bluuebunny/crossref_metadata_2025 huggingface dataset:
Dark side of the honeymoon: reconstructing the Asian x European rose breeding history through the lens of genomics
Authors: Leroy Thibault , Albert Elise , Thouroude Tatiana , Baudino Sylvie , Caissard Jean-Claude , Chastellier Annie , Chameau Jérôme , Jeauffre Julien , Loubert Thérèse , Paramita Saretta Nindya , Pernet Alix , Soufflet-Freslon Vanessa , Oghina-Pavie Cristiana , Foucher Fabrice , Oyant Laurence Hibrand-Saint , Clotault Jérémy
Published: June 2023

Roses hold significant symbolic value in Western cultural heritage, often serving as a symbol of love and romance. Despite their ancient cultivation, the appreciation for the phenotypic diversity of roses emerged relatively recently, notably during the 19th century. This period is characterized by a remarkable expansion in the number of varieties, from around 100 to over 8,000, representing a golden age for roses.

To trace the history of rose breeding in Europe and unveil genetic changes during this period, we gathered phenotypic and genetic data from 204 accessions. These included botanical roses and varieties cultivated between 1800 and 1910. Whole-genome sequences from 32 accessions were also included.

Our analysis revealed a temporal shift in the genetic makeup, transitioning from a historical European to a near-Asian genetic background within a few generations. This shift was accompanied by a notable reduction in genetic diversity, attributed to the backcrossing with the less diverse Asian genepool, plus some genomic signatures of selection.

We have generated the largest GWAS catalog for rose to date, offering a valuable resource for future breeding initiatives. We emphasize the critical importance of preserving ancient rose collections to safeguard diversity and ensure a sustainable breeding for the long term.
A mixed methods analysis of youth mental health intervention feasibility and acceptability in a North American city: perspectives from Seattle, Washington
Authors: Mensa-Kwao Augustina , Cuc Ingrid Sub , Concepcion Tessa , Kemp Christopher G. , Hughsam Matthew , Sinha Moitreyee , Collins Pamela Y.
Published: June 2023

Introduction

In March 2021, the Governor of Washington declared a youth mental health crisis. State data revealed high rates of youth suicide and inadequate access to services. This mixed-methods study examines youth and adult perspectives on mental health service gaps and opportunities in Seattle by assessing needs, feasibility, and acceptability of interventions to support youth mental health.

Methods

We interviewed 15 key informants to identify the contextual, structural, and individual-level factors that increase the risk of poor mental health and deter access to care among young people. We complimented these data with a cross-sectional 25-item survey of 117 participants in King County to assess the feasibility and acceptability of interventions for youth mental health. We conducted a deductive thematic qualitative analysis of the interviews and performed descriptive analyses of the quantitative data, using t-tests and χ2tests to summarize and compare participant characteristics stratified by age group.

Results

Qualitative informants attributed challenges to youth mental health to social and relational problems. Example interventions included creating environments that increase belonging and implementation of culturally congruent mental health services. Quantitative study participants rated all evidence-based mental health interventions presented as highly acceptable. However, youth preferred interventions promoting social connectedness, peer support, and holistic approaches to care, while non-youth preferred interventions focused on suicide, alcohol, and substance abuse prevention. Both key informants and survey participants identified schools as the highest priority setting for mental health interventions. There were no significant differences among quantitative outcomes.

Conclusion

Our findings highlight the need for reducing social isolation and increasing social connectedness to support youth mental health. Schools and digital tools were preferred platforms for implementation. Engaging multiple stakeholders, especially young people, and addressing cultural needs and accessibility of mental health resources are important pre-implementation activities for youth mental health intervention in a US city.
Intent matters: how flow & forms of information impact collective navigation
Authors: Hodgson T. M. , Johnston S. T. , Ottobre M. , Painter K. J.
Published: June 2023

The phenomenon of collective navigation has received considerable interest in recent years. A common line of thinking, backed by theoretical studies, is that collective navigation can improve navigation efficiency through the ‘many-wrongs’ principle, whereby individual error is reduced by comparing the headings of neighbours. When navigation takes place in a flowing environment, each individual’s trajectory is influenced by drift. Consequently, a potential discrepancy emerges between an individual’s intended heading and its actual heading. In this study we develop a theoretical model to explore whether collective navigation benefits are altered according to the form of heading information transmitted between neighbours. Navigation based on each individual’s intended heading is found to confer robust advantages across a wide spectrum of flows, via both a marked improvement in migration times and a capacity for a group to overcome flows unnavigable by solitary individuals. Navigation based on individual’s actual headings is far less effective, only offering an improvement under highly favourable currents. For many currents, sharing actual heading information can even lead to journey times that exceed those of individual navigators.
Defects in Mitochondrial Biogenesis Drive Mitochondrial Alterations in PINK1-deficient Human Dopamine Neurons
Authors: Wang Hu , Chen Rong , Xiao Liming , Kumar Manoj , Acevedo-Cintrón Jesús , Siuda Joanna , Koziorowski Dariusz , Wszolek Zbigniew K. , Dawson Valina L. , Dawson Ted M.
Published: June 2023

