bluuebunny/crossref_metadata_2025 huggingface dataset:
In situ visualization of opioid and cannabinoid drug effects using phosphosite-specific GPCR antibodies
Authors: Fritzwanker Sebastian , Nagel Falko , Kliewer Andrea , Stammer Viviane , Schulz Stefan
Published: June 2022

G protein-coupled receptors (GPCRs) are important signal transducers that are phosphorylated upon activation at intracellular serine and threonine residues. Although antibodies that specifically recognize the phosphorylation state of GPCRs have been available for many years, efficient immunolocalization of phosphorylated receptors in their tissues of origin has not been possible. Here, we show that phosphorylation of receptors is highly unstable during routine immunohistochemical procedures, requiring the use of appropriate phosphatase inhibitors particular during tissue perfusion, post-fixation, and cryoprotection but not during immunostaining of tissue sections. We provide proof of concept using μ-opioid receptor (MOP) and cannabinoid receptor 1 (CB1) antibodies. Indeed, three of four well-characterized phosphosite-specific MOP antibodies, including pS375-MOP, pT376-MOP, and pT379-MOP, showed robust neuronal immunostaining in brain and spinal cord sections of opioid-treated mice only after inclusion of phosphatase inhibitors. We then extended this approach to the CB1 receptor and demonstrated that one of three newly-generated phosphosite-specific CB1 antibodies, namely pS425-CB1, showed striking staining of fibers and varicosities in brain slices from cannabinoid-treated mice. Although subsequent experiments showed that phospho-CB1 immunostaining was less sensitive to phosphatases, we conclude that the use of phosphatase inhibitors should always be considered in the development of immunohistochemical procedures for new phosphosite-specific GPCR antibodies. In summary, we anticipate that this improved protocol will facilitate the widespread use of phosphorylation state-specific antibodies to monitor the activation of endogenous GPCRs under physiological and pharmacological conditions. Our approach may also prove useful to confirm target engagement of GPCR drug candidates in native tissues.
The G-protein-coupled estrogen receptor, a gene co-expressed with ERα in breast tumors, is regulated by estrogen-ERα signalling in ERα positive breast cancer cells
Authors: Pal Uttariya , Manjegowda Mohan , Singh Neha , Saikia Snigdha , Philip Betty S. , Kalita Deep Jyoti , Rai Avdhesh Kumar , Sarma Anupam , Raphael Vandana , Modi Deepak , Kataki Amal Chandra , Limaye Anil Mukund
Published: June 2022

Purpose

The purpose of this study was to assess the relationship between GPER, a seven transmembrane G-protein coupled estrogen receptor, and ERα in breast tumors, and to make inroads into the mechanistic basis and clinical significance.

Methods

TCGA-BRCA data was mined to examine the relationship between GPER and ERα expression. GPER mRNA, and protein expression were analyzed in ERα-positive or -negative breast tumors from two cohorts using immunohistochemistry, western blotting, or RT-qPCR. The Kaplan-Meier Plotter was employed for survival analysis. The influence of estrogen in vivo was studied by examining GPER expression levels in estrus or diestrus mouse mammary tissues, and the impact of 17β-estradiol (E2) administration in juvenile or adult mice. The effect of E2, or propylpyrazoletriol (PPT, an ERα agonist) stimulation on GPER expression was studied in MCF-7 and T47D cells, with or without tamoxifen or ERα knockdown. ERα-binding to the GPER locus was explored by analysing ChIP-seq data (ERP000380), in silico prediction of estrogen response elements, and chromatin immunoprecipitation assay.

Results

Clinical data revealed significant positive association between GPER and ERα expression in breast tumors. The median GPER expression in ERα-positive tumors was significantly higher than ERα-negative tumors. High GPER expression was significantly associated with longer overall survival of patients with ERα-positive tumors. In vivo experiments showed a positive effect of E2 on GPER expression. E2 induced GPER expression in MCF-7 and T47D cells; an effect mimicked by PPT. Tamoxifen or ERα-knockdown blocked the induction of GPER. Estrogen-mediated induction was associated with increased ERα occupancy in the upstream region of GPER.

Conclusion

GPER expression is positively associated with ERα in breast tumors, and a transcriptional target of the estrogen-ERα signalling axis. More in-depth studies are required to establish the significance of GPER-ERα co-expression, and their interplay in breast tumor development, progression, and treatment.
GADMA2: more efficient and flexible demographic inference from genetic data
Authors: Noskova Ekaterina , Abramov Nikita , Iliutkin Stanislav , Sidorin Anton , Dobrynin Pavel , Ulyantsev Vladimir
Published: June 2022

Background

Inference of complex demographic histories is a source of information about events that happened in the past of studied populations. Existing methods for demographic inference typically require input from the researcher in the form of a parameterized model. With an increased variety of methods and tools, each with its own interface, the model specification becomes tedious and error-prone. Moreover, optimization algorithms used to find model parameters sometimes turn out to be inefficient, for instance, by being not properly tuned or highly dependent on a user-provided initialization. The open-source software GADMA addresses these problems, providing automatic demographic inference. It proposes a common interface for several likelihood engines and provides global parameters optimization based on a genetic algorithm.

Results

Here, we introduce the new GADMA2 software and provide a detailed description of the added and expanded features. It has a renovated core code base, new likelihood engines, an updated optimization algorithm and a flexible setup for automatic model construction. We provide a full overview of GADMA2 enhancements, compare the performance of supported likelihood engines on simulated data and demonstrate an example of GADMA2 usage on two empirical datasets.

