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PubMed2006

Genomic variation in the mitochondrially encoded cytochrome b (MT-CYB) and 16S rRNA (MT-RNR2) genes: characterization of eight endangered Pecoran species.

In an effort to develop species-specific identification markers, we examined genetic variants and molecular signatures within genes encoding mitochondrial cytochrome b and 16S rRNA in eight endangered Pecoran species endemic to the Indian peninsula. Our results revealed that the cytochrome b gene exhibited higher sequence diversity than the 16S rRNA gene, both between and within species. However, the 16S rRNA gene harboured a larger number of species-specific mutation sites compared with the cytochrome b gene, suggesting that it could be useful for species identification. Indeed, we successfully used 'forensically informative nucleotide sequencing' (FINS) analysis of the 16S rRNA gene to identify two previously unknown biological specimens.

Animals↗
PubMed2005

BoS: a large and diverse family of short interspersed elements (SINEs) in Brassica oleracea.

Short interspersed elements (SINEs) are nonautonomous non-LTR retrotransposons that populate eukaryotic genomes. Numerous SINE families have been identified in animals, whereas only a few have been described in plants. Here we describe a new family of SINEs, named BoS, that is widespread in Brassicaceae and present at approximately 2000 copies in Brassica oleracea. In addition to sharing a modular structure and target site preference with previously described SINEs, BoS elements have several unusual features. First, the head regions of BoS RNAs can adopt a distinct hairpin-like secondary structure. Second, with 15 distinct subfamilies, BoS represents one of the most diverse SINE families described to date. Third, several of the subfamilies have a mosaic structure that has arisen through the exchange of sequences between existing subfamilies, possibly during retrotransposition. Analysis of BoS subfamilies indicate that they were active during various time periods through the evolution of Brassicaceae and that active elements may still reside in some Brassica species. As such, BoS elements may be a valuable tool as phylogenetic makers for resolving outstanding issues in the evolution of species in the Brassicaceae family.

Base Pairing↗
PubMed1996

Electronic energy levels and hopping conductivity of an entire molecule of hagfish insulin.

The quantum-chemical calculation of an entire molecule of hagfish insulin was done by the ENFC method in which the matrix elements were calculated at the ab initio level using a minimal basis set with simulation of the aqueous solution environment. The ac conductivity for hagfish insulin was also calculated at the ab initio level by random walk theory. All the results were compared with those of pig insulin. It is shown that the reduction of HOMOs and LUMOs localized on the active sites of hagfish insulin agrees with the decrease in the biological reactivity of the insulin. The analysis of primary hopping events showed that a different sequence could influence the biological activity of insulin through the distribution of the hopping centers and the quantities of the hopping frequencies. The curve of the frequency versus ac conductivity of hagfish insulin shows that the different amino acid sequences of proteins influence the hopping conductivity. However, the electronic properties of native proteins are dominated by the three-dimensional conformations. Finally, the electronic mechanism of trans-membrane signal transforms by insulin and its receptor, which had been proposed by Ye and Ladik, was clearly described.

Amino Acid Sequence↗
PubMed2005

Differentially expressed cortical genes contribute to perivascular deposition in transgenic mice with inducible neuron-specific expression of TGF-beta1.

In the brain the expression of transforming growth factor beta1 (TGF-beta1) is involved both in neuroprotective and neurodegenerative processes. Recently, we have established a transgenic mouse model with inducible neuron-specific expression of TGF-beta1 based on the tetracycline-regulated gene expression system. A long-term expression of TGF-beta1 results in persisting perivascular thioflavin-positive depositions, which did not disappear even though the transgene synthesis was repressed completely by administration of doxycycline. Formation and composition of these depositions are hardly elucidated. The aim of this study was to identify TGF-beta1 responding genes potentially participating in forming these depositions. To address this problem we have compared the cortical mRNA expression pattern of TGF-beta1 expressing mice with mice impeded to express the transgenic protein using oligonucleotide microarray analysis. Differential gene expression was further characterized by quantitative real-time reverse transcription-polymerase chain reaction including animals, where the long-lasting TGF-beta1 expression was repressed. While no change of amyloid precursor protein RNA expression level was detected, various genes strongly involved in calcium homeostasis, tissue mineralization or vascular calcification were identified differentially expressed. It is suggested, that these genes might contribute to the perivascular depositions in the TGF-beta1 expressing mice.

Animals↗
PubMed2005

TA-clustering: cluster analysis of gene expression profiles through Temporal Abstractions.

This paper describes a new technique for clustering short time series of gene expression data. The technique is a generalization of the template-based clustering and is based on a qualitative representation of profiles which are labelled using trend Temporal Abstractions (TAs); clusters are then dynamically identified on the basis of this qualitative representation. Clustering is performed in an efficient way at three different levels of aggregation of qualitative labels, each level corresponding to a distinct degree of qualitative representation. The developed TA-clustering algorithm provides an innovative way to cluster gene profiles. We show the developed method to be robust, efficient and to perform better than the standard hierarchical agglomerative clustering approach when dealing with temporal dislocations of time series. Results of the TA-clustering algorithm can be visualized as a three-level hierarchical tree of qualitative representations and as such easy to interpret. We demonstrate the utility of the proposed algorithm on a set of two simulated data sets and on a study of gene expression data from S. cerevisiae.

Algorithms↗
PubMed2006

Mapping the functional domains of yeast NMD3, the nuclear export adapter for the 60 S ribosomal subunit.

