Distribution of nitrogen fixation and nitrogenase-like sequences amongst microbial genomes

Abstract Background The metabolic capacity for nitrogen fixation is known to be present in several prokaryotic species scattered across taxonomic groups. Experimental detection of nitrogen fixation in microbes requires species-specific conditions, making it difficult to obtain a comprehensive census of this trait. The recent and rapid increase in the availability of microbial genome sequences affords novel opportunities to re-examine the occurrence and distribution of nitrogen fixation genes. The current practice for computational prediction of nitrogen fixation is to use the presence of the nifH and/or nifD genes. Results Based on a careful comparison of the repertoire of nitrogen fixation genes in known diazotroph species we propose a new criterion for computational prediction of nitrogen fixation: the presence of a minimum set of six genes coding for structural and biosynthetic components, namely NifHDK and NifENB. Using this criterion, we conducted a comprehensive search in fully sequenced genomes and identified 149 diazotrophic species, including 82 known diazotrophs and 67 species not known to fix nitrogen. The taxonomic distribution of nitrogen fixation in Archaea was limited to the Euryarchaeota phylum; within the Bacteria domain we predict that nitrogen fixation occurs in 13 different phyla. Of these, seven phyla had not hitherto been known to contain species capable of nitrogen fixation. Our analyses also identified protein sequences that are similar to nitrogenase in organisms that do not meet the minimum-gene-set criteria. The existence of nitrogenase-like proteins lacking conserved co-factor ligands in both diazotrophs and non-diazotrophs suggests their potential for performing other, as yet unidentified, metabolic functions. Conclusions Our predictions expand the known phylogenetic diversity of nitrogen fixation, and suggest that this trait may be much more common in nature than it is currently thought. The diverse phylogenetic distribution of nitrogenase-like proteins indicates potential new roles for anciently duplicated and divergent members of this group of enzymes.

Management of gallstone disease in children: a new protocol based on the experience of a single center

Background/purpose: Gallstones and cholelithiasis are being increasingly diagnosed in children owing to the widespread use of ultrasonography. The treatment of choice is cholecystectomy, and routine intraoperative cholangiography is recommended to explore the common bile duct. The objectives of this study were to describe our experience with the management of gallstone disease in childhood over the last 18 years and to propose an algorithm to guide the approach to cholelithiasis in children based on clinical and ultrasonographic findings. Methods: The data for this study were obtained by reviewing the records of all patients with gallstone disease treated between January 1994 and October 2011. The patients were divided into the following 5 groups based on their symptoms: group 1, asymptomatic; group 2, nonbiliary obstructive symptoms; group 3, acute cholecystitis symptoms; group 4, a history of biliary obstructive symptoms that were completely resolved by the time of surgery; and group 5, ongoing biliary obstructive symptoms. Patients were treated according to an algorithm based on their clinical, ultrasonographic, and endoscopic retrograde cholangiopancreatography (ERCP) findings. Results: A total of 223 patients were diagnosed with cholelithiasis, and comorbidities were present in 177 patients (79.3%). The most common comorbidities were hemolytic disorders in 139 patients (62.3%) and previous bariatric surgery in 16 (7.1%). Although symptoms were present in 134 patients (60.0%), cholecystectomy was performed for all patients with cholelithiasis, even if they were asymptomatic; the surgery was laparoscopic in 204 patients and open in 19. Fifty-six patients (25.1%) presented with complications as the first sign of cholelithiasis (eg, pancreatitis, choledocolithiasis, or acute calculous cholecystitis). Intraoperative cholangiography was indicated in 15 children, and it was positive in only 1 (0.4%) for whom ERCP was necessary to extract the stone after a laparoscopic cholecystectomy (LC). Preoperative ERCP was performed in 11 patients to extract the stones, and a hepaticojejunostomy was indicated in 2 patients. There were no injuries to the hepatic artery or common bile duct in our series. Conclusions: Based on our experience, we can propose an algorithm to guide the approach to cholelithiasis in the pediatric population. The final conclusion is that LC results in limited postoperative complications in children with gallstones. When a diagnosis of choledocolithiasis or dilation of the choledocus is made, ERCP is necessary if obstructive symptoms persist either before or after an LC. Intraoperative cholangiography and laparoscopic common bile duct exploration are not mandatory. Published by Elsevier Inc.

Goal-directed fluid management based on pulse pressure variation monitoring during high-risk surgery: a pilot randomized controlled trial

Abstract Introduction Several studies have shown that maximizing stroke volume (or increasing it until a plateau is reached) by volume loading during high-risk surgery may improve post-operative outcome. This goal could be achieved simply by minimizing the variation in arterial pulse pressure (ΔPP) induced by mechanical ventilation. We tested this hypothesis in a prospective, randomized, single-centre study. The primary endpoint was the length of postoperative stay in hospital. Methods Thirty-three patients undergoing high-risk surgery were randomized either to a control group (group C, n = 16) or to an intervention group (group I, n = 17). In group I, ΔPP was continuously monitored during surgery by a multiparameter bedside monitor and minimized to 10% or less by volume loading. Results Both groups were comparable in terms of demographic data, American Society of Anesthesiology score, type, and duration of surgery. During surgery, group I received more fluid than group C (4,618 ± 1,557 versus 1,694 ± 705 ml (mean ± SD), P < 0.0001), and ΔPP decreased from 22 ± 75 to 9 ± 1% (P < 0.05) in group I. The median duration of postoperative stay in hospital (7 versus 17 days, P < 0.01) was lower in group I than in group C. The number of postoperative complications per patient (1.4 ± 2.1 versus 3.9 ± 2.8, P < 0.05), as well as the median duration of mechanical ventilation (1 versus 5 days, P < 0.05) and stay in the intensive care unit (3 versus 9 days, P < 0.01) was also lower in group I. Conclusion Monitoring and minimizing ΔPP by volume loading during high-risk surgery improves postoperative outcome and decreases the length of stay in hospital. Trial registration NCT00479011