bluuebunny/crossref_metadata_2025 huggingface dataset:
Transcriptomic sexual conflict at two evolutionary timescales revealed by experimental evolution inCaenorhabditis elegans
Authors: Kasimatis Katja R. , Willis John H. , Sedore Christine A. , Phillips Patrick C.
Published: August 2023

Sex-specific regulation of gene expression is the most plausible way for generating sexually differentiated phenotypes from an essentially shared genome. However, since genetic material is shared, sex-specific selection in one sex can have an indirect response in the other sex. From a gene expression perspective, this tethered response can move one sex away from their wildtype expression state and impact potentially many gene regulatory networks. Here, using experimental evolution in the model nematodeCaenorhabditis elegans,we explore the coupling of direct sexual selection on males with the transcriptomic response in males and females over microevolutionary timescales to uncover the extent to which post-insemination reproductive traits share a genetic basis between the sexes. We find that differential gene expression evolved in a sex-specific manner in males, while in females indirect selection causes an evolved response. Almost all differentially expressed genes were downregulated in both evolved males and females. Moreover, 97% of significantly differentially expressed genes in males and 69% of significantly differentially expressed genes in females have wildtype female-biased expression profile. Changes in gene expression profiles were likely driven throughtrans-acting pathways that are shared between the sexes. We found no evidence that the core dosage compensation machinery was impacted by experimental evolution. Together these data suggest a de-feminization of the male transcriptome and masculinization of the female transcriptome driven by direct selection on male sperm competitive ability. Our results indicate that on short evolutionary timescales sexual selection can generate putative sexual conflict in expression space.
Alternating polarity integrates chemical and mechanical cues to drive tissue morphogenesis
Authors: Osterfield Miriam
Published: August 2023

The spatial patterning of molecules within a sheet of cells directs morphogenesis in many epithelial tissues. InScaptodrosophilafollicle cells, Par3/Bazooka and aPKC were previously shown to localize to a set of cell edges destined to elongate and form the base of each eggshell dorsal appendage. This study establishes that the mechanism underlying this localization pattern is an alternating, in-plane polarity of the cells. A candidate screen identified several potential molecular players, whose epistatic relationships were then examined using a custom culture assay. These experiments demonstrated that positive feedback between actin polymerization and PI4P production leads to polarization of these cells individually, while mechanical force coordinates polarization among these cells. This work adds to the growing evidence for a role of mechanics in cell polarity, and also provides an example where morphological differences between species can be understood at the level of changes in fundamental cell biological processes.

InScaptodrosophila, the alternating (left, right, left) polarization in a row of cells drives the formation of up to eight eggshell respiratory filaments. This study uncovers the underlying pathway, which integrates chemical signaling through actin and PI4P with mechanical force.
Data-Driven 3D Shape Analysis Reveals Cell Shape-Fate Relationships in Zebrafish Lateral Line Neuromasts
Authors: Hewitt Madeleine N. , Cruz Iván A. , Raible David W.
Published: August 2023

Cell shape is a powerful readout of cell state, fate, and function. With the advent of sophisticated microscopes, image segmentation algorithms, and numerical shape representations, it is becoming more feasible to study cell shape in developing tissues. However, few studies have analyzed cell shape in three dimensions in living, intact organisms. Here, we took advantage of the favorable imaging qualities of zebrafish lateral line neuromasts to generate a dataset of high resolution images with labeled cells and nuclei. Using a custom Python-based workflow, we performed semi-automated, 3D cell and nucleus segmentation. We then used spherical harmonics and principal components analysis to distill neuromast cell and nuclear shape variation into several interpretable, biologically meaningful parameters. We found that neuromast cell and nuclear shapes vary with cell location and identity. The distinction between hair cells and support cells was discrete and accounted for much of the variation in neuromast cell and nucleus shape, which allowed us to train classifiers to predict hair cell identity from cell and nucleus shape features. Using markers for support cell subpopulations, we found that support cell subtypes also had different shapes from each other; however, shape features did not distinguish as sharply between support cell subtypes, suggesting that support cells vary continuously in shape. To investigate the effects of genetic perturbation that results in loss of a cell type on neuromast cell shape, we examinedatoh1amutants that lack hair cells. We found that neuromasts fromatoh1amutants lacked the cell shape phenotype associated with hair cells, but did not exhibit a mutant-specific cell shape. Our results demonstrate the utility of using 3D cell shape features to characterize, compare, and classify cells in a living, developing organism.
Comprehensive analyses of 1771 transcriptome from seven tissues enhance genetic and biological interpretations of maize complex traits
Authors: Lei Mengyu , Si Huan , Zhu Mingjia , Han Yu , Liu Wei , Dai Yifei , Ji Yan , Liu Zhengwen , Hao Fan , Hao Ran , Zhao Jiarui , Ye Guoyou , Zan Yanjun
Published: August 2023

