Arthropod collection for biodiversity prospection in the Guanacaste Conservation Area, Costa Rica

This study describes the results and collection practices for obtaining arthropod samples to be studied as potential sources of new medicines in a bioprospecting effort. From 1994 to 1998, 1800 arthropod samples of 6-10 g were collected in 21 sites of the Area de Conservaci6n Guancaste (A.C.G) in Northwestern Costa Rica. The samples corresponded to 642 species distributed in 21 orders and 95 families. Most of the collections were obtained in the rainy season and in the tropical rainforest and dry forest of the ACG. Samples were obtained from a diversity of arthropod orders: 49.72% of the samples collected corresponded to Lepidoptera, 15.75% to Coleoptera, 13.33% to Hymenoptera, 11.43% to Orthoptera, 6.75% to Hemiptera, 3.20% to Homoptera and 7.89% to other groups. Different life stages per arthropod species were obtained in most samples, 54.26% of them were adults, 19.90% corresponded to larvae, 6.46% to pupae, 6.12% to pre-pupae, 2.07% to nymphs and 3.74% to other stages. Other materials associated to insects like frass represented 11.20% of the samples collected. Several collecting methods were explored, based on the possibility of accessing the necessary amount of material causing the less impact. Most of the samples were obtained by manual collection (44.38%),. followed by insects breeding (25.73%), light traps (18.80%), different types of nets (10.52%) and other methods (0.16%). In general, collecting methods and practices excluded the use of solvents, mixing different species or life stages in the same bag, which might have introduced undesirable effects in the screening systems for new compounds. Based on the possibility of finding new chemicals in similar samples associated to one arthropod species, the collecting strategy included the generation of several samples from same species, separated according to differences in life stages, collecting sites, ecosystems. seasons, feeding materials or behavioral aspects. This strategy allowed the generation a larger number of samples submitted to bioassays in different areas of pharmaceutical research.     

Long-term intake of edible oils benefits blood pressure and myocardial structure in spontaneously hypertensive rat (SHR) and streptozotocin diabetic SHR

The beneficial effects of edible oils long-term supplementation in blood pressure (BP) and cardiac structure were investigated in spontaneously hypertensive rat (SHR) and streptozotocin diabetic (Db) SHR (45 mg/rat i.p.). Twenty-five 12-week old male SHR were divided into four SHR-Db groups and one SHR group, SHR-Db groups each receiving, respectively, olive oil, palm oil and fish oil, and another SHR-Db group with placebo by gavage on a daily basis for 6 weeks. Myocardial structures were analyzed through light microscopy and stereology. In SHR-Db, the BP and the myocardium were significantly altered by oil supplementation. The BP, the interstitial fibrosis and cardiomyocyte size showed a significant decrease in treated SHR-Db than in SHR or untreated SHR-Db. The myocardial microvasculature and number of cardiomyocytes were higher in all treated groups, especially in fish oil group. Long-term edible oil supplementation showed beneficial effects decreasing BP levels and offsetting adverse myocardial remodeling in diabetic SHR.     

GeneCruiser: a web service for the annotation of microarray data

SUMMARY: GeneCruiser is a web service allowing users to annotate their genomic data by mapping microarray feature identifiers to gene identifiers from databases, such as UniGene, while providing links to web resources, such as the UCSC Genome Browser. It relies on a regularly updated database that retrieves and indexes the mappings between microarray probes and genomic databases. Genes are identified using the Life Sciences Identifier standard. AVAILABILITY: GeneCruiser is freely available in the following forms: Web service and Web application, http://www.genecruiser.org; GenePattern, GeneCruiser access has been integrated into our microarray analysis platform, GenePattern. http://www.genepattern.org.     

Melanocortin subtype-4 receptor agonists containing a piperazine core with substituted aryl sulfonamides

The biological activity for a set of melanocortin-4 receptor (MC4R) agonists containing a piperazine core with an ortho-substituted aryl sulfonamide is described. Compounds from this set had binding and functional activities at MC4R less than 30 nM. The most selective compound in this series was >25,000-fold more potent at MC4R than MC3R, and 490-fold more potent at MC4R than MC5R. This compound also reduced food intake after oral dosing at 25, 50, and 100 mg kg(-1) in fasted mice.     

Molecular classification of multiple tumor types

Using gene expression data to classify tumor types is a very promising tool in cancer diagnosis. Previous works show several pairs of tumor types can be successfully distinguished by their gene expression patterns (Golub et al. 1999, Ben-Dor et al. 2000, Alizadeh et al. 2000). However, the simultaneous classification across a heterogeneous set of tumor types has not been well studied yet. We obtained 190 samples from 14 tumor classes and generated a combined expression dataset containing 16063 genes for each of those samples. We performed multi-class classification by combining the outputs of binary classifiers. Three binary classifiers (k-nearest neighbors, weighted voting, and support vector machines) were applied in conjunction with three combination scenarios (one-vs-all, all-pairs, hierarchical partitioning). We achieved the best cross validation error rate of 18.75% and the best test error rate of 21.74% by using the one-vs-all support vector machine algorithm. The results demonstrate the feasibility of performing clinically useful classification from samples of multiple tumor types.     

