bluuebunny/crossref_metadata_2025_split huggingface dataset:
AXenopusneuromast bioassay for chemical ototoxicity
Authors: Knight V. Bleu , Luna Amanda R. , Serrano Elba E. 
Published: January 2022

ABSTRACTBackgroundOtotoxic chemicals can impair the senses of hearing and balance in mammals through irreversible damage to the mechanosensory bundles of inner ear hair cells. Fish and amphibians are useful models for investigating ototoxicity because their inner ear hair cells, like those of mammals, are susceptible to damage by ototoxins. Moreover, amphibian mechanosensation is augmented by a lateral line organ on the body surface that comprises external mechanosensory hair cells. The lateral line hair cells are arranged in clusters (neuromasts) and are structurally and functionally similar to inner ear hair cells, but are more accessible for experimental manipulation. Herein, we implemented neuromasts of the amphibian (Xenopus)lateral line as an organ system for evaluating the effects of ototoxic chemicals, such as antibiotics, on mechanosensory hair cell bundles.MethodsWe examined the ultrastructure of larvalXenopus laevisneuromasts with scanning electron microscopy (SEM) after larvae were continuously exposed to ototoxic aminoglycoside antibiotics at sub-lethal concentrations (gentamicin; streptomycin; neomycin) for 72 hours.ResultsSEM images demonstrated that 72 hours of exposure to antibiotic concentrations greater than 25 µM reduced the hair cell bundle number in lateral line neuromasts.ConclusionTherapeutic drug studies will benefit from the incorporation of bioassay strategies that evaluate ototoxicity across multiple species including genera of amphibian origin such asXenopus. Our outcomes support the use of theXenopuslateral line for identification of potential ototoxic chemicals and suggest thatXenopusneuromast hair cell bundles can withstand antibiotic exposure. TheXenopusbioassay presented here can be incorporated into drug discovery methodology as a high-resolution phenotypic screen for ototoxic effects.Summary statementDamage to sensory cells of the inner ear by chemical agents such as antibiotics contributes to the growing global prevalence of disorders of hearing and balance. Our results demonstrate that theXenopuslateral line, in conjunction with SEM, affords an accessible organ system for otoxicity screens during the drug discovery pipeline.
DNA origami as a nanomedicine for targeted rheumatoid arthritis therapy through reactive oxygen species and nitric oxide scavenging
Authors: Ma Yuxuan , Lu Zhangwei , Shi Ye , Li Zhe 
Published: January 2022

AbstractHigh levels of reactive oxygen species (ROS) and nitric oxide (NO) generated by M1 macrophages induce inflammation in the development of rheumatoid arthritis (RA). The eliminating of ROS and NO therefore represents an alternative strategy for RA treatment. Because DNA molecules possess ROS- and endogenous NO-scavenging capability, herein, we develop a nanomedicine based on triangular DNA origami nanostructures for targeted RA treatment. We showed that folic acid-modified triangular DNA origami nanostructures (FA-tDONs) could reduce ROS and NO simultaneously inside proinflammatory M1 macrophages, leading to their polarization into anti-inflammatory M2 subtype. Further in vivo studies confirmed that FA-tDONs could actively target inflamed joints in collagen-induced arthritis (CIA) mice, attenuate inflammatory cytokines and alleviate disease progression. This work demonstrated that DNA origami itself could act as a potential nanomedicine for targeted RA treatment.
Genome-scale CRISPR screening reveals that C3aR signaling is critical for rapid capture of fungi by macrophages
Authors: Cohen A. , Jeng E.E. , Voorhies M. , Symington J. , Ali N. , Bassik M.C. , Sil A. 
Published: January 2022

