bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of genetic variation inMacadamiashows evidence of extensive reticulate evolution
Authors: Manatunga Sachini Lakmini , Furtado Agnelo , Topp Bruce , Alam Mobashwer , Mason Patrick J. , Kharabian-Masouleh Ardashir , Henry Robert J
Published: February 2024

The genusMacadamiain the Proteaceae family includes four species. To explore diversity in macadamia genetic resources, a total of 166 wild genotypes, representing all four species, were sequenced. The four species were clearly distinguished as four separate clades in a phylogenetic analysis of nuclear gene CDS.M. integrifoliaandM. tetraphyllaformed a clade that had diverged from a clade includingM. ternifoliaandM. jansenii.The greatest diversity in nuclear and chloroplast genomes was found in the more widely distributedM. integrifoliawhile the rareM. janseniishowed little diversity. The chloroplast phylogeny revealed a much more complex evolutionary history. Multiple chloroplast capture events have resulted in chloroplast genome clades including genotypes from different species. This suggests extensive reticulate evolution inMacadamiadespite the emergence of the four distinct species that are supported by the analysis of their nuclear genomes. The chloroplast genomes showed strong associations with geographical distribution reflecting limited maternal gene movement in these species having large seeds. The nuclear genomes showed lesser geographical differences, probably reflecting longer distance movement of pollen. This improved understanding of the distribution of diversity inMacadamiawill aid conservation of these rare species now found in highly fragmented rainforest remnants.

Highlights

Whole genome sequencing of population of the four species in the Macadamia genus allowed phylogenetic relationships to be determined and revealed significant reticulate evolution.
An ability to respond begins with inner alignment: How phase synchronisation effects transitions to higher levels of agency
Authors: Tissot Tazzio , Levin Mike , Buckley Chris , Watson Richard
Published: February 2024

How do multiple active components at one level of organisation create agential wholes at higher levels of organisation? For example, in organismic development, how does the multi-scale autonomy of the organism arise from the interactions of the molecules, cells and tissues that an organism contains? And, in the major evolutionary transitions, how does a multicellular organism, for example, arise as an evolutionary unit from the selective interests of its unicellular ancestors? We utilise computational models as a way to think about this general question. We take a deliberately minimalistic notion of an agent: a competency to take one of two possible actions to minimise stress. Helping ourselves to this behaviour at the microscale, we focus on conditions where this same type of agency appears spontaneously at a higher level of organisation. We find that a simple process of positive feedback on the timing of individual responses, loosely analogous to the natural phase synchronisation of weakly coupled oscillators, causes such a transition in behaviour. The emergent collectives that arise become, quite suddenly, able to respond to their external stresses in the same (minimal) sense as the original microscale units. This effects a dramatic rescaling of the system behaviour, and a quantifiable increase in problem-solving competency, serving as a model of how higher-level agency emerges from a pool of lower-level agents or active matter. We discuss how this dynamical ‘waking-up’ of higher-level collectives, through the alignment of their internal dynamics, might relate to reproductive/cell-cycle synchronisation in evolutionary transitions and development.
From Sight to Insight: A Multi-task Approach with the Visual Language Decoding Model
Authors: Huang Wei , Yang Pengfei , Tang Ying , Qin Fan , Li Hengjiang , Wu Diwei , Ren Wei , Wang Sizhuo , Zhao Yuhao , Wang Jing , Liu Haoxiang , Li Jingpeng , Zhu Yucheng , Zhou Bo , Sun Jingyuan , Li Qiang , Cheng Kaiwen , Yan Hongmei , Chen Huafu
Published: February 2024

Visual neural decoding aims to unlock the mysteries of how the human brain interprets the visual world. While early studies made some progress in decoding visual activity for singular type of information, they failed to concurrently reveal the multi-level interweaving linguistic information in the brain. Here, we developed a novel Visual Language Decoding Model (VLDM) capable of decoding categories, semantic labels, and textual descriptions from visual perceptual activities simultaneously. We selected the large-scale NSD dataset to ensure the efficiency of the decoding model in joint training and evaluation across multiple tasks. For category decoding, we achieved the effective classification of 12 categories with an accuracy of nearly 70%, significantly surpassing the chance level. For label decoding, we attained the precise prediction of 80 specific semantic labels with a 16-fold improvement over the chance level. For text decoding, the scores of the decoded text surpassed the corresponding baseline levels by remarkable margins on six evaluation metrics. This study contributes significantly to extensive applications in multi-layered brain-computer interfaces, potentially leading to more natural and efficient human-computer interaction experiences.
Predicting genetic biodiversity in salamanders using geographic, climatic, and life history traits
Authors: Parsons Danielle J. , Green Abigail E. , Carstens Bryan C. , Pelletier Tara A.
Published: February 2024

The geographic distribution of genetic variation within a species reveals information about its evolutionary history, including responses to historical climate change and dispersal ability across various habitat types. We combine genetic data from salamander species with geographic, climatic, and life history data collected from open-source online repositories to develop a machine learning model designed to identify the traits that are most predictive of unrecognized genetic lineages. We find evidence of hidden diversity distributed throughout the clade Caudata that is largely the result of variation in climatic variables. We highlight some of the difficulties in using machine-learning models on open-source data that are often messy and potentially taxonomically and geographically biased.
LineageVAE: Reconstructing Historical Cell States and Transcriptomes toward Unobserved Progenitors
Authors: Majima Koichiro , Kojima Yasuhiro , Minoura Kodai , Abe Ko , Hirose Haruka , Shimamura Teppei
Published: February 2024

