bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Combination of CRISPR/Cas9 and Standardized RNAi as a Versatile Platform for the Characterization of Gene Function
Authors: Wissel Sebastian , Kieser Anja , Yasugi Tetsuo , Duchek Peter , Roitinger Elisabeth , Gokcezade Joseph , Steinmann Victoria , Gaul Ulrike , Mechtler Karl , Förstemann Klaus , Knoblich Jürgen A , Neumüller Ralph A 
Published: June 2016

AbstractTraditional loss-of-function studies in Drosophila suffer from a number of shortcomings, including off-target effects in the case of RNA interference (RNAi) or the stochastic nature of mosaic clonal analysis. Here, we describe minimal in vivo GFP interference (miGFPi) as a versatile strategy to characterize gene function and to conduct highly stringent, cell type-specific loss-of-function experiments in Drosophila. miGFPi combines CRISPR/Cas9-mediated tagging of genes at their endogenous locus with an immunotag and an exogenous 21 nucleotide RNAi effector sequence with the use of a single reagent, highly validated RNAi line targeting this sequence. We demonstrate the utility and time effectiveness of this method by characterizing the function of the Polymerase I (Pol I)-associated transcription factor Tif-1a, and the previously uncharacterized gene MESR4, in the Drosophila female germline stem cell lineage. In addition, we show that miGFPi serves as a powerful technique to functionally characterize individual isoforms of a gene. We exemplify this aspect of miGFPi by studying isoform-specific loss-of-function phenotypes of the longitudinals lacking (lola) gene in neural stem cells. Altogether, the miGFPi strategy constitutes a generalized loss-of-function approach that is amenable to the study of the function of all genes in the genome in a stringent and highly time effective manner.
Meiotic Interactors of a Mitotic Gene TAO3 Revealed by Functional Analysis of its Rare Variant
Authors: Gupta Saumya , Radhakrishnan Aparna , Nitin Rachana , Raharja-Liu Pandu , Lin Gen , Steinmetz Lars M , Gagneur Julien , Sinha Himanshu 
Published: June 2016

Abstract
Studying the molecular consequences of rare genetic variants has the potential to identify novel and hitherto uncharacterized pathways causally contributing to phenotypic variation. Here, we characterize the functional consequences of a rare coding variant of TAO3, previously reported to contribute significantly to sporulation efficiency variation in Saccharomyces cerevisiae. During mitosis, the common TAO3 allele interacts with CBK1—a conserved NDR kinase. Both TAO3 and CBK1 are components of the RAM signaling network that regulates cell separation and polarization during mitosis. We demonstrate that the role of the rare allele TAO3(4477C) in meiosis is distinct from its role in mitosis by being independent of ACE2—a RAM network target gene. By quantitatively measuring cell morphological dynamics, and expressing the TAO3(4477C) allele conditionally during sporulation, we show that TAO3 has an early role in meiosis. This early role of TAO3 coincides with entry of cells into meiotic division. Time-resolved transcriptome analyses during early sporulation identified regulators of carbon and lipid metabolic pathways as candidate mediators. We show experimentally that, during sporulation, the TAO3(4477C) allele interacts genetically with ERT1 and PIP2, regulators of the tricarboxylic acid cycle and gluconeogenesis metabolic pathways, respectively. We thus uncover a meiotic functional role for TAO3, and identify ERT1 and PIP2 as novel regulators of sporulation efficiency. Our results demonstrate that studying the causal effects of genetic variation on the underlying molecular network has the potential to provide a more extensive understanding of the pathways driving a complex trait.
Evolution of the Insertion-Deletion Mutation Rate Across the Tree of Life
Authors: Sung Way , Ackerman Matthew S , Dillon Marcus M , Platt Thomas G , Fuqua Clay , Cooper Vaughn S , Lynch Michael 
Published: June 2016

