bluuebunny/crossref_metadata_2025 huggingface dataset:
Machine Learning-GWAS reveals the role ofWSD1gene for cuticular wax ester biosynthesis and key genomic regions controlling early maturity in bread wheat
Authors: Tekeu Honoré , Jean Martine , Ngonkeu Eddy L. M. , Belzile François
Published: November 2023

This study employed Machine Learning-Genome-Wide Association Study (ML-GWAS) to identify genomic regions linked to cuticular wax ester biosynthesis (SW) and early maturity (DM) in wheat. Using a dataset with 170 wheat accessions and 74K SNPs, four GWAS tools (MLM, CMLM, FarmCPU, and BLINK) and five machine learning techniques (RF, ANN, SVR, CNN, and SVM) were applied. A highly significant SW association was found on chromosome 1A, with the peak SNP (chr1A:556842331) explaining 50% of the phenotypic variation. A promising candidate gene,TraesCS1A01G385500, was identified as an ortholog of Arabidopsis thaliana’sWSD1gene, which plays a crucial role in very long-chain (VLC) wax ester biosynthesis. For DM, four QTLs were detected on chromosomes 4B (two QTLs), 2A, and 5A. Haplotype analysis revealed that alleles TT significantly contribute to cuticular wax ester biosynthesis and early maturity in wheat varieties. The study underscores the superior performance of ML models, especially when combined with advanced multi-locus GWAS models like BLINK and FarmCPU, with significantly lower p-values for identifying relevant QTLs compared to traditional methods. ML approaches hold potential for revolutionizing the study of complex genetic traits, offering insights to enhance wheat crops’ resilience and quality. ML-GWAS emerges as a compelling tool for genomic-based breeding, enabling breeders to develop improved wheat varieties with greater precision and efficiency.
The hepatocyte Epidermal Growth Factor Receptor (EGFR) pathway regulates the cellular interactome within the liver fibrotic niche
Authors: Gonzalez-Sanchez Ester , Vaquero Javier , Caballero-Diaz Daniel , Grzelak Jan , Fusté Noel P , Bertran Esther , Amengual Josep , Garcia-Saez Juan , Martín-Mur Beatriz , Gut Marta , Esteve-Codina Anna , Alay Ania , Coulouarn Cedric , Calero Silvia , Valdecantos Pilar , Valverde Angela M. , Sánchez Aránzazu , Herrera Blanca , Fabregat Isabel
Published: November 2023

Background & Aims

Liver fibrosis is the consequence of chronic liver injury in the presence of an inflammatory component. Although the main executors of this activation are known, the mechanisms that lead to the inflammatory process that mediates the production of profibrotic factors are not well characterized. The Epidermal Growth Factor Receptor (EGFR) signaling in hepatocytes is essential for the regenerative process of the liver; however, its potential role in regulating the fibrotic niche is not yet clear.

Approach & Results

Our group generated a mouse model that expresses an inactive truncated form of the EGFR specifically in hepatocytes (ΔEGFR mice). Here, we have analyzed the response of WT and ΔEGFR mice to chronic treatment with CCl4.

Results

indicated that the hallmarks of liver fibrosis were attenuated in CCl4-treated ΔEGFR mice when compared to WT mice, coinciding with a faster resolution of the fibrotic process and an ameliorated damage. The absence of EGFR activity in hepatocytes induced changes in the pattern of immune cells in the liver, with a notable change in the population of M2 macrophages, more related to fibrosis resolution, as well as an increase in the population of lymphocytes related to eradication of the damage. Transcriptomic analysis of hepatocytes and secretome studies from extracellular media inin vitrostudies allowed to elucidate the specific molecular mechanisms regulated by EGFR that mediate hepatocyte production of both pro-inflammatory and pro-fibrotic mediators.

Conclusions

Our results support a pro-inflammatory and pro-fibrogenic role for the hepatocyte EGFR pathway during chronic liver damage.
Targeting cellular cathepsins inhibits hepatitis E virus infection
Authors: Klöhn Mara , Burkard Thomas , Janzen Juliana , Schrader Jil Alexandra , Gömer André , Brown Richard J. P. , Dao Thi Viet Loan , Kinast Volker , Brüggemann Yannick , Todt Daniel , Steinmann Eike
Published: November 2023

Background and Aims

The hepatitis E virus (HEV) is estimated to be responsible for 70,000 deaths annually, yet therapy options remain limited. In the pursuit of effective antiviral therapies, targeting viral entry holds promise and has proven effective for other hepatotropic viruses. However, the precise mechanisms and host factors required during HEV entry remain unclear. Cellular proteases have emerged as a class of host factors required for viral surface protein activation and productive cell entry by many viruses. Hence, we investigated the functional requirement and therapeutic potentials of cellular proteases during HEV infection.

Approach and Results

Using our recently established HEV cell culture model and subgenomic HEV replicons, we found that blocking lysosomal cathepsins (CTS) with small molecule inhibitors, impedes HEV infection without affecting replication. Most importantly, the pan-cathepsin inhibitor K11777 robustly suppressed HEV infections with an EC50of ∼ 0.01 nM. Inhibition by K11777, devoid of notable toxicity in hepatoma cells until micromolar concentrations, was also observed in differentiated HepaRG andex vivoin primary human hepatocytes. Furthermore, through time-of-addition experiments, we confirmed that HEV entry is potently blocked by inhibition of cathepsins and cathepsin L (CTSL) knockout cells were less permissive to HEV suggesting that CTSL is critical for HEV infection.

