bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of neuropeptides in regulating ecdysis and reproduction in the hemimetabolous insect Rhodnius prolixus
Authors: Sterkel Marcos , Volonté Mariano , Albornoz Maximiliano G. , Wulff Juan Pedro , del Huerto Sánchez Mariana , Terán Paula María , Ajmat María Teresa , Ons Sheila 
Published: April 2022

AbstractIn ecdysozoan animals, moulting entails the production of a new exoskeleton and the shedding of the old one during ecdysis. It is induced by a pulse of ecdysone that regulates the expression of different hormonal receptors and activates a peptide-mediated signalling cascade. In Holometabola, the peptidergic cascade regulating ecdysis has been well described. However, very little functional information regarding the neuroendocrine regulation of ecdysis is available for Hemimetabola, which displays an incomplete metamorphosis.Here, we studied neuropeptides related to ecdysis regulation in the hemi-metabolous insect Rhodnius prolixus. The RNA interference-mediated reduction of ETH expression in fourth instar nymphs resulted in lethality at the expected time of ecdysis, thereby showing its crucial role in this process. Furthermore, the results revealed the involvement of ETH in the regulation of reproductive fitness. Different from holometabolous, the knockdown of ETH in adult females led to failures in egg hatching without affecting the oviposition. Most of the first instar nymphs hatched from the eggs laid by females injected with dsEH, dsCCAP and dsOKA died at the expected time of ecdysis, indicating the crucial involvement of these genes for post-embryonic development. No phenotypes were observed upon CZ knockdown in nymphs or adult females. The conservation of the role of these neuropeptides in regulating ecdysis and reproduction throughout the class Insecta is discussed.Summary statementThe information provided here is of interest for evolutive studies on the neuroendocrine regulation of ecdysis and reproduction in insects, and the research for new targets to control pest insects.
Co-expression of recombinant human collagen α1(III) chain with viral prolyl 4-Hydroxylase in P. pastoris GS115
Authors: Fang Jiayuan , Ma Ze , Liu Dongyue , Wang Zhaoguo , Zheng Shuo , Wu Hongyan , Xia Peijun , Chen Xi , Yang Rui , Hao Linlin 
Published: April 2022

AbstractProlyl 4-hydroxylase (P4H) is essential to maintain the stable triple-helix structure and function of human collagen α1(Ш) chain (COL3A1). To obtain hydroxylated human COL3A1, the human COL3A1 and the viral P4H A085R were co-expressed in P. pastoris GS115. The sequence of human COL3A1 without N-terminal and C-terminal was selected for expression. Colony PCR analysis and sequencing after transfection showed that the target gene had inserted successfully. Real-time quantitative PCR (RT-qPCR) indicated that human COL3A1 and P4H were expressed at the mRNA levels. SDS-PAGE and Western blotting analysis of supernatant from the recombinant methylotrophic yest culture showed that recombinant human COL3A1 (rhCOL3A1) was secreted into the culture medium with an apparent molecular mass of approximately 130 kDa. It was noted that the rhCOL3A1 expession quantity was higest at 120 h of induction. Furthermore, mass spectrometry analysis demonstrated that the rhCOL3A1 was expressed successfully. His-tagged rhCOL3A1 protein was purified by Ni-affinity column.
The Computational Neuroanatomy of Predictive Dynamics of Pain Perception
Authors: Ishikawa Ryota , Izawa Jun 
Published: April 2022

