bluuebunny/crossref_metadata_2025_split huggingface dataset:
A balance of outward and linear inward ionic currents is required for the generation of slow wave oscillations
Authors: Golowasch Jorge , Bose Amitabha , Guan Yinzheng , Salloum Dalia , Roeser Andrea , Nadim Farzan 
Published: May 2017

AbstractRegenerative inward currents help produce slow oscillations through a negative-slope conductance region of their current-voltage relationship that is well approximated by a linear negative conductance. We used dynamic clamp injections of a linear current with this conductance,INL, to explore why some neurons can generate intrinsic slow oscillations whereas others cannot. We addressed this question, in synaptically isolated neurons of the crabCancer borealis, after blocking action potentials. The pyloric network consists of distinct pacemaker group and follower neurons, all of which express the same complement of ionic currents. When the pyloric dilator (PD) neuron, a member of the pacemaker group, was injected withINLusing dynamic clamp, it consistently produced slow oscillations. In contrast, the lateral pyloric (LP) or ventral pyloric (VD) follower neurons, failed to oscillate withINL. To understand these distinct behaviors, we compared outward current levels of PD, LP and VD neurons. We found that LP and VD neurons had significantly larger high-threshold potassium currents (IHTK) than PD, and LP had lower transient potassium current,IA. ReducingIHTKpharmacologically enabled both LP and VD neurons to produce oscillations withINL, whereas modifyingIAlevels did not affectINL-induced oscillations. Using phase-plane and bifurcation analysis of a simplified model cell, we demonstrate that large levels ofIHTKcan blockINL-induced oscillatory activity, whereas generation of oscillations is almost independent ofIAlevels. These results demonstrate the importance of a balance between inward pacemaking currents and high-threshold K+current levels in determining slow oscillatory activity.
Thermal acclimation mitigates cold-induced paracellular leak from theDrosophilagut
Authors: MacMillan Heath A. , Yerushalmi Gil , Jonusaite Sima , Kelly Scott P. , Donini Andrew 
Published: May 2017

AbstractWhen chilled to temperatures below their critical thermal minimum, chill susceptible insects can suffer tissue damage and die. The mechanisms that cause this chilling injury are not well understood but a growing body of evidence suggests that a loss of ion and water homeostasis in the cold leads to hemolymph hyperkalemia that depolarizes cells, leading to cell death. The apparent root of this cascade of issues is the net leak of osmolytes down their concentration gradients in the cold. Many insects, however, are capable of adjusting their thermal physiology, and cold-acclimatedDrosophilacan maintain homeostasis and avoid chilling injury better than warm-acclimated flies. Here, we test whether the cold-induced loss of osmotic homeostasis is associated with a loss of epithelial barrier function inDrosophila, and provide the first evidence of cold-induced epithelial barrier failure in an invertebrate. Flies exposed to 0° C had increased rates of paracellular leak through the gut epithelia, but cold acclimation reduced paracellular permeability, both before and during cold stress, and improved cold tolerance. This adjustment in barrier function was associated with changes in the abundance of select septate junction proteins and the appearance of a tortuous ultrastructure in subapical intercellular regions of contact between adjacent midgut epithelial cells. Thus, cold causes paracellular leak in a chill susceptible insect and cold acclimation can mitigate this effect, at least partly through changes in the composition and structure of transepithelial barriers.Summary Statement:Chilling disrupts barrier function of the gut of flies and cold acclimation can mitigate this problem through changes in paracellular occluding junctions.
Multi-omic analysis of a hyper-diverse plant metabolic pathway reveals evolutionary routes to biological innovation
Authors: Moghe Gaurav D. , Leong Bryan J. , Hurney Steven , Daniel Jones A. , Last Robert L. 
Published: May 2017

