bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome Analysis Reveals that Vitamin A Metabolism in the Liver Affects Feed Efficiency in Pigs
Authors: Zhao Yunxia , Hou Ye , Liu Fei , Liu An , Jing Lu , Zhao Changzhi , Luan Yu , Miao Yuanxin , Zhao Shuhong , Li Xinyun 
Published: October 2016

Abstract
Feed efficiency (FE) is essential for pig production. In this study, 300 significantly differentially expressed (DE) transcripts, including 232 annotated genes, 28 cis-natural antisense transcripts (cis-NATs), and 40 long noncoding RNAs (lncRNAs), were identified between the liver of Yorkshire pigs with extremely high and low FE. Among these transcripts, 25 DE lncRNAs were significantly correlated with 125 DE annotated genes at a transcriptional level. These DE genes were enriched primarily in vitamin A (VA), fatty acid, and steroid hormone metabolism. VA metabolism is regulated by energy status, and active derivatives of VA metabolism can regulate fatty acid and steroid hormones metabolism. The key genes of VA metabolism (CYP1A1, ALDH1A2, and RDH16), fatty acid biosynthesis (FASN, SCD, CYP2J2, and ANKRD23), and steroid hormone metabolism (CYP1A1, HSD17B2, and UGT2B4) were significantly upregulated in the liver of high-FE pigs. Previous study with the same samples indicated that the mitochondrial function and energy expenditure were reduced in the muscle tissue of high-FE pigs. In conclusion, VA metabolism in liver tissues plays important roles in the regulation of FE in pigs by affecting energy metabolism, which may mediate fatty acid biosynthesis and steroid hormone metabolism. Furthermore, our results identified novel transcripts, such as cis-NATs and lncRNAs, which are also involved in the regulation of FE in pigs.
Distinct and Overlapping Requirements for Cyclins A, B, and B3 inDrosophilaFemale Meiosis
Authors: Bourouh Mohammed , Dhaliwal Rajdeep , Rana Ketki , Sinha Sucheta , Guo Zhihao , Swan Andrew 
Published: October 2016

AbstractMeiosis, like mitosis, depends on the activity of the cyclin dependent kinase Cdk1 and its cyclin partners. Here, we examine the specific requirements for the three mitotic cyclins, A, B, and B3 in meiosis of Drosophila melanogaster. We find that all three cyclins contribute redundantly to nuclear envelope breakdown, though cyclin A appears to make the most important individual contribution. Cyclin A is also required for biorientation of homologs in meiosis I. Cyclin B3, as previously reported, is required for anaphase progression in meiosis I and in meiosis II. We find that it also plays a redundant role, with cyclin A, in preventing DNA replication during meiosis. Cyclin B is required for maintenance of the metaphase I arrest in mature oocytes, for spindle organization, and for timely progression through the second meiotic division. It is also essential for polar body formation at the completion of meiosis. With the exception of its redundant role in meiotic maturation, cyclin B appears to function independently of cyclins A and B3 through most of meiosis. We conclude that the three mitotic cyclin-Cdk complexes have distinct and overlapping functions in Drosophila female meiosis.
Transcriptome Profiling in Rat Inbred Strains and Experimental Cross Reveals Discrepant Genetic Architecture of Genome-Wide Gene Expression
Authors: Kaisaki Pamela J , Otto Georg W , Argoud Karène , Collins Stephan C , Wallis Robert H , Wilder Steven P , Yau Anthony C Y , Hue Christophe , Calderari Sophie , Bihoreau Marie-Thérèse , Cazier Jean-Baptiste , Mott Richard , Gauguier Dominique 
Published: October 2016

