bluuebunny/crossref_metadata_2025 huggingface dataset:
Language model-based B cell receptor sequence embeddings can effectively encode receptor specificity
Authors: Wang Meng , Patsenker Jonathan , Li Henry , Kluger Yuval , Kleinstein Steven H.
Published: June 2023

High throughput sequencing of B cell receptors (BCRs) is increasingly applied to study the immense diversity of antibodies. Learning biologically meaningful embeddings of BCR sequences is beneficial for predictive modeling and interpretability. Several embedding methods have been developed for BCRs, but no direct performance benchmarking exists. Moreover, the impact of the input sequence length and paired-chain information on the prediction remains to be explored. We evaluated the performance of multiple embedding models to predict BCR sequence properties and receptor specificity. Despite the differences in model architectures, most embeddings effectively capture BCR sequence properties and specificity. BCR-specific embeddings slightly outperform general protein language models in predicting specificity. In addition, incorporating full-length heavy chains and paired light chain sequences improve the prediction performance of all embeddings. This study provides insights into the properties of BCR embeddings to improve downstream prediction applications for antibody analysis and discovery.
DNA methylation governs the sensitivity of repeats to restriction by the HUSH-MORC2 corepressor
Authors: Pandiloski Ninoslav , Horvath Vivien , Karlsson Ofelia E. , Christoforidou Georgia , Dorazehi Fereshteh , Koutounidou Symela , Matas Jon , Gerdes Patricia , Garza Raquel , Jönsson Marie E. , Adami Anita , Atacho Diahann , Johansson Jenny G. , Englund Elisabet , Kokaia Zaal , Jakobsson Johan , Douse Christopher H.
Published: June 2023

The human silencing hub (HUSH) complex binds to transcripts of LINE-1 retrotransposons (L1s) and other genomic repeats, recruiting MORC2 and other effectors to remodel chromatin. However, how HUSH and MORC2 operate alongside DNA methylation, a central epigenetic regulator of repeat transcription, remains poorly understood. Here we interrogate this relationship in human neural progenitor cells (hNPCs), a somatic model of brain development that tolerates removal of DNA methyltransferase DNMT1. Upon loss of MORC2 or HUSH subunit TASOR in hNPCs, L1s remain silenced by robust promoter methylation. However, genome demethylation and activation of evolutionarily-young L1s attracts MORC2 binding. Simultaneous depletion of DNMT1 and MORC2 causes massive accumulation of L1 transcripts. We identify the same mechanistic hierarchy at pericentromeric α-satellites and clustered protocadherin genes, repetitive elements important for chromosome structure and neurodevelopment respectively. Our data delineate the independent epigenetic control of repeats in somatic cells, with implications for understanding the vital functions of HUSH-MORC2 in hypomethylated contexts throughout human development.
Microbiome remodeling through bacterial competition and host behavior enables rapid adaptation to environmental toxins
Authors: Kim Dan , Pérez-Carrascal Olga Maria , DeSousa Catherin , Jung Da Kyung , Bohley Seneca , Wijaya Lila , Trang Kenneth , Khoury Sarah , Shapira Michael
Published: June 2023

Human activity is altering the environment in a rapid pace, challenging the adaptive capacities of genetic variation within animal populations. Animals also harbor extensive gut microbiomes, which play diverse roles in host health and fitness and may help expanding host capabilities. The unprecedented scale of human usage of xenobiotics and contamination with environmental toxins describes one challenge against which bacteria with their immense biochemical diversity would be useful, by increasing detoxification capacities. To explore the potential of bacteria-assisted rapid adaptation, we usedCaenorhabditis elegansworms harboring a defined microbiome, and neomycin as a model toxin, harmful for the worm host and neutralized to different extents by some microbiome members. Worms raised in the presence of neomycin showed delayed development and decreased survival but were protected when colonized by neomycin-resistant members of the microbiome. Two distinct mechanisms facilitated this protection: gut enrichment driven by altered bacterial competition for the strain best capable of modifying neomycin; and host avoidance behavior, which depended on the conserved JNK homolog KGB-1, enabling preference and acquisition of neomycin-protective bacteria. We further tested the consequences of adaptation, considering that enrichment for protective strains may represent dysbiosis. We found that neomycin-adapted gut microbiomes caused increased susceptibility to infection as well as an increase in gut lipid storage, suggesting metabolic remodeling. Our proof-of-concept experiments support the feasibility of bacteria-assisted host adaptation and suggest that it may be prevalent. The results also highlight trade-offs between toxin adaptation and other traits of fitness.
SR-BI regulates the synergistic mast cell response by modulating the plasma membrane-associated cholesterol pool
Authors: Capellmann Sandro , Kauffmann Marlies , Arock Michel , Huber Michael
Published: June 2023

