bluuebunny/crossref_metadata_2025 huggingface dataset:
Histone variants shape chromatin states in Arabidopsis
Authors: Jamge Bhagyshree , Lorković Zdravko J. , Axelsson Elin , Osakabe Akihisa , Shukla Vikas , Yelagandula Ramesh , Akimcheva Svetlana , Kuehn Annika Luisa , Berger Frédéric
Published: March 2023

How different intrinsic sequence variation or regulatory modifications of histones regulate nucleosome interactions with transcription remain unclear. By contrast with H3 and H2B variants, H2A variants occupy specific domains of chromatin inArabidopsis thaliana.Broad domains of chromatin are affected by the loss of remodelers that affect the deposition or the exchange of H2A variants. Notably, the chromatin remodeler DECREASED IN DNA METHYLATION (DDM1) is required to maintain enrichment in all markers of constitutive heterochromatin including DNA methylation, H3K9me1/2 and the variant H2A.W. To test the importance of histone variants in the organization of chromatin we investigated how histone variants and histone modifications assemble in theArabidopsis thalianagenome and showed that a limited number of chromatin states divide euchromatin and heterochromatin into several subdomains. We found that histone variants are as significant as histone modifications in determining the composition of chromatin states. Particularly strong associations were observed between H2A variants and specific combinations of histone modifications. To study the role of H2A variants in organizing chromatin states we determined the role the chromatin remodeler DECREASED IN DNA METHYLATION (DDM1) in the organization of chromatin states. We showed that the loss of DDM1 prevented the exchange of the histone variant H2A.Z to H2A.W in constitutive heterochromatin, resulting in significant effects on the definition and distribution of chromatin states in and outside of heterochromatin. We thus propose that dynamic exchanges of histone variants control the organization of histone modifications into chromatin states, acting as molecular landmarks.
Causal Effects of Pupil Size on Visual Processing
Authors: Mathôt Sebastiaan , Berberyan Hermine , Büchel Philipp , Ruuskanen Veera , Vilotijević Ana , Kruijne Wouter
Published: March 2023

The size of the eyes’ pupils determines how much light enters the eye and also how well this light is focused. Through this route, pupil size shapes the earliest stages of visual processing. Yet causal effects of pupil size on vision are poorly understood and rarely studied. Here we report the effects of both experimentally induced and spontaneous changes in pupil size on visual processing as measured through EEG. We compare these to the effects of stimulus intensity and covert visual attention, because previous studies have shown that these factors all have comparable effects on some common measures of early visual processing, such as detection performance and steady-state visual evoked potentials; yet it is still unclear whether these are superficial similarities, or rather whether they reflect similar underlying processes. Using a mix of neural-network decoding, ERP analyses, and time-frequency analyses, we find that induced pupil size, spontaneous pupil size, stimulus intensity, and covert visual attention all affect EEG responses, mainly over occipital and parietal electrodes, but—crucially—that they do so in qualitatively different ways. Induced and spontaneous pupil-size changes mainly modulate activity patterns (but not overall power or intertrial coherence) in the high-frequency beta range; this may reflect a causal effect of pupil size on oculomotor activity and/ or visual processing. In addition, spontaneous (but not induced) pupil size tends to correlate positively with intertrial coherence in the alpha band; this may reflect a non-causal relationship, mediated by arousal. Taken together, our findings suggest that pupil size has qualitatively different effects on visual processing from stimulus intensity and covert visual attention. This shows that pupil size causally affects visual processing, and provides concrete starting points for further study of this important yet understudied earliest stage of visual processing.
“Anthropogenic Threats and Conservation Practices: Evaluating LULC Changes in Relocated Villages of Panna Tiger Reserve, Madhya Pradesh, India”
Authors: Khan Susmita
Published: March 2023

Protected areas globally, including India, face anthropogenic threats despite environmental and forest protection laws. To reduce these pressures, conservation related settlement evacuation from protected areas has been a common conservation practice for decades in many countries. Controversies aside, studies have shown that evacuation of settlements from protected areas has a positive impact on forest cover change and biodiversity increase. Here in this study, we conducted this study for the 14 relocated village sites of Panna Tiger Reserve to see the changes in major Land use Land cover changes over 15 years (2004-2019). We observed a significant increase in forested areas in those regions over time, as well as prominent changes in different land cover classes. The increase in Grassland, Open Forest, and Dense Forest from 2004 to 2019 was significant, and settlements in relocated areas were mainly converted to different forest types. Additionally, fieldwork and camera trap data showed that the relocated sites with established woodlands and other forest classes supported higher animal diversity and species composition compared to other sites. This study provides a knowledge base for conservation and management practices by identifying significant changes in various land use and land cover classes.
Sirtuin3 ensures the metabolic plasticity of neurotransmission during glucose deprivation
Authors: Tiwari Anupama , Hashemiaghdam Arsalan , Laramie Marissa A. , Maschi Dario , Haddad Tristaan , Stunault Marion I. , Bergom Carmen , Javaheri Ali , Klyachko Vitaly , Ashrafi Ghazaleh
Published: March 2023

Neurotransmission is an energetically expensive process that underlies cognition. During intense electrical activity or dietary restrictions, glucose levels in the brain plummet, forcing neurons to utilize alternative fuels. However, the molecular mechanisms of neuronal metabolic plasticity remain poorly understood. Here, we demonstrate that glucose-deprived neurons activate the CREB and PGC1α transcriptional program that induces the expression of the mitochondrial deacetylase Sirtuin 3 (Sirt3) bothin vitroandin vivo. We show that Sirt3 localizes to axonal mitochondria and stimulates mitochondrial oxidative capacity in hippocampal nerve terminals. Sirt3 plays an essential role in sustaining synaptic transmission in the absence of glucose by powering the retrieval of synaptic vesicles after release. These results demonstrate that the transcriptional induction of Sirt3 ensures the metabolic plasticity of synaptic transmission.

