bluuebunny/crossref_metadata_2025 huggingface dataset:
ZNF91 is an endogenous repressor of the molecular phenotype associated with X-linked dystonia-parkinsonism (XDP)
Authors: Rosenkrantz Jimi L. , Raghib Sanaz , Brandorff J. Elias , Kapadia Ashni , Vaine Christine A. , Bragg D. Cristopher , Farmiloe Grace , Jacobs Frank M.J.
Published: October 2023

Background

X-linked dystonia-parkinsonism (XDP) is a severe neurodegenerative disorder resulting from the insertion of an intronic SINE-Alu-VNTR (SVA) retrotransposon in theTAF1gene. Recent research has revealed that the pathogenic XDP-SVA insertion leads to dysregulation ofTAF1transcription, including increased intron retention and decreased expression of exons surrounding the insertion. The Krüppel-associated box (KRAB) zinc finger protein, ZNF91, is a critical repressor of SVA retrotransposons. However, it remains unclear whether ZNF91 is able to repress the XDP-SVA insertion and how this influences the XDP-associated molecular phenotype. In this study, we investigate the role of ZNF91 in repressing the XDP-SVA insertion and its impact on the molecular phenotype associated with XDP.

Methods

Here, we used CRISPR/Cas9 to genetically delete ZNF91 in induced pluripotent stem cell (iPSC) lines derived from XDP patients, as well as isogenic control iPSC lines that lack the XDP-SVA insertion. Total RNA sequencing and capture RNA-sequencing were used to confirm ZNF91 deletion and to assessTAF1transcriptional changes between conditions. Furthermore, publicly available transcriptomic data from whole blood and different brain regions were used to assess ZNF91 expression levels across ages.

Results

We found that genetic deletion of ZNF91 exacerbates the molecular phenotype associated with the XDP-SVA insertion in patient cells, while no difference was observed when ZNF91 was deleted from isogenic control cells. Additionally, we observed a significant age-related reduction in ZNF91 expression in whole blood and brain, indicating a potential role of ZNF91 in the age-dependent onset of XDP.

Conclusions

These findings indicate that ZNF91 plays a crucial role in controlling the molecular phenotype associated with XDP. Since ZNF91 is a critical epigenetic repressor of SVAs, this suggests that epigenetic silencing of the XDP-SVA minimizes the severity of the molecular phenotype. Our results showing that ZNF91 expression levels significantly decrease with age provide a potential explanation for the age-related progressive neurodegenerative character of XDP. Collectively, our study provides important insights into the protective role of ZNF91 in XDP pathogenesis and suggests that modulating ZNF91 levels or targeted repression of the XDP-SVA could be novel therapeutic strategies worth exploring.
Changes in reward-induced neural activity upon Cafeteria Diet consumption
Authors: Heijkoop R. , Lalanza J.F. , Solanas M. , Álvarez-Monell A. , Subias-Gusils A. , Escorihuela R.M. , Snoeren E.M.S.
Published: October 2023

Excessive consumption of highly palatable foods rich in sugar and fat, often referred to as “junk” or “fast” foods, plays a central role in the development of obesity. The highly palatable characteristics of these foods activate hedonic and motivational mechanisms to promote food-seeking behavior and overeating, which is largely regulated by the brain reward system. Excessive junk food consumption can alter the functioning of this reward system, but exact mechanisms of these changes are still largely unknown. This study investigated whether long-term junk food consumption, in the form of Cafeteria (CAF) diet, can alter the reward system in adult, female Long-Evans rats, and whether different regimes of CAF diet influence the extent of these changes. To this end, rats were exposed to a 6-week diet with either standard chow, orad libitumdaily access to CAF diet, 30% restricted but daily access to CAF diet, or one-day-a-week (intermittent)ad libitumaccess to CAF diet, after which c-Fos expression in the Nucleus Accumbens (NAc), Prefrontal Cortex (PFC), and Ventral Tegmental Area (VTA) following consumption of a CAF reward of choice was examined. We found that all CAF diet regimes decreased c-Fos expression in the NAc-shell when presented with a CAF reward, while no changes in c-Fos expression upon the different diet regimes were found in the PFC, and possibly the VTA. Our data suggests that long-term junk food exposure can affect the brain reward system, resulting in an attenuated activity of the NAc-shell.
DrugMap: A quantitative pan-cancer analysis of cysteine ligandability
Authors: Takahashi Mariko , Chong Harrison B. , Zhang Siwen , Lazarov Matthew J. , Harry Stefan , Maynard Michelle , White Ryan , Murrey Heather E. , Hilbert Brendan , Neil Jason R. , Gohar Magdy , Ge Maolin , Zhang Junbing , Durr Benedikt R. , Kryukov Gregory , Tsou Chih-Chiang , Brooijmans Natasja , Alghali Aliyu Sidi Omar , Rubio Karla , Vilanueva Antonio , Harrison Drew , Koglin Ann-Sophie , Ojeda Samuel , Karakyriakou Barbara , Healy Alexander , Assaad Jonathan , Makram Farah , Rachman Inbal , Khandelwal Neha , Tien Pei-Chieh , Popoola George , Chen Nicholas , Vordermark Kira , Richter Marianne , Patel Himani , Yang Tzu-yi , Griesshaber Hanna , Hosp Tobias , van den Ouweland Sanne , Hara Toshiro , Bussema Lily , Dong Rui , Shi Lei , Rasmussen Martin Q. , Domingues Ana Carolina , Lawless Aleigha , Fang Jacy , Yoda Satoshi , Nguyen Linh Phuong , Reeves Sarah Marie , Wakefield Farrah Nicole , Acker Adam , Clark Sarah Elizabeth , Dubash Taronish , Fisher David E. , Maheswaran Shyamala , Haber Daniel A. , Boland Genevieve , Sade-Feldman Moshe , Jenkins Russel , Hata Aaron , Bardeesy Nabeel , Suva Mario L. , Martin Brent , Liau Brian , Ott Christopher , Rivera Miguel N. , Lawrence Michael S. , Bar-Peled Liron
Published: October 2023