The high-affinity IgE receptor FcεRI is the fundamental mast cell (MC) receptor responsible for the involvement of MCs in IgE-associated allergic disorders. Activation of the FcεRI is achieved via crosslinking by multivalent antigen (Ag) recognized by IgE, which results in degranulation and pro-inflammatory cytokine production. In comparison to the T and B cell receptor complexes, for which several co-receptors that orchestrate the initial signaling have been described, information is scarce about FcεRI-associated proteins. Additionally, it is not completely clear how FcεRI signaling synergizes with input from other receptors and how potential regulators affect this synergistic response. We aimed at identifying new regulators of FcεRI and found that the HDL receptor SR-BI (gene name:Scarb1/SCARB1) is expressed in MCs, functionally associates with FcεRI and regulates the local plasma membrane cholesterol content in cholesterol-rich plasma membrane nanodomains as shown by using the cholesterol-sensitive probe GFP-D4. This impacted on the activation of murine MCs upon co-stimulation of the FcεRI with different receptors known to synergize with FcεRI-signaling pathways. Amongst them we investigated the co-activation of the FcεRI with the receptor tyrosine kinase KIT, the IL-33 receptor and GPCRs activated by adenosine or PGE2.Scarb1-deficient bone marrow-derived MCs (BMMCs) showed reduced cytokine secretion in response to these co-stimulation conditions suggesting a role for plasma membrane-associated cholesterol regulating MC-driven inflammation. MimickingScarb1deficiency by membrane cholesterol depletion employing MβCD, we identified PKB and PLCγ1 as cholesterol-sensitive signaling molecules activated downstream of FcεRI in BMMCs. Specifically, when murine MCs were stimulated with SCF and Ag in combination, PLCγ1 activation appeared to be drastically boosted and this could be mitigated by cholesterol depletion. Inhibiting SR-BI in BMMCs phenocopied this effect. Similarly, SR-BI inhibition also attenuated the synergistic response to PGE2and anti-IgE in the human ROSAKITWTmast cell line suggesting that SR-BI is a crucial regulator of synergistic MC activation by regulating the local plasma membrane cholesterol concentration.
Exact Sketch-Based Read Mapping
Authors: Schulz Tizian , Medvedev Paul
Published: June 2023

Given a sequencing read, the broad goal of read mapping is to find the location(s) in the reference genome that have a “similar sequence”. Traditionally, “similar sequence” was defined as having a high alignment score and read mappers were viewed as heuristic solutions to this well-defined problem. For sketch-based mappers, however, there has not been a problem formulation to capture what problem an exact sketch-based mapping algorithm should solve. Moreover, there is no sketch-based method that can find all possible mapping positions for a read above a certain score threshold.

In this paper, we formulate the problem of read mapping at the level of sequence sketches. We give an exact dynamic programming algorithm that finds all hits above a given similarity threshold. It runs in 𝒪 (|t| + |p| +ℓ2) time and Θ(ℓ2) space, where |t| is the number ofk-mers inside the sketch of the reference, |p| is the number ofk-mers inside the read’s sketch andℓis the number of times thatk-mers from the pattern sketch occur in the sketch of the text. We evaluate our algorithm’s performance in mapping long reads to the T2T assembly of human chromosome Y, where ampliconic regions make it desirable to find all good mapping positions. For an equivalent level of precision as minimap2, the recall of our algorithm is 0.88, compared to only 0.76 of minimap2.

2012 ACM Subject Classification

Applied computing → Computational biology
The essential inter-domain interaction between NUDT9H and channel domain of human TRPM2 is also accomplished in trans
Authors: Ehrlich Wiebke , Kühn Frank J.P.
Published: June 2023

Channel function of human transient receptor potential melastatin type 2 (hsTRPM2) essentially depends on its C-terminal domain NUDT9H, which is homologous to the human Nudix hydrolase NUDT9. This cytosolic enzyme specifically binds and cleaves adenosine 5′-diphosphate ribose (ADPR), which in turn represents the principal agonist of TRPM2. For hsTRPM2 the experimental data strongly suggest, that binding of ADPR to NUDT9H as well as to a separate N-terminal binding pocket induces channel gating. Recent cryogenic electron microscopy (cryo-EM) analyses have provided the first concrete clues as to how NUDT9H interacts with the channel domain. In the present study we take an alternative approach by testing co-expression of NUDT9H together with a C-terminally truncated non-functional variant of hsTRPM2. Our data obtained from co-immunoprecipitation and proximity ligation assays reveal that NUDT9H and channel domain also specifically interact when co-expressed as independent proteins. Most importantly, calcium imaging as well as whole-cell patch-clamp recordings demonstrate that this in-trans interaction restores channel function, after stimulation either with intracellular ADPR or with extracellular hydrogen peroxide. Moreover, point mutation N1326D within the NUDT9H domain previously shown to be essential for TRPM2 function significantly reduces co-immunoprecipitation of NUDT9H as well as ADPR-dependent channel activity. These findings open up new possibilities to identify the molecular determinants of this crucial inter-domain interaction.
Entropy predicts early MEG, EEG and fMRI responses to natural images
Authors: Muukkonen I. , Salmela V.R.
Published: June 2023

To reduce the redundancy in the input, the human visual system employs efficient coding. Therefore, images with varying entropy (amount of information) should elicit distinct brain responses. Here, we show that a simple entropy model outperforms all current models, including many deep neural networks, in predicting early MEG/EEG and fMRI responses to visual objects. This suggests that the neural populations in the early visual cortex adapt to the information in natural images.
Investigating apparent differences between standard DKI and axisymmetric DKI and its consequences for biophysical parameter estimates
Authors: Oeschger Jan Malte , Tabelow Karsten , Mohammadi Siawoosh
Published: June 2023

Purpose

Identify differences between the acquisition-time efficient axisymmetric diffusion kurtosis imaging (DKI) model and standard DKI and their consequences on biophysical parameter estimates using standard DKI parameters as the ground truth.