AbstractMutations are the ultimate source of variation used for evolutionary adaptation, while also being predominantly deleterious and a source of genetic disorders. Understanding the rate of insertion-deletion mutations (indels) is essential to understanding evolutionary processes, especially in coding regions, where such mutations can disrupt production of essential proteins. Using direct estimates of indel rates from 14 phylogenetically diverse eukaryotic and bacterial species, along with measures of standing variation in such species, we obtain results that imply an inverse relationship of mutation rate and effective population size. These results, which corroborate earlier observations on the base-substitution mutation rate, appear most compatible with the hypothesis that natural selection reduces mutation rates per effective genome to the point at which the power of random genetic drift (approximated by the inverse of effective population size) becomes overwhelming. Given the substantial differences in DNA metabolism pathways that give rise to these two types of mutations, this consistency of results raises the possibility that refinement of other molecular and cellular traits may be inversely related to species-specific levels of random genetic drift.
Genomic and Transcriptomic Associations Identify a New Insecticide Resistance Phenotype for the Selective Sweep at the Cyp6g1 Locus of Drosophila melanogaster
Authors: Battlay Paul , Schmidt Joshua M , Fournier-Level Alexandre , Robin Charles 
Published: June 2016

Abstract
Scans of the Drosophila melanogaster genome have identified organophosphate resistance loci among those with the most pronounced signature of positive selection. In this study, the molecular basis of resistance to the organophosphate insecticide azinphos-methyl was investigated using the Drosophila Genetic Reference Panel, and genome-wide association. Recently released full transcriptome data were used to extend the utility of the Drosophila Genetic Reference Panel resource beyond traditional genome-wide association studies to allow systems genetics analyses of phenotypes. We found that both genomic and transcriptomic associations independently identified Cyp6g1, a gene involved in resistance to DDT and neonicotinoid insecticides, as the top candidate for azinphos-methyl resistance. This was verified by transgenically overexpressing Cyp6g1 using natural regulatory elements from a resistant allele, resulting in a 6.5-fold increase in resistance. We also identified four novel candidate genes associated with azinphos-methyl resistance, all of which are involved in either regulation of fat storage, or nervous system development. In Cyp6g1, we find a demonstrable resistance locus, a verification that transcriptome data can be used to identify variants associated with insecticide resistance, and an overlap between peaks of a genome-wide association study, and a genome-wide selective sweep analysis.
Assessing Predictive Properties of Genome-Wide Selection in Soybeans
Authors: Xavier Alencar , Muir William M , Rainey Katy Martin 
Published: June 2016

AbstractMany economically important traits in plant breeding have low heritability or are difficult to measure. For these traits, genomic selection has attractive features and may boost genetic gains. Our goal was to evaluate alternative scenarios to implement genomic selection for yield components in soybean (Glycine max L. merr). We used a nested association panel with cross validation to evaluate the impacts of training population size, genotyping density, and prediction model on the accuracy of genomic prediction. Our results indicate that training population size was the factor most relevant to improvement in genome-wide prediction, with greatest improvement observed in training sets up to 2000 individuals. We discuss assumptions that influence the choice of the prediction model. Although alternative models had minor impacts on prediction accuracy, the most robust prediction model was the combination of reproducing kernel Hilbert space regression and BayesB. Higher genotyping density marginally improved accuracy. Our study finds that breeding programs seeking efficient genomic selection in soybeans would best allocate resources by investing in a representative training set.
Saccharomyces cerevisiae TORC1 Controls Histone Acetylation by Signaling Through the Sit4/PP6 Phosphatase to Regulate Sirtuin Deacetylase Nuclear Accumulation
Authors: Workman Jason J , Chen Hongfeng , Laribee R Nicholas 
Published: June 2016