Mutations and loss of activity in the protein kinase PINK1 play a role in the pathogenesis of Parkinson’s disease (PD). PINK1 regulates many aspects of mitochondrial quality control including mitochondrial autophagy (mitophagy), fission, fusion, transport, and biogenesis. Defects in mitophagy are though to play a predominant role in the loss of dopamine (DA) neurons in PD. Here we show that, although there are defects in mitophagy in human DA neurons lacking PINK1, mitochondrial deficits induced by the absence of PINK1 are primarily due to defects in mitochondrial biogenesis. Upregulation of PARIS and the subsequent down regulation of PGC-1α accounts for the mitochondrial biogenesis defects. CRISPR/Cas9 knockdown of PARIS completely restores the mitochondrial biogenesis defects and mitochondrial function without impacting the deficits in mitophagy due to the absence of PINK1. These results highlight the importance mitochondrial biogenesis in the pathogenesis of PD due to inactivation or loss of PINK1 in human DA neurons.
A co-ordinated transcriptional programme in the maternal liver supplies LC-PUFAs to the conceptus using phospholipids
Authors: Amarsi Risha , Furse Samuel , Cleaton Mary AM , Maurel Sarah , Mitchell Alice L , Ferguson-Smith Anne C. , Cenac Nicolas , Williamson Catherine , Koulman Albert , Charalambous Marika
Published: June 2023

Essential fatty acids (EFAs) and their derivatives, the long and very long chain polyunsaturated fatty acids (LC-PUFAs), are preferentially transported by the mother to the fetus. Failure to supply EFAs is strongly linked with stillbirth, fetal growth restriction, and impaired neurodevelopmental outcomes. However, dietary supplementation during pregnancy is unable to simply reverse these outcomes, suggesting imperfectly understood interactions between dietary EFA intake and the molecular mechanisms of maternal supply. Here we combine untargeted lipidomics with transcriptional profiling of healthy and genetically-manipulated murine models to understand the maternal adaptations required to provide LC-PUFAs to the developing fetus. We discovered a late pregnancy-specific, selective activation of the Liver X Receptor signalling pathway which dramatically increases maternal supply of LC-PUFAs within circulating phospholipids. Crucially, genetic ablation of this pathway in the mother reduced LC-PUFA accumulation by the fetus. Overall our work suggests new molecular strategies for improving maternal-fetal transfer of these important lipids.
Adhesion energy controls lipid binding-mediated endocytosis
Authors: Groza Raluca , Schmidt Kita Valerie , Müller Paul Markus , Ronchi Paolo , Schlack-Leigers Claire , Neu Ursula , Puchkov Dmytro , Dimova Rumiana , Matthäus Claudia , Taraska Justin , Weikl Thomas R. , Ewers Helge
Published: June 2023

Several bacterial toxins and viruses can deform membranes through multivalent binding to lipids for clathrin-independent endocytosis. However, it remains unclear, how membrane deformation and endocytic internalization are mechanistically linked. Here we show that many lipid-binding virions induce membrane deformation and clathrin-independent endocytosis, suggesting a common mechanism based on multivalent lipid binding by globular particles. We create a synthetic cellular system consisting of a lipid-anchored receptor in the form of GPI-anchored anti-GFP nanobodies and a multivalent globular binder exposing 180 regularly-spaced GFP molecules on its surface. We show that these globular, 40 nm diameter, particles bind to cells expressing the receptor, deform the plasma membrane upon adhesion and become endocytosed in a clathrin-independent manner. We explore the role of the membrane adhesion energy in endocytosis by using receptors with affinities varying over 7 orders of magnitude. Using this system, we find that once a threshold in adhesion energy is overcome to allow for membrane deformation, endocytosis occurs reliably. Multivalent, binding-induced membrane deformation by globular binders is thus sufficient for internalization to occur and we suggest it is the common, purely biophysical mechanism for lipid-binding mediated endocytosis of toxins and pathogens.
The highly and perpetually upregulated thyroglobulin gene is a hallmark of functional thyrocytes
Authors: Ullrich Simon , Leidescher Susanne , Feodorova Yana , Thanisch Katharina , Fini Jean-Baptiste , Kaspers Bernd , Weber Frank , Markova Boyka , Führer Dagmar , Romitti Mirian , Krebs Stefan , Blum Helmut , Leonhardt Heinrich , Costagliola Sabine , Heuer Heike , Solovei Irina
Published: June 2023

Abnormalities are indispensable for studying normal biological processes and mechanisms. In the present work, we draw attention to the remarkable phenomenon of a perpetually and robustly upregulated gene, the thyroglobulin gene (Tg). The gene is expressed in the thyroid gland and, as it has been recently demonstrated, forms so-called transcription loops, easily observable by light microscopy. Using this feature, we show thatTgis expressed at a high level from the moment a thyroid cell acquires its identity and both alleles remain highly active over the entire life of the cell, i.e. for months or years depending on the species. We demonstrate that this high upregulation is characteristic of thyroglobulin genes in all major vertebrate groups. We provide evidence thatTgis not influenced by the thyroid hormone status, does not oscillate round the clock and is expressed during both the exocrine and endocrine phases of thyrocyte activity. We conclude that the thyroglobulin gene represents a valuable model to study the maintenance of a high transcriptional upregulation.

