bluuebunny/crossref_metadata_2025_split huggingface dataset:
What are we missing by using hydrophilic enrichment? Improving bacterial glycoproteome coverage using total proteome and FAIMS analysis
Authors: Izaham Ameera Raudah Ahmad , Ang Ching-Seng , Nie Shuai , Bird Lauren E. , Williamson Nicholas A. , Scott Nichollas E. 
Published: July 2020

ABSTRACTHydrophilic Interaction Liquid Chromatography (HILIC) glycopeptide enrichment is an indispensable tool for the high-throughput characterisation of glycoproteomes. Despite its utility, HILIC enrichment is associated with a number of short comings including requiring large amounts of starting material, potentially introducing chemical artefacts such as formylation, and biasing/under-sampling specific classes of glycopeptides. Here we investigate HILIC enrichment independent approaches for the study of bacterial glycoproteomes. Using three Burkholderia species (B. cenocepacia, B. dolosaandB. ubonensis) we demonstrate that short aliphaticO-linked glycopeptides are typically absent from HILIC enrichments yet are readily identified in whole proteome samples. Using Field Asymmetric Waveform IMS (FAIMS) fractionation we show that at low compensation voltages (CVs) short aliphatic glycopeptides can be enriched from complex samples providing an alternative means to identify glycopeptides recalcitrant to hydrophilic based enrichment. Combining whole proteome and FAIMS analysis we show that the observable glycoproteome of these Burkholderia species is at least 30% larger than initially thought. Excitingly, the ability to enrich glycopeptides using FAIMS appears generally applicable, with theN-linked glycopeptides ofCampylobacter fetus subsp. fetusalso enrichable at low FAIMS CVs. Taken together, these results demonstrate that FAIMS provides an alternative means to access glycopeptides and is a valuable tool for glycoproteomic analysis.
A toxin-antitoxin system associated transcription factor ofCaulobacter crescentuscan influence cell cycle-regulated gene expression during the SOS response
Authors: Ghosh Koyel , Ankær Brejndal Kamilla , Kirkpatrick Clare L. 
Published: July 2020

AbstractToxin-antitoxin (TA) systems are widespread in bacterial chromosomes but their functions remain enigmatic. Although many are transcriptionally upregulated by stress conditions, it is unclear what role they play in cellular responses to stress and to what extent the role of a given TA system homologue varies between different bacterial species. In this work we investigate the role of the DNA damage-inducible TA system HigBA ofCaulobacter crescentusin the SOS response and discover that in addition to the toxin HigB affecting cell cycle gene expression through inhibition of the master regulator CtrA, HigBA possesses a transcription factor third component, HigC, which both auto-regulates the TA system and acts independently of it. Through HigC, the system exerts downstream effects on antibiotic (ciprofloxacin) resistance and cell cycle gene expression. HigB and HigC had inverse effects on cell cycle gene regulation, with HigB reducing and HigC increasing the expression of CtrA-dependent promoters. Neither HigBA nor HigC had any effect on formation of persister cells in response to ciprofloxacin. Rather, their role in the SOS response appears to be as transcriptional and post-transcriptional regulators of cell cycle-dependent gene expression, transmitting the status of the SOS response as a regulatory input into the cell cycle control network via CtrA.ImportanceAlmost all bacteria respond to DNA damage by upregulating a set of genes that helps them to repair and recover from the damage, known as the SOS response. The set of genes induced during the SOS response varies between species, but frequently includes toxin-antitoxin systems. However, it is unknown what the consequence of inducing these systems is, and whether they provide any benefit to the cells. We show here that the DNA damage-induced TA system HigBA of the asymmetrically dividing bacteriumCaulobacter crescentusaffects the cell cycle regulation of this bacterium. HigBA also has a transcription factor encoded immediately downstream of it, named here HigC, which controls expression of the TA system and potentially other genes as well. Therefore, this work identifies a new role for TA systems in the DNA damage response, distinct from non-specific stress tolerance mechanisms which had been proposed previously.
Direct morpho-chemical characterization of elusive plant residues from Aurignacian Pontic Steppe ground stones
Authors: Birarda G. , Cagnato C. , Pantyukhina I. , Stani C. , Cefarin N. , Sorrentino G. , Badetti E. , Marcomini A. , Lubritto C. , Khlopachev G. , Covalenco S. , Obada T. , Skakun N. , Vaccari L. , Longo L. 
Published: July 2020