Conclusions

In summary, our study highlights the pivotal role of lysosomal cathepsins, especially CTSL, in the HEV entry process. The profound anti-HEV efficacy of the pan-cathepsin inhibitor, K11777, especially with its notable safety profile in primary cells, further underscores its potential as a promising therapeutic candidate.
Discovery of a Novel Chemotype as DYRK1A Inhibitors against Alzheimer’s disease: Computational Modeling and Biological Evaluation
Authors: Qiu Nianzhuang , Qian Chenliang , Guo Tingting , Wang Yaling , Jin Hongwei , Yao Mingli , Li Mei , Guo Tianyang , Lv Yuli , Si Xinxin , Wu Song , Wang Hao , Zhang Xuehui , Xia Jie
Published: November 2023

Dual specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) plays an essential role in tau and Aβ pathology closely related to Alzheimer’s disease (AD). Accumulative evidence has demonstrated DYRK1A inhibition is able to reduce the pathological features of AD. Nevertheless, there is no approved DYRK1A inhibitors for clinical use as anti-AD drugs. This is somewhat the lack of effective and safe chemotypes of DYRK1A inhibitors. To address this issue, we carried outin silicoscreening,in vitroassays andin vivoefficacy evaluation with the aim to discover a new class of DYRK1A inhibitors for potential treatment of AD. Byin silicoscreening, we selected and purchased 16 potential DYRK1A inhibitors from the Specs chemical library. Among them, compoundQ17(Specs ID: AO-476/40829177) potently inhibited DYRK1A. The hydrogen bonds between compoundQ17and each of three amino acid residues named GLU239, LEU241 and LYS188, were uncovered by molecular docking and molecular dynamics simulation. The cell-based assays showed that compoundQ17could protect SH-SY5Y cells from okadaic acid (OA)-induced injury by targeting DYRK1A. More importantly, compoundQ17significantly improved cognitive dysfunction in 3×Tg-AD mice, ameliorated pathological changes, and reduced the expression of DYRK1A, GSK-3β and GSK-3β (pSer9), attenuated tau hyperphosphorylation and Aβ deposition as well. In summary, our computational modeling strategy is effective to identify novel chemotypes of DYRK1A inhibitors with great potential to treat AD, and the identified compoundQ17in this study is worthy of further study.

Graphic Abstract
Systematic elucidation of independently modulated genes inLactobacillus plantarumreveals a trade-off between secondary and primary metabolism
Authors: Qiu Sizhe , Huang Yidi , Liang Shishun , Zeng Hong , Yang Aidong
Published: November 2023

Lactobacillus plantarumis a probiotic bacteria widely used in food and health industries, but its gene regulatory information is limited in existing databases, which impedes the research of its physiology and its applications. To obtain a better understanding of the transcriptional regulatory network ofL. plantarum, independent component analysis (ICA) of its transcriptomes was used to derive 45 sets of independently modulated genes (iModulons). Those iModulons were annotated for associated transcription factors (TFs) and functional pathways, and active iModulons in response to different growth conditions were identified and characterized in detail. Eventually, the analysis of iModulon activities reveals a trade-off between regulatory activities of secondary and primary metabolism inL. plantarum.
Preclinical lentiviral vector-mediated hematopoietic stem and progenitor cell gene therapy corrects Pompe disease-related muscle and neurological manifestations
Authors: Yoon John K. , Schindler Jeffrey W. , Loperfido Mariana , Baricordi Cristina , DeAndrade Mark P. , Jacobs Mary E. , Treleaven Christopher , Plasschaert Robert N. , Yan Aimin , Barese Cecilia N. , Dogan Yildirim , Chen Vicky Ping , Fiorini Claudia , Hull Fritz , Barbarossa Luigi , Unnisa Zeenath , Ivanov Daniel , Kutner Robert H. , Guda Swaroopa , Oborski Christine , Maiwald Tim , Michaud Véronique , Rothe Michael , Schambach Axel , Pfeifer Richard , Mason Chris , Biasco Luca , van Til Niek P.
Published: November 2023

Pompe disease, a rare genetic neuromuscular disorder, is caused by a deficiency of acid alpha-glucosidase (GAA), leading to the accumulation of glycogen in lysosomes and the progressive development of muscle weakness. The current standard treatment, enzyme replacement therapy (ERT), is not curative and demonstrates poor penetration into skeletal muscle and the central and peripheral nervous systems, susceptibility to immune responses against the recombinant enzyme, and the need for high doses and frequent infusions. To overcome these limitations, lentiviral vector-mediated hematopoietic stem and progenitor cell (HSPC) gene therapy has been proposed as a next-generation approach for treating Pompe disease. This study demonstrates the potential of lentiviral HSPC gene therapy to reverse the pathological effects of Pompe disease in a preclinical mouse model. It includes a comprehensive safety assessment via integration site analysis, along with single-cell RNA sequencing analysis of CNS samples to gain insights into the underlying mechanisms of phenotype correction.