SUMMARY STATEMENT

The thyroglobulin gene is highly and permanently expressed in thyrocytes of all vertebrates, at any condition and round the clock, offering a unique model to study mechanisms of high upregulation maintenance and chromatin dynamics
Familiarity-taxis: A bilateral approach to view-based navigation
Authors: Steinbeck Fabian , Kagioulis Efsthathios , Dewar Alex , Philippides Andy , Nowotny Thomas , Graham Paul
Published: June 2023

Many insects use view-based navigation, or snapshot matching, to return to familiar locations, or navigate routes. This relies on egocentric memories being matched to current views of the world. Previous snapshot navigation algorithms have used full panoramic vision for the comparison of memorised images with query images to establish a measure of familiarity, which leads to a recovery of the original heading direction from when the snapshot was taken. Many aspects of insect sensory systems are lateralised with steering being derived from the comparison of left and right signals like a classic Braitenberg vehicle. Here we investigate whether view-based route navigation can be implemented using bilateral visual familiarity comparisons. We found that the difference in familiarity between estimates from left and right fields of view can be used as a steering signal to recover the original heading direction. This finding extends across many different sizes of field of view and visual resolutions. In insects, steering computations are implemented in a brain region called the Lateral Accessory Lobe, within the Central Complex. In a simple simulation we show with a SNN model of the LAL an existence proof of how bilateral visual familiarity could drive a search for a visually defined goal.
A Chicken Tapasin ortholog can chaperone empty HLA molecules independently of other peptide-loading components
Authors: Papadaki Georgia F. , Woodward Claire H. , Young Michael C. , Winters Trenton J. , Burslem George M. , Sgourakis Nikolaos G.
Published: June 2023

Human Tapasin (hTapasin) is the main chaperone of MHC-I molecules, enabling peptide loading and antigen repertoire optimization across HLA allotypes. However, it is restricted to the endoplasmic reticulum (ER) lumen as part of the protein loading complex (PLC) and therefore is highly unstable when expressed in recombinant form. Additional stabilizing co-factors such as ERp57 are required to catalyze peptide exchangein vitro, limiting uses for the generation of pMHC-I molecules of desired antigen specificities. Here, we show that the chicken Tapasin (chTapasin) ortholog can be expressed recombinantly at high yields in stable form, independently of co-chaperones. chTapasin can bind the human HLA-B*37:01 with low micromolar-range affinity to form a stable tertiary complex. Biophysical characterization by methyl-based NMR methods reveals that chTapasin recognizes a conserved β2m epitope on HLA-B*37:01, consistent with previously solved X-ray structures of hTapasin. Finally, we provide evidence that the B*37:01/chTapasin complex is peptide-receptive and can be dissociated upon binding of high-affinity peptides. Our results highlight the use of chTapasin as a stable scaffold for future protein engineering applications aiming to expand the ligand exchange function on human MHC-I and MHC-like molecules.
Effect of Acute Stress on Working Memory in Pilots: Investigating the Modulatory Role of Memory Load
Authors: Liang Yaowei , Peng Xing , Liu Yueying , Zhu Qi , Xu Zhi , Yang Jiazhong
Published: June 2023

The effect of acute stress on working memory (WM) has not been extensively investigated in demanding tasks, although many practitioners, such as pilots, frequently face varying working memory demands. The current study investigated how acute stress modulates pilots’ WM performance. Forty-two pilots were randomly assigned to the stress group or the control group. The stress group experienced acute stress induced by the modified Trier Social Stress Test (TSST), whereas the control group did not receive any stress induction. Both groups performed N-back tasks under varying degrees of memory load (0-back, 1-back, and 2-back). State-Trait Anxiety Inventory scores, heart rates, and salivary cortisol concentrations were measured in the experiment to determine the extent of induced stress. The results revealed that (1) The modified TSST effectively induced acute stress in the stress group. (2) As rising of memory load, the reaction time expectedly increased while accuracy decreased. (3) An interaction between the stress and control group was found for accuracy, indicating that acute stress might contribute to higher accuracy in moderate WM load (1-back). These suggestions support the emotion regulation hypothesis, in which acute stress induces heightened emotional states that impact WM performance. Furthermore, the current study explored the interplay between acute stress and memory load in a specific population, offering insights into potential pilots’ stress management strategies and training programs to improve pilots’ WM abilities. These applications would be beneficial for strengthening pilots’ coping mechanisms in emergencies and guaranteeing flight safety.
Cellular endosomal potassium ion flux regulates arenavirus uncoating during virus entry
Authors: Shaw Amelia B. , Tse Hiu Nam , Byford Owen , Plahe Grace , Moon-Walker Alex , Ollmann-Saphire Erica , Whelan Sean P. J. , Mankouri Jamel , Fontana Juan , Barr John N.
Published: June 2023

Lymphocytic choriomeningitis virus (LCMV) is a model arenavirus that causes fatalities within immunocompromised populations. To enter cells, the LCMV envelope fuses with endosomal membranes, for which two requirements are low pH and interaction between LCMV GP spike and receptor CD164. LCMV subsequently uncoats, where genome-associated NP separates from Z matrix. To further examine LCMV entry, an siRNA screen identified K+channels as important for LCMV infection, and pharmacological inhibition confirmed K+involvement during entry. We tracked incoming virions along their entry pathway under physiological conditions, where uncoating was signified by separation of NP and Z. In contrast, K+channel blockade, prevented uncoating, trapping virions within Rab7 and CD164-positive endosomes, identifying K+as a third LCMV entry requirement. K+did not increase GP/CD164 binding, thus we suggest K+mediates uncoating by modulating NP/Z interactions within the virion interior. These results suggest repurposing licensed K+channel inhibitors represents a potential anti-arenaviral strategy.
The metabolic role of vitamin D in children’s neurodevelopment: a network study
Authors: Marzio Margherita De , Lasky-Su Jessica , Chu Su H. , Prince Nicole , Litonjua Augusto A. , Weiss Scott T. , Kelly Rachel S. , Glass Kimberly R.
Published: June 2023