By analyzing 1771 RNA-seq datasets from seven tissues in a maize diversity panel, we explored the landscape of multi-tissue transcriptome variation and evolution patterns of tissue-specific genes, and built a comprehensive multi-tissue gene regulation atlas to understand the genetic regulation of maize complex trait. Using transcriptome-wide association analysis, we linked tissue-specific expression variation of 45 genes to variation of 11 agronomic traits. Through integrative analyses of tissue-specific gene regulatory variation with genome-wide association studies, we detected relevant tissue types and candidate genes for a number of agronomic traits, including leaf during the day for anthesis-silking interval (GRMZM2G093210), leaf during the day for kernel Zeinoxanthin level (GRMZM2G143202), and root for ear height (GRMZM2G700665), highlighting the contribution from tissue-specific gene expression to variation of agronomic trait. Our findings provide novel insights into the genetic and biological mechanisms underlying complex traits in maize, and the multi-tissue regulatory atlas serves as a primary source for biological interpretation, functional validation, and genomic improvement of maize.
Modeling Single Cell Trajectory Using Forward-Backward Stochastic Differential Equations
Authors: Zhang Kevin , Zhu Junhao , Kong Dehan , Zhang Zhaolei
Published: August 2023

Recent advances in single-cell sequencing technology have provided opportunities for mathematical modeling of dynamic developmental processes at the single-cell level, such as inferring developmental trajectories. Optimal transport has emerged as a promising theoretical framework for this task by computing pairings between cells from different time points. However, optimal transport methods have limitations in capturing nonlinear trajectories, as they are static and can only infer linear paths between endpoints. In contrast, stochastic differential equations (SDEs) offer a dynamic and flexible approach that can model non-linear trajectories, including the shape of the path. Nevertheless, existing SDE methods often rely on numerical approximations that can lead to inaccurate inferences, deviating from true trajectories. To address this challenge, we propose a novel approach combining forward-backward stochastic differential equations (FBSDE) with a refined approximation procedure. Our FBSDE model integrates the forward and backward movements of two SDEs in time, aiming to capture the underlying dynamics of single-cell developmental trajectories. Through comprehensive benchmarking on multiple scRNA-seq datasets, we demonstrate the superior performance of FBSDE compared to other methods, high-lighting its efficacy in accurately inferring developmental trajectories.
Nuclear translocation of LINE-1 encoded ORF1p alters nuclear envelope integrity and disrupts nucleocytoplasmic transport in human neurons
Authors: Znaidi Rania , Massiani-Beaudoin Olivia , Mailly Philippe , Monnet Héloïse ,   The Brainbank Neuro-CEB Neuropathology Network, Joshi Rajiv L. , Fuchs Julia
Published: August 2023

LINE-1 retrotransposons are emerging as possible culprits in neurodegenerative diseases. However, the molecular mechanisms underlying the pathogenic role of LINE-1 and their encoded proteins ORF1p and ORF2p are still not completely understood. While the endonuclease and reverse transcriptase activities of ORF2p have been associated with DNA damage and inflammation, no pathogenic role has yet been assigned to ORF1p. Using a neuronal model of oxidative stress displaying increased LINE-1 expression, we report here that ORF1p stress-dependently translocated into the nucleus, localized to the nuclear envelope and directly interacted with nuclear import proteins, nuclear pore complex components and the inner nuclear lamina. Stress-dependent targeting of nuclear envelope components by ORF1p altered nuclear envelope integrity, disrupted nucleocytoplasmic transport and induced heterochromatin destructuration, features associated with neurodegenerative diseases and aging. Neurons of post-mortem Parkinson disease (PD) patients and non-PD affected controls expressed ORF1p and nuclear ORF1p levels correlated with altered nuclear shape in PD. Overexpression of ORF1p in neurons in the absence of stress recapitulated nuclear envelope dysfunctions and increased nuclear ORF1p levels correlated with a loss of nuclear circularity. Stress-induced nuclear alterations were restored by blocking ORF1p nuclear import or by the small molecule remodelin. This study thus reveals a retrotransposition- and ORF2p- independent pathogenic action of ORF1p at the nuclear envelope and points to ORF1p as a novel target for neuroprotection.
Pancreatic islet α cell function and proliferation requires the arginine transporter SLC7A2
Authors: Spears Erick , Stanley Jade E. , Shou Matthew , Yin Linlin , Li Xuan , Dai Chunhua , Bradley Amber , Sellick Katelyn , Poffenberger Greg , Coate Katie C. , Shrestha Shristi , Jenkins Regina , Sloop Kyle W. , Wilson Keith T. , Attie Alan D. , Keller Mark P. , Chen Wenbiao , Powers Alvin C. , Dean E. Danielle
Published: August 2023

Interrupting glucagon signaling decreases gluconeogenesis and the fractional extraction of amino acids by liver from blood resulting in lower glycemia. The resulting hyperaminoacidemia stimulates α cell proliferation and glucagon secretion via a liver-α cell axis. We hypothesized that α cells detect and respond to circulating amino acids levels via a unique amino acid transporter repertoire. We found thatSlc7a2ISLC7A2is the most highly expressed cationic amino acid transporter in α cells with its expression being three-fold greater in α than β cells in both mouse and human. Employing cell culture, zebrafish, and knockout mouse models, we found that the cationic amino acid arginine and SLC7A2 are required for α cell proliferation in response to interrupted glucagon signaling. Ex vivoandin vivoassessment of islet function inSlc7a2−/−mice showed decreased arginine-stimulated glucagon and insulin secretion. We found that arginine activation of mTOR signaling and induction of the glutamine transporter SLC38A5 was dependent on SLC7A2, showing that both’s role in α cell proliferation is dependent on arginine transport and SLC7A2. Finally, we identified single nucleotide polymorphisms inSLC7A2associated with HbA1c. Together, these data indicate a central role for SLC7A2 in amino acid-stimulated α cell proliferation and islet hormone secretion.
Plant allometry derived from Metabolic Scaling Theory and segregated by tissue functionality
Authors: Sopp S. , Valbuena R.
Published: August 2023