Highlights

Glucose deprivation drives transcriptional reprogramming of neuronal metabolism via CREB and PGC1α.

Glucose or food deprivation trigger the neuronal expression of mitochondrial deacetylase sirtuin 3 (Sirt3) bothin vitroandin vivo.

Sirt3 stimulates oxidative ATP synthesis in nerve terminals.

Sirt3 sustains the synaptic vesicle cycle in the absence of glucose.
Biodiversity shows unique responses to land-use change across regional biomes
Authors: Bevan Peggy , Ferreira Guilherme Braga , Ingram Daniel J , Rowcliffe Marcus , Young Lucy , Freeman Robin , Jones Kate E.
Published: March 2023

Biogeography has a critical influence on how ecological communities respond to threats and how effective conservation interventions are designed. For example, the resilience of ecological communities is linked to environmental and climatic features, and the nature of threats impacting ecosystems also varies geographically. Understanding community-level threat responses may be most accurate at fine spatial scales, however collecting detailed ecological data at such a high resolution would be prohibitively resource intensive. In this study, we aim to find the spatial scale that could best capture variation in community-level threat responses whilst keeping data collection requirements feasible. Using a database of biodiversity records with extensive global coverage, we modelled species richness and total abundance (the responses) across land-use types (reflecting threats), considering three different spatial scales: biomes, biogeographical realms, andregional biomes(the interaction between realm and biome). We then modelled data from three highly sampled biomes separately to ask how responses to threat differ between regional biomes and taxonomic group. We found strong support for regional biomes in explaining variation in species richness and total abundance compared to biomes or realms alone. Our biome case studies demonstrate that there is a high variation in magnitude and direction of threat responses across both regional biomes and taxonomic group, but all groups in tropical forest showed a consistently negative response, whilst many taxon-regional biome groups showed no clear response to threat in temperate forest and tropical grassland. Our results suggest that the taxon-regional biome unit has potential as a reasonable spatial and ecological scale for understanding how ecological communities respond to threats and designing effective conservation interventions to bend the curve on biodiversity loss.
Endothelial Histone Deacetylase 1 Activity Impairs Kidney Microvascular NO Signaling in Rats fed a High Salt Diet
Authors: Dunaway Luke S. , Cook Anthony K. , Botta Davide , Molina Patrick A. , d’Uscio Livius V. , Katusic Zvonimir S. , Pollock David M. , Inscho Edward W. , Pollock Jennifer S.
Published: March 2023

Aim

We aimed to identify new mechanisms by which a high salt diet (HS) decreases NO production in kidney microvascular endothelial cells. Specifically, we hypothesized HS impairs NO signaling through a histone deacetylase 1 (HDAC1)-dependent mechanism.

Methods

Male Sprague Dawley rats were fed normal salt diet (NS; 0.49% NaCl) or high salt diet (4% NaCl) for two weeks. NO signaling was assessed by measuring L-NAME induced vasoconstriction of the afferent arteriole using the blood perfused juxtamedullary nephron (JMN) preparation. In this preparation, kidneys were perfused with blood from a donor rat on a matching or different diet to that of the kidney donor. Kidney endothelial cells were isolated with magnetic activated cell sorting and HDAC1 activity was measured.

Results

We found that HS impaired NO signaling in the afferent arteriole. This was restored by inhibition of HDAC1 with MS-275. Consistent with these findings, HDAC1 activity was increased in kidney endothelial cells. We further found the loss of NO to be dependent upon the diet of the blood donor rather than the diet of the kidney donor and the plasma from HS fed rats to be sufficient to induce dysfunction suggesting a humoral factor, we termedPlasmaDerivedEndothelial-dysfunctionMediator (PDEM), mediates the endothelial dysfunction. The antioxidants, PEG-SOD and PEG-catalase, as well as the NOS cofactor, tetrahydrobiopterin, restored NO signaling.