One Sentence Summary:Preclinical hematopoietic stem cell gene therapy for the treatment of Pompe disease.
Utilizing gene co-expression networks with the rat kidney TXG-MAPr tool to enhance safety assessment, biomarker identification and human translation
Authors: Kunnen Steven J. , Callegaro Giulia , Sutherland Jeffrey J. , Trairatphisan Panuwat , van Kessel Hugo , Wijaya Lukas S. , Chung Git , Pye Keith , Goldstein Keith M. , Teague Claire R. , Fisher Ciaran P. , Saez-Rodriguez Julio , Brown Colin , Elmore Susan A. , Heinz-Taheny Kathleen M. , Stevens James L. , van de Water Bob
Published: November 2023

Toxicogenomic data represent a valuable source of biological information at molecular and cellular level to understand unanticipated organ toxicities. Weighted gene co-expression networks analysis can reduce the complexity of gene-level transcriptomic data to a set of biological response-networks useful for providing insights into mechanisms of drug-induced adverse outcomes. In this study, we have built co-regulated gene networks (modules) from the TG-GATEs and DrugMatrix rat kidney datasets consisting of time- and dose-response data for 180 compounds, including nephrotoxicants. Data from the 347 modules were incorporated into the rat kidney TXG-MAPr web tool, a user-friendly interface that enables visualization and analysis of module perturbations, quantified by a module eigengene score (EGS) for each treatment condition. Several modules annotated for cellular stress, renal injury and inflammation were statistically associated with concurrent renal pathologies, including modules that contain both well-known and novel renal biomarker genes. In addition, many rat kidney modules contain well annotated, robust gene networks that are preserved across transcriptome datasets, suggesting that these biological networks translate to other (drug-induced) kidney injury cases. Moreover, preservation analysis of human kidney transcriptomic data provided a quantitative metric to assess the likelihood that rat kidney modules, and the associated biological interpretation, translate from non-clinical species to human. In conclusion, the rat kidney TXG-MAPr enables uploading and analysis of kidney gene expression data in the context of rat kidney co-expression networks, which could identify possible safety liabilities and/or mechanisms that can lead to adversity for chemical or drug candidates.
Aging in zebrafish is associated with reduced locomotor activity and strain-dependent changes in predator avoidance behaviors related to anxiety
Authors: Hudock Jacob , Kenney Justin W.
Published: November 2023

Aging is associated with a wide range of physiological and behavioral changes in many species. Like humans, zebrafish exhibit gradual senescence, and thus may be a useful model organism for identifying evolutionarily conserved mechanisms related to aging. Here, we compared behavior in the novel tank test of young (6-month-old) and middle aged (12-month-old) zebrafish from two strains (TL and TU) and both sexes. We find that this modest age difference results in a reduction in locomotor activity and strain dependent changes in predator avoidance behaviors related to anxiety. Older TL fish have an elevation in bottom dwelling whereas older TU fish have a decrease in thigmotaxis. We found no consistent effects of age on either short-term (within session) or long-term (1 day later) habituation to the novel tank. Our findings support the use of zebrafish for the study of how age affects locomotion and how genetics interacts with age to alter the regulation of emotional behaviors in response to novelty.
VAV2-Dependent Regulation of Ribosome Biogenesis in Keratinocytes and Oral Squamous Cell Carcinoma
Authors: Fernández-Parejo Natalia , Lorenzo-Martín L. Francisco , García-Pedrero Juana M. , Rodrigo Juan P. , Dosil Mercedes , Bustelo Xosé R.
Published: November 2023

VAV2 is an activator of RHO GTPases that promotes and maintains regenerative proliferation-like states in normal keratinocytes and oral squamous cell carcinoma (oSCC) cells, respectively. Here, we demonstrate that VAV2 also plays critical roles in the regulation of ribosome biogenesis in those cells, a program associated with poor prognosis of human papilloma virus negative oSCC patients. Mechanistic analyses indicate that VAV2 regulates this process in a catalysis-dependent manner using a conserved pathway composed of the GTPases RAC1 and RHOA, members of the PAK and ROCK family kinases, and the transcriptional factors c-MYC and YAP/TAZ. This pathway directly promotes RNA polymerase I activity and the ensuing synthesis of 47S pre-rRNA precursors. This process is further consolidated by the upregulation of ribosome biogenesis factors and the acquisition of the YAP/TAZ-dependent cell undifferentiation state. Finally, we show that RNA polymerase I is a therapeutic Achilles’ heel for both keratinocytes and hnSCC patient derived cells endowed with high VAV2 catalytic activity. Collectively, these findings highlight the therapeutic potential of the VAV2 and ribosome biogenesis pathways in both preneoplastic and late progression stages of oSCC.
Structure prediction of protein-ligand complexes from sequence information with Umol
Authors: Bryant Patrick , Kelkar Atharva , Guljas Andrea , Clementi Cecilia , Noé Frank
Published: November 2023

Protein-ligand docking is an established tool in drug discovery and development to narrow down potential therapeutics for experimental testing. However, a high-quality protein structure is required and often the protein is treated as fully or partially rigid. Here we develop an AI system that can predict the fully flexible all-atom structure of protein-ligand complexes directly, given a multiple sequence alignment representation of the protein and a SMILES string representing the ligand. At a high accuracy threshold, unseen protein-ligand complexes can be predicted more accurately than for RoseTTAFold-AA, and at medium accuracy even classical docking methods that use known protein structures as input are surpassed. The high accuracy presented here suggests that the goal of AI-based drug discovery is one step closer, but there is still a way to go to fully grasp the complexity of protein-ligand interactions. Umol is available at:https://github.com/patrickbryant1/Umol
Highly resolved genomes as a tool for studying speciation history of two closely related louse lineages with different host specificities
Authors: Martinů Jana , Tarabai Hassan , Štefka Jan , Hypša Václav
Published: November 2023

