bluuebunny/crossref_metadata_2025 huggingface dataset:
Orbitofrontal thickness and network associations as transdiagnostic signature of negative symptoms along the bipolar-schizophrenia spectrum
Authors: Franz Marlene , Kebets Valeria , Berg Xaver , Georgiadis Foivos , Burrer Achim , Brakowski Janis , Kaiser Stefan , Seifritz Erich , Homan Philipp , Walton Esther , van Erp Theo G. M. , Turner Jessica A. , Misic Bratislav , Valk Sofie L. , Yeo B.T. Thomas , Bernhardt Boris C. , Kirschner Matthias
Published: July 2024

Negative symptoms are core features of schizophrenia (SCZ) and also prevalent in bipolar disorder (BD). While orbitofrontal cortex (OFC) alterations have been implicated in the development of negative symptoms, their contributions across disorders remain to be established. Here, we tested how OFC thickness and related network associations relate to severity of negative symptom dimensions across the BD-SCZ spectrum. We included 50 individuals with SCZ, 49 with BD, alongside 122 controls. We assessed amotivation and diminished expression and estimated thickness in the medial and lateral OFC as regions-of-interest as well as 64 other cortical regions. Across BD and SCZ, reduced right lateral and bilateral medial OFC thickness were specifically associated with amotivation, but not diminished expression or other clinical factors. We then generated OFC structural co-variation networks to evaluate how the system-level embedding of the OFC would link to brain-wide cortical maps of negative symptoms. We found that medial OFC co-variation networks spatially correlated with the cortical maps of both negative symptom dimensions. Confirmatory analyses in independent SCZ data from the ENIGMA consortium (n=4,474) revealed similar associations with lateral OFC co-variation networks. Finally, the brain-wide cortical alteration pattern of amotivation was significantly correlated with normative functional and structural white-matter connectivity profiles of the right medial and left lateral OFC as well as adjacent prefrontal and limbic regions. Our work identifies OFC alterations as a possible transdiagnostic signature of amotivation and provide insights into network associations underlying the system-wide cortical alterations of negative symptoms across SCZ and BD.
Methods for joint modelling of longitudinal omics data and time-to-event outcomes: Applications to lysophosphatidylcholines in connection to aging and mortality in the Long Life Family Study
Authors: Arbeev Konstantin G. , Bagley Olivia , Ukraintseva Svetlana V. , Kulminski Alexander , Stallard Eric , Schwaiger-Haber Michaela , Patti Gary J. , Gu Yian , Yashin Anatoliy I. , Province Michael A.
Published: July 2024

Studying relationships between longitudinal changes in omics variables and risks of events requires specific methodologies for joint analyses of longitudinal and time-to-event outcomes. We applied two such approaches (joint models [JM], stochastic process models [SPM]) to longitudinal metabolomics data from the Long Life Family Study focusing on understudied associations of longitudinal changes in lysophosphatidylcholines (LPC) with mortality and aging-related outcomes (23 LPC species, 5,790 measurements of each in 4,011 participants, 1,431 of whom died during follow-up). JM analyses found that higher levels of the majority of LPC species were associated with lower mortality risks, with the largest effect size observed for LPC 15:0/0:0 (hazard ratio: 0.715, 95% CI (0.649, 0.788)). SPM applications to LPC 15:0/0:0 revealed how the association found in JM reflects underlying aging-related processes: decline in robustness to deviations from optimal LPC levels, better ability of males’ organisms to return to equilibrium LPC levels (which are higher in females), and increasing gaps between the optimum and equilibrium levels leading to increased mortality risks with age. Our results support LPC as a biomarker of aging and related decline in robustness/resilience, and call for further exploration of factors underlying age-dynamics of LPC in relation to mortality and diseases.
The Contribution of the membrane-bound complement regulatory proteins CD46 and CD55 in phases of acute lymphocytic leukemia (ALL) and acute myelogenous leukemia (AML)
Authors: Saeed Lobna Onsi , Ammar Perihan Ashraf , AbdElaziz Hisham , Abou-Aisha Khaled , Farag Noha Samir , El-Azizi Mohamed
Published: July 2024

