Genome-wide survey of putative Serine/Threonine protein kinases in cyanobacteria-3

<p><b>Copyright information:</b></p><p>Taken from "Genome-wide survey of putative Serine/Threonine protein kinases in cyanobacteria"</p><p>http://www.biomedcentral.com/1471-2164/8/395</p><p>BMC Genomics 2007;8():395-395.</p><p>Published online 30 Oct 2007</p><p>PMCID:PMC2176072.</p><p></p>structed as described in Methods. Strain names are as in Figure 1. Bootstrap values >50% are indicated on the branches. Additional domain names are also given following the gene names. STKs from subfamily cbSTKI-TM are marked in red and bold and those from cbSTKI-I are marked in red, bold, and italics. STKs with additional domains from cbSTKII are marked in bold and some major additional domains are marked in color: green WD40; blue DUF323; purple TPR; and magenta pentapeptide. Members of the family cbSTKIII family are highlighted in a cyan box. Archaeal and eukaryotic STK proteins are in yellow boxes

Genome-wide survey of putative Serine/Threonine protein kinases in cyanobacteria-5

<p><b>Copyright information:</b></p><p>Taken from "Genome-wide survey of putative Serine/Threonine protein kinases in cyanobacteria"</p><p>http://www.biomedcentral.com/1471-2164/8/395</p><p>BMC Genomics 2007;8():395-395.</p><p>Published online 30 Oct 2007</p><p>PMCID:PMC2176072.</p><p></p>as was described in Methods. Numbers appearing at the nodes corresponded to the values produced by bootstrap analysis (1000 replicates). Names of marine nitrogen-fixing strains are marked in yellow boxes. Filamentous diazotrophic strains capable of heterocyst differentiation are marked in cyan boxes. This tree is similar to that obtained by Ashby and Houmard [22]. Percentages in brackets represent total STKs as a percentage of total proteins and total additional domains as a percentage of total STKs

Genome-wide survey of putative Serine/Threonine protein kinases in cyanobacteria-1

<p><b>Copyright information:</b></p><p>Taken from "Genome-wide survey of putative Serine/Threonine protein kinases in cyanobacteria"</p><p>http://www.biomedcentral.com/1471-2164/8/395</p><p>BMC Genomics 2007;8():395-395.</p><p>Published online 30 Oct 2007</p><p>PMCID:PMC2176072.</p><p></p>uences in purple were selected to cover the diversity of species and structural characteristics; 6 sequences in red are of proteins reported to possess phosphorylation or autophosphorylation activity; 5 sequences in yellow were not originally annotated as protein kinases or Serine/Threonine Protein Kinases; and 9 sequences in green were those showing some deviations from the canonical domains of Hanks and Hunter [13]. Each sequence is denoted by the species name followed by the gene names. The 12 conserved subdomains are indicated by Roman numerals according to Hanks and Hunter. Highly conserved eukaryotic and cyanobacteria-specific amino-acid residues are indicated above and below the alignment sequences respectively, using the single-letter amino-acid classes of Hanks and Hunter. Symbols, used to denote the various features according to Hanks and Hunter, are as follows: uppercase letters, universally conserved amino acid residues; lowercase letters, highly conserved amino acid residues; o, positions conserving non-polar residues; *, positions conserving polar residues; +, positions conserving small residues with near neutral polarity; and -, positions within a subdomain with no pattern of conserved amino acids. The number in parentheses preceding each sequence refers to the number of amino acid residues preceeding the sequence shown

Genome-wide survey of putative Serine/Threonine protein kinases in cyanobacteria-6

<p><b>Copyright information:</b></p><p>Taken from "Genome-wide survey of putative Serine/Threonine protein kinases in cyanobacteria"</p><p>http://www.biomedcentral.com/1471-2164/8/395</p><p>BMC Genomics 2007;8():395-395.</p><p>Published online 30 Oct 2007</p><p>PMCID:PMC2176072.</p><p></p>uences in purple were selected to cover the diversity of species and structural characteristics; 6 sequences in red are of proteins reported to possess phosphorylation or autophosphorylation activity; 5 sequences in yellow were not originally annotated as protein kinases or Serine/Threonine Protein Kinases; and 9 sequences in green were those showing some deviations from the canonical domains of Hanks and Hunter [13]. Each sequence is denoted by the species name followed by the gene names. The 12 conserved subdomains are indicated by Roman numerals according to Hanks and Hunter. Highly conserved eukaryotic and cyanobacteria-specific amino-acid residues are indicated above and below the alignment sequences respectively, using the single-letter amino-acid classes of Hanks and Hunter. Symbols, used to denote the various features according to Hanks and Hunter, are as follows: uppercase letters, universally conserved amino acid residues; lowercase letters, highly conserved amino acid residues; o, positions conserving non-polar residues; *, positions conserving polar residues; +, positions conserving small residues with near neutral polarity; and -, positions within a subdomain with no pattern of conserved amino acids. The number in parentheses preceding each sequence refers to the number of amino acid residues preceeding the sequence shown