Cysteine-focused chemical proteomic platforms have accelerated the clinical development of covalent inhibitors of a wide-range of targets in cancer. However, how different oncogenic contexts influence cysteine targeting remains unknown. To address this question, we have developedDrugMap, an atlas of cysteine ligandability compiled across 416 cancer cell lines. We unexpectedly find that cysteine ligandability varies across cancer cell lines, and we attribute this to differences in cellular redox states, protein conformational changes, and genetic mutations. Leveraging these findings, we identify actionable cysteines in NFκB1 and SOX10 and develop corresponding covalent ligands that block the activity of these transcription factors. We demonstrate that the NFκB1 probe blocks DNA binding, whereas the SOX10 ligand increases SOX10-SOX10 interactions and disrupts melanoma transcriptional signaling. Our findings reveal heterogeneity in cysteine ligandability across cancers, pinpoint cell-intrinsic features driving cysteine targeting, and illustrate the use of covalent probes to disrupt oncogenic transcription factor activity.
Open-source instrumented object to study dexterous object manipulation
Authors: Córdova Bulens David , du Bois de Dunilac Sophie , Delhaye Benoit , Lefèvre Philippe , Redmond Stephen J.
Published: October 2023

Humans use tactile feedback to perform skillful manipulation. When tactile sensory feedback is unavailable, for instance, if the fingers are anesthetized, dexterity is severely impaired. Imaging the deformation of the finger pad skin when in contact with a transparent plate provides information about the tactile feedback received by the central nervous system. Indeed, skin deformations are transduced into neural signals by the mechanoreceptors of the finger pad skin. Understanding how this feedback is used for active object manipulation would improve our understanding of human dexterity. In this paper, we present a new device for imaging the skin of the finger pad of one finger during manipulation performed with a precision grip. The device’s weight (300 g) makes it easy to use during unconstrained dexterous manipulation. Using this device, we reproduced the experiment performed in Delhaye et al. 2021a. We extracted the strains aligned with the object’s movement, i.e., the vertical strains in the ulnar and radial parts of the fingerpad, to see how correlated they were with the grip force (GF) adaptation. Interestingly, parts of our results differed from those in Delhaye et al. 2021a due to weight and inertia differences between the devices, with average GF across participants differing significantly. Our results highlight a large variability in the behavior of the skin across participants, with generally low correlations between strain and GF adjustments, suggesting that skin deformations are not the primary driver of GF adaptation in this manipulation scenario.

Significance statement

In this paper, we introduce a new device weighing 300 g and capable of imaging the skin of the finger pad of one finger during manipulation performed with a precision grip. This object is also capable of recording the forces and accelerations applied to the object. We reproduced the experiment performed in Delhaye et al. 2021a using this device. We extracted the strains aligned with the object’s movement to analyze how correlated these strains were with GF adaptation. The behavior of the skin across participants presented a large variability, and we observed low correlations between strain and GF adjustments in most participants. Our results suggest that skin deformations are not the primary driver of GF adaptation in this manipulation scenario.
Photoacoustic Imaging for Non-Invasive Assessment of Physiological Biomarkers of Intestinal Injury in Experimental Necrotizing Enterocolitis
Authors: Weis Jared A. , Rauh Jessica L. , Ellison Maryssa A. , Cruz-Diaz Nildris , Yamaleyeva Liliya M. , Welch Cherrie D. , Zeller Kristen A. , Weis Victoria G.
Published: October 2023

Background

Necrotizing enterocolitis (NEC) is an often-lethal disease of the premature infants’ intestinal tract that is exacerbated by significant difficulties in early and accurate diagnosis. In NEC disease, the intestine often exhibits hypoperfusion and dysmotility, which contributes to advanced disease pathogenesis. However, these physiological features cannot be accurately and quantitively assessed within the current constraints of imaging modalities frequently used in the clinic (plain film X-ray and ultrasound). We have previously demonstrated the ability of photoacoustic imaging (PAI) to non-invasively and quantitively assess intestinal tissue oxygenation and motility in a healthy neonatal rat model. As a first-in-disease application, we evaluated NEC pathogenesis using PAI to assess intestinal health biomarkers in a preclinical neonatal rat experimental model of NEC.

Methods

NEC was induced in neonatal rat pups from birth to 4 days old via hypertonic formula feeding, full-body hypoxic stress, and lipopolysaccharide administration to mimic bacterial colonization. Healthy breastfed (BF) controls and NEC rat pups were imaged at 2- and 4-days old. Intestinal tissue oxygen saturation was measured with PAI imaging for oxy- and deoxyhemoglobin levels. To measure intestinal motility, ultrasound and co-registered PAI cine recordings were used to capture intestinal peristalsis motion and contrast agent (indocyanine green) transit within the intestinal lumen. Additionally, both midplane two-dimensional and volumetric three-dimensional imaging acquisitions were assessed for oxygenation and motility.

