pp-Blast: a "pseudo-parallel" Blast

We have developed a software called pp-Blast that uses the publicly available Blast package and PVM (parallel virtual machine) to partition a multi-sequence query across a set of nodes with replicated or shared databases. Benchmark tests show that pp-Blast running in a cluster of 14 PCs outperformed conventional Blast running in large servers. In addition, using pp-Blast and the cluster we were able to map all human cDNAs onto the draft of the human genome in less than 6 days. We propose here that the cost/benefit ratio of pp-Blast makes it appropriate for large-scale sequence analysis. The source code and configuration files for pp-Blast are available at http://www.ludwig.org.br/biocomp/tools/pp-blast.

Realidade virtual e robótica em cirurgia: aonde chegamos e para onde vamos?

Minimally Invasive Surgery, Telesurgery, Robotics and Virtual Reality represent the technological frontiers that have revolutionized operating practices nowadays. These new technologies aim at improving the quality of assistance offered to patients; thus, they demand from the medical staff more effective measures as far as scientific research, training and expenditure of time and financial resources are concerned. In the past, surgeons have led several medical revolutions, such as the use of antiseptic surgical methods by Semelweiss, the use of anesthesia by Warren, antibiotic therapy, the transplants and the onset of the minimally invasive surgery by Mouret and Perissat. The objective of this article is to present the outreach of this new technology which comprises minimal access, computing, robotics and teletransmission. We have concluded that the new technologies developed in the medical field in the last decades, will offer new options and challenges for the treatment of the surgical patient, leading the scientific knowledge to a new era, the one of the virtual environment.

Spatial variation in the structure and floristic composition of "restinga" vegetation in southeastern Brazil

We examined large-scale spatial variation of structural parameters and floristic composition in open Clusia scrub, a vegetation type of the Brazilian "restingas" (sandy coastal plain vegetation). This vegetation is organized in islands separated by sandy stretches with sparse herbaceous vegetation. We located 12 sample areas on three consecutive beach ridges, lying parallel to the coastline and at different distances from the ocean, in close proximity to two lagoons (Cabiúnas and Comprida). Each sample area was divided into three strips. We used the line intercept method to sample all woody plants ³ 50 cm tall. We used nested ANOVA to verify structural variation between different sampling scales. TWINSPAN analysis was performed to examine the variation in floristic composition between areas. The overall diversity index was 3.07. Six species are repeatedly dominant throughout the entire sampling area. There was homogeneity in relation to diversity and species richness between beach ridges but not within beach ridges. Floristic composition and structural parameters did not vary in relation to distance from the sea but floristic composition did vary as a function of proximity to Cabiúnas or Comprida lagoon. Differences in plant cover between sample areas may be related to the paleoformation of this sandy coastal plain.

Effect of a leucine-supplemented diet on body composition changes in pregnant rats bearing Walker 256 tumor

Cancer patients present high mobilization of host protein, with a decrease in lean body mass and body fat depletion occurring in parallel to neoplastic growth. Since leucine is one of the principal amino acids used by skeletal muscle for energy, we investigated the changes in body composition of pregnant tumor-bearing rats after a leucine-supplemented diet. Sixty pregnant Wistar rats divided into six groups were fed a normal protein diet (18%, N) or a leucine-supplemented diet (3% L-leucine, L). The pregnant groups were: control (CN), Walker 256 carcinoma-bearing rats (WN), control rats pair-fed with tumor-bearing rats (pfN), leucine-supplemented (CL), leucine-supplemented tumor-bearing (WL), and leucine-supplemented rats pair-fed with tumor-bearing rats (pfL). At the end of pregnancy, all animals were sacrificed and body weight and tumor and fetal weight were determined. The carcasses were then analyzed for water, fat and total, collagen and non-collagen nitrogen content. Carcass weight was reduced in the WN, WL, pfN and pfL groups compared to control. The lean body mass and total carcass nitrogen were reduced in both tumor-bearing groups. Despite tumor growth and a decrease in fetal weight, there was a slight decrease in collagen (7%) and non-collagen nitrogen (8%) in the WL group compared with the WN group which showed a decrease of 8 and 12%, respectively. Although the WL group presented severe tumor growth effects, total carcass nitrogen and non-collagen nitrogen were particularly higher in this leucine-supplemented group compared to the WN group. These data suggest that the leucine-supplemented diet had a beneficial effect, probably attenuating body wasting.