Characterization of Trapped Lignin-Degrading Microbes in Tropical Forest Soil

Lignin is often the most difficult portion of plant biomass to degrade, with fungi generally thought to dominate during late stage decomposition. Lignin in feedstock plant material represents a barrier to more efficient plant biomass conversion and can also hinder enzymatic access to cellulose, which is critical for biofuels production. Tropical rain forest soils in Puerto Rico are characterized by frequent anoxic conditions and fluctuating redox, suggesting the presence of lignin-degrading organisms and mechanisms that are different from known fungal decomposers and oxygen-dependent enzyme activities. We explored microbial lignin-degraders by burying bio-traps containing lignin-amended and unamended biosep beads in the soil for 1, 4, 13 and 30 weeks. At each time point, phenol oxidase and peroxidase enzyme activity was found to be elevated in the lignin-amended versus the unamended beads, while cellulolytic enzyme activities were significantly depressed in lignin-amended beads. Quantitative PCR of bacterial communities showed more bacterial colonization in the lignin-amended compared to the unamended beads after one and four weeks, suggesting that the lignin supported increased bacterial abundance. The microbial community was analyzed by small subunit 16S ribosomal RNA genes using microarray (PhyloChip) and by high-throughput amplicon pyrosequencing based on universal primers targeting bacterial, archaeal, and eukaryotic communities. Community trends were significantly affected by time and the presence of lignin on the beads. Lignin-amended beads have higher relative abundances of representatives from the phyla Actinobacteria, Firmicutes, Acidobacteria and Proteobacteria compared to unamended beads. This study suggests that in low and fluctuating redox soils, bacteria could play a role in anaerobic lignin decomposition

Insights into the Musa genome: Syntenic relationships to rice and between Musa species

<p>Abstract</p> <p>Background</p> <p><it>Musa </it>species (Zingiberaceae, Zingiberales) including bananas and plantains are collectively the fourth most important crop in developing countries. Knowledge concerning <it>Musa </it>genome structure and the origin of distinct cultivars has greatly increased over the last few years. Until now, however, no large-scale analyses of <it>Musa </it>genomic sequence have been conducted. This study compares genomic sequence in two <it>Musa </it>species with orthologous regions in the rice genome.</p> <p>Results</p> <p>We produced 1.4 Mb of <it>Musa </it>sequence from 13 BAC clones, annotated and analyzed them along with 4 previously sequenced BACs. The 443 predicted genes revealed that Zingiberales genes share GC content and distribution characteristics with eudicot and Poaceae genomes. Comparison with rice revealed microsynteny regions that have persisted since the divergence of the Commelinid orders Poales and Zingiberales at least 117 Mya. The previously hypothesized large-scale duplication event in the common ancestor of major cereal lineages within the Poaceae was verified. The divergence time distributions for <it>Musa</it>-Zingiber (Zingiberaceae, Zingiberales) orthologs and paralogs provide strong evidence for a large-scale duplication event in the <it>Musa </it>lineage after its divergence from the Zingiberaceae approximately 61 Mya. Comparisons of genomic regions from <it>M. acuminata </it>and <it>M. balbisiana </it>revealed highly conserved genome structure, and indicated that these genomes diverged circa 4.6 Mya.</p> <p>Conclusion</p> <p>These results point to the utility of comparative analyses between distantly-related monocot species such as rice and <it>Musa </it>for improving our understanding of monocot genome evolution. Sequencing the genome of <it>M. acuminata </it>would provide a strong foundation for comparative genomics in the monocots. In addition a genome sequence would aid genomic and genetic analyses of cultivated <it>Musa </it>polyploid genotypes in research aimed at localizing and cloning genes controlling important agronomic traits for breeding purposes.</p

Notes for genera: basal clades of Fungi (including Aphelidiomycota, Basidiobolomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota)

Compared to the higher fungi (Dikarya), taxonomic and evolutionary studies on the basal clades of fungi are fewer in number. Thus, the generic boundaries and higher ranks in the basal clades of fungi are poorly known. Recent DNA based taxonomic studies have provided reliable and accurate information. It is therefore necessary to compile all available information since basal clades genera lack updated checklists or outlines. Recently, Tedersoo et al. (MycoKeys 13:1--20, 2016) accepted Aphelidiomycota and Rozellomycota in Fungal clade. Thus, we regard both these phyla as members in Kingdom Fungi. We accept 16 phyla in basal clades viz. Aphelidiomycota, Basidiobolomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota. Thus, 611 genera in 153 families, 43 orders and 18 classes are provided with details of classification, synonyms, life modes, distribution, recent literature and genomic data. Moreover, Catenariaceae Couch is proposed to be conserved, Cladochytriales Mozl.-Standr. is emended and the family Nephridiophagaceae is introduced

Individualized Risk of Surgical Complications: An Application of the Breast Reconstruction Risk Assessment Score.