Conclusion

We conclude that HS activates endothelial HDAC1 through PDEM leading to decreased NO signaling. This study provides novel insights into the molecular mechanisms by which a HS decreases renal microvascular endothelial NO signaling.
Class-imbalanced Unsupervised and Semi-Supervised Domain Adaptation for Histopathology Images
Authors: Hosseini S. Maryam , Shafique Abubakr , Babaie Morteza , Tizhoosh H.R.
Published: March 2023

In dealing with the lack of sufficient annotated data and in contrast to supervised learning, unsupervised, self-supervised, and semi-supervised domain adaptation methods are promising approaches, enabling us to transfer knowledge from rich labeled source domains to different (but related) unlabeled target domains, reducing distribution discrepancy between the source and target domains. However, most existing domain adaptation methods do not consider the imbalanced nature of the real-world data, affecting their performance in practice. We propose to overcome this limitation by proposing a novel domain adaptation approach that includes two modifications to the existing models. Firstly, we leverage the focal loss function in response to class-imbalanced labeled data in the source domain. Secondly, we introduce a novel co-training approach to involve pseudo-labeled target data points in the training process. Experiments show that the proposed model can be effective in transferring knowledge from source to target domain. As an example, we use the classification of prostate cancer images into low-cancerous and high-cancerous regions.
A high soluble-fibre allele in wheat encodes a defective cell wall peroxidase responsible for dimerization of ferulate moieties on arabinoxylan
Authors: Mitchell Rowan A.C. , Oszvald Maria , Pellny Till K. , Freeman Jackie , Halsey Kirstie , Sparks Caroline A. , Huttly Alison , Specel Sebastien , Leverington-Waite Michelle , Griffiths Simon , Shewry Peter R. , Lovegrove Alison
Published: March 2023

Increasing dietary fibre (DF) intake is an important target to improve health and an attractive strategy for this is to increase the fibre content of staple foods, particularly white bread which is the staple food in many countries. DF in wheat white flour is derived principally from the endosperm cell wall polysaccharide arabinoxylan (AX) and the water-extractable form of this (WE-AX) accounts for the majority of soluble dietary fibre (SDF), which is believed to confer particular health benefits. We previously identified QTLs for soluble dietary fibre (SDF) on 1B and 6B chromosomes in wheat in biparental populations. Here we show that the 6B high SDF allele encodes a peroxidase protein (PER1-v) with a single missense compared to the more common low SDF form (PER1). Wheat lines with the natural PER1-v allele and with an induced knock-out mutation in PER1 showed similar characteristics of reduced dimerization of ferulate associated with water-extractable WE-AX. Decreased ferulate dimerization is associated with decreased cross-linking of the WE-AX chains and increased solubility of AX. Transiently expressed PER1_RFP fusion driven by native promoter in wheat endosperm was shown to localise to cell walls whereas PER1-v_RFP did not; we therefore propose that PER1-v lacks capacity to dimerise AX ferulatein vivodue to mis-localisation. PER1 is the first peroxidase reported to be responsible for oxidative coupling of ferulate on AX, a key process in all grass cell walls. Understanding its role and the effect of variants on AX properties offers a route to control the properties of wheat DF in the human diet.
Sensitive cluster-free differential expression testing.
Authors: Missarova Alsu , Rosen Leah Ursula , Dann Emma , Satija Rahul , Marioni John
Published: March 2023

Comparing molecular features, including the identification of genes with differential expression (DE) between conditions, is a powerful approach for characterising disease-specific phenotypes. When testing for DE in single-cell RNA sequencing data, current pipelines first assign cells into discrete clusters (or cell types), followed by testing for differences within each cluster. Consequently, the sensitivity and specificity of DE testing are limited and ultimately dictated by the granularity of the cell type annotation, with discrete clustering being especially suboptimal for continuous trajectories. To overcome these limitations, we present miloDE - a cluster-free framework for differential expression testing. We build on the Milo approach, introduced for differential cell abundance testing, which leverages the graph representation of single-cell data to assign relatively homogenous, neighbouring cells into overlapping neighbourhoods. We address key differences between differential abundance and expression testing at the level of neighbourhood assignment, statistical testing, and multiple testing correction. To illustrate the performance of miloDE we use both simulations and real data, in the latter case identifying a transient haemogenic endothelia-like state in chimeric mouse embryos lacking Tal1 as well as uncovering distinct transcriptional programs that characterise changes in macrophages in patients with Idiopathic Pulmonary Fibrosis. miloDE is available as an open-source R package at https://github.com/MarioniLab/miloDE.
Abnormal enteric nervous system and motor activity in the ganglionic proximal bowel of Hirschsprung’s disease
Authors: Edwards Brian S. , Stiglitz Emma S. , Davis Brian M. , Smith-Edwards Kristen M.
Published: March 2023

Hirschsprung’s disease (HSCR) is a congenital defect in which the enteric nervous system (ENS) does not develop in the distal bowel, requiring surgical removal of the portions of bowel without ENS ganglia (‘aganglionic’) and reattachment of the ‘normal’ proximal bowel with ENS ganglia. Unfortunately, many HSCR patients have persistent dysmotility (e.g., constipation, incontinence) and enterocolitis after surgery, suggesting that the remaining bowel is not normal despite having ENS ganglia. Anatomical and neurochemical alterations have been observed in the ENS-innervated proximal bowel from HSCR patients and mice, but no studies have recorded ENS activity to define the circuit mechanisms underlying post-surgical HSCR dysfunction. Here, we generated a HSCR mouse model with a genetically-encoded calcium indicator to map the ENS connectome in the proximal colon. We identified abnormal spontaneous and synaptic ENS activity in proximal colons from GCaMP-Ednrb-/-mice with HSCR that corresponded to motor dysfunction. Many HSCR-associated defects were also observed in GCaMP-Ednrb+/-mice, despite complete ENS innervation. Results suggest that functional abnormalities in the ENS-innervated bowel contribute to post-surgical bowel complications in HSCR patients, and HSCR-related mutations that do not cause aganglionosis may cause chronic colon dysfunction in patients without a HSCR diagnosis.
Predatory fireflies and their toxic firefly prey have evolved distinct toxin resistance strategies
Authors: Yang Lu , Borne Flora , Betz Anja , Aardema Matthew L. , Zhen Ying , Peng Julie , Visconti Regina , Wu Mariana , Roland Bartholomew P. , Talsma Aaron D. , Palladino Mike J. , Petschenka Georg , Andolfatto Peter
Published: March 2023

