bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of candidate genes for gelatinization temperature, gel consistency and pericarp color by GWAS in rice based on SLAF-sequencing
Authors: Yang Xinghai , Xia Xiuzhong , Zeng Yu , Nong Baoxuan , Zhang Zongqiong , Wu Yanyan , Xiong Faqian , Zhang Yuexiong , Liang Haifu , Deng Guofu , Li Danting 
Published: February 2018

AbstractRice is an important cereal in the world, uncovering the genetic basis of agronomic traits in rice landraces genes associated with agronomically important traits is indispensable for both understanding the genetic basis of phenotypic variation and efficient crop improvement. Gelatinization temperature, gel consistency and pericarp color are important indices of rice cooking and eating quality evaluation and potential nutritional importance, which attract wide attentions in the application of genetic and breeding. To dissect the genetic basis of gelatinization temperature (GT), gel consistency (GC) and pericarp color (PC), a total of 419 rice landraces core germplasm collections consisting of 330indicalines, 78japonicalines and 11 uncertain varieties were grown, collected, then GT, GC, PC were measured for two years, and sequenced using Specific Locus Amplified Fragment Sequencing (SLAF) technology. In this study, 261,385,070 clean reads and 56,768 polymorphic SLAF tags were obtained, which a total of 211,818 single nucleotide polymorphisms (SNPs) were discovered. With 208,993 SNPs meeting the criterion of minor allele frequency (MAF) > 0.05 and integrity> 0.5, the phylogenetic tree and population structure analysis were performed for all 419 rice landraces, and the whole panel mainly separated into six subpopulations based on population structure analysis. Genome-wide association study (GWAS) was carried out for the whole panel,indicasubpanel andjaponicasubpanel with subset SNPs respectively. One quantitative trait locus (QTL) on chromosome 6 for GT was detected in the whole panel andindicasubpanel, and one QTL associated with GC was located on chromosome 6 in the whole panel andindicasubpanel. For the PC trait, 8 QTLs were detected in the whole panel on chromosome 1, 3, 4, 7, 8, 10 and 11, and 7 QTLs in theindicasubpanel on chromosome 3, 4, 7, 8, 10 and 11. The loci on chromosome 3, 8, 10 and 11 have not been identified previously, and they may be the candidate genes of pericarp color. For the three traits, no QTL was detected injaponicasubpanel probably because of the polymorphism repartition between the subpanel, or small population size ofjaponicasubpanel. This paper provides new gene resources and insights into the molecular mechanisms of important agricultural trait of rice phenotypic variation and genetic improvement of rice quality variety breeding.
Differences in firing efficiency, chromatin and transcription underlie the developmental plasticity of the Arabidopsis originome
Authors: Sequeira-Mendes J. , Vergara Z. , Peiró R. , Morata J. , Aragüez I. , Costas C. , Mendez-Giraldez R. , Casacuberta J.M. , Bastolla U. , Gutierrez C. 
Published: February 2018

AbstractEukaryotic genome replication depends on thousands of DNA replication origins (ORIs) that constitute the originome. A major challenge is to learn ORI biology in multicellular organisms in the context of growing organs to understand their developmental plasticity. We have determined the originome and chromatin landscape of Arabidopsis thaliana at two stages of postembryonic development. ORIs associate with multiple chromatin signatures including TSS but also regulatory regions and heterochromatin, where ORIs colocalize with retrotransposons. In addition, quantitative analysis of ORI activity led us to conclude that strong ORIs have high GC content and clusters of GGN trinucleotides. Development primarily influences ORI firing strength rather than ORI location. ORIs that preferentially fire at early developmental stages colocalize with GC-rich heterochromatin whereas at later stages with transcribed genes, perhaps as a consequence of changes in chromatin features associated with developmental processes. Our study provides the originome of an organism at the postembryo stage that should allow us to study ORI biology in response to development, environment and mutations with a quantitative approach. In a wider scope, the computational strategies developed here can be transferred to other eukaryotic systems.
Evidence for genetic correlations and bidirectional, causal effects between smoking and sleep behaviours
Authors: Gibson Mark , Munafò Marcus R , Taylor Amy E , Treur Jorien L. 
Published: February 2018

