bluuebunny/crossref_metadata_2025 huggingface dataset:
Nearly half of adults with symptoms of sexually transmitted infections (STIs) did not seek clinical care: A population-based study of treatment-seeking behavior among adults in Rakai, Uganda
Authors: Ogale Yasmin P. , Kennedy Caitlin E. , Nalugoda Fred , Mpagazi Josephine , Jackson Jade C. , Galiwango Ronald , Ssekubugu Robert , Kigozi Godfrey , Denison Julie A. , Gaydos Charlotte A. , Kagaayi Joseph , Grabowski M. Kathryn
Published: February 2023

Understanding treatment-seeking behavior is critical to the treatment and control of sexually transmitted infections (STIs), yet current data on STI treatment-seeking in low-resource settings is scarce. This study aims to describe STI treatment-seeking behavior and identify factors associated with seeking treatment at a clinic among adults with STI-related symptoms in rural Uganda. The STI prevalence study (STIPS) conducted a population-based survey and STI testing among all consenting adults aged 18–49 in two communities in rural south-central Uganda. Of 1,825 participants, 962 individuals self-reported STI symptoms in the past six months; we present descriptive data on treatment-seeking and STI prevalence among these individuals. We used multivariable Poisson regressions with robust variance to determine the sociodemographic and symptom-related factors independently associated with seeking STI treatment at a clinic and assessed the association with previous clinic treatment-seeking and current STI diagnosis. Forty-three percent of adults who reported STI-related symptoms in the past six months said they did not seek any treatment. Among those who did, 58% sought treatment at a private clinic, 28% at a government clinic, 9% at a pharmacy/drug store, 3% at a traditional healer, 2% at a market/shop, and 5% at another location. Among both men and women, having multiple STI related symptoms was positively associated with clinic treatment seeking (men=PRR: 1.73, 95%CI: 1.36-2.21; women=PR: 1.41, 95%CI: 1.12-1.78). Approximately one-third of men and women who reported previously seeking clinic treatment for their symptoms were diagnosed with a curable STI at the time of the survey. In this setting, nearly half of adults with STI-related symptoms are not seeking clinical care and many who report having sought treatment recent STI symptoms have curable STIs. Future studies should explore barriers to care-seeking and strategies to improve STI services.
Systematic identification of structure-specific protein–protein interactions
Authors: Holfeld Aleš , Schuster Dina , Sesterhenn Fabian , Stalder Patrick , Haenseler Walther , Barrio-Hernandez Inigo , Ghosh Dhiman , Vowles Jane , Cowley Sally A. , Nagel Luise , Khanppnavar Basavraj , Beltrao Pedro , Korkhov Volodymyr M. , Riek Roland , Souza Natalie de , Picotti Paola
Published: February 2023

Protein–protein interactions (PPIs) mediate numerous essential functions and regulatory events in living organisms. The physical interactome of a protein can be abnormally altered in response to external and internal cues, thus modulating cell physiology and contributing to human disease. In particular, neurodegenerative diseases due to the accumulation of aberrantly folded and aggregated proteins may lead to alterations in protein interactomes. Identifying changes in the interactomes of normal and disease states of proteins could help to understand molecular disease mechanisms, but current interactomics methods are limited in the ability to pinpoint structure-specific PPIs and their interaction interfaces on a proteome-wide scale. Here, we adapted limited proteolysis–mass spectrometry (LiP–MS) to systematically identify putative structure-specific PPIs by probing protein structural alterations within cellular extracts upon treatment with specific structural states of a given protein. We demonstrate the feasibility of our method to detect well-characterized PPIs, including antibody–target protein interactions and interactions with membrane proteins, and show that it pinpoints PPI interfaces. We then applied the LiP–MS approach to study the structure-specific interactors of the Parkinson’s disease hallmark protein alpha-synuclein (aSyn). We identified several previously known interactors of both aSyn monomer and amyloid fibrils and provide a resource of novel putative structure-specific interactors for further studies. This approach is applicable to identify structure-specific interactomes of any protein, including posttranslationally modified and unmodified, or metabolite-bound and unbound structural states of proteins.
RGS14 is neuroprotective against seizure-induced mitochondrial oxidative stress and pathology in hippocampus
Authors: Harbin Nicholas H , Lustberg Daniel J , Hurst Cheyenne , Pare Jean-Francois , Crotty Kathryn M , Waters Alaina L , Yeligar Samantha M , Smith Yoland , Seyfried Nicholas T , Weinshenker David , Hepler John R
Published: February 2023

