bluuebunny/crossref_metadata_2025_split huggingface dataset:
Engineering gene overlaps to sustain genetic constructs in vivo
Authors: Decrulle Antoine L. , Frenoy Antoine , Meiller-Legrand Thomas A. , Bernheim Aude , Lotton Chantal , Gutierrez Arnaud , Lindner Ariel B. 
Published: June 2019

AbstractEvolution is often an obstacle to the engineering of stable biological systems due to the selection of mutations inactivating costly gene circuits. Gene overlaps induce important constraints on sequences and their evolution. We show that these constraints can be harnessed to increase the stability of synthetic circuits by purging loss-of-function mutations. We combine computational and synthetic biology approaches to rationally design an overlapping reading frame expressing an essential gene within an existing gene to protect. Our algorithm succeeded in creating overlapping reading frames in 80% ofE. coligenes. Experimentally, scoring mutations in both genes of such overlapping construct, we found that a significant fraction of mutations impacting the gene to protect have a deleterious effect on the essential gene. Such an overlap thus protects a costly gene from removal by natural selection by associating the benefit of this removal with a larger or even lethal cost. In our synthetic constructs, the overlap converts many of the possible mutants into evolutionary dead-ends, effectively changing the fitness landscape and reducing the evolutionary potential of the system.
Vapor inhalation of cannabidiol (CBD) in rats
Authors: Javadi-Paydar Mehrak , Creehan Kevin M. , Kerr Tony M. , Taffe Michael A. 
Published: June 2019

AbstractCannabidiol (CBD) is increasingly available in e-cigarette liquids and other products. CBD use has been promoted for numerous purported benefits which have not been rigorously assessed in preclinical studies. The objective of this study was to further validate an inhalation model to assess CBD effects in the rat. The primary goal was to determine plasma CBD levels after vapor inhalation and compare that with the levels observed after injection. Secondary goals were to determine if hypothermia is produced in male Sprague-Dawley rats and if CBD affects nociception measured by the warm water tail-withdrawal assay. Blood samples were collected from rats exposed for 30 minutes to vapor generated by an e-cigarette device using CBD (100, 400 mg/mL in the propylene glycol vehicle). Separate experiments assessed the body temperature response to CBD in combination with nicotine (30 mg/mL) and the anti-nociceptive response to CBD. Vapor inhalation of CBD produced concentration-related plasma CBD levels in male and female Wistar rats that were within the range of levels produced by 10 or 30 mg/kg, CBD, i.p.. Dose-related hypothermia was produced by CBD in male Sprague-Dawley rats and this was partially attenuated by 5-HT1a receptor blockade. Nicotine (30 mg/mL) inhalation enhanced the effect of CBD. CBD inhalation had no effect on anti-nociception alone or in combination with Δ9-tetrahydrocannabinol inhalation. The vapor-inhalation approach is a suitable pre-clinical model for the investigation of the effects of inhaled CBD. This route of administration produces hypothermia in rats, while i.p. injection does not at comparable plasma CBD levels.
Do These Crayfish Make Me Look Fat? Body Condition Correlates To Prey Abundance In Three Hellbender (Cryptobranchus Alleganiensis) Populations
Authors: Hecht Kirsten , Nickerson Max , Freake Michael , Colclough Phil , Stofer Katie 
Published: June 2019

AbstractIn ecological studies body condition is often measured as an indicator of animal health or well-being. The Hellbender (Cryptobranchus alleganiensis) is a threatened salamander species found throughout the montane regions of the eastern United States. Although few young individuals have historically been found in the wild, recent studies in Blue Ridge Physiographic Regions have uncovered larvae in several streams. In Little River, Tennessee, differences in the crayfish population, the principal component of the adult Hellbender diet, was hypothesized as a potential reason for the large number of immature individuals, and lack of large adults. To investigate this hypothesis, we compared body condition of Hellbenders in three streams with different crayfish relative frequencies. Body condition of Hellbenders was positively correlated with crayfish relative frequencies, with Hellbenders in the stream with the highest crayfish relative frequency exhibiting the highest expected mass per total length.
Time-varying nodal measures with temporal community structure: a cautionary note to avoid misinterpretation
Authors: Thompson WH , Kastrati G , Finc K , Wright J , Shine JM , Poldrack RA 
Published: June 2019

