bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards measuring growth rates of pathogens during infections by D2O-labeling lipidomics
Authors: Neubauer Cajetan , Sessions Alex L. , Booth Ian R. , Bowen Benjamin P. , Kopf Sebastian H. , Newman Dianne K. , Dalleska Nathan F. 
Published: May 2018

ABSTRACTRATIONALEMicrobial growth rate is an important physiological parameter that is challenging to measurein situ, partly because microbes grow slowly in many environments. Recently, it has been demonstrated that generation times ofS. aureusin cystic fibrosis (CF) infections can be determined by D2O-labeling of actively synthesized fatty acids. To improve species specificity and allow growth rate monitoring for a greater range of pathogens during the treatment of infections, it is desirable to accurately quantify trace incorporation of deuterium into phospholipids.METHODSLipid extracts of D2O-treatedE. colicultures were measured on LC-ESI-MS instruments equipped with TOF and Orbitrap mass analyzers, and used for comparison with the analysis of fatty acids by isotope-ratio GC-MS. We then develop an approach to enable tracking of lipid labeling, by following the transition from stationary into exponential growth in pure cultures. Lastly, we apply D2O-labeling lipidomics to clinical samples from CF patients with chronic lung infections.RESULTSLipidomics facilitates deuterium quantification in lipids at levels that are useful for many labeling applications (>0.03 at% D). In theE. colicultures, labeling dynamics of phospholipids depend largely on their acyl chains and between phospholipids we notice differences that are not obvious from absolute concentrations alone. For example, cyclopropyl-containing lipids reflect the regulation of cyclopropane fatty acid synthase, which is predominantly expressed at the beginning of stationary phase. The deuterium incorporation into a lipid that is specific forS. aureusin CF sputum, indicates an average generation time of the pathogen on the order of one cell doubling per day.CONCLUSIONSThis study demonstrates how trace level measurement of stable isotopes in intact lipids can be used to quantify lipid metabolism in pure cultures and provides guidelines that enable growth rate measurements in microbiome samples after incubation with a low percentage of D2O.
A physiological drop in pH decreases mitochondrial respiration, and AMPK and Akt signalling, in L6 myocytes
Authors: Genders Amanda J , Martin Sheree D , McGee Sean L , Bishop David J 
Published: May 2018

AbstractExercise stimulates mitochondrial biogenesis and increases mitochondrial respiratory function and content. However, during high-intensity exercise muscle pH can decrease below pH 6.8 with a concomitant increase in lactate concentration. This drop in muscle pH is associated with reduced exercise-induced mitochondrial biogenesis, whilst increased lactate may act as a signaling molecule to affect mitochondrial biogenesis. Therefore, in this study we wished to determine the impact of altering pH and lactate concentration in L6 myotubes on genes and proteins known to be involved in mitochondrial biogenesis. We also examined mitochondrial respiration in response to these perturbations. Differentiated L6 myotubes were exposed to normal (pH 7.5), low (pH 7.0) or high pH (pH 8.0) media with and without 20 mM sodium L-lactate for 1 and 6 h. Low pH and 20 mM Sodium L-Lactate resulted in decreased Akt (Ser473) and AMPK (T172) phosphorylation at 1 h compared to controls, whilst at 6 h the nuclear localisation of HDAC5 was decreased. When the pH was increased both Akt (Ser473) and AMPK (T172) phosphorylation was increased at 1 h. Overall increased lactate decreased the nuclear content of HDAC5 at 6 h. Exposure to both high and low pH media significantly decreased basal mitochondrial respiration, ATP turnover, and maximum mitochondrial respiratory capacity. These data indicate that muscle pH affects several metabolic signalling pathways, including those required for mitochondrial function.
Activity-dependent netrin-1 secretion drives synaptic insertion of GluA1-containing AMPA receptors in the hippocampus
Authors: Glasgow Stephen D. , Labrecque Simon , Beamish Ian V. , Aufmkolk Sarah , Gibon Julien , Han Dong , Harris Stephanie N. , Dufresne Paul , Wiseman Paul W. , Anne McKinney R. , Séguéla Philippe , Koninck Paul De , Ruthazer Edward S. , Kennedy Timothy E. 
Published: May 2018