AbstractPain perception is an active process that regulates nociceptive inputs by descending opioidergic signals, in which the brain encodes pain-related predictive and corrective terms, after having made Bayesian-like inferences about noxious amplitudes. Offset analgesia (OA), a large reduction of tonic pain after a small nociceptive termination, is typical empirical evidence of on-line pain modulation through prediction and its correction. However, the basic computational structure underlying OA is not understood. Here, we adopted a constructive approach, formulated the inference of noxious amplitudes with a Kalman filter model, i.e., a recursive Bayesian computation, and then deduced the computational structure for OA, in which an interaction between two latent state variables was implemented. Simulation results suggested that the unidirectional interaction of the two states with two dissociable roles (an integral over time and a derivative of stimulus changes) is crucial for OA. Our results, combined with previous anatomical studies, suggest a computational basis of neural connectivity for pain. The ACC and aINS interact to compute a descending prediction to the brainstem, i.e. PAG, while ascending inputs are filtered in the thalamus and delivered to the cortices as prediction errors. Thus, we suggest dissociable, computational roles of the ACC and aINS in pain processing.Author SummaryUnderstanding the computational theory of pain perception is crucial for clarifying why some painful syndromes become chronic. Here, we propose a computational neuroanatomical model of endogenous pain modulation and we simulate a model for offset analgesia. We first demonstrate through model comparisons that the brain encodes at least two distinct states to estimate ongoing nociception: a derivative of input changes and its integral. We suggest that its neural substrate comprises hierarchical circuits composed of cortices, the thalamus, and brainstem. Second, we show that the computational basis of disrupted pain modulation in patients is pseudo-neglect of actual sensory inputs, with bias toward the internal prediction. Our results are the first to provide a neurocomputational mechanism of pain perception dynamics and a factor that determines its functionality.
Isolation, purification, and characterisation of a phage tail-like bacteriocin from the insect pathogenic bacterium Brevibacillus laterosporus
Authors: Babar Tauseef Khan , Glare Travis R. , Hampton John G. , Hurst Mark R.H. , Narciso Josefina O. 
Published: April 2022

AbstractThe gram-positive and spore-forming bacterium Brevibacillus laterosporus (Bl) belongs to the Brevibacillus brevis phylogenetic cluster. Isolates of the species have demonstrated pesticidal potency against a wide range of invertebrate pests and plant diseases. Two New Zealand isolates, Bl 1821L and Bl 1951, are under development as biopesticides for control of diamondback moth and other pests. However, due to often restricted growth of these endemic isolates, production can be an issue. During investigations of the cause of the disrupted growth, electron micrographs of crude lysate of Bl 1821L showed the presence of phages tail-like structures. PEG 8000 precipitated lysate harbouring the putative phage tail-like particles demonstrated broad-spectrum activity against several gram-positive bacteria. SDS-PAGE of purified and concentrated lysate showed a prominent protein band of ∼48 kD from where transmission electron microscopy revealed the presence of polysheath-like structures. N-terminal sequencing of the ∼48 kD protein mapped to a gene with weak predicted amino acid homology to a Bacillus PBSX phage-like element xkdK, the translated product of which shared >90% amino acid similarity to the phage tail-sheath protein of another Bl published genome, LMG15441. An xkdK homolog was also identified in the Bl 1951 genome. However, genome comparison of the region around the xkdK gene between Bl 1821L and Bl 1951 found differences including two glycine rich protein encoding genes which contain imperfect repeats (1700 bp) in Bl 1951, while a putative phage region resides in the analogous Bl 1821L region. Although comparative analysis of the genomic organisation of Bl 1821L and Bl 1951 PBSX-like region with the defective phages PBSX, PBSZ, and PBP 180 of Bacillus subtilis isolates 168 and W23, and Bacillus phage PBP180 revealed low amino acids similarity, the genes encode similar functional proteins in similar arrangements, including phage tail-sheath (XkdK), tail (XkdO), holin (XhlB), and N-acetylmuramoyl-L-alanine (XlyA). AMPA analysis identified a bactericidal stretch of 13 amino acids in the ∼48 kD sequenced protein of Bl 1821L. Assays of purified ∼48 kD protein of Bl 1821L caused a decrease of 34.2% in the number of viable cells of Bl 1951, 18 hours after treatment as compared to the control.Significance of the studyThis study for the first time isolated, purified, and characterised putative phage tail-like bacteriocins (PTLBs) from the insect pathogenic isolates of Brevibacillus laterosporus. Identified PTLBs caused a decrease in the number of viable cells of Bl 195, 18 hours after treatment as compared to control. Therefore, it is likely that the putative PTLBs might have implications in harnessing the insecticidal potential of this useful bacterium.
Self-avoidance alone does not explain the function of Dscam1 in mushroom body axonal wiring
Authors: Dong Haiyang , Guo Pengjuan , Zhang Jian , Wu Lili , Fu Ying , Li Lei , Zhu Yanda , Du Yiwen , Shi Jilong , Zhang Shixin , Li Guo , Xu Bingbing , Bian Lina , Zhu Xiaohua , You Wendong , Shi Feng , Yang Xiaofeng , Huang Jianhua , Jin Yongfeng 
Published: April 2022