AbstractIn network neuroscience, temporal network models have gained popularity. In these models, network properties have been related to cognition and behaviour. Here we demonstrate that calculating nodal properties that are dependent on temporal community structure (such as the participation coefficient) in time-varying contexts can potentially lead to misleading results. Specifically, with regards to the participation coefficient, increases in integration can be inferred when the opposite is occuring. Further, we present a temporal extension to the participation coefficient measure (temporal participation coefficient) that circumnavigates this problem by jointly considering all community partitions assigned to a node through time. The proposed method allows us to track a node’s integration through time while adjusting for the possible changes in the community structure of the overall network.
Dynamic pneumococcal genetic adaptations support bacterial growth and inflammation during coinfection with influenza
Authors: Smith Amanda P. , Lane Lindey C. , Opijnen Tim van , Woolard Stacie , Carter Robert , Iverson Amy , Burnham Corinna , Vogel Peter , Roeber Dana , Hochu Gabrielle , Johnson Michael D.L. , McCullers Jonathan A. , Rosch Jason , Smith Amber M. 
Published: June 2019

AbstractStreptococcus pneumoniae(pneumococcus) is one of the primary bacterial pathogens that complicates influenza virus infections. These bacterial coinfections increase influenza-associated morbidity and mortality through a number of immunological and viral-mediated mechanisms, but the specific bacterial genes that contribute to post-influenza pathogenicity are not known. Here, we used genome-wide transposon mutagenesis (Tn-Seq) to reveal bacterial genes that confer improved fitness in influenza-infected hosts. The majority of the 32 identified genes are involved in bacterial metabolism, including nucleotide biosynthesis, amino acid biosynthesis, protein translation, and membrane transport. We generated single-gene deletion (SGD) mutants of five identified genes: SPD1414, SPD2047 (cbiO1),SPD0058 (purD), SPD1098, and SPD0822 (proB), to investigate their effect onin vivofitness, disease severity, and host immune responses. Growth of SGD mutants was slightly attenuatedin vitroandin vivo, but each still grew to high titers in the lungs of mock- and influenza-infected hosts. Despite high bacterial loads, mortality was significantly reduced or delayed with all SGD mutants. Time-dependent reductions in pulmonary neutrophils, inflammatory macrophages, and select proinflammatory cytokines and chemokines were also observed. Immunohistochemical staining further revealed that neutrophil phenotype and distribution was altered in the lungs of influenza-SGD coinfected animals. These studies demonstrate a critical role for specific bacterial genes and for bacterial metabolism in driving virulence and modulating immune function during influenza-associated bacterial pneumonia.
Modulation of post-traumatic immune response using anti-IL-1 therapy for improved visual outcomes: Anti-IL-1 improves post-traumatic visual outcomes
Authors: Evans Lucy P. , Woll Addison W. , Wu Shu , Todd Brittany P. , Hehr Nicole , Hedberg-Buenz Adam , Anderson Michael G. , Newell Elizabeth A. , Ferguson Polly J. , Mahajan Vinit B. , Harper Mathew M. , Bassuk Alexander G. 
Published: June 2019