AbstractThe fungal pathogen Histoplasma capsulatum (Hc) invades, replicates within, and destroys macrophages. To interrogate the molecular mechanisms underlying this interaction, we conducted a host-directed CRISPR-Cas9 screen and identified 361 genes that modify macrophage susceptibility to Hc infection, greatly expanding our understanding of host gene networks targeted by Hc. We identified pathways that have not been previously implicated in Hc interaction with macrophages, including the ragulator complex (involved in nutrient stress sensing), glycosylation enzymes, protein degradation machinery, mitochondrial respiration genes, solute transporters, and the ER membrane complex (EMC). The highest scoring protective hits included the complement C3a receptor (C3aR), a G-protein coupled receptor (GPCR) that recognizes the complement fragment C3a. Although it is known that the complement system reacts with the fungal surface, leading to opsonization and release of small peptide fragments such as C3a, a role for C3aR in macrophage susceptibility to fungi has not been elucidated. We demonstrated that whereas C3aR is dispensable for macrophage phagocytosis of bacteria and latex beads, it is critical for optimal macrophage capture of pathogenic fungi, including Hc, the ubiquitous fungal pathogen Candida albicans, and the causative agent of Valley Fever Coccidioides posadasii. We showed that C3aR localizes to the early phagosome during H. capsulatum infection where it coordinates the formation of actin-rich membrane protrusions that promote Hc capture. We also showed that the EMC promotes surface expression of C3aR, likely explaining its identification in our screen. Taken together, our results provide new insight into host processes that affect Hc-macrophage interactions and uncover a novel and specific role for C3aR in macrophage recognition of fungi.
Improvement of field-deployable metagenomic virus detection by a simple pretreatment method
Authors: Fomsgaard Anna S. , Rasmussen Morten , Spiess Katja , Fomsgaard Anders , Belsham Graham J. , Fonager Jannik 
Published: January 2022

AbstractAs both the current COVID-19 pandemic and earlier pandemics have shown, animals are the source for some of the deadliest viral pathogens, which can spread to humans. Therefore, early detection at the point of incidence is crucial to both prevent and understand the threats posed to human health from pathogens in animal reservoirs. Often, the exact genetic nature of these zoonotic pathogens is unknown and advanced laboratory facilities do not exist in most field settings and therefore the development of methods for unbiased metagenomic and point of incidence detection is crucial in order to identify novel viral pathogens in animals with zoonotic and pandemic potential.Here we addressed some of these issues by developing a metagenomic Nanopore next-generation sequencing (mNGS) method for nucleic acids extracted from clinical samples from patients with SARS-CoV-2. To reduce the non-RNA viral genetic components in the samples, we used DNase pretreatment in a syringe followed by filtration and found that these pretreatments increased the number of SARS-CoV2 reads by > 500-fold compared with no pretreatment.The simple protocol, described here, allows for fast (within 6 hours) metagenomic detection of RNA viruses in biological samples exemplified by SARS-CoV-2 detection in clinical throat swabs. This method could also be applied in field settings for point of incidence detection of virus pathogens, thus eliminating the need for transport of infectious samples, cold storage and a specialized laboratory.HighlightsHere we present a field-deployable metagenomic Nanopore protocol for RNA virus detection.SARS-CoV-2 detection used as proof-of-concept.Analysis of simple methods for non-viral nucleic acid depletion were tested on SARS-CoV-2 clinical samples.DNase I treatment followed by 0.22µM syringe filtration dramatically increased the number of SARS-CoV-2 reads and virus genome coverage.
An in vitro and computational validation of a novel loss-of-functional mutation in PAX9 associated with non-syndromic tooth agenesis
Authors: Sarkar Tanmoy , Ranjan Prashant , Kanathur Smitha , Gupta Ankush , Das Parimal 
Published: January 2022

AbstractCongenital tooth agenesis (CTA) is one of the most common craniofacial anomalies. Its frequency varies among different population depending upon the genetic heterogeneity. CTA could be of familial or sporadic and syndromic or non-syndromic. Five major genes are found to be associated with non-syndromic CTA namely, PAX9, MSX1, EDA1, AXIN2 and WNT10A. In this study, an India family with CTA was investigated and a novel c.336C>G variation was identified in the exon 3 of PAX9, leading to substitution of evolutionary conserved Cys with Trp at 112 amino acid position located at the functionally significant DNA binding paired domain region. Functional analysis revealed that p.Cys112Trp mutation did not prevent the nuclear localization although mutant protein had higher cytoplasmic retention. EMSA using e5 probe revealed that mutant protein was unable to bind with the paired-domain binding site. Subsequently, GST pull-down assay revealed lower binding activity of the mutant protein with its known interactor MSX1. Further RNA-sequencing of PAX9 over-expressed HEK293, identified two potential novel targets, WNT4 and WNT7b those are up-regulated by wild-type PAX9 but not by mutant. These in vitro results were consistent with the computational results. The in vitro and computational observations altogether suggest that c.336C>G (p.Cys112Trp) variation leads to loss-of-function of PAX9 leading to CTA in this family.
Loss of p53 tumor suppression function drives invasion and genomic instability in models of murine pancreatic cancer
Authors: Tonelli Claudia , Deschênes Astrid , Yao Melissa A. , Park Youngkyu , Tuveson David A. 
Published: January 2022