The complement system is an essential part of the innate immunity where it is involved in the elimination of pathogens and disposal of apoptotic bodies and immune complexes from the body. Membrane-bound complement regulatory proteins (mCRPs) play key roles in controlling complement activity to avoid any accidental damage of host cells. The role of the complement system during the neoplastic transformation of cells is complicated and has been debated for long. On one hand, the complement system generally acts as a participant in the body’s immune surveillance against cancer. However, recent findings have shown that cancerous cells can use the complement components to assist in certain hallmarks which are fundamental for tumor progression such as angiogenesis, proliferation and metastasis. The aim of the current study is to investigate the differential expression of mCRPs; CD46 and CD55 in of acute lymphoid leukemia (ALL) and acute myeloid leukemia (AML). Clinical peripheral blood samples of newly diagnosed AML and ALL patients were used to assess the changes in transcriptional expression levels of CD46 and CD55 compared to age-matched healthy control subjects using quantitative real time PCR (qPCR). Results showed that both CD46 and CD55 were significantly downregulated by 2 to 7 folds in ALL and AML patients compared to healthy controls. The determined downregulation is suggestive of a defense mechanism conducted by leukemic cells to overcome immune defenses. Flow cytometric analysis was conducted for proteomic expression analysis of both proteins on cell surfaces of leukemia patients compared to healthy controls and results showed a reduction in CD46 expression by 1.2 fold and 2.8 fold in CD55 expression in AML patients. Post transcriptional knockdown of both genes was then carried out in HSB-2 leukemic cell model using customized shRNA, followed by flow cytometry analysis to assess the success of CD46 and CD55 silencing step, and ending with cell viability assays. MTT assay results showed a significant reduction in the viability of HSB-2 cells by 3 fold, approximately, following post-transcriptional silencing of CD46 and CD55 suggesting that although the expression of these mCRPs could be normally compromised by cancerous cells to evade complement attack mechanisms, CD46 and CD55 could be vital to the viability and proliferation of cancerous cells at some point in time. Our results suggest the dual role of complement in the tumor microenvironment where a balance between antitumor and tumor-promoting complement activities exists. The multifunctional properties of the complement system could be employed in opposing roles in cancer suggesting that the biological functions of the complement system are much more diverse than a simple elimination of target cells.
Eco-evolutionary dynamics of temperate phages in periodic environments
Authors: Goel Tapan , Beckett Stephen J. , Weitz Joshua S.
Published: July 2024

Bacteriophage (viruses that exclusively infect bacteria) exhibit a continuum of infection mechanisms, including lysis and lysogeny in interactions with bacterial hosts. Recent work has demonstrated the near-term advantages of lysogeny over lysis in conditions of low host availability. Hence, temperate phage which can switch between lytic and lysogenic strategies — both stochastically and responsively — are hypothesized to have an evolutionary advantage in a broad range of conditions. To examine generalized drivers of viral strategies over the near- and long-term, we explore the eco-evolutionary dynamics of temperate viruses in periodic environments with varying levels of host availability and viral mortality. We use a nonlinear system of ordinary differential equation to simulate periodically-forced dynamics that separate a ‘within-epoch’ phase and a ‘between-epoch’ phase, in which a (potentially unequal) fraction of virus particles and lysogens survive. Using this ecological model and invasion analysis, we show and quantify how conflicts can arise between strategies in the near-term that may favor lysis and strategies in the long-term that may favor lysogeny. In doing so, we identify a wide range of conditions in which temperate strategies can outperform obligately lytic or lysogenic strategies. Finally, we demonstrate that temperate strategies can mitigate against the potential local extinction of viruses in stochastically fluctuating environments, providing further evidence of the eco-evolutionary benefits of being temperate.
Long-range somatic structural variation calling from matched tumor-normal co-assembly graphs
Authors: Le Megan K. , Qin Qian , Li Heng
Published: July 2024

The accurate identification of somatic structural variants (SVs) is a problem with significant applications to clinical cancer research. Though technologies such as long-read sequencing have facilitated the development of more accurate SV calling methods, existing somatic SV callers still struggle with achieving high precision. In this work, we present colorSV, a long-read-based method for calling long-range SVs by examining the local topology of joint assembly graphs from matched tumor-normal samples. colorSV is the first somatic SV calling method that uses a co-assembly approach, as well as the first SV caller that identifies variants by examining characteristics of the assembly graph itself. We demonstrate near-perfect precision and sensitivity for calling translocations on the COLO829 cell line, outperforming four existing somatic SV callers (Severus, Sniffles2, nanomonsv, and SAVANA) in both metrics. We also evaluated colorSV for calling translocations on the HCC1395 cell line, finding that our method achieved a good balance between sensitivity and precision (where the sensitivity was only outperformed by Severus, and the precision was only outperformed by nanomonsv). Our work establishes a novel joint assembly-based strategy for characterizing long-range somatic variation, which could be further expanded or modified for the identification of SVs of different types and sizes.
Stromal KITL/SCF promotes pancreas tissue homeostasis and restrains tumor progression
Authors: Oñate M. Kathrina , Oon Chet , Bhattacharyya Sohinee , Low Vivien , Chen Canping , Zhao Xiaofan , Yan Ziqiao , Hang Yan , Kim Seung K. , Xia Zheng , Sherman Mara H.
Published: July 2024

Components of normal tissue architecture serve as barriers to tumor progression. Inflammatory and wound-healing programs are requisite features of solid tumorigenesis, wherein alterations to immune and non-immune stromal elements enable loss of homeostasis during tumor evolution. The precise mechanisms by which normal stromal cell states limit tissue plasticity and tumorigenesis, and which are lost during tumor progression, remain largely unknown. Here we show that healthy pancreatic mesenchyme expresses the paracrine signaling molecule KITL, also known as stem cell factor, and identify loss of stromal KITL during tumorigenesis as tumor-promoting. Genetic inhibition of mesenchymal KITL in the contexts of homeostasis, injury, and cancer together indicate a role for KITL signaling in maintenance of pancreas tissue architecture, such that loss of the stromal KITL pool increased tumor growth and reduced survival of tumor-bearing mice. Together, these findings implicate loss of mesenchymal KITL as a mechanism for establishing a tumor-permissive microenvironment.

