bluuebunny/crossref_metadata_2025 huggingface dataset:
Habitat resource overlap in two broad-ranged sympatric Neotropical forest eagles
Authors: Sutton Luke J. , Anderson David L. , Franco Miguel , Gomes Felipe Bittioli R. , McClure Christopher J.W. , Miranda Everton B.P. , Vargas F. Hernán , Vargas González José de J. , Puschendorf Robert
Published: March 2022

Quantifying resource partitioning between co-occurring species has important ecological and evolutionary implications. Yet, few studies compare resource overlap in both geographic and environmental space. We test whether the habitat requirements of two closely related Neotropical forest eagles, the crested eagle (Morphnus guianensis) and harpy eagle (Harpia harpyja), differ at fine and coarse resolutions across their shared geographic range. Using landcover and topographic covariates, we quantified resource overlap first using higher resolution (30 arc-sec data) generalized linear models (GLMs), and second using coarser-grain (2.5 arc-min data) environmental ordination. The distribution of both eagles was largely explained by canopy species richness and structural complexity with evergreen forest, but with differing responses to landcover and topography, particularly with the harpy eagle more likely in areas of dense evergreen forest. Both eagles were negatively associated with mosaic forest, with this relationship stronger for the crested eagle. Harpy eagle distribution was restricted by higher elevation and terrain roughness, compared to the crested eagle, whose distribution was more restricted by canopy species richness and structure. From the GLMs, resource overlap was > 92 % in geographical space but reduced to 64 % in environmental space. From ordination, resource overlap was 76 % in environmental space, with randomization tests supporting equivalent environmental space for both eagles. Our results suggest that at the biogeographical scale, crested and harpy eagles share environmental space, but there may be subtle differences in fine-scale habitat preference. We recommend habitat resource overlap be assessed in both geographical and environmental space at multiple resolutions to capture the inherent variability in environmental conditions available to co-occurring species.
Structural and functional MRI data differentially predict chronological age and behavioral memory performance
Authors: Soch Joram , Richter Anni , Kizilirmak Jasmin M. , Schütze Hartmut , Feldhoff Hannah , Fischer Larissa , Knopf Lea , Raschick Matthias , Schult Annika , Düzel Emrah , Schott Björn H.
Published: March 2022

Human cognitive abilities decline with increasing chronological age, with decreased explicit memory performance being most strongly affected. However, some older adults show “successful aging”, that is, relatively preserved cognitive ability in old age. One explanation for this could be higher brain structural integrity in these individuals. Alternatively, the brain might recruit existing resources more efficiently or employ compensatory cognitive strategies. Here, we approached this question by testing multiple candidate variables from structural and functional neuroimaging for their ability to predict chronological age and memory performance, respectively. Prediction was performed using support vector machine (SVM) classification and regression across and within two samples of young (N = 106) and older (N = 153) adults. The candidate variables were (i) behavioral response frequencies in an episodic memory test, (ii) recently described fMRI scores reflecting preservation of functional memory networks, (iii) whole-brain fMRI contrasts for novelty processing and subsequent memory, (iv) resting-state fMRI maps quantifying voxel-wise signal fluctuation and (v) gray matter volume estimated from structural MR images. While age group could be reliably decoded from all variables, chronological age within young and older subjects was best predicted from gray matter volume. In contrast, memory performance was best predicted from task-based fMRI contrasts and particularly single-value fMRI scores, whereas gray matter volume has no predictive power with respect to memory performance in healthy adults. Our results suggest that superior memory performance in healthy older adults is better explained by efficient recruitment of memory networks rather than by preserved brain structure.
Improving patient survival by direct targeting of chimeric protein-protein interaction networks
Authors: Tagore Somnath , Frenkel-Morgenstern Milana
Published: March 2022

Protein fusions produced by the “slippage” of two genes or by chromosomal translocations are essential diagnostic biomarkers of cancer. Fusions produce novel protein-protein interactions, which eliminate other interactions by changing protein domains in such fusions. The impact of these changes disseminates along protein-protein interaction networks, thereby altering cancer-promoting activity and creating cancer phenotypes. Currently, for most patients, the determination of appropriate drugs is totally empirical. As such, a personalized therapy approach based on unique patient genomic markers is needed. In this study, we considered 672 aliquot IDs containing 3091 fusions from The Cancer Genome Atlas (TCGA), accounting for 25 cancer sub-types assigned as leukemias, lymphomas, sarcomas, melanoma, glioblastoma and carcinomas. Protein-protein interaction maps showed distinct patterns according to cancer sub-type, reflected as different phenotypic traits. We induced site-directed percolations, i.e., critical transitions, by selective knockouts of genes encoding proteins in a given interaction network so as to identify breakdown points. The number of genes that needed to be knocked out in a site-directed manner before inducing a breakdown ranged from 1-7 based on whether the fusion protein was part of a network hub. Quantitatively, in leukemia, lymphoma, melanoma and glioblastoma, breakdown was achieved in 218 fusion networks when only higher degree hubs were percolated, and in 280 networks when a combination of higher and lower degree hubs was targeted, with an FDR < 0.05. These were subsequently addressed in survival studies. We found that patient survival may be improved by considering ‘breakdown points’ as drug targets.
Temporal dynamics of cognitive flexibility in adolescents with anorexia nervosa: a high density EEG study
Authors: Berchio Cristina , Annen Lucie Clémentine , Bouamoud Ynès , Micali Nadia
Published: March 2022

Cognitive rigidity is a core symptom of anorexia nervosa (AN) and is associated with treatment resistance. Nevertheless, studies on the neural basis of cognitive flexibility (CF) in adolescent AN are rare.

