Complete genome sequence of Sphingobium sp. strain PAMC 28499 reveals a potential for degrading pectin with comparative genomics approach.

BACKGROUND: Spingobium sp. PAMC 28499 is isolated from the glaciers of Uganda. Uganda is a unique region where hot areas and glaciers coexist, with a variety of living creatures surviving, but the survey on them is very poor. The genetic character and complete genome information of Sphingobium strains help with environmental studies and the development of better to enzyme industry. OBJECTIVE: In this study, complete genome sequence of Spingobium sp. PAMC 28499 and comparative analysis of Spingobium species strains isolated from variety of the region. METHODS: Genome sequencing was performed using PacBio sequel single-molecule real-time (SMRT) sequencing technology. The predicted gene sequences were functionally annotated and gene prediction was carried out using the program NCBI non-redundant database. And using dbCAN2 and KEGG data base were degradation pathway predicted and protein prediction about carbohydrate active enzymes (CAZymes). RESULTS: The genome sequence has 64.5% GC content, 4432 coding protein coding genes, 61 tRNAs, and 12 rRNA operons. Its genome encodes a simple set of metabolic pathways relevant to pectin and its predicted degradation protein an unusual distribution of CAZymes with extracellular esterases and pectate lyases. CAZyme annotation analyses revealed 165 genes related to carbohydrate active, and especially we have found GH1, GH2, GH3, GH38, GH35, GH51, GH51, GH53, GH106, GH146, CE12, PL1 and PL11 such as known pectin degradation genes from Sphingobium yanoikuiae. These results confirmed that this Sphingobium sp. strain PAMC 28499 have similar patterns to RG I pectin-degrading pathway. CONCLUSION: In this study, isolated and sequenced the complete genome of Spingobium sp. PAMC 28499. Also, this strain has comparative genome analysis. Through the complete genome we can predict how this strain can store and produce energy in extreme environment. It can also provide bioengineered data by finding new genes that degradation the pectin.

Short-term results and long-term oncologic outcomes between neoadjuvant chemoradiotherapy and adjuvant postoperative chemoradiotherapy for stage III rectal cancer: a case-matched study.

PURPOSE: To compare the short-term perioperative results and long-term oncologic outcomes between patients who underwent neoadjuvant chemoradiotherapy (NCRT) and patients who underwent postoperative adjuvant chemoradiotherapy (ACRT) for stage III rectal cancer. METHODS: From January 1997 to December 2008, a total of 47 patients who were diagnosed as clinical stage III rectal cancer followed by NCRT were matched according to age, gender, and operation method to 47 patients with pathologic stage III rectal cancer who underwent ACRT. Clinical characteristics, surgical and pathologic outcomes, postoperative complications and recovery, and oncologic outcomes were compared between the two groups. RESULTS: There were no significant differences in demographics or preoperative characteristics between the NCRT and ACRT groups. Though more protective ileostomies were performed in the NCRT group, there was no statistical difference in operation times between the two groups. Patients in the NCRT group had a smaller tumor size (P < 0.001) and a smaller number of lymph nodes retrieved (P < 0.001). No differences were observed with respect to morbidity and recovery outcomes between the two groups. During the median 58-month follow-up periods, the NCRT group showed better disease-free survival and overall survival than the ACRT group (P = 0.002, P = 0.001, respectively). CONCLUSIONS: NCRT in comparison to ACRT did not increase the risk of postoperative morbidity and provided better disease-free and overall survival in stage III rectal cancer patients.