A novel scheme to assess factors involved in the reproducibility of DNA-microarray data

Background  

In research laboratories using DNA-microarrays, usually a number of researchers perform experiments, each generating possible sources of error. There is a need for a quick and robust method to assess data quality and sources of errors in DNA-microarray experiments. To this end, a novel and cost-effective validation scheme was devised, implemented, and employed.     

The surface-mosaic model in host-parasite relationships

The dynamics of protein adsorption to a microbial surface could be of significance in host-parasite relationships because non-defense proteins might interfere with the binding of defense proteins. A surface mosaic of defense and non-defense proteins formed on the microbial surface could activate one of the tissue reactivity programs via a binary code (help or silence) generated by the adsorbed proteins. Understanding the mechanisms of the mosaic formation and its evolution might help to identify evasion mechanisms used by virulent microorganisms. This also provides a conceptual framework to design new strategies to control the infectious diseases they cause.     

Synthesis and biological evaluation of aryl azide derivatives of combretastatin A-4 as molecular probes for tubulin

Two new aryl azides, (Z)-1-(3'-azido-4'-methoxyphenyl)-2-(3",4",5"-trimethoxyphenyl)ethene 9 and (Z)-1-(4'-azido-3'-methoxyphenyl)-2-(3",4",5"-trimethoxyphenyl)ethene 5, modeled after the potent antitumor, antimitotic agent combretastatin A-4 (CA-4), have been prepared by chemical synthesis as potentially useful photoaffinity labeling reagents for the colchicine site on beta-tubulin. Aryl azide 9, in which the 3'-hydroxyl group of CA-4 is replaced by an azido moiety, demonstrates excellent in vitro cytotoxicity against human cancer cell lines (NCI 60 cell line panel, average GI50 = 4.07 x 10(-8) M) and potent inhibition of tubulin polymerization (IC50 = 1.4+/-0.1 microM). The 4'-azido analogue 5 has lower activity (NCI 60 cell line panel, average GI50 = 2.28 x 10(-6) M, and IC50 = 5.2+/-0.2 microM for inhibition of tubulin polymerization), suggesting the importance of the 4'-methoxy moiety for interaction with the colchicine binding site on tubulin. These CA-4 aryl azide analogues also inhibit binding of colchicine to tubulin, as does the parent CA-4, and therefore these compounds are excellent candidates for photoaffinity labeling studies.     

Prevalence and Intensity of Soil-Transmitted Helminthiasis,Prevalence of Malaria and Nutritional Status of School Going Children in Honduras

Background

Many small studies have been done in Honduras estimating soil-transmitted helminthiasis (STH) prevalence but a country-wide study was last done in 2005. The country has the highest burden of malaria among all Central American countries. The present study was done to estimate country-wide STH prevalence and intensity, malaria prevalence and nutritional status in school going children.

Methods and Findings

A cross-sectional study was conducted following PAHO/WHO guidelines to select a sample of school going children of 3^rd to 5^th grades, representative of ecological regions in the country. A survey questionnaire was filled; anthropometric measurements, stool sample for STH and blood sample for malaria were taken. Kato-Katz method was used for STH prevalence and intensity and rapid diagnostic tests, microscopy, and polymerase chain reaction (PCR) were used for malaria parasite detection. A total of 2554 students were studied of which 43.5% had one or more STH. Trichuriasis was the most prevalent (34%) followed by ascariasis (22.3%) and hookworm (0.9%). Ecological regions II (59.7%) and VI (55.6%) in the north had the highest STH prevalence rates while IV had the lowest (10.6%). Prevalence of one or more high intensity STH was low (1.6%). Plasmodium vivax was detected by PCR in only 5 students (0.2%), all of which belonged to the same municipality; no P. falciparum infection was detected. The majority of children (83%) had normal body mass index for their respective age but a significant proportion were overweight (10.42%) and obese (4.35%).

Conclusions

Biannual deworming campaigns would be necessary in ecological regions II and VI, where STH prevalence is >50%. High prevalence of obesity in school going children is a worrying trend and portends of future increase in obesity related diseases. Malaria prevalence, both symptomatic and asymptomatic, was low and provides evidence for Honduras to embark on elimination of the disease.     

Phylogenetic Relationships Among JC Virus Strains in Japanese/Koreans and Native Americans Speaking Amerind or Na-Dene

Abstract Many genetic studies using human mtDNA or the Y chromosome have been conducted to elucidate the relationships among the three Native American groups speaking Amerind, Na-Dene, and Eskimo-Aleut. Human polyomavirus JC (JCV) may also help to gain insights into this issue. JCV isolates are classified into more than 10 geographically distinct genotypes (designated subtypes here), which were generated by splits in the three superclusters, Types A, B, and C. A particular subtype of JCV (named MY) belonging to Type B is spread in both Japanese/Koreans and Native Americans speaking Amerind or Na-Dene. In this study, we evaluated the phylogenetic relationships among MY isolates worldwide, using the whole-genome approach, with which a highly reliable phylogeny of JCV isolates can be reconstructed. Thirty-six complete sequences belonging to MY (10 from Japanese/Koreans, 24 from Native Americans, and 2 from others), together with 54 belonging to other subtypes around the world, were aligned and subjected to phylogenetic analysis using the neighbor-joining and maximum-likelihood methods. In the resultant phylogenetic trees, the MY sequences diverged into two Japanese/Korean and five Native American clades with high bootstrap probabilities. Two of the Native American clades contained isolates mainly from Na-Denes and the others contained isolates mainly from Amerinds. The Na-Dene clades were not clustered together, nor were the Amerind clades. In contrast, the two Japanese/Korean clades were clustered at a high bootstrap probability. We concluded that there is no distinction between Amerinds and Na-Denes in terms of indigenous JCVs, although they are linguistically distinguished from each other.