Automatic layout and visualization of biclusters

Background  

Biclustering has emerged as a powerful algorithmic tool for analyzing measurements of gene expression. A number of different methods have emerged for computing biclusters in gene expression data. Many of these algorithms may output a very large number of biclusters with varying degrees of overlap. There are no systematic methods that create a two-dimensional layout of the computed biclusters and display overlaps between them.     

Synthesis and structure-activity relationships of a new series of 2alpha-substituted trans-4,5-dimethyl-4-(3-hydroxyphenyl)piperidine as mu-selective opioid antagonists

Structure-activity relationships at the 2alpha-position of the piperidine ring of the trans-4,5-dimethyl-4-(3-hydroxyphenyl)piperidine mu-opioid antagonist series were investigated. This study showed that only small linear alkyl groups (methyl, propyl) are tolerated at the 2alpha-position of the piperidine ring of this series.     

Effects of aluminum and deferoxamine on concentration of essential elements in animals experimentally intoxicated with aluminum]

To assess the effect of aluminium intoxication in tissues of experimental animals on Ca, Mg, Zn, Cu, and Fe concentration, aluminium nitrate was administered intraperitoneally to mice at a daily dose of 0.27 mMol/kg for 5 weeks. Concentration of Al, Ca, Mg, Zn, Cu, and Fe were analyzed by atomic absorption spectrometry. The Al content in liver and tibia was significantly higher in treated mice in comparison with control group. In Al loaded tissues the significant increase of all tested essential elements was found. To evaluate the results of DFO treatment on essential elements, mice received 6 times intraperitoneally 3.5 mMol/kg of DFO. This treatment had generally no effect on reduction of Al concentration in tibia and liver, as well as on changes in essential elements concentration.     

The effect of a single dose of aflatoxin B1 on the value of nucleolar index of blood lymphocytes and on histological changes in the liver, bursa Fabricii, suprarenal glands and spleen in ducklings

The value of the nucleolar index of blood lymphocytes, as well as histopathological changes in liver, bursa Fabricii, suprarenal glands and spleen in ducklings administered per os a single dose of 1.5 micrograms aflatoxin B1 on the second day of their life, were observed for two weeks. There was a clear correlation observed between morphological changes in the lymphatic system organs and liver and the value of the nucleolar index of peripheral blood lymphocytes on the 13th and 14th day after administration of aflatoxin B1. The results obtained point to different susceptibility of the tested organs and lymphocytes to the action of aflatoxin B1.     

Polymorphism and methylation of the <Emphasis Type="Italic">MC4R</Emphasis> gene in obese and non-obese dogs

The dog is considered to be a useful biomedical model for human diseases and disorders, including obesity. One of the numerous genes associated with human polygenic obesity is MC4R, encoding the melanocortin 4 receptor. The aim of our study was to analyze polymorphisms and methylation of the canine MC4R in relation to adiposity. Altogether 270 dogs representing four breeds predisposed to obesity: Labrador Retriever (n?=?187), Golden Retriever (n?=?38), Beagle (n?=?28) and Cocker Spaniel (n?=?17), were studied. The dogs were classified into three groups: lean, overweight and obese, according to the 5-point Body Condition Score (BCS) scale. In the cohort of Labradors a complete phenotypic data (age, sex, neutering status, body weight and BCS) were collected for 127 dogs. The entire coding sequence as well as 5′ and 3′-flanking regions of the studied gene were sequenced and six polymorphic sites were reported. Genotype frequencies differed considerably between breeds and Labrador Retrievers appeared to be the less polymorphic. Moreover, distribution of some polymorphic variants differed significantly (P?<?0.05) between small cohorts with diverse BCS in Golden Retrievers (c.777T>C, c.868C>T and c.*33C>G) and Beagles (c.-435T>C and c.637G>T). On the contrary, in Labradors no association between the studied polymorphisms and BCS or body weight was observed. Methylation analysis, using bisulfite DNA conversion followed by Sanger sequencing, was carried out for 12 dogs with BCS?=?3 and 12 dogs with BCS?=?5. Two intragenic CpG islands, containing 19 cytosines, were analyzed and the methylation profile did not differ significantly between lean and obese animals. We conclude that an association of the MC4R gene polymorphism with dog obesity or body weight is unlikely, in spite of the fact that some associations were found in small cohorts of Beagles and Golden Retrievers. Also methylation level of this gene is not related with dog adiposity.     

Molecular markers and sentinel organisms for environmental monitoring

Molecular methods are useful for both to monitor anthropogenic viral, bacterial, and protozoan enteropathogens, and to track pathogen specific markers in a complex environment in order to reveal sources of these pathogens. Molecular genetic markers for fecal viruses, bacteria, and protozoans hold promise for monitoring environmental pollution and water quality. The demand for microbiologically safe waters grows exponentially due to the global demographic rise of the human population. Economically important shellfish, such as oysters, which are harvested commercially and preferentially consumed raw can be of public health importance if contaminated with human waterborne pathogens. However, feral molluscan shellfish which do not have an apparent economic value serve as indicators in monitoring aquatic environments for pollution with human waterborne pathogens and for sanitary assessment of water quality. Current technology allows for multiplexed species-specific identification, genotyping, enumeration, viability assessment, and source-tracking of human enteropathogens which considerably enhances the pathogen source-tracking efforts.     