AbstractDynamic trafficking of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid glutamate receptors (AMPARs) to synapses is critical for activity-dependent synaptic plasticity underlying learning and memory, however the identity of key molecular effectors remains elusive. Here, we demonstrate that membrane depolarization and N-methyl-D-aspartate receptor (NMDAR) activation triggers secretion of the chemotropic guidance cue netrin-1 from dendrites. Using selective genetic deletion, we show that netrin-1 expression by excitatory neurons is required for NMDAR-dependent long-term potentiation (LTP) in the adult hippocampus. Further, we demonstrate that application of exogenous netrin-1 is sufficient to trigger the potentiation of excitatory glutamatergic transmission at hippocampal Schaffer collateral synapses via Ca2+-dependent recruitment of GluA1-containing AMPARs, promoting the maturation of immature or nascent synapses. These findings identify a central role for activity-dependent release of netrin-1 as a critical effector of synaptic plasticity in the adult hippocampus.
AgriSeqDB: an online RNA-Seq database for functional studies in agriculturally relevant plant species
Authors: Robinson Andrew J. , Tamiru Muluneh , Salby Rachel , Bolitho Clayton , Williams Andrew , Huggard Simon , Fisch Eva , Unsworth Kathryn , Whelan James , Lewsey Mathew G. 
Published: May 2018

AbstractBackgroundThe genome-wide expression profile of genes in different tissues/cell types and developmental stages is a vital component of many functional genomic studies. Transcriptome data obtained by RNA-sequencing (RNA-Seq) is often deposited in public databases that are made available via data portals. Data visualization is one of the first steps in assessment and hypothesis generation. However, these databases do not typically include visualization tools and establishing one is not trivial for users who are not computational experts. This, as well as the various formats in which data is commonly deposited, makes the processes of data access, sharing and utility more difficult. Our goal was to provide a simple and user-friendly repository that meets these needs for datasets from major agricultural crops.DescriptionAgriSeqDB (https://expression.latrobe.edu.au/agriseqdb), is a database for viewing, analysing and interpreting developmental and tissue/cell-specific transcriptome data from several species, including major agricultural crops such as wheat, rice, maize, barley and tomato. The disparate manner in which public transcriptome data is often warehoused and the challenge of visualizing raw data are both major hurdles to data reuse. The popular eFP browser does an excellent job of presenting transcriptome data in an easily interpretable view, but previous implementation has been mostly on a case-by-case basis. Here we present an integrated visualisation database of transcriptome datasets from six species that did not previously have public-facing visualisations. We combine the eFP browser, for gene-by-gene investigation, with the Degust browser, which enables visualisation of all transcripts across multiple samples. The two visualisation interfaces launch from the same point, enabling users to easily switch between analysis modes. The tools allow users, even those without bioinformatics expertise, to mine into datasets and understand the behaviour of transcripts of interest across samples and time. We have also incorporated an additional graphic download option to simplify incorporation into presentations or publications.ConclusionPowered by eFP and Degust browsers, AgriSeqDB is a quick and easy-to-use platform for data analysis and visualization in five crops and Arabidopsis. Furthermore, it provides a tool that makes it easy for researchers to share their datasets, promoting research collaborations and dataset reuse.
Hhex regulates the specification and growth of the hepatopancreatic ductal system
Authors: Villasenor Alethia , Gauvrit Sébastien , Collins Michelle M. , Parajes Silvia , Maischein Hans-Martin , Stainier Didier 
Published: May 2018

SUMMARYSignificant efforts have advanced our understanding of foregut-derived organ development; however, little is known about the molecular mechanisms that underlie the formation of the hepatopancreatic ductal (HPD) system. Here, we report a role for the homeodomain transcription factor Hhex in directing HPD progenitor specification in zebrafish. Loss of Hhex function results in impaired HPD system formation. We found that Hhex specifies a distinct population of HPD progenitors that gives rise to the cystic duct, common bile duct, and extra-pancreatic duct. Sincehhexis not uniquely expressed in the HPD region but is also expressed in endothelial cells and the yolk syncytial layer (YSL), we tested the role of blood vessels as well as the YSL in HPD formation. We found that blood vessels are required for HPD patterning, but not for HPD progenitor specification. In addition, we found that Hhex is required in both the endoderm and the YSL for HPD development. Our results shed light on the mechanisms necessary to direct endodermal progenitors towards the HPD fate and also advance our understanding of HPD system formation.
C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution
Authors: Kouno Tsukasa , Moody Jonathan , Kwon Andrew , Shibayama Youtaro , Kato Sachi , Huang Yi , Böttcher Michael , Motakis Efthymios , Mendez Mickaёl , Severin Jessica , Luginbühl Joachim , Abugessaisa Imad , Hasegawa Akira , Takizawa Satoshi , Arakawa Takahiro , Furuno Masaaki , Ramalingam Naveen , West Jay , Suzuki Harukazu , Kasukawa Takeya , Lassmann Timo , Hon Chung-Chau , Arner Erik , Carninci Piero , Plessy Charles , Shin Jay W 
Published: May 2018