AbstractThe purpose of this study was to characterize acute changes in inflammatory pathways in the mouse eye following a blast-mediated TBI (bTBI) model, and to determine if modulation of these pathways could protect the structure and function of retinal ganglion cells (RGC). bTBI was induced in C57BL/6J male mice by exposure to three 20 PSI blast waves, with an interblast interval of one hour. Acute cytokine expression in retinal tissue was measured through real-time quantitative polymerase chain reaction (RT-qPCR) 4 hours post-blast. Increased retinal expression of lL-1β, IL-1α, IL-6, and TNFα was observed in bTBI mice exposed to blast when compared to shams, which was associated with activation of microglia and macroglia reactivity, assessed via immunohistochemistry with IBA-1 and GFAP, respectively, 1 week post-blast. Inhibition of the IL-1 pathway was accomplished using anakina, an IL-1RI antagonist. Retinal function and structure were evaluated 4 weeks post-injury using pattern electroretinogram (PERG) and optical coherence tomography (OCT), respectively. After bTBI, anakinra treatment resulted in a preservation of RGC function and RGC structure when compared to saline treated bTBI mice. Optic nerve integrity analysis demonstrated a tred of decreased suggesting that IL-1 blockade also prevents axonal damage after blast. Blast exposure results in increased retinal inflammation including upregulation of pro-inflammatory cytokines and activation of resident microglia and macroglia. This may partially explain the RGC loss we observed in this model as blockade of the acute inflammatory response after injury with the IL-1R1 antagonist anakinra resulted in preservation of RGC function and structure.Significance StatementBlast-mediated traumatic brain injury (bTBI) affects military members and civilians as a direct result of combat, workplace accidents, or intentional terrorist attacks. The retina is a central nervous system (CNS) tissue that is vulnerable to blast exposure. Individuals with bTBI often report visual dysfunction, but the mechanisms of ocular injury are poorly understood. This study demonstrates that damaging neuroinflammation contributes to retinal injury following blast-mediated TBI. We also identified anakinra, an anti-IL-1 therapy currently utilized for other diseases, as a potential pharmacologic agent that could prevent ocular damage after blast. These findings will aide in the development of novel treatments for vision preservation.
A robust metatranscriptomic technology for population-scale studies of diet, gut microbiome, and human health
Authors: Hatch Andrew , Horne James , Toma Ryan , Twibell Brittany L. , Somerville Kalie M. , Pelle Benjamin , Canfield Kinga P. , Genkin Matvey , Banavar Guruduth , Perlina Ally , Messier Helen , Klitgord Niels , Vuyisich Momchilo 
Published: June 2019

ABSTRACTA functional readout of the gut microbiome is necessary to enable precise control of the gut microbiome’s functions, which support human health and prevent or minimize a wide range of chronic diseases. Stool metatranscriptomic analysis offers a comprehensive functional view of the gut microbiome, but despite its usefulness, it has rarely been used in clinical studies due to its complexity, cost, and bioinformatic challenges. This method has also received criticism due to potential intra-sample variability, rapid changes, and RNA degradation. Here, we describe a robust and automated stool metatranscriptomic method, called Viomega, which was specifically developed for population-scale studies. Viomega includes sample collection, ambient temperature sample preservation, total RNA extraction, physical removal of ribosomal RNAs (rRNAs), preparation of directional Illumina libraries, Illumina sequencing, taxonomic classification based on a database of >110,000 microbial genomes, and quantitative microbial gene expression analysis using a database of ~100 million microbial genes. We applied this method to 10,000 human stool samples, and performed several small-scale studies to demonstrate sample stability and consistency. In summary, Viomega is an inexpensive, high throughput, automated, and accurate sample-to-result stool metatranscriptomic technology platform for large-scale studies and a wide range of applications.
Single cell RNA-sequencing reveals cellular heterogeneity and trajectories of lineage specification during murine embryonic limb development
Authors: Kelly Natalie H. , Huynh Nguyen P.T. , Guilak Farshid 
Published: June 2019

ABSTRACTThe coordinated spatial and temporal regulation of gene expression in the murine hindlimb determines the identity of mesenchymal progenitors and the development of diversity of musculoskeletal tissues they form. Hindlimb development has historically been studied with lineage tracing of individual genes selected a priori, or at the bulk tissue level, which does not allow for the determination of single cell transcriptional programs yielding mature cell types and tissues. To identify the cellular trajectories of lineage specification during limb bud development, we used single cell mRNA sequencing (scRNA-seq) to profile the developing murine hindlimb between embryonic days (E)11.5-E18.5. We found cell type heterogeneity at all time points, and the expected cell types that form the mouse hindlimb. In addition, we used RNA fluorescence in situ hybridization (FISH) to examine the spatial locations of cell types and cell trajectories to understand the ancestral continuum of cell maturation. This data provides a resource for the transcriptional program of hindlimb development that will support future studies of musculoskeletal development and generate hypotheses for tissue regeneration.
Prefix Block-Interchanges on Binary and Ternary Strings
Authors: Rahman Md. Khaledur , Rahman M. Sohel 
Published: June 2019