Plant allometry is key for determining the role of forests in global carbon cycles, through the calculation of tree biomass using proxy measurements such as tree diameters or heights. Metabolic Scaling Theory (MST) considers the general principles that underpin allometry, but MST scaling relationships have been challenged on their lack of fit to empirical data and global applicability. Many authors have thus optimised their model forms for statistical performance over theory based approaches. We postulated that MST scaling is applicable only to the proportion of plant tissue with supportive functionality, meaning that as plants evolved tissues of specialized conductive functionality (e.g vessels) their allometry progressed into more complex relationships. Our generalised MST (gMST) models were thus created by considering conductive lumen as unsupportive area, and consequentially removing it from the original MST 2/3 scaling. According to this principle, we deducted generalized gMST relationships with mechanistically deducted coefficients. We found that the gMST height-diameter scaling outperformed current state of the art equations that are widely used within the tropics and that the model performed well across all tested ecoregions. Furthermore, the proposed aboveground biomass models performed similarly to widely used models in the literature within the tropics. The results presented indicate that the further development of generalised allo-metric models remains a research priority given the importance of assessing and monitoring global forest carbon fluxes. The height-diameter models presented can thus be of much use to the wider community in further refining carbon stock estimates globally, providing a universally applicable theoretical framework.
Chemotherapeutic regulation of the ROS/MondoA-dependent TXNIP/GDF15 axis; and derivation of a new organoid metric as a predictive biomarker
Authors: Deng Jinhai , Pan Teng , Hong Yourae , Liu Zaoqu , Zhou Xingang , An Zhengwen , Li Lifeng , Alfano Giovanna , Li Gang , Dolcetti Luigi , Evans Rachel , Vicencio Jose M , Vlckova Petra , Chen Yue , Monypenny James , De Carvalho Gomes Camila Araujo , Ng Kenrick , McCarthy Caitlin , Yang Xiaoping , Hu Zedong , Porter Joanna C. , Tape Christopher J , Yin Mingzhu , Rodriguez-Justo Manuel , Tejpar Sabine , Beatson Richard , Ng Tony
Published: August 2023

Chemotherapy, the standard of care treatment for cancer patients with advanced disease, has been increasingly recognised to activate host immune responses to produce durable outcomes. Here, in colorectal adenocarcinoma (CRC) we identify chemotherapy-induced Thioredoxin Interacting Protein (TXNIP),a MondoA-dependent tumor suppressor gene, as a negative regulator of Growth/Differentiation Factor 15 (GDF15). GDF15 is a negative prognostic factor in CRC and promotes the differentiation of regulatory T cells (Tregs), through CD48 ligation. Intriguingly, multiple models including patient-derived tumor organoids demonstrate that loss of TXNIP/GDF15 axis functionality is associated with advanced disease or chemotherapeutic resistance, with transcriptomic or proteomic GDF15/TXNIP ratios showing potential as a prognostic biomarker. These findings illustrate a potentially common pathway where chemotherapy-induced epithelial stress drives local immune remodelling for patient benefit, with disruption of this pathway seen in refractory or advanced cases.
Design of a Biohybrid Materials Circuit with Binary Decoder Functionality
Authors: Mohsenin Hasti , Wagner Hanna J. , Rosenblatt Marcus , Kemmer Svenja , Drepper Friedel , Huesgen Pitter , Timmer Jens , Weber Wilfried
Published: August 2023

Synthetic biology applies concepts from electrical engineering and information processing to endow cells with computational functionality. Transferring the underlying molecular components into materials and wiring them according to topologies inspired by electronic circuit boards has yielded materials systems that perform selected computational operations. However, the limited functionality of available building blocks is restricting the implementation of advanced information-processing circuits into materials. Here, we engineer a set of protease-based biohybrid modules the bioactivity of which can either be induced or inhibited. Guided by a quantitative mathematical model and following a design-build-test-learn cycle, we wire the modules according to circuit topologies inspired by electronic signal decoders, a fundamental motif in information processing. We design a 2-input/4-output binary decoder for the detection of two small molecules in a material framework that could perform regulated outputs in form of distinct protease activities. The here demonstrated smart material system is strongly modular and could be used for biomolecular information processing for example in advanced biosensing or drug delivery applications.
Pharmacophoric-based ML model to filter candidate E3 ligands and predict E3 Ligase binding probabilities
Authors: Karki Reagon , Gadiya Yojana , Shetty Simran , Gribbon Phillip , Zaliani Andrea
Published: August 2023