Abstract

Single-cell RNA sequencing (scRNA-seq) enables comprehensive characterization of the cell state. However, its destructive nature prohibits measuring gene expression changes during dynamic processes such as embryogenesis. Although recent studies integrating scRNA-seq with lineage tracing have provided clonal insights between progenitor and mature cells, challenges remain. Because of their experimental nature, observations are sparse, and cells observed in the early state are not the exact progenitors of cells observed at later time points. To overcome these limitations, we developed LineageVAE, a novel computational methodology that utilizes deep learning based on the property that cells sharing barcodes have identical progenitors. This approach transforms scRNA-seq observations with an identical lineage barcode into sequential trajectories toward a common progenitor in a latent cell state space. Using hematopoiesis and reprogrammed fibroblast datasets, we demonstrate the capability of LineageVAE to reconstruct unobservable cell state transitions, historical transcriptome, and regulatory dynamics toward progenitor cell states at single-cell resolution.
Profiling Glioma Stem Cell Dynamics via 3D-based Cell Cycle Reporter Assays
Authors: Lubanska Dorota , Roye-Azar Antonio , Alrashed Sami , Cieslukowski Alan , Soliman Mohamed , deCarvalho Ana C. , Shamisa Abdalla , Kulkarni Swati , Porter Lisa A.
Published: February 2024

Successful containment of unwanted cell cycle progression in tumours such as glioblastoma (GBM) requires targeted therapeutic approaches which rely on understanding cell cycle dynamics in response to microenvironmental stimuli. Glioma Stem Cells (GSCs) can drive tumour initiation, recurrence, therapy resistance, and are often attributed to the heterogeneity and plasticity of GBM.In vitromodels using patient-derived GSCs provide a life relevant tool for exploration of complex molecular mechanisms underlying the aggressive characteristics of GBM. Introduction of 3D tissue culture systems permits the study of spatial complexity of the tumour mass and enables control over diverse conditions within the surrounding microenvironment. This chapter demonstrates detailed methods to study spatio-temporal changes to the cell cycle dynamics using available fluorescent cell cycle reporter systems in combination with bioinformatics-based signal intensity and localization analysis. We present a successful approach that investigates the 3D cell cycle dynamics of GSC populations. This approach utilizes GBM neurosphere and organoid cultures, which are assessed over time and under therapeutic pressure. These models can be further explored, manipulated, and customized to serve specific experimental designs.
Varying selection pressure for a Na+sensing site in epithelial Na+channel subunits reflect divergent roles in Na+homeostasis
Authors: Wang Xue-Ping , Srinivasan Priyanka , Hamdaoui Mustapha El , Grytz Rafael , Kashlan Ossama B.
Published: February 2024

The epithelial Na+channel (ENaC) emerged early in vertebrates and has played a role in Na+and fluid homeostasis throughout vertebrate evolution. We previously showed that proteolytic activation of the channel evolved at the water to land transition of vertebrates. Sensitivity to extracellular Na+, known as Na+self-inhibition, reduces ENaC function when Na+concentrations are high and is a distinctive feature of the channel. A fourth ENaC subunit, δ, emerged in jawed fishes from an α subunit gene duplication. Here, we analyzed 846 α and δ subunit sequences and found that a key Asp in a postulated Na+binding site was nearly always present in the α subunit, but frequently lost in the δ subunit (e.g., human). Analysis of site evolution and codon substitution rates provide evidence that the ancestral α subunit had the site and that purifying selection for the site relaxed in the δ subunit after its divergence from the α subunit, coinciding with a loss of δ subunit expression in renal tissues. We also provide evidence that the proposed Na+binding site in the α subunit is a bona fide site by conferring novel function to channels comprising human δ subunits. Together, our findings provide evidence that ENaC Na+self-inhibition improves fitness through its role in Na+homeostasis in vertebrates.
Evidence for a transfer-to-trap mechanism of fluorophore concentration quenching in lipid bilayers
Authors: Meredith Sophie A. , Kusunoki Yuka , Evans Stephen D. , Morigaki Kenichi , Connell Simon D. , Adams Peter G.
Published: February 2024