RGS14 is a complex multifunctional scaffolding protein that is highly enriched within pyramidal cells (PCs) of hippocampal area CA2. There, RGS14 suppresses glutamate-induced calcium influx and related G protein and ERK signaling in dendritic spines to restrain postsynaptic signaling and plasticity. Previous findings show that, unlike PCs of hippocampal areas CA1 and CA3, CA2 PCs are resistant to a number of neurological insults, including degeneration caused by temporal lobe epilepsy (TLE). While RGS14 is protective against peripheral injury, similar roles for RGS14 during pathological injury in hippocampus remain unexplored. Recent studies show that area CA2 modulates hippocampal excitability, generates epileptiform activity and promotes hippocampal pathology in animal models and patients with TLE. Because RGS14 suppresses CA2 excitability and signaling, we hypothesized that RGS14 would moderate seizure behavior and early hippocampal pathology following seizure activity. Using kainic acid (KA) to induce status epilepticus (KA-SE) in mice, we show loss of RGS14 (RGS14 KO) accelerated onset of limbic motor seizures and mortality compared to wild type (WT) mice, and that KA-SE upregulated RGS14 protein expression in CA2 and CA1 PCs of WT. Utilizing proteomics, we saw loss of RGS14 impacted the expression of a number of proteins at baseline and after KA-SE, many of which associated unexpectedly with mitochondrial function and oxidative stress. RGS14 was shown to localize to the mitochondria in CA2 PCs of mice and reduce mitochondrial respirationin vitro. As a readout of oxidative stress, we found RGS14 KO dramatically increased 3-nitrotyrosine levels in CA2 PCs, which was greatly exacerbated following KA-SE and correlated with a lack of superoxide dismutase 2 (SOD2) induction. Assessing for hallmarks of seizure pathology in RGS14 KO, we observed worse neuronal injury in area CA3 (but none in CA2 or CA1), and a lack of microgliosis in CA1 and CA2 compared to WT. Together, our data demonstrates a newly appreciated neuroprotective role for RGS14 against intense seizure activity in hippocampus. Our findings are consistent with a model where, after seizure, RGS14 is upregulated to support mitochondrial function and prevent oxidative stress in CA2 PCs, limit seizure onset and hippocampal neuronal injury, and promote microglial activation in hippocampus.
Isolating objective and subjective filling-in using the Drift Diffusion Model
Authors: Dekel Ron , Sagi Dov , Zomet Ativ , Levi Dennis M. , Polat Uri
Published: February 2023

Spatial context is known to influence the behavioral sensitivity (d’) and the decision criterion (c) for detection of low-contrast targets. Of interest here is the effect on the decision criterion. Polat and Sagi (2007) demonstrated that for a Gabor target positioned between two similar co-aligned high contrast flankers, observers’ reports of seeing the target (Hit and False-Alarm) decreased with increasing target-flankers distance. This effect was more pronounced when distance was randomized within testing blocks compared to when it was fixed. According to Signal-Detection-Theory (SDT), the latter result suggests that the decision-criterion is adjusted to a specific, distance-dependent combination of signal (S) and Noise (N) when the S and N statistics are fixed, but not when they vary across trials. However, SDT cannot differentiate between changes in the decision-bias (criterion-shift) and changes introduced by variations in S and N (signal-shift). To circumvent this limitation of SDT, we analyze reaction-time data (RT) within the framework of the Drift-Diffusion-Model (DDM). We performed an RT analysis of target-flanker interactions using data from Polat & Sagi (2007) and Zomet et al. (2008; 2016). The analysis revealed a stronger dependence on flankers for faster RTs and a weaker dependence for slower RTs. The results are explained by DDM, where an evidence accumulation process depends on the flankers via a change in the rate of the evidence (signal-shift), and on observers’ prior via a change in the starting point (criterion-shift), leading to RT-independent and RT-dependent effects, respectively. The RT-independent distance-dependent response-bias is attributed to the observers’ inability to learn multiple internal distributions required to accommodate the distance-dependent effects of the flankers on both the Signal and Noise.
Lung viral infection modelling in a bioengineered whole-organ
Authors: Tommasini Fabio , Benoist Thomas , Shibuya Soichi , Woodall Maximillian N.J. , Naldi Eleonora , Orr Jessica C. , Giobbe Giovanni Giuseppe , Maughan Elizabeth F. , Hynds Robert E. , Gjinovci Asllan , Hutchinson J. Ciaran , Arthurs Owen J. , Janes Sam M. , Elvassore Nicola , Smith Claire M. , Michielin Federica , Pellegata Alessandro Filippo , De Coppi Paolo
Published: February 2023

Lung infections are one of the leading causes of death worldwide, and this situation has been exacerbated by the emergence of COVID-19. Pre-clinical modelling of viral infections has relied on cell cultures that lack 3D structure and the context of lung extracellular matrices. Here, we propose a bioreactor-based, whole-organ lung model of viral infection. The bioreactor takes advantage of an automated system to achieve efficient decellularization of a whole rat lung, and recellularization of the scaffold using primary human bronchial cells. Automatization allowed for the dynamic culture of airway epithelial cells in a breathing-mimicking setup that led to an even distribution of lung epithelial cells throughout the distal regions. In the sealed bioreactor system, we demonstrate proof-of-concept for viral infection with the engineered lung by infecting primary human airway epithelial cells. Moreover, to assess the possibility of drug screening in this model, we demonstrate the efficacy of the broad-spectrum antiviral Remdesivir. This whole-organ scale lung infection model represents a step towards modelling viral infection of human cells in a 3D context, providing a powerful tool to investigate the mechanisms of the early stages of pathogenic infections and the development of effective treatment strategies for respiratory diseases.
Risk assessment during nest defense against three simulated predators by female northern house wrens (Troglodytes aedon)
Authors: Eggleston Ross C. , Fornara Josephina H. , Davis Kyle M. , Dong Jess , Reichard Dustin G.
Published: February 2023