Conclusions

We demonstrate the better performance of a genetic algorithm in GADMA2 by comparing it to the initial version and other existing optimization approaches. Our experiments on simulated data indicate that GADMA2’s likelihood engines are able to provide accurate estimations of demographic parameters even for misspecified models. We improve model parameters for two empirical datasets of inbred species.
Characterizing phytoplankton communities in the absence of resource-based competition
Authors: Behrenfeld Michael J. , Bisson Kelsey M. , Boss Emmanuel , Gaube Peter , Karp-Boss Lee
Published: June 2022

Abstract

Under most natural marine conditions, phytoplankton cells suspended in the water column are too distantly spaced for direct competition for resources to be a routine occurrence. Accordingly, resource-based competitive exclusion should be rare. In contrast, contemporary ecosystem models typically predict an exclusion of larger phytoplankton size classes under low-nutrient conditions, an outcome interpreted as reflecting the competitive advantage of small cells having much higher nutrient ‘affinities’ than larger cells. Here, we develop mechanistically-focused expressions for steady-state, nutrient-limited phytoplankton growth that are consistent with the discrete, distantly-spaced cells of natural populations. These expressions are then encompassed in an ecosystem model that sustains diversity across all size classes over the full range in nutrient concentrations observed in the ocean. In other words, our model does not exhibit resource-based competitive exclusion between size classes. We show that the basis for species exclusions in earlier models is not a reflection of size-dependent nutrient ‘affinities’, but rather a consequence of inappropriate descriptions of non-grazing phytoplankton mortality.
Alterations in protein kinase networks in astrocytes and neurons derived from patients with familial Alzheimer’s Disease
Authors: Henkel Nicholas D. , Joyce Alex , Shedroff Elizabeth , Imami Ali Sajid , Alganem Khaled , Hamoud Abdul-rizaq , Xu Chongchong , Siciliano Benjamin , Ma Tao , Wen Zhexing , McCullumsmith Robert E.
Published: June 2022

Neurons and astrocytes derived from Alzheimer’s Disease (AD) patient induced pluripotent stem cells are an evolving technology used to study the pathogenesis and etiology of AD. As the utility of mouse models of AD are increasingly coming into questions, using iPSC technology may offer an opportunity to study this disease with human substrates. Herein, we using a hypothesis generating platform, the PamGene12 Kinome Array, to identify core protein kinases in neurons and astrocytes derived from familial AD patient iPSCs. We identified five core protein kinases in these cells and examined the pathways in which they are enriched. Importantly, we complement our findings using an in-silico approach with postmortem AD brain datasets. While these protein kinases have been conceptualized in the context of traditional AD pathology, they have not been explored in the context of aberrant signaling in the pathophysiology of the disease.
Improved two-step testing of genome-wide gene-environment interactions
Authors: Kawaguchi Eric S. , Kim Andre E. , Lewinger Juan Pablo , Gauderman W. James
Published: June 2022

Two-step tests for gene-environment (G×E) interactions exploit marginal SNP effects to improve the power of a genome-wide interaction scan (GWIS). They combine a screening step based on marginal effects used to ‘bin’ SNPs for weighted hypothesis testing in the second step to deliver greater power over single-step tests while preserving the genome-wide type I error. However, the presence of many SNPs with detectable marginal effects on the trait of interest can reduce power by ‘displacing’ true interactions with weaker marginal effects and by adding to the number of tests that need to be corrected for multiple testing. We introduce a new significance-based allocation into bins for step 2G×Etesting that overcomes the displacement issue and propose a computationally efficient approach to account for multiple testing within bins. Simulation results demonstrate that these simple improvements can provide substantially greater power than current methods under several scenarios. An application to a multi-study collaboration for understanding colorectal cancer (CRC) reveals aG×Sex interaction located within the SMAD7 gene.
A PTP1B-Cdk3 signaling axis promotes cell cycle progression of human glioblastoma cells through an Rb-E2F dependent pathway
Authors: Villamar-Cruz Olga , Loza-Mejía Marco Antonio , Vivar-Sierra Alonso , Saldivar-Cerón Héctor Iván , Patiño-López Genaro , Efraín Olguín Jonadab , Terrazas Luis Ignacio , Armas-López Leonel , Ávila-Moreno Federico , Saha Sayanti , Chernoff Jonathan , Camacho-Arroyo Ignacio , Arias-Romero Luis Enrique
Published: June 2022

Protein tyrosine phosphatase 1B (PTP1B) plays a key role in developing different types of cancer. However, the molecular mechanism underlying this effect is unclear. To identify possible molecular targets of PTP1B that mediate its positive role in tumorigenesis, we undertook a SILAC-based phosphoproteomic approach, which allowed us to identify the Cyclin-dependent kinase 3 (Cdk3) as a novel PTP1B substrate. Molecular docking studies revealed stable interactions between the PTP1B catalytic domain and Cdk3. In addition, we observed that PTP1B dephosphorylates a Cdk3 derived peptide at Tyrosine residue 15in vitroand interacts with endogenous Cdk3 in the nucleus and cytoplasm of human glioblastoma (GB) cells. Finally, we found that the pharmacological inhibition of PTP1B or its depletion with siRNA leads to cell cycle arrest with the diminished activity of Cdk3, the consequent hypophosphorylation of Rb, and the down-regulation of E2F and its target genes Cdk1, Cyclin A, and Cyclin E1. These data delineate a novel signaling pathway from PTP1B to Cdk3 required for efficient cell cycle progression in an Rb-E2F dependent manner in human GB cells and suggest new therapeutic strategies for treating these tumors.
The landscape of pediatric procedural sedation in UK & Irish emergency departments; a PERUKI study
Authors: Hall Dani , Moriarty Tadgh , Roland Damian , O’Sullivan Ronan , Blackburn Carol , Hartshorn Stuart , Messahel Shrouk , Lyttle Mark D
Published: June 2022