AbstractThe genome rearrangement problem computes the minimum number of operations that are required to sort all elements of a permutation. A block-interchange operation exchanges two blocks of a permutation which are not necessarily adjacent and in a prefix block-interchange, one block is always the prefix of that permutation. In this paper, we focus on applying prefix block-interchanges on binary and ternary strings. We present upper bounds to group and sort a given binary/ternary string. We also provide upper bounds for a different version of the block-interchange operation which we refer to as the ‘restricted prefix block-interchange’. We observe that our obtained upper bound for restricted prefix block-interchange operations on binary strings is better than that of other genome rearrangement operations to group fully normalized binary strings. Consequently, we provide a linear-time algorithm to solve the problem of grouping binary normalized strings by restricted prefix block-interchanges. We also provide a polynomial time algorithm to group normalized ternary strings by prefix block-interchange operations. Finally, we provide a classification for ternary strings based on the required number of prefix block-interchange operations.
Bacterial Controller Aided Wound Healing: A Case Study in Dynamical Population Controller Design
Authors: Green Leopold N. , Hu Chelsea Y. , Ren Xinying , Murray Richard M. 
Published: June 2019

AbstractWound healing is a complicated biological process consisting of many types of cellular dynamics and functions regulated by chemical and molecular signals. Recent advances in synthetic biology have made it possible to predictably design and build closed-loop controllers that can function appropriately alongside biological species. In this paper we develop a simple dynamical population model mimicking the sequential relay-like dynamics of cellular populations involved in the wound healing process. Our model consists of four nodes and five signals whose parameters we can tune to simulate various chronic healing conditions. We also develop a set of regulator functions based on type-1 incoherent feed forward loops (IFFL) that can sense the change from acute healing to incomplete chronic wounds, improving the system in a timely manner. Both the wound healing and type-1 IFFL controller architectures are compatible with available synthetic biology experimental tools for potential applications.
Placenta microbiome diversity is associated with maternal pre-pregnancy obesity and placenta biogeography
Authors: Benny Paula A. , Al-Akwaa Fadhl M. , Dirkx Corbin , Schlueter Ryan J. , Wolfgruber Thomas K. , Chern Ingrid Y. , Hoops Suzie , Knights Dan , Garmire Lana X. 
Published: June 2019

AbstractRecently there has been considerable debate in the scientific community regarding the placenta as the host of a unique microbiome. No studies have addressed the associations of clinical conditions such as maternal obesity, or localizations on the placental microbiome. We examined the placental microbiome in a multi-ethnic maternal pre-pregnant obesity cohort using controls for environmental contaminants and an optimized microbiome protocol to enrich low bacterial biomass samples. We confirmed that a distinct placenta microbiome does exist, as compared to the environmental background. The placenta microbiome consists predominantly of Lactobacillus, Enterococcus and Chryseobacterium. Moreover, the microbiome in the placentas of obese pre-pregnant mothers are less diverse when compared to those of mothers of normal pre-pregnancy weight. Lastly, microbiome richness also decreases from the maternal side to fetal side. In summary, our study reveals associations of placental microbiome with placenta biogeography and with maternal pre-pregnant obesity.
Three-dimensional analysis of β-cell proliferation by a novel mouse model
Authors: Tokumoto Shinsuke , Yabe Daisuke , Tatsuoka Hisato , Usui Ryota , Fauzi Muhammad , Botagarova Ainur , Goto Hisanori , Herrera Pedro Luis , Ogura Masahito , Inagaki Nobuya 
Published: June 2019

SummaryInducing β-cell proliferation could inhibit diabetes progression. Many factors have been suggested as potential β-cell mitogens, but their impact on β-cell replication has not been confirmed due to the lack of a standardized β-cell proliferation assay. In this study, we developed a novel method that specifically labels replicating β cells and yields more reproducible results than current immunohistochemical assays. We established a mouse line expressing the fluorescent ubiquitination-based cell cycle indicator (Fucci2a) reporter only in β cells through Cre-mediated recombination under the control of the rat insulin promoter (RIP-Cre;Fucci2aR). Three-dimensional imaging of optically cleared pancreas tissue from these mice enabled the quantification of replicating β cells in islets and morphometric analysis of islets following mitogen treatment. Intravital imaging of RIP-Cre;Fucci2aR mice revealed cell cycle progression of β cells. Thus, this novel mouse line is a powerful tool for spatiotemporal analysis of β-cell proliferation in response to mitogen stimulation.
Transient transcriptome sequencing: computational pipeline to quantify genome-wide RNA kinetic parameters and transcriptional enhancer activity
Authors: Villamil Gabriel , Wachutka Leonhard , Cramer Patrick , Gagneur Julien , Schwalb Björn 
Published: June 2019