Autism spectrum disorder (ASD) is a neurodevelopmental disorder with various proposed environmental risk factors and a rapidly increasing prevalence. Mounting evidence suggests a potential role of vitamin D deficiency in ASD pathogenesis, though the causal mechanisms remain largely unknown. Here we investigate the impact of vitamin D on child neurodevelopment through an integrative network approach that combines metabolomic profiles, clinical traits, and neurodevelopmental data from a pediatric cohort. Our results show that vitamin D deficiency is associated with changes in the metabolic networks of tryptophan, linoleic, and fatty acid metabolism. These changes correlate with distinct ASD-related phenotypes, including delayed communication skills and respiratory dysfunctions. Additionally, our analysis suggests the kynurenine and serotonin sub-pathways may mediate the effect of vitamin D on early childhood communication development. Altogether, our findings provide metabolome-wide insights into the potential of vitamin D as a therapeutic option for ASD and other communication disorders.
Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data
Authors: Bryce-Smith Sam , Burri Dominik , Gazzara Matthew R. , Herrmann Christina J. , Danecka Weronika , Fitzsimmons Christina M. , Wan Yuk Kei , Zhuang Farica , Fansler Mervin M. , Fernández José M. , Ferret Meritxell , Gonzalez-Uriarte Asier , Haynes Samuel , Herdman Chelsea , Kanitz Alexander , Katsantoni Maria , Marini Federico , McDonnel Euan , Nicolet Ben , Poon Chi-Lam , Rot Gregor , Schärfen Leonard , Wu Pin-Jou , Yoon Yoseop , Barash Yoseph , Zavolan Mihaela
Published: June 2023

The tremendous rate with which data is generated and analysis methods emerge makes it increasingly difficult to keep track of their domain of applicability, assumptions, and limitations and consequently, of the efficacy and precision with which they solve specific tasks. Therefore, there is an increasing need for benchmarks, and for the provision of infrastructure for continuous method evaluation. APAeval is an international community effort, organized by the RNA Society in 2021, to benchmark tools for the identification and quantification of the usage of alternative polyadenylation (APA) sites from short-read, bulk RNA-sequencing (RNA-seq) data. Here, we reviewed 17 tools and benchmarked eight on their ability to perform APA identification and quantification, using a comprehensive set of RNA-seq experiments comprising real, synthetic, and matched 3′-end sequencing data. To support continuous benchmarking, we have incorporated the results into the OpenEBench online platform, which allows for seamless extension of the set of methods, metrics, and challenges. We envisage that our analyses will assist researchers in selecting the appropriate tools for their studies. Furthermore, the containers and reproducible workflows generated in the course of this project can be seamlessly deployed and extended in the future to evaluate new methods or datasets.
Researcher effects on the biological structure and edaphic conditions of field sites and implications for management
Authors: Rinehart Shelby A , Dybiec Jacob M , Richardson Parker , Walker Janet B , Peabody James D , Cherry Julia A
Published: June 2023

Field studies are necessary for understanding natural processes, but they can disturb the environment. Despite researchers acknowledging these effects, no studies have empirically tested the direct (e.g., harvesting plants) and indirect effects (i.e., trampling) of researcher activities on biological structure and edaphic conditions. We leveraged field studies in Alabama and California to monitor the recovery of tidal marshes following research activities. Researcher effects on animals, plants, and sediment conditions remained prevalent almost one year after the disturbance ended. For instance, trampled plots had 14-97% lower plant cover than undisturbed plots after >10 months of recovery. Researcher effects also impacted plant composition, leading to increased subordinate species abundance. We encourage field researchers to adopt strategies that reduce their scientific footprints, including reducing field visits, limiting field team size, and considering ways to limit potential environmental impacts during study design.
The activation of INF2 by Piezo1/Ca2+is required for mesenchymal to amoeboid transition in confined environments
Authors: Kar Neelakshi , Caruso Alexa P. , Prokopiou Nicos , Logue Jeremy S.
Published: June 2023

To invade heterogenous tissues, transformed cells may undergo a mesenchymal to amoeboid transition (MAT). However, the molecular mechanisms regulating this transition are poorly defined. In invasive melanoma cells, we demonstrate that intracellular [Ca2+] increases with the degree of confinement in a Piezo1 dependent fashion. Moreover, Piezo1/Ca2+is found to drive amoeboid and not mesenchymal migration in confined environments. Consistent with a model in which Piezo1 senses tension at the plasma membrane, the percentage of cells using amoeboid migration is further increased in undulating microchannels. Surprisingly, amoeboid migration was not promoted by myosin light chain kinase (MLCK), which is sensitive to intracellular [Ca2+]. Instead, we report that Piezo1/Ca2+activates inverted formin-2 (INF2) to induce widespread actin cytoskeletal remodeling. Strikingly, the activation of INF2 is found to promote de-adhesion, which in turn facilitates MAT. Using micropatterned surfaces, we demonstrate that cells require INF2 to effectively migrate in environments with challenging mechanochemical properties.

