Diversity of fungi in mangrove ecosystem

The present study was taken with an objective to asses the occurrence of fungi on leaves, bark and pneumatophores from the selected mangroves, fungi from soil and water was also recorded and physicochemical parameters of soil and water were noted. Maximum number of fungi was isolated from soil. Pneumatophores of Avicennia marina showed more fungal count than leaf and bark of other mangroves.Aspergillus spp were found to be dominant among the various fungal species isolated from the mangrove ecosystem

Complete Genomic Characterization of a Pathogenic A.II Strain of Francisella tularensis Subspecies tularensis

Francisella tularensis is the causative agent of tularemia, which is a highly lethal disease from nature and potentially from a biological weapon. This species contains four recognized subspecies including the North American endemic F. tularensis subsp. tularensis (type A), whose genetic diversity is correlated with its geographic distribution including a major population subdivision referred to as A.I and A.II. The biological significance of the A.I – A.II genetic differentiation is unknown, though there are suggestive ecological and epidemiological correlations. In order to understand the differentiation at the genomic level, we have determined the complete sequence of an A.II strain (WY96-3418) and compared it to the genome of Schu S4 from the A.I population. We find that this A.II genome is 1,898,476 bp in size with 1,820 genes, 1,303 of which code for proteins. While extensive genomic variation exists between “WY96” and Schu S4, there is only one whole gene difference. This one gene difference is a hypothetical protein of unknown function. In contrast, there are numerous SNPs (3,367), small indels (1,015), IS element differences (7) and large chromosomal rearrangements (31), including both inversions and translocations. The rearrangement borders are frequently associated with IS elements, which would facilitate intragenomic recombination events. The pathogenicity island duplicated regions (DR1 and DR2) are essentially identical in WY96 but vary relative to Schu S4 at 60 nucleotide positions. Other potential virulence-associated genes (231) varied at 559 nucleotide positions, including 357 non-synonymous changes. Molecular clock estimates for the divergence time between A.I and A.II genomes for different chromosomal regions ranged from 866 to 2131 years before present. This paper is the first complete genomic characterization of a member of the A.II clade of Francisella tularensis subsp. tularensis

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Grand Challenges for Biological and Environmental Research: A Long-Term Vision

The interactions and feedbacks among plants, animals, microbes, humans, and the environment ultimately form the world in which we live. This world is now facing challenges from a growing and increasingly affluent human population whose numbers and lifestyles are driving ever greater energy demand and impacting climate. These and other contributing factors will make energy and climate sustainability extremely difficult to achieve over the 20-year time horizon that is the focus of this report. Despite these severe challenges, there is optimism that deeper understanding of our environment will enable us to mitigate detrimental effects, while also harnessing biological and climate systems to ensure a sustainable energy future. This effort is advanced by scientific inquiries in the fields of atmospheric chemistry and physics, biology, ecology, and subsurface science - all made possible by computing. The Office of Biological and Environmental Research (BER) within the Department of Energy's (DOE) Office of Science has a long history of bringing together researchers from different disciplines to address critical national needs in determining the biological and environmental impacts of energy production and use, characterizing the interplay of climate and energy, and collaborating with other agencies and DOE programs to improve the world's most powerful climate models. BER science focuses on three distinct areas: (1) What are the roles of Earth system components (atmosphere, land, oceans, sea ice, and the biosphere) in determining climate? (2) How is the information stored in a genome translated into microbial, plant, and ecosystem processes that influence biofuel production, climate feedbacks, and the natural cycling of carbon? (3) What are the biological, geochemical, and physical forces that govern the behavior of Earth's subsurface environment? Ultimately, the goal of BER science is to support experimentation and modeling that can reliably predict the outcomes and behaviors of complex biological and environmental systems, leading to robust solutions for DOE missions and strategic goals. In March 2010, the Biological and Environmental Research Advisory Committee held the Grand Challenges for Biological and Environmental Research: A Long-Term Vision workshop to identify scientific opportunities and grand challenges for BER science in the coming decades and to develop an overall strategy for drafting a long-term vision for BER. Key workshop goals included: (1) Identifying the greatest scientific challenges in biology, climate, and the environment that DOE will face over a 20-year time horizon. (2) Describing how BER should be positioned to address those challenges. (3) Determining the new and innovative tools needed to advance BER science. (4) Suggesting how the workforce of the future should be trained in integrative system science. This report lays out grand research challenges for BER - in biological systems, climate, energy sustainability, computing, and education and workforce training - that can put society on a path to achieve the scientific evidence and predictive understanding needed to inform decision making and planning to address future energy needs, climate change, water availability, and land use

Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities

Background Sequencing the expressed genetic information of an ecosystem (metatranscriptome) can provide information about the response of organisms to varying environmental conditions. Until recently, metatranscriptomics has been limited to microarray technology and random cloning methodologies. The application of high-throughput sequencing technology is now enabling access to both known and previously unknown transcripts in natural communities. Methodology/Principal Findings We present a study of a complex marine metatranscriptome obtained from random whole-community mRNA using the GS-FLX Pyrosequencing technology. Eight samples, four DNA and four mRNA, were processed from two time points in a controlled coastal ocean mesocosm study (Bergen, Norway) involving an induced phytoplankton bloom producing a total of 323,161,989 base pairs. Our study confirms the finding of the first published metatranscriptomic studies of marine and soil environments that metatranscriptomics targets highly expressed sequences which are frequently novel. Our alternative methodology increases the range of experimental options available for conducting such studies and is characterized by an exceptional enrichment of mRNA (99.92%) versus ribosomal RNA. Analysis of corresponding metagenomes confirms much higher levels of assembly in the metatranscriptomic samples and a far higher yield of large gene families with >100 members, ~91% of which were novel. Conclusions/Significance This study provides further evidence that metatranscriptomic studies of natural microbial communities are not only feasible, but when paired with metagenomic data sets, offer an unprecedented opportunity to explore both structure and function of microbial communities – if we can overcome the challenges of elucidating the functions of so many never-seen-before gene families

Hirschsprung disease in Down syndrome: An opportunity for improvement

•National cohort of pediatric patients with Hirschsprung disease used to compare those with and without Down syndrome.•Patients with Down syndrome have delays in diagnosis and poorer outcomes than those with Hirschsprung disease alone.•Earlier suspicion of Hirschsprung disease in patients with Down syndrome may improve outcomes. Down syndrome (DS) is the most common abnormality associated with Hirschsprung disease (HD). It has been suggested patients with HD and DS have worse outcomes, however the literature is controversial. The Kids’ Inpatient Database (KID) from 2003 to 2012 was used to identify newborns with HD. Demographics, hospital characteristics, and outcomes were compared among patients with and without DS using standard statistical tests. There were 481 patients identified with HD, of which 45 (9%) had DS. Patients with DS were older at the time of first rectal biopsy (6 [3–11] days vs. 4 [3–6] days, p = 0.012). There were no differences in operative versus non-operative management in patients with and without DS (p = 0.706). Hospital length of stay was longer in the DS cohort (22 [13–33] days vs. 15 [10–24] days, p = 0.019), and patients with DS were more likely to have a concomitant diagnosis of wound infection (<12% vs. 3%, p = 0.002) and necrotizing enterocolitis (<14% vs. 5%, p = 0.018). The mortality rate for patients with DS was four times higher than those without DS (< 5% vs. < 0.8%, p = 0.018). In this nationwide cohort of patients with Hirschsprung disease, those with Down syndrome experienced delays in diagnosis and worse outcomes. Level III. Treatment study, retrospective comparative study

Outcomes for Ladd's procedure: Does approach matter?