AbstractIn the accompanying chapter (Gressel, Lidschreiber, Cramer), we describe the detailed experimental protocol for transient transcriptome sequencing (TT-seq). TT-seq detects metabolically labeled, newly synthesized RNA fragments genome-wide in living cells. TT-seq can monitor gene activity and the dynamics of enhancer landscapes with great sensitivity, but this requires careful computational analysis of the data. In this manuscript, we present the bioinformatics workflow used to analyze TT-seq data. In particular, we describe pre-processing steps, including a reliable and robust normalization strategy, and several downstream analysis tools that enable the user to quantify RNA synthesis, splicing and degradation activities. Together, these tools form a comprehensive analysis pipeline that can be adapted to almost any TT-seq application.
Elucidating the Influence of Linker Histone Variants on Chromatosome Dynamics and Energetics
Authors: Woods Dustin C. , Wereszczynski Jeff 
Published: June 2019

AbstractLinker histones are epigenetic regulators that bind to nucleosomes and alter chromatin structures and dynamics. Biophysical studies have revealed two binding modes in the linker histone/nucleosome complex, the chromatosome, where the linker histone is either centered on or askew from the dyad axis. Each has been posited to have distinct effects on chromatin, however the molecular and thermodynamic mechanisms that drive them and their dependence on linker histone compositions remain poorly understood. We present molecular dynamics simulations of chromatosomes with the globular domain of two linker histone variants, generic H1 (genGH1) and H1.0 (GH1.0), to determine how their differences influence chromatosome structures, energetics, and dynamics. Results show that both unbound linker histones adopt a single compact conformation. Upon binding, DNA flexibility is reduced, resulting in increased chromatosome compaction. While both variants enthalpically favor on-dyad binding, energetic benefits are significantly higher for GH1.0, suggesting that GH1.0 is more capable than genGH1 of overcoming the large entropic reduction required for on-dyad binding which helps rationalize experiments that have consistently demonstrated GH1.0 in on-dyad states but that show genGH1 in both locations. These simulations highlight the thermodynamic basis for different linker histone binding motifs, and details their physical and chemical effects on chromatosomes.
Lower dormancy with rapid germination is an important strategy for seeds in an arid zone with unpredictable rainfall
Authors: Duncan Corrine , Schultz Nick , Lewandrowski Wolfgang , Good Megan , Cook Simon 
Published: June 2019

AbstractSeed germination traits are key drivers of population dynamics, yet they are under-represented in community ecology studies, which have predominately focussed on adult plant and seed morphological traits. We studied the seed traits and germination strategy of eight woody plant species to investigate regeneration strategies in the arid zone of eastern Australia. To cope with stochastic and minimal rainfall, we predict that arid seeds will either have rapid germination across a wide range of temperatures, improved germination under cooler temperatures, or dormancy and/or longevity traits to delay or stagger germination across time. To understand how temperature affects germination responses, seeds of eight keystone arid species were germinated under laboratory conditions, and under three diurnal temperatures (30/20°C, 25/15°C and 17/7°C) for 30 days. Seeds of species in this study are currently stored for minesite restoration projects, hence we tested for decline in seed viability across 24 months in dry storage at similar storage conditions (≈20°C). Six of the eight arid species studied had non-dormant, rapidly germinating seeds, and only two species had physiological dormancy traits. Seed longevity differed widely between species, from one recalcitrant species surviving only months in storage (P50 = <3 months) and one serotinous species surviving for many years (P50 = 84 months). Our results highlight the importance of understanding the reproductive strategies of plant species in arid environments. Rapid germination, the dominant seed trait of species included in this study, allows arid species to capitalise on sporadic rainfall. However, some species also exhibit dormancy and delayed germination; this an alternative strategy which spreads the risk of germination failure over time. We highlight important seed traits and germination strategies of plants from an arid zone with stochastic rainfall and discuss the implications for their restoration.