Sucking lice of the suborder Anoplura are permanent ectoparasites with specific lifestyle and highly derived features. Currently, genomic data are only available for a single species, the human lousePediculus humanus. In this study we present genomes of two distinct lineages, with different host spectra, of a rodent lousePolyplax serrata. Genomes of these ecologically different lineages are closely similar in gene content, display a high level of synteny, but they also differ by a few duplications/translocations and single inversion. Compared toP. humanus, the twoP. serratagenomes are noticeably larger (139 Mbp vs. 111 Mbp) and encode a higher number of genes. Similar toP. humanus, they are significantly reduced in sensory-related categories such as vision and olfaction. Utilizing a genome-wide set of genes, we perform phylogenetic reconstruction and evolutionary dating of theP. serratalineages. Obtained estimates reveal their relatively deep origin (approx. 6.5 Mya), comparable to the time of split between the human and chimpanzee licePediculus humanusandP. schaeffi. This dating supports the view that theP. serratalineages are likely to represent two cryptic species with different host spectra. Historical demographies of the two lineages show glaciation-related population size (Ne) reduction, but recent restoration of Ne was seen only in the less host specific lineage. Together with the louse genomes, we analyze genomes of their bacterial symbiontLegionella polyplacis, and evaluate their potential complementarity in synthesis of amino acids and B vitamins. We show that both systems,Polyplax/LegionellaandPediculus/Riesia, display almost identical patterns, with symbionts involved in synthesis of B vitamins but not amino acids.
Generation of human induced pluripotent stem cell (hiPSC) lines from patients with extreme high and low polygenic scores for QT interval
Authors: Mitchell Devyn , Ullah Rizwan , Vanags Loren , Shen Alex , Jones Luke , O’Neill Matthew , Davogustto Giovanni , Shaffer Christian , Roden Dan , Shoemaker Ben , Williams Hollie , Strickland Teresa , Agee Taylor , Johnson Christopher , Kroncke Brett
Published: November 2023

Long QT syndrome (LQTS) is an inherited cardiac arrhythmia syndrome with congenital and drug-induced presentations and known monogenic and polygenic contributions. LQTS represents a significant clinical challenge due to its complex genetic underpinning and propensity for fatal arrhythmias. In this study, we generated induced pluripotent stem cells (iPSCs) reprogrammed from peripheral blood mononuclear cells (PBMCs) of six patients with extreme polygenic scores for short and long corrected QT intervals. iPSC lines were rigorously validated for genomic integrity through karyotyping and targeted mutation analysis specific to a lengthened or shortened QT interval. Pluripotency was confirmed by expression of key markers TRA 1-60, TRA 1-81, SOX2, OCT4, NANOG, and REX1 via quantitative PCR and immunofluorescence. Subsequent cardiac induction successfully generated cardiomyocytes that were further characterized. This patient-specific approach will enable us to better understand variable expressivity and penetrance of LQTS. Rigorously validated iPSC lines serve as a vital resource for elucidating the molecular mechanisms underlying LQTS. Our study provides a robust and clinically relevant resource to facilitate our understanding the genetic and cellular complexity of LQTS.
HiCMC: High-Efficiency Contact Matrix Compressor
Authors: Adhisantoso Yeremia Gunawan , Körner Tim , Müntefering Fabian , Ostermann Jörn , Voges Jan
Published: November 2023

Chromosome organization plays an important role in biological processes such as replication, regulation, and transcription. One way to study the relationship between chromosome structure and its biological functions is through Hi-C studies, a genome-wide method for capturing chromosome conformations. Such studies generate vast amounts of data. The problem is exacerbated by the fact that chromosome organization is dynamic, requiring snapshots at different points in time, further increasing the amount of data to be stored. We present a novel approach called the High-Efficiency Contact Matrix Compressor (HiCMC) for efficient compression of Hi-C data. By modeling the underlying structures found in the contact matrix, such as compartments and domains, HiCMC outperforms CMC by approximately 8% and more than 50% against cooler, LZMA, and bzip2 over the state of the art across multiple cell lines and resolutions. In addition, the domain information that is embedded in the data can be used to speed up downstream analysis. HiCMC is available athttps://github.com/sXperfect/hicmc.
Proteomics of Patient-derived Breast Tumours Identifies a Pro-migratory Osteomodulin-Cyclin Dependent Kinase 1 Axis which Drives Bone Metastasis
Authors: Parsons Joseph , Harrison Hannah , Kedward Thomas , Fullwood Paul , Cabral Sara , Spence Katherine , Barden Danielle , Ferguson Jennifer , Watson Joanne , Behan Caron , Ali Nisha , Smith Michael P. , O’Brien Ciara , Clarke Robert B. , Francavilla Chiara
Published: November 2023