AbstractSingle-cell transcriptomic profiling is a powerful tool to explore cellular heterogeneity. However, most of these methods focus on the 3’-end of polyadenylated transcripts and provide only a partial view of the transcriptome. We introduce C1 CAGE, a method for the detection of transcript 5’-ends with an original sample multiplexing strategy in the C1™ microfluidic system. We first quantified the performance of C1 CAGE and found it as accurate and sensitive as other methods in C1 system. We then used it to profile promoter and enhancer activities in the cellular response to TGF-β of lung cancer cells and discovered subpopulations of cells differing in their response. We also describe enhancer RNA dynamics revealing transcriptional bursts in subsets of cells with transcripts arising from either strand within a single-cell in a mutually exclusive manner, which was validated using single molecule fluorescence in-situ hybridization.
Ultrasensitive capture of human herpes simplex virus genomes directly from clinical samples reveals extraordinarily limited evolution in cell culture
Authors: Greninger Alexander L. , Roychoudhury Pavitra , Xie Hong , Casto Amanda , Cent Anne , Pepper Gregory , Koelle David M. , Huang Meei-Li , Wald Anna , Johnston Christine , Jerome Keith R. 
Published: May 2018

AbstractHerpes simplex viruses (HSV) are difficult to sequence due to their large DNA genome, high GC content, and the presence of repeats. To date, most HSV genomes have been recovered from culture isolates, raising concern that these genomes may not accurately represent circulating clinical strains. We report the development and validation of a DNA oligonucleotide hybridization panel to recover near complete HSV genomes at abundances up to 50,000-fold lower than previously reported. Using copy number information on herpesvirus and host DNA background via quantitative PCR, we developed a protocol for pooling for cost-effective recovery of more than 50 HSV-1 or HSV-2 genomes per MiSeq run. We demonstrate the ability to recover >99% of the HSV genome at >100X coverage in 72 hours at viral loads that allow whole genome recovery from latently-infected ganglia. We also report a new computational pipeline for rapid HSV genome assembly and annotation. Using the above tools and a series of 17 HSV-1-positive clinical swabs sent to our laboratory for viral isolation, we show limited evolution of HSV-1 during viral isolation in human fibroblast cells compared to the original clinical samples. Our data indicate that previous studies using low passage clinical isolates of herpes simplex viruses are reflective of the viral sequences present in the lesion and thus can be used in phylogenetic analyses. We also detect superinfection within a single sample with unrelated HSV-1 strains recovered from separate oral lesions in an immunosuppressed patient during a 2.5-week period, illustrating the power of direct-from-specimen sequencing of HSV.ImportanceHerpes simplex viruses affect more than 4 billion people across the globe, constituting a large burden of disease. Understanding global diversity of herpes simplex viruses is important for diagnostics and therapeutics as well as cure research and tracking transmission among humans. To date, most HSV genomics has been performed on culture isolates and DNA swabs with high quantities of virus. We describe the development of wet-lab and computational tools that enable the accurate sequencing of near-complete genomes of HSV-1 and HSV-2 directly from clinical specimens at abundances >50,000-fold lower than previously sequenced and at significantly reduced cost. We use these tools to profile circulating HSV-1 strains in the community and illustrate limited changes to the viral genome during the viral isolation process. These techniques enable cost-effective, rapid sequencing of HSV-1 and HSV-2 genomes that will help enable improved detection, surveillance, and control of this human pathogen.
Development and Validation of a Method for Human Papillomavirus Genotyping Based on Molecular Beacon Probes
Authors: Lyu Jiangfeng , Yu Yuefeng , Ren Xuyi 
Published: May 2018