Among the plethora of E3 Ligases, only a few have been utilized for the novel PROTAC technology. However, extensive knowledge of the preparation of E3 ligands and their utilization for PROTACs is already present in several databases. Here we provide, together with an analysis of functionalized E3 ligands, a comprehensive list of trained ML models to predict the probability to be an E3 ligase binder. We compared the different algorithms based on the different description schemes used and identified that the pharmacophoric-based ML approach was the best. Due to the peculiar pharmacophores present in E3 ligase binders and the presence of an explainable model, we were able to show the capability of our ErG model to filter compound libraries for fast virtual screening or focused library design. A particular focus was also given to target E3 ligase prediction and to find a subset of candidate E3 ligase binders within known public and commercial compound collections.
Asexual lineages of a cosmopolitan pest aphid are associated with different climatic niches
Authors: Godefroid Martin , Meynard Christine N , Clamens Anne-Laure , Popkin Megan , Jousselin Emmanuelle
Published: August 2023

Asexual lineages often exhibit broader distributions and can thrive in extreme habitats compared to their sexual counterparts. Two hypotheses have been proposed to explain this phenomenon. The general-purpose genotype model posits that selection favours a few versatile asexual genotypes with wide environmental tolerance, enabling their long-term persistence across diverse conditions. Conversely, the frozen niche variation model suggests that selection favours specialised genotypes with minimal niche overlap among them and their sexual relatives, potentially leading to competition-driven exclusion of both sexual and asexual relatives. To investigate these hypotheses, we examined ecological niche differentiation among six globally distributed obligate asexual lineages of the cosmopolitan aphid pest,Brachycaudus helichrysi. We initially investigated the presence of different endosymbionts across clones, as endosymbionts play a major role in aphid niche differentiation. Subsequently, we conducted multivariate analyses to explore climatic niche divergence among clones. We provide evidence for climatic niche specialisation in asexual lineages, which is not related to variations in endosymbiont associations. Therefore, despite their apparent global distribution,B. helichrysiclones exhibit characteristics of specialised genotypes, which aligns with the frozen niche variation hypothesis. This study represents the first comprehensive evidence of climatic adaptation in aphid superclones, providing novel insights into their global distribution.
Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes
Authors: Polêto Marcelo D. , Lemkul Justin A.
Published: August 2023

Abstract

The formation of G-quadruplexes (GQs) occurs in guanine-rich sequences of DNA and RNA, producing highly stable and structurally diverse noncanonical nucleic acid structures. GQs play crucial roles in regulating transcription, translation, and replication; and maintaining the genome, among others, thus changes to their structures can lead to diseases such as cancer. Previous studies using polarizable molecular dynamics simulations have shown differences in ion binding properties between telomeric and TERRA GQs despite architectural similarities. Here, we used volume-based metady-namics and repulsive potential simulations in conjunction with polarizable force fields to quantify the impact of ion binding on GQ dynamics and ion binding free energies. Furthermore, we describe how GQs exert electric fields on their surroundings to link dynamics with variations in electronic structure. Our findings provide new insights into the energetic, physical, and conformational properties of GQs and expose subtle, but important, differences between DNA and RNA GQs with the same fold.
Long duration environmental biosensing by recording analyte detection in DNA using recombinase memory
Authors: Kalvapalle Prashant Bharadwaj , Sridhar Swetha , Silberg Jonathan J. , Stadler Lauren B.
Published: August 2023

Microbial biosensors that convert environmental information into real-time visual outputs are limited in their sensing abilities in complex environments, such as soil and wastewater. Alternative reporter outputs are needed that stably record the presence of analytes. Here, we test the performance of recombinase-memory biosensors that sense a sugar (arabinose) and a microbial communication molecule (3-oxo-C12- homoserine lactone) over 8 days (∼70 generations) following analyte exposure. These biosensors use analyte sensing to trigger the expression of a recombinase which flips a segment of DNA, creating a genetic memory, and initiates fluorescent protein expression. The initial designs failed over time due to unintended DNA flipping in the absence of the analyte and loss of the flipped state after exposure to the analyte. Biosensor performance was improved by decreasing recombinase expression, removing the fluorescent protein output, and using qPCR to read out stored information. Application of memory biosensors in wastewater isolates achieved memory of analyte exposure in an uncharacterizedPseudomonasisolate. By returning these engineered isolates to their native environments, recombinase-memory systems are expected to enable longer duration andin situinvestigation of microbial signaling, community shifts, and gene transfer beyond the reach of traditional environmental biosensors.

IMPORTANCE

Living microbial sensors can monitor chemicals and biomolecules in the environment in real-time, but they remain limited in their ability to function on the week, month, and year timescales. To determine if environmental microbes can be programmed to record the detection of analytes over longer timescales, we evaluated whether the sensing of a microbial signaling molecule could be recorded through a DNA rearrangement. We show that off-the-shelf DNA memory is suboptimal for long-duration information storage, use iterative design to enable robust functioning over more than a week, and demonstrate DNA memory in an uncharacterized wastewaterPseudomonasisolate. Memory biosensors will be useful for monitoring the role of quorum sensing in wastewater biofilm formation, and variations of this design are expected to enable studies of ecological processesin situthat are currently challenging to monitor using real-time biosensors and analytical instruments.
Mapping the functional form of the trade-off between infection resistance and reproductive fitness under dysregulated immune signaling
Authors: Critchlow Justin T. , Prakash Arun , Zhong Katherine Y. , Tate Ann T.
Published: August 2023