Breast cancer remains a leading cause of mortality, predominantly due to the development of metastases to vital organs. At present, predictive biomarkers of organ specific metastasis and therapies targeted to the metastatic niche are limited. Here, to identify the molecular determinants of breast cancer metastasis we analysed patient-derived breast tumours by combining quantitative proteomics, bioinformatics, and functional assaysin vitroandin vivo.We identified elevated levels of the protein Osteomodulin (OMD) associated with breast cancer bone metastases in patient-derived samples. OMD overexpression in the breast cancer MDA-MB-231 cell model significantly increases cell migrationin vitroand promotes the formation of bone metastasesin vivo. Phosphoproteomics analysis of MDA-MB-231 cells expressing OMD identifies active Cyclin-dependent kinase 1 (CDK1) downstream of OMD. The importance of the OMD-CDK1 axis was validated using two independent phosphoproteomics datasets analysing patient-derived breast cancer samples. We also show that the OMD-CDK1 axis drives cell migration and cell viabilityin vitroand the formation of bone metastasesin vivo. Finally, CDK1 inhibition reducesin vitrocell viability of an independent cohort of metastatic patient samples showing high CDK1 activity. Therefore, the OMD-CDK1 axis will determine which breast cancer patients develop bone metastases and is a therapeutic target to treat or prevent breast cancer bone metastases.
Morphine-context associative memory and locomotor sensitization in mice are modulated by sex and context in a dose-dependent manner
Authors: Hámor Peter U. , Hartmann Matthew C. , Garcia Aaron , Liu Dezhi , Pleil Kristen E.
Published: November 2023

Sex differences in opioid use, development of opioid used disorder, and relapse behaviors indicate potential variations in opioid effects between men and women. The locomotor and interoceptive effects of opioids play essential roles in opioid addiction, and uncovering the neural mechanisms underlying these effects remain crucial for developing effective treatments. In this study, we examined the dose-dependent effects of morphine on locomotor sensitization and the strength and stability of morphine-context associations in the conditioned place preference (CPP) paradigm in male and female mice, as well as the relationships between these measures. We observed that while CPP is similar between sexes, the locomotor effects of repeated morphine administration and withdrawal differentially contributed to the strength and stability of morphine-context associations. Specifically, females exhibited higher morphine-induced hyperlocomotion than males regardless of the context in which morphine was experienced. Greater locomotor sensitization to morphine in females than males emerged in a dose-dependent manner only when there was sufficient context information for CPP to be established. Additionally, the relationships between the locomotor effects of morphine and the strength and stability of CPP were different in males and females. In females, positive acute and sensitizing locomotor effects of morphine were correlated with a higher CPP score, while the opposite direction of this relationship was found in males. These results suggest that different aspects of the subjective experience of morphine intoxication and withdrawal are important for morphine abuse-related behaviors and highlight the importance of sex-specific responses in the context of opioid addiction.
The development of hepatic steatosis depends on the presence of liver-innervating parasympathetic cholinergic neurons in mice fed a high-fat diet
Authors: Hwang Jiyeon , Okada Junichi , Liu Li , Pessin Jeffrey E. , Schwartz Gary J. , Jo Young-Hwan
Published: November 2023

Hepatic lipid metabolism is regulated by the autonomic nervous system of the liver, with the sympathetic innervation being extensively studied, while the parasympathetic efferent innervation is less understood despite its potential importance. In this study, we investigate the consequences of disrupted brain-liver communication on hepatic lipid metabolism in mice exposed to obesogenic conditions. We found that a subset of hepatocytes and cholangiocytes are innervated by parasympathetic nerve terminals originating from the dorsal motor nucleus of the vagus. The elimination of the brain-liver axis by deleting parasympathetic cholinergic neurons innervating the liver prevents hepatic steatosis and promotes browning of inguinal white adipose tissue (ingWAT). The loss of liver-innervating cholinergic neurons increases hepaticCyp7b1expression and fasting serum bile acid levels. Furthermore, knockdown of the G protein-coupled bile acid receptor 1 gene in ingWAT reverses the beneficial effects of the loss of liver-innervating cholinergic neurons, leading to the reappearance of hepatic steatosis. Deleting liver-innervating cholinergic neurons has a small but significant effect on body weight, which is accompanied by an increase in energy expenditure. Taken together, these data suggest that targeting the parasympathetic cholinergic innervation of the liver is a potential therapeutic approach for enhancing hepatic lipid metabolism in obesity and diabetes.
Competition and Cooperation of Assembly Sequences in Recurrent Neural Networks
Authors: Stöber Tristan M. , Lehr Andrew B. , Fyhn Marianne , Kumar Arvind
Published: November 2023

Neural activity sequences are ubiquitous in the brain and play pivotal roles in functions such as long-term memory formation and motor control. While conditions for storing and reactivating individual sequences have been thoroughly characterized, it remains unclear how multiple sequences may interact when activated simultaneously in recurrent neural networks. This question is especially relevant for weak sequences, comprised of fewer neurons, competing against strong sequences. Using a non-linear rate model with discrete, pre-configured assemblies, we demonstrate that weak sequences can compensate for their competitive disadvantage either by increasing excitatory connections between subsequent assemblies or by cooperating with other co-active sequences. Further, our model suggests that such cooperation can negatively affect sequence speed unless subsequently active assemblies are paired. Our analysis, validated by an analytically tractable linear approximation, characterizes the conditions for successful sequence progression in isolated, competing, and cooperating sequences, and identifies the distinct contributions of recurrent and feed-forward projections. This proof-of-principle study shows how even disadvantaged sequences can be prioritized for reactivation, a process which has recently been implicated in hippocampal memory processing.
Vectorized instructive signals in cortical dendrites during a brain-computer interface task
Authors: Francioni Valerio , Tang Vincent D. , Toloza Enrique H.S. , Brown Norma J. , Harnett Mark T.
Published: November 2023

