bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of siRNA silencing on the susceptibility of the fish cell line CHSE-214 toYersinia ruckeri
Authors: Menanteau-Ledouble Simon , Schachner Oskar , Lawrence Mark L. , El-Matbouli Mansour 
Published: May 2019

AbstractBacterial pathogens are known to co-opt mechanisms of the host cells’ physiology to gain intracellular entrance. Among the facultative intracellular bacteria isYersinia ruckeri, an enterobacterium mostly known as the causative agent of enteric redmouth disease in salmonid fish. In the present study, we applied RNA inhibition to silence twenty pre-selected genes on the genome of a fish cell line (CHSE-214) followed by a gentamycin assay to quantify the effect of this silencing on the susceptibility of the cells to infection. It was found that silencing of 16 out of 20 genes significantly reduced the number ofY. ruckerirecovered at the end of the gentamycin assay. Among the genes with the strongest impact were Rab1A, actin and Rac1, which is consistent with our previous findings that N-acetylcysteine, a chemical inhibitor of Rac1, completely prevented invasion of cells byY. ruckeri. Conversely, silencing of the Rho GTPase activating protein had no statistically significant effect, possibly becauseY. ruckeri, like some other members of theYersiniagenus is able to activate Rho GTPase directly. Similarly, the effect of silencing E-cadherin was not statistically significant, suggesting that this might not be a target for the adhesion molecules ofY. ruckeri. Taken together, these findings improve our understanding of the infection process byY. ruckeriand of the interactions between this bacterial pathogen and host cells.ImportanceIntracellular invasiveness is a mean for bacterial pathogen to gain shelter from the immune system as well as access nutrients. The enterobacteriumY. ruckeriis well characterised as a facultative intracellular pathogen. However, the mechanisms of invasion scrutiny. Investigations have mostly focused on the bacterial virulence rather than on the host’s mechanisms hicjacked during invasion. The present findings therefore allow us to better understand the interaction between this important potentially zoonotic pathogen of fish and host cells in vitro.
Population receptive field and connectivity properties of the early visual cortex in human albinism
Authors: Ahmadi Khazar , Herbik Anne , Wagner Markus , Kanowski Martin , Thieme Hagen , Hoffmann Michael B. 
Published: May 2019

AbstractIn albinism, the pathological decussation of the temporal retinal afferents at the optic chiasm leads to superimposed representations of opposing hemifields in the visual cortex. Here, we assessed the equivalence of the two representations and the cortico-cortical connectivity of the early visual areas. Applying fMRI-based population receptive field (pRF)-mapping (both hemifield and bilateral mapping) and connective field (CF)-modeling, we investigated the early visual cortex in 6 albinotic participants and 4 controls. In albinism, superimposed retinotopic representations of the contra- and ipsilateral visual hemifield were observed on the hemisphere contralateral to the stimulated eye. This was confirmed by the observation of bilateral pRFs during bilateral mapping. Hemifield mapping revealed similar pRF-sizes for both hemifield representations throughout V1 to V3. The typical increase of V1-sampling extent for V3 compared to V2 was not found for the albinotic participants. The similarity of the pRF-sizes for opposing visual hemifield representations highlights the equivalence of the two maps in the early visual cortex. The altered V1-sampling extent in V3 indicates the adaptation of cortico-cortical connections to the abnormal input of the visual cortex. These findings thus suggest that conservative developmental mechanisms are complemented by alterations of the extrastriate cortico-cortical connectivity.HighlightspRF mapping confirms cortical overlay of opposing visual hemifields in albinism.Equivalent information processing of both hemifields is indicated by similar pRF sizes.CF modeling indicates changes to the cortico-cortical connections at the level of V3.
Extremely fast and accurate open modification spectral library searching of high-resolution mass spectra using feature hashing and graphics processing units
Authors: Bittremieux Wout , Laukens Kris , Noble William Stafford 
Published: May 2019