Immune responses benefit organismal fitness by clearing parasites but also exact costs associated with immunopathology and energetic investment. Hosts manage these costs by tightly regulating the induction of immune signaling to curtail excessive responses and restore homeostasis. Despite the theoretical importance of turning off the immune response to mitigate these costs, experimentally connecting variation in the negative regulation of immune responses to organismal fitness remains a frontier in evolutionary immunology. In this study, we used a doseresponse approach to manipulate the RNAi-mediated knockdown efficiency ofcactus(IκBα), a central regulator of Toll pathway signal transduction in flour beetles (Tribolium castaneum). By titratingcactusactivity along a continuous gradient, we derived the shape of the relationship between immune response investment and traits associated with host fitness, including infection susceptibility, lifespan, fecundity, body mass, and gut homeostasis.Cactusknock-down increased the overall magintude of inducible immune responses and delayed their resolution in a dsRNA dose-dependent manner, promoting survival and resistance following bacterial infection. However, these benefits were counterbalanced by dsRNA dose-dependent costs to lifespan, fecundity, body mass, and gut integrity. Our results allowed us to move beyond the qualitative identification of a trade-off between immune investment and fitness to actually derive its functional form. This approach paves the way to quantitatively compare the evolution and impact of distinct regulatory elements on life-history trade-offs and fitness, filling a crucial gap in our conceptual and theoretical models of immune signaling network evolution and the maintenance of natural variation in immune systems.
Colorful Lizards and the Conflict of Collection
Authors: Goodman Colin M. , Claunch Natalie M. , Steele Zachary T. , Episcopio-Sturgeon Diane J. , Romagosa Christina M.
Published: August 2023

Invasive species threaten biodiversity and their management is economically burdensome. Research on the indirect effects of introduced species are often focused on indirect ecological effects, with little focus on the more difficult to capture but critically important societal impacts. Often understated are the social costs of invasive species such as conflicts between invasive species managers and public stakeholders. Chameleons are popular in the pet trade and have been introduced throughout Florida, and their presence often attracts private collectors. After locating a population of panther chameleons (Furcifer pardalis) within a suburban neighborhood in central Florida, we administered anonymous questionnaires to residents to explore how this introduction and the ensuing species collection has affected them. Respondents had knowledge of chameleon presence but most expressed low concern about chameleon presence. Respondents who had observed chameleons in the area expressed more concern for their safety given the activities of private collectors. Our study highlights the importance of recognizing the social impacts of species introductions in urban environments, particularly the attention these species can draw and the mixed perception of these species among stakeholders.
Network shape intelligence outperforms AlphaFold2 intelligence in vanilla protein interaction prediction
Authors: Abdelhamid Ilyes , Muscoloni Alessandro , Rotscher Danny Marc , Lieber Matthias , Markwardt Ulf , Cannistraci Carlo Vittorio
Published: August 2023

For decades, scientists and engineers have been working to predict protein interactions, and network topology methods have emerged as extensively studied techniques. Recently, approaches based on AlphaFold2 intelligence, exploiting 3D molecular structural information, have been proposed for protein interaction prediction, they are promising as potential alternatives to traditional laboratory experiments, and their design and performance evaluation is compelling.

Here, we introduce a new concept of intelligence termed Network Shape Intelligence (NSI). NSI is modelled via network automata rules which minimize external links in local communities according to a brain-inspired principle, as it draws upon the local topology and plasticity rationales initially devised in brain network science and then extended to any complex network. We show that by using only local network information and without the need for training, these network automata designed for modelling and predicting network connectivity can outperform AlphaFold2 intelligence in vanilla protein interactions prediction. We find that the set of interactions mispredicted by AlphaFold2 predominantly consists of proteins whose amino acids exhibit higher probability of being associated with intrinsically disordered regions. Finally, we suggest that the future advancements in AlphaFold intelligence could integrate principles of NSI to further enhance the modelling and structural prediction of protein interactions.
Transport of metformin metabolites by guanidinium exporters of the Small Multidrug Resistance family
Authors: Lucero Rachael M. , Demirer Kemal , Yeh Trevor Justin , Stockbridge Randy B.
Published: August 2023

Proteins from the Small Multidrug Resistance (SMR) family are frequently associated with horizontally transferred multidrug resistance gene arrays found in bacteria from wastewater and the human-adjacent biosphere. Recent studies suggest that a subset of SMR transporters might participate in metabolism of the common pharmaceutical metformin by bacterial consortia. Here, we show that both genomic and plasmid-associated transporters of the SMRGdxfunctional subtype export byproducts of microbial metformin metabolism, with particularly high export efficiency for guanylurea. We use solid supported membrane electrophysiology to evaluate the transport kinetics for guanylurea and native substrate guanidinium by four representative SMRGdxhomologues. Using an internal reference to normalize independent electrophysiology experiments, we show that transport rates are comparable for genomic and plasmid-associated SMRGdxhomologues, and using a proteoliposome-based transport assay, we show that 2 proton:1 substrate transport stoichiometry is maintained. Additional characterization of guanidinium and guanylurea export properties focuses on the structurally characterized homologue, Gdx-Clo, for which we examined the pH dependence and thermodynamics of substrate binding and solved an x-ray crystal structure with guanylurea bound. Together, these experiments contribute in two main ways. By providing the first detailed kinetic examination of the structurally characterized SMRGdxhomologue Gdx-Clo, they provide a functional framework that will inform future mechanistic studies of this model transport protein. Second, this study casts light on a potential role for SMRGdxtransporters in microbial handling of metformin and its microbial metabolic byproducts, providing insight into how native transport physiologies are co-opted to contend with new selective pressures.