AbstractThe diversity of life on Earth is a result of continual innovations in molecular networks influencing morphology and physiology. Plant specialized metabolism produces hundreds of thousands of compounds, offering striking examples of these innovations. To understand how this novelty is generated, we investigated the evolution of the Solanaceae family-specific, trichome-localized acylsugar biosynthetic pathway using a combination of mass spectrometry, RNA-seq, enzyme assays, RNAi and phylogenetics in non-model species. Our results reveal that hundreds of acylsugars are produced across the Solanaceae family and even within a single plant, revealing this phenotype to be hyper-diverse. The relatively short biosynthetic pathway experienced repeated cycles of innovation over the last 100 million years that include gene duplication and divergence, gene loss, evolution of substrate preference and promiscuity. This study provides mechanistic insights into the emergence of plant chemical novelty, and offers a template for investigating the ∼300,000 non-model plant species that remain underexplored.
Examination of signatures of recent positive selection on genes involved in human sialic acid biology
Authors: Moon Jiyun M. , Aronoff David M. , Capra John A. , Abbot Patrick , Rokas Antonis 
Published: May 2017

AbstractSialic acids are nine carbon sugars ubiquitously found on the surfaces of vertebrate cells and are involved in various immune response-related processes. In humans, at least 58 genes spanning diverse functions, from biosynthesis and activation to recycling and degradation, are involved in sialic acid biology. Because of their role in immunity, sialic acid biology genes have been hypothesized to exhibit elevated rates of evolutionary change. Consistent with this hypothesis, several genes involved in sialic acid biology have experienced higher rates of non-synonymous substitutions in the human lineage than their counterparts in other great apes, perhaps in response to ancient pathogens that infected hominins millions of years ago (paleopathogens). To test whether sialic acid biology genes have also experienced more recent positive selection during the evolution of the modern human lineage, reflecting adaptation to contemporary cosmopolitan or geographically-restricted pathogens, we examined whether their protein-coding regions showed evidence of recent hard and soft selective sweeps. This examination involved the calculation of four measures that quantify changes in allele frequency spectra, extent of population differentiation, and haplotype homozygosity caused by recent hard and soft selective sweeps for 55 sialic acid biology genes using publicly available whole genome sequencing data from 1,668 humans from three ethnic groups. To disentangle evidence for selection from confounding demographic effects, we compared the observed patterns in sialic acid biology genes to simulated sequences of the same length under a model of neutral evolution that takes into account human demographic history. We found that the patterns of genetic variation of most sialic acid biology genes did not significantly deviate from neutral expectations and were not significantly different among genes belonging to different functional categories. Those few sialic acid biology genes that significantly deviated from neutrality either experienced soft sweeps or population-specific hard sweeps. Interestingly, while most hard sweeps occurred on genes involved in sialic acid recognition, most soft sweeps involved genes associated with recycling, degradation and activation, transport, and transfer functions. We propose that the lack of signatures of recent positive selection for the majority of the sialic acid biology genes is consistent with the view that these genes regulate immune responses against ancient rather than contemporary cosmopolitan or geographically restricted pathogens.
Systematic genetic dissection of chitin degradation and uptake inVibrio cholerae
Authors: Hayes Chelsea A. , Dalia Triana N. , Dalia Ankur B. 
Published: May 2017

SUMMARYVibrio choleraeis a natural resident of the aquatic environment, where a common nutrient is the chitinous exoskeletons of microscopic crustaceans. Chitin utilization requires chitinases, which degrade this insoluble polymer into soluble chitin oligosaccharides. These oligosaccharides also serve as an inducing cue for natural transformation inVibriospecies. There are 7 predicted endochitinase-like genes in theV. choleraegenome. Here, we systematically dissect the contribution of each gene to growth on chitin as well as induction of natural transformation. Specifically, we created a strain that lacks all 7 putative chitinases and from this strain, generated a panel of strains where each expresses a single chitinase. We also generated expression plasmids to ectopically express all 7 chitinases in our chitinase deficient strain. Through this analysis, we found that low levels of chitinase activity are sufficient for natural transformation, while growth on insoluble chitin as a sole carbon source requires more robust and concerted chitinase activity. We also assessed the role that the three uptake systems for the chitin degradation products GlcNAc, (GlcNAc)2, and (GlcN)2, play in chitin utilization and competence induction. Cumulatively, this study provides mechanistic details for how this pathogen utilizes chitin to thrive and evolve in its environmental reservoir.ORIGINALITY-SIGNIFICANCE STATEMENTVibrio cholerae, the causative agent of the diarrheal disease cholera, interacts with the chitinous shells of crustacean zooplankton in the aquatic environment, which serves as an environmental reservoir for this pathogen. It degrades and utilizes chitin-derived products as a source of carbon and nitrogen. Also, chitin serves as an inducing cue for natural transformation – an important mechanism of horizontal gene transfer in this species. Here, we systematically dissect the genes required for chitin degradation and uptake, and characterize the role of these genes for growth on chitin as a nutrient and during chitininduced natural transformation. Thus, this study provides mechanistic details for how this pathogen utilizes chitin to thrive and evolve in its environmental reservoir.
Improved Split Fluorescent Proteins for Endogenous Protein Labeling
Authors: Feng Siyu , Sekine Sayaka , Pessino Veronica , Li Han , Leonetti Manuel D. , Huang Bo 
Published: May 2017