ABSTRACTPancreatic ductal adenocarcinoma (PDA) is a deadly disease with few treatment options. There is an urgent need to better understand the molecular mechanisms that drive disease progression, with the ultimate aim of identifying early detection markers and clinically actionable targets. To investigate the transcriptional and morphological changes associated with pancreatic cancer progression, we analyzed the KrasLSLG12D/+; Trp53LSLR172H/+; Pdx1-Cre (KPC) mouse model. We have identified an intermediate cellular event during pancreatic carcinogenesis in the KPC mouse model of PDA that is represented by a subpopulation of tumor cells that express KrasG12D, p53R172H and one allele of wild-type Trp53. In vivo, these cells represent a histological spectrum of pancreatic intraepithelial neoplasia (PanIN) and acinar-to-ductal metaplasia (ADM) and rarely proliferate. Following loss of wild-type p53, these precursor lesions undergo malignant de-differentiation and acquire invasive features. We have established matched organoid cultures of pre-invasive and invasive cells from murine PDA. Expression profiling of the organoids led to the identification of markers of the pre-invasive cancer cells in vivo and mechanisms of disease aggressiveness.
Novel enhancers of guanylyl cyclase-A activity via allosteric modulation
Authors: Andresen Henriette , Pérez-Ternero Cristina , Robinson Jerid , Dickey Deborah M , Hobbs Adrian J , Potter Lincoln R , Levy Finn Olav , Cataliotti Alessandro , Moltzau Lise Román 
Published: January 2022

ABSTRACTNatriuretic peptide receptor (NPR)-A (also known as NPR-A, NPR1 or guanylyl cyclase-A, GC-A) is an attractive but challenging target to activate with small molecules. GC-A is activated by endogenous atrial natriuretic peptide (ANP) and B-type natriuretic peptide (BNP), and this activation leads to the production of 3’,5’-cyclic guanosine monophosphate (cGMP). This system plays an important role in the regulation of cardiovascular and renal homeostasis. However, utilization of this receptor as a drug target has so far been limited to peptides, even though small molecule modulators allow oral administration and longer half-life. We have identified small molecular allosteric enhancers of GC-A, which strengthened ANP or BNP activation in various in vitro and ex vivo systems. These compounds do not mediate their actions through previously described allosteric binding sites or via known mechanisms of action. In addition, their selectivity and activity are dependent on only one amino acid in GC-A. Our findings show that there is a novel allosteric binding site on GC-A, which can be targeted by small molecules that increase the signaling effects of ANP and BNP.
NeoRdRp: A comprehensive dataset for identifying RNA-dependent RNA polymerase of various RNA viruses from metatranscriptomic data
Authors: Sakaguchi Shoichi , Urayama Syun-ichi , Takaki Yoshihiro , Hirosuna Kensuke , Wu Hong , Suzuki Youichi , Nunoura Takuro , Nakano Takashi , Nakagawa So 
Published: January 2022

AbstractRNA viruses are distributed throughout various environments, and most RNA viruses have recently been identified by metatranscriptome sequencing. However, due to the high nucleotide diversity of RNA viruses, it is still challenging to identify novel RNA viruses from metatranscriptome data. To overcome this issue, we created a dataset of RNA-dependent RNA polymerase (RdRp) domains that are essential for all RNA viruses belonging to Orthornavirae. Genes with RdRp domains from various RNA viruses were clustered based on their amino acid sequence similarity. For each cluster, a multiple sequence alignment was generated, and a hidden Markov model (HMM) profile was created if the number of sequences was greater than three. We further refined the 426 HMM profiles by detecting the RefSeq RNA virus sequences and subsequently combined the hit sequences with the RdRp domains. As a result, a total of 1,182 HMM profiles were generated from 12,502 RdRp domain sequences, and the dataset was named NeoRdRp. Almost all NeoRdRp HMM profiles successfully detected RdRp domains, specifically in the UniProt dataset. Furthermore, we compared the NeoRdRp dataset with two previously reported methods for RNA virus detection using metatranscriptome sequencing data. Our methods successfully identified most of the RNA viruses in the datasets; however, some RNA viruses were not detected, as in the cases of the other two methods. The NeoRdRp can be repeatedly improved by adding new RdRp sequences and is applicable as a system for detecting various RNA viruses from diverse metatranscriptome data.
The gut microbiota affects the social network of honeybees
Authors: Liberti Joanito , Kay Tomas , Quinn Andrew , Kesner Lucie , Frank Erik T. , Cabirol Amélie , Richardson Thomas O. , Engel Philipp , Keller Laurent 
Published: January 2022

