bluuebunny/crossref_metadata_2025 huggingface dataset:
Complementary approaches to dissect late leaf rust resistance in an interspecific raspberry population
Authors: Prado Melina , da Silva Allison Vieira , Campos Gabriela Romêro , Reis Borges Karina Lima , Yassue Rafael Massahiro , Husein Gustavo , Akens Felix Frederik , Sposito Marcel Bellato , Amorim Lilian , Behrouzi Pariya , Bustos-Korts Daniela , Fritsche-Neto Roberto
Published: January 2024

Over the last ten years, global raspberry production has increased by 47.89%, based on the red species (Rubus idaeus). However, the black raspberry species (Rubus occidentalis), although less consumed, is resistant to one of the most important diseases for the crop, the late leaf rust caused byAcculeastrum americanumfungus, to which the red ones are susceptible. In this context, genetic resistance is the most sustainable way to control the disease, mainly because there are no registered fungicides for late leaf rust in the crop in Brazil. Therefore, the aim was to understand the genetic architecture that controls resistance to late rust in raspberries. For that, we used an interspecific diversity panel between the cited above species, two different statistical approaches to associate the phenotypes to the markers (GWAS and copula graphical models), and two phenotyping methodologies from the first to the seventeenth day after inoculation (high-throughput phenotyping with a multispectral camera and traditional phenotyping by disease severity scores). Our findings indicate that a locus of higher effect possibly controls the resistance to late leaf rust, as both GWAS and the network suggested the same marker. Furthermore, a candidate defense-related gene cluster is close to this marker. Finally, the best stage to evaluate for disease severity is thirteen days after inoculation, confirmed by both traditional and high-throughput phenotyping. Although the network and GWAS indicated the same higher effect genomic region, the network identified other different regions complementing the genetic control comprehension.
Blood-based targeted metabolipidomics reveals altered omega fatty acid-derived lipid mediators in relapsing-remitting multiple sclerosis patients
Authors: Zahoor Insha , Waters Jeffrey , Ata Nasar , Datta Indrani , Pedersen Theresa L. , Cerghet Mirela , Poisson Laila , Markovic-Plese Silva , Rattan Ramandeep , Taha Ameer Y. , Newman John W. , Giri Shailendra
Published: January 2024

Unresolved and uncontrolled inflammation is considered a hallmark of pathogenesis in chronic inflammatory diseases like multiple sclerosis (MS), suggesting a defective resolution process. Inflammatory resolution is an active process partially mediated by endogenous metabolites of dietary polyunsaturated fatty acids (PUFA), collectively termed specialized pro-resolving lipid mediators (SPMs). Altered levels of resolution mediators have been reported in several inflammatory diseases and may partly explain impaired inflammatory resolution. Performing LC-MS/MS-based targeted lipid mediator profiling, we observed distinct changes in fatty acid metabolites in serum from 30 relapsing-remitting MS (RRMS) patients relative to 30 matched healthy subjects (HS). Robust linear regression revealed 12 altered lipid mediators after adjusting for confounders (p <0.05). Of these, 15d-PGJ2, PGE3, and LTB5 were increased in MS while PGF2a, 8,9-DiHETrE, 5,6-DiHETrE, 20-HETE, 15-HETE, 12-HETE, 12-HEPE, 14-HDoHE, and DHEA were decreased in MS compared to HS. In addition, 12,13-DiHOME and 12,13-DiHODE were positively correlated with expanded disability status scale values (EDSS). Using Partial Least Squares, we identified several lipid mediators with high VIP scores (VIP > 1: 32% - 52%) of which POEA, PGE3, DHEA, LTB5, and 12-HETE were top predictors for distinguishing between RRMS and HS (AUC =0.75) based on the XGBoost Classifier algorithm. Collectively, these findings suggest an imbalance between inflammation and resolution. Altogether, lipid mediators appear to have potential as diagnostic and prognostic biomarkers for RRMS.
Targeting glioblastoma tumor hyaluronan to enhance therapeutic interventions that regulate metabolic cell properties
Authors: Neves Edward R , Anand Achal , Mueller Joseph , Remy Roddel A , Xu Hui , Selting Kim A , Sarkaria Jann N. , Harley Brendan AC , Pedron-Haba Sara
Published: January 2024

Despite extensive advances in cancer research, glioblastoma (GBM) still remains a very locally invasive and thus challenging tumor to treat, with a poor median survival. Tumor cells remodel their microenvironment and utilize extracellular matrix to promote invasion and therapeutic resistance. We aim here to determine how GBM cells exploit hyaluronan (HA) to maintain proliferation using ligand-receptor dependent and ligand-receptor independent signaling. We use tissue engineering approaches to recreate the three-dimensional tumor microenvironment in vitro, then analyze shifts in metabolism, hyaluronan secretion, HA molecular weight distribution, as well as hyaluronan synthetic enzymes (HAS) and hyaluronidases (HYAL) activity in an array of patient derived xenograft GBM cells. We reveal that endogenous HA plays a role in mitochondrial respiration and cell proliferation in a tumor subtype dependent manner. We propose a tumor specific combination treatment of HYAL and HAS inhibitors to disrupt the HA stabilizing role in GBM cells. Taken together, these data shed light on the dual metabolic and ligand - dependent signaling roles of hyaluronan in glioblastoma.