It is important to understand the behaviours of fluorescent molecules because, firstly, they are often utilized as probes in biophysical experiments and, secondly, they are crucial cofactors in biological processes such as photosynthesis. A phenomenon called ‘fluorescence quenching’ occurs when fluorophores are present at high concentrations but the mechanisms for quenching are debated. Here, we used a technique called ‘in-membrane electrophoresis’ to generate concentration gradients of fluorophores within a supported lipid bilayer (SLB), across which quenching was expected to occur. Fluorescence lifetime imaging microscopy (FLIM) provides images where the fluorescence intensity in each pixel is correlated to fluorescence lifetime: the intensity provides information about the location and concentration of fluorophores and the lifetime reveals the occurrence of energy-dissipative processes. FLIM was used to compare the quenching behaviour of three commonly-used fluorophores: Texas Red (TR), nitrobenzoaxadiazole (NBD) and 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY). FLIM images provided evidence of quenching in regions where the fluorophores accumulated but the degree of quenching varied between the different fluorophores. The relationship between quenching and concentration was quantified and the ‘critical radius for trap formation’, representing the relative quenching strength, was calculated as 2.70, 2.02 and 1.14 nm, for BODIPY, TR and NBD, respectively. The experimental data supports the theory that quenching takes place via a ‘transfer-to-trap’ mechanism which proposes, firstly, that excitation energy is transferred between fluorophores and may reach a ‘trap site’ resulting in immediate energy dissipation and, secondly, that trap sites are formed in a concentration-dependent manner. Some previous work suggested that quenching occurs only when fluorophores aggregate, or form long-lived dimers, but our data and this theory argues that traps may be ‘statistical pairs’ of fluorophores that exist only transiently. Our findings should inspire future work to assess whether these traps can be charge-transfer states, excited state dimers or something else.
Epigenetic repression of cFos supports sequential formation of distinct spatial memories
Authors: Franzelin Andreas , Lamothe-Molina Paul J. , Gee Christine E. , Formozov Andrey , Schreiter Eric R. , Morellini Fabio , Oertner Thomas G.
Published: February 2024

Expression of the immediate early gene cFos modifies the epigenetic landscape of activated neurons with downstream effects on synaptic plasticity. The production of cFos is inhibited by a long-lived isoform of another Fos family gene, ΔFosB. It has been speculated that this negative feedback mechanism may be critical for protecting episodic memories from being overwritten by new information. Here, we investigate the influence of ΔFosB inhibition on cFos expression and memory. Hippocampal neurons in slice culture produce more cFos on the first day of stimulation compared to identical stimulation on the following day. This downregulation affects all hippocampal subfields and requires histone deacetylation. Overexpression of ΔFosB in individual pyramidal neurons effectively suppresses cFos, indicating that accumulation of ΔFosB is the causal mechanism. Water maze training of mice over several days leads to accumulation of ΔFosB in granule cells of the dentate gyrus, but not in CA3 and CA1. Because the dentate gyrus is thought to support pattern separation and cognitive flexibility, we hypothesized that inhibiting the expression of ΔFosB would affect reversal learning, i.e., the ability to successively learn new platform locations in the water maze. The results indicate that pharmacological HDAC inhibition, which prevents cFos repression, impairs reversal learning, while learning and memory of the initial platform location remain unaffected. Our study supports the hypothesis that epigenetic mechanisms tightly regulate cFos expression in individual granule cells to orchestrate the formation of time-stamped memories.
The Representation of Decision Variables in Orbitofrontal Cortex is Longitudinally Stable
Authors: Zhang Manning , Livi Alessandro , Carter Mary , Schoknecht Heide , Burkhalter Andreas , Holy Timothy E. , Padoa-Schioppa Camillo
Published: February 2024

The computation and comparison of subjective values underlying economic choices rely on the orbitofrontal cortex (OFC). In this area, distinct groups of neurons encode the value of individual options, the binary choice outcome, and the chosen value. These variables capture both the input and the output of the choice process, suggesting that the cell groups found in OFC constitute the building blocks of a decision circuit. Here we show that this neural circuit is longitudinally stable. Using two-photon calcium imaging, we recorded from mice choosing between different juice flavors. Recordings of individual cells continued for up to 20 weeks. For each cell and each pair of sessions, we compared the activity profiles using cosine similarity, and we assessed whether the cell encoded the same variable in both sessions. These analyses revealed a high degree of stability and a modest representational drift. A quantitative estimate indicated this drift would not randomize the circuit within the animal’s lifetime.
Interplay between Mg2+and Ca2+at multiple sites of the ryanodine receptor
Authors: Nayak Ashok R. , Rangubpit Warin , Will Alex H. , Hu Yifan , Castro-Hartmann Pablo , Lobo Joshua J. , Dryden Kelly , Lamb Graham D. , Sompornpisut Pornthep , Samsó Montserrat
Published: February 2024

RyR1 is an intracellular Ca2+channel important in excitable cells. Ca2+activates it at low concentrations and inhibits it at high concentrations. Mg2+is the main physiological RyR1 inhibitor, an effect that is overridden upon activation. Despite the significance of Mg2+-mediated inhibition, the molecular-level mechanisms remain unclear. We determined two cryo-EM structures of RyR1 with Mg2+up to 2.8 Å resolution, identifying multiple Mg2+binding sites. Mg2+inhibits at the known Ca2+activating site and we propose that the EF hand domain is an inhibitory divalent cation sensor. Both divalent cations bind to ATP within a crevice, contributing to the precise transmission of allosteric changes within the enormous channel protein. Notably, Mg2+inhibits RyR1 by interacting with the gating helices as validated by molecular dynamics. This structural insight enhances our understanding of how Mg2+inhibition is overcome during excitation.
Sequence-based genome-wide association studies reveal the polygenic architecture ofVarroa destructorresistance in Western honey beesApis mellifera
Authors: Eynard Sonia E. , Mondet Fanny , Basso Benjamin , Bouchez Olivier , Le Conte Yves , Dainat Benjamin , Decourtye Axel , Genestout Lucie , Guichard Matthieu , Guillaume François , Labarthe Emmanuelle , Locke Barbara , Mahla Rachid , de Miranda Joachim , Neuditschko Markus , Phocas Florence , Tabet Kamila , Vignal Alain , Servin Bertrand
Published: February 2024