SUMMARYAlternative splicing of Drosophila Dscam1 into 38,016 isoforms provides neurons with a unique molecular code for self-recognition and self-avoidance. A canonical model suggests that homophilic binding of identical Dscam1 isoforms on sister branches of mushroom body (MB) axons supports segregation with high fidelity, even when only a single isoform is expressed. Here we generated a series of mutant flies with a single exon 4, 6, or 9 variant, encoding 1,584, 396, or 576 potential isoforms, respectively. Surprisingly, most of the mutants in the latter two groups exhibited obvious defects in the growth, branching, and segregation of MB axonal sister branches. This demonstrates that repertoires of 396 and 576 Dscam1 isoforms were not sufficient for normal patterning of axonal branches. Moreover, reducing Dscam1 levels largely reversed the defects caused by reduced isoform diversity, suggesting a functional link between Dscam1 expression levels and isoform diversity. Taken together, these results indicate that canonical self-avoidance alone does not explain the function of Dscam1 in MB axonal wiring.
The sphingolipid inhibitor myriocin increases susceptibility of Candida auris to amphotericin B
Authors: Stieber Hanna , Junghanns Lara , Wilhelm Hannah , Batliner Maria , Aldejohann Alexander Maximilian , Kurzai Oliver , Martin Ronny 
Published: April 2022

AbstractThe emerging human fungal pathogen Candida auris can cause of hospital outbreaks by transmission between patients and / or medical care staff. It is known for a fast adaption to environmental stress and antifungal treatment. Besides resistance to fluconazole in most isolates, C. auris frequently shows limited susceptibility to echinocandins and even to amphotericin B. Therefore, multidrug resistance (MDR) is frequently found in clinical isolates, leading to a need for new therapeutic targets and compounds. One of those targets could be sphingolipids which are an integral part of the cell membrane and are important for membrane fluidity and the formation of lipid rafts. Here, we show that myriocin-mediated inhibition of the de novo sphingolipid biosynthesis caused severe growth defects in C. auris. Sublethal myriocin concentrations increase fungal susceptibility to amphotericin B and anidulafungin. While the effect is limited for anidulafungin, even isolates that show phenotypic resistance to amphotericin B became susceptible in presence of myriocin. A large-scale screening of 59 clinical isolates validated these initial results and showed that inhibition of the de novo sphingolipid biosynthesis increases C. auris susceptibility to amphotericin B. These observations open new options for future therapeutic strategies and illustrate that sphingolipids might play a pivotal role for the ability of C. auris to develop resistance against amphotericin B.
Cis mutagenesis in vivo reveals extensive noncanonical functions of Dscam1 isoforms in neuronal wiring
Authors: Zhang Shixin , Yang Xi , Dong Haiyang , Xu Bingbing , Wu Lili , Zhang Jian , Li Guo , Guo Pengjuan , Li Lei , Fu Ying , Du Yiwen , Zhu Yanda , Shi Feng , Huang Jianhua , He Haihuai , Jin Yongfeng 
Published: April 2022

AbstractDrosophila Dscam1 encodes ten thousand of cell recognition molecules via alternative splicing, which is required for nervous function. However, the underlying mechanism has not fully understood. Here we revealed extensive noncanonical functions of Dscam1 isoform diversity in neuronal wiring. We generated a series of allelic cis mutations in Dscam1, encoding normal number of isoforms albeit with altered isoform composition. Despite normal dendritic self-avoidance and self/non-self discrimination in da neurons, which is consistent with canonical self-avoidance model, these mutants exhibited strikingly distinct spectra of phenotypic defects in three classes of neurons: up to ∼60% defects in mushroom bodies, a significantly increased branching and growth in da neurons, and mild axonal branching defects in mechanosensory neurons. These data suggest that proper Dscam1 isoform composition is required for axon and dendrite growth in diverse neurons. This unprecedented splicing-tuned regulation unlocks new insights into the molecular mechanisms that Dscam1 isoform diversity is engaged in.
High-throughput proteomics of nanogram-scale samples with Zeno SWATH DIA
Authors: Wang Ziyue , Mülleder Michael , Batruch Ihor , Chelur Anjali , Textoris-Taube Kathrin , Schwecke Torsten , Hartl Johannes , Causon Jason , Castro-Perez Jose , Demichev Vadim , Tate Stephen , Ralser Markus 
Published: April 2022

