Isoelectric point prediction from the amino acid sequence of a protein

Proteins often do not migrate as expected in two dimensional electrophoresis based on their primary sequence. The predicted isoelectric point (pI) frequently does not coincide with experimental pI values obtained in the laboratory. The reasons for these differences led to this study. Initially, 2DE data from the E. coli proteome was collected and formatted. This dataset was split into three parts each consisting of different levels of pI discrepancy (ΔpI). The protein sequence data for each ΔpI subset was run through a pipeline. At each stage of the pipeline the data were analyzed by comparing each of the three ΔpI subsets to one another. The pipeline consisted of a naïve approach (considering individual amino acid frequencies), followed by the application four different alphabets to represent sequences in a simpler way by grouping similar amino acids based on their charge, functional, chemical, and hydrophobic properties . The final step in the pipeline involved investigating the dipeptides of all of these sequences using both the 20 amino acid alphabet and the simplified groupings. An evaluation of the alphabet dipeptide analysis demonstrated the existence of certain dipeptide sequences which correlate well with differences between predicted pI and experimental pI

Explaining the Price of Voluntary Carbon Offsets

This paper investigates factors that explain the large variability in the price of voluntary carbon offsets. We estimate hedonic price functions using a variety of provider- and project-level characteristics as explanatory variables. We find that providers located in Europe sell offsets at prices that are approximately 30 percent higher than providers located in either North America or Australasia. Contrary to what one might expect, offset prices are generally higher, by roughly 20 percent, when projects are located in developing or least-developed nations. But this result does not hold for forestry-based projects. We find evidence that forestry-based offsets sell at lower prices, and the result is particularly strong when projects are located in developing or least-developed nations. Offsets that are certified under the Clean Development Mechanism or the Gold Standard, and therefore qualify for emission reductions under the Kyoto Protocol, sell at a premium of more than 30 percent; however, third-party certification from the Voluntary Carbon Standard, one of the largest certifiers, is associated with a price discount. Variables that have no effect on offset prices are the number of projects that a provider manages and a provider’s status as for-profit or not-for-profit.

STRUCTURAL EVOLUTION OF AFRICAN CICHLID GENOMES

An unanswered question in biology is how the evolution of genome structure supports or accompanies diversification and speciation on different time scales. African cichlid fishes are a well-documented system ideal for studying rapid evolution, due to their phenotypic diversity and high number of speciation events over the last several million years. I generated two de novo genome assemblies of the riverine cichlid Oreochromis niloticus (tilapia) and the Lake Malawi cichlid Metriaclima zebra using high-coverage long-read sequencing data and anchored the assemblies to chromosomes using several genetic and physical maps, to produce two high-quality anchored references. By comparing these chromosome-scale assemblies to integrated recombination, transcriptome, and resequencing data of multiple genera and species, I identified and characterized many large novel genome rearrangement events. These rearrangements included multiple novel sex-determination inversions, several metacentric-acrocentric karyotype differences via centromere assembly and placement, and wide regions of suppressed recombination in genera- and species-level crosses of Lake Malawi cichlids. Karyotype evolution in cichlids was further analyzed with long-read sequencing, specifically revealing the complex structure and content of a highly repetitive supernumerary chromosome present in some but not all individuals of a population across a wide range of eukaryotes, including many cichlid species. These supernumerary "B" chromosomes are shown to be limited to female Lake Malawi cichlids and have a unique evolutionary history with B chromosomes present in Lake Victorian cichlids male and females. This work reveals how structural genomic changes impact a rapidly evolving clade, while providing high-quality resources for the community, a context for previous genetic studies, and a robust platform for future genome research in cichlids

Epidemiology and Impact of Abdominal Oblique Injuries in Major and Minor League Baseball.

