Biomedical cloud computing with Amazon Web Services

In this overview to biomedical computing in the cloud, we discussed two primary ways to use the cloud (a single instance or cluster), provided a detailed example using NGS mapping, and highlighted the associated costs. While many users new to the cloud may assume that entry is as straightforward as uploading an application and selecting an instance type and storage options, we illustrated that there is substantial up-front effort required before an application can make full use of the cloud's vast resources. Our intention was to provide a set of best practices and to illustrate how those apply to a typical application pipeline for biomedical informatics, but also general enough for extrapolation to other types of computational problems. Our mapping example was intended to illustrate how to develop a scalable project and not to compare and contrast alignment algorithms for read mapping and genome assembly. Indeed, with a newer aligner such as Bowtie, it is possible to map the entire African genome using one m2.2xlarge instance in 48 hours for a total cost of approximately $48 in computation time. In our example, we were not concerned with data transfer rates, which are heavily influenced by the amount of available bandwidth, connection latency, and network availability. When transferring large amounts of data to the cloud, bandwidth limitations can be a major bottleneck, and in some cases it is more efficient to simply mail a storage device containing the data to AWS (http://aws.amazon.com/importexport/). More information about cloud computing, detailed cost analysis, and security can be found in references.     

Phylogenetic constraints on digesta separation: Variation in fluid throughput in the digestive tract in mammalian herbivores

The relevance of the mean retention time (MRT) of particles through the gastrointestinal tract (GIT) is well understood and MRT(particle)GIT is an important parameter in digestion models. Solute markers have been used to estimate MRT(solute)GIT (or 'fluid passage') in animals, but the relevance of this measure is less evident and is usually sought in its relation to MRT(particle)GIT. The ratio between the two measures indicates the degree of 'digesta washing', with little washing occurring at ratios of 1, aborad washing at ratios >1 (where the solute marker travels faster than the particle marker), and orad (retrograde) washing at ratios <1 (where the solute marker travels slower than the particle marker). We analysed digesta washing in a dataset of 98 mammalian species including man of different digestion types (caecum, colon and nonruminant foregut fermenters, and ruminants), controlling for phylogeny; a subset of 72 species allowed testing for the influence of food intake level. The results indicate that MRT(solute)GIT and the degree of digesta washing are related to digestion type, whereas variation in MRT(particle)GIT is influenced mainly by effects of body mass and food intake. Thus, fluid throughput and digesta washing emerge as important correlates of digestive anatomy. Most importantly, primates appear constrained to little digesta washing compared to non-primate mammalian herbivores, regardless of their digestion type. These results may help explain the absence of primates from certain herbivore niches and represent a drastic example of a physiologic limitation in a phylogenetic group. More experimental research is required to illuminate relative benefits and costs of digesta washing.     

Urinary thromboxane B2 and thromboxane receptors in bladder cancer: opportunity for detection and monitoring

We have previously found increased expression of thromboxane synthase (TXAS) and thromboxane receptor (TP) beta isoform in the tissues of patients with bladder cancer. Studies in cell lines and mice have indicated a potential significant role of the thromboxane signaling pathway in the pathogenesis of human bladder cancer. This study was designed to determine if the changes observed in the tissues of patients with bladder cancer were mirrored by changes in the urine of these patients. We found increased levels of thromboxane B(2) (TXB(2)) the major metabolite of TXAS and increased levels of the TPβ receptor. These results raised the possibility that patients with bladder cancer may be followed for progression or remission of their disease by quantitation of these substances in their urine.     

Resistance training vs. static stretching: effects on flexibility and strength

Morton, SK, Whitehead, JR, Brinkert, RH, and Caine, DJ. Resistance training vs. static stretching: Effects on flexibility and strength. J Strength Cond Res 25(12): 3391-3398, 2011-The purpose of this study was to determine how full-range resistance training (RT) affected flexibility and strength compared to static stretching (SS) of the same muscle-joint complexes in untrained adults. Volunteers (n = 25) were randomized to an RT or SS training group. A group of inactive volunteers (n = 12) served as a convenience control group (CON). After pretesting hamstring extension, hip flexion and extension, shoulder extension flexibility, and peak torque of quadriceps and hamstring muscles, subjects completed 5-week SS or RT treatments in which the aim was to stretch or to strength train the same muscle-joint complexes over similar movements and ranges. Posttests of flexibility and strength were then conducted. There was no difference in hamstring flexibility, hip flexion, and hip extension improvement between RT and SS, but both were superior to CON values. There were no differences between groups on shoulder extension flexibility. The RT group was superior to the CON in knee extension peak torque, but there were no differences between groups on knee flexion peak torque. The results of this preliminary study suggest that carefully constructed full-range RT regimens can improve flexibility as well as the typical SS regimens employed in conditioning programs. Because of the potential practical significance of these results to strength and conditioning programs, further studies using true experimental designs, larger sample sizes, and longer training durations should be conducted with the aim of confirming or disproving these results.     