Honey bees,Apis mellifera, have experienced the full impacts of globalisation, including the recent invasion by the parasitic miteVarroa destructorwhich has become one of the main causes of colony losses worldwide. Despite its lethal effects, some colonies have developed defence strategies conferring colony resistance and, assuming non-null heritability, selective breeding of naturally resistant bees could be a sustainable way to fight infestations. Here we report on the largest genome-wide association study performed on honey bees to understand the genetic basis of multiple phenotypes linked to varroa resistance. This study was performed on whole genome sequencing of more than 1,500 colonies belonging to different ancestries and combined in a meta-analysis. Results show that varroa resistance is polygenic. A total of 60 genetic markers were identified as having a significant impact in at least one of the tested populations pinpointing several regions of the honey bee genome. Our results also support strategies for genomic selection in honey bee breeding.
Blockade of TREM2 ameliorates pulmonary inflammation and fibrosis by modulating sphingolipid metabolism
Authors: Gu Xueqing , Kang Hanyujie , Cao Siyu , Tong Zhaohui , Song Nan
Published: February 2024

Pulmonary fibrosis is a chronic interstitial lung disease involving systemic inflammation and abnormal collagen deposition. Dysregulations in lipid metabolism, such as macrophage-dependent lipid catabolism, have been recognized as critical factors for the development of pulmonary fibrosis. However, little is known about the signaling pathways involved and the key regulators. Here we found that triggering receptor expressed on myeloid cells 2 (TREM2) plays a pivotal role in regulating the lipid handling capacities of pulmonary macrophages and triggering fibrosis. By integrating analysis of single-cell and bulk RNA sequencing data from patients and mice with pulmonary fibrosis, we revealed that pulmonary macrophages consist of heterogeneous populations with distinct pro-fibrotic properties, and found that both sphingolipid metabolism and the expression of chemotaxis-related genes are elevated in fibrotic lungs. TREM2, a sensor recognizing multiple lipid species, is specifically upregulated in a subset of monocyte- derived macrophages. Blockade of TREM2 by gene knock-out or soluble TREM2 administration can both attenuate bleomycin-induced pulmonary fibrosis. By utilizing scRNA Seq and lipidomics, we found thatTrem2deficiency downregulates the synthesis of various sphingomyelins, and inhibits the expression of chemokines such asCcl2. Together, our findings not only reveal the alterations in lipidomic profiles and the atlas of pulmonary macrophages during pulmonary fibrosis, but also suggest that targeting TREM2, the crucial regulator affecting both pulmonary sphingolipid metabolism and the chemokines secretion, can benefit pulmonary fibrosis patients in the future.
Comparative analyses of adsorbed circulating proteins in the PMMA and PES hemodiafilters in patients on predilution online hemodiafiltration
Authors: Islam Md. Shoriful , Ema Shingo , Nabi Md. Mahamodun , Rahman Md. Muedur , Waliullah A.S.M. , Yan Jing , Ferdous Rafia , Sakamoto Takumi , Takahashi Yutaka , Kato Akihiko , Sato Tomohito , Kahyo Tomoaki , Setou Mitsutoshi
Published: February 2024

Acute and chronic inflammation are common in patients with end-stage kidney disease (ESKD). So, the adsorption of pro-inflammatory cytokines by the hollow fiber has been expected to modify the inflammatory dysregulation in ESKD patients. However, it remains to be determined in detail what molecules of fiber materials can preferably adsorb proteins from the circulating circuit. We aimed this study to analyze directly the adsorbed proteins in the polymethyl methacrylate (PMMA) and polyethersulfone (PES) membranes in patients on predilution online hemodiafiltration (OL-HDF). To compare the adsorbed proteins in the PMMA and PES hemodiafilters membrane, we initially performed predilution OL-HDF using the PES (MFX-25Seco) membrane while then switched to the PMMA (PMF™-A) membrane under the same condition in three patients. We extracted proteins from the collected hemodiafilters by extraction, then SDS-PAGE of the extracted sample, protein isolation, in-gel tryptic digestion, and nano-LC MS/MS analyses. The concentrations of adsorbed proteins from the PMMA and PES membrane extracts were 35.6±7.9 µg/µL and 26.1±9.2 µg/µL. SDS-PAGE analysis revealed distinct variations of adsorbed proteins mainly in the molecular weight between 10 to 25 kDa. By tryptic gel digestion and mass spectrometric analysis, the PMMA membrane exhibited higher adsorptions of β2 microglobulin, dermcidin, retinol-binding protein-4, and lambda-1 light chain than those from the PES membrane. In contrast, amyloid A-1 protein was adsorbed more potently in the PES membrane. Western blot analyses revealed that the PMMA membrane adsorbed interleukin-6 (IL-6) approximately 5 to 118 times compared to the PES membrane. These findings suggest that PMMA-based OL-HDF therapy may be useful in controlling inflammatory status in ESKD patients.
The Gehan test identifies life-extending compounds overlooked by the log-rank test in the NIA Interventions Testing Program: Metformin, Enalapril, caffeic acid phenethyl ester, green tea extract, and 17-dimethylaminoethylamino-17-demethoxygeldanamycin hydrochloride
Authors: Jiang Nisi , Gelfond Jonathan , Liu Qianqian , Strong Randy , Nelson James F.
Published: February 2024