AbstractThe gut microbiota influences animal neurophysiology and behavior but has not previously been documented to affect emergent group-level behaviors. Here we combine gut microbiota manipulation with automated behavioral tracking of honeybee sub-colonies to show that the microbiota increases the rate and specialization of social interactions. Microbiota colonization was associated with higher abundances of one third of metabolites detected in the brain, including several amino acids, and a subset of these metabolites were significant predictors of social interactions. Colonization also affected brain transcriptional processes related to amino acid metabolism and epigenetic modification in a brain region involved in sensory perception. These results demonstrate that the gut microbiota modulates the emergent colony social network of honeybees, likely via changes in chromatin accessibility and amino acid biosynthesis.
Discovery of a MUC3B gene reconstructs the membrane mucin gene cluster on human chromosome 7
Authors: Lang Tiange , Pelaseyed Thaher 
Published: January 2022

AbstractHuman tissue surfaces are coated with mucins, a family of macromolecular sugar-laden proteins serving diverse functions from lubrication to formation of selective biochemical barriers against harmful microorganisms and molecules. Membrane mucins are a distinct group of mucins that are attached to epithelial cell surfaces where they create a dense glycocalyx facing the extracellular environment. All mucin proteins carry long stretches of tandemly repeated sequences that undergo extensive O-linked glycosylation to form linear mucin domains. However, the repetitive nature of mucin domains makes them prone to recombination and render their genetic sequences particularly difficult to read with standard sequencing technologies. As a result, human mucin genes suffer from significant sequence gaps that have hampered investigation of gene function in health and disease. Here we leveraged a recent human genome assembly to identify a previously unmapped MUC3B gene located within a cluster of four structurally related membrane mucin genes that we entitle the MUC3 cluster at q22 locus in chromosome 7. We found that MUC3B shares high sequence identity with the known MUC3A gene, and that the two genes are governed by evolutionarily conserved regulatory elements. Furthermore, we show that MUC3A, MUC3B, MUC12 and MUC17 in the human MUC3 cluster are exclusively expressed in intestinal epithelial cells. Our results complete existing genetic gaps in the MUC3 cluster that is a conserved genetic unit during primate evolution. We anticipate our results to be the starting point for detection of new polymorphisms in the MUC3 cluster associated with human diseases. Moreover, our study provides the basis for exploration of intestinal mucin gene function in widely used experimental models such as human intestinal organoids and genetic mouse models.
The 24-chain core-shell nanostructure of wood cellulose microfibrils in seed plants
Authors: Chang Chih-Hui , Cai Wenjie , Lin Jer-Horng , Huang Shing-Jong , Lin Ying-Chung Jimmy , Tsao Cheng-Si , Tai Hwan-Ching 
Published: January 2022

AbstractWood cellulose microfibrils (CMFs) are the most abundant organic substance on earth, but their nanostructures are poorly understood. There are controversies regarding the glucan chain number (N) of CMFs during initial synthesis and whether they become fused afterwards. Here, we combined small-angle X-ray scattering (SAXS), solid-state nuclear magnetic resonance (ssNMR) and X-ray diffraction (XRD) analyses to resolve these controversies. We successfully developed SAXS measurement methods for the cross-section aspect ratio and area of the crystalline-ordered CMF core, which showed higher density than the semi-disordered shell. The 1:1 aspect ratio suggested that CMFs remain mostly segregated, not fused. The area measurement revealed the chain number in the core zone (Ncore). The ratio of ordered cellulose over total cellulose, termed Roc, was determined by ssNMR. Using the formula N = Ncore / Roc, we found that the majority of wood CMFs contain 24 chains, conserved between gymnosperm and angiosperm trees. The average wood CMF has a crystalline-ordered core of ∼2.2 nm diameter and a semi-disordered shell of ∼0.5 nm thickness. In naturally and artificially aged wood, we only observed CMF aggregation (contact without crystalline continuity) but not fusion (forming conjoined crystalline unit). This further argued against the existence of partially fused CMFs in new wood, overturning the recently proposed 18-chain fusion hypothesis. Our findings are important for advancing wood structural knowledge and more efficient utilization of wood resources in sustainable bio-economies.
Parasite defensive limb movements enhance signal attraction in male little torrent frogs: insight into the evolution of multimodal signals
Authors: Zhao Longhui , Wang Jichao , Zhang Haodi , Wang Tongliang , Yang Yue , Tang Yezhong , Halfwerk Wouter , Cui Jianguo 
Published: January 2022