AbstractDirect evidence for the intentional processing of starch-rich plants during the Paleolithic is scant, and that evidence is often compromised by concerns over preservation and contamination. Our integrated, multimodal approach couples wear-trace analysis with chemical imaging methods to identify the presence of genuine ancient starch candidates (ASC) on ground stones used in the Pontic Steppe starting around 40,000 years ago. Optical and electron microscopy coupled with infrared spectromicroscopy and imaging provide morphological and chemical profiles for ASCs, that partially match the vibrational polysaccharide features of modern reference starches, highlighting diagenetic differences ranging from partial oxidation to mineralization. The results suggest the intentional processing of roots and tubers by means of mechanical tenderization and shed light on the role of dietary carbohydrates during Homo sapiens’ (HS) colonization of Eurasia, demonstrating a long acquaintance with predictable calorific foods, crucial to maintain homeostasis during the harsh conditions of the Late MIS 3 (40-25 ky).
The tree that hides the forest: identification of common predisposing loci in several hematopoietic cancers and several dog breeds
Authors: Hédan Benoit , Cadieu Edouard , Rimbault Maud , Vaysse Amaury , Devauchelle Patrick , Botherel Nadine , Abadie Jérôme , Quignon Pascale , Derrien Thomas , André Catherine 
Published: July 2020

AbstractHistiocytic sarcoma (HS) is a rare but aggressive cancer in humans and dogs. The spontaneous canine model, with the clinical, epidemiological and histological similarities with human HS and specific breed predispositions, is a unique model/opportunity to unravel the genetic bases of this cancer. In this study, we aimed to identify germline risk factors associated with the development of HS in canine predisposed breeds. We used a methodology that combined several genome-wide association studies in a multi-breed and multi-cancer approach, as well as targeted next generation sequencing, and imputation combining several breeds (Bernese mountain dog, Rottweiler, flat coated retriever and golden retriever) and three haematopoietic cancers (HS, lymphoma and mast cell tumor). Results showed that we not only refined the previously identified HS riskCDKN2Alocus but we identified new loci on canine chromosomes 2, 5, 12, 14, 20, 26 and X. Capture and targeted sequencing of specific loci pointed towards the existence of regulatory variants in non coding regions and/or methylation mechanisms linked to risk haplotypes, leading to strong cancer predispositions in specific dog breeds. Our results showed that these canine cancer predisposing loci appear to be due to the additive effect of several risk haplotype involved also in other haematopoietic cancers such lymphoma or mast cell tumor, illustrating the pleiotropic nature of these canine cancer loci as observed in human oncology, thus reinforcing the interest of predisposed dog breeds to study cancer initiation and progression.
Antimicrobial prodrug activation by the staphylococcal glyoxalase GloB
Authors: Mikati Marwa O. , Miller Justin J. , Osbourn Damon M. , Ghebremichael Naomi , Shah Ishaan T. , Burnham Carey-Ann D. , Heidel Kenneth M. , Yan Victoria C. , Muller Florian L. , Dowd Cynthia S. , Edwards Rachel L. , Odom John Audrey R. 
Published: July 2020