Statement of significance

By analyzing transcriptional programs in healthy and tumor-associated pancreatic mesenchyme, we find that a sub-population of mesenchymal cells in healthy pancreas tissue express the paracrine signaling factor KITL. Loss of mesenchymal KITL is an accompanying and permissive feature of pancreas tumor evolution, with potential implications for cancer interception.
Proteomic analysis of unicellular cyanobacteriumCrocosphaera subtropicaATCC 51142 under extended light or dark growth
Authors: Panda Punyatoya , Giri Swagarika J. , Sherman Louis , Kihara Daisuke , Aryal Uma K.
Published: July 2024

The daily light-dark cycle is a recurrent and predictable environmental phenomenon to which many organisms, including cyanobacteria, have evolved to adapt. Understanding how cyanobacteria alter their metabolic attributes in response to subjective light or dark growth may provide key features for developing strains with improved photosynthetic efficiency and applications in enhanced carbon sequestration and renewable energy. Here, we undertook a label-free proteomic approach to investigate the effect of extended light (LL) or extended dark (DD) conditions on the unicellular cyanobacteriumCrocosphaera subtropicaATCC 51142. We quantified 2287 proteins, of which 603 proteins were significantly different between the two growth conditions. These proteins represent several biological processes, including photosynthetic electron transport, carbon fixation, stress responses, translation, and protein degradation. One significant observation is the regulation of over two dozen proteases, including ATP dependent Clp-proteases (endopeptidases) and metalloproteases, the majority of which were upregulated in LL compared to DD. This suggests that proteases play a crucial role in the regulation and maintenance of photosynthesis, especially the PSI and PSII components. The higher protease activity in LL indicates a need for more frequent degradation and repair of certain photosynthetic components, highlighting the dynamic nature of protein turnover and quality control mechanisms in response to prolonged light exposure. The results enhance our understanding of howCrocosphaera subtropicaATCC51142 adjusts its molecular machinery in response to extended light or dark growth conditions.
PCA-based spatial domain identification with state-of-the-art performance
Authors: Schaub Darius P , Yousefi Behnam , Kaiser Nico , Khatri Robin , Puelles Victor G , Krebs Christian F , Panzer Ulf , Bonn Stefan
Published: July 2024

The identification of biologically meaningful domains is a central step in the analysis of spatial transcriptomic data. Following Occam's razor, we show that a simple PCA-based algorithm for spatial domain identification rivals the performance of ten competing state-of-the-art methods across six single-cell spatial transcriptomic datasets. Our reductionist approach, NichePCA, provides researchers with intuitive domain interpretation and excels in execution speed, robustness, and scalability.
Identification and characterization of anti-epileptic compounds from Papaver somniferum using quantification techniques (GC-MS, FTIR), integrated network pharmacology, molecular docking, and molecular dynamics simulations
Authors: Shahzadi Kiran , Rasool Danish , Irshad Faiza , khalid Ammara , Aslam Sehar , Nazir Aisha
Published: July 2024

Epilepsy is a common neurological condition identified by repetitive seizures that affect the overall quality of life. Existing anti-epileptic drugs have undesirable side effects, necessitating safer alternatives. This study develops an integrated computational framework to discover potential anti-epileptic leads fromPapaver somniferum(opium poppy). Literature and databases were mined to compile all chemicals from Papaver somniferum. PubChem provided structural data, and compounds satisfying drug-likeness and bioavailability criteria were selected. GeneCards, DisGeNET and SwissTargetPrediction identified 344 target genes of the compounds and common targets with epilepsy. Network pharmacology analyses were performed. Cytoscape constructed a compound-target network comprising 5 active constituents and 22 shared targets. Degree distributions revealed molecular interactions. STRING elucidated target connectivity. Hub targets were identified using CytoHubba. GO and KEGG enrichment on 123 targets recognized biological roles and pathways. DAVID and Hiplot characterized functional annotations. Cytoscape visualized a compound-target-pathway association network involving targets, pathways, and compounds related to epilepsy. GC-MS identified 25 compounds in the Papaver somniferum extract. FTIR characterized functional groups. Molecular docking scored compound affinities for 10 targets. Autodock Vina docked 15 constituents into binding pockets. Interactions were validated using Desmond MD simulations of IL6 with scoulerine over 100 ns, assessing RMSD, RMSF, interactions. RMSD/RMSF plots and histograms characterized protein/ligand stability and flexibility. This integrativeInsilicoandInvitroframework facilitates prioritizing Papaver somniferum constituents for epilepsy. Network analyses provided systems-level understanding of multi-target mechanisms. Molecular modeling established structure-activity relationships, validating predicted interactions. Compounds with good ADMET profiles, network centrality, docking scores, and stable simulations emerge as candidates warranting further examination for safer anti-epileptic therapy.
Sepsis-induced NET formation requires MYD88 but is independent of GSDMD and PAD4
Authors: Englert Hanna , Rangaswamy Chandini , Divivier Mylène , Göbel Josephine , Hermans-Borgmeyer Irm , Borgmeyer Uwe , Mowen Kerri A. , Beerens Manu , Frye Maike , Mailer Reiner K. , Gelderblom Mathias , Stavrou Evi X. , Preston Roger J. S. , Schneider Stefan W. , Fuchs Tobias A. , Renné Thomas
Published: July 2024

Neutrophils are peripheral blood-circulating leukocytes that play a pivotal role in host defense against bacterial pathogens which upon activation, they release web-like chromatin structures called neutrophil extracellular traps (NETs).