Summary Statement

Migrating melanoma cells are found to rely on the activation of inverted formin-2 (INF2) by Piezo1/Ca2+for mesenchymal to amoeboid transition (MAT) in confined environments.
TECPR1 provides E3-ligase like activity to the ATG5-ATG12 complex to conjugate LC3/ATG8 to damaged lysosomes
Authors: Wang Yingxue , Jefferson Matthew , Whelband Matthew , Kreuzer Kristine , Mccoll James , Verkade Paul , Mayer Ulrike , Wileman Thomas
Published: June 2023

Autophagosomes deliver cytosolic material to lysosomes to provide amino acids during starvation and to degrade damaged proteins and organelles to maintain tissue homeostasis. Delivery to lysosomes requires LC3/ATG8 (LC3), the major membrane protein of the autophagosome, that uses adaptor proteins to capture cargo and recruits tethering and SNARE proteins to promote fusion with lysosomes. LC3 is also recruited to endo-lysosome compartments in response to increases in vacuolar pH to facilitate degradation of material entering cells by endocytosis. A series of ubiquitin-like reactions conjugate LC3 to amino groups exposed by phosphatidylethanolamine (PE) or phosphatidylserine (PS) in target membranes. The E1 and E2-ubiquitin-like activities of ATG7 and ATG3 use thioester bonds to transfer LC3 to the ATG5-ATG12 conjugate. At the same time binding of ATG16L1 to ATG5-ATG12 provides the E3 ubiquitin-ligase like activity necessary to conjugate LC3 to PE or PS. The ATG5-ATG12 conjugate can also bind TECPR1 (tectonin beta propeller repeat-containing protein) which shares an ATG5 interaction (AIR) region with ATG16L1 and can binds LC3 directly through a LC3 interaction region (LIR). In this study we have used cells lacking ATG16L1 to determine if TECPR1 can substitute for ATG16L1 during LC3 conjugation. The results show that ATG16L1-/-MEFS can conjugate LC3 to lysosomes damaged by chloroquine or LLOMes and conjugation is dependent on the ubiquitin-like enzymes ATG3, ATG5 and ATG7 upstream of ATG16L1. TECPR1, ATG5 and galectin 3 are recruited to LAMP positive damaged lysosomes in the absence of ATG16L1 suggesting that TECPR-1 recruits ATG5-ATG12 to conjugate LC3 to damaged lysosomes. This was confirmed when truncation of TECPR1 at the central PH domain required for lysosome binding prevented LC3 conjugation, and LC3 conjugation could be restored by full length TECPR1. Recruitment of TECPR1 to damaged lysosomes required the N-terminal LIR motif and was partially dependent on the central PH domain that binds PI4P exposed during lysosome repair. TECPR1 can therefore conjugate LC3 to damaged lysosomes independently of ATG16L1 by providing E3 ligase-like activity to ATG5-ATG12. Direct conjugation of LC3 by TECPR1 may contribute to the autophagosome tethering functions reported for TECPR1 by increasing recruitment of cargo receptors, tethering proteins and SNARE proteins required for fusion with lysosomes and protein degradation. TECPR1-dependent conjugation of LC3 may also facilitate lysosome repair pathways involving autophagic lysosomal reformation and transcriptional activation of autophagy by TFEB.
Huntingtin loss in hepatocytes is associated with altered metabolism, adhesion, and liver zonation
Authors: Bragg Robert M. , Coffey Sydney R. , Cantle Jeffrey P. , Hu Shikai , Singh Sucha , Legg Samuel R.W. , McHugh Cassandra A. , Toor Amreen , Zeitlin Scott O. , Kwak Seung , Howland David , Vogt Thomas F. , Monga Satdarshan P. , Carroll Jeffrey B.
Published: June 2023

Huntington’s disease arises from a toxic gain of function in thehuntingtin(HTT) gene. As a result, many HTT-lowering therapies are being pursued in clinical studies, including those that reduce HTT RNA and protein expression in the liver. To investigate potential impacts, we characterized molecular, cellular, and metabolic impacts of chronic HTT lowering in mouse hepatocytes. Lifelong hepatocyte HTT loss is associated with multiple physiological changes, including increased circulating bile acids, cholesterol and urea, hypoglycemia, and impaired adhesion. HTT loss causes a clear shift in the normal zonal patterns of liver gene expression, such that pericentral gene expression is reduced. These alterations in liver zonation in livers lacking HTT are observed at the transcriptional, histological and plasma metabolite level. We have extended these phenotypes physiologically with a metabolic challenge of acetaminophen, for which the HTT loss results in toxicity resistance. Our data reveal an unexpected role for HTT in regulating hepatic zonation, and we find that loss of HTT in hepatocytes mimics the phenotypes caused by impaired hepatic β-catenin function.

Graphical Abstract
Generation of a robust reference gut microbiome dataset for an urban population in Argentina optimized by a machine learning approach
Authors: Rohr Cristian , Sciara Mariela , Brun Bianca , Fay Fabian , Vazquez Martín P.
Published: June 2023

Robust human microbiome analysis requires robust reference datasets obtained from a population that presents similar habits to the one we are trying to assess.

We reported here the construction of a robust reference dataset of healthy individuals from urban and surrounding rural areas of the Argentine population. We screened 200 volunteers with strict inclusion/exclusion criteria. Volunteers were also screened with routine blood clinical test analysis and a complete metabolome profile from blood and urine to remove outliers before inclusion in the Next Generation Sequencing dataset. Sequencing was done on an Illumina MiSeq using the V3-V4 16S rRNA. Using these data, we performed de novo community structure prediction by applying clustering methodology based on seven distance and dissimilarity metrics and two clustering methods to the reference set. Using this approach, we discovered four different enterotypes in this community structure. We then trained a model for the classification of any new sample into the structure of the reference set. Once the new sample was classified, it was compared to the reference ranges of both the enterotype-specific subset and the whole reference set.