Results

NEC pups showed a significant decrease of intestinal tissue oxygenation as compared to healthy BF controls at both ages (2-days old: 55.90% +/-3.77% vs 44.12% +/-7.18%; 4-days old: 56.13% +/-3.52% vs 38.86% +/-8.33%). Intestinal motility, assessed using a computational intestinal deformation analysis, demonstrated a significant reduction in the intestinal motility index in both early (2-day) and established (4-day) NEC. Extensive NEC damage was confirmed with histology and dysmotility was confirmed by small intestinal transit assay.

Conclusions

This study presents PAI as a successful emerging diagnostic imaging modality for both intestinal tissue oxygenation and intestinal motility disease hallmarks in a rat NEC model. PAI presents enormous significance and potential for fundamentally changing current clinical paradigms for detecting and monitoring intestinal pathologies in the premature infant.
Comparison of Tug-of-War Models Assuming Moran versus Branching Process Population Dynamics
Authors: Dinh Khanh N , Kurpas Monika Klara , Kimmel Marek
Published: October 2023

Mutations arising during cancer evolution are typically categorized as either 'drivers' or 'passengers', depending on whether they increase the cell fitness. Recently, McFarland et al. introduced the tug-of-war model for the joint effect of rare advantageous drivers and frequent but deleterious passengers. We examine this model under two common but distinct frameworks, the Moran model and the branching process. We show that frequently used statistics are similar between a version of the Moran model and the branching process conditioned on the final cell count, under different selection scenarios. We infer the selection coefficients for three breast cancer samples, resulting in good fits of the shape of their Site Frequency Spectra. All fitted values for the selective disadvantage of passenger mutations are nonzero, supporting the view that they exert deleterious selection during tumorigenesis that driver mutations must compensate.
Assembly of Protein Complexes In and On the Membrane with Predicted Spatial Arrangement Constraints
Authors: Christoffer Charles , Harini Kannan , Archit Gupta , Kihara Daisuke
Published: October 2023

Membrane proteins play crucial roles in various cellular processes, and their interactions with other proteins in and on the membrane are essential for their proper functioning. While an increasing number of structures of more membrane proteins are being determined, the available structure data is still sparse. To gain insights into the mechanisms of membrane protein complexes, computational docking methods are necessary due to the challenge of experimental determination. Here, we introduce Mem-LZerD, a rigid-body membrane docking algorithm designed to take advantage of modern membrane modeling and protein docking techniques to facilitate the docking of membrane protein complexes. Mem-LZerD is based on the LZerD protein docking algorithm, which has been constantly among the top servers in many rounds of CAPRI protein docking assessment. By employing a combination of geometric hashing, newly constrained by the predicted membrane height and tilt angle, and model scoring accounting for the energy of membrane insertion, we demonstrate the capability of Mem-LZerD to model diverse membrane protein-protein complexes. Mem-LZerD successfully performed unbound docking on 13 of 21 (61.9%) transmembrane complexes in an established benchmark, more than shown by previous approaches. It was additionally tested on new datasets of 44 transmembrane complexes and 92 peripheral membrane protein complexes, of which it successfully modeled 35 (79.5%) and 15 (16.3%) complexes respectively. When non-blind orientations of peripheral targets were included, the number of successes increased to 54 (58.7%). We further demonstrate that Mem-LZerD produces complex models which are suitable for molecular dynamics simulation. Mem-LZerD is made available athttps://lzerd.kiharalab.org.
Predictably manipulating photoreceptor light responses to reveal their role in downstream visual responses
Authors: Chen Qiang , Ingram Norianne T. , Baudin Jacob , Angueyra Juan M. , Sinha Raunak , Rieke Fred
Published: October 2023

Computation in neural circuits relies on the judicious use of nonlinear circuit components. In many cases, multiple nonlinear components work collectively to control circuit outputs. Separating the contributions of these different components is difficult, and this limits our understanding of the mechanistic basis of many important computations. Here, we introduce a tool that permits the design of light stimuli that predictably alter rod and cone phototransduction currents - including stimuli that compensate for nonlinear properties such as light adaptation. This tool, based on well-established models for the rod and cone phototransduction cascade, permits the separation of nonlinearities in phototransduction from those in downstream circuits. This will allow, for example, direct tests of how adaptation in rod and cone phototransduction affects downstream visual signals and perception.
Conifers concentrate large numbers of NLR immune receptor genes on one chromosome
Authors: Woudstra Yannick , Tumas Hayley , van Ghelder Cyril , Hung Tin Hang , Ilska Joana J. , Girardi Sebastien , A’Hara Stuart , McLean Paul , Cottrell Joan , Bohlmann Joerg , Bousquet Jean , Birol Inanc , Woolliams John A. , MacKay John J.
Published: October 2023

Nucleotide-binding domain and Leucine-rich Repeat (NLR) immune receptor genes form a major line of defence in plants, acting in both pathogen recognition and resistance machinery activation. NLRs are reported to form large gene clusters in limber pine (Pinus flexilis) but it is unknown how widespread this genomic architecture may be among the extant species of conifers (Pinophyta). We used comparative genomic analyses to assess patterns in the abundance, diversity and genomic distribution of NLR genes. Chromosome-level whole genome assemblies and high-density linkage maps in the Pinaceae, Cupressaceae, Taxaceae and other gymnosperms were scanned for NLR genes using existing and customised pipelines. Discovered genes were mapped across chromosomes and linkage groups, and analysed phylogenetically for evolutionary history. Conifer genomes are characterised by dense clusters of NLR genes, highly localised on one chromosome. These clusters are rich in TNL-encoding genes, which seem to have formed through multiple tandem duplication events. In contrast to angiosperms and non-coniferous gymnosperms, genomic clustering of NLR genes is ubiquitous in conifers. NLR-dense genomic regions are likely to influence a large part of the plant’s resistance, informing our understanding of adaptation to biotic stress and the development of genetic resources through breeding.