Differences in the Clinical Outcome of Osteomyelitis by Treating Specialty: Orthopedics or Infectology

Osteomyelitis is a heterogeneous infection with regard to etiology and treatment, and currently no single management protocol exists. Management of the condition is typically an interdisciplinary approach between orthopedics and infectious disease; however, the orthopedist is often the person who manages treatment. The aim of the study was to determine differences in the outcome of osteomyelitis according to its treating specialty and to identify factors associated with the recurrence of the disease. An ambispective cohort study of 129 patients with osteomyelitis was conducted and the proportions for qualitative variables and central tendency and dispersion measures for quantitative variables were calculated; the latter were tested for normality using the Shapiro-Wilk test. A bivariate analysis was conducted with measures of association based on the chi square test and crude relative risk. A logistic regression model was applied and statistical significance was set at p < 0.05, including the model of relevant clinical variables that fit the Hosmer-Lemeshow test. We found that 70% of patients were treated either by orthopedics or infectious disease. Patients who were treated by an orthopedist alone presented a greater risk of relapse or reinfection (RR = 4.6; 95% CI 2.3;8.9). Risk factors of osteomyelitis recurrence as determined in the regression model included the following: age of 57 years or older (RR = 1.3; 95% 0.3;5.2), long bones (RR = 1.9; 95% CI 0.5;7.1), fracture (RR = 5.0; 95% CI 0.4;51.4), monotherapy (RR = 3.0; 95% CI 0.6;14.5), receiving less than 4 weeks of antibiotics (RR = 1.5; 95% CI 0.2;10.1), inadequate treatment (RR = 3.1; 95% CI 0.4;20.1), and receiving orthopedics treatment (RR = 5.5; 95% CI 1.6;18.2). Most patients evaluated jointly by orthopedics and infectious disease received adequate treatment for osteomyelitis and had fewer relapses.     

GRP78(BiP) facilitates the cytosolic delivery of anthrax lethal factor (LF) in vivo and functions as an unfoldase in vitro

Anthrax toxin is an A/B bacterial protein toxin which is composed of the enzymatically active Lethal Factor (LF) and/or Oedema Factor (EF) bound to Protective Antigen 63 (PA63) which functions as both the receptor binding and transmembrane domains. Once the toxin binds to its cell surface receptors it is internalized into the cell and traffics through Rab5- and Rab7-associated endosomal vesicles. Following acidification of the vesicle lumen, PA63 undergoes a dynamic change forming a beta-barrel that inserts into and forms a pore through the endosomal membrane. It is widely recognized that LF, and the related fusion protein LFnDTA, must be completely denatured in order to transit through the PA63 formed pore and enter the eukaryotic cell cytosol. We demonstrate by protease protection assays that the molecular chaperone GRP78 mediates the unfolding of LFnDTA and LF at neutral pH and thereby converts these proteins from a trypsin resistant to sensitive conformation. We have used immunoelectron microscopy and gold-labelled antibodies to demonstrate that both GRP78 and GRP94 chaperones are present in the lumen of endosomal vesicles. Finally, we have used siRNA to demonstrate that knock-down of GRP78 results in the emergence of resistance to anthrax lethal toxin and oedema toxin action.     

The structural basis of cyclic diguanylate signal transduction by PilZ domains

The second messenger cyclic diguanylate (c-di-GMP) controls the transition between motile and sessile growth in eubacteria, but little is known about the proteins that sense its concentration. Bioinformatics analyses suggested that PilZ domains bind c-di-GMP and allosterically modulate effector pathways. We have determined a 1.9 A crystal structure of c-di-GMP bound to VCA0042/PlzD, a PilZ domain-containing protein from Vibrio cholerae. Either this protein or another specific PilZ domain-containing protein is required for V. cholerae to efficiently infect mice. VCA0042/PlzD comprises a C-terminal PilZ domain plus an N-terminal domain with a similar beta-barrel fold. C-di-GMP contacts seven of the nine strongly conserved residues in the PilZ domain, including three in a seven-residue long N-terminal loop that undergoes a conformational switch as it wraps around c-di-GMP. This switch brings the PilZ domain into close apposition with the N-terminal domain, forming a new allosteric interaction surface that spans these domains and the c-di-GMP at their interface. The very small size of the N-terminal conformational switch is likely to explain the facile evolutionary diversification of the PilZ domain.