Toxic cardiotonic steroids (CTS) act as a defense mechanism in many firefly species (Lampyridae) by inhibiting a crucial enzyme called Na+,K+-ATPase (NKA). While most fireflies produce these toxins internally, species of the genusPhoturisacquire them from a surprising source: predation on other fireflies. The contrasting physiology of toxin exposure and sequestration betweenPhoturisand other firefly genera suggests that distinct strategies may be required to prevent self-intoxication. Our study demonstrates that bothPhoturisand their firefly prey have evolved highly-resistant NKAs. Using an evolutionary analysis of the specific target of CTS (ATPα) in fireflies, and gene-editing inDrosophila, we find that the initial steps towards resistance were shared amongPhoturisand other firefly lineages. However, thePhoturislineage subsequently underwent multiple rounds of gene duplication and neofunctionalization, resulting in the development of ATPα paralogs that are differentially expressed and exhibit increasing resistance to CTS. In contrast, other firefly species have maintained a single copy. Our results implicate gene duplication as a facilitator in the transition ofPhoturisto its distinct ecological role as predator of toxic firefly prey.

One-Sentence Summary

Gene duplication and neofunctionalization distinguish firefly predators from their toxic firefly prey.
Enthesis Maturation in Engineered Ligaments is Differentially Driven by Loads that Mimic Slow Growth Elongation and Rapid Cyclic Muscle Movement
Authors: Brown M. Ethan , Puetzer Jennifer L.
Published: March 2023

Entheses are complex attachments that translate load between elastic-ligaments and stiff-bone via organizational and compositional gradients. Neither natural healing, repair, nor engineered replacements restore these gradients, contributing to high re-tear rates. Previously, we developed a novel culture system which guides ligament fibroblasts in high-density collagen gels to develop early postnatal-like entheses, however further maturation is needed. Mechanical cues, including slow growth elongation and cyclic muscle activity, are critical to enthesis developmentin vivobut these cues have not been widely explored in engineered entheses and their individual contribution to maturation is largely unknown. Our objective here was to investigate how slow stretch, mimicking ACL growth rates, and intermittent cyclic loading, mimicking muscle activity, individually drive enthesis maturation in our system so to shed light on the cues governing enthesis development, while further developing our engineered replacements. Interestingly, we found these loads differentially drive organizational maturation, with slow stretch driving improvements in the interface/enthesis region, and cyclic load improving the ligament region. However, despite differentially affecting organization, both loads produced improvements to interface mechanics and zonal composition. This study provides new insight into how mechanical cues differentially affect enthesis development, while producing some of the most organized engineered enthesis to date.
Conserved features of eye movement related eardrum oscillations (EMREOs) across humans and monkeys
Authors: Lovich Stephanie N , King Cynthia D , Murphy David L.K. , Abbasi Hossein , Bruns Patrick , Shera Christopher A , Groh Jennifer
Published: March 2023

Auditory and visual information involve different coordinate systems, with auditory spatial cues anchored to the head and visual spatial cues anchored to the eyes. Information about eye movements is therefore critical for reconciling visual and auditory spatial signals. The recent discovery of eye movement-related eardrum oscillations (EMREOs) suggests that this process could begin as early as the auditory periphery. How this reconciliation might happen remains poorly understood. Because humans and monkeys both have mobile eyes and therefore both must perform this shift of reference frames, comparison of the EMREO across species can provide insights to shared and therefore important parameters of the signal. Here we show that rhesus monkeys, like humans, have a consistent, significant EMREO signal that carries parametric information about eye displacement as well as onset times of eye movements. The dependence of the EMREO on the horizontal displacement of the eye is its most consistent feature, and is shared across behavioral tasks, subjects, and species. Differences chiefly involve the waveform frequency (higher in monkeys than in humans) and patterns of individual variation (more prominent in monkeys than humans), and the waveform of the EMREO when factors due to horizontal and vertical eye displacements were controlled for.
Differential universal ortholog composition ofCoffea arabicaL. sub-genomes and its contribution to regulatory networks governing essential biological processes
Authors: Ribeiro Thales Henrique Cherubino , Oliveira Raphael Ricon de , Antonio Chalfun-Junior
Published: March 2023

