Search

Artificial selection has produced varieties of domesticated maize that thrive in temperate climates around the world. However, the direct progenitor of maize, teosinte, is indigenous only to a relatively small range of tropical and subtropical latitudes and grows poorly or not at all outside of this region. Tripsacum, a sister genus to maize and teosinte, is naturally endemic to the majority of areas in the western hemisphere where maize is cultivated. A full-length reference transcriptome for Tripsacum dactyloides generated using long-read Iso-Seq data was used to characterize independent adaptation to temperate climates in this clade. Genes related to phospholipid biosynthesis, a critical component of cold acclimation in other cold-adapted plant lineages, were enriched among those genes experiencing more rapid rates of protein sequence evolution in T. dactyloides. In contrast with previous studies of parallel selection, we find that there is a significant overlap between the genes that were targets of artificial selection during the adaptation of maize to temperate climates and those that were targets of natural selection in temperate-adapted T. dactyloides. Genes related to growth, development, response to stimulus, signaling, and organelles were enriched in the set of genes identified as both targets of natural and artificial selection.

Figure S2. (A and B) Plate clone formation assays were conducted in the indicated cells. The data are presented in triplicates as the meanâ Âąâ S.D. (PDF 4660 kb)

Figure S1. (A, B and C) OS, RFS and DMFS K-M curve for breast cancer patients with either GTSE1 high or GTSE1 low mRNA expression based on PROGgeneV2 database. (PDF 1460 kb)

Figure S3. (A) Overexpression of GTSE1 could promote cell migration in MCF7 cells compared with control cells. (B and C) Silencing or overexpression of GTSE1 markedly changed cell migration as detected by wound-healing assay. (D and E) Quantification data for C and D. *p

Figure S4. (A and B) The gating of MDA-MB-231 siNC and siGTSE1 group cells were treated with 5-fluorouracil (5μg/ml) for 48 h and test for apoptosis respectively. (C and D) The gating of MDA-MB-468 siNC and siGTSE1 group cells were treated with 5-fluorouracil (0.9μg/ml) for 48 h and test for apoptosis respectively. (E and F) The gating of MDA-MB-231-vector and overexpression of GTSE1 group cells were treated with 5-fluorouracil (5μg/ml) for 48 h, then test its apoptosis rate respectively. (G and H) The gating of MCF7-vector and overexpression of GTSE1 group cells were treated with 5-fluorouracil (20μg/ml) for 48 h, then test its apoptosis rate respectively. (PDF 3207 kb)

RNA sequencing (RNA-seq) providing genome-wide expression datasets has been successfully used to study gene expression patterns and regulation mechanism among multiple samples. Gene co-expression networks (GCNs) studies within or across species showed that coordinated genes in expression patterns are often functionally related. For potatoes, a large amount of publicly available transcriptome datasets have been generated but an optimal GCN detecting expression patterns in different genotypes, tissues and environmental conditions, is lacking. We constructed a potato GCN using 16 published RNA-Seq datasets covering 11 cultivars from native habitat worldwide. The correlations of gene expression were assessed pair-wisely and biologically meaningful gene modules which are highly connected in GCN were identified. One of the primitively native-farmer-selected cultivars in the Andes, ssp.Andigena, had relative far distance in gene expression patterns with other modern varieties. GCN in further enriched 134 highly and specifically co-expressed genes in ssp.Andigena associated with potato disease and stress resistance, which underlying the dramatic shift in evolutionary pressures during potato artificial domestication. In total, the network was consisted of into 14 gene models that involves in a variety of plant processes, which sheds light on how gene modules organized intra- and inter-varieties in the context of evolutionary divergence and provides a basis of information resource for potato gene functional studies.

Colorectal cancer (CRC) is the third most commonly diagnosed cancer. Celastrol exhibits anti-tumor activities in a variety of cancers. However, the effect of Celastrol on human CRC and the underlying mechanisms still need to be elucidated. The present study aimed to use in vitro and in vivo methods to clarify the anti-tumor effect of Celastrol and use protein microarrays to explore its mechanisms. We demonstrated that Celastrol effectively inhibited SW480 CRC cell proliferation. Two weeks of Celastrol gavage significantly inhibited the growth of xenografts in nude mice. A total of 69 candidate proteins were identified in the protein microarray experiment, including the most highly enriched protein Shoc2, which is a scaffold protein that modulates cell motility and metastasis through the ERK pathway. Celastrol significantly inhibited ERK1/2 phosphorylation in cell lines and xenograft tumors. Down-regulation of Shoc2 expression using Shoc2 siRNA also inhibited ERK1/2 phosphorylation. Furthermore, down-regulation of Shoc2 expression also significantly inhibited proliferation, colony formation, and migration functions of tumor cells. In addition, the LD0 of Celastrol by gavage is equal or more than 80 mg/kg in C57 male mice. In summary, we unraveled the anti-CRC function of Celastrol and confirmed for the first time that it inhibited the ERK1/2 pathway through binding to Shoc2.