Study objective

Approximately 250,000 children undergo pediatric procedural sedation (PPS) in UK & Irish emergency departments (ED) annually. PPS practice in our setting has not been described as fully as in other high income countries. We aimed to evaluate PPS in UK and Irish EDs.

Methods

Online survey distributed through Pediatric Emergency Research in the UK and Ireland (PERUKI) during June 2020. One respondent per ED completed the survey, including questions on agents, fasting, training and governance. Results are presented using descriptive statistics.

Results

61/72 (85%) sites responded, of which PPS was performed in 50 (82%). Intravenous ketamine was the most common agent (43/50; 86%), followed by variable concentration nitrous oxide (13/50; 26%). Fasting practices varied widely across sites and agents: 24/45 (53.3%) of sites delivering ketamine/es-ketamine PPS required fasting compared to 2/13 (15.4%) before variable concentration nitrous oxide. 49/72 (68.1%) provided complete responses on training; internal training packages existed in under half (22/49, 44.9%). Most had a guideline (43/61; 70.5%) and documentation proforma (39/61; 63.9%). Databases existed in 24/61 (39.3%).

Conclusion

We have demonstrated widespread PPS use, but non-standardized practice. This leads to potential issues of risk and variability, highlighting a need for a UK and Ireland sedation package to standardize PPS practice and data collection, informed by international guidance and evidence. We propose development of a prospective ED sedation registry to facilitate data collection to support research within this area.
The formation of the Indo-Pacific montane avifauna
Authors: Reeve Andrew Hart , Kennedy Jonathan David , Pujolar José Martín , Petersen Bent , Blom Mozes P. K. , Alström Per , Haryoko Tri , Ericson Per G. P. , Irestedt Martin , Nylander Johan A. A. , Jønsson Knud Andreas
Published: June 2022

Mountain biotas have considerable conservation and research importance, but the formation of montane communities remains incompletely understood. Study of Indo-Pacific island faunas has inspired two main hypotheses for the generation of montane diversity. The first posits that montane populations arise via direct colonization from other mountain areas, while the second invokes recruitment from adjacent lowland populations. We sought to reconcile these apparently conflicting hypotheses by asking whether a species’ ancestral geographic origin determines its mode of mountain colonization. To this end, island-dwelling passerine birds at the faunal crossroads between Eurasia and Australo-Papua provide an ideal study system. We recovered the phylogenetic relationships of the region’s montane species, and used this information to reconstruct their ancestral geographic ranges, elevational ranges, and migratory behavior. We also performed genomic population studies of three super-dispersive montane species/clades with broad island distributions. Eurasian-origin species populated archipelagos via direct colonization between mountains. This mode of colonization appears related to ancestral adaptations to cold and seasonal Palearctic climates, specifically short-distance migration. Australo-Papuan-origin mountain populations, by contrast, evolved from lowland ancestors, and highland distribution mostly precludes their further colonization of island mountains. The patterns and processes revealed for this group are compatible with taxon cycles, a hypothesized process of lowland lineage expansion followed by montane relictualization. Collectively, our analyses explain much of the distributional variation within a complex biological system, and provide a synthesis of two seemingly discordant hypotheses for montane community formation.
T cell receptor convergence is an indicator of antigen-specific T cell response in cancer immunotherapies
Authors: Pan Ming Yao , Li Bo
Published: June 2022

T cells are potent at eliminating pathogens and playing a crucial role in the adaptive immune response. T cell receptor (TCR) convergence describes T cells that share identical TCRs with the same amino acid sequences but have different DNA sequences due to codon degeneracy. We conducted a systematic investigation of TCR convergence using single-cell immune profiling and bulk TCRβ-sequence (TCR-seq) data obtained from both mouse and human samples, and uncovered a strong link between antigen-specificity and convergence. This association was stronger than T cell expansion, a putative indicator of antigen-specific T cells. By using flow sorted tetramer+single T cell data, we discovered that convergent T cells were enriched for a neoantigen-specific CD8+effector phenotype in the tumor microenvironment. Moreover, TCR convergence demonstrated better prediction accuracy for immunotherapy response than the existing TCR repertoire indexes. In conclusion, convergent T cells are likely to be antigen-specific and might be a novel prognostic biomarker for anti-cancer immunotherapy.
Modeling of Aberrant Epithelial Reprogramming in Idiopathic Pulmonary Fibrosis using Human Induced Pluripotent Stem Cell-derived Alveolar Organoids
Authors: Ptasinski Victoria , Monkley Susan J. , Öst Karolina , Tammia Markus , Overed-Sayer Catherine , Hazon Petra , Wagner Darcy E. , Murray Lynne A.
Published: June 2022