Plain language summary

NLR immune receptor genes are important in pest, disease and drought resistance of plants. In the giga-genomes of conifers, they concentrate on very small chromosomal regions. These regions act as important reservoirs for NLR diversity and can be used in breeding to improve the resilience of conifer trees.
Assessing nanobody interaction with SARS-CoV-2 Nsp9
Authors: Esposito Gennaro , Hunashal Yamanappa , Percipalle Mathias , Fogolari Federico , Venit Tomas , Leonchiks Ainars , Gunsalus Kristin C. , Piano Fabio , Percipalle Piergiorgio
Published: October 2023

The interaction between SARS-CoV-2 non-structural protein Nsp9 and the nanobody 2NSP90 was investigated by NMR spectroscopy using the paramagnetic perturbation methodology PENELOP (Paramagnetic Equilibrium vs Nonequilibrium magnetization Enhancement or LOss Perturbation). The Nsp9 monomer is an essential component of the replication and transcription complex (RTC) that reproduces the viral gRNA for subsequent propagation. Therefore preventing Nsp9 recruitment in RTC would represent an efficient antiviral strategy that could be applied to different coronaviruses, given the Nsp9 relative invariance. The NMR results were consistent with a previous characterization suggesting a 4:4 Nsp9-to-nanobody stoichiometry with the occurrence of two epitope pairs on each of the Nsp9 units that establish the inter-dimer contacts of Nsp9 tetramer. The oligomerization state of Nsp9 was also analyzed by molecular dynamics simulations and both dimers and tetramers resulted plausible. However a different distribution of the mapped epitopes on the tetramer surface with respect to the former 4:4 complex could also be possible, as well as different stoichiometries of the Nsp9-nanobody assemblies such as the 2:2 stoichiometry suggested by the recent crystal structure of the Nsp9 complex with 2NSP23 (PDB ID: 8dqu), a nanobody exhibiting essentially the same affinity as 2NSP90. The experimental NMR evidence, however, ruled out the occurrence in liquid state of the relevant Nsp9 conformational change observed in the same crystal structure.
A public resource of single cell transcriptomes and multiscale networks from persons with and without Alzheimer’s disease
Authors: Wang Qi , Antone Jerry , Alsop Eric , Reiman Rebecca , Funk Cory , Bendl Jaroslav , Dudley Joel T , Liang Winnie S , Karr Timothy L , Roussos Panos , Bennett David A , De Jager Philip L , Serrano Geidy E , Beach Thomas G , Keuren-Jensen Kendall Van , Mastroeni Diego , Reiman Eric M , Readhead Benjamin P
Published: October 2023

The emergence of technologies that can support high-throughput profiling of single cell transcriptomes offers to revolutionize the study of brain tissue from persons with and without Alzheimer’s disease (AD). Integration of these data with additional complementary multiomics data such as genetics, proteomics and clinical data provides powerful opportunities to link observed cell subpopulations and molecular network features within a broader disease-relevant context. We report here single nucleus RNA sequencing (snRNA-seq) profiles generated from superior frontal gyrus cortical tissue samples from 101 exceptionally well characterized, aged subjects from the Banner Brain and Body Donation Program in combination with whole genome sequences. We report findings that link common AD risk variants withCR1expression in oligodendrocytes as well as alterations in peripheral hematological lab parameters, with these observations replicated in an independent, prospective cohort study of ageing and dementia. We also observed an AD-associated CD83(+) microglial subtype with unique molecular networks that encompass many known regulators of AD-relevant microglial biology, and which are associated with immunoglobulin IgG4 production in the transverse colon. These findings illustrate the power of multi-tissue molecular profiling to contextualize snRNA-seq brain transcriptomics and reveal novel disease biology. The transcriptomic, genetic, phenotypic, and network data resources described within this study are available for access and utilization by the scientific community.
Presynaptic inhibition selectively suppresses leg proprioception in behavingDrosophila
Authors: Dallmann Chris J. , Luo Yichen , Agrawal Sweta , Chou Grant M. , Cook Andrew , Brunton Bingni W. , Tuthill John C.
Published: October 2023

Controlling arms and legs requires feedback from proprioceptive sensory neurons that detect joint position and movement. Proprioceptive feedback must be tuned for different behavioral contexts, but the underlying circuit mechanisms remain poorly understood. Using calcium imaging in behavingDrosophila, we find that the axons of position-encoding leg proprioceptors are active across behaviors, whereas the axons of movement-encoding leg proprioceptors are suppressed during walking and grooming. Using connectomics, we identify a specific class of interneurons that provide GABAergic presynaptic inhibition to the axons of movement-encoding proprioceptors. The predominant synaptic inputs to these interneurons are descending neurons, suggesting they are driven by predictions of leg movement originating in the brain. Calcium imaging from both the interneurons and their descending inputs confirmed that their activity is correlated with self-generated but not passive leg movements. Overall, our findings elucidate a neural circuit for suppressing specific proprioceptive feedback signals during self-generated movements.
Cellular rules underlying psychedelic control of prefrontal pyramidal neurons
Authors: Ekins Tyler G , Brooks Isla , Kailasa Sameer , Rybicki-Kler Chloe , Jedrasiak-Cape Izabela , Donoho Ethan , Mashour George A. , Rech Jason , Ahmed Omar J
Published: October 2023