The aim of this study was to investigate temporal brain dynamics of CF in adolescents with AN and their tendency to experience anxiety. To address this aim, participants performed a Dimensional Change Card Sorting task during high-density EEG recording. Transient state and stable traits of anxiety were measured with the State-Trait Anxiety Inventory. Data were collected on 22 girls with AN, and 23 healthy controls (HC) (aged 12-20 years old). Evoked potentials were investigated using microstates analysis. Effects of trait and state anxiety on microstates parameters were investigated performing correlations across groups and in the AN group only.

Adolescents with AN did not differ from HC with respect to behavioral switching cost, despite a greater overall accuracy. Adolescents with AN showed altered visual orienting processes (N100 micro-state), and earlier attentional processing to task switching (P300b microstate) when compared to HC. Reduced activation in a network involving the pre-central cortex, the cerebellum, and the posterior cingulate was identified in adolescents with AN. Trait and state anxiety were correlated with atypical AN microstates across groups.

The present findings suggest CF manifests with inefficient behavioral and neural strategies in adolescents with AN, at early stages in the illness. Additionally, this study provides evidence that transient and stable tendencies to experience anxiety could represent a vulnerability to developing CF impairments in adolescent AN.
Stable working memory and perceptual representations in macaque lateral prefrontal cortex during naturalistic vision
Authors: Roussy Megan , Corrigan Benjamin , Luna Rogelio , Gulli Roberto A. , Sachs Adam J. , Palaniyappan Lena , Martinez-Trujillo Julio C.
Published: March 2022

Primates use perceptual and mnemonic visuospatial representations to perform everyday functions. Neurons in the lateral prefrontal cortex (LPFC) have been shown to encode both of these representations during tasks where eye movements are strictly controlled and visual stimuli are reduced in complexity. This raises the question of whether perceptual and mnemonic representations encoded by LPFC neurons remain robust during naturalistic vision — in the presence of a rich visual scenery and during eye movements. Here we investigate this issue by training macaque monkeys to perform working memory and perception tasks in a visually complex virtual environment that requires navigation using a joystick and allows for free visual exploration of the scene. We recorded the activity of 3950 neurons in the LPFC (areas 8a and 9/46) of two rhesus macaques using multi-electrode arrays, and measured eye movements using video tracking. We found that navigation trajectories to target locations and eye movement behavior differed between the perception and working memory tasks suggesting that animals employed different behavioral strategies. Single neurons were tuned to target location during cue encoding and working memory delay and neural ensemble activity was predictive of the animals’ behavior. Neural decoding of target location was stable throughout the working memory delay epoch. However, neural representations of similar target locations differed between the working memory and perception tasks. These findings indicate that during naturalistic vision, LPFC neurons maintain robust and distinct neural codes for mnemonic and perceptual visuospatial representations.

Significance Statement

We show that LPFC neurons encode working memory and perceptual representations during a naturalistic task set in a virtual environment. We show that despite eye movement and complex visual input, neurons maintain robust working memory representations of space which are distinct from neuronal representations for perception. We further provide novel insight on the use of virtual environments to construct behavioral tasks for electrophysiological experiments.
siRNA-mediated gene knockdown via electroporation in hydrozoan jellyfish embryos
Authors: Masuda-Ozawa Tokiha , Fujita Sosuke , Nakamura Ryotaro , Watanabe Hiroshi , Kuranaga Erina , Nakajima Yu-ichiro
Published: March 2022

As the sister group to bilaterians, cnidarians stand in a unique phylogenetic position that provides insight into evolutionary aspects of animal development, physiology, and behavior. While cnidarians are classified into two types, sessile polyps and free-swimming medusae, most studies at the cellular and molecular levels have been conducted on representative polyp-type cnidarians and have focused on establishing techniques of genetic manipulation. Recently, gene knockdown by delivery of short hairpin RNAs into eggs via electroporation has been introduced in two polyp-type cnidarians, Nematostella vectensis and Hydractinia symbiolongicarpus, enabling systematic loss-of-function experiments. By contrast, current methods of genetic manipulation for most medusa-type cnidarians, or jellyfish, are quite limited, except for Clytia hemisphaerica, and reliable techniques are required to interrogate function of specific genes in different jellyfish species. Here, we present a method to knock down target genes by delivering small interfering RNA (siRNA) into fertilized eggs via electroporation, using the hydrozoan jellyfish, Clytia hemisphaerica and Cladonema paciificum. We show that siRNAs targeting endogenous GFP1 and Wnt3 in Clytia efficiently knock down gene expression and result in known planula phenotypes: loss of green fluorescence and defects in axial patterning, respectively. We also successfully knock down endogenous Wnt3 in Cladonema by siRNA electroporation, which circumvents the technical difficulty of microinjecting small eggs. Wnt3 knockdown in Cladonema causes gene expression changes in axial markers, suggesting a conserved Wnt/β-catenin-mediated pathway that controls axial polarity during embryogenesis. Our gene-targeting siRNA electroporation method is applicable to other animals, including and beyond jellyfish species, and will facilitate the investigation and understanding of myriad aspects of animal development.
Resting-state connectivity underlying cognitive control’s association with perspective taking in callous-unemotional traits
Authors: Winters Drew E. , Leopold Daniel R. , McKell Carter R. , Sakai Joseph T.
Published: March 2022