The National Institute on Aging Interventions Testing Program (ITP) has so far identified 12 compounds that extend the lifespan of genetically heterogeneous mice using the log-rank test. However, the log-rank test is relatively insensitive to any compound that does not uniformly reduce mortality across the lifespan. This test may thus miss compounds that only reduce mortality before midlife, for example, a plausible outcome if a compound only mitigates risk factors before midlife or if its efficacy is reduced at later ages. We therefore reanalyzed all data collected by the ITP from 2004-2022 using the Gehan test, which is more sensitive to mortality differences earlier in the life course and does not assume a uniformly reduced mortality hazard across the lifespan. The Gehan test identified 5 additional compounds, metformin, enalapril, 17-dimethylaminoethylamino-17-demethoxygeldanamycin hydrochloride (17-DMAG), caffeic acid phenethyl ester (CAPE), and green tea extract (GTE), which significantly increased survival but were previously missed by the log-rank test. Three (metformin, enalapril, and 17-DMAG) were only effective in males and two (CAPE and GTE) were only effective in females. In addition, 1,3-butanediol, which by log-rank analysis increased survival in females but not males, increased survival in males by the Gehan test. These results suggest that statistical tests sensitive to non-uniformity of drug efficacy across the lifespan should be included in the standard statistical testing protocol to minimize overlooking geroprotective interventions.
An explanation for the sister repulsion phenomenon in Patterson’s f-statistics
Authors: Atağ Gözde , Waldman Shamam , Carmi Shai , Somel Mehmet
Published: February 2024

Patterson’s f-statistics are among the most heavily utilized tools for analysing genome-wide allele frequency data for demographic inference. Beyond studying admixture,f3andf4statistics are also used for clustering populations to identify groups with similar histories. However, previous studies have noted an unexpected behaviour of f-statistics: multiple populations from a certain region systematically show higher genetic affinity to a more distant population than to their neighbours, a pattern that is mismatched with alternative measures of genetic similarity. We call this counter-intuitive pattern “sister repulsion”. We first present a novel instance of sister repulsion, where genomes from Bronze Age East Anatolian sites show higher affinity towards Bronze Age Greece rather than each other. This is observed both usingf3- andf4-statistics, contrasts with archaeological/historical expectation, and also contradicts genetic affinity patterns captured using PCA or MDS on genetic distances. We then propose a simple demographic model to explain this pattern, where sister populations receive gene flow from a genetically distant source. We calculatef3- andf4-statistics using simulated genetic data with varying population genetic parameters, confirming that low-level gene flow from an external source into populations from one region can create sister repulsion in f-statistics. Unidirectional gene flow between the studied regions (without an external source) can likewise create repulsion. Meanwhile, similar to our empirical observations, MDS analyses of genetic distances still cluster sister populations together. Overall, our results highlight the impact of low-level admixture events when inferring demographic history using f-statistics.
Comparative Multi-omic Mapping of Human Pancreatic Islet Endoplasmic Reticulum and Cytokine Stress Responses Provides Insights into Type 2 Diabetes Genetics
Authors: Sokolowski Eishani Kumar , Kursawe Romy , Selvam Vijay , Bhuiyan Redwan M. , Thibodeau Asa , Zhao Chi , Spracklen Cassandra N. , Ucar Duygu , Stitzel Michael L.
Published: February 2024

Endoplasmic reticulum (ER) and inflammatory stress responses are two pathophysiologic factors contributing to islet dysfunction and failure in Type 2 Diabetes (T2D). However, how human islet cells respond to these stressors and whether T2D-associated genetic variants modulate these responses is unknown. To fill this knowledge gap, we profiled transcriptional (RNA-seq) and epigenetic (ATAC-seq) remodeling in human islets exposed toex vivoER (thapsigargin) or inflammatory (IL-1β+IFN-γ) stress. 5,427 genes (∼32%) were associated with stress responses; most were stressor-specific, including upregulation of genes mediating unfolded protein response (e.g.DDIT3, ATF4) and NFKB signaling (e.g.NFKB1, NFKBIA) in ER stress and cytokine-induced inflammation respectively. Islet single-cell RNA-seq profiling revealed strong but heterogeneous beta cell ER stress responses, including a distinct beta cell subset that highly expressed apoptotic genes. Epigenetic profiling uncovered 14,968 stress-responsivecis-regulatory elements (CREs; ∼14%), the majority of which were stressor-specific, and revealed increased accessibility at binding sites of transcription factors that were induced upon stress (e.g. ATF4 for ER stress, IRF8 for cytokine-induced inflammation). Eighty-six stress-responsive CREs overlapped known T2D-associated variants, including 20 residing within CREs that were more accessible upon ER stress. Among these, we linked the rs6917676 T2D risk allele (T) to increasedin vivoaccessibility of an islet ER stress-responsive CRE and allele-specific beta cell nuclear factor bindingin vitro. We showed thatMAP3K5,the only ER stress-responsive gene in this locus, promotes beta cell apoptosis. Consistent with its pro-apoptotic and putative diabetogenic roles,MAP3K5expression inversely correlated with beta cell abundance in human islets and was induced in beta cells from T2D donors. Together, this study provides new genome-wide insights into human islet stress responses and putative mechanisms of T2D genetic variants.
Targeting CD19 for the treatment of autoimmune with a novel T cell engager
Authors: Yuan Andy Qingan , Zhao Likun , Bai Lili , Wang Yang , Yang Isabella , Yuan Ray Qirui , Meng Qingwu , Dai Xuning
Published: February 2024