Additional file 1: of Defective autophagy leads to the suppression of stem-like features of CD271+ osteosarcoma cells

Cell viaiblities of OS cells after chemotherapeutics treatments. (A, B) The indicated SaoS2 and MNNG/HOS cells were treated with Cisplatin (A) or Epicubicin (B) of different doses for 48 h. Then, the cell viability of the indicated cells was detected by CCK8 assay. The data are showen as the mean ± S.D. (n = 3). (PPTX 232 kb

DataSheet_1_Genetic basis of the early heading of high-latitude weedy rice.docx

Japonica rice (Oryza sativa L.) is an important staple food in high-latitude regions and is widely distributed in northern China, Japan, Korea, and Europe. However, the genetic diversity of japonica rice is relatively narrow and poorly adapted. Weedy rice (Oryza sativa f. spontanea) is a semi-domesticated rice. Its headings are earlier than the accompanied japonica rice, making it a potential new genetic resource, which can make up for the defects of wild rice that are difficult to be directly applied to japonica rice improvement caused by reproductive isolation. In this study, we applied a natural population consisting of weedy rice, japonica landrace, and japonica cultivar to conduct a genome-wide association study (GWAS) of the heading date and found four loci that could explain the natural variation of the heading date in this population. At the same time, we developed recombinant inbred lines (RILs) crossed by the early-heading weedy rice WR04-6 and its accompanied japonica cultivar ShenNong 265 (SN265) to carry out a QTL mapping analysis of the heading date and mapped four quantitative trait locus (QTLs) and three epistatic effect gene pairs. The major locus on chromosome 6 overlapped with the GWAS result. Further analysis found that two genes, Hd1 and OsCCT22, on chromosome 6 (Locus 2 and Locus 3) may be the key points of the early-heading character of weedy rice. As minor effect genes, Dth7 and Hd16 also have genetic contributions to the early heading of weedy rice. In the process of developing the RIL population, we introduced fragments of Locus 2 and Locus 3 from the weedy rice into super-high-yielding japonica rice, which successfully promoted its heading date by at least 10 days and expanded the rice suitable cultivation area northward by about 400 km. This study successfully revealed the genetic basis of the early heading of weedy rice and provided a new idea for the genetic improvement of cultivated rice by weedy rice.</p

DataSheet_2_Genetic basis of the early heading of high-latitude weedy rice.xlsx

Japonica rice (Oryza sativa L.) is an important staple food in high-latitude regions and is widely distributed in northern China, Japan, Korea, and Europe. However, the genetic diversity of japonica rice is relatively narrow and poorly adapted. Weedy rice (Oryza sativa f. spontanea) is a semi-domesticated rice. Its headings are earlier than the accompanied japonica rice, making it a potential new genetic resource, which can make up for the defects of wild rice that are difficult to be directly applied to japonica rice improvement caused by reproductive isolation. In this study, we applied a natural population consisting of weedy rice, japonica landrace, and japonica cultivar to conduct a genome-wide association study (GWAS) of the heading date and found four loci that could explain the natural variation of the heading date in this population. At the same time, we developed recombinant inbred lines (RILs) crossed by the early-heading weedy rice WR04-6 and its accompanied japonica cultivar ShenNong 265 (SN265) to carry out a QTL mapping analysis of the heading date and mapped four quantitative trait locus (QTLs) and three epistatic effect gene pairs. The major locus on chromosome 6 overlapped with the GWAS result. Further analysis found that two genes, Hd1 and OsCCT22, on chromosome 6 (Locus 2 and Locus 3) may be the key points of the early-heading character of weedy rice. As minor effect genes, Dth7 and Hd16 also have genetic contributions to the early heading of weedy rice. In the process of developing the RIL population, we introduced fragments of Locus 2 and Locus 3 from the weedy rice into super-high-yielding japonica rice, which successfully promoted its heading date by at least 10 days and expanded the rice suitable cultivation area northward by about 400 km. This study successfully revealed the genetic basis of the early heading of weedy rice and provided a new idea for the genetic improvement of cultivated rice by weedy rice.</p