AbstractOpen modification searching (OMS) is a powerful search strategy to identify peptides with any type of modification. OMS works by using a very wide precursor mass window to allow modified spectra to match against their unmodified variants, after which the modification types can be inferred from the corresponding precursor mass differences. A disadvantage of this strategy, however, is the large computational cost, because each query spectrum has to be compared against a multitude of candidate peptides.We have previously introduced the ANN-SoLo tool for fast and accurate open spectral library searching. ANN-SoLo uses approximate nearest neighbor indexing to speed up OMS by selecting only a limited number of the most relevant library spectra to compare to an unknown query spectrum. Here we demonstrate how this candidate selection procedure can be further optimized using graphics processing units. Additionally, we introduce a feature hashing scheme to convert high-resolution spectra to low-dimensional vectors. Based on these algorithmic advances, along with low-level code optimizations, the new version of ANN-SoLo is up to an order of magnitude faster than its initial version. This makes it possible to efficiently perform open searches on a large scale to gain a deeper understanding about the protein modification landscape. We demonstrate the computational efficiency and identification performance of ANN-SoLo based on a large data set of the draft human proteome.ANN-SoLo is implemented in Python and C++. It is freely available under the Apache 2.0 license at https://github.com/bittremieux/ANN-SoLo.
The use of a centrifuge-free RABiT-II system for high-throughput micronucleus analysis
Authors: Repin Mikhail , Pampou Sergey , Brenner David J. , Garty Guy 
Published: May 2019

AbstractThe cytokinesis-block micronucleus (CBMN) assay is considered as the most suitable biodosimetry method for automation. Previously, we automated this assay on a commercial robotic biotech high-throughput system (RABiT-II) adopting both a traditional and an accelerated micronucleus protocol, both using centrifugation steps for lymphocyte harvesting and washing, after whole blood culturing. Here we describe further development of our accelerated CBMN assay protocol for using on High Throughput/High Content Screening (HTS/HCS) robotic systems without a centrifuge. This opens the way for implementation of the CBMN assay on a wider range of commercial automated HTS/HCS systems and thus increases the potential capacity of dose estimates following a mass-casualty radiological event.
Encoding Information in Synthetic Metabolomes
Authors: Kennedy Eamonn , Arcadia Christopher E. , Geiser Joseph , Weber Peter M. , Rose Christopher , Rubenstein Brenda M. , Rosenstein Jacob K. 
Published: May 2019

AbstractBiomolecular information systems offer numerous potential advantages over conventional semiconductor technologies. Downstream from DNA, the metabolome is an information-rich molecular system with diverse chemical dimensions which could be harnessed for information storage and processing. As a proof of principle of postgenomic data storage, here we demonstrate a workflow for representing abstract data in synthetic metabolomes. Our approach leverages robotic liquid handling for writing digital information into chemical mixtures, and mass spectrometry for extracting the data. We present several kilobyte-scale image datasets stored in synthetic metabolomes, which are decoded with accuracy exceeding 98-99% using multi-mass logistic regression. Cumulatively, >100,000 bits of digital image data was written into metabolomes. These early demonstrations provide insight into the benefits and limitations of postgenomic chemical information systems.
Persistent fibrosis and decreased cardiac function following cardiac injury in theCtenopharyngodon idella(grass carp)
Authors: Long Daniel W , Webb Charles H , Wang Yadong 
Published: May 2019

AbstractFollowing the discovery of heart regeneration in zebrafish, several more species within the Cyprinidae family have been found to have the same capability, suggesting heart regeneration may be conserved within this family. Although gonad regeneration has been observed in grass carp (Ctenopharyngodon idella), one of the largest cyprinid fish, the species’ response to cardiac injury has not been characterized. Surprisingly, we found cardiomyocytes do not repopulate the injured region following cryoinjury to the ventricle, instead exhibiting unresolved fibrosis and decreased cardiac function that persists for the 8-week duration of this study. Compared to other cyprinid fish studied, infiltration of macrophages is delayed and muted in this model. Additionally, fibroblasts are depleted following injury, a phenomenon not previously described in any cardiac model. This study shows that heart regeneration is not conserved among the Cyprinidae family and suggests the important role of non-fibroblasts in chronic fibrosis. Further study of these phenomenon may reveal the underlying differences between regeneration versus unresolved fibrosis in heart disease.Summary statementGrass carp, a member of the Cyprinidae family that includes regenerative zebrafish, do not regenerate functional cardiac tissue after cryoinjury. Instead, healing progresses through collagen deposition and scar formation.
Successive passaging of a plant-associated microbiome reveals robust habitat and host genotype-dependent selection
Authors: Morella Norma M. , Weng Francis Cheng-Hsuan , Joubert Pierre M. , Metcalf C. Jessica E. , Lindow Steven , Koskella Britt 
Published: May 2019