Callous-Unemotional (CU) traits are often associated with impairments in perspective taking and cognitive control (regulating goal directed behavior); and adolescents with CU traits demonstrate aberrant brain activation/connectivity in areas underlying these processes. Together cognitive control and perspective taking are thought to link mechanistically to explain CU traits. Because increased cognitive control demands modulate perspective taking ability among both typically developing samples and individuals with elevated CU traits, understanding the neurophysiological substrates of these constructs could inform efforts to alleviate societal costs of antisocial behavior. The present study uses GIMME to examine the heterogenous functional brain properties (i.e., connection density, node centrality) underlying cognitive control’s influence on perspective taking among adolescents on a CU trait continuum. Results reveal that cognitive control had a negative indirect association with CU traits via perspective taking; and brain connectivity indirectly associated with lower CU traits – specifically the social network via perspective taking and conflict network via cognitive control. Additionally, less negative connection density between the social and conflict networks was directly associated with higher CU traits. Our results support the growing literature on cognitive control’s influence on socio-cognitive functioning in CU traits and extends that work by identifying underlying functional brain properties.
Exploring intra-species diversity through non-redundant pangenome assemblies
Authors: Puente-Sánchez Fernando , Hoetzinger Matthias , Buck Moritz , Bertilsson Stefan
Published: March 2022

At the genome level, microorganisms are highly adaptable both in terms of allele and gene composition. Such heritable traits emerge in response to different environmental niches and can have a profound influence on microbial community dynamics. As a consequence of this, any individual genome or clonal population will contain merely a fraction of the total genetic diversity of any operationally defined “species”, with the collective from that group presenting the broader genomic diversity known as the pangenome. Pangenomes are valuable concepts for studying evolution and adaptation in microorganisms, as they partition genomes into core regions (present in all the genomes, and responsible for housekeeping and species-level niche adaptation) and accessory regions (present only in some genomes, and responsible for ecotype divergence).

Here we present SuperPang, an algorithm capable of producing pangenome assemblies from a set of input genomes of varying quality, including metagenome-assembled genomes or MAGs. SuperPang runs in linear time and its results are complete, non-redundant, preserve gene ordering and contain both coding and non-coding regions. Our approach provides a modular view of the pangenome, identifying operons and genomic islands, and allowing to track their prevalence in different populations. We illustrate our approach by analyzing the intra-species diversity of Polynucleobacter, a clade of ubiquitous freshwater microorganisms characterized by their streamlined genomes and their ecological versatility. We show how SuperPang facilitates the simultaneous analysis of allelic and gene content variation under different environmental pressures, allowing us to study the drivers of microbial diversification at unprecedented resolution.
Xenon LFP Analysis Platform is a Novel Graphical User Interface for Analysis of Local Field Potential from Large-Scale MEA Recordings
Authors: Mahadevan Arjun , Codadu Neela K. , Parrish R. Ryley
Published: March 2022

High-density multi-electrode array (HD-MEA) has enabled neuronal measurements at high spatial resolution to record local field potentials (LFP), extracellular spikes, and network activity with ease. Whilst we have advanced recording systems with over 4000 electrodes, capable of recording data at over 20 kHz, it still presents computational challenges to handle, process, extract, and view information from these large recordings. It can be challenging for researchers to extract and view even a single channel that has more than a billion data points, let alone process a group of channels.

We have created a computational method, and an open-source toolkit built on Python, rendered on a web browser using Plotly’s Dash for extracting and viewing the data, and creating interactive visualization. In addition to extracting and viewing entire or small chunks of data sampled at lower or higher frequencies, respectively, it provides a framework to collect user inputs, analyze channel groups, generate raster plots, view quick summary measures for LFP activity, detect and isolate noise channels, and generate plots and visualization in both time and frequency domain. Incorporated into our Graphical User Interface (GUI), we also have created a novel seizure detection method, which can be used to detect the onset of seizures in all or a selected group of channels and provide the following measures of seizures: distance, duration, and propagation across the region of interest.

We demonstrate the utility of this toolkit, using datasets collected from the 3Brain BioCAM duplex system. For the current analysis, we demonstrate the toolkit and methods with a low sampling frequency dataset (300 Hz) and a group of approximately 400 channels. Using this toolkit, we present novel data demonstrating increased seizure propagation speed from slices of Scn1aHet mice compared to littermate controls.