Methods

Noise-free, synthetic diffusion MRI (dMRI) human brain data are generated using standard DKI and fitted with axisymmetric DKI and standard DKI. Then, the five axisymmetric DKI tensor metrics (AxTM), the parallel and perpendicular diffusivity and kurtosis and mean of the kurtosis tensor, attainable with both DKI models are computed. Next, the five biophysical parameters axon water fraction and dispersion, extra axonal parallel and perpendicular diffusivity and intra axonal parallel diffusivity are estimated from the AxTM using the WMTI-Watson model. Finally, the number of substantially differing voxels (SDV), defined as voxels where estimation results of both DKI models differ more than 5%, is calculated for the AxTM and the biophysical parameters.

Results

For the AxTM, the number of SDV was biggest for the parallel (26%) and perpendicular (51%) kurtosis while the other three AxTM had very few SDV (less than 5%). The biophysical parameters had much more SDV than the AxTM from which they were computed, ranging from 29% to 50%.

Conclusion

Axisymmetric DKI is a viable alternative to standard DKI in studies focusing on effects based on the parallel and perpendicular diffusion and mean of the kurtosis tensor. However, our findings urge caution when using axisymmetric DKI to investigate effects based on the parallel and perpendicular kurtosis or use it to estimate the biophysical parameters.
Utilizing a dual endogenous reporter system to identify functional regulators of aberrant stem cell and differentiation activity in colorectal cancer
Authors: Spisak Sandor , Chen David , Likasitwatanakul Pornlada , Doan Paul , Li Zhixin , Bala Pratyusha , Vizkeleti Laura , Tisza Viktoria , De Silva Pushpamail , Giannakis Marios , Wolpin Brian , Qi Jun , Sethi Nilay S.
Published: June 2023

Aberrant stem cell-like activity and impaired differentiation are central to the development of colorectal cancer (CRC). To identify functional mediators that regulate these key cellular programs in CRC, we developed an endogenous reporter system by genome-editing human CRC cell lines with knock-in fluorescent reporters at the SOX9 and KRT20 locus to report aberrant stem cell-like activity and differentiation, respectively, and then performed pooled genetic perturbation screens. Constructing a dual reporter system that simultaneously monitored aberrant stem cell-like and differentiation activity in the same CRC cell line improved our signal to noise discrimination. Using a focused-library CRISPR screen targeting 78 epigenetic regulators with 542 sgRNAs, we identified factors that contribute to stem cell-like activity and differentiation in CRC. Perturbation single cell RNA sequencing (Perturb-seq) of validated hits nominated SMARCB1 of the BAF complex (also known as SWI/SNF) as a negative regulator of differentiation across an array of neoplastic colon models. SMARCB1 is a dependency in CRC and required forin vivogrowth of human CRC models. These studies highlight the utility of a biologically designed endogenous reporter system to uncover novel therapeutic targets for drug development.
Single cell compendium of the muscle microenvironment in peripheral artery disease reveals capillary endothelial heterogeneity and activation of resident macrophages
Authors: Turiel Guillermo , Desgeorges Thibaut , Masschelein Evi , Birrer Manuela , Zhang Jing , Engelberger Stephan , De Bock Katrien
Published: June 2023

Background

Peripheral artery disease (PAD) is caused by atherosclerosis and chronic narrowing of lower limb arteries leading to decreased muscle perfusion and oxygenation. Current guidelines for treating PAD include endovascular strategies or bypass surgery but long-term outcomes have been suboptimal. This is likely due to our limited understanding of the contribution of the microvasculature as well as other cell types, in particular macrophages, to PAD skeletal muscle pathophysiology. We used single cell sequencing to investigate cellular and transcriptional heterogeneity of the skeletal muscle microenvironment in PAD.

Methods

Samples from the medial head of thegastrocnemiusmuscle of individuals undergoing either lower limb aneurysm surgery (controls) or PAD bypass surgery (PAD) were collected. Samples were either frozen for histological evaluation (control: n=4; PAD: n=6) or were immediately processed for single cell RNA sequencing of mononuclear cells (control: n=4; PAD: n= 4). Bioinformatic tools were used to annotate cell types and their subpopulations, to study transcriptional changes and to analyze cellular interactions.

Results

We generated a dataset comprised of 106,566 high-quality, deep-sequenced cells that compose the muscle microenvironment. Focusing on endothelial cells (ECs) and macrophages, we confirmed the presence of ATF3/4+ECs with angiogenic and immune regulatory capacities in human muscle and found that their transcriptional profile profoundly alters during PAD. Also, capillary ECs display features of endothelial to mesenchymal transition. Furthermore, we identifiedLYVE1hiMHCIIlowresident macrophages as the dominant macrophage population in human muscle, even under a chronic inflammatory condition such as PAD. During PAD,LYVE1hiMHCIIlowmacrophages get activated and acquire a more pro-inflammatory profile. Finally, we map strong intercellular communication in the muscle microenvironment, which is significantly altered in PAD.