Repeated injury of the lung epithelium is proposed to be a main driver of idiopathic pulmonary fibrosis (IPF). However, none of the available therapies target the epithelium and there is a limited amount of human models of fibrotic epithelial damage with suitability for drug screening and discovery. We developed a model of the epithelial reprogramming seen in IPF using alveolar organoids derived from human induced pluripotent stem cells stimulated with a cocktail of pro-fibrotic and inflammatory cytokines. This fibrosis cocktail induced persistent epithelial reprogramming and expression of extracellular matrix. Deconvolution of RNA-seq data indicated that the fibrosis cocktail increased the proportion of cells with theKRT5-/KRT17+aberrant basaloid phenotype, recently identified in the lungs of IPF patients. Treatment with nintedanib and pirfenidone had effects on markers of extracellular matrix, pro-fibrotic mediators and epithelial reprogramming. Thus, our system recapitulates key aspects of IPF and is a promising system for drug discovery.
Rescue of aged muscle stem cell quiescence defects by AKT inhibition revealed with a 3D biomimetic culture assay
Authors: Jacques Erik , Kuang Yinni , Kann Allison P. , Krauss Robert S. , Gilbert Penney M.
Published: June 2022

Adult skeletal muscle harbors a population of muscle stem cells (MuSCs) that are required to repair or reform multinucleated myofibers after tissue injury. In youth, MuSCs return to a reversible state of cell cycle arrest termed ‘quiescence’ after injury resolution. By contrast, a proportion of MuSCs in aged muscle remain in a semi-activated state, causing a premature response to subsequent injury cues that results in incomplete tissue repair and eventual stem cell depletion. Regulation of the balance between MuSC quiescence and activation in youth and in age may hold the key to restoring tissue homeostasis with age, but is incompletely understood. To fill this gap, we developed a simple and tractable in vitro method, with a 96-well footprint, to rapidly inactivate MuSCs freshly isolated from young skeletal muscle tissue, and return them to a quiescent-like state for at least one-week. This was achieved by introducing MuSCs into a three-dimensional (3D) bioartificial niche comprised of a thin sheet of multinucleated myotubes, which we iterate, and analyze temporally, to show that these in vivo niche features provide the minimal cues necessary to inactivate MuSCs and induce quiescence. By seeding the 3D myotube sheets with different starting numbers of MuSCs, the assay revealed cellular heterogeneity and population-level adaptation activities that converged on a common steady-state niche repopulation density; behaviors previously observed only in vivo. Quiescence-associated hallmarks included a Pax7+CalcR+MyoD- c-FOS- molecular signature, in vivo quiescent-like morphologies including oval-shaped nuclei and long cytoplasmic projections with N-cadherin+ tips, as well as the acquisition of polarized niche markers. Leveraging high-content imaging and bespoke CellProfilerTM-based image analysis pipelines, we demonstrate a relationship between morphology and cell fate signatures opening up the possibility of real-time morphology-based screening. Notably, when MuSCs from aged muscle were introduced into the assay, they displayed aberrant proliferative activities, delayed inactivation kinetics, persistence of activation-associated morphologies, and population depletion; quiescence-associated defects that we show are rescued by wortmannin treatment. Thus, the miniaturized assay offers an unprecedented opportunity to systematically investigate long-standing queries in areas such as regulation of adult stem cell pool size and functional heterogeneity within the MuSC population, and to uncover regulators of quiescence in youth and in age.
Not only perception but also grasping actions can obey Weber’s law
Authors: Derzsi Zoltan , Volcic Robert
Published: June 2022

Weber’s law, the principle that the uncertainty of perceptual estimates increases proportionally with object size, is regularly violated when considering the uncertainty of the grip aperture during grasping movements. The origins of this perception-action dissociation are debated and are attributed to various reasons, including different coding of visual size information for perception and action, biomechanical factors, the use of positional information to guide grasping, or, sensorimotor calibration. Here, we contrasted these accounts and compared perceptual and grasping uncertainties by asking people to indicate the visually perceived center of differently sized objects (Perception condition) or to grasp and lift the same objects with the requirement to achieve a balanced lift (Action condition). We found that the variability (uncertainty) of contact positions increased as a function of object size in both perception and action. The adherence of the Action condition to Weber’s law and the consequent absence of a perception-action dissociation contradict the predictions based on different coding of visual size information and sensorimotor calibration. These findings provide clear evidence that human perceptual and visuomotor systems rely on the same visual information and suggest that the previously reported violations of Weber’s law in grasping movements should be attributed to other factors.
Hierarchical differences in the encoding of sound and choice in the subcortical auditory system
Authors: Mackey Chase A. , Dylla Margit , Bohlen Peter , Grigsby Jason , Hrnicek Andrew , Mayfield Jackson , Ramachandran Ramnarayan
Published: June 2022

Detection of sounds is a fundamental function of the auditory system. While studies of auditory cortex have gained substantial insight into detection performance using behaving animals, previous subcortical studies have mostly taken place under anesthesia, in passively listening animals, or have not measured performance at threshold. These limitations preclude direct comparisons between neuronal responses and behavior. To address this, we simultaneously measured auditory detection performance and single-unit activity in the inferior colliculus (IC) and cochlear nucleus (CN) in macaques. The spontaneous activity and response variability of CN neurons were higher than those observed for IC neurons. Signal detection theoretic methods revealed that the magnitude of responses of IC neurons provided more reliable estimates of psychometric threshold and slope compared to the responses of single CN neurons. However, pooling small populations of CN neurons provided reliable estimates of psychometric threshold and slope, suggesting sufficient information in CN population activity. Trial-by-trial correlations between spike count and behavioral response emerged 50-75 ms after sound onset for most IC neurons, but for few neurons in the CN. These results highlight hierarchical differences between neurometric-psychometric correlations in CN and IC, and have important implications for how subcortical information could be decoded.