The polyploidy ofCoffea arabicais an important trait affecting the evolution of this species. Genetic variability is scarce due to its recent origin as an interspecific hybrid from a single successful crossing event betweenCoffea canephoraandCoffea eugenioidesrelatives. To further investigate the genomic composition of an allotetraploid we coupled high-throughput methodologies of co-expression analysis and full-length protein coding genes inference. Many of the expected orthologs were found to be missing from one of the two homoeologous chromosomes. The gene expression machinery is mainly represented by single-copy essential orthologs located in theCoffea eugenioidessub-genome. This result suggests a preference of the transcriptional and RNA processing machinery to be regulated by one parental sub-genome. To understand the operational modules of the sub-genomes transcription, we performed co-expression analysis that revealed 23 co-regulated modules. This system-wide approach clarified how biological processes (i.e., photosynthesis, cell wall biogenesis, translation, transcription, catabolism and biosynthesis) are running in synchrony and reinforces that there is an ongoing selective pressure inC. arabicathat constrains the number of copies of some universal orthologues. Thus, this work contributes to our understanding of genome evolution in recent polyploids and supports crop breeding programs.
Sex- and Age-dependent Skin Mechanics – A Detailed Look in Mice
Authors: Lin Chien-Yu , Sugerman Gabriella P. , Kakaletsis Sotirios , Meador William D. , Buganza Adrian T. , Rausch Manuel K.
Published: March 2023

Skin aging is of immense societal and, thus, scientific interest. Because mechanics play a critical role in skin’s function, a plethora of studies have investigated age-induced changes in skin mechanics. Nonetheless, much remains to be learned about the mechanics of aging skin. This is especially true when considering sex as a biological variable. In our work, we set out to answer some of these questions using mice as a model system. Specifically, we combined mechanical testing, histology, collagen assays, and two-photon microscopy to identify age- and sex-dependent changes in skin mechanics and to relate them to structural, microstructural, and compositional factors. Our work revealed that skin stiffness, thickness, and collagen content all decreased with age and were sex dependent. Interestingly, sex differences in stiffness were age induced. We hope our findings not only further our fundamental understanding of skin aging but also highlight both age and sex as important variables when conducting studies on skin mechanics.
phytools 2.0: An updated R ecosystem for phylogenetic comparative methods (and other things)
Authors: Revell Liam J.
Published: March 2023

Phylogenetic comparative methods comprise the general endeavor of using an estimated phylogenetic tree (or set of trees) to make secondary inferences: about trait evolution, diversification dynamics, biogeography, community ecology, and a wide range of other phenomena or processes. Over the past ten years or so, thephytoolsR package (Revell 2012) has grown to become an important research tools for phylogenetic comparative analysis.phytoolsis a diverse contributed R library now consisting of hundreds of different functions covering a variety of methods and purposes in phylogenetic biology. As of the time of writing,phytoolsincluded functionality for fitting models of trait evolution, for reconstructing ancestral states, for studying diversification on trees, and for visualizing phylogenies, comparative data, and fitted models, as well numerous other tasks related to phylogenetic biology. Here, I describe some significant features of and recent updates tophytools, while also illustrating several popular workflows of thephytoolscomputational software.
Modification of social cheating facilitates the stabilization and chronic infection of polymorphicPseudomonas aeruginosapopulation
Authors: Zhao Kelei , Yang Xiting , Zeng Qianglin , Zhang Yige , Li Heyue , Li Jing Shirley , Liu Huan , Du Liangming , Wu Yi , Huang Gui , Huang Ting , Zhang Yamei , Zhou Hui , Wang Xinrong , Chu Yiwen , Zhou Xikun
Published: March 2023

Chronic infection of the common bacterial pathogenPseudomonas aeruginosafrequently leads to the coexistence of heterogeneous individuals to engage in several group behaviors. However, further evolution of the polymorphicP. aeruginosapopulation, including the dynamic change of social cooperation and its impact on host immune system, still remain elusive. We show that the evolution ofP. aeruginosain the patients with chronic obstructive pulmonary disease frequently selects the isolates deficient in producing the costly and sharable extracellular products for nutrient acquisition. The evolution of polymorphicP. aeruginosapopulation is mainly concentrated on modifying the adaptability oflasRmutants, which are typical cheaters in the competition of quorum-sensing-controlled extracellular proteases. Importantly,lasRmutants with varying degrees of evolution interact with wild-typeP. aeruginosain a framework termed cascaded public goods game to compete for extracellular proteases and siderophores, and thus perpetuate social cooperation under different conditions. Finally, we find that a polymorphic population comprised oflasR-intactP. aeruginosaand evolvedlasR-mutant can minimize the host immune fluctuation for persistent colonization. This study demonstrates the multistage evolution and complex interaction ofP. aeruginosain adaptation to host lungs, and provides an explanation for the success of cooperation in public goods game.
Characterizing the extracellular matrix transcriptome of endometriosis
Authors: Cook Carson J. , Fogg Kaitlin C.
Published: March 2023