Classical psychedelic drugs are thought to increase excitability of pyramidal cells in prefrontal cortex via activation of serotonin 2Areceptors (5-HT2ARs). Here, we instead find that multiple classes of psychedelics dose-dependently suppress intrinsic excitability of pyramidal neurons, and that extracellular delivery of psychedelics decreases excitability significantly more than intracellular delivery. A previously unknown mechanism underlies this psychedelic drug action: enhancement of ubiquitously expressed potassium “M-current” channels that is independent of 5-HT2R activation. Using machine-learning-based data assimilation models, we show that M-current activation interacts with previously described mechanisms to dramatically reduce intrinsic excitability and shorten working memory timespan. Thus, psychedelic drugs suppress intrinsic excitability by modulating ion channels that are expressed throughout the brain, potentially triggering homeostatic adjustments that can contribute to widespread therapeutic benefits.
Multilevel gene expression changes in lineages containing adaptive copy number variants
Authors: Spealman Pieter , de Santana Carolina , De Titir , Gresham David
Published: October 2023

Copy-number variants (CNVs) are an important class of recurrent variants that mediate adaptive evolution. While CNVs can increase the relative fitness of the organism, they can also incur a cost. We previously evolved populations ofSaccharomyces cerevisiaeover hundreds of generations in glutamine-limited (Gln-) chemostats and observed the recurrent evolution of CNVs at theGAP1locus. To understand the role that expression plays in adaptation, both in relation to the adaptation of the organism to the selective condition, and as a consequence of the CNV, we measured the transcriptome, translatome, and proteome of 4 strains of evolved yeast, each with a unique CNV, and their ancestor in Gln-conditions. We find CNV-amplified genes correlate with higher RNA abundance; however, this effect is reduced at the level of the proteome, consistent with post-transcriptional dosage compensation. By normalizing each level of expression by the abundance of the preceding step we were able to identify widespread divergence in the efficiency of each step in the gene in the efficiency of each step in gene expression. Genes with significantly different translational efficiency were enriched for potential regulatory mechanisms including either upstream open reading frames, RNA binding sites for SSD1, or both. Genes with lower protein expression efficiency were enriched for genes encoding proteins in protein complexes. Taken together, our study reveals widespread changes in gene expression at multiple regulatory levels in lineages containing adaptive CNVs highlighting the diverse ways in which adaptive evolution shapes gene expression.
A Novel Semi-automated Proofreading and Mesh Error Detection Pipeline for Neuron Extension
Authors: Joyce Justin , Chalavadi Rupasri , Chan Joey , Tanna Sheel , Xenes Daniel , Kuo Nathanael , Rose Victoria , Matelsky Jordan , Kitchell Lindsey , Bishop Caitlyn , Rivlin Patricia K. , Villafañe-Delgado Marisel , Wester Brock
Published: October 2023

Abstract

The immense scale and complexity of neuronal electron microscopy (EM) datasets pose significant challenges in data processing, validation, and interpretation, necessitating the development of efficient, automated, and scalable error-detection methodologies. This paper proposes a novel approach that employs mesh processing techniques to identify potential error locations near neuronal tips. Error detection at tips is a particularly important challenge since these errors usually indicate that many synapses are falsely split from their parent neuron, injuring the integrity of the connectomic reconstruction. Additionally, we draw implications and results from an implementation of this error detection in a semi-automated proofreading pipeline. Manual proofreading is a laborious, costly, and currently necessary method for identifying the errors in the machine learning based segmentation of neural tissue. This approach streamlines the process of proofreading by systematically highlighting areas likely to contain inaccuracies and guiding proofreaders towards potential continuations, accelerating the rate at which errors are corrected.
Staphylococcal and Non-typhoidalSalmonellainfection statuses in non-human mammals: A potential source of zoonoses in the Greater Accra region of Ghana
Authors: Amoah Linda Ama Owusuaa , Ameade Evans Paul Kwame , Yeboah-Ofori Benjamin , Sampane-Donkor Eric , Bimi Langbong
Published: October 2023

Background

Bacterial zoonoses are readily transmitted from animals to humans and are thrice more likely to lead to emerging or re-emerging diseases. In Ghana, there is a paucity of animal-related bacterial infection surveillance data, significantly affecting how such diseases are accurately targeted for prevention or control. This study sought to investigate the prevalence of two important bacterial infections in some common animals found in two human-dominated landscapes and ascertain if their prevalence was of imminent public health concern. In most Ghanaian communities, dogs, cats and rodents are non-human mammals that are frequently in contact with humans. As such, they were targeted during this cross-sectional study.

Methods

Biological samples collected from animals in households and veterinary institutions were processed using molecular techniques targetingStaphylococcusand Non-typhoidalSalmonellaspecies. Additionally, medical records were sourced from three (3) major health institutions to determine if cases of bacterial zoonoses were of imminent concern.

Results

Overall, the prevalence of staphylococcal and Non-typhoidalSalmonellainfections were 72.5% and 22.8%, respectively. More animals from the urban areas tested positive for Staphylococcal (χ2=5.721;p=0.017) and Non-typhoidalSalmonella(χ2=16.151;p< 0.001) infections compared to those from the peri-urban areas. The medical records also revealed that relatively higher cases of staphylococcal infections were reported within three years (2018-2020), although no significant differences were observed between the urban and peri-urban areas.