New & Noteworthy

The cerebral cortex is widely recognized to play a role in sensory processing and decision-making. Accounts of the neural basis of auditory perception and its dysfunction are based on this idea. However, significantly less attention has been paid to midbrain and brainstem structures in this regard. Here we find that subcortical auditory neurons represent stimulus information sufficient for detection, and predict behavioral choice on a trial-by-trial basis.
Functional divergence in a multi-gene family is a key evolutionary innovation for anaerobic growth in Saccharomyces cerevisiae
Authors: Krause David J. , Hittinger Chris Todd
Published: June 2022

The amplification and diversification of genes into large multi-gene families often marks key evolutionary innovations, but this process often creates genetic redundancy that hinders functional investigations. When the model budding yeast Saccharomyces cerevisiae transitions from aerobic to anaerobic growth conditions, the cell massively induces the expression of seven cell wall mannoproteins (anCWMPs): TIP1, TIR1, TIR2, TIR3, TIR4, DAN1, and DAN4. Here we show that these genes likely derive evolutionarily from a single ancestral anCWMP locus, which was duplicated and translocated to new genomic contexts several times both prior to and following the budding yeast whole genome duplication (WGD) event. Based on synteny and their phylogeny, we separate the anCWMPs into four gene subfamilies. To resolve prior inconclusive genetic investigations of these genes, we constructed a set of combinatorial deletion mutants to determine their contributions toward anaerobic growth in S. cerevisiae. We found that two genes, TIR1 and TIR3, were together necessary and sufficient for the anCWMP contribution to anaerobic growth. Overexpressing either gene alone was insufficient for anaerobic growth, implying that they encode non-overlapping functional roles in the cell during anaerobic growth. We infer from the phylogeny of the anCWMP genes that these two important genes derive from an ancient duplication that predates the WGD event, whereas the TIR1 subfamily experienced gene family amplification after the WGD event. Taken together, the genetic and molecular evidence suggest that one key anCWMP gene duplication event, several auxiliary gene duplication events, and functional divergence underpin the evolution of anaerobic growth in budding yeasts.
First record of monogenean fish parasites in the Upper Lufira basin (Democratic Republic of Congo): dactylogyrids and gyrodactylids infecting Oreochromis mweruensis, Coptodon rendalli and Serranochromis macrocephalus (Teleostei: Cichlidae)
Authors: Kasembele Gyrhaiss Kapepula , Manda Auguste Chocha , Abwe Emmanuel , Pariselle Antoine , Bukinga Fidel Muterezi , Huyse Tine , Jorissen Michiel W.P. , Vreven Emmanuel J. , Luus-Powell Wilmien J. , Smit Willem , Sara Joseph Roderick , Snoeks Jos , Vanhove Maarten P.M.
Published: June 2022

Background

Monogenean parasites have never been formally reported on fish from the Lufira basin. Then it is hypothesised that multiple monogenean species are to be recorded that are new to the region. This study aimed to record the gill monogenean parasite fauna of three cichlid fish species in the Upper Lufira basin by inventorying their diversity (species composition) and analysing their infection parameters (prevalence, mean intensity and abundance).

Methods

Oreochromis mweruensis, Coptodon rendalli, and Serranochromis macrocephalus were selected for the study, given their economic value and their abundance in the Upper Lufira basin. Monogeneans were isolated from the gills and stomach, mounted on glass slides with either Hoyer’s medium or ammonium picrate-glycerin for further identification under a stereomicroscope, based on morphological analysis of genital and haptoral hard parts. Indices of diversity and infections parameters were calculated.

Results

A total of thirteen gill monogenean parasite species (Cichlidogyrus dossoui, C. halli, C. karibae, C. mbirizei, C. papernastrema, C. quaestio, C. sclerosus, C. tiberianus, C. tilapiae, C. zambezensis, Scutogyrus gravivaginus, S. cf. bailloni and Gyrodactylus nyanzae) and one stomach monogenean (Enterogyrus malmbergi) were reported. A species richness of S= 10 for O. mweruensis, S= 6 for C. rendalli and S= 2 for S. macrocephalus were recorded. Five parasite species were reported to be common amongst O. mweruensis and C. rendalli. The most prevalent parasite species were C. halli (P= 80.9%) on O. mweruensis, C. dossoui (P= 92.9%) on C. rendalli and C. karibae and C. zambezensis (both of which P = 9.1%) on S. macrocephalus with a respective mean infection intensity of 7.9 on O. mweruensis, 9.8 on C. rendalli and 5 and 15, respectively, on S. macrocephalus. Results of this study reported new host ranges for five parasites species (C. quaestio, S. cf. bailloni, E. malmbergi on O. mweruensis, C. halli on C. rendalli and C. karibae on S. macrocephalus) as well as new geographical records for three of them (S. cf. bailloni, E. malmbergi, C. karibae).