Significance

The control of aberrant hyaluronan metabolism in the tumor microenvironment can improve the efficacy of current treatments. Bioengineered preclinical models demonstrate potential to predict, stratify and accelerate the development of cancer treatments.
Spatial Morphoproteomic Features Predict Uniqueness of Immune Microarchitectures and Responses in Lymphoid Follicles
Authors: Hu Thomas , Allam Mayar , Kaushik Vikram , Goudy Steven L. , Xu Qin , Mudd Pamela , Manthiram Kalpana , Coskun Ahmet F.
Published: January 2024

Multiplex imaging technologies allow the characterization of single cells in their cellular environments. Understanding the organization of single cells within their microenvironment and quantifying disease-status related biomarkers is essential for multiplex datasets. Here we proposed SNOWFLAKE, a graph neural network framework pipeline for the prediction of disease-status from combined multiplex cell expression and morphology in human B-cell follicles. We applied SNOWFLAKE to a multiplex dataset related to COVID-19 infection in humans and showed better predictive power of the SNOWFLAKE pipeline compared to other machine learning and deep learning methods. Moreover, we combined morphological features inside graph edge features to utilize attribution methods for extracting disease-relevant motifs from single-cell spatial graphs. The underlying subgraphs were further analyzed and associated with disease status across the dataset. We showed that SNOWFLAKE successfully extracted significant low dimensional embedding from subgraphs with a clear separation between disease status and helped characterize unique cellular interactions in the subgraphs. SNOWFLAKE is a generalizable pipeline for the analysis of multiplex imaging data modality by extracting disease-relevant subgraphs guided by graph-level prediction.
Neural interference between real and imagined visual stimuli
Authors: Sulfaro Alexander A , Robinson Amanda K , Carlson Thomas A
Published: January 2024

Evidence suggests that mental imagery and veridical perception recruit similar components of the human visual system. If so, neural representations of imagined and real stimuli should interact with one another, combining constructively or competing antagonistically. To determine if and how real and imagined visual stimuli interact in the brain, we asked participants to mentally visualise white bars at specific orientations after a rhythmic countdown while their brain activity was recorded using electroencephalography. Stimuli were imagined in isolation, or while another stimulus at a highly or poorly congruent orientation appeared on-screen. Multivariate pattern analysis was used to assess whether overlap between imagined and real stimulus features enhanced or diminished stimulus-specific sensory information in the brain. Findings showed that imagined and real orientation could be decoded from brain activity, with real orientation decoding mildly amplified by highly congruent, but not poorly congruent, imagined orientations. Although interactions between real and imagined stimuli were observed, no evidence was detected to suggest that imagined and real stimuli use the same neural activity patterns to encode sensory information. Instead, congruent imagery seemed only to amplify activity which had already been induced by real percepts, targeting late- but not early-stage perceptual representations. Ultimately, this study suggests that imagined and real stimuli interact in a mildly constructive manner, with imagination mostly acting in a modulatory capacity.
System-level analysis of genes mutated in muscular dystrophies reveals a functional pattern associated with muscle weakness distribution
Authors: Ozisik Ozan , Gorokhova Svetlana , Cerino Mathieu , Bartoli Marc , Baudot Anaïs
Published: January 2024

Muscular dystrophies (MDs) are inherited genetic diseases causing weakness and degeneration of muscles. The distribution of muscle weakness differs between MDs, involving distal muscles or proximal muscles. While the mutations in most of the MD-associated genes lead to either distal or proximal onset, there are also genes whose mutations can cause both types of onsets.

We hypothesized that the genes associated with different MD onsets code proteins with distinct cellular functions. To investigate this, we collected the MD-associated genes and assigned them to three onset groups: genes mutated only in distal onset dystrophies, genes mutated only in proximal onset dystrophies, and genes mutated in both types of onsets. We then systematically evaluated the cellular functions of these gene sets with computational strategies based on functional enrichment analysis and biological network analysis.

Our analyses demonstrate that genes mutated in either distal or proximal onset MDs code proteins linked with two distinct sets of cellular processes. Interestingly, these two sets of cellular processes are relevant for the genes that are associated with both onsets. Moreover, the genes associated with both onsets display high centrality and connectivity in the network of muscular dystrophy genes. Our findings support the hypothesis that the proteins associated with distal or proximal onsets have distinct functional characteristics, whereas the proteins associated with both onsets are multifunctional.
Mycobacterium tuberculosisexploits SIRT2 for iron acquisition to facilitate its intracellular survival
Authors: Talukdar Sharmila , Modanwal Radheshyam , Chaubey Gaurav Kumar , Dhiman Asmita , Dilawari Rahul , Raje Chaaya Iyengar , Raje Manoj
Published: January 2024