AbstractThere is increasing interest in the plant microbiome as it relates to both plant health and agricultural sustainability. One key unanswered question is whether we can select for a plant microbiome that is robust after colonization of target hosts. We used a successive passaging experiment to address this question by selecting upon the tomato phyllosphere microbiome. Beginning with a diverse microbial community generated from field-grown tomato plants, we inoculated replicate plants across five plant genotypes for four eight-week long passages, sequencing the microbial community at each passage. We observed consistent shifts in both the bacterial (16S amplicon sequencing) and fungal (ITS amplicon sequencing) communities across replicate lines over time, as well as a general loss of diversity over the course of the experiment suggesting that much of the naturally observed microbial community in the phyllosphere is likely transient or poorly adapted. We found that both host genotype and environment shape microbial composition, but the relative importance of genotype declines through time. Furthermore, using a community coalescence experiment, we found that the bacterial community from the end of the experiment was robust to invasion by the starting bacterial community. These results highlight that selecting for a stable microbiome that is well adapted to a particular host environment is indeed possible, emphasizing the great potential of this approach in agriculture and beyond.Significance StatementThere is great interest in selecting for host-associated microbiomes that confer particular functions to their host, and yet it remains unknown whether selection for a robust and stable microbiome is possible. Here, we use a microbiome passaging approach to measure the impact of host-mediated selection on the tomato phyllosphere (above ground) microbiome. We find robust community selection across replicate lines that is shaped by plant host genotype in early passages, but changes in a genotype-independent manner in later passages. Work such as ours is crucial to understanding the general principles governing microbiome assembly and adaptation, and is widely applicable to both sustainable agriculture and microbiome-related medicine.
The reliability of the isotropic fractionator method for counting total cells and neurons
Authors: Neves Kleber , Menezes Daniel , Rayêe Danielle , Valério-Gomes Bruna , Iack Pamela Meneses , Lent Roberto , Mota Bruno 
Published: May 2019

AbstractBackgroundThe Isotropic Fractionator (IF) is a method used to determine the cellular composition of nervous tissue. It has been mostly applied to assess variation across species, where differences are expected to be large enough not to be masked by methodological error. However, understanding the sources of variation in the method is important if the goal is to detect smaller differences, for example, in same-species comparisons. Comparisons between different mice strains suggest that the IF is consistent enough to detected these differences. Nevertheless, the internal validity of the method has not yet been examined directly.MethodIn this study, we evaluate the reliability of the IF method for the determination of cellular and neuronal numbers. We performed repeated cell counts of the same material by different experimenters to quantify different sources of variation.ResultsIn total cell counts, we observed that for the cerebral cortex most of the variance was at the counter level. For the cerebellum, most of the variance is attributed to the sample itself. As for neurons, random error along with the immunological staining correspond to most of the variation, both in the cerebral cortex and in the cerebellum. Test-retest reliability coefficients were relatively high, especially for cell counts.ConclusionsAlthough biases between counters and random variation in staining could be problematic when aggregating data from different sources, we offer practical suggestions to improve the reliability of the method. While small, this study is a most needed step towards more precise measurement of the brain’s cellular composition.HighlightsMost variance in cell counts was between counters (η = 0.58) for cerebral cortices.For cerebella, most of the variance was attributed to the samples (η = 0.49).Variance in immunocytochemical counts was mostly residual/random (η > 0.8).Test-retest reliability was high (same counter, same sample).Practical suggestions are offered to improve the reliability of the method.
Modeling cell infection via virus-producing cells rather than free infectious virus significantly improves fits ofin vitroviral kinetic data
Authors: Bernhauerová Veronika , Rezelj Veronica V. , Levi Laura I. , Vignuzzi Marco 
Published: May 2019