Offspring predation is one of the greatest obstacles to an organism’s reproductive success, but parents vary in the strength of their response to potential predators. One explanation for this variable investment is that defending current offspring has the potential to lower future reproductive success if the predator is also capable of injuring or killing the parent. Northern house wrens (Troglodytes aedon) are cavity-nesting songbirds that defend against multiple species of nest predators including small mammals, birds of prey, and snakes. Here, we used three different predator decoys: two nest predators - an eastern chipmunk (Tamias striatus) and an eastern ratsnake (Pantherophis alleghaniensis) - as well as a predator of both offspring and adults - a juvenile Cooper’s hawk (Accipiter cooperi) - to elicit nest defense and test whether females use risk assessment to modulate their antipredator behavior. We found that antipredator behaviors were not significantly different between the two nest predators, which posed a high risk to the nestlings, but lower risk to the parents as neither species frequently captures adult wrens outside the nest box. However, female wrens never dove at or attacked the Cooper’s hawk while they frequently attacked both the snake and chipmunk decoys. Neighboring house wrens from adjacent territories were also less likely to respond to the hawk, but more heterospecifics mobbed the hawk than the snake decoy. Collectively, these results show that risk assessment and the strength of the antipredator response varies substantially both within and among species. Female house wrens exhibit plasticity in their nest defense behavior, and they respond to different types of predators in a way that could maximize lifetime fitness while risking the loss of their current offspring.
Nociceptor neuroimmune interactomes reveal cell type- and injury-specific inflammatory pain pathways
Authors: Jain Aakanksha , Gyori Benjamin M. , Hakim Sara , Bunga Samuel , Taub Daniel G , Ruiz-Cantero Mari Carmen , Tong-Li Candace , Andrews Nicholas , Sorger Peter K , Woolf Clifford J
Published: February 2023

Inflammatory pain associated with tissue injury and infections, results from the heightened sensitivity of the peripheral terminals of nociceptor sensory neurons in response to exposure to inflammatory mediators. Targeting immune-derived inflammatory ligands, like prostaglandin E2, has been effective in alleviating inflammatory pain. However, the diversity of immune cells and the vast array of ligands they produce make it challenging to systematically map all neuroimmune pathways that contribute to inflammatory pain. Here, we constructed a comprehensive and updatable database of receptor-ligand pairs and complemented it with single-cell transcriptomics of immune cells and sensory neurons in three distinct inflammatory pain conditions, to generate injury-specific neuroimmune interactomes. We identified cell-type-specific neuroimmune axes that are common, as well as unique, to different injury types. This approach successfully predicts neuroimmune pathways with established roles in inflammatory pain as well as ones not previously described. We found that thrombospondin-1 produced by myeloid cells in all three conditions, is a negative regulator of nociceptor sensitization, revealing a non-canonical role of immune ligands as an endogenous reducer of peripheral sensitization. This computational platform lays the groundwork to identify novel mechanisms of immune-mediated peripheral sensitization and the specific disease contexts in which they act.
crossing3dforest: an R package for evaluating empty space structure in forest ecosystems
Authors: Puletti Nicola , Castronuovo Rossella , Ferrara Carlotta
Published: February 2023

Traditionally, forest structure is mostly described by vegetative elements; however, the complementary empty space also contributes to the forest spatial structure.

We developed an R package (crossing3dforest) to support the entire processing of Terrestrial Laser Scanning point clouds to quantify the size, shape, and connectivity of empty spaces within the mid and low strata of forest stands, using an approach based on the percolation theory. The package functions, which are designed for step-by-step single stand analysis, can be executed sequentially in a pipeline.

A case study is presented to demonstrate thecrossing3dforestpotentials for characterising the forest empty space architecture. TLS point clouds collected in ten different pure beech (Fagus sylvatica L.) stands, representative of five distinct forest management regimes, were analysed and characterised.

The adopted empty space approach can be integrated into forest structural analysis to identify animal-habitat associations and establish appropriate habitat structure for wildlife management.

Graphical abstract
Stroke induces early recurrent vascular events by inflammasome-dependent atherosclerotic plaque rupture
Authors: Cao Jiayu , Roth Stefan , Zhang Sijia , Kopczak Anna , Georgakis Marios K. , Li Xinghai , Dutsch Alexander , Liman Thomas G , Endres Matthias , Brough David , Green Jack P. , Wernsdorf Saskia , Fürle Christina , Carofiglio Olga , Zhu Jie , Asare Yaw ,   DEMDAS Study Group, Dichgans Martin , Sager Hendrik B. , Große Gerrit M. , Liesz Arthur
Published: February 2023

The risk of early recurrent events after stroke remains high despite currently established secondary prevention strategies. Risk is particularly high in patients with atherosclerosis, with more than 10% of patients experiencing early recurrent events. However, despite the enormous medical burden of this clinical phenomenon, the underlying mechanisms leading to increased vascular risk and recurrent stroke are largely unknown. Here, using a novel mouse model of stroke-induced recurrent ischemia, we show that stroke leads to activation of the AIM2 inflammasome in vulnerable atherosclerotic plaques via an increase of circulating cell-free DNA from the ischemic tissue. Enhanced plaque inflammation post-stroke results in plaque destabilization and atherothrombosis, finally leading to arterio-arterial embolism and recurrent stroke within days after the index stroke. We confirm key steps of plaque destabilization also after experimental myocardial infarction and in carotid artery plaque samples from patients with acute stroke. Neutralization of cell-free DNA by DNase treatment or inhibition of inflammasome activation reduced the rate of stroke recurrence after experimental stroke. Our findings present an explanation for the high recurrence rate after incident ischemic events in atherosclerotic patients. The detailed mechanisms uncovered here provide so far clinically uncharted therapeutic targets for which we show high efficacy to prevent recurrent events. Targeting DNA-mediated inflammasome activation after remote tissue injury represents a promising avenue for further clinical development in the prevention of early recurrent events.
Aromatic amino acids in the finger domain of the FMRFamide-gated Na+channel are involved in the FMRFamide recognition and the activation
Authors: Furukawa Yasuo , Tagashira Iori
Published: February 2023