Conclusions

The dataset we present here provides a highly valuable resource for gaining deeper insights into the critical roles that cells in the muscle microenvironment may play in PAD skeletal muscle pathology. We propose that targeting the crosstalk between ECs and macrophages could provide novel insights for developing effective treatments against this disease.
Kinetic and functional analysis of abundant microRNAs in extracellular vesicles from normal and stressed cultures of Chinese Hamster Ovary (CHO) cells
Authors: Belliveau Jessica , Thompson Will , Papoutsakis Eleftherios Terry
Published: June 2023

Chinese hamster ovary (CHO) cells release and exchange large quantities of extracellular vesicles (EVs). EVs are highly enriched in microRNAs (miRs, or miRNAs), which are responsible for most of their biological effects. We have recently shown that the miR content of CHO EVs varies significantly under culture stress conditions. Here, we provide a novel stoichiometric (“per-EV”) quantification of miR and protein levels in large CHO EVs produced under ammonia, lactate, osmotic, and age-related stress. Each stress resulted in distinct EV miR levels, with selective miR loading by parent cells. Our data provide a proof of concept for the use of CHO EV cargo as a diagnostic tool for identifying culture stress. We also tested the impact of three select miRs (let-7a, miR-21, and miR-92a) on CHO cell growth and viability. Let-7a—abundant in CHO EVs from stressed cultures—reduced CHO cell viability, while miR-92a—abundant in CHO EVs from unstressed cultures—promoted cell survival. Overexpression of miR-21 had a slight detrimental impact on CHO cell growth and viability during late exponential-phase culture, an unexpected result based on the reported anti-apoptotic role of miR-21 in other mammalian cell lines. These findings provide novel relationships between CHO EV cargo and cell phenotype, suggesting that CHO EVs may exert both pro- and anti-apoptotic effects on target cells, depending on the conditions under which they were produced.

Graphical Abstract
Atomic description of the reciprocal action between supercoils and melting bubbles on linear DNA
Authors: Burman Matthew , Noy Agnes
Published: June 2023

Although the mechanical response of DNA to physiological torsion and tension is well characterized, the detailed structures are not yet known. By using molecular dynamics simulations on linear DNA with 300 bp, we provide, for the first time, the conformational phase diagram at atomic resolution. Our simulations also reveal the dynamics and diffusion of supercoils. We observe a new state in negative supercoiling, where denaturation bubbles form in AT-rich regions independently of the underlying DNA topology. We thus propose sequence-dependent bubbles could position plectonemes in longer DNA.
Genome-wide kinetic profiling of pre-mRNA 3’ end cleavage
Authors: Ulloa Leslie Torres , Calvo-Roitberg Ezequiel , Pai Athma A.
Published: June 2023

Cleavage and polyadenylation is necessary for the formation of mature mRNA molecules. The rate at which this process occurs can determine the temporal availability of mRNA for subsequent function throughout the cell and is likely tightly regulated. Despite advances in high-throughput approaches for global kinetic profiling of RNA maturation, genome-wide 3’ end cleavage rates have never been measured. Here, we describe a novel approach to estimate the rates of cleavage, using metabolic labeling of nascent RNA, high-throughput sequencing, and mathematical modeling. Using in-silico simulations of nascent RNA-seq data, we show that our approach can accurately and precisely estimate cleavage half-lives for both constitutive and alternative sites. We find that 3’ end cleavage is fast on average, with half-lives under a minute, but highly variable across individual sites. Rapid cleavage is promoted by the presence of canonical sequence elements and an increased density of polyadenylation signals near a cleavage site. Finally, we find that cleavage rates are associated with the localization of RNA Polymerase II at the end of a gene and faster cleavage leads to quicker degradation of downstream read-through RNA. Our findings shed light on the features important for efficient 3’ end cleavage and the regulation of transcription termination.
INDOCYANINE GREEN IMAGING BY VITAL TISSUE SLICES SCANNING ALLOWS FOR THE ISOLATION OF INTACT LIVER MICRO-METASTASIS FOR SINGLE-CELL ANALYSIS
Authors: Roda Niccolò , Stendardo Massimo , Gambino Valentina , Persico Giuseppe , Cossa Andrea , Rodighiero Simona , Priami Chiara , Kaludercic Nina , Pelicci Pier Giuseppe , Giorgio Marco
Published: June 2023

Metastasis represents the deadliest outcome in cancer, leading to the vast majority of cancer-related deaths. Understanding the progression from micro-to macro-metastasis might improve future therapeutic strategies aimed at blocking metastatic disease. However, the difficulty of investigating vital, clinically undetectable, micro-metastases hindered our capacity to unravel phenotypic determinants of micro-metastases. In this work, we leveraged indocyanine green (ICG) dye to detect small sized liver micro-metastases across several cancer models. We exploited a method for infrared fluorescence scanning of fresh tissue and coring of cancer micro-metastases and succeeded in processing them for single-cell RNA sequencing. Our analysis revealed that distinct liver micro-metastases upregulate both shared and specific genes that can successfully predict breast cancer patient prognosis. Moreover, the ontology classification of these genes allowed the validation of several pathways, namely interferon response, extracellular matrix remodeling, and antioxidant response in metastatic progression. Ultimately, we showed that ICG can be successfully used to quantify breast cancer micro- and macro-metastases to lungs, which we showed to be abrogated through inhibition of H2O2-producing enzyme monoamine oxidase. Therefore, the ICG approach allowed us to identify not only determinant of breast cancer metastatization, but also to assess the therapeutic efficacy of targeting these genes which can be further investigated in clinic.
A pathogenic missense mutation in kainate receptors elevates dendritic excitability and synaptic integration through dysregulation of SK channels
Authors: Nomura Toshihiro , Taniguchi Sakiko , Wang Yi-Zhi , Yeh Nai-Hsing , Wilen Anika P , Castillon Charlotte C.M. , Foote Kendall M. , Xu Jian , Armstrong John N. , Savas Jeffrey N. , Swanson Geoffrey T. , Contractor Anis
Published: June 2023