Here, we analyzed and compared the importance of myeloid differentiation factor 88 (MYD88), peptidyl arginine deiminase 4 (PAD4), and gasdermin D (GSDMD) for NET formationin vivofollowing sepsis and neutrophilia challenge. Injection of lipopolysaccharide (LPS)/E. colior the transgenic expression of granulocyte colony-stimulating factor (G-CSF), each induced NET-mediated lethal vascular occlusions in mice with combined genetic deficiency inDnase1 andDnase1l3(D1/D1l3−/−). In accordance with the signaling of toll-like receptors,Myd88/D1/D1l3−/−animals were protected from the formation of lethal intravascular NETs during septic conditions. However, this protection was not observed during neutrophilia. It was unexpected to find that bothGsdmd/D1/D1l3−/−andPad4/D1/D1l3−/−mice were fully capable of forming NETs upon LPS/E.coli challenge. Sepsis equally triggered a similar inflammatory response in these mice characterized by formation of DNA-rich thrombi, vessel occlusions, and mortality from pulmonary embolism, compared toD1/D1l3−/−mice. Pharmacologic GSDMD inhibitors did not reduce PMA-stimulated NET formation inex vivomodels either. Similarly, neither Pad4 nor GSDMD deficiency affected intravascular occlusive NET formation upon neutrophilia challenge. The magnitude of NET production, multi-organ damage, and lethality were comparable to those observed in challenged control mice.

In conclusion, our data indicate that NET formation during experimental sepsis and neutrophilia is regulated by distinct stimulus-dependent pathways that may be independent of canonical PAD4 and GSDMD.

Key points:

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Sepsis triggers vaso-occlusive NET formation inDnase1/Dnase1l3-deficient mice in a myeloid differentiation factor 88-dependent manner

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Peptidyl arginine deiminase 4 and gasdermin D are dispensable for NET formation in sepsis and neutrophilia models

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Myeloid differentiation factor 88, peptidyl arginine deiminase 4 and gasdermin D differ in their importance for NET formationin vivo
Fucosylated and non-fucosylated α2,3 sialosides were detected on the bovine mammary gland tissues
Authors: Hiono Takahiro , Morita Tatsuru , Kosenda Keigo , Otani Yuki , Ichii Osamu , Isoda Norikazu , Sakoda Yoshihiro
Published: July 2024

Receptors for high pathogenicity avian influenza viruses (HPAIVs) in the mammary glands of dairy cattle were detected using various recombinant hemagglutinins (rHAs). Results demonstrated the presence of fucosylated and non-fucosylated α2,3 sialosides, which were typically targeted by the HA of clade 2.3.4.4b HPAIVs.
The dual Ras Association (RA) Domains of Drosophila Canoe have differential roles in linking cell junctions to the cytoskeleton during morphogenesis
Authors: McParland Emily D. , Gurley Noah J. , Wolfsberg Leah R. , Butcher T. Amber , Bhattarai Abhi , Jensen Corbin C. , Johnson Ruth I. , Slep Kevin C. , Peifer Mark
Published: July 2024

During embryonic development and adult homeostasis epithelial cells must change shape and move without disrupting the tissue’s dynamic architecture. This requires robust linkage of cell-cell adherens junctions to the force-generating actomyosin cytoskeleton. Drosophila Canoe and mammalian Afadin play key roles in this linkage. One central task for the field is defining how upstream inputs from Ras-family GTPases regulate Canoe and Afadin. They are unusual in that they share two tandem Ras-association (RA) domains, which, when deleted, virtually eliminate Canoe function. Previous work in vitro suggested RA1 and RA2 differ in their ability to bind GTPases, but their individual functions in vivo remain unknown. Combining bioinformatic and biochemical approaches, we find that both RA1 and RA2 bind to active Rap1 with similar affinities, and that conserved N-terminal extensions play a role in binding. We created Drosophilacanoemutants to test RA1 and RA2 function in vivo. Despite their similar affinities for Rap1, RA1 and RA2 play strikingly different roles. Deleting RA1 virtually eliminates Canoe function in morphogenesis, while mutants lacking RA2 are viable and fertile but have defects in junctional reinforcement in embryos and during pupal eye development. These data significantly expand our understanding of how adherens junction:cytoskeletal linkage is regulated.
Efficient integration of spatial omics data for joint domain detection, matching, and alignment with stMSA
Authors: Shu Han , Chen Jing , Xu Chang , Hu Jialu , Wang Yongtian , Peng Jiajie , Jiang Qinghua , Shang Xuequn , Wang Tao
Published: July 2024

