beta2 and beta4-subunit Ig domain. These isoform-specific glycans may have evolved to facilitate specific functional interactions, for example by redirecting beta-subunit Ig-domains outwards to permit cis or trans supra-clustering within specialized cellular compartments such as the cardiomyocyte perinexal space. Further experimental work is necessary to validate these predictions.
Conservation of the cooling agent binding pocket within the TRPM subfamily
Authors: Huffer Kate , Denley Matthew C.S. , Oskoui Elisabeth V. , Swartz Kenton J.
Published: May 2024

Transient Receptor Potential (TRP) channels are a large and diverse family of tetrameric cation selective channels that are activated by many different types of stimuli, including noxious heat or cold, organic ligands such as vanilloids or cooling agents, or intracellular Ca2+. Structures available for all subtypes of TRP channels reveal that the transmembrane domains are closely related despite their unique sensitivity to activating stimuli. Here we use computational and electrophysiological approaches to explore the conservation of the cooling agent binding pocket identified within the S1-S4 domain of the Melastatin subfamily member TRPM8, the mammalian sensor of noxious cold, with other TRPM channel subtypes. We find that a subset of TRPM channels, including TRPM2, TRPM4 and TRPM5, contain pockets very similar to the cooling agent binding pocket in TRPM8. We then show how the cooling agent icilin modulates activation of TRPM4 to intracellular Ca2+, enhancing the sensitivity of the channel to Ca2+and diminishing outward-rectification to promote opening at negative voltages. Mutations known to promote or diminish activation of TRPM8 by cooling agents similarly alter activation of TRPM4 by icilin, suggesting that icilin binds to the cooling agent binding pocket to promote opening of the channel. These findings demonstrate that TRPM4 and TRPM8 channels share related ligand binding pockets that are allosterically coupled to opening of the pore.
Validating an Immunoassay to Measure Fecal Glucocorticoid Metabolites in Yellow-Bellied Marmots
Authors: Ortiz-Ross Xochitl , Taha Hash Brown , Press Emily , Rhone Sarah , Blumstein Daniel T.
Published: May 2024

The yellow-bellied marmot (Marmota flaviventer) study at the Rocky Mountain Biological Laboratory near Crested Butte, Colorado, USA is the world’s second longest study of free-living mammals. Quantifying physiological stress is essential for understanding their health, reproductive success, and survival in a variable environment. Historically, we used a validated radioimmunoassay (RIA) to measure fecal glucocorticoid metabolites (FGMs). Given the costs and risks of working with radioisotopes, we have shifted to a more sustainable method. Here we evaluate the suitability of two competitive enzyme-linked immunosorbent assays (ELISA) from Cayman Chemical Company (CCC) and Arbor Assays (AA) to measure corticosterone levels in FGMs. The findings revealed that the AA ELISA, unlike the CCC ELISA, consistently matched the RIA in terms of accuracy across high and low corticosterone concentrations, demonstrated superior assay parameters, showed the highest correlations with RIA results and effectively captured the annual variations in FGM concentrations, indicative of its reliability for use in longitudinal studies. We further analytically validated the usage of the AA ELISA for FGMs, confirming its efficacy without matrix effects, thus establishing its suitability for ongoing and future studies of FGMs in marmots. The transition to the AA ELISA from the RIA ensures continued data integrity while enhancing safety and environmental sustainability.
Segatella copri strains adopt distinct roles within a single individual's gut
Authors: Xiao Xieyue , Singh Adarsh , Giometto Andrea , Brito Ilana Lauren
Published: May 2024

Segatella copri is a dominant member of individuals' gut microbiomes worldwide, especially in non-Western populations. Although metagenomic assembly and genome isolation have shed light on the genetic diversity of S. copri, the lack of available isolates from this clade has resulted in a limited understanding of how members' genetic diversity translates into phenotypic diversity. Within the confines of a single gut microbiome, we have isolated 63 strains from diverse lineages of S. copri. We performed comparative analyses that exposed differences in cellular morphologies, preferences in polysaccharide utilization, yield of short-chain fatty acids, and antibiotic resistance across isolates. We further show that exposure to S. copri lineages either evokes strong or muted transcriptional responses in human intestinal epithelial cells. Our study exposes large phenotypic differences within related S. copri isolates, extending this to host-microbe interactions.
Imaging of porphyrin-specific fluorescence in pathogenic bacteria in vitro using a wearable, hands-free system
Authors: Sun Junhong , Vellappan Sangeevan , Akdemir Johnathan , Steier Liviu , Feinbloom Richard , Yadavalli Srujana Samhita
Published: May 2024

Fluorescence imaging is an effective method for detecting porphyrin production in bacteria, leveraging the natural fluorescence properties of porphyrins. Here we use a simple, lightweight, hands-free device for rapid, non-invasive assessments in clinical settings, microbial research, and diagnostic applications. Specifically in this study, we examined 15 bacterial and 2 fungal strains commonly associated with skin, oral, and/or multi-site infections at wound sites for their ability to autofluoresce based on their porphyrin production. We utilized Remel Porphyrin Test Agar and blood agar plates to monitor red fluorescence over several days of growth under aerobic or anaerobic conditions using the wearable REVEAL FC imaging system with a 405 nm violet excitation headlight paired with eyewear carrying 430 nm emission lenses. Fourteen of the fifteen bacteria produced red fluorescence when grown on Porphyrin Test Agar and nine of the fifteen bacteria also displayed red fluorescence on blood agar plates, consistent with their ability to synthesize porphyrins. Taken together, our results elucidate the sensitivity, effectiveness, and convenience of using wearable technology to detect pathogens that produce porphyrin-specific fluorescence. Consequently, the REVEAL system has immense potential to help diagnose wound infections, direct clinical procedures, and guide treatment options in real-time using fluorescence imaging all while minimizing the risk of contamination.