ABSTRACTSelf-complementing split fluorescent proteins (FPs) have been widely used for protein labeling, visualization of subcellular protein localization, and detection of cell-cell contact. To expand this toolset, we have developed a screening strategy for the direct engineering of self-complementing split FPs. Via this strategy, we have generated a yellow-green split-mNeonGreen21-10/11that improves the ratio of complemented signal to the background of FP1-10-expressing cells compared to the commonly used split-GFP1-10/11,as well as a 10-fold brighter red-colored split-sfCherry21-10/11. Based on split-sfCherry2, we have engineered a photoactivatable variant that enables single-molecule localization-based super-resolution microscopy. We have demonstrated dual-color endogenous protein tagging with sfCherry211and GFP11, revealing that endoplasmic reticulum translocon complex Sec61B has reduced abundance in certain peripheral tubules. These new split FPs not only offer multiple colors for imaging interaction networks of endogenous proteins, but also hold the potential to provide orthogonal handles for biochemical isolation of native protein complexes.
LTR_retriever: a highly accurate and sensitive program for identification of LTR retrotransposons
Authors: Ou Shujun , Jiang Ning 
Published: May 2017

ABSTRACTLong terminal-repeat retrotransposons (LTR-RTs) are prevalent in plant genomes. Identification of LTR-RTs is critical for achieving high-quality gene annotation. Based on the well-conserved structure, multiple programs were developed forde novoidentification of LTR-RTs; however, these programs are associated with low specificity and high false discovery rate (FDR). Here we report LTR_retriever, a multithreading empowered Perl program that identifies LTR-RTs and generates high-quality LTR libraries from genomic sequences. LTR_retriever demonstrated significant improvements by achieving high levels of sensitivity (91.8%), specificity (94.7%), accuracy (94.3%), and precision (90.6%) in model plants. LTR_retriever is also compatible with long sequencing reads. With 40k self-corrected PacBio reads equivalent to 4.5X genome coverage in Arabidopsis, the constructed LTR library showed excellent sensitivity and specificity. In addition to canonical LTR-RTs with 5'-TG..CA-3' termini, LTR_retriever also identifies non-canonical LTR-RTs (non-TGCA), which have been largely ignored in genome-wide studies. We identified seven types of non-canonical LTRs from 42 out of 50 plant genomes. The majority of non-canonical LTRs areCopiaelements, with which the LTR is four times shorter than that of otherCopiaelements, which may be a result of their target specificity. Strikingly, non-TGCACopiaelements are often located in genic regions and preferentially insert nearby or within genes, indicating their impact on the evolution of genes and potential as mutagenesis tools.
Amortized Hypothesis Generation
Authors: Dasgupta Ishita , Schulz Eric , Goodman Noah D. , Gershman Samuel J. 
Published: May 2017

