Metabolic reconstruction of sulfur assimilation in the extremophile Acidithiobacillus ferrooxidans based on genome analysis

BACKGROUND: Acidithiobacillus ferrooxidans is a gamma-proteobacterium that lives at pH2 and obtains energy by the oxidation of sulfur and iron. It is used in the biomining industry for the recovery of metals and is one of the causative agents of acid mine drainage. Effective tools for the study of its genetics and physiology are not in widespread use and, despite considerable effort, an understanding of its unusual physiology remains at a rudimentary level. Nearly complete genome sequences of A. ferrooxidans are available from two public sources and we have exploited this information to reconstruct aspects of its sulfur metabolism. RESULTS: Two candidate mechanisms for sulfate uptake from the environment were detected but both belong to large paralogous families of membrane transporters and their identification remains tentative. Prospective genes, pathways and regulatory mechanisms were identified that are likely to be involved in the assimilation of sulfate into cysteine and in the formation of Fe-S centers. Genes and regulatory networks were also uncovered that may link sulfur assimilation with nitrogen fixation, hydrogen utilization and sulfur reduction. Potential pathways were identified for sulfation of extracellular metabolites that may possibly be involved in cellular attachment to pyrite, sulfur and other solid substrates. CONCLUSIONS: A bioinformatic analysis of the genome sequence of A. ferrooxidans has revealed candidate genes, metabolic process and control mechanisms potentially involved in aspects of sulfur metabolism. Metabolic modeling provides an important preliminary step in understanding the unusual physiology of this extremophile especially given the severe difficulties involved in its genetic manipulation and biochemical analysis

Occurrence and paragenesis of diagenetic monazite in the Upper Triassic black shales of the Marvast region, South Yazd, Iran

Upper Triassic-Jurassic black shale at Marvast, Iran, contains grey to green-grey ellipsoidal nodules of monazite ranging from 0.1 to 2 mm across. The presence of host-rock mineral inclusions within the monazite grains, low Th content in the monazite, lack of relict yellow cores (characteristic of igneous monazite), and the absence of monazite in the other sedimentary sequences in the Marvast area rule out a detrital origin for the monazite nodules and suggest authigenic crystallization during sediment compaction. Enrichment of the cores of the monazite grains in mid-range to heavy rare-earth elements (REE) and their rims in La + Ce point to variations in the degree of REE mobility and/or evolving composition of the diagenetic mineralizing fluid during nodule growth. The phosphorus and REE required for monazite crystallization were probably derived from seawater and adsorbed on clays and Fe-Mn hydroxides. The interstitial fluids expelled from the sediments during burial compaction and diagenesis became enriched in P and REE through complexing. The association of the Marvast monazite nodules with the black shale may indicate that organic complexes aided in the mobilization and transport of the REE into the pore fluids. Detailed field investigations in the study area and vicinity show that authigenic monazite in the upper Triassic-Jurassic shale sections is spatially associated with quartz lenses. It is likely that these lenses are surface expressions of shallow intrusive magmas, which provided the heat that promoted the mobilization and redistribution of the REE and P, and initiated precipitation of monazite in the overlying sediments

Third Asia-Pacific consensus recommendations on colorectal cancer screening and postpolypectomy surveillance

The Asia-Pacific region has the largest number of cases of colorectal cancer (CRC) and one of the highest levels of mortality due to this condition in the world. Since the publishing of two consensus recommendations in 2008 and 2015, significant advancements have been made in our knowledge of epidemiology, pathology and the natural history of the adenoma-carcinoma progression. Based on the most updated epidemiological and clinical studies in this region, considering literature from international studies, and adopting the modified Delphi process, the Asia-Pacific Working Group on Colorectal Cancer Screening has updated and revised their recommendations on (1) screening methods and preferred strategies; (2) age for starting and terminating screening for CRC; (3) screening for individuals with a family history of CRC or advanced adenoma; (4) surveillance for those with adenomas; (5) screening and surveillance for sessile serrated lesions and (6) quality assurance of screening programmes. Thirteen countries/regions in the Asia-Pacific region were represented in this exercise. International advisors from North America and Europe were invited to participate

Third Asia-Pacific consensus recommendations on colorectal cancer screening and postpolypectomy surveillance

The Asia-Pacific region has the largest number of cases of colorectal cancer (CRC) and one of the highest levels of mortality due to this condition in the world. Since the publishing of two consensus recommendations in 2008 and 2015, significant advancements have been made in our knowledge of epidemiology, pathology and the natural history of the adenoma-carcinoma progression. Based on the most updated epidemiological and clinical studies in this region, considering literature from international studies, and adopting the modified Delphi process, the Asia-Pacific Working Group on Colorectal Cancer Screening has updated and revised their recommendations on (1) screening methods and preferred strategies; (2) age for starting and terminating screening for CRC; (3) screening for individuals with a family history of CRC or advanced adenoma; (4) surveillance for those with adenomas; (5) screening and surveillance for sessile serrated lesions and (6) quality assurance of screening programmes. Thirteen countries/regions in the Asia-Pacific region were represented in this exercise. International advisors from North America and Europe were invited to participate