Conclusion

The high prevalence of staphylococcal infections in animals and the high number of hospital cases suggest increased exposure to this bacteria and a higher risk of persons residing in these areas to bacterial zoonoses. Data from the study also suggest that rodents are actively and inactively maintaining the cycle of these two bacterial species and as such, a source of concern. Findings underscore the need for active surveillance of bacterial species with zoonotic potential in non-human mammals regularly found in communities, which is fundamental to developing appropriate disease control strategies.
Inhibitory actions of melanin-concentrating hormone in the lateral septum
Authors: Payant Mikayla A , Spencer C Duncan , Chee Melissa J
Published: October 2023

Melanin-concentrating hormone (MCH) neurons can coexpress several neuropeptides or neurotransmitters and send widespread projections throughout the brain. Notably, there is a dense cluster of nerve terminals from MCH neurons in the lateral septum (LS) that innervate LS cells by glutamate release. The LS is also a key region integrating stress- and anxiety-like behaviours that are also emerging roles of MCH neurons. However, it is not known if the MCH peptide acts within the LS or whether MCH target sites are localized. We analysed the projections from MCH neurons in male and female mice anteroposteriorly throughout the LS and found spatial overlap between the distribution pattern of MCH-immunoreactive (MCH-ir) fibers with MCH receptorMchr1mRNA hybridization or MCHR1-ir cells. This overlap was most prominent along the ventral and lateral border of the rostral part of the LS (LSr). Most MCHR1-labeled LS neurons laid adjacent to passing MCH-ir fibers, but some MCH-ir varicosities directly contacted the soma or cilium of MCHR1-labeled LS neurons. We thus performed whole-cell patch-clamp recordings from MCHR1-rich LSr regions to determine if and how LS cells respond to MCH. Bath application of MCH to acute brain slices activated a bicuculline-sensitive chloride current that directly hyperpolarized LS cells. This MCH-mediated hyperpolarization was blocked by calphostin C and suggested that the inhibitory actions of MCH were mediated by protein kinase C-dependent activation of GABAAreceptors. Taken together, these findings defined potential hotspots within the LS that may elucidate the contributions of MCH to stress- or anxiety-related feeding behaviours.

Key points

RESEARCH QUESTION.Melanin-concentrating hormone (MCH) neurons have dense nerve terminals within the lateral septum (LS), a key region underlying stress- and anxiety-like behaviours that are emerging roles of the MCH system, but it is not known if the LS is a MCH target site.

NEUROANATOMY.We found spatial overlap between MCH-immunoreactive fibers,Mchr1mRNA, and MCHR1 protein expression especially along the lateral border of the LS.

ELECTROPHYSIOLOGY.Within MCHR1-rich regions, MCH directly inhibited LS cells by increasing a chloride conductance in a protein kinase C-dependent manner.

SIGNIFICANCE.Electrophysiological MCH effects in brain slices have been elusive and even fewer have described the mechanisms of MCH action. Our findings demonstrated, to our knowledge, the first description of MCHR1 Gq-coupling in brain slices, which was previously predicted in cell or primary culture models only. Together, these findings defined hotspots and mechanistic underpinnings for MCH effects such as in stress- and anxiety-related behaviours.
Architecture and activation of human muscle phosphorylase kinase
Authors: Yang Xiaoke , Zhu Mingqi , Lu Xue , Wang Yuxin , Xiao Junyu
Published: October 2023

The study of phosphorylase kinase (PhK)-regulated glycogen metabolism has contributed to the fundamental understanding of protein phosphorylation. Here we present the high-resolution cryo-electron microscopy structures of human muscle PhK. The 1.3-megadalton PhK α4β4γ4δ4hexadecamer consists of a tetramer of tetramer, wherein four αβγδ modules are connected by the central β4scaffold. The α- and β-subunits possess glucoamylase-like domains, but exhibit no detectable enzyme activities. The α-subunit serves as a bridge between the β-subunit and the γδ subcomplex, and facilitates the γ-subunit to adopt an autoinhibited state. Ca2+-free calmodulin (δ-subunit) binds to the γ-subunit in a compact conformation. Upon binding of Ca2+, a conformational change occurs, allowing for the de-inhibition of the γ-subunit through a spring-loaded mechanism. We also reveal an ADP-binding pocket in the β-subunit, which plays a role in allosterically enhancing PhK activity. These results provide unprecedented molecular insights of this important kinase complex.
Master transcription factor binding sites constitute the core of early replication control elements
Authors: Turner Jesse L. , Hinojosa-Gonzalez Laura , Sasaki Takayo , Uchino Satoshi , Vouzas Athanasios , Soto Mariella S. , Chakraborty Abhijit , Alexander Karen E. , Fitch Cheryl A. , Brown Amber N. , Ay Ferhat , Gilbert David M.
Published: October 2023