Iron availability is a critical factor for both bacteria and humans, and its availability significantly influences host-pathogen dynamics. AsMtbhas coevolved with the human race,Mtbrelentlessly tries to exploit iron from the tightly regulated iron machinery of host. Sirtuins are evolutionary conserved NAD+-dependent deacetylases involved in various cellular processes including infection. Notably, the cytosolic protein, Sirtuin 2 regulates cellular iron homeostasis in hepatocytes and afterMtbinfection, SIRT2 translocates to the nucleus leading to decreased protective immune response. However, the underlying mechanism as to howMtbexploits SIRT2 for iron acquisition remains unknown. In the current study, we observe that the decreased bacillary load in SIRT2 inhibited or knock down cells is due to low availability of iron to the bacilli. Inhibition or knockdown of SIRT2 inMtbinfected cells displays differential modulation of iron import and export proteins suggesting ongoing tussle by host to limit the bioavailability of iron to pathogen. More specifically, by flow cytometry analysis, we show significant upregulation of cell surface Apo Tf and GAPDH in infected SIRT2 inhibited macrophages. Thus, in SIRT2 depleted state, we delineate a different mechanism of iron export occurring through Apo Tf and GAPDH during infection in contrast to the classical iron exporter Fpn1. Collectively, our findings showed the importance of SIRT2-mediated iron regulation inMtbpathogenesis and can encourage designing of novel host-targeted therapeutics.
CGRP inhibits SARS-CoV-2 infection of bronchial epithelial cells and its pulmonary levels correlate with viral clearance in critical COVID-19 patients
Authors: Barbosa Bomfim Caio César , Genin Hugo , Cottoignies-Callamarte Andréa , Gallois-Montbrun Sarah , Murigneux Emilie , Sams Anette , Rosenberg Arielle R , Belouzard Sandrine , Dubuisson Jean , Kosminder Olivier , Pène Frédéric , Terrier Benjamin , Bomsel Morgane , Ganor Yonatan
Published: January 2024

Upon infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), patients with critical coronavirus disease 2019 (COVID-19) present with life-threatening respiratory distress, pulmonary damage and cytokine storm. One unexplored hub in COVID-19 is the neuropeptide calcitonin gene-related peptide (CGRP), which is highly abundant in the airways and could converge in multiple aspects of COVID-19-related pulmonary pathophysiology. Whether CGRP affects SARS-CoV-2 infection directly remains elusive. We show that in critical COVID-19 patients, CGRP is increased in both plasma and lungs. Importantly, CGRP pulmonary levels are elevated in early SARS-CoV-2-positive patients, and restore to baseline upon subsequent viral clearance in SARS-CoV-2-negative patients. We further show that CGRP and its stable analogue SAX directly inhibit infection of bronchial Calu-3 epithelial cells with SARS-CoV-2 Omicron and Alpha variants in a dose-dependent manner. Both pre- and post-infection treatment with GRRP and/or SAX is enough to block SARS-CoV-2 productive infection of Calu3 cells. CGRP-mediated inhibition occurs via activation of the CGRP receptor and involves down-regulation of SARS-CoV-2 entry receptors at the surface of Calu-3 cells. Together, we propose that increased pulmonary CGRP mediates beneficial viral clearance in critical COVID-19 patients, by directly inhibiting SARS-CoV-2 infection. Hence, CGRP-based interventions could be harnessed for management of COVID-19.

Brief summary

Pulmonary levels of the neuropeptide CGRP are increased in critical COVID-19 patients, and could clear virus by directly inhibiting SRAS-CoV-2 infection of bronchial epithelia cells.
Mean Shift Clustering as a Loss Function for Accurate and Segmentation-aware Localization of Macromolecules in Cryo-electron Tomography
Authors: Lamm Lorenz , Righetto Ricardo D. , Peng Tingying
Published: January 2024

Cryo-electron tomography allows us to visualize and analyze the native cellular environment on a molecular level in 3D. To reliably study structures and interactions of proteins, they need to be accurately localized. Recent detection methods train a segmentation network and use post-processing to determine protein locations, often leading to inaccurate and inconsistent locations.

We present an end-to-end learning approach for more accurate protein center identification by introducing a differentiable, scoremap-guided Mean Shift clustering implementation. To make training computationally feasible, we sample random cluster points instead of processing the entire image.

We show that our Mean Shift loss leads to more accurate cluster center positions compared to the classical Dice loss. When combining these loss functions, we can enhance 3D protein shape preservation and improve clustering with more accurate, localization-focused score maps. In addition to improved protein localization, our method provides more efficient training with sparse ground truth annotations, due to our point sampling strategy.
Deciphering the diversity and sequence of extracellular matrix and cellular spatial patterns in lung adenocarcinoma using topological data analysis
Authors: Yoon Iris H.R. , Jenkins Robert , Colliver Emma , Zhang Hanyun , Novo David , Moore David , Ramsden Zoe , Rullan Antonio , Fu Xiao , Yuan Yinyin , Harrington Heather A. , Swanton Charles , Byrne Helen M. , Sahai Erik
Published: January 2024

Extracellular matrix (ECM) organization influences cancer development and progression. It modulates the invasion of cancer cells and can hinder the access of immune cells to cancer cells. Effective quantification of ECM architecture and its relationship to the position of different cell types is, therefore, important when investigating the role of ECM in cancer development. Using topological data analysis (TDA), particularly persistent homology and Dowker persistent homology, we develop a novel analysis pipeline for quantifying ECM architecture, spatial patterns of cell positions, and the spatial relationships between distinct constituents of the tumour microenvironment. We apply the pipeline to 44 surgical specimens of lung adenocarcinoma from the lung TRACERx study stained with picrosirius red and haematoxylin. We show that persistent homology effectively encodes the architectural features of the tumour microenvironment. Inference using pseudo-time analysis and spatial mapping to centimetre scale tissues suggests a gradual and progressive route of change in ECM architecture, with two different end states. Dowker persistent homology enables the analysis of spatial relationship between any pair of constituents of the tumour microenvironment, such as ECM, cancer cells, and leukocytes. We use Dowker persistent homology to quantify the spatial segregation of cancer and immune cells over different length scales. A combined analysis of both topological and non-topological features of the tumour microenvironment indicates that progressive changes in the ECM are linked to increased immune exclusion and reduced oxidative metabolism.
Swinging lever mechanism of myosin directly demonstrated by time-resolved cryoEM
Authors: Klebl David P. , McMillan Sean N. , Risi Cristina , Forgacs Eva , Virok Betty , Atherton Jennifer L. , Stofella Michele , Winkelmann Donald A. , Sobott Frank , Galkin Vitold E. , Knight Peter J. , Muench Stephen P. , Scarff Charlotte A. , White Howard D.
Published: January 2024