Numerous rarede novovariants that cause neurodevelopmental disorders (NDDs) occur within genes encoding synaptic proteins, including ionotropic glutamate receptors (iGluRs). However, in many cases it remains unclear how damaging missense variants affect brain function. Here we determined the physiological consequences of an NDD causing missense mutation in theGRIK2kainate receptor (KAR) gene, that results in a single amino acid change p.Ala657Thr in the GluK2 receptor subunit. We engineered the equivalent mutation in the mouseGrik2gene, yielding a GluK2(A657T) mouse, to better understand the human disorder and determine how hippocampal neuronal function is disrupted. Synaptic KAR currents in hippocampal CA3 pyramidal neurons from heterozygous A657T mice exhibited slow decay kinetics, consistent with incorporation of the mutant subunit into functional receptors. Unexpectedly, CA3 neurons demonstrated elevated action potential spiking due to down-regulation of the small conductance Ca2+activated K+channel (SK), which mediates the post-spike afterhyperpolarization (AHP). The reduction in SK activity resulted in increased CA3 dendritic excitability, increased EPSP-spike coupling and lowered the threshold for the induction of LTP of the associational commissural (AC) synapses in the distal dendrites of CA3 neurons. Pharmacological inhibition of SK channels in wild-type (WT) mice increased dendritic excitability and EPSP-spike coupling, mimicking the phenotype in A657T mice and suggesting a causative role for attenuated SK activity in aberrant excitability observed in the mutant mice. These findings demonstrate that a disease-associated missense mutation inGRIK2leads to altered signaling through neuronal KARs, pleiotropic effects on neuronal and dendritic excitability, and implicate these processes in neuropathology in patients with genetic NDDs.
The development of brain pericytes requires expression of the transcription factornkx3.1in intermediate precursors
Authors: Ahuja Suchit , Adjekukor Cynthia , Li Qing , Kocha Katrinka M. , Rosin Nicole , Labit Elodie , Sinha Sarthak , Narang Ankita , Long Quan , Biernaskie Jeff , Huang Peng , Childs Sarah J.
Published: June 2023

Brain pericytes are one of the critical cell types that regulate endothelial barrier function and activity, thus ensuring adequate blood flow to the brain. The genetic pathways guiding undifferentiated cells into mature pericytes are not well understood. We show here that pericyte precursor populations from both neural crest and head mesoderm of zebrafish express the transcription factornkx3.1develop into brain pericytes. We identify the gene signature of these precursors, and show that annkx3.1, foxf2a, andcxcl12b-expressing pericyte precursor population is present around the basilar artery prior to artery formation and pericyte recruitment. The precursors later spread throughout the brain and differentiate to express canonical pericyte markers. Cxcl12b-Cxcr4 signaling is required for pericyte attachment and differentiation. Further, bothnkx3.1andcxcl12b are necessary and sufficient in regulating pericyte number as loss inhibits and gain increases pericyte number. Through genetic experiments we have defined a precursor population for brain pericytes and identified genes critical for their differentiation.
MEBRAINS 1.0: a new population-based macaque atlas
Authors: Balan Puiu F , Zhu Qi , Li Xiaolian , Niu Meiqi , Rapan Lucija , Funck Thomas , Bakker Rembrandt , Palomero-Gallagher Nicola , Vanduffel Wim
Published: June 2023

Due to their fundamental relevance, the number of anatomical macaque brain templates is constantly growing. Novel templates aim to alleviate limitations of previously published atlases and offer the foundation to integrate multiscale multimodal data. Typical limitations of existing templates include their reliance on one subject, their unimodality (usually only T1 or histological images), or lack of anatomical details. The MEBRAINS template overcomes these limitations by using a combination of T1 and T2 images, from the same 10 animals (Macaca mulatta), which are averaged by the multi-brain toolbox for diffeomorphic registration and segmentation. The resulting volumetric T1 and T2 templates are supplemented with high quality white and gray matter surfaces built with FreeSurfer. Human-curated segmentations of pial surface, white/gray matter interface and major subcortical nuclei were used to analyse the relative quality of the MEBRAINS template. Recently published 3D maps of the macaque inferior parietal lobe and (pre)motor cortex were warped to the MEBRAINS surface template, thus populating it with a parcellation scheme based on cyto- and receptor architectonic analyses. Finally, 9 CT scans of the same monkeys were registered to the T1 modality and co-registered to the template. Through its main features (multi-subject, multi-modal, volume-and-surface, traditional and deep learning-based segmentations), MEBRAINS aims to improve integration of multi-modal multi-scale macaque data and is quantitatively equal or better compared to currently widely used macaque templates. The template is integrated in the EBRAINS and Scalable Brain Atlas web-based infrastructures, each of which comes with its own suite of spatial registration tools.
Improved detection and phylogenetic analysis of plant proteins containing LysM domains
Authors: Dallachiesa Dardo , Aguilar O. Mario , Lozano Mauricio J
Published: June 2023