Finally, we challenged the robustness of this methodology using samples from two test case volunteers with clinically proven gut dysbiosis in a time-series sampling with dietary interventions. Our results pointed to the need to carefully analyze the results of gut microbiome in the context of enterotype-specific rather than to a whole population dataset.
Bruno 1 regulates cytoskeleton dynamics and a temporal splicing transition to promote myofibril assembly, growth and maturation inDrosophilaflight muscle
Authors: Nikonova Elena , Canela Grimau Marc , Barz Christiane , Esser Alexandra , Bouterwek Jessica , Roy Akanksha , Gensler Heidemarie , Heß Martin , Straub Tobias , Forne Ignasi , Spletter Maria L.
Published: June 2023

Muscles undergo developmental transitions in gene expression and alternative splicing that are necessary to refine sarcomere structure and contractility. CUG-BP and ETR-3-like (CELF) family RNA binding proteins are important regulators of RNA processing during myogenesis that are misregulated in diseases such as myotonic dystrophy (DM1). Here we report a conserved function for Bruno 1 (Bru1, Arrest), a CELF1/2 family homolog inDrosophila, during early muscle myogenesis. Loss of Bru1 in flight muscles results in disorganization of the actin cytoskeleton leading to aberrant myofiber compaction and defects in pre-myofibril formation. Temporally-restricted rescue and RNAi knockdown demonstrate that early cytoskeletal defects interfere with subsequent steps in sarcomere growth and maturation. Early defects are distinct from a later requirement forbru1to regulate sarcomere assembly dynamics during myofiber maturation. We identify an imbalance in growth in sarcomere length and width during later stages of development as the mechanism driving abnormal radial growth, myofibril fusion and the formation of hollow myofibrils inbru1mutant muscle. Molecularly, we characterize a genome-wide transition from immature to mature sarcomere gene isoform expression in flight muscle development that is blocked inbru1mutants. We further demonstrate that temporally restricted Bru1 rescue can partially alleviate hypercontraction in late pupal and adult stages, but it cannot restore myofiber function or correct structural deficits. Our results reveal the conserved nature of CELF function in regulating cytoskeletal dynamics in muscle development, and demonstrate that defective RNA processing due to misexpression of CELF proteins causes wide-reaching structural defects and progressive malfunction of affected muscles that cannot be rescued by late-stage gene replacement.
Metabolic engineering ofCorynebacterium glutamicumfor the production of anthranilate from glucose and xylose
Authors: Mutz Mario , Brüning Vincent , Brüsseler Christian , Müller Moritz-Fabian , Noack Stephan , Marienhagen Jan
Published: June 2023

Anthranilate and its derivative aniline are important basic chemicals for the synthesis of polyurethanes as well as various dyes and food additives. Today, aniline is mainly chemically produced from petroleum-derived benzene, but it could be also obtained more sustainably by decarboxylation of the microbially produced shikimate pathway intermediate anthranilate. In this study,Corynebacterium glutamicumwas engineered for the microbial production of anthranilate from a carbon source mixture of glucose and xylose. First, a feedback-resistant 3-deoxy- arabinoheptulosonate-7-phosphate synthase fromE. coli, catalyzing the first step of the shikimate pathway, was functionally introduced intoC. glutamicumto enable anthranilate production. Modulation of the translation efficiency of the genes for the shikimate kinase (aroK) and the anthranilate phosphoribosyltransferase (trpD) improved product formation. Deletion of two genes, one for a putative phosphatase (nagD) and one for a quinate/shikimate dehydrogenase (qsuD), abolished by-product formation of glycerol and quinate. However, the introduction of an engineered anthranilate synthase (TrpEG) unresponsive to feedback inhibition by tryptophan had the most pronounced effect on anthranilate production. Component I of this enzyme (TrpE) was engineered using a biosensor-basedin vivoscreening strategy for identifying variants with increased feedback-resistance in a semi-rational library of TrpE muteins. The final strain accumulated up to 5.9 g/L (43 mM) anthranilate in defined CGXII medium from a mixture of glucose and xylose in bioreactor cultivations. We believe that the constructedC. glutamicumvariants are not only limited to anthranilate production, but could also be suitable for the synthesis of other biotechnologically interesting shikimate pathway intermediates, or any other aromatic compound derived thereof.
A computational model predicts sex-specific responses to calcium channel blockers in mammalian mesenteric vascular smooth muscle
Authors: Hernandez-Hernandez Gonzalo , O’Dwyer Samantha C. , Matsumoto Collin , Tieu Mindy , Fong Zhihui , Yang Pei-Chi , Lewis Timothy J. , Santana L. Fernando , Clancy Colleen E.
Published: June 2023