BACKGROUND: Oblique injuries are known to be a common cause of time out of play for professional baseball players, and prior work has suggested that injury rates may be on the rise in Major League Baseball (MLB). PURPOSE: To better understand the current incidence of oblique injuries, determine their impact based on time out of play, and to identify common injury patterns that may guide future injury prevention programs. STUDY DESIGN: Descriptive epidemiological study. METHODS: Using the MLB Health and Injury Tracking System, all oblique injuries that resulted in time out of play in MLB and Minor League Baseball (MiLB) during the 2011 to 2015 seasons were identified. Player demographics such as age, position/role, and handedness were included. Injury-specific factors analyzed included the following: date of injury, timing during season, days missed, mechanism, side, treatment, and reinjury status. RESULTS: A total of 996 oblique injuries occurred in 259 (26%) MLB and 737 (74%) MiLB players. Although the injury rate was steady in MiLB, the MLB injury rate declined (P = .037). A total of 22,064 days were missed at a mean rate of 4413 days per season and 22.2 days per injury. The majority of these occurred during batting (n = 455, 46%) or pitching (n = 348, 35%), with pitchers losing 5 days more per injury than batters (P \u3c .001). The leading side was injured in 77% of cases and took 5 days longer to recover from than trailing side injuries (P = .009). Seventy-nine (7.9%) players received either a corticosteroid or platelet-rich plasma injection, and the mean recovery time was 11 days longer compared with those who did not receive an injection (P \u3c .001). CONCLUSION: Although the rate of abdominal oblique injuries is on the decline in MLB, this is not the case for MiLB, and these injuries continue to represent a significant source of time out of play in professional baseball. The vast majority of injuries occur on the lead side, and these injuries result in the greatest amount time out of play. The benefit of injections for the treatment of oblique injuries remains unknown

Comparative analysis of a sex chromosome from the blackchin tilapia, Sarotherodon melanotheron

Background Inversions and other structural polymorphisms often reduce the rate of recombination between sex chromosomes, making it impossible to fine map sex-determination loci using traditional genetic mapping techniques. Here we compare distantly related species of tilapia that each segregate an XY system of sex-determination on linkage group 1. We use whole genome sequencing to identify shared sex-patterned polymorphisms, which are candidates for the ancestral sex-determination mutation. Results We found that Sarotherodon melanotheron segregates an XY system on LG1 in the same region identified in Oreochromis niloticus. Both species have higher densities of sex-patterned SNPs, as well as elevated number of ancestral copy number variants in this region when compared to the rest of the genome, but the pattern of differentiation along LG1 differs between species. The number of sex-patterned SNPs shared by the two species is small, but larger than expected by chance, suggesting that a novel Y-chromosome arose just before the divergence of the two species. We identified a shared sex-patterned SNP that alters a Gata4 binding site near Wilms tumor protein that might be responsible for sex-determination. Conclusions Shared sex-patterned SNPs, insertions and deletions suggest an ancestral sex-determination system that is common to both S. melanotheron and O. niloticus. Functional analyses are needed to evaluate shared SNPs near candidate genes that might play a role in sex-determination of these species. Interspecific variation in the sex chromosomes of tilapia species provides an excellent model system for understanding the evolution of vertebrate sex chromosomes. (Résumé d'auteur

An improved genome reference for the African cichlid, Metriaclima zebra

Funding for Open Access provided by the UMD Libraries Open Access Publishing Fund.Background: Problems associated with using draft genome assemblies are well documented and have become more pronounced with the use of short read data for de novo genome assembly. We set out to improve the draft genome assembly of the African cichlid fish, Metriaclima zebra, using a set of Pacific Biosciences SMRT sequencing reads corresponding to 16.5x coverage of the genome. Here we characterize the improvements that these long reads allowed us to make to the state-of-the-art draft genome previously assembled from short read data. Results: Our new assembly closed 68 % of the existing gaps and added 90.6Mbp of new non-gap sequence to the existing draft assembly of M. zebra. Comparison of the new assembly to the sequence of several bacterial artificial chromosome clones confirmed the accuracy of the new assembly. The closure of sequence gaps revealed thousands of new exons, allowing significant improvement in gene models. We corrected one known misassembly, and identified and fixed other likely misassemblies. 63.5 Mbp (70 %) of the new sequence was classified as repetitive and the new sequence allowed for the assembly of many more transposable elements. Conclusions: Our improvements to the M. zebra draft genome suggest that a reasonable investment in long reads could greatly improve many comparable vertebrate draft genome assemblies.https://doi.org/10.1186/s12864-015-1930-