Isocitrate dehydrogenase 1 R132C mutation occurs exclusively in microsatellite stable colorectal cancers with the CpG island methylator phenotype

The CpG Island Methylator Phenotype (CIMP) is fundamental to an important subset of colorectal cancer; however, its cause is unknown. CIMP is associated with microsatellite instability but is also found in BRAF mutant microsatellite stable cancers that are associated with poor prognosis. The isocitrate dehydrogenase 1 (IDH1) gene causes CIMP in glioma due to an activating mutation that produces the 2-hydroxyglutarate oncometabolite. We therefore examined IDH1 alteration as a potential cause of CIMP in colorectal cancer. The IDH1 mutational hotspot was screened in 86 CIMP-positive and 80 CIMP-negative cancers. The entire coding sequence was examined in 81 CIMP-positive colorectal cancers. Forty-seven cancers varying by CIMP-status and IDH1 mutation status were examined using Illumina 450K DNA methylation microarrays. The R132C IDH1 mutation was detected in 4/166 cancers. All IDH1 mutations were in CIMP cancers that were BRAF mutant and microsatellite stable (4/45, 8.9%). Unsupervised hierarchical cluster analysis identified an IDH1 mutation-like methylation signature in approximately half of the CIMP-positive cancers. IDH1 mutation appears to cause CIMP in a small proportion of BRAF mutant, microsatellite stable colorectal cancers. This study provides a precedent that a single gene mutation may cause CIMP in colorectal cancer, and that this will be associated with a specific epigenetic signature and clinicopathological features.     

Mathematical and computational modeling in biology at multiple scales

A variety of topics are reviewed in the area of mathematical and computational modeling in biology, covering the range of scales from populations of organisms to electrons in atoms. The use of maximum entropy as an inference tool in the fields of biology and drug discovery is discussed. Mathematical and computational methods and models in the areas of epidemiology, cell physiology and cancer are surveyed. The technique of molecular dynamics is covered, with special attention to force fields for protein simulations and methods for the calculation of solvation free energies. The utility of quantum mechanical methods in biophysical and biochemical modeling is explored. The field of computational enzymology is examined.     

Comparative tests of ectoparasite species richness in seabirds

Background  

The diversity of parasites attacking a host varies substantially among different host species. Understanding the factors that explain these patterns of parasite diversity is critical to identifying the ecological principles underlying biodiversity. Seabirds (Charadriiformes, Pelecaniformes and Procellariiformes) and their ectoparasitic lice (Insecta: Phthiraptera) are ideal model groups in which to study correlates of parasite species richness. We evaluated the relative importance of morphological (body size, body weight, wingspan, bill length), life-history (longevity, clutch size), ecological (population size, geographical range) and behavioural (diving versus non-diving) variables as predictors of louse diversity on 413 seabird hosts species. Diversity was measured at the level of louse suborder, genus, and species, and uneven sampling of hosts was controlled for using literature citations as a proxy for sampling effort.     

Antiprotozoal and cysteine proteases inhibitory activity of dipeptidyl enoates

A family of dipeptidyl enoates has been prepared and tested against the parasitic cysteine proteases rhodesain, cruzain and falcipain-2 related to sleeping sickness, Chagas disease and malaria, respectively. They have also been tested against human cathepsins B and L1 for selectivity. Dipeptidyl enoates resulted to be irreversible inhibitors of these enzymes. Some of the members of the family are very potent inhibitors of parasitic cysteine proteases displaying k_2nd (M^?1s^?1) values of seven orders of magnitude. In vivo antiprotozoal testing was also performed. Inhibitors exhibited IC₅₀ values in the micromolar range against Plasmodium falciparum, Trypanosoma brucei, Trypanosoma cruzi and even more promising lower values against Leishmania donovanii.     

A New Glucose-6-Phosphate Dehydrogenase Variant, G6PD Orissa (44 Ala→Gly), is the Major Polymorphic Variant in Tribal Populations in India

Deficiency of glucose-6-phosphate dehydrogenase (G6PD) is usually found at high frequencies in areas of the world where malaria has been endemic. The frequency and genetic basis of G6PD deficiency have been studied in Africa, around the Mediterranean, and in the Far East, but little such information is available about the situation in India. To determine the extent of heterogeneity of G6PD, we have studied several different Indian populations by screening for G6PD deficiency, followed by molecular analysis of deficient alleles. The frequency of G6PD deficiency varies between 3% and 15% in different tribal and urban groups. Remarkably, a previously unreported deficient variant, G6PD Orissa (44 Ala→Gly), is responsible for most of the G6PD deficiency in tribal Indian populations but is not found in urban populations, where most of the G6PD deficiency is due to the G6PD Mediterranean (188 Ser→Phe) variant. The K of G6PD Orissa is fivefold higher than that of the normal enzyme. This may be due to the fact that the alanine residue that is replaced by glycine is part of a putative coenzyme-binding site.     

Effect of insectary rearing on host preference and oviposition behavior of the fruit fly parasitoid Diachasmimorpha longicaudata

Diachasmimorpha longicaudata (Ashmead) has been produced in the laboratory for >160 generations on the larvae of oriental fruit fly, Bactrocera dorsalis (Hendel), the propagation hosts raised routinely on a semi-synthetic wheat diet formulation. Choice tests using modified stinging units were conducted in the laboratory to investigate whether insectary rearing had altered the host seeking and oviposition behavior of female parasitoids. Results showed that fruit fly larvae that developed in papaya, Carica papaya L. var. solo, were less preferred for oviposition than fruit fly larvae that developed on wheat diet when both were exposed concurrently to naive D. longicaudata females (= females without prior oviposition experience). The substrates (pureed papaya or wheat diet) in which treatment larvae were exposed to parasitoids did not affect oviposition preference of gravid D. longicaudata for wheat diet-reared fruit fly larvae. Our study demonstrated the possibility that rearing in an insectary system may have modified the parasitization behavior of female D. longicaudata.     

SEXUAL REPRODUCTION AND GENETIC VARIATION IN THE SUBAERIAL ALGA CEPHALEUROS VIRESCENS (ULVOPHYCEAE,CHLOROPHYTA)

Cephaleuros virescens is a pantropical subaerial green alga with no known long‐range dispersal mechanisms. Sexual reproduction is relatively rare and may involve intragametangial fusion of identical, mitotically produced gametes. This situation may be a consequence of adaptation to the subaerial habitat. Genetic variation among populations of C. virescens may be very low and might be positively correlated to the distance (hence, time) separating populations. Thus, assessing the global biogeography of C. virescens requires analysis of what might be low levels of variation. Because C. virescens occurs on literally hundreds of different host species, the question of host‐races must also be considered. Preliminary analysis of local populations of C. virescens, originally obtained as field collections from three different host species and subsequently raised in culture, is the first step in addressing the biogeography of this alga. We are using the AFLP plant mapping protocol by PE Applied Biosystems to detect genetic variability in the three isolates of C. virescens. AFLP is a PCR‐based DNA fingerprinting technique that detects the presence or absence of restriction fragments rather than fragment length differences. Because the number of restriction fragments that can be detected with the AFLP technique is “virtually unlimited,” it is a very powerful tool for assessing the degree of relatedness or variability among cultivars or isolates. AFLP techniques have been used successfully to distinguish morphologically identical bacteria, determine relatedness among soybean accessions, reveal genetic variability within bee samples, and identifyfall armyworm strains and hybrids.