Myosins are essential for producing force and movement in cells through their interactions with F-actin. Generation of movement is proposed to occur through structural changes within the myosin motor domain, fuelled by ATP hydrolysis, that are amplified by a lever swing1, transitioning myosin from a primed (pre-powerstroke) state to a post-powerstroke state. However, the initial, primed actomyosin state, proposed to form prior to lever swing, has never been observed. Nor has the mechanism by which actin catalyses myosin ATPase activity been resolved. To address this, we performed time-resolved cryoEM of a myosin-5 mutant having slow hydrolysis product release. Primed actomyosin was captured 10 ms after mixing primed myosin with F-actin, whereas post-powerstroke actomyosin predominated at 120 ms, with no abundant intermediate structures. The structures were solved to 4.4Å and 4.2Å global resolution respectively. The primed motor binds to actin through its lower 50 kDa subdomain, with the actin-binding cleft open and Pi release prohibited. N-terminal actin interactions with myosin promote rotation of the upper 50 kDa subdomain, which closes the actin-binding cleft, and enables Pi release. Formation of upper 50 kDa subdomain interactions with actin creates the strong-binding interface required for effective force production. The myosin-5 lever swings through an angle of 93°, predominantly along the actin axis, with little twisting, to produce the post-powerstroke state. The magnitude of the lever swing matches the typical step length of myosin-5 walking along actin. These time-resolved structures directly demonstrate the swinging lever mechanism, ending decades of conjecture on how myosin produces force and movement.
Lettuce seedlings rapidly assemble their microbiome from the environment through deterministic processes
Authors: Mohamed Nesma Zakaria , Schena Leonardo , Malacrinò Antonino
Published: January 2024

Plant-associated microorganisms have significant impacts on plant biology, ecology, and evolution. Although several studies have examined the factors driving variations in plant microbiomes, the mechanisms underlying the assembly of the plant microbiome are still poorly understood. In this study, we used gnotobiotic plants to test (i) whether seedlings create a selective environment and drive the assembly of root and leaf microbiomes through deterministic or stochastic processes, and (ii) whether seedlings structure the microbiome that is transferred through seeds using deterministic processes and whether this pattern changes when seedlings are exposed to the environmental microbiome. Our results show that the microbiome of gnotobiotic plants (i.e., inherited through seeds) is not under the selective influence of the host plant but changes quickly when plants are exposed to soil microbiomes. Within one week, plants were able to select microorganisms from the inocula, assemble the root microbiome, and assemble the shoot microbiome. This study supports the hypothesis that plants at early developmental stages might exert strong selective activity on their microbiomes and contribute to clarifying the mechanisms of plant microbiome assembly.
Loss of the E3 ubiquitin ligase TRIM67 alters the post-synaptic density proteome
Authors: McCormick Laura E. , Barker Natalie K. , Herring Laura E. , Gupton Stephanie L.
Published: January 2024

The E3 ubiquitin ligase TRIM67 is enriched in the central nervous system and is required for proper neuronal development. Previously we demonstrated TRIM67 coordinates with the closely related E3 ubiquitin ligase TRIM9 to regulate cytoskeletal dynamics downstream of the netrin-1 during axon guidance and axon branching in early neuronal morphogenesis. Interestingly, loss ofTrim67impacts cognitive flexibility in a spatial learning and memory task. Despite this behavioral phenotype, it was previously uninvestigated if TRIM67 was involved in synapse formation or function. Here we demonstrate TRIM67 localizes to the post-synaptic density (PSD) within dendritic spines. Furthermore, we show that loss ofTrim67significantly changes the PSD proteome, including changes in the regulation of the actin and microtubule cytoskeletons. Collectively, our data propose a synaptic role for TRIM67.
Stable Individual Differences from Dynamic Patterns of Function: Brain Network Flexibility Predicts Openness/Intellect and Intelligence
Authors: Sassenberg Tyler A. , Safron Adam , DeYoung Colin G.
Published: January 2024

Growing understanding of the nature of brain function has led to increased interest in interpreting the properties of large-scale brain networks. Methodological advances in network neuroscience provide means to decompose these networks into smaller functional communities and measure how they reconfigure over time as an index of their dynamic and flexible properties. Recent evidence has identified associations between flexibility and a variety of traits pertaining to complex cognition including creativity and working memory. The present study used measures of dynamic resting-state functional connectivity in data from the Human Connectome Project (N= 994) to test associations with Openness/Intellect and general intelligence, two traits that involve flexible cognition. Using a machine-learning cross-validation approach, we identified reliable associations of intelligence with cohesive flexibility of parcels in large communities across the cortex, and of Openness/Intellect with overall flexibility among parcels in smaller communities. These findings are reasonably consistent with previous theories of the neural correlates of intelligence and Openness/Intellect, and help to expand on previous associations of behavior and dynamic functional connectivity within the context of broader personality dimensions.
Contaminant Spot Check and Removal Assay (ContamSPOT) for Mass Spectrometry Analysis
Authors: Smeriglio Noah , Li Haorong , binti Mazli Wan Nur Atiqah , Bendel Katharine , Hao Ling
Published: January 2024