FMRFamide-gated Na+channel (FaNaC) is a member of the DEG/ENaC family and activated by a neuropeptide, FMRFamide. Structural information about the FMRFamide-dependent gating is, however, still elusive. Because two phenylalanines of FMRFamide are essential for the activation of FaNaC, we hypothesized that aromatic-aromatic interaction between FaNaC and FMRFamide is critical for FMRFamide recognition and/or the activation gating. Here, we focused on eight conserved aromatic residues in the finger domain of FaNaCs and tested our hypothesis by mutagenic analysis andin silicodocking simulations The mutation of conserved aromatic residues in the finger domain reduced the FMRFamide potency, the extent of which were dependent on the mutated position, suggesting that the conserved aromatic residues are more or less involved in the FMRFamide-dependent activation. The kinetics of the FMRFamide-gated currents were also modified substantially in some mutants. The docking simulations revealed the aromatic-aromatic interaction between some conserved aromatic residues in FaNaC and FMRFamide. Collectively, our results suggest that the conserved aromatic residues in the finger domain of FaNaC are important determinants of the ligand recognition and/or the activation gating in FaNaC.
The unknown lipids project: harmonized methods improve compound identification and data reproducibility in an inter-laboratory untargeted lipidomics study
Authors: Shen Tong , Conway Ciara , Rempfert Kaitlin R. , Kyle Jennifer E. , Colby Sean M. , Gaul David A. , Habra Hani , Kong Fanzhou , Bloodsworth Kent J. , Allen Douglas , Evans Bradley S. , Du Xiuxia , Fernandez Facundo M. , Metz Thomas O. , Fiehn Oliver , Evans Charles R.
Published: February 2023

Untargeted lipidomics allows analysis of a broader range of lipids than targeted methods and permits discovery of unknown compounds. Previous ring trials have evaluated the reproducibility of targeted lipidomics methods, but inter-laboratory comparison of compound identification and unknown feature detection in untargeted lipidomics has not been attempted. To address this gap, five laboratories analyzed a set of mammalian tissue and biofluid reference samples using both their own untargeted lipidomics procedures and a common chromatographic and data analysis method. While both methods yielded informative data, the common method improved chromatographic reproducibility and resulted in detection of more shared features between labs. Spectral search against the LipidBlast in silico library enabled identification of over 2,000 unique lipids. Further examination of LC-MS/MS and ion mobility data, aided by hybrid search and spectral networking analysis, revealed spectral and chromatographic patterns useful for classification of unknown features, a subset of which were highly reproducible between labs. Overall, our method offers enhanced compound identification performance compared to targeted lipidomics, demonstrates the potential of harmonized methods to improve inter-site reproducibility for quantitation and feature alignment, and can serve as a reference to aid future annotation of untargeted lipidomics data.
Cognitive reserve counteracts typical neural activity changes related to ageing
Authors: Cespón Jesús , Chupina Irina , Carreiras Manuel
Published: February 2023

Studies have shown that older adults with high Cognitive Reserve (HCR) exhibit better executive functioning than their low CR (LCR) counterparts. However, the neural processes linked to those differences are unclear. This study investigates (1) the neural processes underlying enhanced executive functions in older adults with HCR and (2) how executive control differences are modulated by task difficulty. We recruited 74 participants, who performed two executive control tasks with different difficulty levels while recording the electroencephalogram. The accuracy on both tasks requiring inhibition of irrelevant information was better in the HCR than the LCR group. Also, in the more demanding task, event-related potentials (ERP) latencies related to inhibition and working memory update were faster in HCR than LCR. Moreover, the HCR, but not the LCR, showed larger P300 amplitude in parietal than frontal regions and in the left than right hemisphere, suggesting a posterior to anterior shift of activity and loss of inter-hemispheric asymmetries in LCR participants. These results suggest that high CR counteracts neural activity changes related to ageing. Thus, high levels of CR can be related to maintenance of neural activity patterns typically observed in young adults rather than to deployment of neural compensatory mechanisms.
Near-optimal integration of the magnitude Information of time and numerosity
Authors: Otsuka Taku , Yotsumoto Yuko
Published: February 2023

Magnitude information is often correlated in the external world, providing complementary information about the environment. As if to reflect this relationship, the perceptions of different magnitudes (e.g., time and numerosity) are known to influence one another. Recent studies suggest that such magnitude interaction is similar to cue integration, such as multisensory integration. Here, we tested whether human observers could integrate the magnitudes of two quantities with distinct physical units (i.e., time and numerosity) as abstract magnitude information. The participants compared the magnitudes of two visual stimuli based on time, numerosity, or both. Consistent with the predictions of the maximum likelihood estimation (MLE) model, the participants integrated time and numerosity in a near-optimal manner; the weights for numerosity increased as the reliability of the numerosity information increased, and the integrated estimate was more reliable than either the time or numerosity estimate. Furthermore, the integration approached a statistical optimum as the temporal discrepancy of the acquisition of each piece of information became smaller. These results suggest that magnitude interaction arises through a similar computational mechanism to cue integration. They are also consistent with the idea that different magnitudes are processed by a generalized magnitude system.
Corroborating age with oxygen isotope profiles in otoliths: consequences for estimation of growth, productivity and management reference points in northern pike (Esox lucius)in the southern Baltic Sea
Authors: Rittweg Timo D. , Trueman Clive , Ehrlich Elias , Wiedenbeck Michael , Arlinghaus Robert
Published: February 2023