Eukaryotic genomes replicate in a defined temporal order called the replication timing (RT) program. RT is developmentally regulated with potential to drive cell fate transitions, but mechanisms controlling RT remain elusive. We previously identified “Early Replication Control Elements” (ERCEs) necessary for early RT, domain-wide transcription, 3D chromatin architecture and compartmentalization in mouse embryonic stem cells (mESCs) but, deletions identifying ERCEs were large and encompassed many putative regulatory elements. Here, we show that ERCEs are compound elements whose RT activity can largely be accounted for by multiple sites of diverse master transcription factor binding (subERCEs), distinguished from other such sites by their long-range interactions. While deletion of subERCEs had large effects on both transcription and RT, deleting transcription start sites eliminated nearly all transcription with moderate effects on RT. Our results suggest a model in which subERCEs respond to diverse master transcription factors by functioning both as transcription enhancers and as elements that organize chromatin domains structurally and support early RT, potentially providing a feed-forward loop to drive robust epigenomic change during cell fate transitions.
Rare Genomic Copy Number Variants Implicate New Candidate Genes for Bicuspid Aortic Valve
Authors: Carlisle Steven G. , Albasha Hasan , Michelena Hector , Sabate-Rotes Anna , Bianco Lisa , De Backer Julie , Mosquera Laura Muiño , Yetman Anji T. , Bissell Malenka M , Andreassi Maria Grazia , Foffa Ilenia , Hui Dawn S. , Caffarelli Anthony , Kim Yuli Y. , Guo Dong-Chuan , Citro Rodolfo , De Marco Margot , Tretter Justin T. , McBride Kim L. ,   EBAV Investigators,   BAVCon Investigators, Milewicz Dianna M. , Body Simon C. , Prakash Siddharth K.
Published: October 2023

Bicuspid aortic valve (BAV), the most common congenital heart defect, is a major cause of aortic valve disease requiring valve interventions and thoracic aortic aneurysms predisposing to acute aortic dissections. The spectrum of BAV ranges from early onset valve and aortic complications (EBAV) to sporadic late onset disease. Rare genomic copy number variants (CNVs) have previously been implicated in the development of BAV and thoracic aortic aneurysms. We determined the frequency and gene content of rare CNVs in EBAV probands (n = 272) using genome-wide SNP microarray analysis and three complementary CNV detection algorithms (cnvPartition, PennCNV, and QuantiSNP). Unselected control genotypes from the Database of Genotypes and Phenotypes were analyzed using identical methods. We filtered the data to select large genic CNVs that were detected by multiple algorithms. Findings were replicated in cohorts with late onset sporadic disease (n = 5040). We identified 34 large and rare (< 1:1000 in controls) CNVs in EBAV probands. The burden of CNVs intersecting with genes known to cause BAV when mutated was increased in case-control analysis. CNVs intersecting withGATA4andDSCAMwere enriched in cases, recurrent in other datasets, and segregated with disease in families. In total, we identified potentially pathogenic CNVs in 8% of EBAV cases, implicating alterations of candidate genes at these loci in the pathogenesis of BAV.

Author Summary

Bicuspid aortic valve (BAV) is the most common form of congenital heart disease and can lead to long-term complications such as aortic stenosis, aortic regurgitation, or thoracic aortic aneurysms. Most BAV-related complications arise in late adulthood, but 10-15% of individuals with BAV develop early onset complications before age 30. Copy number variants (CNVs) are genomic structural variations that have been previously implicated in some types of congenital heart disease, including BAV. Here we demonstrate that individuals with early onset complications of BAV are enriched for specific rare CNVs compared to individuals with late-onset BAV disease. We also describe novel CNVs involvingDSCAM, a gene on chromosome 21 that has not previously been associated with the development of BAV. These results may lead to improved risk stratification and targeted therapies for BAV patients.
Prospective analysis of incident disease among individuals of diverse ancestries using genetic and conventional risk factors
Authors: Wang Wei , Eriksson Nicholas , McIntyre Matthew , Quetglas Rafaela Bagur , Koelsch Bertram L. , Hinds David A. , Aslibekyan Stella , Auton Adam , Holmes Michael V. , Shringarpure Suyash S.
Published: October 2023

Background

Human genetics provides opportunities for enhancing disease prediction through polygenic risk scores (PRS).

Method

We used a dataset from 23andMe (6.77M European, 1.30M Latine, and 0.45M African American individuals). Using cross-sectional data for PRS construction and a prospective cohort for evaluation, we estimated PRS-associated cumulative incidences after one year of follow-up for 12 clinical endpoints.

Results

The cumulative incidence of disease at one year was consistently higher among individuals in the top 10% of each PRS. Relative risks (RRs) comparing top to bottom 10% of PRS differed across diseases (e.g. European RR 2.12 for eczema vs 12.53 for T2D). Estimates were similar between Europeans and Latines however were more modest for African Americans (e.g. T2D RR 10.92 for Latines vs. 4.00 for African Americans). Clinical manifestation occurred earlier among those in top vs bottom 10% of polygenic risk: 16yrs for hypertension, and 9.5yrs for T2D. Among participants at elevated conventional risk of CHD or T2D, those in the top 10% PRS had a 10-20 fold higher RR of disease incidence vs those not at conventional risk. Among individuals at high polygenic risk of CHD or T2D, favorable lifestyle characteristics associated with 64-73% lower RR of developing disease over 1-year, with cumulative incidence equivalent to the population average.

Conclusion

In an ancestrally-diverse cohort, individuals in the top 10% PRS had higher 1-year disease incidence and earlier age of clinical manifestation. PRS provided risk stratification beyond conventional risk factors. Lifestyle characteristics markedly lowered disease incidence among those at elevated polygenic risk.
Predicting new onset thought disorder in early adolescence with optimized deep learning implicates environmental-putamen interactions
Authors: de Lacy Nina , Ramshaw Michael J.
Published: October 2023

Background

Thought disorder (TD) is a sensitive and specific marker of risk for schizophrenia onset. Specifying factors that predict TD onset in adolescence is important to early identification of youth at risk. However, there is a paucity of studies prospectively predicting TD onset in unstratified youth populations.