AbstractChikungunya and Zika viruses are arthropod-borne viruses that pose significant threat to public health. Experimental data show that duringin vitroinfection both viruses exhibit qualitatively distinct replication cycle kinetics. Chikungunya viral load rapidly accumulates within the first several hours post infection whereas Zika virus begins to increase at much later times. We sought to characterize these qualitatively distinctin vitrokinetics of chikungunya and Zika viruses by fitting a family of mathematical models to time course viral load datasets. We demonstrate that the standard viral kinetic model, which considers that new infections result only from free virus penetrating susceptible cells, does not fit experimental data as well as a model in which the number of virus-infected cells is the primary determinant of infection rate. We provide biologically meaningful quantifications of the main viral kinetic parameters and show that our results support cell-to-cell or localized transmission as a significant contributor to viral infection with chikungunya and Zika viruses.ImportanceMathematical modeling has become a useful tool to tease out information about virus-host interactions and thus complements experimental work in characterizing and quantifying processes within viral replication cycle. Importantly, mathematical models can fill in incomplete data sets and identify key parameters of infection, provided the appropriate model is used. Thein vitrotime course dynamics of mosquito transmitted viruses, such as chikungunya and Zika, have not been studied by mathematical modeling and thus limits our knowledge about quantitative description of the individual determinants of viral replication cycle. This study employs dynamical modeling framework to show that the rate at which cells become virus-infected is proportional to the number or virus-infected cells rather than free extracellular virus in the milieu, a widely accepted assumption in models of viral infections. Using the refined mathematical model in combination with viral load data, we provide quantification of the main drivers of chikungunya and Zikain vitrokinetics. Together, our results bring quantitative understanding of the basic components of chikungunya and Zika virus dynamics.
Unexpected activity of oral fosfomycin against resistant strains ofEscherichia coliin murine pyelonephritis
Authors: Pourbaix Annabelle , Guérin François , Burdet Charles , Massias Laurent , Chau Françoise , Cattoir Vincent , Fantin Bruno 
Published: May 2019

AbstractFosfomycin-tromethamine activity is well established for oral treatment of uncomplicated lower urinary tract infections but little is known about its potential efficacy in pyelonephritis. Ascending pyelonephritis was induced in mice infected with 6 strains ofEscherichia coli(fosfomycin MICs: 1 μg/ml to 256 μg/ml). Urine pH was 4.5 before infection and 5.5-6.0 during infection. Animals were treated for 24h with fosfomycin (100 mg/kg subcutaneously every 4 hours) and CFU were enumerated in kidneys 24h after the last fosfomycin injection. Peak (20.5 μg/ml at 1h) and trough (3.5 μg/ml at 4h) levels in plasma were comparable to those obtained in human after an oral dose of 3 grams. Fosfomycin treatment significantly reduced bacterial loads in kidneys (3.65 log10CFU/g [min-max=1.83-7.03] and 1.88 log10CFU/g [1.78-5.74] in start-of-treatment control mice and treated mice, respectively,P< 10-6). However, this effect was not found to differ across the 6 study strains (P = 0.71) and between the 3 susceptible and the 3 resistant strains (P=0.09). Three phenomena may contribute to explain this unexpectedin vivoactivity: i) in mice, fosfomycin kidney/plasma concentrations ratio increased from 1 to 7.8 (95% CI, 5.2; 10.4) within 24 hours;in vitro, when pH decreased to 5: (ii) fosfomycin MICs for the 3 resistant strains (64-256 μg/ml) decreased into the susceptible range (16-32 μg/ml) and: iii) maximal growth rates significantly decreased for all strains and were the lowest in urine. These results suggest that local fosfomycin concentrations and physiological conditions may favour fosfomycin activity in pyelonephritis, even against resistant strains.
Carbon monoxide dehydrogenases enhance bacterial survival by oxidising atmospheric CO
Authors: Cordero Paul R.F. , Bayly Katherine , Leung Pok Man , Huang Cheng , Islam Zahra F. , Schittenhelm Ralf B. , King Gary M. , Greening Chris 
Published: May 2019