Using solid supported membrane electrophysiology, structural biology, and binding assays, we characterize binding and transport of metformin metabolites by bacterial SMR transporters, including proteins associated with horizontal gene transfer in wastewater bacteria that degrade metformin.
Transcriptional suppression of sphingolipid catabolism controls pathogen resistance inC. elegans
Authors: Nasrallah Mohamad A. , Peterson Nicholas D. , Salisbury J. Elizabeth , Liu Pengpeng , Page Amanda L. , Tse Samantha Y. , Wani Khursheed A. , Tocheny Claire E. , Pukkila-Worley Read
Published: August 2023

Sphingolipids are required for diverse biological functions and are degraded by specific catabolic enzymes. However, the mechanisms that regulate sphingolipid catabolism are not known. Here we characterize a transcriptional axis that regulates sphingolipid breakdown to control resistance against bacterial infection. From an RNAi screen for transcriptional regulators of pathogen resistance in the nematodeC. elegans, we identified the nuclear hormone receptornhr-66,a ligand-gated transcription factor homologous to human hepatocyte nuclear factor 4. Tandem chromatin immunoprecipitation-sequencing and RNA sequencing experiments revealed that NHR-66 is a transcriptional repressor, which directly targets sphingolipid catabolism genes. Transcriptional de-repression of two sphingolipid catabolic enzymes innhr-66loss-of-function mutants drives the breakdown of sphingolipids, which enhances host susceptibility to infection with the bacterial pathogenPseudomonas aeruginosa. These data define transcriptional control of sphingolipid catabolism in the regulation of cellular sphingolipids, a process that is necessary for pathogen resistance.
WITHDRAWN: L-Carnitine on contrast-induced nephropathy in diabetic rats
Authors: de Oliveira Natalia Abreu , Couto Sheila Marques Fernandes , Borges Fernanda Teixeira , Vattimo Maria de Fátima Fernandes , da Fonseca Cassiane Dezoti
Published: August 2023

Withdrawal Statement

The authors have withdrawn their manuscript owing to improve the data of manuscript. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
MICROGLIAL CELL EXPRESSION OF THE TYPE 2 CANNABINOID RECEPTOR REGULATES IMMUNE-MEDIATED NEUROINFLAMMATION
Authors: Moe Alison , Rayasam Aditya , Sauber Garrett , Shah Ravi K. , Yuan Cheng-Yin , Szabo Aniko , Moore Bob M. , Colonna Marco , Cui Weiguo , Romero Julian , Zamora Anthony E. , Hillard Cecilia J. , Drobyski William R.
Published: August 2023

Neuroinflammation is a recognized complication of immunotherapeutic approaches such as immune checkpoint inhibitor treatment, chimeric antigen receptor therapy, and graft versus host disease (GVHD) occurring after allogeneic hematopoietic stem cell transplantation. While T cells and inflammatory cytokines play a role in this process, the precise interplay between the adaptive and innate arms of the immune system that propagates inflammation in the central nervous system remains incompletely understood. Using a murine model of GVHD, we demonstrate that type 2 cannabinoid receptor (CB2R) signaling plays a critical role in the pathophysiology of neuroinflammation. In these studies, we identify that CB2R expression on microglial cells induces an activated inflammatory phenotype which potentiates the accumulation of donor-derived proinflammatory T cells, regulates chemokine gene regulatory networks, and promotes neuronal cell death. Pharmacological targeting of this receptor with a brain penetrant CB2R inverse agonist/antagonist selectively reduces neuroinflammation without deleteriously affecting systemic GVHD severity. Thus, these findings delineate a therapeutically targetable neuroinflammatory pathway and has implications for the attenuation of neurotoxicity after GVHD and potentially other T cell-based immunotherapeutic approaches.
An automated convergence diagnostic for phylogenetic MCMC analyses
Authors: Berling Lars , Bouckaert Remco , Gavryushkin Alex
Published: August 2023

Assessing convergence of Markov chain Monte Carlo (MCMC) based analyses is crucial but challenging, especially so in high dimensional and complex spaces such as the space of phylogenetic trees (treespace). In practice, it is assumed that the target distribution is the unique stationary distribution of the MCMC and convergence is achieved when samples appear to be stationary. Here we leverage recent advances in computational geometry of the treespace and introduce a method that combines classical statistical techniques and algorithms with geometric properties of the treespace to automatically evaluate and assess practical convergence of phylogenetic MCMC analyses. Our method monitors convergence across multiple MCMC chains and achieves high accuracy in detecting both practical convergence and convergence issues within treespace. Furthermore, our approach is developed to allow for real-time evaluation during the MCMC algorithm run, eliminating any of the chain post-processing steps that are currently required. Our tool therefore improves reliability and efficiency of MCMC based phylogenetic inference methods and makes analyses easier to reproduce and compare. We demonstrate the efficacy of our diagnostic via a well-calibrated simulation study and provide examples of its performance on real data sets. Although our method performs well in practice, a significant part of the underlying treespace probability theory is still missing, which creates an excellent opportunity for future mathematical research in this area.

