An integrated tool for microarray data clustering and cluster validity assessment

SUMMARY: In this paper we present a data mining system, which allows the application of different clustering and cluster validity algorithms for DNA microarray data. This tool may improve the quality of the data analysis results, and may support the prediction of the number of relevant clusters in the microarray datasets. This systematic evaluation approach may significantly aid genome expression analyses for knowledge discovery applications. The developed software system may be effectively used for clustering and validating not only DNA microarray expression analysis applications but also other biomedical and physical data with no limitations. AVAILABILITY: The program is freely available for non-profit use on request at http://www.cs.tcd.ie/Nadia.Bolshakova/Machaon.html CONTACT: Nadia.Bolshakova@cs.tcd.ie.     

Proliferation and cell death of hepatocytes in regenerating fetal rat liver

Proliferation and death of hepatocytes in regenerating liver were studied in 17-day-old fetal white rats. Two days after liver resection (20%), animals were sacrificed every 3 h. In experimental groups, the index of Ki67-positive hepatocytes increased sharply 15 h after liver resection. In all experimental and control groups, the ratio of the index of the metaphase, the longest phase of mitosis, to the mitotic index remained unchanged, indicating the same duration of hepatocyte mitoses in regenerating liver. In regenerating and intact liver, hepatocytes labeled with antibodies to caspase 3 were not detected. Thus, resection of 20% fetal rat liver did not promote enhancement of apoptosis of hepatocytes.     

Isolation and Genetic Study of Erwinia Mutants Devoid of Common Components of the Phosphoenolpyruvate-Dependent Phosphotransferase System

Mutants of bacteria belonging the genus Erwinia(Erwinia chrysanthemi andErwinia carotovora) with pleiotropic disturbances in the utilization of many substrates were obtained through chemical and transposon mutagenesis. Genetic studies revealed that these mutants had defective ptsI or ptsH genes responsible for the synthesis of common components of the phosphoenolpyruvate-dependent phosphotransferase system, enzyme I and the HPr protein, respectively. The ptsI ⁺ allele in both Erwinia species was cloned in vivo. Mapping of obtained mutations indicated that theptsIand ptsH genes ofE. chrysanthemi do not constitute a linkage group. The ptsI gene is located at 100 min of the chromosomal map, whereas theptsH gene is located at 175 min. Sequencing of a portion of theE. chrysanthemi ptsI gene showed that a product of the cloned DNA region had up to 68% homology with the N terminus of Escherichia coli enzyme I.     

Age ratio and survival of Common Rosefinch (<Emphasis Type="Italic">Carpodacus erythrinus</Emphasis>, Passeriformes,Fringillidae) in a local population based on ringing data

The ringing data on Common Rosefinch obtained during thirteen field seasons (2002–2014) at the National Park “Russky Sever” (Vologda region) are analyzed. Birds were trapped in two sites 59 km apart. The age of the birds (yearlings or first breeders and adults) was determined according to the plumage color in every male captured with mist nets. The apparent survival rate of adult individuals was determined using two methods: according to the ratio of males’ age and the CJS model (Lebreton et al., 1992; Bursky, 2011). A total of 713 captures of 657 individuals were analyzed. The ratios of ages in the males from the sites studied did not differ; yearlings amounted to 56% of all males. The rate of survival in the males based on the age ratios was estimated at 44 ± 2%. The apparent survival rate obtained using the CJS model was significantly higher (61 ± 6%). The survival rate of adult rosefinches in two sites did not differ and did not depend on sex. Literature materials on the age ratio and survival of rosefinches in local populations are analyzed. There is a suggestion that the mismatch of the survival rates obtained by two methods and the high proportion of yearling males in the banding captures can be explained by the fact that the majority of individuals of that age category did not participate in nesting.