Abstract
The epigenome responds to changes in the extracellular environment, yet how this information is transmitted to the epigenetic regulatory machinery is unclear. Using a Saccharomyces cerevisiae yeast model, we demonstrate that target of rapamycin complex 1 (TORC1) signaling, which is activated by nitrogen metabolism and amino acid availability, promotes site-specific acetylation of histone H3 and H4 N-terminal tails by opposing the activity of the sirtuin deacetylases Hst3 and Hst4. TORC1 does so through suppression of the Tap42-regulated Sit4 (PP6) phosphatase complex, as sit4Δ rescues histone acetylation under TORC1-repressive conditions. We further demonstrate that TORC1 inhibition, and subsequent PP6 activation, causes a selective, rapid, nuclear accumulation of Hst4, which correlates with decreased histone acetylation. This increased Hst4 nuclear localization precedes an elevation in Hst4 protein expression, which is attributed to reduced protein turnover, suggesting that nutrient signaling through TORC1 may limit Hst4 nuclear accumulation to facilitate Hst4 degradation and maintain histone acetylation. This pathway is functionally relevant to TORC1 signaling since the stress sensitivity of a nonessential TORC1 mutant (tco89Δ) to hydroxyurea and arsenic can be reversed by combining tco89Δ with either hst3Δ, hst4Δ, or sit4Δ. Surprisingly, while hst3Δ or hst4Δ rescues the sensitivity tco89Δ has to low concentrations of the TORC1 inhibitor rapamycin, sit4Δ fails to do so. These results suggest Sit4 provides an additional function necessary for TORC1-dependent cell growth and proliferation. Collectively, this study defines a novel mechanism by which TORC1 suppresses a PP6-regulated sirtuin deacetylase pathway to couple nutrient signaling to epigenetic regulation.
Restriction of Retrotransposon Mobilization inSchizosaccharomyces pombeby Transcriptional Silencing and Higher-Order Chromatin Organization
Authors: Murton Heather E , Grady Patrick J R , Chan Tsun Ho , Cam Hugh P , Whitehall Simon K 
Published: June 2016

AbstractUncontrolled propagation of retrotransposons is potentially detrimental to host genome integrity. Therefore, cells have evolved surveillance mechanisms to restrict the mobility of these elements. In Schizosaccharomyces pombe the Tf2 LTR retrotransposons are transcriptionally silenced and are also clustered in the nucleus into structures termed Tf bodies. Here we describe the impact of silencing and clustering on the mobility of an endogenous Tf2 element. Deletion of genes such as set1+ (histone H3 lysine 4 methyltransferase) or abp1+ (CENP-B homolog) that both alleviate silencing and clustering, result in a corresponding increase in mobilization. Furthermore, expression of constitutively active Sre1, a transcriptional activator of Tf2 elements, also alleviates clustering and induces mobilization. In contrast, clustering is not disrupted by loss of the HIRA histone chaperone, despite high levels of expression, and in this background, mobilization frequency is only marginally increased. Thus, mutations that compromise transcriptional silencing but not Tf bodies are insufficient to drive mobilization. Furthermore, analyses of mutant alleles that separate the transcriptional repression and clustering functions of Set1 are consistent with control of Tf2 propagation via a combination of silencing and spatial organization. Our results indicate that host surveillance mechanisms operate at multiple levels to restrict Tf2 retrotransposon mobilization.
Misiones de cohetería experimental con propelente sólido: Misión séneca, cohete Ainkaa 1
Authors: Urrego Peña José Alejandro , Rojas Mora Fabio Arturo 
Published: June 2016