The effects of chronic betaine supplementation on exercise performance, skeletal muscle oxygen saturation and associated biochemical parameters in resistance trained men

Trepanowski, JF, Farney, TM, McCarthy, CG, Schilling, BK, Craig, SA, and Bloomer, RJ. The effects of chronic betaine supplementation on exercise performance, skeletal muscle oxygen saturation, and associated biochemical parameters in resistance trained men. J Strength Cond Res 25(12): 3461-3471, 2011-We examined the effects of chronic betaine supplementation on exercise performance and associated parameters in resistance trained men. Men were randomly assigned in a double-blind manner using a crossover design to consume betaine (2.5 g of betaine mixed in 500 ml of Gatorade?) or a placebo (500 ml of Gatorade?) for 14 days, with a 21-day washout period. Before and after each treatment period, tests of lower- and upper-body muscular power and isometric force were conducted, including a test of upper-body muscular endurance (10 sets of bench press exercise to failure). Muscle tissue oxygen saturation (StO2) during the bench press protocol was measured via near infrared spectroscopy. Blood samples were collected before and after the exercise test protocol for analysis of lactate, nitrate/nitrite (NOx), and malondialdehyde (MDA). When analyzed using a repeated measures analysis of variance, no significant differences were noted between conditions for exercise performance variables (p > 0.05). However, an increase in total repetitions (p = 0.01) and total volume load (p = 0.02) in the 10-set bench press protocol was noted with betaine supplementation (paired t-tests), with values increasing approximately 6.5% from preintervention to postintervention. Although not of statistical significance (p = 0.14), postexercise blood lactate increased to a lesser extent with betaine supplementation (210%) compared with placebo administration (270%). NOx was lower postintervention as compared with preintervention (p = 0.06), and MDA was relatively unchanged. The decrease in StO2 during the bench press protocol was greater with betaine vs. placebo (p = 0.01), possibly suggesting enhanced muscle oxygen consumption. These findings indicate that betaine supplementation results in a moderate increase in total repetitions and volume load in the bench press exercise, without favorably impacting other performance measures.     

The dual-activity insecticidal protein,Cry2Aa,does not enhance the mosquitocidal activity of Bacillus thuringiensis subsp. israelensis

Cry2Aa, one of the major insecticidal proteins produced by Bacillus thuringiensis subsp. kurstaki HD1, is known to be active against both lepidopteran and dipteran larvae. In order to determine whether Cry2Aa could enhance or synergize the mosquitocidal activity of B. thuringiensis subsp. israelensis, we constructed a plasmid vector that harbored the cry2Aa operon and transformed crystalliferous and acrystalliferous strains of this bacterium. The wild-type B. thuringiensis subsp. israelensis, a recombinant B. thuringiensis subsp. israelensis producing Cry2A along with its native major mosquitocidal proteins, and a recombinant B. thuringiensis subsp. israelensis producing Cry2Aa alone were tested against three major mosquito species — Aedes aegypti, Anopheles gambiae and Culex quinquefasciatus. Our results demonstrated that Cry2Aa does not synergize or enhance the mosquitocidal activity of B. thuringiensis subsp. israelensis against these important vectors of disease.     

Morphological plasticity promotes resistance to phagocyte killing of uropathogenic Escherichia coli

Uropathogenic Escherichia coli proceed through a complex intracellular developmental pathway that includes multiple morphological changes. During intracellular growth within Toll-like receptor 4-activated superficial bladder epithelial cells, a subpopulation of uropathogenic E. coli initiates SulA-mediated filamentation. In this study, we directly investigated the role of bacterial morphology in the survival of uropathogenic E. coli from killing by phagocytes. We initially determined that both polymorphonuclear neutrophils and macrophages are recruited to murine bladder epithelium at times coincident with extracellular bacillary and filamentous uropathogenic E. coli. We further determined that bacillary uropathogenic E. coli were preferentially destroyed when mixed uropathogenic E. coli populations were challenged with cultured murine macrophages in vitro. Consistent with studies using elliptical-shaped polymers, the initial point of contact between the phagocyte and filamentous uropathogenic E. coli influenced the efficacy of internalization. These findings demonstrate that filamentous morphology provides a selective advantage for uropathogenic E. coli evasion of killing by phagocytes and defines a mechanism for the essential role for SulA during bacterial cystitis. Thus, morphological plasticity can be viewed as a distinct class of mechanism used by bacterial pathogens to subvert host immunity.     

Land-use,environment, and their impact on butterfly populations in a mountainous pastoral landscape: species richness and family-level abundance

Extensive grasslands are considered to be of high biodiversity value, but are under threat from intensification and abandonment. We studied butterfly species richness and abundance in 47 hay and grazing meadows in the Picos de Europa, northern Spain in 2004. Nine transects were walked around the perimeter of the meadows from the 1 June to 28 July with butterflies recorded to species or species-group. Land-use, abiotic, and sward variables were also recorded. Change in meadow extent was estimated by comparing a digital map of open meadows with a cadastral map with 1950s provenance. We found: A decrease in open area, mostly attributable to reduction in grazing meadows. 75 or more butterfly species with species richness principally, and positively, influenced by altitude and presence of scrub in the body of the meadow. Hay meadow management was a positive influence on richness of satyrids. When all butterflies were considered together, the only significant factor influencing abundance was Plantago lanceolata (−ve). For sub-groups of the butterfly community there was no consistent pattern, although P. lanceolata was identified as a (−ve) factor in relation to hesperiid, nymphalid, satyrid, and Viola-feeding fritillary groups. Several regression models included components that could be linked to abiotic influences (water, aspect, altitude) but many were indicative of abandonment or relaxation of management intensity (scrub, Pteridium aquilinum, Asphodelus albus), sward components, fragmentation (distance to nearest meadow, number of meadows within 100 m), and land use (hay management, summer grazing). The results are discussed in relation to changing socio-economics, including the potential impact of tourism, and the need for financial instruments to support extensive farming.