Mass spectrometry (MS) analysis is often challenged by contaminations from detergents, salts, and polymers that compromise the data quality and can damage the chromatography and mass spectrometry instruments. However, researchers may not discover contamination issues until after data acquisition. There is no existing contaminant assay that is sensitive enough to detect trace amounts of contaminants from a few microliters of samples prior to MS analysis. To address this crucial need in the field, we developed a sensitive, rapid, and low-cost contaminant spot check and removal assay (ContamSPOT) to detect and quantify trace amounts of contaminants, such as detergents, salts, and other chemicals commonly used in MS sample preparation workflow. Only one microliter of sample was used prior to MS injection to quantify contaminants by ContamSPOT colorimetric or fluorometric assay on a thin layer chromatography (TLC) plate. We also optimized contaminant removal methods to salvage samples with minimal loss when ContamSPOT showed a positive result. ContamSPOT was then successfully applied to evaluate commonly used bottom- up proteomic methods, regarding the effectiveness of removing detergents, peptide recovery, and reproducibility. We expect ContamSPOT to be widely adopted by MS laboratories as a last-step quality checkpoint prior to MS injection. ContamSPOT can also provide a unique readout of sample cleanness for developing and evaluating MS-based sample preparation methods. We provided a practical decision tree and a step-by-step protocol with a troubleshooting guide to facilitate the use of ContamSPOT by other researchers.

Table of Contents (TOC) graphic

(All images used in the TOC graphic are original, in compliance with copyright guidelines.)
Invariant crossmodal equivalence evokes visual imagery from sounds in rhesus monkeys
Authors: Cabrera-Ruiz Elizabeth , Alva Marlen , Mata Miguel , Treviño Mario , Vergara José , Figueroa Tonatiuh , Perez-Orive Javier , Lemus Luis
Published: January 2024

After hearing the words Little Red Riding Hood, many humans instantly visualize a girl wearing a red hood in the woods. However, whether nonhuman primates also evoke such visual imagery from sounds remains an open question. We explored this from direct behavioral measurements from two rhesus macaques trained in a delayed crossmodal equivalence task. In each trial, they listened to a sound, such as a monkey vocalization or a word, and three seconds later, selected a visual equivalent out of a pool of 2 to 4 pictures appearing on a touchscreen. We show that monkeys can be trained to discriminate perceptual objects of numerous properties and furthermore that they perceive as invariant different versions of the learned sounds. We propose two potential mechanisms for the brain to solve this task: acoustic memory or visual imagery. After analyzing the monkeys’ choice accuracies and reaction times in the task, we find that they experience visual imagery when listening to sounds. Therefore, the ability of rhesus monkeys to perceive crossmodal equivalences between learned categories poses rhesus monkeys as an ideal model organism for studying high-order cognitive processes like semantics and conceptual thinking at the single-neuron level.
Potential pandemic risk of circulating swine H1N2 influenza viruses
Authors: Sage Valerie Le , Rockey Nicole C. , McCarthy Kevin R. , French Andrea J. , Shephard Meredith J. , McBride Ryan , Jones Jennifer E. , Walter Sydney G. , Doyle Joshua D. , Xu Lingqing , Barbeau Dominique J. , Wang Shengyang , Frizzell Sheila A. , Rigatti Lora H. , Myerburg Michael M. , Paulson James C. , McElroy Anita K. , Anderson Tavis K. , Baker Amy L. Vincent , Lakdawala Seema S.
Published: January 2024

Influenza A viruses in swine have considerable genetic diversity and continue to pose a pandemic threat to humans. They were the source of the most recent influenza pandemic, and since 2010, novel swine viruses have spilled over into humans more than 400 times in the United States. Although these zoonotic infections generally result in mild illness with limited onward human transmission, the potential for sustained transmission of an emerging influenza virus between individuals due to lack of population level immunity is of great concern. Compiling the literature on pandemic threat assessment, we established a pipeline to characterize and triage influenza viruses for their pandemic risk and examined the pandemic potential of two widespread swine origin viruses. Our analysis revealed that a panel of human sera collected from healthy adults in 2020 has no cross-reactive neutralizing antibodies against an α-H1 clade strain but do against a γ-H1 clade strain. Swine H1N2 virus from the α-H1 clade (α-swH1N2) replicated efficiently in human airway cultures and exhibited phenotypic signatures similar to the human H1N1 pandemic strain from 2009 (H1N1pdm09). Furthermore, α-swH1N2 was capable of efficient airborne transmission to both naïve ferrets and ferrets with prior seasonal influenza immunity. Ferrets with H1N1pdm09 pre-existing immunity had reduced α-swH1N2 viral shedding from the upper respiratory tract and cleared the infection faster. Despite this, H1N1pdm09-immune ferrets that became infected via the air could still onward transmit α-swH1N2 with an efficiency of 50%. Taken together, these results indicate that this α-swH1N2 strain has a higher pandemic potential, but a moderate level of impact since there is reduced replication fitness in animals with prior immunity.
Tissue Inhibitor of Metalloproteinase 3 (TIMP3) mutations increase glycolytic activity and dysregulate glutamine metabolism in RPE cells
Authors: Grenell Allison , Singh Charandeep , Raju Monisha , Wolk Alyson , Dalvi Sonal , Jang Geeng-Fu , Crabb John S. , Hershberger Courtney E. , Manian Kannan , Crabb John W. , Singh Ruchira , Du Jianhai , Anand-Apte Bela
Published: January 2024