AbstractWe describe a new assay system for the genotyping of human papillomavirus (HPV) based on linear-after-the-exponential-PCR and melting curve analysis. This system can detect and identify the 23 most common HPV strains (types 6, 11, 16, 18, 31, 33, 35, 39,42, 45, 51, 52, 53, 56, 58, 59, 66, 68, 70, 73, 81, 82, and 83) in two sealed reaction tubes within 2 h. The sensitivity and specificity of this new system was validated using cloned HPV DNA and clinical samples. The detection limit was 5–500 copies/reaction depending on the genotype, and no cross-reactivity was observed with any other low-risk HPV or pathogen that was commonly found in the female genital tract. When compared with the HPV GenoArray test kit, the testing of 1104 clinical samples produced a good overall agreement between the two methods of 98.37% (95% CI: 97.44%–98.97%) and a kappa value of 0.954. Thus, this new HPV genotyping assay system represents a simple, rapid, universally applicable, sensitive, and highly specific detection methodology that should be useful for cervical lesion screening and, thus, is potentially of great value in future clinical applications.
Genotype by environment interactions for the shade avoidance syndrome in the plantAntirrhinum majus, the snapdragon
Authors: Mousset Mathilde , Marin Sara , Archambeau Juliette , Blot Christel , Bonhomme Vincent , Garaud Laura , Pujol Benoit 
Published: May 2018

AbstractA classical example of phenotypic plasticity in plants is the set of trait changes in response to shade,i.e.the shade avoidance syndrome. There is widespread evidence that plants in low light conditions often avoid shade by growing taller or by increasing their photosynthetic efficiency. This plastic response is expected to have evolved in response to selection in several species, yet there is limited evidence for its genetic variation within populations, which is required for any evolutionary response to selection. In this study, we investigated the shade avoidance syndrome in snapdragon plants (Antirrhinum majus) by using a common garden approach on four natural populations from the Mediterranean region. Our results showed that, in the four populations, individual plants reacted strongly to the presence of shade by growing longer shoots, longer internodes, and increasing their specific leaf area. Our results also revealed genetic variation for the plastic response within these populations, as well as few genetic constraints to its evolution. Our findings imply that the plastic response to shade has the potential to evolve in response to selection in natural populations ofA. majus.
Oral health-related quality of life in elderly women participating in a coexistence group in southern Brazil: Oral health and quality of life in elderly women
Authors: Dallasta Thaís Cauduro , Medina Vanessa Bischoff , Dallepiane Loiva Beatriz 
Published: May 2018

AbstractThe objective of this work was to evaluate the association between quality of life with the oral health in elderly women participating in a coexistence group in Southern Brazil. Study of the descriptive type, analytical, cross-sectional approach, with women aged 60 years or more, participants of a coexistence group in a city in Southern Brazil. Data collection used the instrument Oral Health Impact Profile (OHIP-14). The study had the participation of 64 elderly women aged between 60 and 88 years old with a mean of 69.8 ± 7.31 years. The areas that presented the highest values were “Physical Pain”, “Psychological Distress” and “Physical Disability”. The highest averages of the total scores of the OHIP-14 occurred in individuals with lower family income and low education, who showed signs of depression, changes in taste, difficulty to feel the taste of certain foods and malnutrition. Low education, change of taste and malnutrition by the arm circumference were associated with poor quality of life arising from oral disorders.
Dynamics of supercoiled DNA with complex knots: large-scale rearrangements and persistent multi-strand interlocking
Authors: Coronel Lucia , Suma Antonio , Micheletti Cristian 
Published: May 2018

AbstractKnots and supercoiling are both introduced in bacterial plasmids by catalytic processes involving DNA strand passages. While the effects on plasmid organization has been extensively studied for knotting and supercoiling taken separately, much less is known about their concurrent action. Here, we use molecular dynamics simulations and oxDNA, an accurate mesoscopic DNA model, to study the kinetic and metric changes introduced by complex (five-crossing) knots and supercoiling in 2kbp-long DNA rings. We find several unexpected results. First, the conformational ensemble is dominated by two distinct states, differing in branchedness and knot size. Secondly, fluctuations between these states are as fast as the metric relaxation of unknotted rings. In spite of this, certain boundaries of knotted and plectonemically-wound regions can persist over much longer timescales. These pinned regions involve multiple strands that are interlocked by the cooperative action of topological and supercoiling constraints. Their long-lived character may be relevant for the simplifying action of topoisomerases.
Highly Multiplexed Genome Engineering Using CRISPR/Cas9 gRNA Arrays
Authors: Kurata Morito , Wolf Natalie K. , Lahr Walker S. , Weg Madison T. , Lee Samantha , Hui Kai , Shiraiwa Masano , Webber Beau R. , Moriarity Branden 
Published: May 2018