Plants perceive N-acetyl-d-glucosamine-containing oligosaccharides that play a role in the interaction with bacteria and fungi, both pathogenic and symbiotic, through cell-surface receptors that belong to the Receptor-Like Kinase (RLK) or Receptor-Like Protein (RLP) families. Structurally characterised proteins from these families have been shown to contain a tight bundle of three LysM domains in their extracellular domain. However, the identification of LysM domains of RLK/Ps using sequence based methods has led to some ambiguity, as some proteins have been annotated with one or only two LysM domains. This missing annotation was likely produced by the failure of the LysM hidden Markov model (HMM) from the PFAM database to correctly identify some LysM domains in proteins of plant origin. In this work, we provide improved HMMs for LysM domain detection in plants, that were built from the structural alignment of manually curated LysM domain structures from PDB and AlphaFold. Furthermore, we evaluated different sets of ligand-specific HMMs that were able to correctly classify a limited set of fully characterised RLK/Ps by their ligand specificity. In contrast, the phylogenetic analysis of the extracellular region of RLK/Ps, or of their individual LysM domains, was unable to discriminate these proteins by their ligand specificity. The HMMs reported here will allow a more sensitive detection of plant proteins containing LysM domains and help improve their characterisation.
Impact of random 50-base sequences inserted into an intron on splicing inSaccharomyces cerevisiae
Authors: Perchlik Molly , Sasse Alexander , Mostafavi Sara , Fields Stanley , Cuperus Josh T.
Published: June 2023

Intron splicing is a key regulatory step in gene expression in eukaryotes. Three sequence elements required for splicing – 5’ and 3’ splice sites and a branch point – are especially well- characterized inSaccharomyces cerevisiae, but our understanding of additional intron features that impact splicing in this organism is incomplete, due largely to its small number of introns. To overcome this limitation, we constructed a library inS. cerevisiaeof random 50-nucleotide elements (N50) individually inserted into the intron of a reporter gene and quantified canonical splicing and the use of cryptic splice sites by sequencing analysis. More than 70% of approximately 140,000 N50 elements reduced splicing by at least 20% compared to the intron control. N50 features, including higher GC content, presence of GU repeats and stronger predicted secondary structure of its pre-mRNA, correlated with reduced splicing efficiency. A likely basis for the reduced splicing of such a large proportion of variants is the formation of RNA structures that pair N50 bases – such as the GU repeats – with other bases specifically within the reporter pre-mRNA analyzed. However, neither convolutional neural network nor linear models were able to explain more than a small fraction of the variance in splicing efficiency across the library, suggesting that complex non-linear interactions in RNA structures are not accurately captured by RNA structure prediction methods given the limited number of variants. Our results imply that the specific context of a pre-mRNA may determine the bases allowable in an intron to prevent secondary structures that reduce splicing.
Assessment of Nutrient Composition and utilization of some popular wild Edible fruits of Kumaun Himalayan Region as Anti-oxidant agents
Authors: Pandey Neelaxi , Ghosh Puja , Muhasina K. M , Bisht Satpal Singh , Jha Abhishek
Published: June 2023

Food and Nutrition security is the main problem faced by developing and underdeveloped countries. Proper utilization of wild edible plants for nutrition security is a great choice for reducing the wastage of these powerful foods. The present investigation has been made to understand the nutritional and phytochemical parameter of selected underutilized fruits such asDiospyros kaki, Pyrus pashia, Ficus semicordata, Diploknema butyracea, Pyracantha crenulata, andRubus niveus. The proximate analyses showed thatDiospyros kakiis most promising fruit with 44.86± 0.4 mg/g carbohydrate, 9.29±0.80 mg/g protein, 81.31±0.4, 7% moisture and 1.1±0.11% little amount of ash content. Micronutrient iron was quantify highest inPyracantha crenulata(3.52±0.24mg/100g) and zinc inRubus niveus(8.13±0.05 mg/100g). Phytochemical screening was recorded in the ethanolic and aqueous extract, in which Phenolic and flavonoid content were highest in ethanolic extract ofRubus niveus;64.05±0.13mg GAE/gm, 108.83±2.93mg QE/ g extract respectively and tannin content was highest in case ofDiospyros kaki(79.94±0.40mg TAE/100g of extract). The free radical scavenging activity of fruits have been analyzed by DPPH, H2O2and NO assay; it was observed that the ethanolic extract ofRubus niveusfruit is most promising with an IC50value 16.97μg/ml. In contrast, aqueous extract scored IC50value 28.86μg/ml. The lowest IC50value was found in aqueous extract ofDiospyros kakii.e., 81.9 μg/ml in DPPH assay. The potential usage of these plants will help the people of these regions to combat nutrient deficiency diseases. Further development of research may help us to come out with powerful functional foods using these fruits.

Graphical Abstract
A widespread proteinaceous sulfur storage compartment in bacteria
Authors: Benisch Robert , Andreas Michael P. , Giessen Tobias W.
Published: June 2023

Intracellular compartmentalization is essential for all cells and enables the regulation and optimization of metabolism1. One of the main functions of subcellular compartments is the storage of nutrients2–4. As bacteria do generally not possess membrane-bound organelles, they often have to rely on functionally analogous protein-based compartments2,5–7. Encapsulin nanocompartments are one of the most prevalent protein-based compartmentalization strategies found in prokaryotes5,8. Here we show that desulfurase encapsulins represent a novel sulfur storage compartment in bacteria able to sequester large amounts of crystalline elemental sulfur. We determined the 1.78 Å cryo-EM structure of a 24 nm desulfurase-loaded encapsulin highlighting the molecular details of the protein shell and desulfurase encapsulation. We found that elemental sulfur crystals can be formed inside encapsulin shells in a desulfurase-dependent manner with L-cysteine acting as the sulfur donor. Intracellular sulfur accumulation can be influenced by the concentration and type of sulfur source in growth media. The selectively permeable protein shell allows the long-term intracellular storage of redox-labile elemental sulfur by excluding cellular reducing agents from its interior. We found that encapsulation substantially improves desulfurase activity and stability while also preventing substrate inhibition. These findings represent the first example of a dedicated and widespread storage system for the essential element sulfur in bacteria and provide the basis for understanding how this novel protein-based storage compartment is integrated within bacterial metabolism.
Multiprotein Assemblies, Phosphorylation and Dephosphorylation in Neuronal Cytoskeleton
Authors: Kurochkina Natalya , Sapio Matthew R. , Iadarola Michael J. , Hall Bradford E , Kulkarni Ashok B.
Published: June 2023