<p>Este documento expone la metodología y los resultados obtenidos en el desarrollo de una investigación sistemática, que trata sobre a la implementación de misiones de cohetería experimental. En este proceso se obtuvieron, datos y resultados que permitieron corroborar de forma experimental, conceptos de propulsión, aerodinámica y balística propios de una aeronave tipo cohete sin elementos de control activo a bordo. Para el estudio e implementación de esta misión, se generó un método dividido en etapas por las cuales se guió el desarrollo del proyecto; primero se realizó la etapa de validación y el<br />diseño preliminar en forma teórica, se continuó con la etapa de simulación, utilizando un software especializado y culminó con la etapa del proceso constructivo y el procedimiento de disparo. La puesta en marcha de esta misión de cohetería experimental permitió alcanzar, propulsado por un combustible tipo “candy” compuesto por nitrato de potasio y sorbitol, un apogeo del cohete Ainkaa 1 de 780 m sobre la superficie de lanzamiento, con una velocidad de impacto de 526 Km/h, un tiempo de quemado de 3.2s entre otros datos, para configurar esta misión dentro de la categoría de alta potencia.</p>
Effect of grapevine latent buds (<em>Vitis vinifera</em> L., cv. Merlot) chilling on their starch content: biochimical and cytological approachs
Authors: Koussa Tayeb , Cholet Céline , Cherrad Monique 
Published: June 2016

<p style="text-align: justify;">Biochimical analysis and photonic microscopy observations of starch were investigated in latent buds of <em>Vitis vinifera </em>L. (cv. Merlot) collected during their dormancy phase and during their cold storage at 2°C. Biochimical analysis showed that starch levels of grapevine latent buds was high (70 mg/g DW). Microscopical observations confirmed this result and showed a gradient of starch content in different regions of bud in which the foliars primordiums and scales were the starch richer. Buds conservation at 2°C reduced their starch content but this decrease begun only after 9 days of chilling corresponding to the time necessary for budbreak and for the beginning of increase the bud burst ability. The hydrolysis of starch seems begun at the first in apex and then propaged to the other regions of bud. In the scales, the most exposed region to cold, storage at 2°C during 56 days induced an increase of cellular tannins content and cell walls polysaccharides. These results were discuted in relation to the increase of bud burst ability and to their cold acclimatation.</p>
Yield Performance of Calocybe indica on Different Agricultural Subatrate
Authors: Patel Pinkal , Trivedi Ratna 
Published: June 2016

The Milky mushroom, Calocybe Indica was cultivated on different agricultural substrate, paddy straw, wheat straw, sugarcane trace and mango dry leaves. The spawning was done by sterilization of all the four substrate. The bags were kept in mushroom growing room with the maintenance of temperature and humidity 30̊ c-35̊ c and 70-80 % respectively. The minimum days requires for completion of spawn run (18.4 days), primordial formation (25.2 days) and days for first harvest (32.4 days) was first observed on cultivation with Paddy straw. The maximum yield on fresh weight basis and biological efficiency (134.86 %) was also found to be as the same treatment with the Paddy straw as a substrate. The biological efficiency of wheat straw was at par with Sugarcane trace as substrate which was 85.07 % and 85.02 % respectively.
A Comparative Study of Competitive Anxiety between Basketball and Volleyball Players
Authors: Singh Anita , Parmar Devender Singh 
Published: June 2016

Anxiety is a psychological and physiological state characterized by somatic, emotional, cognitive and behavioral components. The root meaning of the word anxiety is `to vex or trouble. The objective of this paper is to compare the competitive anxiety between basketball and volleyball players. For this purpose 40 Male intercollegiate players from Basketball (20) and Volleyball (20) were taken as sample. For the purpose of this study the standardized Rainer Marten (SCAT, 1990) Scale was used. The Questionnaire was administers in small groups during the intercollegiate Basketball and Volleyball tournament. The results of the study have revealed that there is no significant difference between the competitive anxiety of Basketball and Volleyball players of intercollegiate, as no significant difference has seen in the mean score at the Basketball and Volleyball players on competitive anxiety. Therefore it may be said that there is no influence of competitive anxiety at the Basketball and Volleyball players of inter-college level.
Data Mining Technique Applied To DNA Sequencing
Authors: Jamuna R. 
Published: June 2016