Abstract
To test the impact of genetic heterogeneity on cis- and trans-mediated mechanisms of gene expression regulation, we profiled the transcriptome of adipose tissue in 20 inbred congenic strains derived from diabetic Goto–Kakizaki (GK) rats and Brown–Norway (BN) controls, which contain well-defined blocks (1–183 Mb) of genetic polymorphisms, and in 123 genetically heterogeneous rats of an (GK × BN)F2 offspring. Within each congenic we identified 73–1351 differentially expressed genes (DEGs), only 7.7% of which mapped within the congenic blocks, and which may be regulated in cis. The remainder localized outside the blocks, and therefore must be regulated in trans. Most trans-regulated genes exhibited approximately twofold expression changes, consistent with monoallelic expression. Altered biological pathways were replicated between congenic strains sharing blocks of genetic polymorphisms, but polymorphisms at different loci also had redundant effects on transcription of common distant genes and pathways. We mapped 2735 expression quantitative trait loci (eQTL) in the F2 cross, including 26% predominantly cis-regulated genes, which validated DEGs in congenic strains. A hotspot of &gt;300 eQTL in a 10 cM region of chromosome 1 was enriched in DEGs in a congenic strain. However, many DEGs among GK, BN and congenic strains did not replicate as eQTL in F2 hybrids, demonstrating distinct mechanisms of gene expression when alleles segregate in an outbred population or are fixed homozygous across the entire genome or in short genomic regions. Our analysis provides conceptual advances in our understanding of the complex architecture of genome expression and pathway regulation, and suggests a prominent impact of epistasis and monoallelic expression on gene transcription.
Genomic, Transcriptomic, and Proteomic Analysis Provide Insights Into the Cold Adaptation Mechanism of the Obligate Psychrophilic Fungus Mrakia psychrophila
Authors: Su Yao , Jiang Xianzhi , Wu Wenping , Wang Manman , Hamid M Imran , Xiang Meichun , Liu Xingzhong 
Published: October 2016

Abstract
Mrakia psychrophila is an obligate psychrophilic fungus. The cold adaptation mechanism of psychrophilic fungi remains unknown. Comparative genomics analysis indicated that M. psychrophila had a specific codon usage preference, especially for codons of Gly and Arg and its major facilitator superfamily (MFS) transporter gene family was expanded. Transcriptomic analysis revealed that genes involved in ribosome and energy metabolism were upregulated at 4°, while genes involved in unfolded protein binding, protein processing in the endoplasmic reticulum, proteasome, spliceosome, and mRNA surveillance were upregulated at 20°. In addition, genes related to unfolded protein binding were alternatively spliced. Consistent with other psychrophiles, desaturase and glycerol 3-phosphate dehydrogenase, which are involved in biosynthesis of unsaturated fatty acid and glycerol respectively, were upregulated at 4°. Cold adaptation of M. psychrophila is mediated by synthesizing unsaturated fatty acids to maintain membrane fluidity and accumulating glycerol as a cryoprotectant. The proteomic analysis indicated that the correlations between the dynamic patterns between transcript level changes and protein level changes for some pathways were positive at 4°, but negative at 20°. The death of M. psychrophila above 20° might be caused by an unfolded protein response.
Proper Sterol Distribution Is Required for Candida albicans Hyphal Formation and Virulence
Authors: McCourt Paula , Liu Hsing-Yin , Parker Josie E , Gallo-Ebert Christina , Donigan Melissa , Bata Adam , Giordano Caroline , Kelly Steven L , Nickels Joseph T 
Published: October 2016

Abstract
Candida albicans is an opportunistic fungus responsible for the majority of systemic fungal infections. Multiple factors contribute to C. albicans pathogenicity. C. albicans strains lacking CaArv1 are avirulent. Arv1 has a conserved Arv1 homology domain (AHD) that has a zinc-binding domain containing two cysteine clusters. Here, we explored the role of the CaAHD and zinc-binding motif in CaArv1-dependent virulence. Overall, we found that the CaAHD was necessary but not sufficient for cells to be virulent, whereas the zinc-binding domain was essential, as Caarv1/Caarv1 cells expressing the full-length zinc-binding domain mutants, Caarv1C3S and Caarv1C28S, were avirulent. Phenotypically, we found a direct correlation between the avirulence of Caarv1/Caarv1, Caarrv1AHD, Caarv1C3S, and Caarv1C28S cells and defects in bud site selection, septa formation and localization, and hyphal formation and elongation. Importantly, all avirulent mutant strains lacked the ability to maintain proper sterol distribution. Overall, our results have established the importance of the AHD and zinc-binding domain in fungal invasion, and have correlated an avirulent phenotype with the inability to maintain proper sterol distribution.
CRISPR/Cas9-Mediated Genome Editing and Mutagenesis of EcChi4 in Exopalaemon carinicauda
Authors: Gui Tianshu , Zhang Jiquan , Song Fengge , Sun Yuying , Xie Shijun , Yu Kuijie , Xiang Jianhai 
Published: October 2016