Phosphoregulation and depolymerization-driven movement of the Dam1 complex do not require ring formation

During mitosis, kinetochores form persistent attachments to microtubule tips and undergo corrective detachment in response to phosphorylation by Ipl1 (Aurora B) kinase. The Dam1 complex is required to establish and maintain bi-oriented attachment to microtubule tips in vivo, and it contains multiple sites phosphorylated by Ipl1 (Refs 2, 3, 4, 5, 6, 7, 8, 9, 10). Moreover, a number of kinetochore-like functions can be reconstituted in vitro with pure Dam1 complex. These functions are believed to derive from the ability of the complex to self-assemble into rings. Here we show that rings are not necessary for dynamic microtubule attachment, Ipl1-dependent modulation of microtubule affinity or the ability of Dam1 to move processively with disassembling microtubule tips. Using two fluorescence-based assays, we found that the complex exhibited a high affinity for microtubules (Kd of approximately 6 nM) that was reduced by phosphorylation at Ser 20, a single Ipl1 target residue in Dam1. Moreover, individual complexes underwent one-dimensional diffusion along microtubules and detached 2.5-fold more frequently after phosphorylation by Ipl1. Particles consisting of one to four Dam1 complexes - too few to surround a microtubule - were captured and carried by disassembling tips. Thus, even a small number of binding elements could provide a dynamic, phosphoregulated microtubule attachment and thereby facilitate accurate chromosome segregation.     

Capillaria hepatica (Nematoda) infections in human-habituated mountain gorillas (Gorilla gorilla beringei) of the Parc National de Volcans, Rwanda

Habituation to humans of free-ranging populations of endangered mountain gorillas (Gorilla gorilla beringei) raised concern of anthropozoonotic transmission of parasitic helminths and protozoans. Examinations of liver tissue of 19 gorillas found dead in the Parc National de Volcans, Rwanda, revealed 10 cases of hepatic nematodiasis due to Capillaria hepatica. Identifiable C. hepatica eggs were present in the liver of 4 gorillas (3 juveniles, 1 adult), and nematode cross-sections were found in 1 juvenile gorilla. Six other adult gorillas had areas of periportal and subcapsular fibrosis with calcified eggs. Histologically, the lesions surrounded by the areas of mild inflammatory reaction were characterized by subcapsular, periportal foci of fibrosis in which were embedded numerous C. hepatica eggs. Control of hepatic capillariasis in the remaining populations of mountain gorillas should be focused on eradication or control of populations of rodent pests (i.e., mice and rats) that sustain the reservoir of C. hepatica in habitats shared by gorillas and humans.     

Characterization of 3-chlorobenzoate degrading aerobic bacteria isolated under various environmental conditions

The rates of bacterial growth in nature are often restricted by low concentrations of oxygen or carbon substrates. In the present study the metabolic properties of 24 isolates that had been isolated using various concentrations of 3-chlorobenzoate, benzoate and oxygen as well as using continuous culture at high and low growth rates were determined to investigate the effects of these parameters on the metabolism of monoaromatic compounds. Bacteria were enriched from different sampling sites and subsequently isolated. In batch culture this was done both under low oxygen (2% O(2)) and air-saturated concentrations. Chemostat enrichments were performed under either oxygen or 3-chlorobenzoate limiting conditions. Bacteria metabolizing aromatics with gentisate or protocatechuate as intermediates (gp bacteria) as well as bacteria metabolizing aromatic compounds via catechols (cat bacteria) were isolated from batch cultures when either benzoate or 3CBA were used as C sources, regardless of the enrichment conditions applied. In contrast, enrichments performed in chemostats at low dilution rates resulted in gp-type organisms only, whereas at high dilution rates cat-type organisms were enriched, irrespective of the oxygen and 3-chlorobenzoate concentration used during enrichment. It is noteworthy that the gp-type of bacteria possessed relatively low μ(max) values on 3CBA and benzoate along with relatively high substrate and oxygen affinities for these compounds. This is in contrast with cat-type of bacteria, which seemed to be characterized by high maximum specific growth rates on the aromatic substrates and relatively high apparent half saturation constants. In contrast, bacteria degrading chlorobenzoate via gentisate or protocatechuate may possibly be better adapted to conditions leading to growth at reduced rates such as low oxygen and low substrate concentrations.     

Risk of handling as a route of exposure to infectious waterborne Cryptosporidium parvum oocysts via Atlantic blue crabs (Callinectes sapidus)

Commercial Atlantic blue crabs (Callinectes sapidus) were exposed to 2.0x10(4) infectious waterborne oocysts of Cryptosporidium parvum. The study demonstrated that blue crabs can transfer C. parvum oocysts to persons involved in handling or preparing crabs and that they may contaminate other surfaces or products during storage.