Spatial omics (SO) is a powerful methodology that enables the study of genes, proteins, and other molecular features within the spatial context of tissue architecture. With the growing availability of SO datasets, researchers are eager to extract biological insights from larger datasets for a more comprehensive understanding. However, existing approaches focus on batch effect correction, often neglecting complex biological patterns in tissue slices, complicating feature integration and posing challenges when combining transcriptomics with other omics layers. Here, we introduce stMSA (SpaTial Multi-Slice/omics Analysis), a deep graph contrastive learning model that incorporates graph auto-encoder techniques. stMSA is specifically designed to produce batch-corrected representations while retaining the distinct spatial patterns within each slice, considering both intra- and inter-batch relationships during integration. Extensive evaluations show that stMSA outperforms state-of-the-art methods in distinguishing tissue structures across diverse slices, even when faced with varying experimental protocols and sequencing technologies. Furthermore, stMSA effectively deciphers complex developmental trajectories by integrating spatial proteomics and transcriptomics data, and excels in cross-slice matching and alignment for 3D tissue reconstruction.
Impact of preanalytical factors on liquid biopsy in the canine cancer model
Authors: Megquier Kate , Husted Christopher , Rhoades Justin , White Michelle E. , Genereux Diane P. , Chen Frances L. , Xiong Kan , Kwon Euijin , Swofford Ross , Painter Corrie , Adalsteinsson Viktor , London Cheryl A. , Gardner Heather L. , Karlsson Elinor K.
Published: July 2024

While liquid biopsy has potential to transform cancer diagnostics through minimally-invasive detection and monitoring of tumors, the impact of preanalytical factors such as the timing and anatomical location of blood draw is not well understood. To address this gap, we leveraged pet dogs with spontaneous cancer as a model system, as their compressed disease timeline facilitates rapid diagnostic benchmarking. Key liquid biopsy metrics from dogs were consistent with existing reports from human patients. The tumor content of samples was higher from venipuncture sites closer to the tumor and from a central vein. Metrics also differed between lymphoma and non-hematopoietic cancers, urging cancer-type-specific interpretation. Liquid biopsy was highly sensitive to disease status, with changes identified soon after post chemotherapy administration, and trends of increased tumor fraction and other metrics observed prior to clinical relapse in dogs with lymphoma or osteosarcoma. These data support the utility of pet dogs with cancer as a relevant system for advancing liquid biopsy platforms.
Effects of ketamine on GABAergic and glutamatergic activity in the mPFC: biphasic recruitment of GABA function in antidepressant-like responses
Authors: Fogaça Manoela V. , Daher Fernanda , Picciotto Marina R.
Published: July 2024

Major depressive disorder (MDD) is associated with disruptions in glutamatergic and GABAergic activity in the medial prefrontal cortex (mPFC), leading to altered synaptic formation and function. Low doses of ketamine rapidly rescue these deficits, inducing fast and sustained antidepressant effects. While it is suggested that ketamine produces a rapid glutamatergic enhancement in the mPFC, the temporal dynamics and the involvement of GABA interneurons in its sustained effects remain unclear. Using simultaneous photometry recordings of calcium activity in mPFC pyramidal and GABA neurons, as well as chemogenetic approaches inGad1-Cremice, we explored the hypothesis that initial effects of ketamine on glutamate signaling trigger subsequent enhancement of GABAergic responses, contributing to its sustained antidepressant responses. Calcium recordings revealed a biphasic effect of ketamine on activity of mPFC GABA neurons, characterized by an initial transient decrease (phase 1, <30 min) followed by an increase (phase 2, >60 min), in parallel with a transient increase in excitation/inhibition levels (10 min) and lasting enhancement of glutamatergic activity (30-120 min). Previous administration of ketamine enhanced GABA neuron activity during the sucrose splash test (SUST) and novelty suppressed feeding test (NSFT), 24 h and 72 h post-treatment, respectively. Chemogenetic inhibition of GABA interneurons during the surge of GABAergic activity (phase 2), or immediately before the SUST or NSFT, occluded ketamine’s behavioral actions. These results indicate that time-dependent modulation of GABAergic activity is required for the sustained antidepressant-like responses induced by ketamine, suggesting that approaches to enhance GABAergic plasticity and function are promising therapeutic targets for antidepressant development.
‘Tuning’ of ribosome levels mediated by RNase I and hibernating ribosomes
Authors: Minami Atsushi , Tanzawa Takehito , Yang Zhuohao , Funatsu Takashi , Kuzuyama Tomohisa , Yoshida Hideji , Kato Takayuki , Ogawa Tetsuhiro
Published: July 2024

Ribosomes consume vast energy to synthesize proteins, so controlling the ribosome abundance is a significant concern for cells. Ribonucleases mediate ribosome degradation in response to stresses, while some ribosomes deactivate translational activity and protect themselves from degradation, called ribosome hibernation. RNase T2 is an endoribonuclease found in almost all organisms, and they are thought to be involved in the degradation of ribosomal RNA. Although it was recently reported that the activity ofEscherichia coliRNase T2, called RNase I, depends on the environmental conditions, the regulation mechanism remains elusive. Here, we report how rRNA degradation by RNase I is regulated by hibernating ribosomes. Combining the biochemical, cryo-electron microscopy, and single-molecule analyses, we found that hibernating ribosome is an inhibitor by forming a complex with RNase I. Moreover, RNase I does not bind to the translating ribosome, so rRNA is protected. On the other hand, RNase I degrades the rRNA of each subunit dissociated from stalled ribosomes on aberrant mRNA bytrans-translation. Under stress conditions, and even in the actively growing phase, some ribosomes are stalling or pausing. Although such ribosomes were thought to be recycled after being rescued, our results add a new insight that they are not recycled but degraded. These findings have broad implications for understanding the regulation of ribosome levels, which is critical for cellular homeostasis and response to environmental stresses.
Ranking Single Fluorescent Protein Based Calcium Biosensor Performance by Molecular Dynamics Simulations
Authors: Berksoz Melike , Atilgan Canan
Published: July 2024