With advances in HD-MEA recording systems with high spatial and temporal resolution, limited tools are available for researchers to view and process these big datasets. We now provide a user-friendly toolkit to analyze LFP activity obtained from large-scale MEA recordings with translatable applications to EEG recordings, and demonstrate the utility of this new graphic user interface with novel biological findings.
AMP-kinase mediates adaptation of glioblastoma cells to conditions of the tumour microenvironment
Authors: Lorenz Nadja I. , Sauer Benedikt , Zeiner Pia S. , Strecker Maja I. , Luger Anna-Luisa , Schulte Dorothea , Mittelbronn Michel , Alekseeva Tijna , Sevenich Lisa , Harter Patrick N. , Münch Christian , Steinbach Joachim P. , Ronellenfitsch Michael W.
Published: March 2022

AMP-activated protein kinase (AMPK) is a central cellular energy sensor that regulates metabolic activity. We hypothesised that in glioblastoma (GB), AMPK plays a pivotal role in balancing metabolism under conditions of the tumour microenvironment, which is characterised by fluctuating and often low nutrient and oxygen availability. Impairment of this network could thus interfere with tumour progression.

AMPK activity was modulated genetically by CRISPR/Cas9-based double knockout (DKO) of the catalytic α1 and α2 subunits in human GB cells and effects were confirmed by pharmacological AMPK inhibition using BAY3827 and an inactive control compound in primary GB cell lines.

We found that metabolic adaptation of GB cells under energy stress conditions (hypoxia, glucose deprivation) was dependent on AMPK and accordingly that, AMPK DKO cells were more vulnerable to glucose-deprivation or inhibition of glycolysis and sensitised to hypoxia-induced cell death. This effect was rescued by reexpression of the AMPK α2 subunit. Similar results were observed using the selective pharmacological AMPK inhibitor BAY3827. Mitochondrial biogenesis was regulated AMPK-dependently with a reduced mitochondrial mass and mitochondrial membrane potential in AMPK DKO GB cells. In vivo, AMPK DKO GB cells showed impaired tumour growth and tumour formation in CAM assays as well as in an orthotopic glioma mouse model.

Our study highlights the importance of AMPK for GB cell adaptation towards energy depletion and emphasises the role of AMPK for tumour formation in vivo. Moreover, we identified mitochondria as central downstream effectors of AMPK signalling. The development of AMPK inhibitors could open opportunities for the treatment of hypoxic tumours.
S6K1 phosphorylates Cdk1 and MSH6 to regulate DNA repair
Authors: Amar-Schwartz Adi , Ben-Hur Vered , Jbara Amina , Cohen Yuval , Barnabas Georgina , Siegfried Zahava , Mashahreh Bayan , Hassouna Fouad , Shilo Asaf , Abu-Odeh Mohammad , Berger Michael , Wiener Reuven , Aqeilan Rami I. , Geiger Tamar , Karni Rotem
Published: March 2022

The mTORC1 substrate, S6 Kinase 1 (S6K1), is involved in the regulation of cell growth, ribosome biogenesis, glucose homeostasis and adipogenesis. Accumulating evidence has suggested a role for mTORC1 signaling in the DNA damage response. This is mostly based on the findings that mTORC1 inhibitors sensitized cells to DNA damage. However, a direct role of the mTORC1-S6K1 signaling pathway in DNA repair and the mechanism by which this signaling pathway regulates DNA repair is unknown. In this study, we discovered a novel role for S6K1 in regulating DNA repair through the coordinated regulation of the cell cycle, homologous recombination (HR) DNA repair (HRR) and mismatch DNA repair (MMR) mechanisms. Here we show that S6K1 orchestrates DNA repair by phosphorylation of Cdk1 at serine 39, causing G2/M cell cycle arrest enabling homologous recombination and by phosphorylation of MSH6 at serine 309, enhancing MMR. Moreover, breast cancer cells harboring RPS6KB1 gene amplification show increased resistance to several DNA damaging agents and S6K1 expression is associated with poor survival of breast cancer patients treated with chemotherapy. Our findings reveal an unexpected function of S6K1 in the DNA repair pathway, serving as a tumorigenic barrier by safeguarding genomic stability.
Rapid differentiation of regulatory CD4+ T cells in the infarcted myocardium blunts in situ inflammation
Authors: Delgobo Murilo , Weiß Emil , Ashour Diyaa ElDin , Popiolkowski Lisa , Arampatzi Panagiota , Stangl Verena , Arias-Loza Paula , Rainer Peter P. , Saliba Antoine-Emmanuel , Ludewig Burkhard , Hofmann Ulrich , Frantz Stefan , Ramos Gustavo Campos
Published: March 2022

Background

Myocardial infarction (MI) is a sterile inflammatory condition associated with tissue injury that results in the activation of T helper cell targeting cardiac antigens. However, the differentiation trajectories and in situ activity of heart-specific CD4+T cells activated in the MI context remain poorly understood.

Methods

Herein, we combined T-cell receptor transgenic models targeting myocardial protein, single-cell transcriptomics, and functional phenotyping to elucidate how the myosin-specific CD4+ T cells (TCR-M) differentiate in the murine infarcted myocardium and ultimately influence tissue repair. Furthermore, we adoptively transferred heart-specific T-cells that were pre-differentiated in vitro towards pro-inflammatory versus regulatory phenotypic states to dissect how they differentially regulate post-myocardial infarction (MI) inflammation.