Autoimmune disorder, affecting more than twenty million in United States and billions of people worldwide, occurs when human immune system mistakenly attacks its own body. Autoreactive B cells, particularly the autoantibodies they produce, play a critical role in the etiology, progress, prognosis, and pathogenesis of multiple autoimmune diseases. While targeting B cells medicines, such as anti-CD19 or anti-CD20 monoclonal antibodies have produced promise in both pre-clinic models and some clinic practices, many patients failed to respond, ended less satisfactory outcome, or relapsed to monoclonal antibody therapies. Novel therapies are desperately needed to fight this challenge. In this study, based upon a symmetrical format, namely fusion of IgG and scFv technology (FIST), an anti-CD19xCD3 T cell engager (TCE) YK012, developed to treat B-cell malignancies such as precursor pre-B acute lymphatic leukemia (ALL) and non-Hodgkin’s lymphoma (NHL), was expanded to explore the treatment of autoimmune diseases by bringing T cells to CD19 positive B cells, including autoreactive B cell populations. Even as bivalent binding to CD3, YK012 has so significantly reduced binding affinity to TCR compared to other TCEs that, free YK012 alone does activate T cells at all. In contrast, in the presence of CD19-expressing Raji target cells and mediated by YK012, T cells can be activated in a dose-dependent manner, measured by upregulation of NFAT-reporter, CD25, IFN-γ and granzyme B expression. Crosslinking of B cell with T cell by YK012, the conjugation elicited T cell-mediated potent but mild cytotoxicity only to CD19-positive Raji cells. Additionally, YK012 elicited much reduced cytokines releasein vitrocompared to that of Blincyto®biosimilar, implying a potentially me-better therapeutics replacement in clinics for B-cell related diseases. In twoin vivopharmacological studies, YK012 alleviated the pathology symptoms of a collagen-induced arthritis model and almost completely depleted the peripheral B cell in human stem cell-transplanted murine model. In summary, this study demonstrated that YK012, a FIST platform designed TCE, has the potential to treat B cell-mediated diseases including autoimmune indications with possible better efficacy and less side effects in clinical practices.
An open-source MRI compatible frame for multimodal presurgical mapping in macaque and capuchin monkeys
Authors: Liang Lucy , Zimmermann Rollin Isabela , Alikaya Aydin , Ho Jonathan C. , Santini Tales , Bostan Andreea C. , Schwerdt Helen N. , Stauffer William R. , Ibrahim Tamer S. , Pirondini Elvira , Schaeffer David J.
Published: February 2024

Highlights:

We present a compact MRI-compatible stereotaxic frame for large nonhuman primates.

The design is 3D printable, inexpensive, and matches size of an adult human head.

Enabled real-time, accurate, MRI-guided deep-brain viral vector injection.

Facilitated multimodal alignment for deep-brain electrophysiology planning.

All computer-aided-design files are modularized and publicly available and editable.

Background

High-precision neurosurgical targeting in nonhuman primates (NHPs) often requires presurgical anatomy mapping with noninvasive neuroimaging techniques (MRI, CT, PET), allowing for translation of individual anatomical coordinates to surgical stereotaxic apparatus. Given the varied tissue contrasts that these imaging techniques produce, precise alignment of imaging-based coordinates to surgical apparatus can be cumbersome. MRI-compatible stereotaxis with radiopaque fiducial markers offer a straight-forward and reliable solution, but existing commercial options do not fit in conformal head coils that maximize imaging quality.

New method

We developed a compact MRI-compatible stereotaxis suitable for a variety of NHP species (Macaca mulatta,Macaca fascicularis, andCebus apella) that allows multimodal alignment through technique-specific fiducial markers.

Comparison with existing methods

With the express purpose of compatibility with clinically available MRI, CT, and PET systems, the frame is no larger than a human head, while allowing for imaging NHPs in the supinated position. This design requires no marker implantation, special software, or additional knowledge other than the operation of a common large animal stereotaxis.

Results

We demonstrated the applicability of this 3D-printable apparatus across a diverse set of experiments requiring presurgical planning: 1) We demonstrate the accuracy of the fiducial system through a within-MRI cannula insertion and subcortical injection of viral vectors. 2) We also demonstrated accuracy of multimodal (MRI and CT) alignment and coordinate transfer to guide a surgical robot electrode implantation for deep-brain electrophysiology.