The open source package for the phylogenetic inference framework BEAST2, called ASM, that implements these methods, making them accessible through a user-friendly GUI, is available fromhttps://github.com/rbouckaert/asm/. The open source Python package, called tetres, that provides an interface for these methods enabling their applications beyond BEAST2 can be accessed athttps://github.com/bioDS/tetres/.
Ubiquitin phosphorylation accelerates protein aggregation and promotes neurodegeneration in the aging brain
Authors: Chen Cong , Yi Hua-Wei , Zhang Yi , Wang Tong , Gao Tong-Yao , Lou Zhi-Lin , Wei Tao-Feng , Lu Yun-Bi , Li Ting-Ting , Zhang Wei-Ping , Tang Chun
Published: August 2023

Ser65-phosphorylated ubiquitin (pUb) was found elevated in neurons of aged and neurodegenerative brains. Yet little is known whether a causative link exists between pUb level and brain aging. Here we show that the knockout ofpink1, a Ub kinase, abolished pUb elevation and decelerated protein aggregation in aged mouse brains and cells with proteasomal inhibition. Conversely, over-expression of PINK1 but not the kinase-dead version increased the pUb level and accelerated protein aggregation by suppressing of proteasomal degradation. Furthermore, PINK1 over-expression in mouse hippocampus neurons increased pUb level and protein aggregation, slowly leading to mitochondrial injury, neurodegeneration, and cognitive impairment. Notably, the neuronal damages induced by PINK1 were rescued by the dominant negative Ub/S65A mutant, while Ub/S65E phosphomimetic mutant caused neuronal death. Together, an incidental increase of Ub phosphorylation can progressively and cumulatively cause the decline of Ub-dependent proteasomal activity, consequenting promotes neurodegeneration in the aging brain.
Species-Agnostic Transfer Learning for Cross-species Transcriptomics Data Integration without Gene Orthology
Authors: Park Youngjun , Muttray Nils Paul , Hauschild Anne-Christin
Published: August 2023

Novel hypotheses in biomedical research are often developed or validated in model organisms such as mice and zebrafish and thus play a crucial role, particularly in studying disease mechanisms and treatment responses. However, due to biological differences between species, translating these findings into human applications remains challenging. Moreover, commonly used orthologous gene information is often incomplete, particularly for non-model organisms, and entails a significant information loss during gene-id conversion. To address these issues, we present a novel methodology for species-agnostic transfer learning with heterogeneous domain adaptation. We built on the cross-domain structure-preserving projection and extended the algorithm toward out-of-sample prediction, a common challenge in biomedical sequencing data. Our approach not only allows knowledge integration and translation across various species without relying on gene orthology but also identifies similar GO biological processes amongst the most influential genes composing the latent space for species integration. Subsequently, this enables the identification and functional annotation of genes missing from public orthology databases. Finally, we evaluated our approach with four different single-cell sequencing datasets focusing on out-of-sample prediction and compared it against related machine-learning approaches. In summary, the developed model outperforms all related methods working without prior knowledge when predicting unseen cell types based on other species’ data. The results demonstrate that our novel approach allows knowledge transfer beyond species barriers without the dependency on known gene orthology but utilizing the entire gene sets.
Machine Learning-Driven Phenotype Predictions based on Genome Annotations
Authors: Edirisinghe Janaka N. , Goyal Samaksh , Brace Alexander , Colasanti Ricardo , Gu Tianhao , Sadhkin Boris , Zhang Qizhi , Kamimura Roy , Henry Christopher S.
Published: August 2023

Over the past two decades, there has been a remarkable and exponential expansion in the availability of genome sequences, encompassing a vast number of isolate genomes, amounting to hundreds of thousands, and now extending to millions of metagenome-assembled genomes. The rapid and accurate interpretation of this data, along with the profiling of diverse phenotypes such as respiration type, antimicrobial resistance, or carbon utilization, is essential for a wide range of medical and research applications.

Here, we leverage sequenced-based functional annotations obtained from the RAST annotation algorithm as predictors and employ six machine learning algorithms (K-Nearest Neighbors, Gaussian Naive Bayes, Support Vector Machines, Neural Networks, Logistic Regression, and Decision Trees) to generate classifiers that can accurately predict phenotypes of unclassified bacterial organisms. We apply this approach in two case studies focused on respiration types (aerobic, anaerobic, and facultative anaerobic) and Gram-stain types (Gram negative and Gram positive). We demonstrate that all six classifiers accurately classify the phenotypes of Gram stain and respiration type, and discuss the biological significance of the predicted outcomes. We also present four new applications that have been deployed in The Department of Energy Systems Biology Knowledgebase (KBase) that enable users to: (i) Upload high-quality data to train classifiers; (ii) Annotate genomes in the training set with the RAST annotation algorithm; (iii) Build six different genome classifiers; and (iv) Predict the phenotype of unclassified genomes. (https://narrative.kbase.us/#catalog/modules/kb_genomeclassification)
The spreading of facultative H3K9me3-heterochromatin drives congenital disease
Authors: Wang Chen , Zhang Wei , Chen Xue-Lin , Wang Wen-Fei , Li Yong-Hao , Chang Jian-Feng , Guo Xiao-Bo , Jing Yuan-Ya , Li Ya-Bin , Lu Xin-Yi , Li Yu-Tong , Liu Kai , Ni Jian-Quan , Sun Fang-Lin
Published: August 2023