AbstractIntroductionCigarette smokers are at increased risk of poor sleep behaviours. However, it is largely unknown whether these associations are due to shared (genetic) risk factors and/or causal effects (which may be bi-directional).MethodsWe obtained summary-level data of genome-wide association studies of smoking (smoking initiation (n=74,035), cigarettes per day (n=38,181) and smoking cessation (n=41,278)) and sleep behaviours (sleep duration and chronotype, or ‘morningness’) (n=128,266) and insomnia (n=113,006)). Using LD score regression, we calculated genetic correlations between smoking and sleep behaviours. To investigate causal effects, we employed Mendelian randomization (MR), both with summary-level data and individual level data (n=333,581 UK Biobank participants). For MR with summary-level data, individual genetic variants were combined with inverse-variance weighted meta-analysis, weighted median regression and MR Egger regression methods.ResultsWe found positive genetic correlations between insomnia and smoking initiation (rg=0.27, 95% CI 0.06 to 0.49) and insomnia and cigarettes per day (rg=0.15, 0.01 to 0.28), and negative genetic correlations between sleep duration and smoking initiation (rg=-0.14, -0.26 to -0.01) and chronotype and smoking cessation (rg=-0.18, -0.31 to -0.06). MR analyses provided strong evidence that smoking more cigarettes per day causally decreases the odds of being a morning person, and weak evidence that insomnia causally increases smoking heaviness and decreases smoking cessation odds.ConclusionsSmoking and sleep behaviours show moderate genetic correlation. Heavier smoking seems to causally affect circadian rhythm and there is some indication that insomnia increases smoking heaviness and hampers cessation. Our findings point to sleep as a potentially interesting smoking treatment target.
Hybridization and rampant mitochondrial introgression among fire salamanders in peninsular Italy
Authors: Bisconti Roberta , Porretta Daniele , Arduino Paola , Nascetti Giuseppe , Canestrelli Daniele 
Published: February 2018

ABSTRACTDiscordance between mitochondrial and nuclear patterns of population genetic structure is providing key insights into the eco-evolutionary dynamics between and within species, and their assessment is highly relevant to biodiversity monitoring practices based on DNA barcoding approaches. Here, we investigate the population genetic structure of the fire salamanderSalamandra salamandrain peninsular Italy. Both mitochondrial and nuclear markers clearly identified two main population groups. However, nuclear and mitochondrial zones of geographic transition between groups were located 600 km from one another. The overall pattern of genetic variation, together with morphological and fossil data, suggest that a rampant mitochondrial introgression triggered the observed mitonuclear discordance, following a post-glacial secondary contact between lineages. Moreover, at a shallower level of population structure, we observed evidence of asymmetric introgression of nuclear genes between two sub-groups in southern Italy. Our results clearly show the major role played by reticulate evolution in shaping the structure ofSalamandra salamandrapopulations and, together with similar findings in other regions of the species’ range, contribute to identify the fire salamander as a particularly intriguing case to investigate the complexity of mechanisms triggering patterns of mitonuclear discordance in animals.
Perceived timing of active head movement at different speeds
Authors: Sachgau Carolin , Chung William , Barnett-Cowan Michael 
Published: February 2018

AbstractThe central nervous system must determine which sensory events occur at the same time. Actively moving the head corresponds with large changes in the relationship between the observer and the environment, sensorimotor processing, and spatiotemporal perception. Numerous studies have shown that head movement onset must precede the onset of other sensory events in order to be perceived as simultaneous, indicating that head movement perception is slow. Active head movement perception has been shown to be slower than passive head movement perception and dependent on head movement velocity, where participants who move their head faster than other participants require the head to move even earlier than comparison stimuli to be perceived as simultaneous. These results suggest that head movement perception is slower (i.e., suppressed) when the head moves faster. The present study used a within-subjects design to measure the point of subjective simultaneity (PSS) between active head movement speeds and a comparison sound stimulus. Our results clearly show that i) head movement perception is faster when the head moves faster within-subjects, ii) active head movement onset must still precede the onset of other sensory events (Average PSS: -123 to -52 ms) in order to be perceived as occurring simultaneously even at the fastest speeds (Average peak velocity: 76°/s to 257°/s). We conclude that head movement perception is slow, but that this delay is minimized with increased speed. While we do not provide evidence against sensory suppression, which requires active versus passive head movement comparison, our results do rule out velocity-based suppression.
Impaired Spatial Reorientation in the 3xTg-AD Mouse Model of Alzheimer’s Disease
Authors: Stimmell Alina C. , Baglietto-Vargas David , Moseley Shawn C. , Lapointe Valérie , Thompson Lauren M. , LaFerla Frank M. , McNaughton Bruce L. , Wilber Aaron A. 
Published: February 2018