AbstractThe ability to conduct high-quality proteomic experiments in high throughput has opened new avenues in clinical research, drug discovery, and systems biology. Next to an increase in quantitative precision, recent developments in high-throughput proteomics have also gained proteomic depth, to the extent that earlier gaps between classic and high-throughput experiments have significantly narrowed. Here we introduce and benchmark Zeno SWATH, a data-independent acquisition technique that employs a linear ion trap pulsing (Zeno trap pulsing) in order to increase proteomic depth and dynamic range in proteomic experiments. Combined with the high acquisition speed, these gains in sensitivity are particularly attractive for conducting high-throughput proteomics experiments with high chromatographic flow rates and fast gradients. We demonstrate that when combined with either micro-flow- or analytical-flow-rate chromatography, Zeno SWATH increases protein identification in complex samples 5- to 10-fold when compared to current SWATH acquisition methods on the same instrument. Using 20-min micro-flow chromatography, Zeno SWATH identified > 6,000 proteins from a 62.5 ng load of human cell lysate with more than 5,000 proteins consistently quantified in triplicate injections with a median CV of 6%. Using 5-min analytical-flow-rate chromatography (800 µl/min), Zeno SWATH identified 4,907 proteins from a triplicate injection of 2 µg of a human cell lysate; or more than 3,000 proteins from 250 ng tryptic digest. Zeno SWATH hence facilitates precise proteomic experiments with small sample amounts using a fast and robust high flow-rate chromatographic method, broadening the application space that requires precise proteomic experiments on a large scale.
Pneumococcal Evasion of Antibiotics via Metabolic Adaptation During Infection
Authors: Dao Tina H. , Echlin Haley , McKnight Abigail , Marr Enolia S. , Junker Julia , Jia Qidong , Hayden Randall , Rosch Jason W. 
Published: April 2022

ABSTRACTStreptococcus pneumoniae is a major human pathogen of global health concern, causing a range of mild to severe infections, including acute otitis media, pneumonia, sepsis, and meningitis. The rapid emergence of antibiotic resistance among S. pneumoniae isolates poses a serious public health problem worldwide. Resistant pneumococcal strains have rendered the mainstay treatment with beta-lactams, fluoroquinolones, and macrolides, ineffective. Antibiotic resistance in S. pneumoniae has spread globally via the emergence of de novo mutations and horizontal transfer of resistance. Fluoroquinolone resistance in S. pneumoniae is an intriguing case because the prevalence of fluoroquinolone resistance does not correlate with increasing usage, as is often the case with other classes of antibiotics. In this study, we demonstrated that deleterious fitness costs constrain the emergence of individual fluoroquinolone resistance mutations in either topoisomerase IV or gyrase A in S. pneumoniae. Generation of double point mutations in the target enzymes in topoisomerase IV and gyrase A conferred high-level fluoroquinolone resistance while restoring fitness comparable to the sensitive wild-type. During an in vivo model of antibiotic resistance evolution, S. pneumoniae was able to circumvent deleterious fitness costs imposed by resistance determinants through development of antibiotic tolerance through metabolic adaptation that reduced the production of reactive oxygen species, an effect that could be recapitulated pharmacologically. The metabolic mutants conferring tolerance resulted in a fitness benefit during infection following antibiotic treatment with fluroquinolones. These data suggest that emergence of fluoroquinolone resistance is tightly constrained in S. pneumoniae by host fitness tradeoffs and that mutational pathways involving metabolic networks to enable tolerance phenotypes may be an important contributor to the evasion of antibiotic mediated killing.
CanSig: a tool for benchmarking malignant state discovery in single-cell RNA-Seq data
Authors: Barkmann Florian , Yates Josephine , Czyz Pawel , Kraft Agnieszka , Glettig Marc , Beerenwinkel Niko , Boeva Valentina 
Published: April 2022

AbstractSingle-cell RNA sequencing (scRNA-seq) facilitates the discovery of gene signatures that define cell states across patients, which could be used in patient stratification and drug discovery. However, the lack of standardization in computational methodologies to analyse these data impedes the reproducibility of signature detection. To address this, we developed CanSig, a comprehensive benchmarking tool that evaluates methods for identifying transcriptional signatures in cancer. CanSig integrates metrics for batch correction and biological signal conservation with a gene signature correlation metric to score according to rediscovery, cross-dataset reproducibility, and clinical relevance. We applied CanSig to ten methods and to ten scRNA-seq datasets from four human cancer types—glioblastoma, breast cancer, lung adenocarcinoma, and cutaneous squamous cell carcinoma— representing 116 patients and 105,000 malignant cells. Our results identify BBKNN as a leading method. We showed that the signatures identified with these methods correlate with clinically relevant outcomes, including patient survival and lymph node metastasis. Thus, CanSig establishes a standardized framework for reproducible cancer transcriptomics analysis.
This is GlycoQL
Authors: Hayes Catherine , Daponte Vincenzo , Mariethoz Julien , Lisacek Frederique 
Published: April 2022