Results

Flow cytometry and single-cell transcriptomics findings reveled that transferred TCR-M cells rapidly acquired an induced regulatory phenotype (iTreg) in the infarcted myocardium and blunt local inflammation. Myocardial TCR-M cells differentiated into two main lineages enriched with cell activation and pro-fibrotic transcripts (e.g. Tgfb1) or with suppressor immune checkpoints (e.g. Pdcd1), which we also found in human myocardial tissue. These cells produced high levels of latency-associated peptide (LAP) and inhibited interleukine-17 (IL-17) responses. Notably, TCR-M cells that were pre-differentiated in vitro towards a regulatory phenotype maintained a stable in vivo FOXP3 expression and anti-inflammatory activity when adoptively transferred prior to MI induction. In contrast, TCR-M cells that were pre-differentiated in vitro towards a pro-inflammatory TH17 phenotype were partially converted towards a regulatory phenotype in the injured myocardium and blunted myocardial inflammation.

Conclusions

These findings reveal that the myocardial milieu provides a suitable environment for iTreg differentiation and reveals novels mechanisms by which the healing myocardium shapes local immunological processes.
Structural basis of transcription antitermination by Qλ: NusA induces refolding of Qλ to form nozzle for RNA polymerase exit channel
Authors: Yin Zhou , Bird Jeremy G. , Kaelber Jason T. , Nickels Bryce E. , Ebright Richard H.
Published: March 2022

Lambdoid bacteriophage Q proteins are transcription antipausing and antitermination factors that enable RNA polymerase (RNAP) to read through pause and termination sites. Q proteins load onto RNAP engaged in promoter-proximal pausing at a Q binding element (QBE) and adjacent sigma-dependent pause element to yield a Q-loading complex, and translocate with RNAP as a pausing-deficient, termination-deficient Q-loaded complex. In previous work, we showed that the Q protein from bacteriophage 21 (Q21) functions by forming a “nozzle” that narrows and extends the RNAP RNA-exit channel, preventing formation of pause and termination RNA hairpins. Here, we report atomic structures of four states on the pathway of antitermination by the Q protein from bacteriophage λ (Qλ), a Q protein that shows no sequence similarity to Q21 and that, unlike Q21, requires the transcription elongation factor NusA for efficient antipausing and antitermination. We report structures of Qλ, the Qλ-QBE complex, the NusA-free “pre-engaged” Qλ-loading complex, and the NusA-containing “engaged” Qλ-loading complex. The results show that Qλ, like Q21, forms a nozzle that narrows and extends the RNAP RNA-exit channel, preventing formation of RNA hairpins. However, the results show that Qλ has no three-dimensional structural similarity to Q21, employs a different mechanism of QBE recognition than Q21, and employs a more complex process for loading onto RNAP than Q21, involving recruitment of Qλ to form a “pre-engaged” loading complex, followed by NusA-facilitated refolding of Qλ to form an “engaged” loading complex. The results establish Qλ and Q21 are not structural homologs and are solely functional analogs.

SIGNIFICANCE STATEMENT

Bacteriophage Q proteins are textbook examples of regulators of gene expression that function at the level of transcription antitermination. Here, we report structures defining the mechanism of antitermination by the Q protein of bacteriophage λ (Qλ). The results show Qλ forms a “nozzle” that narrows and extends the RNA polymerase RNA-exit channel, precluding the formation of terminator RNA hairpins. The results show Qλ exhibits no structural similarity to the Q protein of bacteriophage 21 (Q21), employs a different mechanism for DNA binding than Q21, and employs a more complex process of loading onto RNA polymerase than Q21. We conclude Qλ and Q21 are not structural homologs and are solely functional analogs, akin to a bird wing and a bat wing.
Fast synaptic-like axo-axonal transmission from striatal cholinergic interneurons onto dopaminergic fibers
Authors: Kramer Paul F. , Brill-Weil Samuel , Cummins Alex C. , Zhang Renshu , Camacho-Hernandez Gisela A. , Newman Amy H. , Eldridge Mark A. , Averbeck Bruno B. , Khaliq Zayd M.
Published: March 2022

Transmission from striatal cholinergic interneurons (CINs) controls dopamine release through nicotinic acetylcholine receptors (nAChRs) on dopaminergic axons. Anatomical studies suggest that cholinergic terminals signal predominantly through non-synaptic volume transmission. However, the influence of cholinergic transmission on electrical signaling in axons remains unclear. We examined axo-axonal transmission from CINs onto dopaminergic axons using perforated-patch recordings which revealed rapid spontaneous EPSPs with properties characteristic of fast synapses. Pharmacology showed that axonal EPSPs (axEPSPs) were mediated primarily by high-affinity α6-containing receptors. Remarkably, axEPSPs triggered spontaneous action potentials locally in dopaminergic axons, suggesting these axons perform integration to convert synaptic input into spiking, a function associated with somatodendritic compartments. We investigated cross-species validity of cholinergic axo-axonal transmission by recording dopaminergic axons in macaque putamen and found similar axEPSPs. Thus, we reveal that fast synaptic-like neurotransmission underlies cholinergic signaling onto dopaminergic axons, providing insight into how nicotinic receptors shape electrical signaling directly in axon terminals.
ChromDMM: A Dirichlet-Multinomial Mixture Model For Clustering Heterogeneous Epigenetic Data
Authors: Osmala Maria , Eraslan Gökçen , Lähdesmäki Harri
Published: March 2022

Motivation

Research on epigenetic modifications and other chromatin features at genomic regulatory elements elucidates essential biological mechanisms including the regulation of gene expression. Despite the growing number of epigenetic datasets, new tools are still needed to discover novel distinctive patterns of heterogeneous epigenetic signals at regulatory elements.

