Atlas – a data warehouse for integrative bioinformatics

Background  

We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development.     

Occurrence of oestrogenic pollutants and widespread feminisation of male tilapia in peri-urban dams in Bulawayo,Zimbabwe

Peri-urban water bodies are at risk from excessive pollution as they are direct sinks for urban effluents. The occurrence of oestrogenic and androgenic endocrine disrupting chemicals (EDCs) in effluents and water bodies around the city of Bulawayo, Zimbabwe, and their effects on wild fish was investigated in 2013. Effluent and water were sampled from sewage treatment plants, an urban stream, and effluent-polluted dams, and were compared with a ‘pristine’ dam upstream of Bulawayo. Organic pollutants were extracted by solid-phase extraction and tested for EDCs using a yeast oestrogen/androgen screen. Oestrogenic and androgenic potencies were expressed as 17β-oestradiol equivalent (EEq) or dihydrotestosterone equivalent (TEq). Tilapia and catfish from the dams were analysed for gonado-somatic indices and testis histopathology. Effluents from STPs, which directly flow into Umguza Dam, had EEq of 33 ng l^?1 and 55 ng l^?1, respectively. Umguza Dam, Khami Dam and Matsheumhlope Stream had EEqs of 237 ng l^–1, 9 ng l^?1 and 2 ng l^?1, respectively. Androgenic activity was detected in only one STP (TEq = 93 ng l^?1). Tilapia sampled from effluent-polluted dams had high incidences of testis-ova, but catfish had no signs of reproductive dysfunction. These findings underscore the need for greater attention to EDCs in developing countries where there is scant literature regarding their occurrence and impacts.     

A comparative map of bovine chromosome 19 based on a combination of mapping on a bacterial artificial chromosome scaffold map, a whole genome radiation hybrid panel and the human draft sequence

We have constructed a medium density physical map of bovine chromosome 19 using a combination of mapping loci on both a bovine bacterial artificial chromosome (BAC) scaffold map and a whole genome radiation hybrid (WGRH) panel. The resulting map contains 70 loci spanning the length of bovine chromosome 19. Three contiguous groups of BACs were identified on the basis of multiple loci mapping to individual BAC clones. Bovine chromosome 19 was found in this study to be comprised almost entirely from regions of human chromosome 17, with a small region putatively assigned to human chromosome 10. Fourteen breakpoints between the bovine and human chromosomes were detected, with a possibility of five more based on ordering of the WGRH map.     

The Interaction of Genetic and Environmental Factors in the Control of Amylase Gene Expression in DROSOPHILA MELANOGASTER

A number of previous studies have established that amylase activity can vary between Drosophila strains which are maintained under identical laboratory conditions. In addition, we have recently shown that all strains examined so far are subject to glucose repression of amylase activity. In this study, we show that the degree of glucose repression can vary between strains. Moreover, the glucose repression effect is much more pronounced in larvae than in adult flies. Our results lead to the conclusion that the strain-specific differences in activity and the dietary effects are not independent phenomena. These results have implications for the interpretation of many studies on amylase activity variation, including those experiments which have been designed to link amylase activity variations with fitness differences in nature. A question that naturally arises concerns the molecular basis for these strain-specific variations in the degree of glucose repression of this eukaryotic gene.     

Conformation of aspartate aminotransferase in crystals

X-ray study of chicken cytosolic aspartate aminotransferase revealed conformational changes in the protein of two kinds: (1) a shift of the small domain adjacent to substrate-binding area due to interaction of the protein with two carboxyl groups of substrate and (2) a change in inclination of the coenzyme plane due to replacement of C = N bond of the coenzyme with Lys-258 by C = N bond with a substrate. An asymmetry in subunit behaviour is observed in both cases: the domain is shifted in one subunit and the coenzyme is rotated in other. Substrate-binding properties of each subunit are strictly dependent on the protein conformation in substrate-binding area.