Vectorization of teaching signals is a key element of virtually all modern machine learning algorithms, including backpropagation, target propagation and reinforcement learning. Vectorization allows a scalable and computationally efficient solution to the credit assignment problem by tailoring instructive signals to individual neurons. Recent theoretical models have suggested that neural circuits could implement single-phase vectorized learning at the cellular level by processing feedforward and feedback information streams in separate dendritic compartments1–5. This presents a compelling, but untested, hypothesis for how cortical circuits could solve credit assignment in the brain. We leveraged a neurofeedback brain-computer interface (BCI) task with an experimenter-defined reward function to test for vectorized instructive signals in dendrites. We trained mice to modulate the activity of two spatially intermingled populations (4 or 5 neurons each) of layer 5 pyramidal neurons in the retrosplenial cortex to rotate a visual grating towards a target orientation while we recorded GCaMP activity from somas and corresponding distal apical dendrites. We observed that the relative magnitudes of somatic versus dendritic signals could be predicted using the activity of the surrounding network and contained information about task-related variables that could serve as instructive signals, including reward and error. The signs of these putative teaching signals both depended on the causal role of individual neurons in the task and predicted changes in overall activity over the course of learning. Furthermore, targeted optogenetic perturbation of these signals disrupted learning. These results provide the first biological evidence of a vectorized instructive signal in the brain, implemented via semi-independent computation in cortical dendrites, unveiling a potential mechanism for solving credit assignment in the brain.
Plastid genome evolution in leafless members of the orchid subfamily Orchidoideae, with a focus onDegranvillea dermaptera
Authors: Barrett Craig F. , Pace Matthew C. , Corbett Cameron W.
Published: November 2023

Premise

Leafless, heterotrophic plants are prime examples of organismal modification, the genomic consequences of which have received considerable interest. In particular, plastid genomes (plastomes) are being sequenced at a high rate, allowing continual refinement of conceptual models of reductive evolution in heterotrophs. Yet, numerous sampling gaps exist, hindering the ability to conduct comprehensive phylogenomic analyses in these plants.

Methods

We sequenced and analyzed the plastome ofDegranvillea dermaptera, a rarely collected, leafless orchid species from South America about which little is known, including its phylogenetic affinities.

Key Results

We revealed the most reduced plastome sequenced to date among the orchid subfamily Orchidoideae.Degranvilleahas lost the majority of genes found in leafy autotrophic species, is structurally rearranged, and has similar gene content to the most reduced plastomes among the orchids. We found strong evidence for the placement ofDegranvilleawithin the subtribe Spiranthinae using models that explicitly account for heterotachy, or lineage-specific evolutionary rate variation over time. We further found evidence of relaxed selection on several genes and correlations among substitution rates and several other “traits” of the plastome among leafless members of orchid subfamily Orchidoideae.

Conclusions

Our findings advance knowledge on the phylogenetic relationships and paths of plastid genome evolution among the orchids, which have experienced more independent transitions to heterotrophy than any other plant family. This study demonstrates the importance of herbarium collections in comparative genomics of poorly known species of conservation concern.
Evolution in action: Brown-headed Cowbirds (Molothrus ater) adapt songs to 50 years of Ohio urbanization
Authors: Ruscitelli Kristen , Provost Kaiya
Published: November 2023

Technological advances in the last century have allowed humans to rapidly alter the landscape, resulting in a global loss of biodiversity. Of such alterations, is the conversion of rural land into urban space. In birds, urbanization has been found to impact song to facilitate improved auditory communication between conspecifics in areas with increased background noise. Given that birdsong is an important reproductive behavior, it is possible that urbanization promotes the evolution of birdsong through differences in fitness between individuals in urban acoustic environments. Here, we investigated if urbanization across Ohio impacts song characteristics of Brown-headed Cowbirds (Molothrus ater), a brood parasite associated with cropland and other altered habitats. To assess change inM. atersong over space and time, we compared syllable shape and syllable properties with metrics of urbanization. It was found thatM. atersong differs significantly across geographic space and time, and is associated with changes in urbanization. Cowbird song of conspecifics in preferred habitat, such as cropland, demonstrates different syllable shape than conspecifics in urban space. This suggests that urbanization could facilitate change inM. atersong over time. These results provide additional insight into how anthropogenic habitat alteration facilitates cultural evolution in birds, and allows for increased understanding of how human behavior contributes to altered ecological interactions.
Replacement of Arabidopsis H2A.Z with human H2A.Z orthologs reveals extensive functional conservation and limited importance of the N-terminal tail sequence for Arabidopsis development
Authors: Sijacic Paja , Holder Dylan H. , Krall Ellen G , Willett Courtney G. , Foroozani Maryam , Deal Roger B.
Published: November 2023