ABSTRACTWith the rising prevalence of multidrug-resistance, there is an urgent need to develop novel antibiotics. Many putative antibiotics demonstrate promising in vitro potency but fail in vivo due to poor drug-like qualities (e.g. serum half-life, oral absorption, solubility, toxicity). These drug-like properties can be modified through the addition of chemical protecting groups, creating “prodrugs” that are activated prior to target inhibition. Lipophilic prodrugging techniques, including the attachment of a pivaloyloxymethyl group, have garnered attention for their ability to increase cellular permeability by masking charged residues and the relative ease of the chemical prodrugging process. Unfortunately, pivaloyloxymethyl prodrugs are rapidly activated by human sera, rendering any membrane permeability qualities absent during clinical treatment. Identification of the bacterial prodrug activation pathway(s) will allow for the development of host-stable and microbe-targeted prodrug therapies. Here, we use two zoonotic staphylococcal species, S. schleiferi and S. pseudintermedius, to establish the mechanism of carboxy ester prodrug activation. Using a forward genetic screen, we identify a conserved locus in both species encoding the enzyme hydroxyacylglutathione hydrolase (GloB), whose loss-of-function confers resistance to carboxy ester prodrugs. We enzymatically characterize GloB and demonstrate that it is a functional glyoxalase II enzyme, which has the capacity to activate carboxy ester prodrugs. As GloB homologs are both widespread and diverse in sequence, our findings suggest that GloB may be a useful mechanism for developing species-or genus-level prodrug targeting strategies.
HTSQualC is a Flexible and One-Step Quality Control Software for High-throughput Sequencing Data Analysis
Authors: Bedre Renesh , Avila Carlos , Mandadi Kranthi 
Published: July 2020

ABSTRACTUse of high-throughput sequencing (HTS) has become indispensable in life science research. Raw HTS data contains several sequencing artifacts, and as a first step it is imperative to remove the artifacts for reliable downstream bioinformatics analysis. Although there are multiple stand-alone tools available that can perform the various quality control steps separately, availability of an integrated tool that can allow one-step, automated quality control analysis of HTS datasets will significantly enhance handling large number of samples parallelly. Here, we developed HTSQualC, a stand-alone, flexible, and easy-to-use software for one-step quality control analysis of raw HTS data. HTSQualC can evaluate HTS data quality and perform filtering and trimming analysis in a single run. We evaluated the performance of HTSQualC for conducting batch analysis of HTS datasets with 322 samples with an average ∼1M (paired end) sequence reads per sample. HTSQualC accomplished the QC analysis in ∼3 hours in distributed mode and ∼31 hours in shared mode, thus underscoring its utility and robust performance. In addition to command-line execution, we integrated HTSQualC into the free, open-source, CyVerse cyberinfrastructure resource as a GUI interface, for wider access to experimental biologists who have limited computational resources and/or programming abilities.
Optimization of a bacterial three-hybrid assay throughin vivotitration of an RNA-DNA adapter-protein
Authors: Wang Clara D. , Mansky Rachel , LeBlanc Hannah , Gravel Chandra M. , Berry Katherine E. 
Published: July 2020

ABSTRACTNon-coding RNAs regulate gene expression in every domain of life. In bacteria, small RNAs (sRNAs) regulate gene expression in response to stress and are often assisted by RNA-chaperone proteins, such as Hfq. We have recently developed a bacterial three-hybrid (B3H) assay that detects the strong binding interactions of certainE. colisRNAs with proteins Hfq and ProQ. Despite the promise of this system, the signal-to-noise has made it challenging to detect weaker interactions. In this work, we use Hfq-sRNA interactions as a model system to optimize the B3H assay, so that weaker RNA-protein interactions can be more reliably detected. We find that the concentration of the RNA-DNA adapter is an important parameter in determining the signal in the system, and have modified the plasmid expressing this component to tune its concentration to optimal levels. In addition, we have systematically perturbed the binding affinity of Hfq-RNA interactions to define, for the first time, the relationship between B3H signal andin vitrobinding energetics. The new pAdapter construct presented here substantially expands the range of detectable interactions in the B3H assay, broadening its utility. This improved assay will increase the likelihood of identifying novel protein-RNA interactions with the B3H system, and will facilitate exploration of the binding mechanisms of these interactions.
The supramolecular landscape of growing human axons
Authors: Hoffmann Patrick C. , Giandomenico Stefano L. , Ganeva Iva , Wozny Michael R. , Sutcliffe Magdalena , Kukulski Wanda , Lancaster Madeline A. 
Published: July 2020