Abstract
The development of the type II clustered regularly interspaced short palindromic repeats (CRISPR) system has resulted in the revolution of genetic engineering, and this technology has been applied in the genome editing of various species. However, there are no reports about target-specific genome editing in shrimp. In this research, we developed a microinjection method for the ridgetail white prawn Exopalaemon carinicauda and successfully applied CRISPR/Cas9 technology to the genome editing of E. carinicauda. Through coinjection of mRNA of Cas9 nuclease and gRNA specialized for E. carinicauda chitinase 4 (EcChi4), shrimps with indel mutations were obtained. Further analysis showed that the mutations could be transmitted to the next generation. This is the first time that site-specific genome editing has been successfully demonstrated in a decapod, and will further contribute to the study of functional genomics in decapods.
In Silico Whole Genome Sequencer and Analyzer (iWGS): a Computational Pipeline to Guide the Design and Analysis of de novo Genome Sequencing Studies
Authors: Zhou Xiaofan , Peris David , Kominek Jacek , Kurtzman Cletus P , Hittinger Chris Todd , Rokas Antonis 
Published: October 2016

Abstract
The availability of genomes across the tree of life is highly biased toward vertebrates, pathogens, human disease models, and organisms with relatively small and simple genomes. Recent progress in genomics has enabled the de novo decoding of the genome of virtually any organism, greatly expanding its potential for understanding the biology and evolution of the full spectrum of biodiversity. The increasing diversity of sequencing technologies, assays, and de novo assembly algorithms have augmented the complexity of de novo genome sequencing projects in nonmodel organisms. To reduce the costs and challenges in de novo genome sequencing projects and streamline their experimental design and analysis, we developed iWGS (in silicoWhole Genome Sequencer and Analyzer), an automated pipeline for guiding the choice of appropriate sequencing strategy and assembly protocols. iWGS seamlessly integrates the four key steps of a de novo genome sequencing project: data generation (through simulation), data quality control, de novo assembly, and assembly evaluation and validation. The last three steps can also be applied to the analysis of real data. iWGS is designed to enable the user to have great flexibility in testing the range of experimental designs available for genome sequencing projects, and supports all major sequencing technologies and popular assembly tools. Three case studies illustrate how iWGS can guide the design of de novo genome sequencing projects, and evaluate the performance of a wide variety of user-specified sequencing strategies and assembly protocols on genomes of differing architectures. iWGS, along with a detailed documentation, is freely available at https://github.com/zhouxiaofan1983/iWGS.
Extensive Epigenetic Changes Accompany Terminal Differentiation of Mouse Hepatocytes After Birth
Authors: Cannon Matthew V , Pilarowski Genay , Liu Xiuli , Serre David 
Published: October 2016

Abstract
DNA methylation is traditionally thought to be established during early development and to remain mostly unchanged thereafter in healthy tissues, although recent studies have shown that this epigenetic mark can be more dynamic. Epigenetic changes occur in the liver after birth, but the timing and underlying biological processes leading to DNA methylation changes are not well understood. We hypothesized that this epigenetic reprogramming was the result of terminal differentiation of hepatocyte precursors. Using genomic approaches, we characterized the DNA methylation patterns in mouse liver from E18.5 until adulthood to determine if the timing of the DNA methylation change overlaps with hepatocyte terminal differentiation, and to examine the genomic context of these changes and identify the regulatory elements involved. Out of 271,325 CpGs analyzed throughout the genome, 214,709 CpGs changed DNA methylation by more than 5% (e.g., from 5 to 10% methylation) between E18.5 and 9 wk of age, and 18,863 CpGs changed DNA methylation by more than 30%. Genome-scale data from six time points between E18.5 and P20 show that DNA methylation changes coincided with the terminal differentiation of hepatoblasts into hepatocytes. We also showed that epigenetic reprogramming occurred primarily in intergenic enhancer regions while gene promoters were less affected. Our data suggest that normal postnatal hepatic development and maturation involves extensive epigenetic remodeling of the genome, and that enhancers play a key role in controlling the transition from hepatoblasts to fully differentiated hepatocytes. Our study provides a solid foundation to support future research aimed at further revealing the role of epigenetics in stem cell biology.
Drosophila CG2469 Encodes a Homolog of Human CTR9 and Is Essential for Development
Authors: Chaturvedi Dhananjay , Inaba Mayu , Scoggin Shane , Buszczak Michael 
Published: October 2016