Filament systems are comprised of fibrous and globular cytoskeletal proteins and are key elements regulating cell shape, rigidity, and dynamics. The cellular localization and assembly of neurofilaments depend on phosphorylation by kinases. The involvement of the BRCA1 (Breast cancer associated protein 1)/BARD1 (BRCA1-associated RING domain 1) pathways in Alzheimer disease (AD) is suggested by colocalization studies. In particular, BRCA1 accumulation within neurofibrillary tangles and colocalization with tau aggregates in the cytoplasm of AD patients implicates the involvement of mutant forms of BRCA1/BARD1 proteins in disease pathogenesis. The purpose of this study is to show that the location of mutations in the translated BARD1, specifically within ankyrin repeats, has strong correlation with the Cdk5 motifs for phosphorylation.

Mapping of the mutation sites on the protein’s three-dimensional structure and estimation of the backbone dihedral angles show transitions between the canonical helical and extended conformations of the tetrapeptide sequence of ankyrin repeats.

Clustering of mutations in BARD1 ankyrin repeats near the N-termini of the helices with T/SXXH motifs provides a basis for conformational transitions that might be necessary to ensure the compatibility of the substrate with active site geometry and accessibility of the substrate to the kinase.

Ankyrin repeats are interaction sites for phosphorylation-dependent dynamic assembly of proteins including those involved in transcription regulation and signaling, and present potential targets for the design of new drugs.
Structural insights into a single semi-clathrate hydrate formed in a confined environment of porous protein crystal
Authors: Maity Basudev , Tian Jiaxin , Furuta Tadaomi , Abe Satoshi , Ueno Takafumi
Published: June 2023

Water behavior on protein surfaces influences protein structure and function. Antifreeze Proteins (AFPs) have been intensively studied in context of biological cytotechnology. AFPs inhibit growth of ice microcrystals by forming unique water-cluster networks which are influenced by protein surface morphology and hydrophobicity. Such unique water-cluster networks have been identified as semi-clathrate structures in crystals and are believed to be stabilized by intermolecular interactions within the confined environment. However, there is little atomic-level information about the process of formation of semi-clathrates and the structural units of water-clathrate networks. We identified a single semi-clathrate formed on the pore surface of ferritin crystal which has a structure similar to that of a natural AFP. Comparison of ferritin mutants and determination of temperature-dependent structures revealed that semi-clathrate water molecules on an ⍺-helix undergo structural alterations with increasing temperature. Lowering the temperature regenerates the semi-clathrate structure. Water molecules hydrogen-bonded to main chain carbonyl groups are stably immobilized at room temperature and serve as starting points for clathrate formation. These findings provide a mechanistic understanding of water networks in AFPs and guidelines for designing new cryomaterials.
Membrane contact sites regulate vacuolar fission via sphingolipid metabolism
Authors: Hanaoka Kazuki , Nishikawa Kensuke , Ikeda Atsuko , Schlarmann Philipp , Yamashita Sayumi , Nakaji Aya , Fujii Sotaro , Funato Kouichi
Published: June 2023

Membrane contact sites (MCSs) are junctures that perform important roles including coordinating lipid metabolism. Previous studies have indicated that vacuolar fission/fusion processes are coupled with modifications in the membrane lipid composition. However, it has been still unclear whether MCS-mediated lipid metabolism controls the vacuolar morphology. Here we report that deletion of tricalbins (Tcb1, Tcb2, Tcb3), tethering proteins at endoplasmic reticulum (ER)-plasma membrane (PM) and ER-Golgi contact sites, alters fusion/fission dynamics and causes vacuolar fragmentation in the yeastSaccharomyces cerevisiae. In addition, we show that the sphingolipid precursor phytosphingosine accumulates in tricalbin-deleted cells, triggering the vacuolar division. Detachment of the nucleus vacuole junction (NVJ), an important contact site between the vacuole and the perinuclear ER, restored vacuolar morphology in both cells subjected to high exogenous phytosphingosine and Tcb3-deleted cells, supporting that phytosphingosine transport across the NVJ induces vacuole division. Thus, our results suggest that vacuolar morphology is maintained by MCSs through the metabolism of sphingolipids.
Cardiomyocytes Deficiency of SENP1 Promotes Myocardial Fibrosis via Paracrine Action
Authors: Liu Zhihao , Bian Xiyun , Li Lan , Liu Li , Feng Chao , Wang Ying , Ni Jingyu , Li Sheng , Lu Dading , Li Yanxia , Ma Chuanrui , Yu Tian , Xiao Xiaolin , Xue Na , Wang Yuxiang , Zhang Chunyan , Ma Xiaofang , Gao Xiumei , Fan Xiaohui , Liu Xiaozhi , Fan Guanwei
Published: June 2023

Background

SENP1 (Sentrin-specific protease 1) is involved in heart disease by regulating intracellular SUMOylation. However, the role of cell type-specific SENP1 in the setting of myocardial infarction (MI) remains to be defined. We determined whether cardiomyocyte-specific SENP1 regulates maladaptive remodeling in the ischemic heart.