Genetically Encoded Fluorescent Biosensors (GEFBs) have become indispensable tools for visualizing biological processes in vivo. A typical GEFB is composed of a sensory domain (SD) which undergoes a conformational change upon ligand binding and a genetically fused fluorescent protein (FP). Ligand binding in the SD allosterically modulates the chromophore environment and changes its spectral properties. Single fluorescent (FP)-based biosensors, a subclass of GEFBs, offer a simple experimental setup; they are easy to produce in living cells, structurally stable and simple due to their single-wavelength operation. However, they pose a significant challenge for structure optimization, especially concerning the length and residue content of linkers between the FP and SD which affect how well the chromophore responds to conformational change in the SD. In this work, we use classical all-atom molecular dynamics simulations to analyze the dynamic properties of a series of calmodulin-based calcium biosensors, all with different FP-SD interaction interfaces and varying degrees of calcium binding dependent fluorescence change. Our results indicate that biosensor performance can be predicted based on distribution of water molecules around the chromophore and shifts in hydrogen bond occupancies between the ligand-bound and ligand-free sensor structures.
Understanding human amygdala function with artificial neural networks
Authors: Jang Grace , Kragel Philip A.
Published: July 2024

Abstract

The amygdala is a cluster of subcortical nuclei that receives diverse sensory inputs and projects to the cortex, midbrain and other subcortical structures. Numerous accounts of amygdalar contributions to social and emotional behavior have been offered, yet an overarching description of amygdala function remains elusive. Here we adopt a computationally explicit framework that aims to develop a model of amygdala function based on the types of sensory inputs it receives, rather than individual constructs such as threat, arousal, or valence. Characterizing human fMRI signal acquired as participants viewed a full-length film, we developed encoding models that predict both patterns of amygdala activity and self-reported valence evoked by naturalistic images. We use deep image synthesis to generate artificial stimuli that distinctly engage encoding models of amygdala subregions that systematically differ from one another in terms of their low-level visual properties. These findings characterize how the amygdala compresses high-dimensional sensory inputs into low-dimensional representations relevant for behavior.
Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases
Authors: Litinetskaya Anastasia , Shulman Maiia , Hediyeh-zadeh Soroor , Moinfar Amir Ali , Curion Fabiola , Szałata Artur , Omidi Alireza , Lotfollahi Mohammad , Theis Fabian J.
Published: July 2024

Multimodal analysis of single-cell samples from healthy and diseased tissues at various stages provides a comprehensive view that identifies disease-specific cells, their molecular features and aids in patient stratification. Here, we present MultiMIL, a novel weakly-supervised multimodal model designed to construct multimodal single-cell references and prioritize phenotype-specific cells via patient classification. MultiMIL effectively integrates single-cell modalities, even when they only partially overlap, providing robust representations for downstream analyses such as phenotypic prediction and cell prioritization. Using a multiple-instance learning approach, MultiMIL aggregates cell-level measurements into sample-level representations and identifies disease-specific cell states through attention-based scoring. We demonstrate that MultiMIL accurately identifies disease-specific cell states in blood and lung samples, identifying novel disease-associated genes and achieving superior patient classification accuracy compared to existing methods. We anticipate MultiMIL will become an essential tool for querying single-cell multiomic atlases, enhancing our understanding of disease mechanisms and informing targeted treatments.
Remote organ cancer adversely alters renal function and induces kidney injury, inflammation, and fibrosis
Authors: Hammouri Dana , Orwick Andrew , Doll Mark , Vega Dianet Sanchez , Shah Parag P. , Clarke Christopher J. , Clem Brian , Beverly Levi J. , Siskind Leah J.
Published: July 2024

Approximately 30% of cancer patients experience kidney complications, which hinder optimal cancer management, imposing a burden on patients’ quality of life and the healthcare system. The etiology of kidney complications in cancer patients is often attributed to nephrotoxic oncological therapies. However, the direct impact of cancer on kidney health is underestimated, as most nephrotoxic oncological therapies have been studied in animal models that do not have cancer. Our previous study demonstrated that advanced lung cancer adversely alters kidney physiology and function, and exacerbates chemotherapy-induced nephrotoxicity, indicating lung cancer-kidney crosstalk. This study examines whether this phenomenon is specific to the employed cancer model. Female and male mice of various strains were injected with different cell lines representing human and mouse lung cancer, breast cancer, and melanoma, and their kidney tissues were analyzed for toxicity and fibrosis. The impact of cancer on the kidney varied by cancer type. Breast cancer and specific subtypes of lung cancer, including KRAS- and EGFR-mutant cancer, pathologically altered kidney physiology and function in a manner dependent on the metastatic potential of the cell line. This was independent of mouse strain, sex, and cancer cell line origin. Moreover, tumor DNA was not detected in the renal tissue, excluding metastases to the kidney as a causative factor for the observed pathological alterations. Lewis lung carcinoma and B16 melanoma did not cause nephrotoxicity, regardless of the tumor size. Our results confirm cancer-kidney crosstalk in specific cancer types and highlight gaps in understanding the risk of renal complications in cancer patients. In the era of precision medicine, further research is essential to identify at-risk oncology populations, enabling early detection and management of renal complications.
Marsupial immune protection is shaped by enhancer sharing and gene cluster duplication of cathelicidin antimicrobial peptides
Authors: Park Jongbeom , Ke Wenfan , Kaage Aellah , Feigin Charles Y. , Pritykin Yuri , Donia Mohamed S. , Mallarino Ricardo
Published: July 2024