Study Design

We used deep learning optimized with artificial intelligence (AI) to analyze 5,777 multimodal features obtained at 9-10 years from youth and their parents in the ABCD study, including 5,014 neural metrics, to prospectively predict new onset TD cases at 11-12 years. The design was replicated for all prevailing TD cases at 11-12 years.

Study Results

Optimizing performance with AI, we were able to achieve 92% accuracy and F1 and 0.96 AUROC in prospectively predicting the onset of TD in early adolescence. Structural differences in the left putamen, sleep disturbances and the level of parental externalizing behaviors were specific predictors of new onset TD at 11-12 yrs, interacting with low youth prosociality, the total parental behavioral problems and parent-child conflict and whether the youth had already come to clinical attention. More important predictors showed greater inter-individual variability.

Conclusions

This study provides robust person-level, multivariable signatures of early adolescent TD which suggest that structural differences in the left putamen in late childhood are a candidate biomarker that interacts with psychosocial stressors to increase risk for TD onset. Our work also suggests that interventions to promote improved sleep and lessen parent-child psychosocial stressors are worthy of further exploration to modulate risk for TD onset.
Automated 3D multi-color single-molecule localization microscopy
Authors: Power Rory M. , Tschanz Aline , Zimmermann Timo , Ries Jonas
Published: October 2023

Since its inception, single molecule localization microscopy (SMLM) has enabled imaging scientists to visualize biological structures with unprecedented resolution. Particularly powerful implementations capable of 3D, multi-color and high-throughput imaging have yielded key biological insights although widespread access to such technologies has been limited. The purpose of this protocol is to provide a guide for interested researchers to establish high-end SMLM in their laboratories. We detail the initial configuration and subsequent assembly of the SMLM, including instructions for alignment of all optical pathways, software/hardware integration and operation of the instrument. We describe validation steps including the preparation and imaging of test- and biological samples with structures of well-defined geometry and assist the user in troubleshooting and benchmarking performance. Additionally, we provide a walkthrough of the reconstruction of a super-resolved dataset from acquired raw images using the Super-resolution Microscopy Analysis Platform (SMAP). Depending on the instrument configuration, the cost of components is in the range $80,000 – 160,000, a fraction of the cost of a commercial instrument. A builder with some experience of optical systems is expected to require 3 - 6 months from the start of system construction to attain high-quality 3D and multi-color biological images.
Super-Resolution Imaging of Fast Morphological Dynamics of Neurons in Behaving Animals
Authors: Zhang Yujie , Bai Lu , Wang Xin , Zhao Yuchen , Zhang Tianlei , Ye Lichen , Du Xufei , Zhang Zhe , Du Jiulin , Wang Kai
Published: October 2023

Neurons are best studied in their native working states in which their functional and morphological dynamics support animals’ natural behaviors. Super-resolution microscopy can potentially reveal these dynamics in much higher details but has been challenging in behaving animals due to severe motion artifacts. Here, we report multiplexed line-scanning structured illumination microscopy, which could tolerate motions of up to 50 μm/s while achieving 150 and 100 nm lateral resolutions in its linear and nonlinear forms respectively over large fields-of-view. We continuously imaged the dynamics of spinules in dendritic spines and axonal boutons volumetrically over thousands of frames and tens of minutes in mouse brains during sleep-wake cycles. Super-resolution imaging of axonal boutons revealed their prevalent spinule dynamics on a scale of seconds. Simultaneous two-color imaging further enabled analyses of the correlation between the spatial distributions of diverse PSD-95 clusters and the structural dynamics of dendrites in the brains of awake mice.
Structural Requirements for Reverse Transcription by a Diversity-generating Retroelement
Authors: Handa Sumit , Biswas Tapan , Chakraborty Jeet , Ghosh Gourisankar , Paul Blair G. , Ghosh Partho
Published: October 2023

Diversity-generating retroelements (DGRs) create massive protein sequence variation in ecologically diverse microbes. Variation occurs during reverse transcription of a protein-encoding RNA template coupled to misincorporation at adenosines. In the prototypicalBordetellabacteriophage DGR, the template must be surrounded by upstream and downstream RNA segments for cDNA synthesis by the reverse transcriptase bRT and associated protein Avd. The function of the surrounding RNA was unknown. Cryo-EM revealed that this RNA enveloped bRT and lay over barrel-shaped Avd, forming an intimate ribonucleoprotein (RNP).

An abundance of essential interactions between RNA structural elements and bRT-Avd precisely positioned an RNA homoduplex for initiation of cDNA synthesis bycis-priming. Our results explain how the surrounding RNA primes cDNA synthesis, promotes processivity, terminates polymerization, and strictly limits mutagenesis to select proteins through mechanisms that are likely conserved in DGRs from distant taxa.
Viral envelope proteins fused to multiple distinct fluorescent reporters to probe receptor binding
Authors: Tomris Ilhan , van der Woude Roosmarijn , de Paiva Droes Rocha Rebeca , Torrents de la Peña Alba , Ward Andrew B. , de Vries Robert P.
Published: October 2023

Enveloped viruses carry one or multiple proteins with receptor binding functionalities. Functional receptors can either be glycans, proteinaceous or both, recombinant protein approaches are instrumental to gain more insight into these binding properties. Visualizing and measuring receptor binding normally entails antibody detection or direct labelling, whereas direct fluorescent fusions are attractive tools in molecular biology. Here we report a suite of different fluorescent fusions, both N- and/or C-terminal, for influenza A virus hemagglutinins and SARS-CoV-2 spike RBD. The proteins contained a total of three or six fluorescent protein barrels and were applied directly to cells to determine receptor binding properties.