In recent years, the matrisome, a set of proteins that make up the extracellular matrix (ECM) or are closely involved in ECM behavior, has been shown to have great importance for characterizing and understanding disease pathogenesis and progression. The matrisome is especially critical for examining diseases characterized by extensive tissue remodeling. Endometriosis is characterized by the extrauterine growth of endometrial tissue, making it an ideal condition to study through the lens of matrisome gene expression. While large gene expression datasets have become more available, and gene dysregulation in endometriosis has been the target of several studies, the gene expression profile of the matrisome specifically in endometriosis has not been well characterized. In our study, we explored three Gene Expression Omnibus (GEO) DNA microarray datasets containing endometriosis and healthy samples of eutopic endometrium. We established that matrisome gene expression alone can stratify healthy and endometriosis samples and identified the matrisome genes and gene networks that hold inferential significance for the onset and progression of endometriosis. Furthermore, we found that menstrual cycle phase accounted for over a third of the variance of matrisome gene expression within the samples. Taken together, these findings may aid in developing futurein vitromodels of disease and identifying novel treatment strategies for this underserved patient population.
Inhibition of muscarinic receptor signaling protects human enteric inhibitory neurons against platin chemotherapy toxicity
Authors: Richter Mikayla N , Farahvashi Sina , Samuel Ryan M , Majd Homa , Chemel Angeline K , Ramirez Jonathan T , Majd Alireza , Scantlen Megan D , Elder Nicholas , Cesiulis Andrius , Garcia Kristle , Joshi Tanvi , Keefe Matthew G , Samiakalantari Bardia , Turkalj Elena M , Yu Johnny , Arab Abolfazl , Yin Keyi , Culbertson Bruce , Vora Bianca , Xiong Chenling , Kattah Michael G , Irannejad Roshanak , Kroetz Deanna L , Nowakowski Tomasz J , Goodarzi Hani , Fattahi Faranak
Published: March 2023

GI toxicity is a common dose-limiting adverse effect of platin chemotherapy treatment. Up to 50% of cancer survivors continue to experience symptoms of chronic constipation or diarrhea induced by their chemotherapy for many years after their treatment. This drug toxicity is largely attributed to damage to enteric neurons that innervate the GI tract and control GI motility. The mechanisms responsible for platin-induced enteric neurotoxicity and potential preventative strategies have remained unknown. Here, we use human pluripotent stem cell derived enteric neurons to establish a new model system capable of uncovering the mechanism of platin-induced enteric neuropathy. Utilizing this scalable system, we performed a high throughput screen and identified drug candidates and pathways involved in the disease. Our analyses revealed that excitotoxicity through muscarinic cholinergic signaling is a key driver of platin-induced enteric neuropathy. Using single nuclei transcriptomics and functional assays, we discovered that this disease mechanism leads to increased susceptibility of specific neuronal subtypes, including inhibitory nitrergic neurons, to platins. Histological assessment of the enteric nervous system in platin-treated patients confirmed the selective loss of nitrergic neurons. Finally, we demonstrated that pharmacological and genetic inhibition of muscarinic cholinergic signaling is sufficient to rescue enteric neurons from platin excitotoxicityin vitroand can prevent platin-induced constipation and degeneration of nitrergic neurons in mice. These studies define the mechanisms of platin-induced enteric neuropathy and serve as a framework for uncovering cell type-specific manifestations of cellular stress underlying numerous intractable peripheral neuropathies.
LRRC8A anion channels modulate vasodilation via association with Myosin Phosphatase Rho Interacting Protein (MPRIP)
Authors: Choi Hyehun , Miller Michael R. , Nguyen Hong-Ngan , Rohrbough Jeffrey C. , Koch Stephen R. , Boatwright Naoko , Yarboro Michael T. , Sah Rajan , McDonald W. Hayes , Reese J. Jeffrey , Stark Ryan J. , Lamb Fred S.
Published: March 2023

Background

In vascular smooth muscle cells (VSMCs), LRRC8A volume regulated anion channels (VRACs) are activated by inflammatory and pro-contractile stimuli including tumor necrosis factor alpha (TNFα), angiotensin II and stretch. LRRC8A physically associates with NADPH oxidase 1 (Nox1) and supports its production of extracellular superoxide (O2-•).

Methods and Results

Mice lacking LRRC8A exclusively in VSMCs (Sm22α-Cre, KO) were used to assess the role of VRACs in TNFα signaling and vasomotor function. KO mesenteric vessels contracted normally to KCl and phenylephrine, but relaxation to acetylcholine (ACh) and sodium nitroprusside (SNP) was enhanced compared to wild type (WT). 48 hours ofex vivoexposure to TNFα (10ng/ml) markedly impaired dilation to ACh and SNP in WT but not KO vessels. VRAC blockade (carbenoxolone, CBX, 100 μM, 20 min) enhanced dilation of control rings and restored impaired dilation following TNFα exposure. Myogenic tone was absent in KO rings. LRRC8A immunoprecipitation followed by mass spectroscopy identified 35 proteins that interacted with LRRC8A. Pathway analysis revealed actin cytoskeletal regulation as the most closely associated function of these proteins. Among these proteins, the Myosin Phosphatase Rho-Interacting protein (MPRIP) links RhoA, MYPT1 and actin. LRRC8A-MPRIP co-localization was confirmed by confocal imaging of tagged proteins, Proximity Ligation Assays, and IP/western blots which revealed LRRC8A binding at the second Pleckstrin Homology domain of MPRIP. siLRRC8A or CBX treatment decreased RhoA activity in cultured VSMCs, and MYPT1 phosphorylation at T853 was reduced in KO mesenteries suggesting that reduced ROCK activity contributes to enhanced relaxation. MPRIP was a target of redox modification, becoming oxidized (sulfenylated) after TNFα exposure.