Conclusions

This study highlights the richness of monogenean communities in the Upper Lufira basin and is a starting point for future helminthological studies, e.g. on the use of fish parasites as indicators of anthropogenic impacts.
SpiDec: Computing Binodals and Interfacial Tension of Biomolecular Condensates From Simulations of Spinodal Decomposition
Authors: Mazarakos Konstantinos , Prasad Ramesh , Zhou Huan-Xiang
Published: June 2022

Phase separation of intrinsically disordered proteins (IDPs) is a phenomenon associated with many essential cellular processes, but a robust method to compute the binodal from molecular dynamics simulations of IDPs modeled at the all-atom level in explicit solvent is still elusive, due to the difficulty in preparing a suitable initial dense configuration and in achieving phase equilibration. Here we present SpiDec as such a method, based on spontaneous phase separation via spinodal decomposition that produces a dense slab when the system is initiated at a homogeneous, low density. After illustrating the method on four model systems, we apply SpiDec to a tetrapeptide modeled at the all-atom level and solvated in TIP3P water. The concentrations in the dense and dilute phases agree qualitatively with experimental results and point to binodals as a sensitive property for force-field parameterization. SpiDec may prove useful for the accurate determination of the phase equilibrium of IDPs.

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An efficient not-only-linear correlation coefficient based on machine learning
Authors: Pividori Milton , Ritchie Marylyn D. , Milone Diego H. , Greene Casey S.
Published: June 2022

Correlation coefficients are widely used to identify patterns in data that may be of particular interest. In transcriptomics, genes with correlated expression often share functions or are part of disease-relevant biological processes. Here we introduce the Clustermatch Correlation Coefficient (CCC), an efficient, easy-to-use and not-only-linear coefficient based on machine learning models. CCC reveals biologically meaningful linear and nonlinear patterns missed by standard, linear-only correlation coefficients. CCC captures general patterns in data by comparing clustering solutions while being much faster than state-of-the-art coefficients such as the Maximal Information Coefficient. When applied to human gene expression data, CCC identifies robust linear relationships while detecting nonlinear patterns associated, for example, with sex differences that are not captured by linear-only coefficients. Gene pairs highly ranked by CCC were enriched for interactions in integrated networks built from protein-protein interaction, transcription factor regulation, and chemical and genetic perturbations, suggesting that CCC could detect functional relationships that linear-only methods missed. CCC is a highly-efficient, next-generation not-only-linear correlation coefficient that can readily be applied to genome-scale data and other domains across different data types.
The C. elegans Observatory: High-throughput exploration of behavioral aging
Authors: Kerr Rex A. , Roux Antoine , Goudeau Jerome , Kenyon Cynthia
Published: June 2022

Organisms undergo a variety of characteristic changes as they age, suggesting a substantial commonality in the mechanistic basis of aging. Experiments in model organisms have revealed a variety of cellular systems that impact lifespan, but technical challenges have prevented a comprehensive evaluation of how these components impact the trajectory of aging, and many components likely remain undiscovered. To facilitate the deeper exploration of aging trajectories at sufficient scale to enable primary screening, we have created the C. elegans Observatory, an automated system for monitoring the behavior of group-housed C. elegans throughout their lifespans. One Observatory consists of a set of computers running custom software to control an incubator containing custom imaging and motion-control hardware. In its standard configuration, the Observatory cycles through trays of standard 6 cm plates, running four assays per day on up to 576 plates per incubator. High-speed image processing captures a range of behavioral metrics including movement speed and stimulusinduced turning, and a data processing pipeline continuously computes summary statistics. The Observatory software includes a web interface that allows the user to input metadata and to view graphs of the trajectory of behavioral aging as the experiment unfolds. Compared to manual use of a plate-based C. elegans tracker, the Observatory reduces effort required by close to two orders of magnitude. Within the Observatory, reducing function of known lifespan genes with RNA interference (RNAi) gives the expected phenotypic changes, including extended motility in daf-2(RNAi) and progeria in hsf-1(RNAi). Lifespans scored manually from worms raised in conventional conditions match those scored from images captured by the Observatory. We have used the Observatory for a small candidate-gene screen and identified an extended youthful vigor phenotype for tank-1(RNAi) and a progeric phenotype for cdc-42(RNAi). By utilizing the Observatory, it is now feasible to conduct whole-genome screens for an aging-trajectory phenotype, thus greatly increasing our ability to discover and analyze new components of the aging program.
The requirement of GW182 in miRNA-mediated gene silencing inDrosophilalarval development
Authors: Matsuura-Suzuki Eriko , Kiyokawa Kaori , Iwasaki Shintaro , Tomari Yukihide
Published: June 2022

microRNAs (miRNAs) regulate a wide variety of biological processes by silencing their target genes. Argonaute (AGO) proteins load miRNAs to form RNA-induced silencing complex (RISC), which mediates translational repression and/or mRNA decay of the targets. A scaffold protein called GW182 directly binds AGO and the CCR4-NOT deadenylase complex, initiating the mRNA decay reaction. Although previous studies have demonstrated the critical role of GW182 in cultured cells as well as in cell-free systems, its biological significance in living organisms remains poorly explored, especially inDrosophila melanogaster. Here, we generatedgw182-null flies using the CRISPR/Cas9 system and found that, unexpectedly, they can survive until an early second instar larval stage. Moreover, in vivo miRNA reporters can be effectively repressed ingw182-null first instar larvae. Nevertheless,gw182-null flies have defects in the expression of chitin-related genes and the formation of the larval trachea system, preventing them to complete the larval development. Our results highlight the importance of both GW182-dependent and -independent silencing mechanisms in vivo.
Effective Representation Learning via The Integrated Self-Supervised Pre-training models of StyleGAN2-ADA and DINO for Colonoscopy Images
Authors: Kim Jong-Yeup , Tangriberganov Gayrat , Jung Woochul , Kim Dae Sung , Koo Hoon Sup , Lee Suehyun , Kim Sun Moon
Published: June 2022