Results

We introduce ChromDMM, a product Dirichlet-multinomial mixture model for clustering genomic regions that are characterised by multiple chromatin features. ChromDMM extends the mixture model framework by profile shifting and flipping that can probabilistically account for inaccuracies in the position and strand-orientation of the genomic regions. Owing to hyper-parameter optimisation, ChromDMM can also regularise the smoothness of the epigenetic profiles across the consecutive genomic regions. With simulated data, we demonstrate that ChromDMM clusters, shifts, and strand-orients the profiles more accurately than previous methods. With ENCODE data, we show that the clustering of enhancer regions in the human genome reveals distinct patterns in several chromatin features. We further validate the enhancer clusters by their enrichment for transcriptional regulatory factor binding sites.

Availability

The software is available at https://github.com/MariaOsmala/ChromDMM
Multiplexed Label-Free Biomarker Detection by Targeted Disassembly of Variable-Length DNA Payload Chains
Authors: Aquilina Matthew , Dunn Katherine E.
Published: March 2022

Simultaneously studying different types of biomarkers (DNA, RNA, proteins, metabolites) has the potential to significantly improve understanding and diagnosis for many complex diseases. However, extracting biomarkers of different types involves using several technically complex or expensive methodologies, often requiring specialized laboratories and personnel. Streamlining detection through the use of a single multiplexed assay would greatly facilitate the process of accessing and interpreting patient biomarker data. In this work, we present a method for multiplexed biomarker detection based on variable-length DNA payload chains, which are systematically disassembled in the presence of specific biomolecular targets, leading to fragments of different sizes that yield characteristic band patterns in gel electrophoresis. This strategy has enabled us to detect with high sensitivity and specificity DNA sequences including BRCA1, an RNA sequence (miR-141) and the steroid aldosterone. We show that our assay can be multiplexed, enabling simultaneous detection of different types of biomarker. Furthermore, we show that our method suffers no loss of sensitivity when conducted in fetal bovine serum and can be applied using capillary electrophoresis, which may be more amenable to automation and integration in healthcare settings.

ToC Graphic
Lis1-dynein drives corona compaction and error-correction at kinetochores
Authors: Mitevska Olivera , Lam Pak Wing , Auckland Philip
Published: March 2022

Mitotic cell division requires that kinetochores form microtubule attachments that can segregate chromosomes and control mitotic progression via the spindle assembly checkpoint. During prometaphase, kinetochores shed a distal domain called the fibrous corona as microtubule attachments form and mature. This shedding is mediated, in part, by the minus-end directed motor dynein, which ‘strips’ kinetochore cargoes along K-fibre microtubules towards the pole. While the main molecular players are well understood, relatively little is known about how dynein stripping is regulated and how it responds to increasing microtubule occupancy. Lis1 is a conserved dynein regulator that associates with kinetochores and is mutated in the severe neurodevelopmental disease lissencephaly. Here, we have combined loss-of-function studies, high-resolution imaging and engineered separation-of-function mutants to define how Lis1 contributes to dynein-mediated corona stripping. We show that cells depleted of Lis1 fail to fully dissemble the corona and delay in metaphase as a result of persistent checkpoint activation. Furthermore, we find that while kinetochore-tethered Lis1-dynein is required for attachment error-correction, the contribution of Lis1 to corona disassembly can be mediated by a rapidly cycling cytosolic pool. These findings support the idea that Lis1 contextualises dynein function at kinetochores to maintain corona disassembly into metaphase and prevent chromosome mis-segregation.
The general anesthetic isoflurane inhibits calcium activity in cerebrovascular endothelial cells and disrupts vascular tone
Authors: Shi Lingyan , Rodríguez-Contreras Adrián
Published: March 2022

Calcium signaling in cerebrovascular endothelial cells (CVECs) has been identified to play key physiological and pathological roles in blood brain barrier function and neurovascular coupling, which involve dynamic changes in vessel diameter. However, there are no studies that measured correlated changes in vessel diameter and calcium activity in CVECs in vivo. In this study, we used the general anesthetic isoflurane (ISO) to induce a maximally dilated state in cortical blood vessels and measured the effects of the manipulation on CVEC calcium reporter activity in awake Cdh5BAC-GCaMP mice by use of two-photon fluorescence microscopy through thinned skull cranial windows. For the first time, we report dual effects of ISO on calcium activity in cerebral blood vessels of different diameter. During anesthesia induction ISO exposure triggered a short latency synchronous increase in calcium activity, followed by a period of activity suppression in small, medium, and large diameter vessels. Furthermore, during anesthesia maintenance calcium activity was desynchronized, and the relationship between vascular tone and calcium activity was disrupted in all vessel types. Based on these results we propose that there is a feedback mechanism between intracellular calcium fluctuations in CVECs and the maintenance of cerebrovascular tone.
Comparative Genome Analysis ofLactobacillus acidophilusIsolates from Different Ecological Niches
Authors: Liu Xudong , Hu Tongyuan , Lin Xiaoqian , Liang Hewei , Li Wenxi , Jin Xin , Xiao Liang , Fang Xiaodong , Zou Yuanqiang
Published: March 2022