BACKGROUND: Risk discussion is a central tenet of the dialogue between surgeon and patient. Risk calculators have recently offered a new way to integrate evidence-based practice into the discussion of individualized patient risk and expectation management. Focusing on the comprehensive Tracking Operations and Outcomes for Plastic Surgeons (TOPS) database, we endeavored to add plastic surgical outcomes to the previously developed Breast Reconstruction Risk Assessment (BRA) score. METHODS: The TOPS database from 2008 to 2011 was queried for patients undergoing breast reconstruction. Regression models were constructed for the following complications: seroma, dehiscence, surgical site infection (SSI), explantation, flap failure, reoperation, and overall complications. RESULTS: Of 11,992 cases, 4439 met inclusion criteria. Overall complication rate was 15.9%, with rates of 3.4% for seroma, 4.0% for SSI, 6.1% for dehiscence, 3.7% for explantation, 7.0% for flap loss, and 6.4% for reoperation. Individualized risk models were developed with acceptable goodness of fit, accuracy, and internal validity. Distribution of overall complication risk was broad and asymmetric, meaning that the average risk was often a poor estimate of the risk for any given patient. These models were added to the previously developed open-access version of the risk calculator, available at http://www.BRAscore.org. CONCLUSIONS: Population-based measures of risk may not accurately reflect risk for many individual patients. In this era of increasing emphasis on evidence-based medicine, we have developed a breast reconstruction risk assessment calculator from the robust TOPS database. The BRA Score tool can aid in individualizing-and quantifying-risk to better inform surgical decision making and better manage patient expectations

The Use of Patient Registries in Breast Surgery: a Comparison of the Tracking Operations and Outcomes for Plastic Surgeons and National Surgical Quality Improvement Program Data Sets.

BACKGROUND: The National Surgical Quality Improvement Program (NSQIP) and the Tracking Operations and Outcomes for Plastic Surgeons (TOPS) registries gather outcomes for plastic surgery procedures. The NSQIP collects hospital data using trained nurses, and the TOPS relies on self-reported data. We endeavored to compare the TOPS and NSQIP data sets with respect to cohort characteristics and outcomes to better understand the strengths and weakness of each registry as afforded by their distinct data collection methods. STUDY DESIGN: The 2008 to 2011 TOPS and NSQIP databases were queried for breast reductions and breast reconstructions. Propensity score matching identified similar cohorts from the TOPS and NSQIP databases. Shared 30-day surgical and medical complications rates were compared across matched cohorts. RESULTS: The TOPS captured a significantly greater number of wound dehiscence occurrences (4.77%-5.47% vs 0.69%-1.17%, all P0.05). CONCLUSIONS: The TOPS and NSQIP capture significantly different patient populations, with TOPS\u27 self-reported data allowing for the inclusion of private practices. This self-reporting limits TOPS\u27 ability to identify medical complications; surgical complications and readmissions, however, were not underreported. Many surgical complications are captured by TOPS at a higher rate due to its broader definitions, and others are not captured by NSQIP at all. The TOPS and NSQIP provide complementary information with different strengths and weakness that together can guide evidence-based decision making in plastic surgery

Combining Abdominal and Cosmetic Breast Surgery Does Not Increase Short-term Complication Rates: A Comparison of Each Individual Procedure and Pretreatment Risk Stratification Tool.

BACKGROUND: Combined abdominal and breast surgery presents a convenient and relatively cost-effective approach for accomplishing both procedures. OBJECTIVES: This study is the largest to date assessing the safety of combined procedures, and it aims to develop a simple pretreatment risk stratification method for patients who desire a combined procedure. METHODS: All women undergoing abdominoplasty, panniculectomy, augmentation mammaplasty, and/or mastopexy in the TOPS database were identified. Demographics and outcomes for combined procedures were compared to individual procedures using χ(2) and Student\u27s t-tests. Multiple logistic regression provided adjusted odds ratios for the effect of a combined procedure on 30-day complications. Among combined procedures, a logistic regression model determined point values for pretreatment risk factors including diabetes (1 point), age over 53 (1), obesity (2), and 3+ ASA status (3), creating a 7-point pretreatment risk stratification tool. RESULTS: A total of 58,756 cases met inclusion criteria. Complication rates among combined procedures (9.40%) were greater than those of aesthetic breast surgery (2.66%; P \u3c .001) but did not significantly differ from abdominal procedures (9.75%; P = .530). Nearly 77% of combined cases were classified as low-risk (0 points total) with a 9.78% complication rates. Medium-risk patients (1 to 3 points) had a 16.63% complication rate, and high-risk (4 to 7 points) 38.46%. CONCLUSIONS: Combining abdominal and breast procedures is safe in the majority of patients and does not increase 30-day complications rates. The risk stratification tool can continue to ensure favorable outcomes for patients who may desire a combined surgery. LEVEL OF EVIDENCE: 4 Risk