In order to reach better performance in visual representation learning from image or video dataset, huge amount of annotated data are on demand. However, collecting and annotating large-scale datasets are costly and time-consuming tasks. Especially, in a domain like medical, it is hard to access patient images because of the privacy concerns and also not knowing what exactly to annotate without expert effort. One of the solutions to obviate the hassle is to use Self-Supervised learning methods (SSL) and Generative Adversarial Networks (GANs) together. SSL and GANs are quickly advancing fields. GANs have unique capability to create unlabeled data sources containing photo-realistic images while SSL methods are able to learn general image and video features from large-scale data without using any human-annotated labels. In this work, we explore leveraging the power of recently introduced StyleGAN2-ada and Self-Supervised Pre-Training of Dino together for the pretext task. Our underlying insight is also that leveraging the current approaches with Transfer Learning (TF) together brings benefit on doing pretext task in medical domain. By the strategy of unifying these two approaches, we propose the integrated version and use it derive representation learning on polyp dataset.
CeGAL: revisiting a widespread fungal-specific TF family using an in silico error-aware approach to identify missing zinc cluster domains
Authors: Mayer Claudine , Vogt Arthur , Uslu Tuba , Scalzitti Nicolas , Poch Olivier , Thompson Julie D.
Published: June 2022

Transcription factors (TF) regulate gene activity in eukaryotic cells by binding specific regions of genomic DNA. In fungi, the most abundant TF class contains a fungal-specific ‘GAL4-like’ Zn2C6 DNA binding domain (DBD), while the second class contains another fungal-specific domain, known as ‘fungal_trans’ or Middle Homology Domain (MHD), whose function remains largely uncharacterized. Remarkably, almost a third of MHD-containing TF in public sequence databases apparently lack DNA binding activity, since they are not predicted to contain a DBD. Here, we reassess the domain organization of these ‘MHD-only’ proteins using an in silico error-aware approach. Our large-scale analysis of ~17000 MHD-only TF sequences showed that the vast majority (>90%) result from gene annotation errors, thus contradicting previous findings that the MHD-only TF are widespread in fungi. We show that they are in fact exceptional cases, and that the Zn2C6-MHD domain pair represents the canonical domain signature defining a new TF family composed of two fungal-specific domains. We call this family CeGAL, after the most characterized members: Cep3, whose 3D structure has been determined and GAL4, an archetypal eukaryotic TF. This definition should improve the classification of the Zn2C6 TF and provide critical insights into fungal gene regulatory networks.

IMPORTANCE

In fungi, extensive efforts focus on genome-wide characterization of potential Transcription Factors (TFs) and their targets genes to provide a better understanding of fungal processes and a rational for transcriptional manipulation. The second most abundant families of fungal-specific TFs, characterized by a Middle Homology Domain, are major regulators of primary and secondary metabolisms, multidrug resistance and virulence. Remarkably, one third of these TFs do not have a DNA Binding Domain (DBD-orphan) and thus are excluded from genome-wide studies. This particularity has been the subject of debate for many years. By computationally inspecting the close genomic environment of about 20,000 DBD-orphan TFs from a wide range of fungal species, we reveal that more than 90% contained sequences encoding a zinc-finger DBD. This analysis implies that the arrays of DBD containing TFs and their control DNA-sequences in target genes need to be reconsidered and expands the combinatorial regulation degree of the crucial fungal processes controlled by this TF family.
A single-nucleus transcriptomics study of alcohol use disorder in the nucleus accumbens
Authors: van den Oord Edwin J.C.G. , Xie Lin Y , Zhao Min , Aberg Karolina A. , Clark Shaunna L.
Published: June 2022

Alcohol use disorder (AUD) is a significant public health problem. Gene expression studies offer promising opportunities to better understand the underlying pathogenic processes. As cell-types differ in their function, gene expression profiles will typically vary across cell-types. When studying bulk tissue, failure to account for this cellular diversity has a detrimental impact on the ability to detect disease associations. We therefore assayed the transcriptomes of 32,531 individual nuclei extracted from the nucleus accumbens (NAc) of 9 donors with AUD and 9 controls. Our study identified 17 clearly delineated cell-types. We detected 26 transcriptome-wide significant association signals (q-value<0.1) that mainly involved medium spiny neurons with both D1-type and D2-type dopamine receptors, microglia and oligodendrocytes. A significantly higher number of findings than expected by chance replicated in an existing single nucleus gene expression study of alcohol dependence in the pre-frontal cortex (enrichment ratio 1.91, P value 0.019). The alcohol related genes and pathways detected for each cell-type were consistent with the functions of those cell-types reported in the literature. Thus, for the neurons we observed alcohol related neurodegeneration, disruption of circadian rhythms, alterations in glucose metabolism, and changes in synaptic plasticity. For microglia we found neuroinflammation and immune-related processes and for oligodendrocytes disruptions in myelination. This identification of the specific cell-types from which the association signals originate is key for designing proper follow-up experiments and, eventually, for developing new and targeted clinical interventions.
COVID-19 redux: clinical, virologic, and immunologic evaluation of clinical rebound after nirmatrelvir/ritonavir
Authors: Epling Brian P. , Rocco Joseph M. , Boswell Kristin L. , Laidlaw Elizabeth , Galindo Frances , Kellogg Anela , Das Sanchita , Roder Allison , Ghedin Elodie , Kreitman Allie , Dewar Robin L. , Kelly Sophie E. M. , Kalish Heather , Rehman Tauseef , Highbarger Jeroen , Rupert Adam , Kocher Gregory , Holbrook Michael R. , Lisco Andrea , Manion Maura , Koup Richard A. , Sereti Irini
Published: June 2022