AbstractIn early Alzheimer’s disease (AD) spatial navigation is impaired; however, the precise cause of this impairment is unclear. Recent evidence suggests that getting lost in new surroundings is one of the first impairments to emerge in AD. It is possible that getting lost in new surroundings represents a failure to use distal cues to get oriented in space. Therefore, we set out to look for impaired use of distal cues for spatial orientation in a mouse model of amyloidosis (3xTg-AD). To do this, we trained mice to shuttle to the end of a track and back to an enclosed start box to receive a water reward. Then, mice were trained to stop in an unmarked reward zone to receive a brain stimulation reward. The time required to remain in the zone for a reward was increased across training, and the track was positioned in a random start location for each trial. We found that 6-month female, but not male, 3xTg-AD mice were impaired. Male and female mice had only intracellular pathology and male mice had less pathology, particularly in the dorsal hippocampus. Thus, AD may cause spatial disorientation as a result of impaired use of landmarks.
Titer estimation for quality control (TEQC) method: a practical approach for optimal production of protein complexes using the baculovirus expression vector system
Authors: Imasaki Tsuyoshi , Wenzel Sabine , Yamada Kentaro , Bryant Megan L. , Takagi Yuichiro 
Published: February 2018

AbstractThe baculovirus expression vector system (BEVS) is becoming the method of choice for expression of many eukaryotic proteins and protein complexes for biochemical, structural and pharmaceutical studies. Significant technological advancement has made generation of recombinant baculoviruses easy, efficient and user-friendly. However, there is a tremendous variability in the amount of proteins made using the BEVS, including different batches of virus made to express the same proteins. Yet, what influences the overall production of proteins or protein complexes remains largely unclear. Many downstream applications, particularly protein structure determination, require purification of large quantities of proteins in a repetitive manner, calling for a reliable experimental set-up to obtain the protein or protein complexes of interest consistently. During our investigation of optimizing the expression of the Mediator Head module, we discovered that the ‘initial infectivity’ was an excellent indicator of overall production of protein complexes. Further, we show that this initial infectivity can be mathematically described as a function of multiplicity of infection (MOI), correlating recombinant protein yield and virus titer. All these findings led us to develop the Titer Estimation for Quality Control (TEQC) method, which enables researchers to estimate initial infectivity, titer/MOI values in a simple and affordable way, and to use these values to quantitatively optimize protein expressions utilizing BEVS in a highly reproducible fashion.
Sequencing Metrics of Human Genomes Extracted from Single Cancer Cells Individually Isolated in a Valveless Microfluidic Device
Authors: Marie Rodolphe , Pødenphant Marie , Koprowska Kamila , Bærlocher Loic , Vulders Roland C.M. , Wilding Jennifer , Ashley Neil , McGowan Simon J. , van Strijp Dianne , van Hemert Freek , Olesen Tom , Agersnap Niels , Bilenberg Brian , Sabatel Celine , Schira Julien , Kristensen Anders , Bodmer Walter , van der Zaag Pieter J. , Mir Kalim U. 
Published: February 2018

AbstractSequencing the genomes of individual cells enables the direct determination of genetic heterogeneity amongst cells within a population. We have developed an injection-moulded valveless microfluidic device in which single cells from colorectal cell (LS174T, LS180 and RKO) lines and fresh colorectal cancers are individually trapped, their genomes extracted and prepared for sequencing, using multiple displacement amplification (MDA). Ninety nine percent of the DNA sequences obtained mapped to a reference human genome, indicating that there was effectively no contamination of these samples from non-human sources. In addition, most of the reads are correctly paired, with a low percentage of singletons (0.17 ± 0.06 %) and we obtain genome coverages approaching 90%. To achieve this high quality, our device design and process shows that amplification can be conducted in microliter volumes as long as extraction is in sub-nanoliter volumes. Our data also demonstrates that high quality single cell sequencing can be achieved using a relatively simple, inexpensive and scalable device.
Shugoshin is essential for meiotic prophase checkpoints inC. elegans
Authors: Bohr Tisha , Nelson Christian R. , Giacopazzi Stefani , Lamelza Piero , Bhalla Needhi 
Published: February 2018