Accurate and precise age estimates are crucial for assessing the life-history of fish and providing management advice for fisheries, but age validation studies remain rare or absent in many species. Aging from scales is common, as it is non-lethal, but potential for underaging old fish exists. Using 85 northern pike (Esox lucius) collected from the southern Baltic Sea in Germany as a model, we corroborated age readings based on annual cycles of oxygen isotopes (δ18O) in otoliths to infer the timing and validity of growth, so as to compare results with visual age estimations from scales and otoliths. Otoliths were accurate and precise, while age readings from scales systematically underestimated the age of old pike. Fitting population-level von Bertalanffy growth models to the size-at-age data estimated viaδ18O-profiling, otoliths or scales revealed a larger terminal length (L∞) and a lower body growth coefficientkin scale-aged fish compared to otolith and corroborated age data. Populating an age-structured model with structure-specific growth model parameters demonstrated that the maximum sustainable yield (MSY) was estimated to be about 37% lower using scale-informed growth models relative to growth models fitted to corroborated and otolith-based size-at-age data. Thus, pike populations assessed and modeled based on scale age readings might appear less productive than they really are. Using scale-based ages to inform management regulations may therefore result in too conservative management and lost biomass yield, while instilling unrealistic angler expectations as to the trophy potential of the fishery.
Effect of crocin and treadmill exercise on oxidative stress and heart damage in diabetic rats
Authors: Pourmousavi Laleh , Asadi Rasoul Hashemkandi , Zehsaz Farzad , Jadidi Roghayeh Pouzesh
Published: February 2023

Objective

in diabetes the production of free radicals and inflammatory agents in the heart tissue is increased and the expression of genes associated with the induction of apoptosis is altered. Considering the importance of common cardiovascular disorders in diabetes, this study investigated the effect of eight weeks of aerobic exercise and kerosene use alone, as well as tissue damage and oxidative stress caused by diabetes in the heart of adult rats.

Materials and Methods

To induce diabetes, streptozotocin 50 mg/kg was injected as a single dose intraperitoneally. After 72 hours, blood glucose levels were monitored by a glucometer, and blood glucose above 250 mg/dl was considered diabetes. Continuous treadmill exercise was performed for eight weeks by placing the animal on the treadmill. Next, the animals were anesthetized, and samples were taken from the hearts and frozen in liquid nitrogen. Then, superoxide dismutase (SOD), glutathione peroxidase (GPx), and malondialdehyde (MDA) were measured in the cardiac tissue. Finally, the hearts of half of the animals were immediately immersed in formalin solution for histological changes.

Results

According to our findings, diabetes increased lipid peroxidation, which was characterized by increased MDA levels in the control diabetes group and decreased SOD and GPx levels (P<0.05). It also changes the balance of expression of genes associated with apoptosis control, increased Bcl-2-associated X (Bax) expression, and decreased Bcl-2 expression (P <0.05). Also, we observed the induction of apoptosis in cardiac tissue. Using eight weeks of continuous exercise and administration of crocin significantly reduced blood sugar levels and lipid peroxidation and increased the activity of antioxidant enzymes and Bcl- 2 gene expression compared to the diabetes control group. In addition, continuous exercise and kerosene improved the oxidative stress parameters in the control group.

Conclusions

The results of this study showed that diabetes could cause oxidative stress and heart dysfunction. Moreover, simultaneously and separately, aerobic exercise with treadmill and crocin administration can reduce these disorders and prevent apoptosis in the heart tissue.
Benchmarking algorithms for joint integration of unpaired and paired single-cell RNA-seq and ATAC-seq data
Authors: Lee Michelle Y. Y. , Kaestner Klaus H. , Li Mingyao
Published: February 2023

Single-cell RNA-sequencing (scRNA-seq) measures gene expression in single cells, while single-nucleus ATAC-sequencing (snATAC-seq) enables the quantification of chromatin accessibility in single nuclei. These two data types provide complementary information for deciphering cell types/states. However, when analyzed individually, scRNA-seq and snATAC-seq data often produce conflicting results regarding cell type/state assignment. In addition, there is a loss of power as the two modalities reflect the same underlying cell types/states. Recently, it has become possible to measure both gene expression and chromatin accessibility from the same nucleus. Such paired data make it possible to directly model the relationships between the two modalities. However, given the availability of the vast amount of single-modality data, it is desirable to integrate the paired and unpaired single-modality data to gain a comprehensive view of the cellular complexity. Here, we benchmarked the performance of seven existing single-cell multi-omic data integration methods. Specifically, we evaluated whether these methods are able to uncover peak-gene associations from single-modality data, and to what extent the multiome data can provide additional guidance for the analysis of the existing single-modality data. Our results indicate that multiome data are helpful for annotating single-modality data, but the number of cells in the multiome data is critical to ensure a good cell type annotation. Additionally, when generating a multiome dataset, the number of cells is more important than sequencing depth for cell type annotation. Lastly, Seurat v4 is the best at integrating scRNA-seq, snATAC-seq, and multiome data even in the presence of complex batch effects.
Aryl hydrocarbon receptor knockout accelerates PanIN formation and fibro-inflammation in a mutantKras-driven pancreatic cancer model
Authors: Walcheck Morgan T. , Schwartz Patrick B. , Carrillo Noah D. , Matkowsky Kristina A. , Nukaya Manabu , Bradfield Christopher A. , Ronnekleiv-Kelly Sean M.
Published: February 2023