Mutations in Tissue Inhibitor of Metalloproteinases 3 (TIMP3) cause Sorsby’s Fundus Dystrophy (SFD), a dominantly inherited, rare form of macular degeneration that results in vision loss. TIMP3 is synthesized primarily by retinal pigment epithelial (RPE) cells, which constitute the outer blood-retinal barrier. Quantitative proteomics and RNAseq analysis on the choroid/RPE of mice expressing mutant TIMP3 identified a dysregulation in metabolic processes. We examined the effects of mutant TIMP3 on RPE metabolism using human ARPE-19 cells expressing mutant S179C TIMP3 and patient-derived induced pluripotent stem cell-derived RPE (iRPE) carrying the S204C TIMP3 mutation. Stable isotope tracing experiments demonstrated enhanced glucose utilization and glycolytic activity in mutant RPE concomitantly with altered glutamine utilization. This study provides important information on the dysregulation of the metabolome of RPE cells in SFD and implicates a potential commonality with other retinal degenerative diseases, emphasizing RPE cellular metabolism as a therapeutic target.
Climate change, age acceleration, and the erosion of fitness in polar bears
Authors: Newediuk Levi , Richardson Evan S , Biddlecombe Brooke A. , Kassim Haziqa , Kathan Leah , Lunn Nicholas , Rivkin L Ruth , Salama Ola E , Schmidt Chloé , Jones Meaghan J , Garroway Colin J
Published: January 2024

Climate change is increasingly disrupting evolved life history strategies and reducing population viability in wild species. Using estimates of epigenetic age acceleration, a cellular biomarker of lifetime stress and the expression of age-related phenotypes, we found that polar bears aged approximately one year faster for each degree of warming since the 1960s. Age acceleration was also associated with reproducing early in life, linking this cellular process to well-established life history theory. However, we found evidence for the erosion of fitness as epigenetic aging accelerated and temperatures increased. Finally, using a large pedigree, we found adaptive potential in our study population was approximately zero. Global temperatures will soon reach the levels of warming currently experienced by Arctic species, which could impose widespread physiological costs and limit adaptive capacities worldwide.
A Supervised Contrastive Framework for Learning Disentangled Representations of Cell Perturbation Data
Authors: Tu Xinming , Hütter Jan-Christian , Wang Zitong Jerry , Kudo Takamasa , Regev Aviv , Lopez Romain
Published: January 2024

CRISPR technology, combined with single-cell RNA-Seq, has opened the way to large scale pooled perturbation screens, allowing more systematic interrogations of gene functions in cells at scale. However, such Perturb-seq data poses many analysis challenges, due to its high-dimensionality, high level of technical noise, and variable Cas9 efficiency. The single-cell nature of the data also poses its own challenges, as we observe the heterogeneity of phenotypes in the unperturbed cells, along with the effect of the perturbations. All in all, these characteristics make it difficult to discern subtler effects. Existing tools, like mixscape and ContrastiveVI, provide partial solutions, but may oversimplify biological dynamics, or have low power to characterize perturbations with a smaller effect size. Here, we address these limitations by introducing the Supervised Contrastive Variational Autoencoder (SC-VAE). SC-VAE integrates guide RNA identity with gene expression data, ensuring a more discriminative analysis, and adopts the Hilbert-Schmidt Independence Criterion as a way to achieve disentangled representations, separating the heterogeneity in the control population from the effect of the perturbations. Evaluation on large-scale data sets highlights SC-VAE’s superior sensitivity in identifying perturbation effects compared to ContrastiveVI, scVI and PCA. The perturbation embeddings better reflect known protein complexes (evaluated on CORUM), while its classifier offers promise in identifying assignment errors and cells escaping the perturbation phenotype. SC-VAE is readily applicable across diverse perturbation data sets.
Graph Learning for Cortical Parcellation from Tensor Decompositions of Resting-State fMRI
Authors: Liu Yijun , Li Jian , Wisnowski Jessica L. , Leahy Richard M.
Published: January 2024

Cortical parcellation has long been a cornerstone in the field of neuroscience, enabling the cerebral cortex to be partitioned into distinct, non-overlapping regions that facilitate the interpretation and comparison of complex neuroscientific data. In recent years, these parcellations have frequently been based on the use of resting-state fMRI (rsfMRI) data. In parallel, methods such as independent components analysis have long been used to identify large-scale functional networks with significant spatial overlap between networks. Despite the fact that both forms of decomposition make use of the same spontaneous brain activity measured with rsfMRI, a gap persists in establishing a clear relationship between disjoint cortical parcellations and brain-wide networks. To address this, we introduce a novel parcellation framework that integrates NASCAR, a three-dimensional tensor decomposition method that identifies a series of functional brain networks, with state-of-the-art graph representation learning to produce cortical parcellations that represent near-homogeneous functional regions that are consistent with these brain networks. Further, through the use of the tensor decomposition, we avoid the limitations of traditional approaches that assume statistical independence or orthogonality in defining the underlying networks. Our findings demonstrate that these parcellations are comparable or superior to established atlases in terms of homogeneity of the functional connectivity across parcels, task contrast alignment, and architectonic map alignment. Our methodological pipeline is highly automated, allowing for rapid adaptation to new datasets and the generation of custom parcellations in just minutes, a significant advancement over methods that require extensive manual input. We describe this integrated approach, which we refer to asUntamed, as a tool for use in the fields of cognitive and clinical neuroscientific research. Parcellations created from the Human Connectome Project dataset usingUntamed, along with the code to generate atlases with custom parcel numbers, are publicly available athttps://untamed-atlas.github.io.
Light-based juxtacrine signaling between synthetic cells
Authors: Moghimianavval Hossein , Loi Kyle J. , Hwang Sung-Won , Bashirzadeh Yashar , Liu Allen P.
Published: January 2024