Marsupial neonates are born with immature immune systems, making them vulnerable to pathogens. While neonates receive maternal protection, they can also independently combat pathogens, though the mechanisms remain unknown. Using the sugar glider (Petaurus breviceps) as a model, we investigated immunological defense strategies of marsupial neonates. Cathelicidins – a family of antimicrobial peptides expanded in the genomes of marsupials – are highly expressed in developing neutrophils. Sugar glider cathelicidins reside in two genomic clusters and their coordinated expression is achieved by enhancer sharing within clusters and long-range physical interactions between clusters. These cathelicidins modulate immune responses and have potent antimicrobial effects, sufficient to provide protection in a mouse model of sepsis. Lastly, cathelicidins have a complex evolutionary history, where marsupials and monotremes are the only tetrapods that retained two cathelicidin clusters. Thus, cathelicidins are critical mediators of marsupial immunity, and their evolution reflects the life history-specific immunological needs of these animals.
Longitudinal Decline of Exercise Capacity in Male and Female Mice
Authors: Pajski Megan L. , Maroto Rosario , Byrd Chris , Graber Ted G.
Published: July 2024

The population of older adults is exponentially expanding. Alongside aging comes the onset of chronic disease, decline of functional capacity, and reduced quality of life. Thus, this population increase will stress the capacity and financial viability of health and long-term care systems. Developing pre-clinical models for age-related functional decline is imperative to advancing therapies that extend healthspan and prolong independence. Previously in a cross-sectional study, we established a powerful composite scoring system we termed CFAB (comprehensive functional assessment battery). CFAB measures physical function and exercise capacity using well-validated determinants to measure overall motor function, fore-limb strength, four-limb strength/endurance, aerobic capacity, and volitional exercise/activity rate. In the current work, we used CFAB to track cohorts of male and female C57BL/6 mice over the lifespan (measuring CFAB at 6, 12, 18, 24, and 28 months of age). Overall, we found statistically significantly declining function as the mice aged, with some differences between males and females in trajectory and slope. We also determined that body mass changes presented differently between sexes, and tracked body composition (fat percentage, using magnetic resonance imagery) in females. In a subset of mice, we trackedin vivocontractile physiology noting declines in plantar flexor maximum isometric torque. In summary, our data suggest that males and females declined at different rates. We confirmed the efficacy of CFAB to track longitudinal changes in exercise capacity and physical fitness in both males and females, further validating the system to track age-related functional decline.
Galanin receptor 1 expressing neurons in hippocampal-prefrontal circuitry modulate goal directed attention and impulse control
Authors: Messanvi Fany , Visocky Vladimir , Senneca Carolyn , Berkun Kathleen , Taori Maansi , Bradley Sean P. , Wang Huikun , Tejeda Hugo , Chudasama Yogita
Published: July 2024

While amino acid neurotransmitters are the main chemical messengers in the brain, they are co-expressed with neuropeptides which are increasingly recognized as modulators of cognitive pathways. For example, the neuropeptide galanin has been implicated in a wide range of pathological conditions in which frontal and temporal structures are compromised. In a recent study in rats, we discovered that direct pharmacological stimulation of galanin receptor type 1 (GalR1) in the ventral prefrontal cortex (vPFC) and ventral hippocampus (vHC) led to opposing effects on attention and impulse control behavior. In the present study, we investigate how subtypes of neurons expressing GalR1 in these two areas differentially contribute to these behaviors. We first establish that GalR1 is predominantly expressed in glutamatergic neurons in both the vPFC and HC. We develop a novel viral approach to gain genetic access to GalR1-expressing neurons and demonstrate that optogenetic excitation of GalR1 expressing neurons in the vPFC, but not vHC, selectively disrupts attention in a complex behavioral task. Finally, using fiber photometry, we measure the bulk calcium dynamics in GalR1-expressing neurons during the same task to demonstrate opposing activity in vPFC and vHC. These results are consistent with our previous work demonstrating differential behavioral effects induced by GalR1 activating in vPFC and vHC. These results indicate the distinct neuromodulatory and behavioral contributions of galanin mediated by subclasses of neurons in the hippocampal and prefrontal circuitry.
Efficientin situepitope tagging of rice genes by nuclease-mediated prime editing
Authors: Li Xueqi , Zhang Sujie , Wang Chenyang , Ren Bin , Yan Fang , Li Shaofang , Spetz Carl , Huang Jinguang , Zhou Xueping , Zhou Huanbin
Published: July 2024