Clinical rebound of COVID-19 after nirmatrelvir/ritonavir treatment has been reported. We performed clinical, virologic, and immune measurements in seven patients with symptomatic rebound, six after nirmatrelvir/ritonavir treatment and one without previous treatment. There was no evidence of severe disease or impaired antibody and T-cell responses in people with rebound symptoms.
DORA-compliant measures to assess research quality and impact in biomedical institutions: review of published research, international best practice and Delphi survey
Authors: Gagliardi Anna R , Chen Rob HC , Boury Himani , Albert Mathieu , Chow James , DaCosta Ralph S , Hoffman Michael , Keshavarz Behrang , Kontos Pia , Liu Jenny , McAndrews Mary Pat , Protze Stephanie
Published: June 2022

Objective

The San Francisco Declaration on Research Assessment (DORA) advocates for assessing biomedical research quality and impact, yet academic organizations continue to employ traditional measures such as Journal Impact Factor. We aimed to identify and prioritize measures for assessing research quality and impact.

Methods

We conducted a review of published and grey literature to identify measures of research quality and impact, which we included in an online survey. We assembled a panel of researchers and research leaders, and conducted a two-round Delphi survey to prioritize measures rated as high (rated 6 or 7 by ≥ 80% of respondents) or moderate (rated 6 or 7 by ≥ 50% of respondents) importance.

Results

We identified 50 measures organized in 8 domains: relevance of the research program, challenges to research program, or productivity, team/open science, funding, innovations, publications, other dissemination, and impact. Rating of measures by 44 panelists (60%) in Round One and 24 (55%) in Round Two of a Delphi survey resulted in consensus on the high importance of 5 measures: research advances existing knowledge, research plan is innovative, an independent body of research (or fundamental role) supported by peer-reviewed research funding, research outputs relevant to discipline, and quality of the content of publications. Five measures achieved consensus on moderate importance: challenges to research productivity, potential to improve health or healthcare, team science, collaboration, and recognition by professional societies or academic bodies. There was high congruence between researchers and research leaders across disciplines.

Conclusions

Our work contributes to the field by identifying 10 DORA-compliant measures of research quality and impact, a more comprehensive and explicit set of measures than prior efforts. Research is needed to identify strategies to overcome barriers of use of DORA-compliant measures, and to “de-implement” traditional measures that do not uphold DORA principles yet are still in use.
Helicobacter pylori promotes colorectal carcinogenesis by deregulating intestinal immunity and inducing a mucus-degrading microbiota signature
Authors: Ralser Anna , Dietl Alisa , Jarosch Sebastian , Engelsberger Veronika , Wanisch Andreas , Janssen Klaus Peter , Vieth Michael , Quante Michael , Haller Dirk , Busch Dirk H. , Deng Li , Mejías-Luque Raquel , Gerhard Markus
Published: June 2022

OBJECTIVE

H. pylori infection is the most prevalent bacterial infection worldwide. Besides being the most important risk factor for gastric cancer development, epidemiological data show that infected individuals harbor a nearly two-fold increased risk to develop colorectal cancer (CRC). However, a direct causal and functional connection between H. pylori infection and colon cancer is lacking.

DESIGN

We infected two Apc-mutant mouse models and C57BL/6 mice with H. pylori and conducted a comprehensive analysis of H. pylori-induced changes in intestinal immune responses and epithelial signatures via flow cytometry, chip cytometry, immunohistochemistry and single cell RNA sequencing. Microbial signatures were characterized and evaluated in germ-free mice and via stool transfer experiments.

RESULTS

H. pylori infection accelerated tumor development in Apc-mutant mice. We identified a unique H. pylori-driven immune alteration signature characterized by a reduction in regulatory T-cells and proinflammatory T-cells. Furthermore, in the intestinal and colonic epithelium, H. pylori induced pro-carcinogenic STAT3 signaling and a loss of goblet cells, changes that have been shown to contribute - in combination with pro-inflammatory and mucus degrading microbial signatures - to tumor development. Similar immune and epithelial alterations were found in human colon biopsies from H. pylori-infected patients. Housing of Apc-mutant mice under germ-free conditions ameliorated, and early antibiotic eradication of H. pylori infection normalized the tumor incidence to the level of uninfected controls.

CONCLUSIONS

Our studies provide evidence that H. pylori infection is a strong causal promoter of colorectal carcinogenesis. Therefore, implementation of H. pylori status into preventive measures of CRC should be considered.