CpG islands (CGIs) play a vital role in genome analysis as genomic markers. Identification of the CpG pair has contributed not only to the prediction of promoters but also to the understanding of the epigenetic causes of cancer. In the human genome [1] wherever the dinucleotides CG occurs the C nucleotide (cytosine) undergoes chemical modifications. There is a relatively high probability of this modification that mutates C into a T. For biologically important reasons the mutation modification process is suppressed in short stretches of the genome, such as ‘start’ regions. In these regions [2] predominant CpG dinucleotides are found than elsewhere. Such regions are called CpG islands. DNA methylation is an effective means by which gene expression is silenced. In normal cells, DNA methylation functions to prevent the expression of imprinted and inactive X chromosome genes. In cancerous cells, DNA methylation inactivates tumor-suppressor genes, as well as DNA repair genes, can disrupt cell-cycle regulation. The most current methods for identifying CGIs suffered from various limitations and involved a lot of human interventions. This paper gives an easy searching technique with data mining of Markov Chain in genes. Markov chain model has been applied to study the probability of occurrence of C-G pair in the given gene sequence. Maximum Likelihood estimators for the transition probabilities for each model and analgously for the model has been developed and log odds ratio that is calculated estimates the presence or absence of CpG is lands in the given gene which brings in many facts for the cancer detection in human genome.
The Perfection of Interpreting By Non-Linguist Interpreters
Authors: Yulianti Ni Ketut Dewi 
Published: June 2016

An interpreter is a person who converts a thought or expression in a source language into an expression with a comparable meaning in a target language in real time. The function of interpreters is to convey every semantic element (tone and register) and every intention and feeling of the message that the source-language speaker is directing to target-language recipients. Interpreting (oral translation) is not an easy job. In written translation, a translator has time to consider and revise each word and sentence before delivering their product to the client. While an interpreter’s goal is to achieve total accuracy at all times, details of the original (source) speech can be missed and interpreters can ask for clarification from the speaker. This paper deals with the perfection of interpreting by non-linguist interpreters in Bhagawad Gita class in Sri Sri Jaganath Gaurangga Temple in Denpasar, and it has been presented in 2ndTranscon (International Translation Conference) in Jakarta, but hasn’t been published yet. There are some interpreters at the temple that have no special background knowledge about linguistics, especially translation / interpreting, but they can deliver the message from the source language (SL) English into the target Language (TL) Indonesian perfectly. The cross-culture understanding that they have and their knowledge background about the text (Bhagavad Gita) play an important role in this case. The interpreters have been interviewed for the purpose of this paper to find out the factors that affect the perfection of interpreting for non-linguist interpreters.
Study of Medical Waste and Its Management at Wangaya Hospital in Denpasar
Authors: Muliarta I Nengah 
Published: June 2016

Medical waste has three forms; solid, liquid and gas which derives from hospital activities which contains microorganism, chemical material and radioactive substances. Based on description above, this research was necessary to be conducted to handle the negative impact of medical waste to the environment. The research objectives were 1) in order to know the medical waste management system of Wangaya Hospital in Denpasar, and 2) studying more about medical waste quality of Wangaya Hospital in Denpasar. The research was a case study in using method that was designed by combining the observation data with the laboratory data analyses. The research location was in Denpasar of Wangaya Hospital (B type) regarding on the high occupancy rate of the patient was compared to other hospital (B type) in Bali. The research results was to show that 1) the medical waste management of Wangaya Hospital in Denpasar was suitable yet to meet the procedure of medical waste from Decree of Minister of health No.1204 in 2004, regarding Health Condition of Environmental Hospital. The laboratory results show that the medical waste quality in Denpasar Wangaya Hospital was above the maximum of standard limit based on Decree of Minister No. 58/MENLH/12/2004. The ashes of incinerated medical waste contained a Hg heavy metal until 2,39 ppm. Based on the research results it was concluded that the management system of medical waste in Denpasar Wangaya Hospital was suitable yet with the procedure, and the medical waste quality of outputs that was released into the environment still exceeding the maximum standard limit. Therefore, it is recommended that Denpasar Wangaya Hospital should undertake the evaluation in management system of the medical waste and its treatment plan to reduce the effluent in its output products in order to comply with the standard limit.