Methods

We generated cardiomyocyte-specific SENP1 knockout and overexpression mice to assess cardiac function and ventricular remodeling responses under physiological and pathological conditions. Adult mouse cardiomyocytes and fibroblasts were separated to observe the paracrine effects of cardiomyocytes. DIA proteomic assay and bioinformatic analysis were performed to detect differential proteins in primary cardiomyocytes. Single-cell sequencing data were analyzed to identify key cardiomyocyte cluster regulated by SENP1 after MI. Mass spectrometry was performed to search for key effector proteins regulated by SENP1.

Results

SENP1 expression reduced in post-infarction mice and patients with heart failure. Cardiomyocyte-specific SENP1 deficiency (genetic or adeno-associated virus (AAV)-mediated) triggered a myocardial fibrotic response and progressive cardiac dysfunction. MI exacerbated the poor ventricular remodeling response mediated by SENP1 deletion, SENP1 overexpression improved cardiac function and reduced fibrosis. Further, we found that increased cardiac fibrosis in the cardiomyocyte-specific SENP1 deletion mice, associated with increased Fn expression and secretion in cardiomyocytes, promoted fibroblast activation in response to myocardial injury. Mechanistically, SENP promoted deSUMOylation of the HSP90ab1 (heat shock protein 90 alpha, class B, member 1) Lys72 and ubiquitin-dependent degradation, which reduced HSP90ab1-mediated phosphorylation of STAT3 (signal transducer and activator of transcription 3) and transcriptional activation of Fn, and then reduced fibroblast activation in the indirect coculture model. On the other hand, AAV-mediated mutation of the HSP90ab1 Lys72 ameliorated adverse ventricular remodeling and dysfunction post-MI.

Conclusions

SENP1 is essential for repressing STAT3-mediated Fn transcription by regulating deSUMOylation of HSP90ab1. Blockade of HSP90ab1 SUMOylation at the Lys72 site is a novel therapy effective in reversing adverse ventricular remodeling post-MI.

Abstract Figure
Small-field visual projection neurons detect translational optic flow and support walking control
Authors: Isaacson Mathew D. , Eliason Jessica L. M. , Nern Aljoscha , Rogers Edward M. , Lott Gus K. , Tabachnik Tanya , Rowell William J. , Edwards Austin W. , Korff Wyatt L. , Rubin Gerald M. , Branson Kristin , Reiser Michael B.
Published: June 2023

Animals rely on visual motion for navigating the world, and research in flies has clarified how neural circuits extract information from moving visual scenes. However, the major pathways connecting these patterns of optic flow to behavior remain poorly understood. Using a high-throughput quantitative assay of visually guided behaviors and genetic neuronal silencing, we discovered a region inDrosophila’s protocerebrum critical for visual motion following. We used neuronal silencing, calcium imaging, and optogenetics to identify a single cell type, LPC1, that innervates this region, detects translational optic flow, and plays a key role in regulating forward walking. Moreover, the population of LPC1s can estimate the travelling direction, such as when gaze direction diverges from body heading. By linking specific cell types and their visual computations to specific behaviors, our findings establish a foundation for understanding how the nervous system uses vision to guide navigation.
Identification of a new human polyomavirus in distinct populations and tissues
Authors: Torres Carolina , Correa Rita M. , Picconi María A. , Buck Christopher B. , Mbayed Viviana A.
Published: June 2023

Objectives

This work aimed to characterize a novel human polyomavirus (HPyV) with cutaneous tropism.

Methods

Swabs of healthy skin (forehead) of 75 immunocompetent individuals from Argentina were screened for HPyV through sequence amplification techniques. Publicly available metagenomic datasets were also analyzed.

Results

A previously unknown polyomavirus sequence was detected in two skin swab samples. A nearly identical sequence was detected in public datasets representing metagenomic surveys of human skin and feces. Further analyses showed that the new polyomavirus diverges from its nearest relative, human polyomavirus 6 (HPyV6), by 17.3-17.7% (in nucleotides for the large T antigen), which meets criteria for a new species designation in the genusDeltapolyomavirus.

The screening also revealed more distant HPyV6 relatives in macaque genital and chimpanzee fecal datasets. Since polyomaviruses are generally thought to cospeciate with mammalian hosts, the high degree of similarity to HPyV6 suggests the new polyomavirus species is human-tropic.

Conclusions

A novel polyomavirus was identified and characterized from samples of distinct populations and tissues. We suggest the common name human polyomavirus 16 (HPyV16).
Hippocampal Codes for Real-World Human Navigation
Authors: Graves Kathryn N. , Letrou Ariadne , Gray Tyler E. , Quraishi Imran H. , Turk-Browne Nicholas B.
Published: June 2023

As animals move through the world, the hippocampus represents their location, direction, and speed. Parallel studies in humans have been mostly limited to virtual navigation because of physical constraints of suitable neural recording technologies. However, there are known differences between real-world and virtual navigation, leaving open the question of how the hippocampus supports real-world navigation in humans. Here we report evidence from ambulatory patients with chronic brain implants that the location, direction, and speed of humans walking along a linear track are represented in local field potentials from the hippocampus. We further show in a subset of patients who were tested twice after long delays that these representations can be reliable over time. These findings provide the first demonstration of multiple, stable neural codes for real-world navigation in the human hippocampus.