The function of the smooth muscle cells lining the walls of mammalian systemic arteries and arterioles is to regulate the diameter of the vessels to control blood flow and blood pressure. Here, we describe anin-silicomodel, which we call the “Hernandez-Hernandez model”, of electrical and Ca2+signaling in arterial myocytes based on new experimental data indicating sex-specific differences in male and female arterial myocytes from murine resistance arteries. The model suggests the fundamental ionic mechanisms underlying membrane potential and intracellular Ca2+signaling during the development of myogenic tone in arterial blood vessels. Although experimental data suggest that KV1.5 channel currents have similar amplitudes, kinetics, and voltage dependencies in male and female myocytes, simulations suggest that the KV1.5 current is the dominant current regulating membrane potential in male myocytes. In female cells, which have larger KV2.1 channel expression and longer time constants for activation than male myocytes, predictions from simulated female myocytes suggest that KV2.1 plays a primary role in the control of membrane potential. Over the physiological range of membrane potentials, the gating of a small number of voltage-gated K+channels and L-type Ca2+channels are predicted to drive sex-specific differences in intracellular Ca2+and excitability. We also show that in an idealized computational model of a vessel, female arterial smooth muscle exhibits heightened sensitivity to commonly used Ca2+channel blockers compared to male. In summary, we present a new model framework to investigate the potential sex-specific impact of anti-hypertensive drugs.
Differences in Hepatocellular Iron Metabolism Underlie Sexual Dimorphism in Hepatocyte Ferroptosis
Authors: Tao Hui , Dar Hamid Y , Tian Cheng , Banerjee Somesh , Glazer Evan S , Srinivasan Shanthi , Zhu Liqin , Pacifici Roberto , He Peijian
Published: June 2023

Males show higher incidence and severity than females in hepatic injury and many liver diseases, but the mechanisms are not well understood. Ferroptosis, an iron-mediated lipid peroxidation-dependent death, plays an important role in the pathogenesis of liver diseases. We determined whether hepatocyte ferroptosis displays gender difference, accounting for sexual dimorphism in liver diseases. Compared to female hepatocytes, male hepatocytes were much more vulnerable to ferroptosis by iron and pharmacological inducers including RSL3 and iFSP1. Male but not female hepatocytes exhibited significant increases in mitochondrial Fe2+and mitochondrial ROS (mtROS) contents. Female hepatocytes showed a lower expression of iron importer transferrin receptor 1 (TfR1) and mitochondrial iron importer mitoferrin 1 (Mfrn1), but a higher expression of iron storage protein ferritin heavy chain 1 (FTH1). It is well known that TfR1 expression is positively correlated with ferroptosis. Herein, we showed that silencing FTH1 enhanced while knockdown of Mfrn1 decreased ferroptosis in HepG2 cells. Removing female hormones by ovariectomy (OVX) did not dampen but rather enhanced hepatocyte resistance to ferroptosis. Mechanistically, OVX potentiated the decrease in TfR1 and increase in FTH1 expression. OVX also increased FSP1 expression in ERK-dependent manner. Elevation in FSP1 suppressed mitochondrial Fe2+accumulation and mtROS production, constituting a novel mechanism of FSP1-mediated inhibition of ferroptosis. In conclusion, differences in hepatocellular iron handling between male and female account, at least in part, for sexual dimorphism in induced ferroptosis of the hepatocytes.
Thanks to repetition, dustbathing detection can be automated combining accelerometry and wavelet analysis
Authors: Fonseca R.G. , Flesia A.G. , Spanevello F.C. , de la Fuente M.V. , Bosch M.C. , Marin R.H. , Barberis L. , Kembro J.M.
Published: June 2023

Dustbathing is performed by many groups of birds, including Galliformes. It consists of a well-defined orderly sequence of movements. Repetitive changes in body position during dustbathing can be automatically detected through data processing of body mounted accelerometer recordings, specifically the complex Morlet continuous wavelet transform. The approach was tested in 13 adult male Japanese quail(Coturnix japonica) fitted with a backpack containing a triaxial accelerometer and video-recorded during at least 6h. Rhythmicity (period 25-60s) in the y-axis acceleration vector is reflected as large power values, and is associated almost exclusively to dustbathing events. Thus, by implementing a threshold value we detected events automatically with an accuracy of 80% (range 66-100%). We show potential uses for characterizing temporal dynamics (e.g. daily rhythms) of dustbathing and for the assessment of intra- and inter-individual variability over long-term studies, even within large complex environments (e.g. natural environments or breeding facilities).

Summary statement

We propose a method for automatically detecting dustbathing (i.e a behavior performed by many groups of birds, including Galliformes) from triaxial accerometer recoding using a wavelet technique.
TOMM40 and TOMM22 of the Translocase Outer Mitochondrial Membrane Complex rescue statin-impaired mitochondrial dynamics, morphology, and mitophagy in skeletal myotubes
Authors: Yang Neil V. , Rogers Sean , Guerra Rachel , Pagliarini David J. , Theusch Elizabeth , Krauss Ronald M.
Published: June 2023

Background

Statins are the drugs most commonly used for lowering plasma low-density lipoprotein (LDL) cholesterol levels and reducing cardiovascular disease risk. Although generally well tolerated, statins can induce myopathy, a major cause of non-adherence to treatment. Impaired mitochondrial function has been implicated as a cause of statin-induced myopathy, but the underlying mechanism remains unclear. We have shown that simvastatin downregulates transcription ofTOMM40andTOMM22, genes that encode major subunits of the translocase of outer mitochondrial membrane (TOM) complex which is responsible for importing nuclear-encoded proteins and maintaining mitochondrial function. We therefore investigated the role ofTOMM40andTOMM22in mediating statin effects on mitochondrial function, dynamics, and mitophagy.

Methods

Cellular and biochemical assays and transmission electron microscopy were used to investigate effects of simvastatin andTOMM40andTOMM22expression on measures of mitochondrial function and dynamics in C2C12 and primary human skeletal cell myotubes.