Overexpressing CLCA2 impairs NPC cell migration and silencing CLCA2 promotes NPC cell migration ability in vitro. (PDF 492Â kb)

Soybean mosaic virus (SMV) disease is one of the most serious and broadly distributed soybean (Glycine max (L.) Merr.) diseases. Here, we combine the advantages of association and linkage analysis to identify and fine-map the soybean genes associated with resistance to SMV strain SC7. A set of 191 soybean accessions from different geographic origins and 184 recombinant inbred lines (RILs) derived from Kefeng No.1 (resistant) × Nannong 1138-2 (susceptible) were used in this study. The SC7 resistance genes were previously mapped to a 2.65 Mb region on chromosome 2 and a 380 kb region on chromosome 13. Among 19 single nucleotide polymorphisms (SNPs) detected via association analysis in the study, the SNP BARC-021625-04157 was located in the 2.65 Mb region, and the SNP BARC-041671-08065 was located near the 380 kb region; three genes harboring the SNPs were probably related to SC7 resistance. The resistance gene associated with BARC-021625-04157 was then fine-mapped to a region of approximately 158 kb on chromosome 2 using 184 RILs. Among the 15 genes within this region, one NBS-LRR type gene, one HSP40 gene and one serine carboxypeptidase-type gene might be candidate SC7 resistance genes. These results will be useful for map-based cloning and marker-assisted selection in soybean breeding programs.

Accurate and fast performance estimation is necessary to drive design space exploration and thus support important design decisions. Current techniques are either time consuming or not accurate enough. In this paper, we solve these problems by presenting a hybrid method for multimedia multiprocessor system-on-chip (MPSoC) performance estimation. A general coverage analysis tool GNU gcov is employed to profile the execution statistics during the native simulation. To tackle the complexity and keep the analysis and simulation manageable, the orthogonalization of communication and computation parts is adopted. The estimation result of the computation part is annotated to a transaction accurate model for further analysis, by which a gradual refinement of MPSoC performance estimation is supported. The implementation and its experimental results prove the feasibility and efficiency of the proposed method.

Artificial selection has produced varieties of domesticated maize which thrive in temperate climates around the world. However, the direct progenitor of maize, teosinte, is indigenous only to a relatively small range of tropical and sub-tropical latitudes and grows poorly or not at all outside of this region. Tripsacum, a sister genus to maize and teosinte, is naturally endemic to the majority of areas in the western hemisphere where maize is cultivated. A full-length reference transcriptome for Tripsacum dactyloides generated using long-read isoseq data was used to characterize independent adaptation to temperate climates in this clade. Genes related to phospholipid biosynthesis, a critical component of cold acclimation on other cold adapted plant lineages, were enriched among those genes experiencing more rapid rates of protein sequence evolution in T. dactyloides. In contrast with previous studies of parallel selection, we find that there is a significant overlap between the genes which were targets of artificial selection during the adaptation of maize to temperate climates and those which were targets of natural selection in temperate adapted T. dactyloides. This overlap between the targets of natural and artificial selection suggests genetic changes in crop-wild relatives associated with adaptation to new environments may be useful guides for identifying genetic targets for breeding efforts aimed at adapting crops to a changing climate.

The domestication of diverse grain crops from wild grasses resulted from artificial selection for a suite of overlapping traits producing changes referred to in aggregate as ”domestication syndrome”. Parallel phenotypic change can be accomplished by either selection on orthologous genes, or selection on non-orthologous genes with parallel phenotypic effects. To determine how often artificial selection for domestication traits in the grasses targeted orthologous genes, we employed resequencing data from wild and domesticated accessions of Zea (maize) and Sorghum (sorghum). Many ”classic” domestication genes identified through QTL mapping in populations resulting from wild/domesticated crosses indeed show signatures of parallel selection in both maize and sorghum. However, the overall number of genes showing signatures of parallel selection in both species is not significantly different from that expected by chance. This suggests that, while a small number of genes will extremely large phenotypic effects have been targeted repeatedly by artificial selection during domestication, the optimization portion of domestication targeted small and largely non-overlapping subsets of all possible genes which could produce equivalent phenotypic alterations.

The diamond search (DS) algorithm is one of the most efficient block matching motion estimation algorithms by far and has already been applied in MPEG2/4. Through our research, we found that there is still some redundancy in the algorithm. In this paper, an improved new difference based search (DBS) algorithm is proposed. Simulation results demonstrate that the new algorithm outperforms the well-known diamond search (DS) algorithm and four step-searches (4SS). It obtains almost the same Peak Signal to Noise Ratio (PSNR) while requires less computations than the DS algorithm and 4SS algorithm.