Cell signaling through direct physical cell-cell contacts plays vital roles in biology during development, angiogenesis, and immune response. Intercellular communication mechanisms between synthetic cells constructed from the bottom up are majorly reliant on diffusible chemical signals, thus limiting the range of responses in receiver cells. Engineering contact-dependent signaling between synthetic cells promises to unlock more complicated signaling schemes with different types of responses. Here, we design and demonstrate a light-activated contact-dependent communication tool for synthetic cells. We utilize a split bioluminescent protein to limit signal generation exclusively to contact interfaces of synthetic cells, driving the recruitment of a photoswitchable protein in receiver cells, akin to juxtacrine signaling in living cells. Our modular design not only demonstrates contact-dependent communication between synthetic cells but also provides a platform for engineering orthogonal contact-dependent signaling mechanisms.
An expanded view of ligandability in the allosteric enzyme PTP1B from computational reanalysis of large-scale crystallographic data
Authors: (Skaist) Mehlman Tamar , Ginn Helen M. , Keedy Daniel A.
Published: January 2024

The recent advent of crystallographic small-molecule fragment screening presents the opportunity to obtain unprecedented numbers of ligand-bound protein crystal structures from a single high-throughput experiment, mapping ligandability across protein surfaces and identifying useful chemical footholds for structure-based drug design. However, due to the low binding affinities of most fragments, detecting bound fragments from crystallographic datasets has been a challenge. Here we report a trove of 65 new fragment hits across 59 new liganded crystal structures for PTP1B, an “undruggable” therapeutic target enzyme for diabetes and cancer. These structures were obtained from computational analysis of data from a large crystallographic screen, demonstrating the power of this approach to elucidate many (∼50% more) “hidden” ligand-bound states of proteins. Our new structures include a fragment hit found in a novel binding site in PTP1B with a unique location relative to the active site, one that validates another new binding site recently identified by simulations, one that links adjacent allosteric sites, and, perhaps most strikingly, a fragment that induces long-range allosteric protein conformational responses via a previously unreported intramolecular conduit. Altogether, our research highlights the utility of computational analysis of crystallographic data, makes publicly available dozens of new ligand-bound structures of a high-value drug target, and identifies novel aspects of ligandability and allostery in PTP1B.
Mesophyll-Specific Circadian Dynamics of CAM Induction in the Ice Plant Unveiled by Single-Cell Transcriptomics
Authors: Perron Noé , Dervinis Christopher , Pereira Wendell , Barbazuk Brad , Kirst Matias
Published: January 2024

Crassulacean acid metabolism (CAM) is an evolutionary modification of the C3photosynthetic carbon dioxide fixation pathway used by approximately 7% of terrestrial plants to live in drought-prone environments. Facultative CAM species, such asMesembryanthemum crystallinum(common ice plant), possess the unique ability to switch from C3to CAM photosynthesis in response to high-salinity and water-deficit stress. Here we characterized the environmentally-triggered transition from C3to CAM in the ice plant using single nucleus RNA sequencing (snRNA-seq) to identify its putative regulators, supported by a novel high-quality assembled and annotated genome. Analysis of snRNA-seq datasets from ice plant leaves transitioning between C3and CAM collected at dawn and dusk revealed substantial transcriptional changes in mesophyll cells at the onset of CAM induction. Notably, our findings identify mesophyll sub-cell types engaged in either CAM or C3photosynthesis at dusk. Cell trajectory inference analysis reconstructed both 24-hour CAM and C3cycles, enabling a direct comparison of gene expression profiles in these pathways. This comparative study uncovered divergent expression patterns of key circadian clock genes in CAM and C3cell trajectories, pointing to a connection between circadian regulation and CAM induction.
Balancing stability, dynamics and kinetics in phase separation of intrinsically disordered proteins
Authors: Zhang Guoqing , Chu Xiakun
Published: January 2024