ABSTRACTThe CRISPR/Cas9 system is an RNA guided nuclease system that evolved as a mechanism of adaptive immunity in bacteria. This system has been adopted for numerous genome engineering applications in research and recently, therapeutics. The CRISPR/Cas9 system has been largely implemented by delivery of Cas9 as protein, RNA, or plasmid along with a chimeric crRNA-tracrRNA guide RNA (gRNA) under the expression of a pol III promoter, such as U6. Using this approach, multiplex genome engineering has been achieved by delivering several U6-gRNA plasmids targeting multiple loci. However, this approach is limiting due to the efficiently of delivering multiple plasmids to a single cell at one time. To augment the capability and accessibility of multiplexed genome engineering, we developed an efficient golden gate based method to assemble gRNAs linked by optimalCsy4ribonuclease sequences to deliver up to 10 gRNAs as a single gRNA array transcript. Here we report the optimal expression of our guide RNA array under a strong pol II promoter. This system can be implemented alongside the myriad of CRISPR applications, allowing users to model complex biological processes requiring numerous gRNAs.
A retinal circuit generating a dynamic predictive code for orientated features
Authors: Johnston Jamie , Seibel Sofie-Helene , Darnet Léa Simone Adele , Renninger Sabine , Orger Michael , Lagnado Leon 
Published: May 2018

SummarySensory systems must reduce the transmission of redundant information to function efficiently. One strategy is to continuously adjust the sensitivity of neurons to suppress responses to common features of the input while enhancing responses to new ones. Here we image both the excitatory synaptic inputs and outputs of retinal ganglion cells to understand how such dynamic predictive coding is implemented in the analysis of spatial patterns. Synapses of bipolar cells become tuned to orientation through presynaptic inhibition generating lateral antagonism in the orientation domain. Individual ganglion cells receive excitatory synapses tuned to different orientations but feedforward inhibition generates a high-pass filter that only transmits the initial activation of these inputs, thereby removing redundancy. These results demonstrate how a dynamic predictive code can be implemented by circuit motifs common to many parts of the brain.
Immunobiochemical reconstruction of influenza lung infection - Melanoma skin cancer interactions
Authors: Nikolaev Evgeni V. , Zloza Andrew , Sontag Eduardo D. 
Published: May 2018

AbstractOur recent experimental results that combine a mouse model of influenza A virus (IAV) infection (A/H1N1/PR8) and a highly aggressive model of infection-unrelated cancer, B16-F10 skin melanoma, showed that acute influenza infection of the lung promotes distal melanoma growth in the dermis of the flank and leads to decreased host survival. Here, we proceed to ground the experimental observations in a mechanistic immunobiochemical model that incorporates the T cell receptor signaling pathway, various transcription factors, and a gene regulatory network (GRN). A core component of our model is a biochemical motif, which we call a Triple Incoherent Feed-Forward Loop (TIFFL), and which reflects known interactions between IRF4, Blimp-1, and Bcl-6. The different activity levels of the TIFFL components, as a function of the cognate antigen levels and the given inflammation context, manifest themselves in phenotypically distinct outcomes. Specifically, both the TIFFL reconstruction and quantitative estimates obtained from the model allowed us to formulate a hypothesis that it is the loss of the fundamental TIFFL-induced adaptation of the expression of PD-1 receptors on anti-melanoma CD8+ T cells that constitutes the essence of the previously unrecognized immunologic factor that promotes the experimentally observed distal tumor growth in the presence of acute non-ocogenic infection. We therefore hope that this work can further highlight the importance of adaptive mechanisms by which immune functions contribute to the balance between self and non-self immune tolerance, adaptive resistance, and the strength of TCR-induced activation, thus contributing to the understanding of a broader complexity of fundamental interactions between pathogens and tumors.