Results

Knockdown ofTOMM40andTOMM22in skeletal cell myotubes impaired mitochondrial oxidative function, increased production of mitochondrial superoxide, reduced mitochondrial cholesterol and CoQ levels, disrupted mitochondrial dynamics and morphology, and increased mitophagy, with similar effects resulting from simvastatin treatment. Overexpression ofTOMM40andTOMM22in simvastatin-treated muscle cells rescued statin effects on mitochondrial dynamics, but not on mitochondrial function or cholesterol and CoQ levels. Moreover, overexpression of these genes resulted in an increase in number and density of cellular mitochondria.

Conclusion

These results confirm that TOMM40 and TOMM22 are central in regulating mitochondrial homeostasis and demonstrate that downregulation of these genes by statin treatment mediates disruption of mitochondrial dynamics, morphology, and mitophagy, effects that may contribute to statin-induced myopathy.

GRAPHICAL ABSTRACT
TheVEGFG-quadruplex forming promoter is repaired via long-patch BER
Authors: Hussen Adil , Kravitz Haley L. , Freudenthal Bret D. , Whitaker Amy M.
Published: June 2023

In response to oxidative damage, base excision repair (BER) enzymes perturb the structural equilibrium of theVEGFpromoter between B-form and G4 DNA conformations, resulting in epigenetic-like modifications of gene expression. However, the mechanistic details remain enigmatic, including the activity and coordination of BER enzymes on the damaged G4 promoter. To address this, we investigated the ability of each BER factor to conduct its repair activity onVEGFpromoter G4 DNA substrates by employing pre-steady-state kinetics assays andin vitrocoupled BER assays. OGG1 was able to initiate BER on double-strandedVEGFpromoter G4 DNA substrates. Moreover, pre-steady-state kinetics revealed that compared to B-form DNA, APE1 repair activity on the G4 was decreased ∼2-fold and is the result of slower product release as opposed to inefficient strand cleavage. Interestingly, Pol β performs multiple insertions on G4 substates via strand displacement DNA synthesis in contrast to a single insertion on B-form DNA. The multiple insertions inhibit ligation of the Pol β products, and hence BER is not completed on theVEGFG4 promoter substrates through canonical short-patch BER. Instead, repair requires the long-patch BER flap-endonuclease activity of FEN1 in response to the multiple insertions by Pol β prior to ligation. Because the BER proteins and their repair activities are a key part of theVEGFtranscriptional enhancement in response to oxidative DNA damage of the G4VEGFpromoter, the new insights reported here on BER activity in the context of this promoter are relevant toward understanding the mechanism of transcriptional regulation.
Wound-Induced Syncytia Outpace Mononucleate Neighbors duringDrosophilaWound Repair
Authors: White James S. , Su Jasmine J. , Ruark Elizabeth M. , Hua Junmin , Shane Hutson M. , Page-McCaw Andrea
Published: June 2023

All organisms have evolved to respond to injury. Cell behaviors like proliferation, migration, and invasion replace missing cells and close wounds. However, the role of other wound-induced cell behaviors is not understood, including the formation of syncytia (multinucleated cells). Wound-induced epithelial syncytia were first reported around puncture wounds in post-mitoticDrosophilaepidermal tissues, but have more recently been reported in mitotically competent tissues such as theDrosophilapupal epidermis and zebrafish epicardium. The presence of wound-induced syncytia in mitotically active tissues suggests that syncytia offer adaptive benefits, but it is unknown what those benefits are. Here, we usein vivolive imaging to analyze wound-induced syncytia in mitotically competentDrosophilapupae. We find that almost half the epithelial cells near a wound fuse to form large syncytia. These syncytia use several routes to speed wound repair: they outpace diploid cells to complete wound closure; they reduce cell intercalation during wound closure; and they pool the resources of their component cells to concentrate them toward the wound. In addition to wound healing, these properties of syncytia are likely to contribute to their roles in development and pathology.
Glucose-stimulated KIF5B-driven microtubule sliding organizes microtubule networks in pancreatic beta cells
Authors: Bracey Kai M. , Noguchi Pi’illani , Edwards Courtney , Cario Alisa , Gu Guoqiang , Kaverina Irina
Published: June 2023

In pancreatic islet beta cells, molecular motors use cytoskeletal polymers microtubules as tracks for intracellular transport of insulin secretory granules. Beta-cell microtubule network has a complex architecture and is non-directional, which provide insulin granules at the cell periphery for rapid secretion response, yet to avoid over-secretion and subsequent hypoglycemia. We have previously characterized a peripheral sub-membrane microtubule array, which is critical for withdrawal of excessive insulin granules from the secretion sites. Microtubules in beta cells originate at the Golgi in the cell interior, and how the peripheral array is formed is unknown. Using real-time imaging and photo-kinetics approaches in clonal mouse pancreatic beta cells MIN6, we now demonstrate that kinesin KIF5B, a motor protein with a capacity to transport microtubules as cargos, slides existing microtubules to the cell periphery and aligns them to each other along the plasma membrane. Moreover, like many physiological beta-cell features, microtubule sliding is facilitated by a high glucose stimulus. These new data, together with our previous report that in high glucose sub-membrane MT array is destabilized to allow for robust secretion, indicate that MT sliding is another integral part of glucose-triggered microtubule remodeling, likely replacing destabilized peripheral microtubules to prevent their loss over time and beta-cell malfunction.