AbstractBayesian models of cognition posit that people compute probability distributions over hypotheses, possibly by constructing a sample-based approximation. Since people encounter many closely related distributions, a computationally efficient strategy is to selectively reuse computations – either the samples themselves or some summary statistic. We refer to these reuse strategies asamortized inference. In two experiments, we present evidence consistent with amortization. When sequentially answering two related queries about natural scenes, we show that answers to the second query vary systematically depending on the structure of the first query. Using a cognitive load manipulation, we find evidence that people cache summary statistics rather than raw sample sets. These results enrich our notions of how the brain approximates probabilistic inference.
DNA damage checkpoint dynamics drive cell cycle phase transitions
Authors: Chao Hui Xiao , Poovey Cere E. , Privette Ashley A. , Grant Gavin D. , Chao Hui Yan , Cook Jeanette G. , Purvis Jeremy E. 
Published: May 2017

ABSTRACTDNA damage checkpoints are cellular mechanisms that protect the integrity of the genome during cell cycle progression. In response to genotoxic stress, these checkpoints halt cell cycle progression until the damage is repaired, allowing cells enough time to recover from damage before resuming normal proliferation. Here, we investigate the temporal dynamics of DNA damage checkpoints in individual proliferating cells by observing cell cycle phase transitions following acute DNA damage. We find that in gap phases (G1 and G2), DNA damage triggers an abrupt halt to cell cycle progression in which the duration of arrest correlates with the severity of damage. However, cells that have already progressed beyond a proposed “commitment point” within a given cell cycle phase readily transition to the next phase, revealing a relaxation of checkpoint stringency during later stages of certain cell cycle phases. In contrast to G1 and G2, cell cycle progression in S phase is significantly less sensitive to DNA damage. Instead of exhibiting a complete halt, we find that increasing DNA damage doses leads to decreased rates of S-phase progression followed by arrest in the subsequent G2. Moreover, these phase-specific differences in DNA damage checkpoint dynamics are associated with corresponding differences in the proportions of irreversibly arrested cells. Thus, the precise timing of DNA damage determines the sensitivity, rate of cell cycle progression, and functional outcomes for damaged cells. These findings should inform our understanding of cell fate decisions after treatment with common cancer therapeutics such as genotoxins or spindle poisons, which often target cells in a specific cell cycle phase.
Quadratization: From conductance-based models to caricature models with parabolic nonlinearities
Authors: Turnquist Axel G. R. , Rotstein Horacio G. 
Published: May 2017

DefinitionQuadratizationof biophysical (conductance-based) models having a parabolic-like voltage nullcline in the subthreshold voltage regime refers to the process by which these models are substituted by “caricature” models having a strictly parabolic voltage nullcline and a linear nullcline for the recovery variable. We refer to the latter as quadratic or parabolic models. The parabolic-like and strictly parabolic voltage nullclines coincide at their extrema (minima or maxima) and are well approximated by each other in vicinities of these extrema whose size depend on the model parameters. Quadratic models are simplified by a change of variables that translates these extrema into the origin of the phase-plane diagram. A further simplification (parameter reduction) can be achieved by nondimensionalizing the quadratic models. This procedure can be extended to three-dimensional models having a parabolic-cylinder-like shaped voltage nullsurface and to models having time-dependent inputs and synaptic currents.
Estimation of universal and taxon-specific parameters of prokaryotic genome evolution
Authors: Sela Itamar , Wolf Yuri I. , Koonin Eugene V. 
Published: May 2017

AbstractOur recent study on mathematical modeling of microbial genome evolution indicated that, on average, genomes of bacteria and archaea evolve in the regime of mutation-selection balance defined by positive selection coefficients associated with gene acquisition that is counter-acted by the intrinsic deletion bias. This analysis was based on the strong assumption that parameters of genome evolution are universal across the diversity of bacteria and archaea, and yielded extremely low values of the selection coefficient. Here we further refine the modeling approach by taking into account evolutionary factors specific for individual groups of microbes using two independent fitting strategies, an ad hoc hard fitting scheme and an hierarchical Bayesian model. The resulting estimate of the mean selection coefficient ofs∼10-10associated with the gain of one gene implies that, on average, acquisition of a gene is beneficial, and that microbial genomes typically evolve under a weak selection regime that might transition to strong selection in highly abundant organisms with large effective population sizes. The apparent selective pressure towards larger genomes is balanced by the deletion bias, which is estimated to be consistently greater than unity for all analyzed groups of microbes. The estimated values ofsare more realistic than the lower values obtained previously, indicating that global and group-specific evolutionary factors synergistically affect microbial genome evolution that seems to be driven primarily by adaptation to existence in diverse niches.
The opposite effects of nitric oxide donor, S‐nitrosoglutathione, on myocardial ischaemia/reperfusion injury in diabetic and non‐diabetic mice
Authors: Liu Yi , Xia Chenhai , Wang Rutao , Zhang Jinglong , Yin Tao , Ma Yanzuo , Tao Ling 
Published: May 2017

