A Comparative Faunal Analysis of British Military Contexts at Brimstone Hill Fortress, St. Kitts, West Indies

The Caribbean island of St. Kitts was one of the wealthiest colonies in the British Empire during the late 17th through early 19th centuries because of its production and export of sugar. The British sought to defend the island from foreign invaders by building a large military fortification on the island called Brimstone Hill Fortress. Built beginning in 1690, the fort was home to a community of enslaved Africans, British army officers, British Royal Engineers, and enlisted soldiers up until its abandonment in the mid 1800s. To feed such a diverse workforce, the British military utilized imported provisions such as preserved fish and barreled beef and pork in combination with locally available livestock and produce. The diets of those residing at Brimstone Hill varied according to military rank and ethnic origin. Zooarchaeological analysis of faunal assemblages from BSH5 (enlisted men’s occupation) and BSH6 (British military officers) are examined and compared to faunal data already analyzed from enslaved African and British army officers living quarters. The analysis shows differences in the relative proportions of mammals, birds, and fish at each occupation. The enlisted men at BSH5 consumed relatively more fish and beef compared to those residing at BSH6 whose diet consisted mostly of locally raised sheep and goat. Data from skeletal part frequencies and stable carbon isotope analysis reveal that some of the beef consumed at BSH5 was barreled. This comparative analysis aids in the understanding of how the British military chose to provision its diverse population and in doing so further delineated the social ranks within the fortress walls

Genome assembly forensics: finding the elusive mis-assembly

A collection of software tools is combined for the first time in an automated pipeline for detecting large-scale genome assembly errors and for validating genome assemblies

Desformylgramicidin: A Model Channel with an Extremely High Water Permeability

AbstractThe water conductivity of desformylgramicidin exceeds the permeability of gramicidin A by two orders of magnitude. With respect to its single channel hydraulic permeability coefficient of 1.1·10−12cm3s−1, desformylgramicidin may serve as a model for extremely permeable aquaporin water channel proteins (AQP4 and AQPZ). This osmotic permeability exceeds the conductivity that is predicted by the theory of single-file transport. It was derived from the concentration distributions of both pore-impermeable and -permeable cations that were simultaneously measured by double barreled microelectrodes in the immediate vicinity of a planar bilayer. From solvent drag experiments, approximately five water molecules were found to be transported by a single-file process along with one ion through the channel. The single channel proton, potassium, and sodium conductivities were determined to be equal to 17pS (pH 2.5), 7 and 3pS, respectively. Under any conditions, the desformyl-channel remains at least 10 times longer in its open state than gramicidin A

Phytophthora sojae Avirulence Effector Avr3b is a Secreted NADH and ADP-ribose Pyrophosphorylase that Modulates Plant Immunity

Plants have evolved pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI) to protect themselves from infection by diverse pathogens. Avirulence (Avr) effectors that trigger plant ETI as a result of recognition by plant resistance (R) gene products have been identified in many plant pathogenic oomycetes and fungi. However, the virulence functions of oomycete and fungal Avr effectors remain largely unknown. Here, we combined bioinformatics and genetics to identify Avr3b, a new Avr gene from Phytophthora sojae, an oomycete pathogen that causes soybean root rot. Avr3b encodes a secreted protein with the RXLR host-targeting motif and C-terminal W and Nudix hydrolase motifs. Some isolates of P. sojae evade perception by the soybean R gene Rps3b through sequence mutation in Avr3b and lowered transcript accumulation. Transient expression of Avr3b in Nicotiana benthamiana increased susceptibility to P. capsici and P. parasitica, with significantly reduced accumulation of reactive oxygen species (ROS) around invasion sites. Biochemical assays confirmed that Avr3b is an ADP-ribose/NADH pyrophosphorylase, as predicted from the Nudix motif. Deletion of the Nudix motif of Avr3b abolished enzyme activity. Mutation of key residues in Nudix motif significantly impaired Avr3b virulence function but not the avirulence activity. Some Nudix hydrolases act as negative regulators of plant immunity, and thus Avr3b might be delivered into host cells as a Nudix hydrolase to impair host immunity. Avr3b homologues are present in several sequenced Phytophthora genomes, suggesting that Phytophthora pathogens might share similar strategies to suppress plant immunity

Temperature Dependence of Fast and Slow Gating Relaxations of ClC-0 Chloride Channels

The chloride channel from the Torpedo electric organ, ClC-0, is the best studied member of a large gene-family (Jentsch, T.J. 1996. Curr. Opin. Neurobiol. 6:303–310.). We investigate the temperature dependence of both the voltage- and chloride-dependent fast gate and of the slow gate of the “double-barreled” ClC-0 expressed in Xenopus oocytes. Kinetics of the fast gate exhibit only a moderate temperature dependence with a Q10 of 2.2. Steady-state popen of the fast gate is relatively independent of temperature. The slow gate, in contrast, is highly temperature sensitive. Deactivation kinetics at positive voltages are associated with a Q10 of ∼40. Steady-state open probability of the slow gate (popenslow(V)) can be described by a Boltzmann distribution with an apparent gating valence of ≈2 and a variable “offset” at positive voltages. We note a positive correlation of this offset (i.e., the fraction of channels that are not closed by the slow gate) with the amount of expression. This offset is also highly temperature sensitive, being drastically decreased at high temperatures. Paradoxically, the maximum degree of activation of the slow gate also decreases at higher temperatures. The strong temperature dependence of the slow gate was also observed at the single channel level in inside-out patches. The results imply that within a Markovian-type description at least two open and two closed states are needed to describe slow gating. The strong temperature dependence of the slow gate explains the phenotype of several ClC-0 point-mutants described recently by Ludewig et al. (Ludewig, U., T.J. Jentsch, and M. Pusch. 1996. J. Physiol. (Lond.). In press). The large Q10 of slow gating kinetics points to a complex rearrangement. This, together with the correlation of the fraction of noninactivating channels with the amount of expression and the fact that the slow gate closes both protochannels simultaneously suggests that the slow gate is coupled to subunit interaction of the multimeric ClC-0 channel