Objectives

The pathogenesis of pancreas cancer (PDAC) remains poorly understood, hindering efforts to develop a more effective therapy for PDAC. Recent discoveries show the aryl hydrocarbon receptor (AHR) plays a crucial role in the pathogenesis of several cancers, and can be targeted for therapeutic effect. However, its involvement in PDAC remains unclear. Therefore, we evaluated the role of AHR in the development of PDACin vivo.

Methods

We created a global AHR-null, mutantKras-driven PDAC mouse model (A-/-KC) and evaluated the changes in PDAC precursor lesion formation (Pan-IN 1, 2, and 3) and associated fibro-inflammation between KC and A-/-KC at 5 months of age. We then examined the changes in the immune microenvironment followed by single-cell RNA-sequencing analysis to evaluate concomitant transcriptomic changes.

Results

We found a significant increase in PanIN-1 lesion formation and PanIN-1 associated fibro-inflammatory infiltrate in A-/-KC vs KC mice. This was associated with significant changes in the adaptive immune system, particularly a decrease in the CD4+/CD8+ T-cell ratio, as well as a decrease in the T-regulatory/Th17 T-cell ratio suggesting unregulated inflammation.

Conclusion

These findings show the loss of AHR results in heightenedKras-induced PanIN formation, through modulation of immune cells within the pancreatic tumor microenvironment.
Systematic comparison of temporal transcriptional responses to hepatotoxicants in primary human hepatocytes and HepaRG cells using concentration-response modelling of gene co-expression networks
Authors: Kunnen Steven J. , Arnesdotter Emma , Willenbockel Christian Tobias , Vinken Mathieu , van de Water Bob
Published: February 2023

Next generation risk assessment of chemicals revolves around the use of mechanistic information without animal experimentation. In this regard, toxicogenomics has proven to be a useful tool to elucidate the underlying mechanisms of adverse effects of xenobiotics. In the present study, two widely used humanin vitrohepatocyte culture systems, namely primary human hepatocytes (PHH) and human hepatoma HepaRG cells, were exposed to liver toxicants known to induce liver cholestasis, steatosis or necrosis. Benchmark concentration-response modelling was applied to transcriptomics gene co-expression networks (modules) in order to derive benchmark concentrations (BMCs) and to gain mechanistic insight into the hepatotoxic effects. BMCs derived by concentration-response modelling of gene co-expression modules recapitulated concentration-response modelling of individual genes. Although PHH and HepaRG cells showed overlap in deregulated genes and modules by the liver toxicants, PHH demonstrated a higher responsiveness, based on the lower BMCs of co-regulated gene modules. Such BMCs can be used as point of departure (PoD) for assessing module-associated cellular (stress) pathways/processes. This approach identified clear PoDs of around Cmaxlevels for the tested drugs, while for cosmetics ingredients the BMCs were 10-100 fold higher than the estimated plasma concentrations. This approach could serve next generation risk assessment practice to identify early responsive modules at low BMCs, that could be linked to key events in liver adverse outcome pathways. In turn, this can assist in delineating potential hazards of new test chemicals usingin vitrosystems and used in a risk assessment when BMCs are paired with chemical exposure assessment.
A chemoproteomic platform for reactive fragment profiling against the deubiquitinases
Authors: Cookson Rosa , Vuorinen Aini , Pettinger Jonathan , Kennedy Cassandra R. , Kirkpatrick Joanna M. , Peltier-Heap Rachel E. , Powell Andrew , Snijders Ambrosius P. , Skehel Mark , House David , Rittinger Katrin , Bush Jacob T.
Published: February 2023

Chemoproteomics is a powerful method capable of detecting interactions between small molecules and the proteome, however its use as a high-throughput screening method for chemical libraries has so far been limited. To address this need, we have further developed a chemoproteomics workflow to screen cysteine reactive covalent fragments in cell lysates against the deubiquitinating (DUB) enzymes using activity-based protein profiling. By using targeted ubiquitin probes, we have addressed sensitivity and affinity limitations, enabling target identification and covalent fragment library profiling in a 96-well plate format. The use of data independent acquisition (DIA) methods for MS analysis combined with automated Evosep liquid chromatography (LC) reduced instrument runtimes to 21 minutes per sample and simplified the workflow. In this proof-of-concept study, we have profiled 138 covalent fragments against 57 DUB proteins and validated four hit fragments against OTUD7B and UCHL3 through site identification experiments and orthogonal biochemical activity assays.

Graphical abstract
Environment Modulates Protein Heterogeneity Through Transcriptional and Translational Stop Codon Miscoding
Authors: Romero Romero Maria Luisa , Kirilenko Anastasiia , Poehls Jonas , Richter Doris , Jumel Tobias , Shevchenko Anna , Toth-Petroczy Agnes
Published: February 2023

Stop codon miscoding events give rise to longer proteins, which may alter the protein’s function and thereby generate short-lasting phenotypic variability from a single gene.