Heterochromatin marked by trimethylated histone 3 at lysine 9 (H3K9me3) plays fundamental roles in reprogramming to direct cell fate determination in higher eukaryotes. However, the upstream factors that guide the establishment and spreading of H3K9me3-heterochromatin, leading to human developmental malformations, remain elusive. In this study, we found that Cdk13, a member of RNA polymerase II (RNAPII) kinase, suppresses congenital heart syndrome by preventing global facultative H3K9me3-heterochromatin spreading. Additionally, Cdk13 directs the phosphorylation of a large set of heterochromatin proteins at specific sites, which are required for the interaction between HP1 and histone H3K9 methyltransferases. Furthermore, we identified a compound, an inhibitor of heterochromatin regulators, that can alleviate syndromic heart defects inCdk13-mutant mice through the inhibition of H3K9me3-heterochromatin spreading. In summary, this study reveals a novel role and mechanism of Cdk13-triggered facultative H3K9me3-heterochromatin spreading in human genetic disease and paves the way for the treatment of congenital heart syndrome.
Mesothelial cells exhibit characteristics of perivascular cells in anin vitroangiogenesis assay
Authors: Koukorava Chrysa , Ward Kelly , Ahmed Katie , Dauleh Sumaya , Pereira Sofia M , Taylor Arthur , Haddrick Malcolm , Cross Michael J , Wilm Bettina
Published: August 2023

Mesothelial cells have been shown to have remarkable plasticity towards mesenchymal cell types during development and in disease situations. Here, we have characterized the potential of mesothelial cells to undergo changes towards perivascular cells using an in vitro angiogenesis assay. We demonstrate that GFP-labelled mesothelial cells (GFP-MCs) aligned closely and specifically with endothelial networks formed when human dermal microvascular endothelial cells (HDMECs) were cultured in the presence of VEGF-A165 on normal human dermal fibroblasts (NHDFs) for a 7-day period. The co-culture with GFP-MCs had a positive effect on branch point formation indicating that the cells supported endothelial tube formation. We interrogated the molecular response of the GFP- MCs to the angiogenic co-culture by qRT-PCR and found that the pericyte markerNg2was upregulated when the cells were co-cultured with HDMECs on NHDFs, indicating a change towards a perivascular phenotype. When GFP-MCs were cultured on the NHDF feeder layer, they upregulated the epithelial-mesenchymal transition markerZeb1and lost their circularity while increasing their size, indicating a change to a more migratory cell type. We analysed the pericyte- like behavior of the GFP-MCs in a 3D cardiac microtissue (spheroid) with cardiomyocytes, cardiac fibroblasts and cardiac endothelial cells where the mesothelial cells showed alignment with the endothelial cells. These results indicate that mesothelial cells have the potential to adopt a perivascular phenotype and associate with endothelial cells to potentially support angiogenesis.
Osteocalcin of maternal and embryonic origins synergize to establish homeostasis in offspring
Authors: Pinto Danilo Correa , Delgado Isabella Canal , Yang Haiyang , Clemenceau Alisson , Corvelo André , Narzisi Giuseppe , Musunuri Rajeeva , Berger Julian Meyer , Hendricks Lauren E. , Tokumura Kazuya , Luo Na , Li Hongchao , Oury Franck , Ducy Patricia , Yadav Vijay K. , Li Xiang , Karsenty Gerard
Published: August 2023

Many physiological functions regulated by osteocalcin are affected in adult offspring of mothers experiencing an unhealthy pregnancy. Furthermore, osteocalcin signaling during gestation influences cognition and adrenal steroidogenesis in adult mice. Together these observations suggest that osteocalcin functions during pregnancy may be a broader determinant of organismal homeostasis in adult mammals than previously thought. To test this hypothesis, we analyzed in unchallenged wildtype andOsteocalcin-deficient, newborn, and adult mice of various genotypes and origin, and that were maintained on different genetic backgrounds, the functions of osteocalcin in the pancreas, liver and testes and their molecular underpinnings. This analysis revealed that providing mothers are themselvesOsteocalcin-deficient,Osteocalcinhaploinsufficiency in embryos hampers insulin secretion, liver gluconeogenesis, glucose homeostasis, testes steroidogenesis in adult offspring; inhibits cell proliferation in developing pancreatic islets and testes; and disrupts distinct programs of gene expression in these organs and in the brain. This study indicates that through their synergistic regulation of multiple physiological functions, osteocalcin ofmaternal and embryonic origins contributes to the establishment and maintenance of organismal homeostasis in newborn and adult offspring.