Conclusions

Interaction of Nox1/LRRC8A with MPRIP/RhoA/MYPT1/actin may allow redox regulation of the cytoskeleton and link Nox1 activation to both inflammation and vascular contractility.
Administration of the glutamate-modulating drug riluzole after stress reverses its delayed effects on the amygdala
Authors: Datta Siddhartha , Rashid Zubin , Naskar Saptarnab , Chattarji Sumantra
Published: March 2023

Extracellular glutamate levels are elevated across brain regions immediately after stress. Despite sharing common features in their genesis, the patterns of stress-induced plasticity that eventually take shape are strikingly different between these brain areas. While stress impairs structure and function in the hippocampus, it has the opposite effect on the amygdala. Riluzole, an FDA-approved drug known to modulate glutamate release and facilitate glutamate clearance, prevents stress-induced deficits in the hippocampus. But, whether the same drug is also effective in countering the opposite effects of stress in the amygdala remains unexplored. We addressed this question by using a rat model wherein even a single 2-hour acute immobilization stress causes a delayed build-up, 10 days later, in anxiety-like behavior, alongside stronger excitatory synaptic connectivity in the basolateral amygdala (BLA). This temporal profile – several days separating the acute stressor and its delayed impact – allowed us to test if these effects can be reversed by administering riluzole in the drinking waterafteracute stress. Post-stress riluzole not only prevented the delayed increase in anxiety-like behavior on the elevated plus-maze, but also reversed the increase in spine-density on BLA neurons 10 days later. Further, stress-induced increase in the frequency of miniature excitatory postsynaptic currents recorded in BLA slices, 10 days later, was reversed by the same post-stress riluzole administration. Together, these findings underscore the importance of therapeutic strategies, aimed at glutamate uptake and modulation, in correcting the delayed behavioral, physiological, and morphological effects of stress on the amygdala.

Significance statement

Stress disorders are characterized by impaired cognitive function alongside enhanced emotionality. Consistent with this, the same stress elicits contrasting effects in the rodent hippocampus versus amygdala. This poses a therapeutic challenge – the same pharmacological intervention against stress has to counter these opposite effects. Yet, the immediate consequence of stress – enhanced extracellular glutamate – is similar across these two areas. To target this common feature, we treated rats with riluzole, a drug that prevents stress-induced glutamate surge. Although the drug was administered after the end of stress, it reversed its delayed impact on amygdalar structure and function. Since riluzole also enhances glutamate-uptake through glial-transporters and is approved for human use, these results highlight the importance of therapeutic strategies focused on neuron-astrocyte interactions.
Bowel Colonization by Non-Commensal Fungi in Neonatal Obstructive Cholangitis and Biliary Atresia
Authors: Huang Song-Wei , Lin Chia-Ray , Chang Ya-Hui , Ni Yen-Hsuan , Chen Huey-Ling , Liu Hong-Hsing
Published: March 2023

Up to two-thirds of biliary atresia (BA) patients need liver transplantation after the standard Kasai portoenterostomy treatment. Unrelenting cholangitis often precedes the full-blown presentation of BA. Using ribosomal 18S sequencing, here we report bowel colonization by non-commensalAspergillusfungi in one case of neonatal obstructive cholangitis. Continuous oral fluconazole treatment resolved obstructive cholangitis completely. Colonization by non-commensalAspergillusandCerrenawere additionally identified in 2 BA cases. In brief, bowel colonization by non-commensal fungi could be a treatable cause of neonatal obstructive cholangitis and potentially BA at an early stage.
Exploring the vomeronasal organ in an endangered antelope species
Authors: Torres Mateo V. , Ortiz-Leal Irene , Ferreiro Andrea , Rois José Luis , Sanchez-Quinteiro Pablo
Published: March 2023

The dama gazelle is a threatened and scarcely studied species of northern Africa. Human pressure has depleted the population of dama gazelles from tens of thousands to a few hundred individuals. Since 1970, after deriving from a founder population of the last 17 surviving individuals in the Western Sahara, it has been reproduced naturally in captivity. Although certain aspects of the reproductive biology of the dama gazelle have been established in preparation for the future implementation of assisted reproductive technology there is a lack of information regarding the role of semiochemical-mediated communication in the sexual behavior of the dama gazelle. This is partially due to the lack of a neuroanatomical and morphofunctional characterization of the dama gazelle vomeronasal organ (VNO); the sensory organ responsible for the processing of pheromones. This study aims to determine the presence in the dama gazelle of a VNO fully equipped to carry out its neurosensory function and to contribute to the understanding of the interspecific variability of the VNO of ruminants. Employing histological, lectin-histochemical and immunohistochemical techniques we have performed a detailed morphofunctional evaluation of the dama gazelle VNO along its entire longitudinal axis. The findings suggest that studies of the VNO should take a similar approach, as there are significant structural and neurochemical transformations that the organ exhibits as a whole. This study contributes to the understanding of the VNO in dama gazelles and provides a basis for future studies on semiochemical-mediated communication and reproductive management of this species.
Unveiling Convergent and Divergent Intrinsic Brain Network Alternations in Depressed Adolescents Engaged Non-Suicidal Self-Injurious Behaviors with and without Suicidal Attempts
Authors: Li Linling , Liang Zhen , Li Guohua , Xu Hong , Yang Xing , Liu Xia , Zhang Xin , Wang Jianhong , Zhang Zhiguo , Zhou Yongjie
Published: March 2023