In order to systematically assess the frequency and origin of stop codon miscoding events, we designed a library of reporters. We introduced premature stop codons into mScarlet that enabled high-throughput quantification of protein synthesis termination errors inE.coliusing fluorescent microscopy. We found that under stress conditions, stop codon miscoding may occur with a rate as high as 80%, depending on the nucleotide context, suggesting that evolution frequently samples stop codon miscoding events. The analysis of selected reporters by mass spectrometry and RNA-seq showed that not only translation but also transcription errors contribute to stop codon miscoding. The RNA polymerase is more likely to misincorporate a nucleotide at premature stop codons. Proteome-wide detection of stop codon miscoding by mass spectrometry revealed that temperature regulates the expression of cryptic sequences generated by stop codon miscoding inE.coli.

Overall, our findings suggest that the environment influences the accuracy of protein production, which increases protein heterogeneity when the organisms need to adapt to new conditions.
Unraveling the causal genes and transcriptomic determinants of human telomere length
Authors: Chang Ying , Zhou Yao , Zhou Junrui , Li Wen , Cao Jiasong , Shen Yongmei , Fan Xutong , Yang Hongxi , Dong Xiaobao , Zhang Shijie , Yi Xianfu , Shuai Ling , Shi Lei , Liu Zhe , Yang Jie , Hao Jihui , Chen Kexin , Huang Dandan , Wang Feng , Li Mulin Jun
Published: February 2023

Telomere length (TL) shortening is a pivotal indicator of biological aging and is associated with many human diseases. The genetic determinates of human TL have been widely investigated, however, most existing studies were conducted based on adult tissues which are heavily influenced by lifetime exposure. Based on the analyses of terminal restriction fragment (TRF) length of telomere, individual genotypes, and gene expressions on 166 healthy placental tissues, we systematically interrogated TL-modulated genes and their potential functions. We found that placental TL is relatively longer across human tissues and which maintenance is mostly connected to genes responsible for alternative lengthening of telomeres. Trans-ancestral TL genome-wide association studies (GWASs) on 644,553 individuals identified 20 novel genetic associations and provided increased polygenic determination of human TL. Next, we integrated the powerful TL GWAS with placental expression quantitative trait locus (eQTL) mapping to prioritize 31 likely causal genes, among which 4 were functionally validated, includingMMUT, RRM1, KIAA1429, andYWHAZ. Finally, modeling transcriptomic signatures and TRF-based TL improved the prediction performance of human TL. This study deepened our understanding of causal genes and transcriptomic determinants of human TL, promoting the mechanistic research on fine-grained TL regulation.
The role of cuticular hydrocarbons in intraspecific aggression in the invasive antCardiocondyla obscurior
Authors: Drakula Maja , Buellesbach Jan , Schrader Lukas
Published: February 2023

Cuticular hydrocarbons (CHCs) are important cues for nestmate discrimination and intraspecific aggression in ants. In invasive ants, diminished CHC profile diversity is suspected to contribute to the ecological and evolutionary success of populations by reducing intraspecific aggression between colonies. The antCardiocondyla obscuriorhas successfully colonized habitats around the world, reaching high local population densities. However, despite being invasive, colonies still react aggressively against each other, especially in interactions with non-nestmate alate queens. Here, we study whether CHCs are relevant for antagonistic interactions in this species, by combining behavioral experiments with gas-chromatography coupled with mass spectrometry (GC-MS). We show that queen and worker CHC profiles show pronounced quantitative as well as qualitative differences, that queens with depleted CHC profiles receive virtually no aggression from non-nestmates, and that aggression levels are positively correlated with the naturally occurring CHC profile differences between colonies. These findings provide first empirical evidence for a role of CHCs and chemical diversity in antagonistic behaviors against foreign queens in this species. They further suggest that invasive populations ofC. obscuriorare multicolonial and polydomous.
Role of Complementarity-Determining Regions 1 and 3 in Pathologic Amyloid Formation by Human Immunoglobulin κ1 Light Chains
Authors: Klimtchuk Elena S. , Peterle Daniele , Bullitt Esther A. , Connors Lawreen H. , Engen John R. , Gursky Olga
Published: February 2023

Immunoglobulin light chain (LC) amyloidosis is a life-threatening disease whose understanding and treatment is complicated by vast numbers of patient-specific mutations. To address molecular origins of the disease, we explored 14 patient-derived and engineered proteins related to κ1-family germline genes IGKVLD-33*01 and IGKVLD-39*01. Hydrogen-deuterium exchange mass spectrometry analysis of local conformational dynamics in full-length recombinant LCs and their fragments was integrated with studies of thermal stability, proteolytic susceptibility, amyloid formation, and amyloidogenic sequence propensities using spectroscopic, electron microscopic and bioinformatics tools. The results were mapped on the atomic structures of native and fibrillary proteins. Proteins from two κ1 subfamilies showed unexpected differences. Compared to their germline counterparts, amyloid LC related to IGKVLD-33*01 was less stable and formed amyloid faster, whereas amyloid LC related to IGKVLD-39*01 had similar stability and formed amyloid slower. These and other differences suggest different major factors influencing amyloid formation. In 33*01-related amyloid LC, these factors involved mutation-induced destabilization of the native structure and probable stabilization of amyloid. The atypical behaviour of 39*01-related amyloid LC tracked back to increased dynamics/exposure of amyloidogenic segments in βC’Vand βEVthat could initiate aggregation, combined with decreased dynamics/exposure near the Cys23-Cys88 disulfide whose rearrangement is rate-limiting to amyloidogenesis. The results suggest distinct amyloidogenic pathways for closely related LCs and point to the antigen-binding, complementarity-determining regions CDR1 and CDR3, which are linked via the conserved internal disulfide, as key factors in amyloid formation by various LCs.
Large-scale high-density brain-wide neural recording in nonhuman primates
Authors: Trautmann Eric M. , Hesse Janis K. , Stine Gabriel M. , Xia Ruobing , Zhu Shude , O’Shea Daniel J. , Karsh Bill , Colonell Jennifer , Lanfranchi Frank F. , Vyas Saurabh , Zimnik Andrew , Steinmann Natalie A. , Wagenaar Daniel A. , Andrei Alexandru , Lopez Carolina Mora , O’Callaghan John , Putzeys Jan , Raducanu Bogdan C. , Welkenhuysen Marleen , Churchland Mark , Moore Tirin , Shadlen Michael , Shenoy Krishna , Tsao Doris , Dutta Barundeb , Harris Timothy
Published: February 2023