Lactobacillus acidophilushas been extensively applied in plentiful probiotic products and is mostly found in the gastrointestinal tract, vagina, and oral cavity of human and animal, and fermented foods. Although several studies have been performed to investigate the beneficial characteristics and genome function ofL. acidophilus, comparative genomic analysis remains scarce. In this study, we collected 74L. acidophilusgenomes from our gut bacterial genome collection and the public database and conducted a comprehensive comparative genomic analysis. The analysis of average nucleotide identity (ANI), phylogenetic, gene distribution of COG and KEGG database, carbohydrates utilization, and secondary metabolites revealed the potential correlation of the genomic diversity and niches adaptation ofL. acidophilusfrom different perspectives. In addition, the pan-genome ofL. acidophiluswas found to be open, with metabolism, information storage and processing genes mainly distributed in the core genome. Phage- and peptidase-associated genes were found in the genome of the specificity of animal-derived strains, which were related to adaptation of animal gut. SNP analysis showed the differences of the utilization of Vitamin B12 in cellular ofL. acidophilusstrains from animal gut and others. This work provides new insights for the genomic diversity analysis ofLactobacillus acidophilusand uncovers the ecological adaptation of the specific strains.
Deterioration of patients with mental disorders in Denmark coinciding with the invasion of Ukraine
Authors: Østergaard Søren Dinesen , Rohde Christopher , Jefsen Oskar Hougaard
Published: March 2022

The Russian invasion of Ukraine on February 24, 2022 has led to a humanitarian crisis of immense proportions. In turn, this will, inevitably, also lead to a mental health crisis among those affected by the war - either directly or by proxy. The mental health impact of the war in Ukraine is also likely to affect people beyond the borders of the countries directly involved. Here, we investigated whether Danish patients with mental disorders seem to be affected by the war in Ukraine. Specifically, we searched the Electronic Patient Record system of the Psychiatric Services of the Central Denmark Region in the period from January 1, 2022 to March 8, 2022 for clinical notes containing the word *ukrain* (*irrespective of letters and symbols prior to- or following ukrain). We then manually assessed (read) 100 randomly drawn notes containing *ukrain* to determine whether they described worsening of the mental health/symptoms of the patients that was likely attributable to the war in Ukraine. We identified a total of 16,341 adult patients (57% women, mean age 40 years, SD=18) who were registered with at least one clinical note in the Electronic Patient Record system of the Psychiatric Services of the Central Denmark Region in the period from January 1, 2022 to March 8, 2022. During this period, 567,647 clinical notes were entered into the electronic patient record system. Among these, 502 notes from 369 unique patients contained *ukrain* with a sharp rise in incidence following the Russian invasion of Ukraine on February 24, 2022. Among the 100 randomly drawn clinical notes containing *ukrain* (stemming from 94 unique patients), 62 notes from 58 unique patients described worsening of the mental health/symptoms of the patients that seemed attributable to the war in Ukraine. Although causal inference is challenging in this regard, the results of this study suggest that even individuals remotely distanced from the war in Ukraine may be psychologically affected by it - serving as an early warning sign of the potential width of the negative mental health impact from the war, which will, inevitably, hit the Ukrainian population the hardest.
RNAseq analysis reveals prominent and distinct expressed variants that are related to disease severity in SARS-CoV-2 infected patients with mild-to-severe disease
Authors: Okendo Javan , Okanda David
Published: March 2022

Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to be a significant public health challenge globally. SARS-CoV-2 is a novel virus, and the understanding of what constitutes expressed RNAseq variants in healthy, convalescent, severe, moderate and to those admitted at the Intensive Care Unit (ICU) is yet to be presented. We set to characterize the different expressed RNAseq variants in healthy, severe, moderate, ICU, and convalescent individuals.

Materials and methods

The bulk RNA sequencing data with identifier PRJNA639275 was download from Sequence Reads Archive (SRA). The individuals were divided into: (i) healthy, n=34, severe, n=16, ICU, n=8, moderate, n=8, and convalescent, n=2. Fastqc version 0.11.9 and Cutadapt version 3.7 was used to asses the reads quality and to perform adapter trimming respectively. STAR was using to align reads to the reference genome and GATK best practice was followed to call variants using rnavar pipeline, part of the nf-core pipelines.

Results

Our analysis demonstrated that convalescent, moderate, severe and those admitted to the ICU are characterized by different sets of unique RNAseq variants. The data shows that the individuals who recover from SARS-CoV-2 infection have the same set of expressed variants as in the healthy controls. We showed that the healthy and SARS-CoV-2 infected individuals display different sets of expressed varinats which is characteristic of the patient phenotype.

