Differential gene expression in an elite hybrid rice cultivar (Oryza sativa, L) and its parental lines based on SAGE data

<p>Abstract</p> <p>Background</p> <p>It was proposed that differentially-expressed genes, aside from genetic variations affecting protein processing and functioning, between hybrid and its parents provide essential candidates for studying heterosis or hybrid vigor. Based our serial analysis of gene expression (SAGE) data from an elite Chinese super-hybrid rice (<it>LYP9</it>) and its parental cultivars (<it>93-11 </it>and <it>PA64s</it>) in three major tissue types (leaves, roots and panicles) at different developmental stages, we analyzed the transcriptome and looked for candidate genes related to rice heterosis.</p> <p>Results</p> <p>By using an improved strategy of tag-to-gene mapping and two recently annotated genome assemblies (<it>93-11 and PA64s</it>), we identified 10,268 additional high-quality tags, reaching a grand total of 20,595 together with our previous result. We further detected 8.5% and 5.9% physically-mapped genes that are differentially-expressed among the triad (in at least one of the three stages) with <it>P</it>-values less than 0.05 and 0.01, respectively. These genes distributed in 12 major gene expression patterns; among them, 406 up-regulated and 469 down-regulated genes (<it>P </it>< 0.05) were observed. Functional annotations on the identified genes highlighted the conclusion that up-regulated genes (some of them are known enzymes) in hybrid are mostly related to enhancing carbon assimilation in leaves and roots. In addition, we detected a group of up-regulated genes related to male sterility and 442 down-regulated genes related to signal transduction and protein processing, which may be responsible for rice heterosis.</p> <p>Conclusion</p> <p>We improved tag-to-gene mapping strategy by combining information from transcript sequences and rice genome annotation, and obtained a more comprehensive view on genes that related to rice heterosis. The candidates for heterosis-related genes among different genotypes provided new avenue for exploring the molecular mechanism underlying heterosis.</p

TripleRE: Knowledge Graph Embeddings via Tripled Relation Vectors

Translation-based knowledge graph embedding has been one of the most important branches for knowledge representation learning since TransE came out. Although many translation-based approaches have achieved some progress in recent years, the performance was still unsatisfactory. This paper proposes a novel knowledge graph embedding method named TripleRE with two versions. The first version of TripleRE creatively divide the relationship vector into three parts. The second version takes advantage of the concept of residual and achieves better performance. In addition, attempts on using NodePiece to encode entities achieved promising results in reducing the parametric size, and solved the problems of scalability. Experiments show that our approach achieved state-of-the-art performance on the large-scale knowledge graph dataset, and competitive performance on other datasets

Tarımsal Pazarlamada Alternatif Pazarlama Ağı Olan Elektronik Ticaretin(E-Ticaret) SWOT Analizi ile Değerlendirilmesi

Dünya ticaretinde meydana gelen zorunlu rekabet, firmaları farklı pazarlama sistemlerine yöneltmiştir. Türkiye tarımında üretim sorunundan ziyade pazarlama sorunu olduğu görülmektedir. Bu yönde pazarlama alternatifleri aranmaktadır. E-ticaret tarımsal pazarlamada olanakları fazla olan bir sistemdir. Türkiye’de bu sistemin uygulanabilirliğinin artırılması tarımda pazarlama ile ilgili birçok sorunu ortadan kaldıracaktır. E-ticaretin tarımsal pazarlamada aktif olarak kullanılmasıyla tarıma dayalı ve bağlı sanayi kuruluşları ve üreticileri için ürünlerinin pazarlamasında kolaylık sağlanacak ve ülkenin her yeri potansiyel pazar konumunda olacaktır. Bu çalışmada e-ticaretin tarım sektörüne sunduğu olanaklar, fırsatlar, tehditler, eksiklikler ve tarım sektörüne katkısı ele alınmıştır. Zaman ve mekan sınırlaması olmadan internet ve bilgisayar aracılığıyla e-ticaretin ulusal ve uluslararası arz talep dengesinin kurulması, aktif ve canlı pazarlamanın sağlanmasında önemli rolleri üstleneceği görülmüştür. Tarımsal pazarlama sorunlarının azaltılması noktasında da önemli bir araç olarak karşımıza çıkmaktadır

Two species of Naididae (Annelida, Clitellata) from southern Tibet, China

One new species of Naidinae (Oligochaeta, Naididae), Nais badia sp. n. and one new record species from China, Tubifex montanus Kowalewski, 1919 (Tubificinae) are found in southern Tibet. The new species is distinguished from congeners by its large area of reddish brown pigment in the anterior segments I–VIII, serrate hairs, pectinate needles with 1–2 intermediate teeth, ventral chaetae partly with 1–2 fine intermediate teeth and wave-like movements. The new material of the species Tubifex montanus differs slightly from the previous descriptions by its vas deferens entering atrium subapically, wide ental end of penial sheath and smooth hair chaetae

Records of Naididae and Lumbriculidae (Clitellata) from Tibet, China, with description of a new species of Nais

Cui, Yongde, He, Xuebao, Peng, Yu, Wang, Hongzhu (2015): Records of Naididae and Lumbriculidae (Clitellata) from Tibet, China, with description of a new species of Nais. Zootaxa 3956 (4): 513-530, DOI: 10.11646/zootaxa.3956.4.

Genetic Variation and Phylogeography of <i>Lumbriculus variegatus</i> (Annelida: Clitellata: Lumbriculidae) Based on Mitochondrial Genes

Lumbriculus variegatus is a typical cold-water worm and is mainly distributed in the Tibetan Plateau and Northeast in China. The current study aimed to explore the genetic diversity and phylogeography of L. variegatus sampled from different geographical regions based on concatenated (COI + 16S rRNA, 879 bp) genes. Among 63 L. variegatus specimens, 29 haplotypes were identified with high haplotype diversity (h = 0.923) and nucleotide diversity (π = 0.062). The Bayesian phylogenetic analysis and Median-joining haplotype network revealed two lineages, or species, of L. variegatus. Taxa belonging to lineage I was mainly distributed in the Tibetan Plateau of China, North America, and Sweden, while lineage II composed taxa from Northeast China, southern China, and Sweden. The analysis of molecular variance indicated that the genetic difference was mainly due to differences between lineages. Neutrality tests showed that the overall L. variegatus have a stable population since the time of origin. Divergence time analysis suggested that L. variegatus originated from the Triassic period of Mesozoic in 235 MYA (95%HPD: 199–252 MYA), and the divergence between different lineages of L. variegatus began from the next 170 million years