High-density, integrated silicon electrodes have begun to transform systems neuroscience, by enabling large-scale neural population recordings with single cell resolution. Existing technologies, however, have provided limited functionality in nonhuman primate species such as macaques, which offer close models of human cognition and behavior. Here, we report the design, fabrication, and performance of Neuropixels 1.0-NHP, a high channel count linear electrode array designed to enable large-scale simultaneous recording in superficial and deep structures within the macaque or other large animal brain. These devices were fabricated in two versions: 4416 electrodes along a 45 mm shank, and 2496 along a 25 mm shank. For both versions, users can programmatically select 384 channels, enabling simultaneous multi-area recording with a single probe. We demonstrate recording from over 3000 single neurons within a session, and simultaneous recordings from over 1000 neurons using multiple probes. This technology represents a significant increase in recording access and scalability relative to existing technologies, and enables new classes of experiments involving fine-grained electrophysiological characterization of brain areas, functional connectivity between cells, and simultaneous brain-wide recording at scale.
LncRNA MALAT1/microRNA-30b axis regulate macrophage polarization and function
Authors: Ahmad Imran , Naqvi Raza Ali , Valverde Araceli , Naqvi Afsar R.
Published: February 2023

Introduction

Macrophages (Mφ) can polarize towards the proinflammatory M1 or proresolving M2 phenotype to control diverse biological processes such as inflammation, and tissue regeneration. Noncoding RNAs play critical roles in numerous biological pathways; however, their functional interaction in the regulation of Mφ polarization and immune responses remain unclear.

Objectives

To examine relationship between lncRNA (MALAT1) and microRNA (miR-30b) in shaping macrophage polarization and immune functions.

Methods

Expression of MALAT1 and miR-30b was examined in differentiating M1/M2 Mφ, human and murine inflamed gingival biopsies by RT-qPCR. MALAT1 and miR-30b direct interaction was examined by dual luciferase assays. Impact of MALAT1 knockdown and miR-30b overexpression was examined on macrophage polarization markers, bacterial phagocytosis, antigen uptake/processing and cytokine profiles.

Results

MALAT1 expression displays a time-dependent induction during Mφ differentiation and, upon challenge with TLR4 agonist (E. coliLPS). Knockdown of MALAT1 enhanced the expression of M2Mφ markers without affecting the M1Mφ markers, suggesting that MALAT1 favors the M1 phenotype by suppressing M2 polarization. MALAT1 knockdown Mφ exhibit reduced antigen uptake and processing, bacterial phagocytosis, and bactericidal activity, strongly supporting its critical role in regulating innate immune functions. Consistent with this, MALAT1 knockdown showed impaired cytokine secretion upon challenge with LPS. Importantly, MALAT1 exhibit an antagonistic expression pattern with all five members of the miR-30 family during M2Mφ differentiation. Dual-luciferase assays validated a novel sequence on MALAT1 that interacts with miR-30b, a microRNA that promotes the M2 phenotype. Phagocytosis and antigen processing assays unequivocally demonstrated that MALAT1 and miR-30b are functionally antagonistic. In human subjects with periodontal disease and murine model of ligature-induced periodontitis, we observed higher levels of MALAT1, and downregulation of miR-30b that correlates with higher M1Mφ markers expression in gingival tissues suggesting a pro-inflammatory function of MALAT1.

Conclusion

MALAT1/miR-30b antagonistic interaction shapes Mφ polarizationin vitroand in inflamed gingival biopsies.
Statistically inferred neuronal connections in subsampled neural networks strongly correlate with spike train covariance
Authors: Liang Tong , Brinkman Braden A. W.
Published: February 2023

Statistically inferred neuronal connections from observed spike train data are often skewed from ground truth by factors such as model mismatch, unobserved neurons, and limited data. Spike train covariances, sometimes referred to as “functional connections,” are often used as a proxy for the connections between pairs of neurons, but reflect statistical relationships between neurons, not anatomical connections, and moreover are not casual. Connections inferred by maximum likelihood inference, by contrast, can be constrained to be causal. However, we show in this work that the inferred connections in spontaneously active networks modeled by stochastic leaky integrate-and-fire networks strongly reflect covariances between neurons, not causal information, when many neurons are unobserved or when neurons are weakly coupled. This phenomenon occurs across different network structures, including random networks and balanced excitatory-inhibitory networks.