AbstractThe conserved factor Shugoshin is dispensable inC. elegansfor the two-step loss of sister chromatid cohesion that directs the proper segregation of meiotic chromosomes. We show that theC. elegansortholog of Shugoshin, SGO-1, is required for checkpoint activity in meiotic prophase. This role in checkpoint function is similar to that of the meiotic chromosomal protein, HTP-3. Nullsgo-1mutants exhibit additional phenotypes similar to that of a partial loss of function allele of HTP-3: premature synaptonemal complex disassembly, the activation of alternate DNA repair pathways and an inability to recruit a conserved effector of the DNA damage pathway, HUS-1. SGO-1 localizes to pre-meiotic nuclei, when HTP-3 is present but not yet loaded onto chromosome axes, suggesting an early role in regulating meiotic chromosome metabolism. We propose that SGO-1 acts during pre-meiotic replication to ensure fully functional meiotic chromosome architecture, rendering these chromosomes competent for checkpoint activity and normal progression of meiotic recombination. Given that most research on Shugoshin has been focused on its regulation of sister chromatid cohesion in meiosis, this novel role may be conserved but previously uncharacterized in other organisms. Further, our findings expand the repertoire of Shugoshin’s functions beyond coordinating regulatory activities at the centromere.
Insights into Parkinson’s disease from computational models of the basal ganglia
Authors: Humphries Mark D. , Obeso Jose , Dreyer Jakob Kisbye 
Published: February 2018

AbstractMovement disorders arise from the complex interplay of multiple changes to neural circuits. Successful treatments for these disorders could interact with these complex changes in myriad ways, and as a consequence their mechanisms of action and their amelioration of symptoms are incompletely understood. Using Parkinson’s disease as a case-study, we review here how computational models are a crucial tool for taming this complexity, across causative mechanisms, consequent neural dynamics, and treatments. For mechanisms, we review models that capture the effects of losing dopamine on basal ganglia function; for dynamics, we discuss models that have transformed our understanding of how beta-band (15-30 Hz) oscillations arise in the parkinsonian basal ganglia. For treatments, we touch on the breadth of computational modelling work trying to understand the therapeutic actions of deep brain stimulation. Collectively, models from across all levels of description are providing a compelling account of the causes, symptoms, and treatments for Parkinson’s disease.
TheAquilegiagenome: adaptive radiation and an extraordinarily polymorphic chromosome with a unique history
Authors: Filiault Danièle , Ballerini Evangeline S. , Mandáková Terezie , Aköz Gökçe , Derieg Nathan , Schmutz Jeremy , Jenkins Jerry , Grimwood Jane , Shu Shengqiang , Hayes Richard D. , Hellsten Uffe , Barry Kerrie , Yan Juying , Mihaltcheva Sirma , Karafiátová Miroslava , Nizhynska Viktoria , Lysak Martin A. , Hodges Scott A. , Nordborg Magnus 
Published: February 2018

AbstractThe columbine genusAquilegiais a classic example of an adaptive radiation, involving a wide variety of pollinators and habitats. Here we present the genome assembly ofA. coerulea‘Goldsmith’, complemented by high-coverage sequencing data from 10 wild species covering the world-wide distribution. Our analyses reveal extensive allele sharing among species and demonstrate that introgression and selection played a role in theAquilegiaradiation. We also present the remarkable discovery that the evolutionary history of an entire chromosome differs from that of the rest of the genome – a phenomenon which we do not fully understand, but which highlights the need to consider chromosomes in an evolutionary context.
Transition State Characteristics During Cell Differentiation
Authors: Brackston Rowan D. , Lakatos Eszter , Stumpf Michael P.H. 
Published: February 2018

