Gene function prediction from synthetic lethality networks via ranking on demand.

MOTIVATION: Synthetic lethal interactions represent pairs of genes whose individual mutations are not lethal, while the double mutation of both genes does incur lethality. Several studies have shown a correlation between functional similarity of genes and their distances in networks based on synthetic lethal interactions. However, there is a lack of algorithms for predicting gene function from synthetic lethality interaction networks. RESULTS: In this article, we present a novel technique called kernelROD for gene function prediction from synthetic lethal interaction networks based on kernel machines. We apply our novel algorithm to Gene Ontology functional annotation prediction in yeast. Our experiments show that our method leads to improved gene function prediction compared with state-of-the-art competitors and that combining genetic and congruence networks leads to a further improvement in prediction accuracy.

Application of neural networks to the ranking of perinatal variables influencing birthweight.

In this paper we compare Multi-Layer Perceptrons (a neural network type) with Multivariate Linear Regression in predicting birthweight from nine perinatal variables which are thought to be related. Results show, that seven of the nine variables, i.e., gestational age, mother's body-mass index (BMI), sex of the baby, mother's height, smoking, parity and gravidity, are related to birthweight. We found no significant relationship between birthweight and each of the two variables, i.e., maternal age and social class.

Age and size composition, growth rate, reproductive biology, and habitats of the West Australian dhufish (Glaucosoma hebraicum) and their relevance to the management of this species

Samples of the commercially and recreationally important West Australian dhufish (Glaucosoma hebraicum) were obtained from the lower west coast of Australia by a variety of methods. Fish <300 mm TL were caught over flat, hard substrata and low-lying limestone reefs, whereas larger fish were caught over larger limestone and coral reef formations. Maximum total lengths, weights, and ages were 981 mm, 15.3 kg, and 39 years, respectively, for females and 1120 mm, 23.2 kg, and 41 years, respectively, for males. The von Bertalanffy growth curves for females and males were significantly different. The values for L∞, k, and t0 in the von Bertalanffy growth equations were 929 mm, 0.111/year, and –0.141 years, respectively, for females, and 1025 mm, 0.111/year, and –0.052 years, respectively, for males. Preliminary estimates of total mortality indicated that G. hebraicum is now subjected to a level of fishing pressure that must be of concern to fishery managers. Glaucosoma hebraicum, which spawns between November and April and predominantly between December and March, breeds at a wide range of depths and is a multiple spawner. The L50’s for females and males at first maturity, i.e. 301 and 320 mm, respectively, were attained by about the end of the third year of life and are well below the minimum legal length (MLL) of 500 mm. Because females and males did not reach the MLL until the end of their seventh and sixth years of life, respectively, they would have had, on average, the opportunity of spawning during four and three spawning seasons, respectively, before they reached the MLL. However, because G. hebraicum caught in water depths >40 m typically die upon release, a MLL is of limited use for conserving this species. Alternative approaches, such as restricting fishing activity in highly fished areas, reducing daily bag limits for recreational fishermen, introducing quotas or revising specific details of certain commercial hand-line licences (or doing both) are more likely to provide effective conservation measures.

Study on regional differences in soil-water characteristics and their relevance to aquaculture productivity and fish disease

A total of 45 ponds used for fish polyculture were investigated in three zones of Bangladesh to identify the differences among the zones in respect to aqua-ecology, culture practices, fish productivity and health management. Four hundred and fifty fish from three zones were clinically examined by naked eye and histopathology. Out of total number of fish examined, 45 fish from Dhaka zones were examined for parasites and bacteria in addition to histopathology. Faded and haemorrhagic gill, skin, fin, scale loss and lesions were observed during fish examination. Aeromonas spp. Pseudomonas spp. and Streptococcus spp. were isolated respectively from 56%, 46% and 39% affected fish. Among the five water quality parameters analyzed, the highest average hardness and alkalinity respectively were recorded in Rajshahi (156 ppm and 142 ppm) followed by Dhaka (146 ppm and 132 ppm) and Chittagong (81 ppm and 90 ppm). The highest average pH was recorded in Mymensingh (7.52) followed by Rajshahi (7.13) and Chittagong (7.05). Water holding capacity of soil in Rajshahi zone was poor compared to other zones and farmers were found to be reluctant to fish farming.

Evolutionary history of the mtDNA 9-bp deletion in Chinese populations and its relevance to the peopling of east and southeast Asia

In total, 1218 Chinese from twelve ethnic groups and nine Han geographic groups were screened for the mtDNA 9-bp deletion motif. The frequency of the 9-bp deletion in all samples was 14.7% but ranged from 0% to 32% in the various ethnic groups. Three individuals had a triplication of the 9-bp segment. Phylogenetic and demographic analyses of the mtDNA hypervariable segment 1 (HVS1) sequences suggest that the 9-bp deletion occurred more than once in China. The majority of the Chinese deletion:haplotypes (about 90%) have a common origin as a mutational event following an initial expansion of modem humans in eastern Asia. Other deletion haplotypes and the three haplotypes with a 9-bp triplication may have arisen independently in the Chinese, presumably by replication error. HVS1 haplotype analysis suggests two possible migration routes of the 9-bp deletion in east and southeast Asia. Both migrations originated in China with one route leading to the Pacific Islands via Taiwan, the other to southeast Asia and possibly the Nicobar Islands. Along both routes of peopling, a decrease in HVS1 diversity of the mtDNA haplotypes is observed. The "Polynesian motif (16217T/C, 16247A/G, and 16261C/T)" and the 16140T/C, 16266C/A, or C/G polymorphisms appear specific to each migration route.

Mitochondrial control region sequence variation within the argali wild sheep (Ovis ammon): evolution and conservation relevance

The phylogenetic relationship of several subspecies of Ovis ammon were analyzed by comparing DNA sequences within the entire mitochondrial D-loop region. Five putative subspecies of ammon (dalai-lamae, darwini, hodgsoni, sairensis and adamerzi) were sampled from four provinces in China [Xinjiang, Qinghai, Gansu and Xizang (Tibet)] and two (servertzovi and nigrimontana) from Uzbekistan. The argalis sampled represent most of the currently recognized putative Subspecies of argali. Analysis of mtDNA sequences revealed high variability within ammon (7.7%), ranging from 2.4 to 11.5%. MaxiMUM-Parsimony tree indicated that nigrimontana from Uzbekistan diverged First, followed by severtzovi from Uzbekistan. The dispersal of argalis into China gave rise to three clades, suggesting that the argali originated in Western Asia and then dispersed throughout the central Asian highlands on a southeastward course. Among the Chinese argalis, mtDNA analysis places dalailamae genetically closer to hodgsoni than to darwini. Severtzovi and.. nigrimontana are two separate subspecies and genetically distinct from the Chinese argali.