Nonsuicidal self-injury (NSSI) and suicidal attempt (SA) frequently occur during depressed adolescents, but the underlying neurobiological mechanisms are poorly understood. The maturation of network connectivity is a central feature of brain development during adolescence. However, few researchers have used resting-state functional magnetic resonance imaging (fMRI) to investigate the similarities and differences in the intrinsic brain networks between NSSI with NSSI+SA in depressed adolescent populations. In this study, we collected self-reported questionnaires and resting-state (fMRI data from a sample of depressed adolescents (N = 114), categorized into three groups: clinical control (non-self-harm), NSSI-only, and NSSI+SA based on their self-harm history. The alternations of FC patterns were identified through support vector machine-based classification, as machine learning approaches can help to overcome the multiple-comparison problems of their multivariate nature. Referring to the convergent alternations between adolescent NSSI with or without a history of SA, the alternations of intra-/inter-network FCs among the Control, SalVAtten, Limbic, and Default networks. Besides, divergent alternations were also observed for depressed adolescents with a history of SA, involving the Limbic, DorsAttn, Visual, and Subcortical networks. Besides, the severity of depressive symptoms only showed a significant correlation with altered FCs in Limbic-DorAttn and Limbic-Visual networks, strengthening the fact that these observed alternations of FC could not all be explained by increased depression severity. The emphasis of this study on the network basis could extend the existing evidence at a circuit level and the observed convergent alternations may explain an underlying neurobiological mechanism pertaining to the continuum of self-destructiveness in adolescents. In addition, our discovery of divergent alternations could help to identify biomarkers that will aid in differentiating those at risk for SA among those engaging in NSSI and contribute to the development of neurobiologically informed interventions.
Clustering predicted structures at the scale of the known protein universe
Authors: Barrio-Hernandez Inigo , Yeo Jingi , Jänes Jürgen , Wein Tanita , Varadi Mihaly , Velankar Sameer , Beltrao Pedro , Steinegger Martin
Published: March 2023

Proteins are key to all cellular processes and their structure is important in understanding their function and evolution. Sequence-based predictions of protein structures have increased in accuracy with over 214 million predicted structures available in the AlphaFold database (AFDB). However, studying protein structures at this scale requires highly efficient methods. Here, we developed a structural-alignment based clustering algorithm - Foldseek cluster - that can cluster hundreds of millions of structures. Using this method we have clustered all structures in AFDB, identifying 2.27M non-singleton structural clusters, of which 31% lack annotations representing likely novel structures. Clusters without annotation tend to have few representatives covering only 4% of all proteins in the AFDB. Evolutionary analysis suggests that most clusters are ancient in origin but 4% seem species specific, representing lower quality predictions or examples of de-novo gene birth. Additionally, we show how structural comparisons can be used to predict domain families and their relationships, identifying examples of remote homology. Based on these analyses we identify several examples of human immune related proteins with remote homology in prokaryotic species which illustrates the value of this resource for studying protein function and evolution across the tree of life.
Transcriptional characterization of iPSC-derived microglia as a model for therapeutic development in neurodegeneration
Authors: Ramaswami Gokul , Yuva-Aydemir Yeliz , Akerberg Brynn , Matthews Bryan , Williams Jenna , Golczer Gabriel , Huang Jiaqi , Huh Dann , Burkly Linda C. , Engle Sandra J. , Sehgal Alfica , Sigova Alla A. , Fremeau Robert T. , Liu Yuting , Bumcrot David
Published: March 2023

Background

Microglia are the resident immune cells in the brain that play a key role in driving neuroinflammation, a hallmark of neurodegenerative disorders. Inducible microglia-like cells have been developed as an in vitro platform for molecular and therapeutic hypothesis generation and testing. However, there has been no systematic assessment of similarity of these cells to primary human microglia along with their responsiveness to external cues expected of primary cells in the brain.

Methods

In this study, we performed transcriptional characterization of commercially available human inducible pluripotent stem cell (iPSC)-derived microglia-like (iMGL) cells by bulk and single cell RNA sequencing to assess their similarity with primary human microglia. To evaluate their stimulation responsiveness, iMGL cells were treated with Liver X Receptor (LXR) pathway agonists and their transcriptional responses characterized by bulk and single cell RNA sequencing.

Results

Bulk transcriptome analyses demonstrate that iMGL cells have a similar overall expression profile to freshly isolated human primary microglia and express many key microglial transcription factors and functional and disease-associated genes. Notably, at the single-cell level, iMGL cells exhibit distinct transcriptional subpopulations, representing both homeostatic and activated states present in normal and diseased primary microglia. Treatment of iMGL cells with LXR pathway agonists induces robust transcriptional changes in lipid metabolism and cell cycle at the bulk level. At the single cell level, we observe heterogeneity in responses between cell subpopulations in homeostatic and activated states and deconvolute bulk expression changes into their corresponding single cell states.

Conclusions

In summary, our results demonstrate that iMGL cells exhibit a complex transcriptional profile and responsiveness, reminiscent of in vivo microglia, and thus represent a promising model system for therapeutic development in neurodegeneration.