SummaryNitric oxide is a potent anti‐apoptotic and cardioprotective molecule in healthy animals. However, recent study demonstrates that overexpression of eNOS exacerbates the liver injury in diabetic animals. whether diabetes may also alter NO's biologic activity in ischaemic/reperfused heart remains unknown. The present experiment was designed to determine whether the nitric oxide donor, S‐nitrosoglutathione, may exert different effects on diabetic and non‐diabetic myocardial ischaemia/reperfusion (MI/R) injury. Diabetic state was induced in mice by multiple intraperitoneal injections of low‐dose streptozotocin (STZ). The control or diabetic mice were subjected to 30 minutes ischaemia and 3 or 24 hours reperfusion. At 10 minutes before reperfusion, diabetic and non‐diabetic mice were received an intraperitoneal injection of S‐nitrosoglutathione (GSNO, a nitric oxide donor, 1 μmol/kg). GSNO attenuated MI/R injury in non‐diabetic mice, as measured by improved cardiac function, reduced infarct size and decreased cardiomyocyte apoptosis. In contrast, GSNO failed to attenuate but, rather, aggravated the MI/R injury in diabetic mice. Mechanically, the diabetic heart exhibited an increased nitrative/oxidative stress level, as measured by peroxynitrite formation, compared with non‐diabetic mice. Co‐administration of GSNO with EUK134 (a peroxynitrite scavenger) or MnTE‐2‐PyP5 (a superoxide dismutase mimetic) or Apocynin (a NADPH oxidase inhibitor) 10 minutes before reperfusion significantly decreased the MI/R‐induced peroxynitrite formation and the MI/R injury. Collectively, the present study for the first time demonstrated that diabetes may cause superoxide overproduction, increase NO inactivation and peroxynitrite formation, and thus convert GSNO from a cardioprotective molecule to a cardiotoxic molecule.
Hot water immersion of Allium hookeri roots for the control of the plant parasitic nematodes Meloidogyne javanica and Pratylenchus coffeae
Authors: Cho Dong‐Hun , Park Bok‐Ri , Chun Jae‐Yong , Noh Young‐Ho , Kim Yang‐Ho , Park Min‐Gu , Kim Dongwoo , Lee Kyeong‐Yeoll 
Published: May 2017

AbstractNematodes are important quarantine pests of bulbous plants such as hooker chives. Although control methods such as fumigation, chemical immersion, and heat are often applied, it has proved difficult to disinfect nematodes from plant roots in quarantine. As heat treatment has been successfully useful for the control of nematodes in other agricultural products in quarantine, we investigated the susceptibility and mortality rates of Meloidogyne javanica and Pratylenchus coffeae, which infest hooker chive roots, using a hot water immersion method. Heat damage to the hooker chive roots was noticeable at temperatures over 50°C. Temperatures for the effective time to kill 99% at 1 min (ET99) for M. javanica and P. coffeae juveniles were 49.3°C and 49.1°C, respectively. However, the time to kill 99% of M. javanica eggs at 48°C and 49°C were 27.0 min and 8.3 min, respectively. Using a thermal equilibrium formula, the optimum commercial scale condition, in a 1400‐L chamber, for nematode control without associated plant damage was water immersion at 48.2°C for 30 min or at 49.2°C for 13 min with a filling ratio less than 12%. This result can be applicable for the nematode disinfestation of hooker chive roots in plant quarantine.