AbstractMotivationWe have previously designed and implemented a tree-based ontology to represent glycan structures with the aim of searching these structures with a glyco-driven syntax. This resulted in creating the GlySTreeM knowledge-base as a linchpin of the matching procedure and we now introduce a query language, called GlycoQL, for the actual implementation of a glycan structure search.ResultsThe methodology is described and illustrated with a use-case focused on SARS-CoV-2 spike protein glycosylation. We show how to enhance site annotation with federated queries involving UniProt and GlyConnect, our glycoprotein database.Availabilitycurrently only available for reviewers at:https://beta.glyconnect.expasy.org/glycoql/Contactcatherine.hayes@unige.ch;frederique.lisacek@sib.swissSupplementary informationSupplementary data are available athttps://glyconnect.expasy.org/glystreem/wiki.
Linkage mapping and genome annotation give novel insights into gene family expansions and regional recombination rate variation in the painted lady (Vanessa cardui) butterfly
Authors: Shipilina Daria , Näsvall Karin , Höök Lars , Vila Roger , Talavera Gerard , Backström Niclas 
Published: April 2022

AbstractGene family expansions and crossing over are two main mechanisms for the generation of novel genetic variants that can be picked up by natural selection. Here, we developed a high-density, pedigree-based linkage map of the painted lady butterfly (Vanessa cardui) – a non-diapausing, highly polyphagous species famous for its long-distance migratory behavior. We also performed detailed annotations of genes and interspersed repetitive elements for a previously developed genome assembly, characterized species-specific gene family expansions and the relationship between recombination rate variation and genomic features. Identified expanded gene families consisted of clusters of tandem duplications with functions associated with protein and fat metabolism, detoxification, and defense against infection - key functions for the painted lady’s unique lifestyle. The detailed assessment of recombination rate variation demonstrated a negative association between recombination rate and chromosome size. Moreover, the recombination landscape along the holocentric chromosomes was bimodal. The regional recombination rate was positively associated with the proportion of short interspersed elements (SINEs), but not the other repeat classes, potentially a consequence of SINEs hijacking the recombination machinery for proliferation. The detailed genetic map developed here will contribute to the understanding of the mechanisms and evolutionary consequences of recombination rate variation in Lepidoptera in general. We conclude that the structure of the painted lady genome has been shaped by a complex interplay between recombination, gene duplications and TE-activity and that specific gene family expansions have been key for the evolution of long-distance migration and the ability to utilize a wide range of host plants.
The EGFR/ErbB inhibitor neratinib modifies the neutrophil phosphoproteome and promotes apoptosis and clearance by airway macrophages
Authors: Herman Kimberly D , Wright Carl G , Marriott Helen M , McCaughran Sam C , Collins Mark O , Renshaw Stephen A , Prince Lynne R 
Published: April 2022

AbstractDysregulated neutrophilic inflammation can be highly destructive in chronic inflammatory diseases due to prolonged neutrophil lifespan and continual release of histotoxic mediators in inflamed tissues. Therapeutic induction of neutrophil apoptosis, an immunologically silent form of cell death, may be beneficial in these diseases, provided that the apoptotic neutrophils are efficiently cleared from the tissue. Our previous research identified ErbB inhibitors as able to induce neutrophil apoptosis and reduce neutrophilic inflammation bothin vitroandin vivo(Rahman et al., 2019). Here we extend that work using a clinical ErbB inhibitor, neratinib, which has the potential to be repurposed in inflammatory diseases. We show that neratinib reduces neutrophilic migration to an inflammatory site in zebrafish larvae. Neratinib upregulates efferocytosis and reduces the number of persisting neutrophil corpses in mouse models of acute, but not chronic, lung injury, suggesting the drug may have therapeutic benefits in acute inflammatory settings. Phosphoproteomics analysis of human neutrophils shows that neratinib modifies the phosphorylation of proteins regulating apoptosis, migration and efferocytosis. This work identifies a potential mechanism for neratinib in treating acute lung inflammation by upregulating the clearance of dead neutrophils and, through examination of the neutrophil phosphoproteome, provides important insights into the mechanisms by which this may be occurring.