Liquid-liquid phase separation is a ubiquitous molecular phe-nomenon that plays crucial roles in a multitude of essential cellular activities. Intrinsically disordered proteins (IDPs), which lack well-defined three-dimensional structures, are prevalent participants in phase separation due to their inherent potential for promoting multivalent binding–the major driving force for this process. Understanding the underlying mechanisms of phase separation is challenging, as phase separation is a complex process, involving numerous molecules and various types of interactions. Here, we used a simplified coarse-grained model of IDPs to investigate the thermodynamic stability of the dense phase, conformational properties of IDPs, chain dynamics and kinetic rates of forming condensates. We focused on the IDP system, in which the oppositely charged IDPs are maximally segregated, inherently possessing a high propensity for phase separation. By varying interaction strengths, salt concentrations and temperatures, we observed that IDPs in the dense phase exhibited highly conserved conformational characteristics, which are more extended than those in the dilute phase. This implies that condensate formation acts as a protective shield, enabling IDPs to maintain conformational ensemble with high resistance to the changes in interactions and environmental conditions. Although the chain motions and global conformational dynamics of IDPs in the condensates are slow due to the high viscosity, local chain flexibility at the short timescales is largely preserved with respect to that at the free state. Strikingly, we observed a non-monotonic relationship between interaction strengths and kinetic rates for forming condensates. As strong interactions of IDPs result in high stable condensates, our results suggest that the thermodynamics and kinetics of phase separation are decoupled and optimized by the speed-stability balance through underlying molecular interactions. Our findings contribute to the molecular-level understanding of phase separation and offer valuable insights into the developments of engineering strategies for precise regulation of biomolecular condensates.
Heterozygosity for neurodevelopmental disorder-associatedTRIOvariants yields distinct deficits in behavior, neuronal development, and synaptic transmission in mice
Authors: Ishchenko Yevheniia , Jeng Amanda T. , Feng Shufang , Nottoli Timothy , Manriquez-Rodriguez Cindy , Nguyen Khanh K. , Carrizales Melissa G. , Vitarelli Matthew J. , Corcoran Ellen E. , Greer Charles A. , Myers Samuel A. , Koleske Anthony J.
Published: January 2024

Genetic variants inTRIOare associated with neurodevelopmental disorders (NDDs) including schizophrenia (SCZ), autism spectrum disorder (ASD) and intellectual disability. TRIO uses its two guanine nucleotide exchange factor (GEF) domains to activate GTPases (GEF1: Rac1 and RhoG; GEF2: RhoA) that control neuronal development and connectivity. It remains unclear how discreteTRIOvariants differentially impact these neurodevelopmental events. Here, we investigate how heterozygosity for NDD-associatedTriovariants –+/K1431M(ASD),+/K1918X(SCZ), and+/M2145T(bipolar disorder, BPD) – impact mouse behavior, brain development, and synapse structure and function. Heterozygosity for differentTriovariants impacts motor, social, and cognitive behaviors in distinct ways that align with clinical phenotypes in humans.Triovariants differentially impact head and brain size with corresponding changes in dendritic arbors of motor cortex layer 5 pyramidal neurons (M1 L5 PNs). Although neuronal structure was only modestly altered in theTriovariant heterozygotes, we observe significant changes in synaptic function and plasticity. We also identified distinct changes in glutamate synaptic release in+/K1431Mand+/M2145Tcortico-cortical synapses. The TRIO K1431M GEF1 domain has impaired ability to promote GTP exchange on Rac1, but+/K1431Mmice exhibit increased Rac1 activity, associated with increased levels of the Rac1 GEF Tiam1. Acute Rac1 inhibition with NSC23766 rescued glutamate release deficits in+/K1431Mvariant cortex. Our work reveals that discrete NDD-associatedTriovariants yield overlapping but distinct phenotypes in mice, demonstrates an essential role for Trio in presynaptic glutamate release, and underscores the importance of studying the impact of variant heterozygosity in vivo.
Auditory and visual gratings elicit distinct gamma responses
Authors: Gulati Divya , Ray Supratim
Published: January 2024

Sensory stimulation is often accompanied by fluctuations at high frequencies (>30Hz) in brain signals. These could be “narrowband” oscillations in the gamma band (30-70 Hz) or non-oscillatory “broadband” high-gamma (70-150 Hz) activity. Narrowband gamma oscillations, which are induced by presenting some visual stimuli such as gratings and have been shown to weaken with healthy aging and the onset of Alzheimer’s Disease, hold promise as potential biomarkers. However, since delivering visual stimuli is cumbersome as it requires head stabilization for eye tracking, an equivalent auditory paradigm could be useful. Although simple auditory stimuli have been shown to produce high-gamma activity, whether specific auditory stimuli can also produce narrowband gamma oscillations is unknown. We tested whether auditory ripple stimuli, which are considered an analogue to visual gratings, could elicit narrowband oscillations in auditory areas. We recorded 64-channel EEG from male and female (18 each) subjects while they either passively fixated on the monitor while viewing static visual gratings, or listened to stationary and moving ripples, played using loudspeakers, with their eyes open or closed. We found that while visual gratings induced narrowband gamma oscillations with suppression in the alpha band (8-12Hz), auditory ripples did not produce narrowband gamma but instead elicited very strong broadband high-gamma response and suppression in the beta band (14-26Hz). Even though we used equivalent stimuli in both modalities, our findings indicate that the underlying neuronal circuitry may not share ubiquitous strategies for stimulus processing.

Significance statement

In the visual cortex, gratings can induce robust narrowband gamma oscillations (30-70Hz). These visual stimulus-induced oscillations can further be used as a biomarker for diagnosing neuronal disorders. However, tasks used to elicit these oscillations are challenging for elderly subjects, and therefore, we tested if we could use auditory stimuli instead. We hypothesized that auditory ripple stimuli, which are analogous to visual gratings, may elicit these narrowband oscillations. We found that ripples induce a broadband high-gamma response (70-150Hz) in human EEG, unlike visual gratings that produce robust gamma. Thus, the underlying neural circuitry in the two areas may not be canonical.