In situepitope tagging is crucial for probing gene expression, protein localization, and the dynamics of protein interactions within their natural cellular context. However, the practical application of this technique in plants presents considerable hurdles. Here, we comprehensively explore the potential of the CRISPR/Cas nuclease-mediated prime editing and different DNA repair pathways in epitope tagging of endogenous rice genes. We find that SpCas9 nuclease/microhomology-mediated end joining (MMEJ)-based prime editing strategy (termed NM-PE) facilitates more straightforward and efficient gene tagging compared to the conventional and other derivative PE method. Furthermore, the PAM-flexible SpRY and ScCas9 nucleases-based prime editors have been engineered and implemented for the tagging of endogenous genes with diverse epitopes, significantly broadening the applicability of NM-PE in rice. Moreover, NM-PE has been successfully adopted in simultaneous tagging ofOsMPK1andOsMPK13in rice plants with c-Myc and HA tags, respectively. Taken together, our results indicate great potential of the NM-PE toolkit in the targeted gene tagging for Rice Protein Tagging Project, gene function study and genetic improvement.
Mechanical problem solving in mice
Authors: Boon Marcus N. , Andresen Niek , Traverso Soledad , Meier Sophia , Schuessler Friedrich , Hellwich Olaf , Lewejohann Lars , Thöne-Reineke Christa , Sprekeler Henning , Hohlbaum Katharina
Published: July 2024

Recent advances in automated tracking tools have sparked a growing interest in studying naturalistic behavior. Yet, traditional decision-making tasks remain the norm for assessing learning behavior in neuroscience. We introduce an alternative sequential decision-making task for studying mouse behavior. It consists of an open-source, 3D-printed “lockbox”, a mechanical riddle that requires four different mechanisms to be solved in sequence to obtain a reward. During the task, the mice move around freely, allowing the expression of complex behavioral patterns. We observed that mice willingly engage in the task and learn to solve it in only a few trials. To analyze how the mice solved the task, we recorded their behavior in a multi-camera setup and developed a custom data analysis pipeline to automatically detect the interactions of the mice with the different lockbox mechanisms for a large corpus of video footage (>300h, 12 mice). The pipeline allows us to further delineate why mouse performance increases over trials. Our analyses suggest that this is not due to an increased interaction time with the task or the acquisition of a smart solution strategy, but primarily due to habituation to the lockbox. Lockboxes may hence be a promising approach to study both abstract sequential decision making and low-level motor learning in a single task that can be rapidly learned by mice.
Enhanced RNAi does not provide efficient innate antiviral immunity in micein vivo
Authors: Kulmann Marcos Iuri Roos , Taborska Eliska , Benköova Brigita , Palus Martin , Drobek Ales , Horvat Filip , Pasulka Josef , Malik Radek , Salyova Eva , Hönig Vaclav , Pellerova Michaela , Borsanyiova Maria , Stepanek Ondrej , Bopegamage Shubhada , Ruzek Daniel , Svoboda Petr
Published: July 2024

In RNA interference (RNAi), long double-stranded RNA (dsRNA) is cleaved by Dicer endonuclease into small RNA interfering RNAs (siRNAs), which guide degradation of complementary RNAs. While RNAi mediates antiviral innate immunity in plants and many invertebrates, vertebrates adopted sequence-independent response and their Dicer produces siRNAs inefficiently because it is adapted to process small hairpin microRNA precursors in the gene-regulating microRNA pathway. Mammalian RNAi is thus a rudimentary pathway of unclear significance. To investigate its antiviral potential, we modified mouse Dicer locus to express a truncated variant (DicerΔHEL1) known to stimulate RNAi. Next, we analyzed how DicerΔHEL1/wtmice respond to four RNA viruses: Coxsackievirus B3 (CVB3) and encephalomyocarditis virus (ECMV) fromPicornaviridae; tick-borne encephalitis virus (TBEV) fromFlaviviridae; and lymphocytic choriomeningitis virus (LCMV) fromArenaviridae. Increased Dicer activity in DicerΔHEL1/wtmice did not elicit any antiviral effect. supporting insignificant antiviral function of endogenous mammalian RNAiin vivo. However, we also report that sufficiently high expression of DicerΔHEL1suppressed LCMV in embryonic stem cells and in a transgenic mouse model. Altogether, mice with increased Dicer activity offer a new benchmark for identifying and studying viruses susceptible to mammalian RNAiin vivo.
Evidence for an efferent-based prediction contributing to implicit motor adaptation
Authors: Szarka Annika , Kim Hyosub E. , Inglis J. Timothy , Chua Romeo
Published: July 2024

Models of sensorimotor adaptation have proposed that implicit adaptation is driven by error signals created by discrepancies between various sensory information sources. While proprioception has been suggested as a critical source for the error signals driving adaptation, the role of an efferent-based motor prediction has largely been neglected. In this study, we examined the effect of dissociating the afferent and efferent information available during implicit adaptation. Participants moved a visual cursor towards targets by applying horizontal forces to a stationary handle at a central home location. During perturbation trials, the cursor followed an invariant path rotated relative to the target. Participants were instructed to ignore this task-irrelevant cursor feedback and to isometrically “reach” towards the target. Participants implicitly adapted in the isometric task, even when the hand never actually moved to the target. Moreover, the level of adaptation surpassed that of a typical clamped reaching paradigm by nearly twofold. This was confirmed in a secondary experiment where participants performed actual reaching movements and demonstrated significantly less adaptation. Our findings suggest that while afferent proprioceptive feedback of hand position around the target most likely plays a role in adaptation, it is not necessary to induce adaptation.