Abstract
Conserved from yeast to humans, the Paf1 complex participates in a number of diverse processes including transcriptional initiation and polyadenylation. This complex typically includes five proteins: Paf1, Rtf1, Cdc73, Leo1, and Ctr9. Previous efforts identified clear Drosophila homologs of Paf1, Rtf1, and Cdc73 based on sequence similarity. Further work showed that these proteins help to regulate gene expression and are required for viability. To date, a Drosophila homolog of Ctr9 has remained uncharacterized. Here, we show that the gene CG2469 encodes a functional Drosophila Ctr9 homolog. Both human and Drosophila Ctr9 localize to the nuclei of Drosophila cells and appear enriched in histone locus bodies. RNAi knockdown of Drosophila Ctr9 results in a germline stem cell loss phenotype marked by defects in the morphology of germ cell nuclei. A molecular null mutation of Drosophila Ctr9 results in lethality and a human cDNA CTR9 transgene rescues this phenotype. Clonal analysis in the ovary using this null allele reveals that loss of Drosophila Ctr9 results in a reduction of global levels of histone H3 trimethylation of lysine 4 (H3K4me3), but does not compromise the maintenance of stem cells in ovaries. Given the differences between the null mutant and RNAi knockdown phenotypes, the germ cell defects caused by RNAi likely result from the combined loss of Drosophila Ctr9 and other unidentified genes. These data provide further evidence that the function of this Paf1 complex component is conserved across species.
The GATOR1 Complex Regulates Metabolic Homeostasis and the Response to Nutrient Stress inDrosophila melanogaster
Authors: Wei Youheng , Reveal Brad , Cai Weili , Lilly Mary A 
Published: October 2016

AbstractTORC1 regulates metabolism and growth in response to a large array of upstream inputs. The evolutionarily conserved trimeric GATOR1 complex inhibits TORC1 activity in response to amino acid limitation. In humans, the GATOR1 complex has been implicated in a wide array of pathologies including cancer and hereditary forms of epilepsy. However, the precise role of GATOR1 in animal physiology remains largely undefined. Here, we characterize null mutants of the GATOR1 components nprl2, nprl3, and iml1 in Drosophila melanogaster. We demonstrate that all three mutants have inappropriately high baseline levels of TORC1 activity and decreased adult viability. Consistent with increased TORC1 activity, GATOR1 mutants exhibit a cell autonomous increase in cell growth. Notably, escaper nprl2 and nprl3 mutant adults have a profound locomotion defect. In line with a nonautonomous role in the regulation of systemic metabolism, expressing the Nprl3 protein in the fat body, a nutrient storage organ, and hemocytes but not muscles and neurons rescues the motility of nprl3 mutants. Finally, we show that nprl2 and nprl3 mutants fail to activate autophagy in response to amino acid limitation and are extremely sensitive to both amino acid and complete starvation. Thus, in Drosophila, in addition to maintaining baseline levels of TORC1 activity, the GATOR1 complex has retained a critical role in the response to nutrient stress. In summary, the TORC1 inhibitor GATOR1 contributes to multiple aspects of the development and physiology of Drosophila.
Improvement of Predictive Ability by Uniform Coverage of the Target Genetic Space
Authors: Bustos-Korts Daniela , Malosetti Marcos , Chapman Scott , Biddulph Ben , van Eeuwijk Fred 
Published: October 2016