Conclusion

The individuals with severe, moderate, those admitted at the ICU, and convalescent individuals display a unique set of variants. The findings in this study will inform the test kit development and SARS-CoV-2 patients classification to enhance management and control of SARS-CoV-2 infection in our population.
Sexual selection on a female copulatory device in an insect with nuptial gifts
Authors: Browne Jessica H. , Gwynne Darryl T.
Published: March 2022

Male genitalia are rapidly evolving structures, often driven sexual selection to increase fertilization success. Although sexual selection on females can be strong in systems where males provide offspring care or feed their mates, sometimes resulting in the evolution of female ornamentation, there are no actual estimates of direct sexual selection on female genitalia. In a New Zealand ground weta,Hemiandrus pallitarsis(Orthoptera: Ensifera, Anostostomatidae), females possess a genitalic device (the accessory organ) that is necessary for successful copulation and the acquisition of glandular food-gifts from males. These nutritious gifts are known to result in sexual competition among females in other ensiferan species. In ground weta, the gifts are probably important in avoiding starvation during a months-long period when caring for (their lifetime production of) eggs and offspring. Here, we test the hypothesis that the accessory organ is a sexually selected device inH. pallitarsisby measuring the female Bateman gradient and directional sexual selection on the accessory organ. Using newly developed and characterized microsatellite loci, we analyze offspring and/or stored sperm to estimate female mating frequency for the first time in ground weta. As predicted, we found positive Bateman gradients for females, and some evidence of directional sexual selection on accessory organ length. Although organ length does not correlate well with female fecundity, it may increase mating success by indicating her condition and thus quality of her offspring care.
Sex-specific role of the circadian transcription factor NPAS2 in opioid tolerance, withdrawal, and analgesia
Authors: Puig Stephanie , Shelton Micah A. , Barko Kelly , Seney Marianne L. , Logan Ryan W.
Published: March 2022

Opioids like fentanyl are the mainstay treatment for chronic pain. Unfortunately, opioids high addiction liability has led to the current opioid crisis. This is in part related to long-term use side-effects, including analgesic tolerance (gradual decrease in analgesia), and physical dependence (withdrawal symptoms upon opioid interruption), causing dose-escalation and preventing usage interruption. Altered circadian rhythmicity and sleep patterns are common in patients on opioid therapy. Prior research showed intricate bidirectional interactions between circadian rhythmicity, opioid analgesic efficacy, and side-effects. However, underlying mechanisms are largely unknown. Neuronal PAS domain protein 2 (NPAS2) is a circadian transcription factor that is highly expressed in structures of the central nervous system that modulate pain and opioids. In this study, we used male and female mice expressing non-functional NPAS2 (NPAS2 deficient, NPAS2-/-) to investigate the role of NPAS2 in fentanyl analgesia, tolerance, hyperalgesia, and dependence. In NPAS2-/- mice, we found that thermal pain thresholds, acute analgesia, and tolerance to a fixed dose of fentanyl were largely like wild-type mice. However, female NPAS2-/- mice augmented behavioral state of analgesic tolerance and exhibited significantly more behavioral symptoms of physical dependence. Conversely, only male NPAS2-/- mice had increased fentanyl-induced hypersensitivity, when compared to matched-sex littermate controls. Together, our findings suggest sex-specific effects of NPAS2 signaling in the regulation of fentanyl-induced tolerance, hyperalgesia, and dependence.
Longitudinal single cell transcriptional and epigenetic mapping of effector, memory, and exhausted CD8 T cells reveals shared biological circuits across distinct cell fates
Authors: Giles Josephine R. , Ngiow Shin Foong , Manne Sasikanth , Baxter Amy E. , Khan Omar , Wang Ping , Staupe Ryan , Abdel-Hakeem Mohamed S. , Huang Hua , Mathew Divij , Painter Mark M. , Wu Jennifer E. , Huang Yinghui Jane , Goel Rishi , Wherry E. John
Published: March 2022

Naïve CD8 T cells can differentiate into effector (TEFF), memory (TMEM), or exhausted (TEX) CD8 T cells. These developmental pathways are associated with distinct transcriptional and epigenetic changes that endow cells with different functional capacities and therefore therapeutic potential. The molecular circuitry underlying these developmental trajectories and the extent of heterogeneity within TEFF, TMEM, TEX populations remain poorly understood. Here, we used the lymphocytic choriomeningitis virus model of acutely-resolved and chronic infection and addressed these gaps by applying longitudinal scRNA-seq and scATAC-seq analysis. These analyses uncovered new subsets, including a subpopulation of TEX expressing NK cell-associated genes, as well as multiple distinct TCF1+ stem/progenitor-like subsets in acute and chronic infection. These data also revealed insights into the reshaping of TEX subsets following PD1 pathway blockade and identified a key role for the cell stress regulator, Btg1, in TEX differentiation. Finally, these results highlighted how the same biological circuits such as cytotoxicity or stem/progenitor pathways can be used by CD8 T cells with highly divergent underlying chromatin landscapes. Thus, this transcriptional and chromatin accessibility landscape map elucidates developmental biology and underlying mechanisms governing TEFF, TMEM, and TEX differentiation.