•Hospital readmission is common after Ladd’s procedure•Laparoscopic Ladd’s procedure results in fewer index complications and lower readmission rates than the open approach•The rate of redo Ladd’s procedure is lower than previously reported Laparoscopic Ladd's procedure has been proven safe and effective for the treatment of malrotation. However, the nationwide utilization and outcomes of elective Ladd's procedure are largely unknown. The Nationwide Readmissions Database from 2010 to 2014 was used to identify patients 0–18 years (excluding newborns) with malrotation who underwent elective Ladd's procedure. Demographics, hospital factors, and outcomes were compared by approach (laparoscopic vs. open) using standard statistical tests and propensity score (PS) matched analysis. Results were weighted for national estimates. 1343 patients (44% male) underwent elective Ladd's procedure via laparoscopic (22%) or open (78%) approach. Laparoscopic approach was more common in large hospitals (26% vs. 16%), patients >13 years (30% vs. 20%), and those with higher income (29% vs. 16%), all p  7 days (20% vs. 8%), more post-operative gastrointestinal dysfunction (12% vs. < 1%), and more nausea, vomiting, and/or diarrhea (16% vs. 6%), all p < 0.001. The overall readmission rates within 30 days and the year of index operation were 8% and 15%, respectively. In the matched cohort, those undergoing laparoscopic Ladd's were less likely to be readmitted than those with the open approach (7% vs. 16%, p < 0.001) and experienced less gastrointestinal issues on readmission (5% vs. 15%, p = 0.002). There were similar rates of post-operative small bowel obstruction (< 3% vs. < 3%, p = 0.840) and volvulus (0% vs. < 1%, p = 0.136). Redo Ladd's procedure was performed in less than 4% of readmissions and all occurred within 5 days of initial hospital discharge. The majority of Ladd's procedures in the U.S. are being performed open, despite comparable outcomes following a laparoscopic approach. Readmission rates are similar with either approach, and the rate of redo Ladd's procedure is lower than previously reported. Level III

Pediatric Gastrostomy Tube Placement: Less Complications Associated with Laparoscopic Approach

There are few nationwide studies comparing outcomes of open, laparoscopic (LAP), and percutaneous endoscopic (PEG) gastrostomy tube (GT) placement in the pediatric population.The Nationwide Readmissions Database from 2010 to 2014 was used to identify patients ≤18 years (excluding newborns) who underwent GT placement. Demographics, hospital characteristics, and outcomes were compared by the GT approach.There were 3278 patients (41% female, age 3 ± 5 years) identified who underwent GT placement (40% open versus 32% PEG versus 28% LAP). Following an open approach, there were higher rates of GT-related complications (10% versus 4% LAP versus 3% PEG) and postoperative gastrointestinal issues (24% versus 12% LAP versus 9% PEG) on index hospitalization, both < .001. Readmission within 30 days and 1 year were 18% and 43%, respectively. Overall readmission rates were not affected by the GT approach (44% open versus 44% LAP versus 43% PEG, = .773). However, readmission for GT-related complications was the lowest following the LAP approach (<0.3% versus 2% open versus 2% PEG, < .001). When those who also underwent fundoplication were excluded, conversion to gastrojejunostomy or jejunostomy (GJ/J) on readmission was higher following open and PEG approaches (4% open versus 2% PEG versus 0% LAP, = .039).Compared with PEG gastrostomy and open gastrostomy, LAP GT placement appears to have lower index complications and reoperation rates, and at least comparable readmission outcomes. Despite these advantages, LAP GT placement remains underutilized

Genome Sequences of Industrially Relevant Saccharomyces cerevisiae Strain M3707, Isolated from a Sample of Distillers Yeast and Four Haploid Derivatives

Saccharomyces cerevisiae strain M3707 was isolated from a sample of commercial distillers yeast, and its genome sequence together with the genome sequences for the four derived haploid strains M3836, M3837, M3838, and M3839 has been determined. Yeasts have potential for consolidated bioprocessing (CBP) for biofuel production, and access to these genome sequences will facilitate their development