AbstractModels describing the process of stem-cell differentiation are plentiful, and may offer insights into the underlying mechanisms and experimentally observed behaviour. Waddington’s epigenetic landscape has been providing a conceptual framework for differentiation processes since its inception. It also allows, however, for detailed mathematical and quantitative analyses, as the landscape can, at least in principle, be related to mathematical models of dynamical systems. Here we focus on a set of dynamical systems features that are intimately linked to cell differentiation, by considering exemplar dynamical models that capture important aspects of stem cell differentiation dynamics. These models allow us to map the paths that cells take through gene expression space as they move from one fate to another, e.g. from a stem-cell to a more specialized cell type. Our analysis highlights the role of the transition state (TS) that separates distinct cell fates, and how the nature of the TS changes as the underlying landscape changes— change that can be induced by e.g. cellular signalling. We demonstrate that models for stem cell differentiation may be interpreted in terms of either a static or transitory landscape. For the static case the TS represents a particular transcriptional profile that all cells approach during differentiation. Alternatively, the TS may refer to the commonly observed period of heterogeneity as cells undergo stochastic transitions.
“Light-box” accelerated growth of poinsettias: LED-only Illumination
Authors: Weerasuriya Charitha , Detez Stewart , Hock Ng Soon , Hughes Andrew , Callaway Michael , Harrison Iain , Katkus Tomas , Juodkazis Saulius 
Published: February 2018

ABSTRACTFor the current commercialized agricultural industry which requires a reduced product lead time to customer and supply all year round, an artificial light emitting diode (LED)-based illumination has high potential due to high efficiency of electrical-to-light conversion. The main advantage of the deployed Red Green Blue Amber LED lighting system is colour mixing capability, which means the ability to generate all the colours in the spectrum by using three or four primary colour LEDs. The accelerated plant growth was carried out in a “light-box” which was made to generate an artificial day/night cycle and had a capability to tune the colour mixing ratio along the colour temperature curve of the chromaticity diagram. The control group of plants form the same initial batch was grown on the same shelf in a greenhouse at the same conditions with addition of artificial illumination by incandescent lamps for few hours. More dense and better quality (hence, commercial value) plants were grown in the light-box. Costs and efficiency projections of LED lamps for horticultural applications is discussed together with required capital investment. The total cost of the “light-box” including LED lamps and electronics was 850 AUD.
Torso-like is a component of the hemolymph and regulates the insulin signalling pathway in Drosophila
Authors: Henstridge Michelle A. , Aulsebrook Lucinda , Koyama Takashi , Johnson Travis K. , Whisstock James C. , Tiganis Tony , Mirth Christen K. , Warr Coral G. 
Published: February 2018

ABSTRACTIn Drosophila key developmental transitions are governed by the steroid hormone ecdysone. A number of neuropeptide-activated signalling pathways control ecdysone production in response to environmental signals, including the insulin signalling pathway, which regulates ecdysone production in response to nutrition. Here, we find that the Membrane Attack Complex/Perforin-like protein Torso-like, best characterised for its role in activating the Torso receptor tyrosine kinase in early embryo patterning, also regulates the insulin signalling pathway in Drosophila. We previously reported that the small body size and developmental delay phenotypes of torso-like null mutants resemble those observed when insulin signalling is reduced. Here we report that, in addition to growth defects, torso-like mutants also display metabolic and nutritional plasticity phenotypes characteristic of mutants with impaired insulin signalling. We further find that in the absence of torso-like the expression of insulin-like peptides is increased, as is their accumulation in the insulin-producing cells. Finally, we show that Torso-like is a component of the hemolymph and that it is required in the prothoracic gland to control developmental timing and body size. Taken together, our data suggest that the secretion of Torso-like from the prothoracic gland influences the activity of insulin signalling throughout the body in Drosophila.ARTICLE SUMMARYIn many animals distinct developmental transitions are crucial for the coordinated progression from the juvenile stage to adulthood. In Drosophila, the transition from an immature larva into a reproductively mature adult is controlled by the steroid hormone ecdysone. Several neuropeptide-activated signalling pathways, including the insulin signalling pathway, regulate ecdysone production in response to environmental cues. Here we find that the perforin-like protein Torso-like regulates the insulin signalling pathway. We show that Torso-like is secreted into circulation where it acts to influence insulin-like peptide activity, revealing a novel mechanism for the regulation of insulin signalling in Drosophila.