AbstractDuring brain development, human axons must extend over great distances in a relatively short amount of time. How the subcellular architecture of the growing axon sustains the requirements for such rapid build-up of cellular constituents has remained elusive. Human axons have been particularly inaccessible to imaging at molecular resolution in a near-native context. Here we apply cryo-correlative light microscopy and electron tomography to growing axonal tracts from human cerebral organoids. Our data reveal a wealth of structural details on the arrangement of macromolecules, cytoskeletal components, and organelles in elongating axon shafts. In particular, the intricate shape of the endoplasmic reticulum is consistent with its role in fulfilling the high demand for lipid biosynthesis to support growth. Furthermore, the scarcity of ribosomes within the growing shaft suggests limited translational competence during expansion of this compartment. These data provide an unprecedented resource and reveal a molecular architecture that helps explain the unique biology of growing human axons.
Soluble corn fiber reduces ovalbumin-induced sinonasal inflammation via the gut microbiota-airway axis
Authors: Jaramillo Sierra A. , Borsom Emily M. , Orsini Gabrielle M. , Kask Oliver , Lee Keehoon , Hirsch Allyson H. , Settles Erik , Shi Xiaojian , Gu Haiwei , Koppisch Andrew T. , Bokulich Nicholas A. , Caporaso J. Gregory , Cope Emily K. 
Published: July 2020

ABSTRACTAsthma is a chronic airway inflammatory disease that affects approximately 300 million people worldwide, causing a substantial healthcare burden. Although there is a large degree of heterogeneity in the inflammatory response of asthmatics, a subset of patients are characterized by type-2 inflammation, which is in part mediated by TH2 cells in both the upper and lower airways. Asthma prevalence is increased in low-socioeconomic-status populations, where disparities in health behavior exist, including a shift toward a western diet characterized by low dietary fiber. Gut microbes metabolize fiber into short chain fatty acids that can reduce type-2 inflammation in peripheral organs, such as the airways. We hypothesized that soluble fiber can reduce ovalbumin (OVA)-induced upper airway inflammation in the context of the unified airway hypothesis, in mice maintained on ingredient-matched western (WD) and control diets (CD) through production of short chain fatty acids. Our results show that soluble fiber reducesIL-4andIL-13gene expression (p<0.05, Mann Whitney) in the sinonasal cavity of CD-fed mice, but this effect was lost in WD-fed mice. This loss of protection in WD-fed mice parallels compositional changes of the cecal and fecal microbiota. Mice fed a soluble fiber supplement while being maintained on a WD had altered microbial communities characterized by lower abundance of fiber fermentering bacteria. This work can be used to develop effective microbiome-based therapeutics as a low-cost method to reduce asthma morbidity.IMPORTANCEPrevious research has supported that western-style diets, typically high-fat and low-fiber, are associated with changes in the gut microbiome and increased inflammation. Western diets are accessible and prominent in low-socioeconomic-status populations, where asthma rates are highest; however, there has yet to be a low-cost asthma therapeutic. For the first time, we investigated whether supplementation with a physiologically relevant quantity of soluble corn fiber can reduce allergic airway inflammation. Our study supports that soluble corn fiber supplementation is associated with compositional shifts of the gut microbiota and reduced airway inflammation, promoting the use of fiber as a low-cost microbiome modifying therapy to reduce asthma-associated inflammation. However, soluble corn fiber in conjunction with a western diet resulted in an alternate gut microbiome composition and loss of protection against allergic airway inflammation. These findings further support the importance of the gut microbiota in host health.
Standardizing carabid pitfall catches for trapping effort; a meta-analysis
Authors: Saska Pavel , Makowski David , Bohan David , van der Werf Wopke 
Published: July 2020