AbstractMany animals rely on complex sexual signals that target multiple senses to attract mates and repel rivals. These multimodal mating displays can however also attract unintended receivers, which can be an important driver of signal complexity. Despite being taxonomically widespread, we often lack insight into how multimodal signals evolve from unimodal signals and in particular what roles unintended eavesdroppers play. Here we assess whether the physical movements of parasite defense behavior increase the complexity and attractiveness of an acoustic sexual signal in the little torrent frog (Amolops torrentis). Calling males of this species often display limb movements in order to defend against blood-sucking parasites such as frog-biting midges that eavesdrop on their acoustic signal. Through mate choice tests we show that some of these midge-evoked movements influence female preference for acoustic signals. Our data suggest that midge-induced movements may be incorporated into a sexual display, targeting both hearing and vision in the intended receiver. Females may play an important role in incorporating these multiple components because they prefer signals which combine multiple programs. Our results thus help to understand the relationship between ecological and sexual selection pressure operating on signalers and how in turn this may influence multimodal signal evolution.
Cell type-specific interpretation of noncoding variants using deep learning-based methods
Authors: Sindeeva Maria , Chekanov Nikolay , Avetisian Manvel , Baranov Nikita , Malkin Elian , Lapin Alexander , Kardymon Olga , Fishman Veniamin 
Published: January 2022

AbstractInterpretation of non-coding genomic variants is one of the most important challenges in human genetics. Machine learning methods have emerged recently as a powerful tool to solve this problem. State-of-the-art approaches allow prediction of transcriptional and epigenetic effects caused by non-coding mutations. However, these approaches require specific experimental data for training and can not generalize across cell types where required features were not experimentally measured. We show here that available epigenetic characteristics of human cell types are extremely sparse, limiting those approaches that rely on specific epigenetic input. We propose a new neural network architecture, DeepCT, which can learn complex interconnections of epigenetic features and infer unmeasured data from any available input. Furthermore, we show that DeepCT can learn cell type-specific properties, build biologically meaningful vector representations of cell types and utilize these representations to generate cell type-specific predictions of the effects of non-coding variations in the human genome.
INFLUENCE OF RAT CENTRAL THALAMIC NEURONS ON FORAGING BEHAVIOR IN A HAZARDOUS ENVIRONMENT
Authors: Herzallah Mohammad M. , Amir Alon , Paré Denis 
Published: January 2022

ABSTRACTThe basolateral amygdala (BL) is a major regulator of foraging behavior. Following BL inactivation, rats become indifferent to predators. However, at odds with the view that the amygdala detects threats and generate defensive behaviors, most BL neurons have reduced firing rates during foraging and at proximity of the predator. In search of the signals determining this unexpected activity pattern, this study considered the contribution of the central medial thalamic nucleus (CMT), which sends a strong projection to BL, mostly targeting its principal neurons. Inactivation of CMT or BL with muscimol abolished the rats’ normally cautious behavior in the foraging task. Moreover, unit recordings revealed that CMT neurons showed large but heterogeneous activity changes during the foraging task, with many neurons decreasing or increasing their discharge rates, with a modest bias for the latter. A generalized linear model revealed that CMT neurons encode many of the same task variables as principal BL cells. However, the nature (inhibitory vs. excitatory) and relative magnitude of the activity modulations seen in CMT neurons differed markedly from those of principal BL cells but were very similar to those of fast-spiking BL interneurons. Together, these findings suggest that, during the foraging task, CMT inputs fire some principal BL neurons, recruiting feedback interneurons in BL, resulting in the widespread inhibition of principal BL cells.