Conclusions

The computer-aided design files and engineering drawings are publicly available, with the modular design allowing for low cost and manageable manufacturing.
Stochastic regimes can hide the attractors in data, reconstruction algorithms can reveal them
Authors: M. S. Arani Babak , R. Carpenter Stephen , H. van Nes Egbert , A. van de Leemput Ingrid , Xu Chi , G. Lind Pedro , Scheffer Marten
Published: February 2024

Tipping points and alternative attractors have become an important focus of research and public discussions about the future of climate, ecosystems and societies. However, empirical evidence for the existence of alternative attractors remains scarce. For example, bimodal frequency distributions of state variables may suggest bistability, but can also be due to bimodality in external conditions. Here, we bring a new dimension to the classical arguments on alternative stable states and their resilience showing that the stochastic regime can distort the relationship between the probability distribution of states and the underlying attractors. Simple additive Gaussian white noise produces a one-to-one correspondence between the modes of frequency distributions and alternative stable states. However, for more realistic types of noise, the number and position of modes of the frequency distribution do not necessarily match the equilibria of the underlying deterministic system. We show that data must represent the stochastic regime as thoroughly as possible. When data are adequate then existing methods can be used to determine the nature of the underlying deterministic system and noise simultaneously. This may help resolve the question of whether there are tipping points, but also how realized states of a system are shaped by stochastic forcing vs internal stability properties.

Open Research Statement

Data and MATLAB codes for results reported here are available in the Github repositoryhttps://github.com/mshoja/Reconst(Babak M. S. Arani 2023) The original data source is cited in the text.
Potential of Photoelectric Stimulation with Ultrasmall Carbon Electrode on Neural Tissue: New Directions in Neuromodulation Technology Development
Authors: Chen Keying , Wu Bingchen , Krahe Daniela , Vazquez Alberto , Siegenthaler James R. , Rechenberg Robert , Li Wen , Cui X. Tracy , Kozai Takashi D.Y.
Published: February 2024

Objective

Neuromodulation technologies have gained considerable attention for its clinical potential in treating neurological disorders and their capacity to advance cognition research. Nevertheless, traditional neuromodulation methods such as electrical stimulation and optogenetics manipulation currently experience technical and biological challenges that hinge their therapeutic potential and chronic research applications. Recently, a promising alternative neuromodulation approach based on the photoelectric effect has emerged. This approach is capable of generating electrical pulses when exposed to near-infrared (NIR) light and allows modulation of neuronal activity without the need for genetic alterations. In this study, we investigate a variety of design strategies aimed at enhancing photoelectric stimulation using minimally invasive, ultrasmall, untethered carbon electrodes.

Approach

A multiphoton laser was employed as the NIR light source. Benchtop investigations were conducted using a three-electrode setup, and chronopotentiometry was used to record photo-stimulated voltage. Forin vivoevaluation, we used Thy1-GCaMP6s mice with acute implantation of ultrasmall carbon electrodes.

Main results

We revealed the beneficial effects of high duty-cycle laser scanning and photovoltaic polymer interfaces on the photo-stimulated voltages of ultrasmall carbon electrodes. Additionally, we demonstrated the promising potential of carbon-based diamond electrodes for photoelectric stimulation and examined the application of photoelectric stimulation in precise chemical delivery by loading mesoporous silica nanoparticles (SNPs) co-deposited with polyethylenedioxythiophene (PEDOT).

Significance

These findings on photoelectric stimulation utilizing ultrasmall carbon electrodes underscore its immense potential for advancing the next generation of neuromodulation technology. This approach offers the opportunity to effectively modulate neural tissue while minimizing invasive implantation-related injuries in freely moving subjects, which hold significant promise for a wide range of applications in neuroscience research and clinical settings.
Structural architecture of a prokaryotic metabolon reveals conserved interfaces mediating multiple protein-protein interactions
Authors: Bhattacharyya Sanchari , Ranganathan Srivastav , Chowdhury Sourav , Adkar Bharat V , Khrapko Mark , Shakhnovich Eugene I
Published: February 2024

Enzymes in a pathway often form metabolons through weak protein-protein interactions (PPI) that localize and protect labile metabolites. Due to their transient nature, the structural architecture of these enzyme assemblies has largely remained elusive, thereby limiting our abilities to re-engineer novel metabolic pathways. Here we delineate a complete PPI map of 1225 interactions in theE. coli1-carbon metabolism pathway using bimolecular fluorescence complementation that can capture transient interactionsin vivoand show strong intra- and inter-pathway clusters within the folate and purine biosynthesis pathways. Further, deep scanning mutagenesis experiments along with AlphaFold predictions and meta-dynamics simulations not only reveal interaction interfaces of all PPI in the folate pathway but also uncovers that most proteins use conserved “dedicated” interfaces distant from their active sites to interact with multiple partners. Overall, this study sheds light on the fundamental features of metabolon biophysics and structural aspects of transient binary complexes.