Abstract
Genome-enabled prediction provides breeders with the means to increase the number of genotypes that can be evaluated for selection. One of the major challenges in genome-enabled prediction is how to construct a training set of genotypes from a calibration set that represents the target population of genotypes, where the calibration set is composed of a training and validation set. A random sampling protocol of genotypes from the calibration set will lead to low quality coverage of the total genetic space by the training set when the calibration set contains population structure. As a consequence, predictive ability will be affected negatively, because some parts of the genotypic diversity in the target population will be under-represented in the training set, whereas other parts will be over-represented. Therefore, we propose a training set construction method that uniformly samples the genetic space spanned by the target population of genotypes, thereby increasing predictive ability. To evaluate our method, we constructed training sets alongside with the identification of corresponding genomic prediction models for four genotype panels that differed in the amount of population structure they contained (maize Flint, maize Dent, wheat, and rice). Training sets were constructed using uniform sampling, stratified-uniform sampling, stratified sampling and random sampling. We compared these methods with a method that maximizes the generalized coefficient of determination (CD). Several training set sizes were considered. We investigated four genomic prediction models: multi-locus QTL models, GBLUP models, combinations of QTL and GBLUPs, and Reproducing Kernel Hilbert Space (RKHS) models. For the maize and wheat panels, construction of the training set under uniform sampling led to a larger predictive ability than under stratified and random sampling. The results of our methods were similar to those of the CD method. For the rice panel, all training set construction methods led to similar predictive ability, a reflection of the very strong population structure in this panel.
Higher Objectives of Islamic Investment Products: Islamizing Indonesian Capital Market
Authors: Soemitra Andri 
Published: October 2016

Indonesian capital market regulators have already accommodated Islamic products as one of Indonesian capital market products. Theoretically, Islamic investment promises three main benefits i.e. spiritual, financial, and social benefits. Realizing Islamic investment in the sense of those three main benefits needs serious effort. This paper discusses the perception of capital market investors. This study suggests that their opinion as to whether or not sharī‘ah capital market products had fulfilled their expectations of Islamic comprehensive objectives. Islamic capital market instruments are part of Islamic instruments. The Islamization of financial institutions and instruments in the modern era has emerged not only to meet Muslims’ need for financial activities but also as the medium to realize the higher objectives of Islam, i.e. maqāṣid al-sharī‘ah in economic and financial activities.DOI: 10.15408/sdi.v23i2.2408
The Reception of Seyyed Hossein Nasr’s Ideas within the Indonesian Intellectual Landscape
Authors: Widiyanto Asfa 
Published: October 2016

This paper examines the appreciation and acceptance of Seyyed Hossein Nasr’s (b. 1933) ideas in the context of intellectual discourse in Indonesia. To do so, it investigates the translation of Nasr’s works into Indonesian, studies on Nasr’s thought, and quotations from Nasr’s works that emerge in the writings of some Indonesian intellectuals. It is especially the notions of Perennialism, “traditional Islam” and scientia sacra that throw light on the process by which his ideas have taken root and gained influence and acceptance in Indonesia. To be more specific, the article scrutinizes the impact of Nasr’s ideas and perspectives on the structure of thought of two Indonesian intellectuals, namely Nurcholish Madjid (1939-2005) and Komaruddin Hidayat (b. 1953). This paper also traces the roots of Nasr’s and Hidayat’s thought in the classical-medieval Islamic tradition, most specifically in Suhrawardi’s School of Illumination, and compares these with those of Madjid and Hidayat.DOI: 10.15408/sdi.v23i2.3002
Ḥizb al-‘Adālah wa al-Rafāhīyah (PKS) wa Siyāsāt al-Huwīyah al-Islāmīyah: Istiratijīyāt Kawādir al-Ḥizb li Ta’ṭīr Qaḍāyā Nukhabihim al-Fasādīyah al-Mālīyah
Authors: Saputra Rangga Eka 
Published: October 2016

This article explains the mechanism of cadre engagement and militancy of Prosperous Justice Party (PKS), as the Islamist party in Indonesia. This study departs from the puzzle that despite their president, Luthfi Hasan Ishaaq, was accused for corruption crime ahead of elections in 2014, but the PKS’s vote still stable from the previous election period (2009). Since PKS is a party cadre, this study argues that the success of the PKS in maintaining the vote in the 2014 election was because of militancy and loyalty of their cadre in doing work collectively for the party. By using the framing approach in the field of social movement, this study concludes that the engagement and militancy of the PKS’s cadre have been influenced by their vigorous framing resources both ideology and identity, as well as the ability of party leaders in mobilizing those resources to their cadre at the lower levels.DOI: 10.15408/sdi.v23i2.3313