Genome-wide polymorphisms between the parents of an elite hybrid rice and the development of a novel set of PCR-based InDel markers.

Genome-wide re-sequencing of the Zhenshan 97 (ZS97) and Milyang 46 (MY46) parents of an elite three-line hybrid rice developed in China resulted in the generation of 9.91 G bases of data with an effective sequencing depth of 11.66x and 11.51x, respectively. Detection of genome-wide DNA polymorphisms, single nucleotide polymorphisms (SNPs), short insertions/deletions (InDels; 1-5 bp), and structural variations (SVs), which is an invaluable variation resource for genetic research and molecular marker-assisted breeding, was conducted by comparing whole-genome re-sequencing data. A total of 364,488 SNPs, 61,181 InDels and 6298 SVs were detected in ZS97 and 364,179 SNPs, 61,984 InDels and 6408 SVs were detected in MY46 compared to the 9311 reference sequence. Synteny analysis of the variation revealed a total of 77,013 identical and 181,737 different SNPs and 15,021 identical and 1205 different InDels between ZS97 and MY46, respectively. A total of 180 InDels 3-8 bp in length between ZS97 and MY46 were selected for experimental validation; 160 polymerase chain reaction products were efficiently separated on 6% non-denaturing polyacrylamide gels. Identification of genome-wide variation among the parents of the elite hybrid as well as the set of 160 polymerase chain reaction-based InDel markers will facilitate future genetic studies and the molecular breeding of hybrid rice.

Comparison of whole-body PET/CT, dedicated high-resolution head and neck PET/CT, and contrast-enhanced CT in preoperative staging of clinically M0 squamous cell carcinoma of the head and neck.

UNLABELLED: The purpose of this study was to compare optimized whole-body (WB) and dedicated high-resolution contrast-enhanced PET/CT protocols and contrast enhanced CT in the preoperative staging of primary squamous cell carcinoma of the head and neck. METHODS: A total of 44 patients with clinically M0 squamous cell carcinoma of the head and neck underwent primary tumor resection and neck dissection within 6 wk of diagnostic imaging. Imaging consisted of a standard WB PET/CT protocol without intravenous contrast enhancement, followed by a high-resolution dedicated head and neck (HN) PET/CT protocol, which included diagnostic-quality contrast-enhanced CT (CECT). Imaging results were compared with histopathology. A 5-point scale was used to designate primary tumor localization and the presence of lymph node metastasis on a per-patient and per-level basis. For cervical nodes, receiver-operating-characteristic curves were generated to determine the differences in performance between the WB and HN PET/CT protocols and CECT. Sensitivity, specificity, positive and negative predictive values, and accuracy were calculated for primary tumor and cervical nodes. RESULTS: No statistical difference was observed between WB and HN PET/CT protocols, both of which significantly outperformed CECT, in the evaluation of the primary tumor. The performance of the HN PET/CT protocol was superior to that of the WB PET/CT in the detection of cervical node metastases, achieving statistical significance on a per-level basis and approaching significance on a per-patient basis, with the greatest advantage in the detection of small positive lymph nodes (<15 mm). No significant difference was observed between the WB PET/CT protocol and CECT in nodal staging, either on a per-patient or on a per-level basis. CONCLUSION: The primary advantage of the dedicated HN PET/CT protocol over the WB protocol or CECT in the staging of head and neck cancer is in the detection of small lymph node metastases.

[The different functions of glnB and glnZ from Azospirillum brasilense YU62 in the control of nitrogen fixation].

The glnB and glnZ genes of A. brasilense have 70% homology at nucleotide sequence. glnB is located in a 3.7 kb Eco RI+ PstI fragment and glnZ is located in a 3.7 kb SalI fragment. Both glnB and glnZ genes were mutagenized by Kmr cassette insertions and glnB- and glnZ- mutants were obtained. glnB- mutant did not have any nitrogenase activity, while glnZ- mutant still has nitrogenase activity. The coding regions of glnB and glnZ were cloned into pVK100 vectors and recombinant plasmids pVK-II and pVK-Z were obtained, respectively. The recombinant plasmids pVK-II and pVK-Z were introduced into glnB- and glnZ- to produce C-glnB and C-glnZ, respectively. C-glnB can restore nitrogenase activity and C-glnZ does not have effect on nitrogenase activity. When pVK-II and pVK-Z were introduced into A. brasilense Yu62 and draT-, respectively, the Yu62-II (containing pVK-II) and draT-II (containing pVK-II) have higher nitrogenase activity than that of wild type Yu62. In contrast, Yu62-Z (containing pVK-Z) and draT-Z (containing pVK-Z) has no effect on nitrogenase activity. The nifA(-)-II (containg pVK-II) and nifA(-)-Z (containing pVK-Z) still have no nitrogenase activity.