Significance statement

Enzymes from the same metabolic pathway often form dynamic assemblies called metabolons, which channel metabolites as well as protect labile intermediates. Yet very little is known about their structural features or what makes these interactions transient. Paucity of such information has particularly affected our ability to engineer novel metabolic pathways, construct multi-scale mathematical models of cells, etc. We address this by obtaining a comprehensive map for 1225 interaction pairs in the essential 1-carbon metabolism pathway ofE. coli. Using both high-throughput experiments and computation, we uncover that metabolon proteins tend to use a conserved dedicated interface to interact with their partners. These results shed light on structural and energetic aspects of PPI in metabolons at near atomic level of resolution.
Mycorrhizal and endophytic fungi structure contrasting but interdependent assembly processes in forest below-ground symbiosis
Authors: Noguchi Mikihito , Toju Hirokazu
Published: February 2024

Interactions between plants and diverse root-associated fungi are essential drivers of forest ecosystem dynamics. The nature of the symbiosis in root systems is potentially dependent on multiple ecological factors/processes such as host/symbiont specificity, background soil microbiome structure, inter-root sharing/dispersal of symbionts, and fungus–fungus interactions within fine roots. Nonetheless, it has remained a major challenge to reveal the mechanisms by which those multiple factors/processes determine the assembly of mycorrhizal and endophytic fungal communities. Based on a framework of joint species distribution modeling, we here examined how root-associated fungal community structure was collectively formed through filtering by host plants, associations with background soil fungi, spatial autocorrelation, and symbiont–symbiont interactions. In our analysis targeting 1,615 root-tip samples collected in a cool-temperate forest dominated by ectomycorrhizal plants, statistical models including all the four ecological factors/processes best explained the fine-scale community structure of root-associated fungi. Meanwhile, among partial models including subsets of those ecological factors/processes, those including background soil microbiome structure and within-root fungus–fungus interactions showed the highest performance. When fine-root distributions of respective fugal species/taxa were examined, ectomycorrhizal fungi tended to show stronger associations with background soil community structure and stronger spatially-autocorrelated patterns than other fungal guilds. In contrast, the distributions of root-endophytic fungi were inferred to depend greatly on fungus–fungus interactions. A network statistical analysis further suggested that some endophytic fungi, such as those belonging to the ascomycete generaPhialocephalaandLeptodontidium, were involved in webs of positive and negative interactions with other root-associated fungi. These results suggest that basic assembly rules can differ between mycorrhizal and endophytic fungi, both of which are major components of forest ecosystems. Consequently, knowledge of how multiple ecological factors/processes differentially drive the assembly of multiple fungal functional guilds is indispensable for comprehensively understanding the mechanisms by which terrestrial ecosystem dynamics are organized by plant–fungal symbiosis.
High-resolution lineage tracking of within-host evolution and strain transmission in a human gut symbiont across ecological scales
Authors: Vasquez Kimberly S. , Wong Daniel P.G.H. , Pedro Miguel F. , Yu Feiqiao Brian , Jain Sunit , Meng Xiandong , Higginbottom Steven K. , DeFelice Brian C. , Neff Norma , Bhatt Ami , Tropini Carolina , Xavier Karina B. , Sonnenburg Justin L. , Good Benjamin H. , Huang Kerwyn Casey
Published: February 2024

Gut bacteria rapidly evolvein vivo, but their long-term success requires dispersal across hosts. Here, we quantify this interplay by tracking >50,000 genomically barcoded lineages of the prevalent commensalBacteroides thetaiotaomicron(Bt) among co-housed mice. We find that adaptive mutations rapidly spread between hosts, overcoming the natural colonization resistance of residentBtstrains. Daily transmission rates varied >10-fold across hosts, but shared selection pressures drove predictable engraftment of specific lineages over time. The addition of a 49-species community shifted the adaptive landscape relative to mono-colonizedBtwithout slowing the rate of evolution, and reduced transmission while still allowing specific mutants to engraft. Whole-genome sequencing uncovered diverse modes of adaptation involving complex carbohydrate metabolism. Complementaryin vitroevolution across 29 carbon sources revealed variable overlap within vivoselection pressures, potentially reflecting synergistic and antagonistic pleiotropies. These results show how high-resolution lineage tracking enables quantification of commensal evolution across ecological scales.
A Model of Ethanol Self-Administration in Head-Fixed Mice
Authors: Ward Amy L. , Winston Kion T. , Buchmaier Sophie A. , Clarke Rachel E. , Bell Marcus S. , Martino Michael R. , Vollmer Kelsey M. , Paniccia Jacqueline , Doncheck Elizabeth M. , Grant R. Ian , Otis James M. , Rinker Jennifer A.
Published: February 2024

Significant advances in neurotechnology, such as the emergence of 2-photon imaging, have enabled unparalleled access to the complex neural circuits that coordinate behavior in rodents. Integration of these techniques would be groundbreaking for the study of animal models of alcohol use disorder (AUD), which is rooted in longitudinal brain adaptations that could be functionally monitored and manipulated at the level of neural circuits from the onset of alcohol use through dependence. However, 2-photon and related methodologies require or are often facilitated by head-fixation, and a lack of head-fixed models have hindered their integration in the study of AUD. Here we present a head-fixed alcohol self-administration model, and find that head-fixed male and female mice will reliably press an active, but not inactive, lever for an oral alcohol reward. The number of alcohol rewards obtained reliably predicted blood alcohol concentrations, at physiologically relevant levels. Furthermore, we demonstrate that mice can extinguish alcohol self-administration when the alcohol reward is omitted, suggesting active lever pressing behavior was alcohol-directed. Following extinction, presentation of alcohol-related cues or a priming reminder of alcohol itself invigorated reinstatement of alcohol seeking, modeling relapse in a manner that mimics decades of work in freely-moving rodent studies. Overall, our head-fixed alcohol self-administration model allows integration of novel technologies that require or are greatly facilitated by head-fixation, improving our ability to study and understand the neural circuits adaptations and computations that underlie AUD.