AbstractCarabid beetles (Coleoptera: Carabidae) provide important ecological services and are frequently used as a bio-indicator in monitoring environmental quality. The abundance and diversity of carabids is usually determined using pitfall trapping, but trap catches are difficult to compare between studies due to variation in trapping effort. The standardization of the catch for trapping effort has not been previously addressed in a global analysis of studies in the literature.The aims of this study are (i) to define a method for estimating the effect of trapping effort on the size of the pitfall catch, and (ii) to explore factors related to study designs, sampling method, study origin, and level of data aggregation to determine how these factors affect the catch per unit effort in pitfall trapping.We conducted a meta-analysis on the activity-density and diversity of carabids across studies, based on published data from Europe and North-America to analyse whether standardization of catch measurements might be possible. Data were extracted from 104 publications, spanning a period of 42 years.The total catch was proportional to the number of trap days, and ranged from 0.19-9.53 beetles/(trap day) across studies (95% range), with a mean of 1.33 beetles/(trap day). The number of species was allometrically related to the trapping effort defined as the product of the number of traps, their perimeter and the time of exposure in the field, and characterized by a power exponent of 0.25. Species richness ranged across studies from 2.30-13.18 species/(m day)0.25(95% range) with a mean of 7.15 species/(m day)0.25. The size of the catch and the number of species were higher in crops with narrow as compared to wide rows. There was no significant change in abundance or diversity of carabids in arable land over the 42 years covered. We also found that increasing trapping effort may not yield more accurate results.The results show that it is possible to standardize activity-density-based catches and species diversity for trapping effort across studies using a power transformation, allowing meta-analysis of such data, e.g. to elucidate factors affecting abundance and diversity of the focal taxa.
Non-synaptic interactions between olfactory receptor neurons, a possible key feature of odor processing in flies
Authors: Pannunzi Mario , Nowotny Thomas 
Published: July 2020

AbstractWhen flies explore their environment, they encounter odors in complex, highly intermittent plumes. To navigate a plume and, for example, find food, they must solve several challenges, including reliably identifying mixtures of odorants and their intensities, and discriminating odorant mixtures emanating from a single source from odorants emitted from separate sources and just mixing in the air. Lateral inhibition in the antennal lobe is commonly understood to help solving these challenges. With a computational model of theDrosophilaolfactory system, we analyze the utility of an alternative mechanism for solving them: Non-synaptic (“ephaptic”) interactions (NSIs) between olfactory receptor neurons that are stereotypically co-housed in the same sensilla.We found that NSIs improve mixture ratio detection and plume structure sensing and they do so more efficiently than the traditionally considered mechanism of lateral inhibition in the antennal lobe. However, we also found that NSIsdecreasethe dynamic range of co-housed ORNs, especially when they have similar sensitivity to an odorant. These results shed light, from a functional perspective, on the role of NSIs, which are normally avoided between neurons, for instance by myelination.Author summaryMyelin is important to isolate neurons and avoid disruptive electrical interference between them; it can be found in almost any neural assembly. However, there are a few exceptions to this rule and it remains unclear why. One particularly interesting case is the electrical interaction between olfactory sensory neurons co-housed in the sensilla of insects. Here, we created a computational model of the early stages of theDrosophilaolfactory system and observed that the electrical interference between olfactory receptor neurons can be a useful trait that can help flies, and other insects, to navigate the complex plumes of odorants in their natural environment.With the model we were able to shed new light on the trade-off of adopting this mechanism: We found that the non-synaptic interactions (NSIs) improve both the identification of the concentration ratio in mixtures of odorants and the discrimination of odorant mixtures emanating from a single source from odorants emitted from separate sources – both highly advantageous. However, they also decrease the dynamic range of the olfactory sensory neurons – a clear disadvantage.