Pebble and Rock Band: Heuristic Resolution of Repeats and Scaffolding in the Velvet Short-Read de Novo Assembler

BACKGROUND: Despite the short length of their reads, micro-read sequencing technologies have shown their usefulness for de novo sequencing. However, especially in eukaryotic genomes, complex repeat patterns are an obstacle to large assemblies. PRINCIPAL FINDINGS: We present a novel heuristic algorithm, Pebble, which uses paired-end read information to resolve repeats and scaffold contigs to produce large-scale assemblies. In simulations, we can achieve weighted median scaffold lengths (N50) of above 1 Mbp in Bacteria and above 100 kbp in more complex organisms. Using real datasets we obtained a 96 kbp N50 in Pseudomonas syringae and a unique 147 kbp scaffold of a ferret BAC clone. We also present an efficient algorithm called Rock Band for the resolution of repeats in the case of mixed length assemblies, where different sequencing platforms are combined to obtain a cost-effective assembly. CONCLUSIONS: These algorithms extend the utility of short read only assemblies into large complex genomes. They have been implemented and made available within the open-source Velvet short-read de novo assembler

Finding optimal threshold for correction error reads in DNA assembling

Background: DNA assembling is the problem of determining the nucleotide sequence of a genome from its substrings, called reads. In the experiments, there may be some errors on the reads which affect the performance of the DNA assembly algorithms. Existing algorithms, e.g. ECINDEL and SRCorr, correct the error reads by considering the number of times each length-k substring of the reads appear in the input. They treat those length-k substrings appear at least M times as correct substring and correct the error reads based on these substrings. However, since the threshold M is chosen without any solid theoretical analysis, these algorithms cannot guarantee their performances on error correction. Results: In this paper, we propose a method to calculate the probabilities of false positive and false negative when determining whether a length-k substring is correct using threshold M. Based on this optimal threshold M that minimizes the total errors (false positives and false negatives). Experimental results on both real data and simulated data showed that our calculation is correct and we can reduce the total error substrings by 77.6% and 65.1% when compared to ECINDEL and SRCorr respectively. Conclusion: We introduced a method to calculate the probability of false positives and false negatives of the length-k substring using different thresholds. Based on this calculation, we found the optimal threshold to minimize the total error of false positive plus false negative. © 2009 Chin et al; licensee BioMed Central Ltd.published_or_final_versio

De novo finished 2.8 Mbp Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads

Motivation: Paired-end sequencing allows circumventing the shortness of the reads produced by second generation sequencers and is essential for de novo assembly of genomes. However, obtaining a finished genome from short reads is still an open challenge. We present an algorithm that exploits the pairing information issued from inserts of potentially any length. The method determines paths through an overlaps graph by using a constrained search tree. We also present a method that automatically determines suited overlaps cutoffs according to the contextual coverage, reducing thus the need for manual parameterization. Finally, we introduce an interactive mode that allows querying an assembly at targeted regions. Results: We assess our methods by assembling two Staphylococcus aureus strains that were sequenced on the Illumina platform. Using 100 bp paired-end reads and minimal manual curation, we produce a finished genome sequence for the previously undescribed isolate SGH-10-168. Availability and implementation: The presented algorithms are implemented in the standalone Edena software, freely available under the General Public License (GPLv3) at www.genomic.ch/edena.php. Contact: [email protected] Supplementary Information: Supplementary data are available at Bioinformatics onlin

Injectable Materials for the Treatment of Myocardial Infarction and Heart Failure: The Promise of Decellularized Matrices

Cardiovascular disease continues to be the leading cause of death, suggesting that new therapies are needed to treat the progression of heart failure post-myocardial infarction. As cardiac tissue has a limited ability to regenerate itself, experimental biomaterial therapies have focused on the replacement of necrotic cardiomyocytes and repair of the damaged extracellular matrix. While acellular and cellular cardiac patches are applied surgically to the epicardial surface of the heart, injectable materials offer the prospective advantage of minimally invasive delivery directly into the myocardium to either replace the damaged extracellular matrix or to act as a scaffold for cell delivery. Cardiac-specific decellularized matrices offer the further advantage of being biomimetic of the native biochemical and structural matrix composition, as well as the potential to be autologous therapies. This review will focus on the requirements of an ideal scaffold for catheter-based delivery as well as highlight the promise of decellularized matrices as injectable materials for cardiac repair