The incorporation of histone variants, distinct paralogs of core histones, into chromatin affects all DNA-templated processes in the cell, including the regulation of transcription. In recent years, much research has been focused on H2A.Z, an evolutionarily conserved H2A variant found in all eukaryotes. In order to investigate the functional conservation of H2A.Z histones during eukaryotic evolution we transformed h2a.z deficient plants with each of the three human H2A.Z variants to assess their ability to rescue the mutant defects. We discovered that human H2A.Z.1 and H2A.Z.2.1 fully complement the phenotypic abnormalities of h2a.z plants despite significant divergence in the N-terminal tail sequences of Arabidopsis and human H2A.Zs. In contrast, the brain-specific splice variant H2A.Z.2.2 has a dominant-negative effect in wild-type plants, mimicking an H2A.Z deficiency phenotype. Furthermore, H2A.Z.1 almost completely re-establishes normal H2A.Z chromatin occupancy in h2a.z plants and restores the expression of more than 84% of misexpressed genes. Finally, we used a series of N-terminal tail truncations of Arabidopsis HTA11 to reveal that the N-terminal tail of Arabidopsis H2A.Z is not necessary for normal plant development but does play an important role in mounting proper environmental stress responses.
The microbial community of rust layer biofilm was driven by seawater microbial community
Authors: Yao Shengxun , Lai Junxiang , Sun Congtao , Pan Zihan , Zhao Maomi , Duan Jizhou , Hou Baorong
Published: November 2023

Microbiologically influenced corrosion (MIC) accounts for approximately 20% of the total corrosion-related losses worldwide, causing significant economic damage each year, particularly in Marine environments. However, there are still no truly effective and eco-friendly protection solutions against MIC, among which the incomplete understanding of the microbial biofilm development on metallic surface is a key limitation. Using 16S rRNA and ITS sequencing, we studied bacterial and fungal communities in rust layer biofilm and seawater. The results showed that Proteobacteria, Cyanobacteria and Bacteroidota were the dominant bacterial phyla, and Ascomycota and Basidiomycota were the dominant fungal phyla both in the rust layer biofilm and seawater. Bacteria like Erythrobacter and Aquimarina, as well as fungi like Aspergillus and Acremonium were were notable microorganisms in the rust layer biofilm. Source analysis revealed differences between biofilm and seawater communities, with 23.08% bacterial and 21.48% fungal communities originating from seawater. Stochastic processes governed biofilm and seawater microbial communities, and network analysis showed coexistence and interaction among bacteria and fungi.

IMPORTANCE

The composition and source analysis of bacterial and fungal communities in the rust layer and seawater were studied, and the interaction of bacteria and fungi in the rust layer was discussed for the first time. Based on these findings, we provided a framework to explain the observed characteristics of microbial communities in rust layer biofilm and presented key evidence supporting the relationship between different microbial structures and interactions with metal corrosion. These findings, from the perspective of microbial ecology, provide a theoretical foundation for studying microbial corrosion in marine environments.
Pseudotime analysis for time-series single-cell sequencing and imaging data
Authors: Li Gang , Kim Hyeon-Jin , Pendyala Sriram , Zhang Ran , Disteche Christine M. , Vert Jean-Philippe , Deng Xinxian , Fowler Douglas M. , Noble William Stafford
Published: November 2023

Many single-cell RNA-sequencing studies have collected time-series data to investigate transcriptional changes concerning various notions of biological time, such as cell differentiation, embryonic development, and response to stimulus. Accordingly, several unsupervised and supervised computational methods have been developed to construct single-cell pseudotime embeddings for extracting the temporal order of transcriptional cell states from these time-series scRNA-seq datasets. However, existing methods, such as psupertime, suffer from low predictive accuracy, and this problem becomes even worse when we try to generalize to other data types such as scATAC-seq or microscopy images. To address this problem, we propose Sceptic, a support vector machine model for supervised pseudotime analysis. Whereas psupertime employs a single joint regression model, Sceptic simultaneously trains multiple classifiers with separate score functions for each time point and also allows for non-linear kernel functions. Sceptic first generates a probability vector for each cell and then aims to predict chronological age via conditional expectation. We demonstrate that Sceptic achieves significantly improved prediction power (accuracy improved by 1.4−38.9%) for six publicly available scRNA-seq data sets over state-of-the-art methods, and that Sceptic also works well for single-nucleus image data. Moreover, we observe that the pseudotimes assigned by Sceptic show stronger correlations with nuclear morphology than the observed times, suggesting that these pseudotimes accurately capture the heterogeneity of nuclei derived from a single time point and thus provide more informative time labels than the observed times. Finally, we show that Sceptic accurately captures sex-specific differentiation timing from both scATAC-seq and scRNA-seq data.
Development of a high-throughput pipeline to characterize microglia morphological states at a single-cell resolution
Authors: Kim Jennifer , Pavlidis Paul , Ciernia Annie Vogel
Published: November 2023

As rapid responders to their environments, microglia engage in functions that are mirrored by their cellular morphology. Microglia are classically thought to exhibit a ramified morphology under homeostatic conditions which switches to an ameboid form during inflammatory conditions. However, microglia display a wide spectrum of morphologies outside of this dichotomy, including rod-like, ramified, ameboid, and hypertrophic states, which have been observed across brain regions, neurodevelopmental timepoints, and various pathological contexts. We used dimensionality reduction and clustering approaches to consider contributions of multiple morphology measures together to define a spectrum of microglial morphological states. Using ImageJ tools, we first developed a semi-automated approach to characterize 27 morphology features from hundreds to thousands of individual microglial cells in a brain subregion-specific manner. Within this pool of morphology measures, we defined distinct sets of highly correlated features that describe different aspects of morphology, including branch length, branching complexity, territory span, and cell circularity. When considered together, these sets of features drove different morphological clusters. Furthermore, our analysis toolset captured morphological states similarly and robustly when applied to independent datasets and using different immunofluorescent markers for microglia. We have compiled our morphology analysis pipeline into an accessible, easy to use, and fully open-source ImageJ macro and R package that the neuroscience community can expand upon and directly apply to their own analyses. Outcomes from this work will supply the field with new tools to systematically evaluate the heterogeneity of microglia morphological states across various experimental models and research questions.
The chikungunya virus E1 glycoprotein fusion loop and hinge alter glycoprotein dynamics leading to cell and host specific changes in infectivity
Authors: Thannickal Sara A. , Battini Leandro , Spector Sophie N. , Noval Maria G. , Álvarez Diego E. , Stapleford Kenneth A.
Published: November 2023