AbstractCarbon monoxide (CO) is a ubiquitous atmospheric trace gas produced by natural and anthropogenic sources. Some aerobic bacteria can oxidize atmospheric CO and, collectively, they account for the net loss of ~250 teragrams of CO from the atmosphere each year. However, the physiological role, genetic basis, and ecological distribution of this process remain incompletely resolved. In this work, we addressed these knowledge gaps through culture-based and culture-independent work. We confirmed through shotgun proteomic and transcriptional analysis that the genetically tractable aerobic soil actinobacteriumMycobacterium smegmatisupregulates expression of a carbon monoxide dehydrogenase by 50-fold when exhausted for organic carbon substrates. Whole-cell biochemical assays in wild-type and mutant backgrounds confirmed that this organism aerobically respires CO, including at sub-atmospheric concentrations, using the enzyme. Contrary to current paradigms on CO oxidation, the enzyme did not support chemolithoautotrophic growth and was dispensable for CO detoxification. However, it significantly enhanced long-term survival, suggesting that atmospheric CO serves a supplemental energy source during organic carbon starvation. Phylogenetic analysis indicated that atmospheric CO oxidation is widespread and an ancestral trait of CO dehydrogenases. Homologous enzymes are encoded by 685 sequenced species of bacteria and archaea, including from seven dominant soil phyla, and we confirmed genes encoding this enzyme are abundant and expressed in terrestrial and marine environments. On this basis, we propose a new survival-centric model for the evolution of CO oxidation and conclude that, like atmospheric H2, atmospheric CO is a major energy source supporting persistence of aerobic heterotrophic bacteria in deprived or changeable environments.
The Solanum tuberosum GBSSI gene: a target for assessing gene and base editing in tetraploid potato
Authors: Veillet Florian , Chauvin Laura , Kermarrec Marie-Paule , Sevestre François , Merrer Mathilde , Terret Zoé , Szydlowski Nicolas , Devaux Pierre , Gallois Jean-Luc , Chauvin Jean-Eric 
Published: May 2019

AbstractGenome editing has recently become a method of choice for basic research and functional genomics, and holds great potential for molecular plant breeding applications. The powerful CRISPR-Cas9 system that typically produces double-strand DNA breaks is mainly used to generate knockout mutants. Recently, the development of base editors has broadened the scope of genome editing, allowing precise and efficient nucleotide substitutions. In this study, we produced mutants in two cultivated elite cultivars of the tetraploid potato (Solanum tuberosum) using stable or transient expression of the CRISPR-Cas9 components to knockout the amylose-producing StGBSSI gene. We set up a rapid, highly sensitive and cost-effective screening strategy based on high-resolution melting analysis followed by direct Sanger sequencing and trace chromatogram analysis. Most mutations consisted of small indels, but unwanted insertions of plasmid DNA were also observed. We successfully created tetra-allelic mutants with impaired amylose biosynthesis, confirming the loss-of-function of the StGBSSI protein. The second main objective of this work was to demonstrate the proof of concept of CRISPR-Cas9 base editing in the tetraploid potato by targeting two loci encoding catalytic motifs of the StGBSSI enzyme. Using a cytidine base editor (CBE), we efficiently and precisely induced DNA substitutions in the KTGGL-encoding locus, leading to discrete variation in the amino acid sequence and generating a loss-of-function allele. The successful application of base editing in the tetraploid potato opens up new avenues for genome engineering in this species.Key MessageThe StGBSSI gene was successfully and precisely edited in the tetraploid potato using gene and base editing strategies, leading to plants with impaired amylose biosynthesis.