Alphaviruses infect both mammals and insects, yet the distinct mechanisms that alphaviruses use to infect different hosts are not well defined. In this study, we characterize CHIKV E1 variants in the fusion loop (E1-M88L) and hinge region (E1-N20Y)in vitroandin vivoto understand how these regions of the E1 glycoprotein contribute to host-specific infection. Through cell culture assays, we found that CHIKV E1-N20Y enhanced infectivity in mosquito cells while the CHIKV E1-M88L variant enhanced virus binding and infectivity in both BHK-21 and C6/36 cells, and led to changes in the virus cholesterol-dependence in BHK-21 cells. Given thesein vitroresults and that residue E1-M88L is in a defined Mxra8 interacting domain, we hypothesized that this residue may be important for receptor usage. However, while the CHIKV E1-M88L variant increased replication in Mxra8-deficient mice compared to WT CHIKV, it was attenuatedin vitroin mouse fibroblasts, suggesting that residue E1-M88 may function in a cell-type dependent manner to alter entry. Finally, using molecular dynamics to understand how potential changes in the E1 glycoprotein may impact the CHIKV glycoprotein E1-E2 complex, we found that E1-M88L and other E1 domain II variants lead to changes in both E1 and E2 dynamics. Taken together, these studies show that key residues in the CHIKV E1 fusion loop and hinge region function through changes in E1-E2 dynamics to facilitate cell- and host-dependent entry.

Importance

Arthropod-borne viruses (arboviruses) are significant global public health threats, and their continued emergence around the world highlights the need to understand how these viruses replicate at the molecular level. The alphavirus class II glycoproteins are critical for virus entry in mosquitoes and mammals, yet how these proteins function is not completely understood. Therefore, to address these gaps in our knowledge, it is critical to dissect how distinct glycoprotein domains functionin vitroandin vivo. Here, we show that changes in the CHIKV E1 fusion loop and hinge contribute to host-specific entry and E1-E2 dynamics, furthering our knowledge of how alphaviruses infect mammals and insects.
Differential activation states of direct pathway striatal output neurons associated with the development of L-DOPA-induced dyskinesia
Authors: Figge David A. , de Amaral Oliveira Henrique , Crim Jack , Cowell Rita M. , Standaert David G. , Eskow Jaunarajs Karen L.
Published: November 2023

L-DOPA-induced dyskinesia (LID) is a debilitating motor side effect arising from chronic dopamine replacement therapy with L-DOPA for the treatment of Parkinson disease (PD). The emergence of LID is linked to heightened sensitivity of striatal dopaminergic signaling and driven by abnormal fluctuations in synaptic dopamine levels following each administration of L- DOPA. This maladaptive plasticity narrows the therapeutic window for L-DOPA treatment, even as the progressive worsening of PD symptoms demands escalating doses. The heterogeneous composition of the striatum, including diverse subpopulations of medium spiny output neurons (MSNs), interneurons, and supporting cells, has complicated the precise identification of the cell(s) underlying LID development and persistence. To elucidate the cellular and molecular mechanisms of LID, we used single nucleus RNA-sequencing (snRNA-seq) to establish a comprehensive striatal transcriptional profile during the development and maintenance of LID in an animal model. Hemiparkinsonian mice were treated with vehicle or L-DOPA for progressive durations (1, 5, or 10 d) and nuclei from the striata were processed for snRNA-seq. Our analysis found that a limited population of dopamine D1 receptor-expressing MSNs (D1-MSNs), arising from both the patch and matrix compartments, formed three subclusters in response to L-DOPA treatment that expressed cellular markers of activation. These activated D1-MSN subpopulations display many of the transcriptional changes previously associated with LID; however, the prevalence and transcriptional behavior of activated D1-MSNs was differentially influenced by the extent of L-DOPA experience. The differentially expressed genes found in these D1-MSNs indicated that acute L-DOPA induced upregulation of multiple plasticity-related transcription factors and regulators of MAPK signaling, while repeated L-DOPA exposure induced numerous genes associated with synaptic remodeling, learning and memory, and transforming growth factor-ß (TGFß) signaling. Notably, repeated L-DOPA led to a sensitization in the expression ofInhba,a member of the activin/TGFß superfamily, in activated D1-MSNs. We tested pharmacological inhibition of its receptor, ALK4, and found that it impaired LID development. Collectively, these data suggest that distinct subsets of D1-MSNs become differentially responsive to L-DOPA due to the aberrant induction of the molecular mechanisms necessary for neuronal entrainment, similar to those processes underlying hippocampal learning and memory formation. Our data further suggests that activin/TGFß signaling may play an essential role in LID development in this subpopulation of D1-MSNs.