Nuclear export of the large ribosomal subunit requires the adapter protein Nmd3p to provide a leucine-rich nuclear export signal that is recognized by the export receptor Crm1. Nmd3p binds to the pre-60 S subunit in the nucleus. After export to the cytoplasm, the release of Nmd3p depends on the ribosomal protein Rpl10p and the GTPase Lsg1p. Here, we have carried out a mutational analysis of Nmd3 to better define the domains responsible for nucleocytoplasmic shuttling and ribosome binding. We show that mutations in two regions of Nmd3p affect 60 S binding, suggesting that its binding to the subunit is multivalent.

Active Transport, Cell Nucleus↗
PubMed2001

Analysis of temporal gene expression profiles: clustering by simulated annealing and determining the optimal number of clusters.

MOTIVATION: Cluster analysis of genome-wide expression data from DNA microarray hybridization studies has proved to be a useful tool for identifying biologically relevant groupings of genes and samples. In the present paper, we focus on several important issues related to clustering algorithms that have not yet been fully studied. RESULTS: We describe a simple and robust algorithm for the clustering of temporal gene expression profiles that is based on the simulated annealing procedure. In general, this algorithm guarantees to eventually find the globally optimal distribution of genes over clusters. We introduce an iterative scheme that serves to evaluate quantitatively the optimal number of clusters for each specific data set. The scheme is based on standard approaches used in regular statistical tests. The basic idea is to organize the search of the optimal number of clusters simultaneously with the optimization of the distribution of genes over clusters. The efficiency of the proposed algorithm has been evaluated by means of a reverse engineering experiment, that is, a situation in which the correct distribution of genes over clusters is known a priori. The employment of this statistically rigorous test has shown that our algorithm places greater than 90% genes into correct clusters. Finally, the algorithm has been tested on real gene expression data (expression changes during yeast cell cycle) for which the fundamental patterns of gene expression and the assignment of genes to clusters are well understood from numerous previous studies.

Algorithms↗
PubMed1996

Molecular genetic diagnosis of von Hippel-Lindau disease: analysis of five Japanese families.

We analyzed deoxyribonucleic acids from blood samples of five Japanese von Hippel-Lindau (VHL) disease families (three familial cases, two new mutations) for the presence of VHL gene mutations by single-strand conformational polymorphism analysis and direct sequencing. Four of the five families showed germ line mutations in VHL gene, comprising 2 missense mutations, 1 deletion, and 1 splice-site mutation. Two families had VHL gene mutations at exon 1; 1 family at exon 3; and 1 family at the splice-site adjacent to exon 3. Presymptomatic patients were accurately diagnosed by these methods. However, one family did not show a VHL gene mutation in the germ line but showed a somatic mutation at exon 2 in the hemangioblastoma tissue. The consequence of the somatic mutation was a microdeletion leading to a frameshift mutation. Our study is the first report of VHL gene analyses of Japanese VHL disease families, and suggests that not only germ line mutation, but also somatic mutation can lead to development of a tumor associated with the VHL disease.

Base Sequence↗
PubMed2004

Clustering gene expression data with temporal abstractions.

This paper describes a new technique for clustering short time series coming from gene expression data. The technique is based on the labelling of the time series through temporal trend abstractions and a consequent clustering of the series on the basis of their labels. Clustering is performed at three different levels of aggregation of the original time series, so that the results are organized and visualized as a three-levels hierarchical tree. Results on simulated and on yeast data are shown. The technique appears robust and efficient and the results obtained are easy to be interpreted.

Algorithms↗
PubMed1994

[Application of DNA polymorphism to forensic medicine].

Recent recombinant DNA technology has provided some novel and powerful methods for forensic science application. Human genomic DNA can be analyzed directly for individual identification and paternity testing on the basis of variations in its sequence. The analysis of DNA isolated from forensic biological evidence provides valuable information relating to the identification of the source of the sample. Restriction fragment length polymorphism (RFLP) testing, using a combination of single locus probe (SLP) that vary highly among individuals, produces a DNA fingerprint or profile. The PCR method using STR (microsatellite) and mitochondrial DNA analysis (mtDNA) is suitable for examination of the forensic biological samples (bloodstains, hairs, seminal stains, bones, tooth). For sex identification of bloodstains, bleached skeletons and teeth, Southern blot hybridization with Y-chromosome specific probe (pHY10; 3.4 kb) and PCR amplifying with sex chromosome specific fragments, can be used. Mitochondrial DNA RFLPs and 9-bp deletion type of mtDNA may suggest the characteristics of the human races. For the purpose of resolving the genetic basis of human uniqueness, we reported the isolation of human-specific sequences using the technique of genome subtraction (HS5, 2282 bp).

Animals↗
PubMedDate not supplied

Nanotechnologies and microchips in genetic diseases.

Microarrays or microchips represent a new area of high technology, which will completely change the methodological approach to basic research and clinical diagnostics. This technology can be used for genotyping, expression profiling and proteome analysis. Genetics and molecular medicine have an expanding need for rapid genotyping, mutational analysis and DNA re-sequencing technologies, i.e. microarrays that have a clear potential for miniaturization, parallelization, and automation and enable high-throughput screening. Expression profiling technology is a new tool for investigating expression patterns, identifying new disease genes either for monogenic disorders or for complex traits, identifying new functional and cellular relationships and identifying new pathways and possible related drugs. This technology has been successfully applied to the study of complex traits, i.e. cardiovascular diseases, cancer and type II diabetes, providing new insights into possible pathogenetic mechanisms and new therapeutical approaches. Finally, microarray can further improve proteome analysis. This review discusses these points.

Gene Expression Profiling↗
PubMed2006

DivergentSet, a tool for picking non-redundant sequences from large sequence collections.

DivergentSet addresses the important but so far neglected bioinformatics task of choosing a representative set of sequences from a larger collection. We found that using a phylogenetic tree to guide the construction of divergent sets of sequences can be up to 2 orders of magnitude faster than the naive method of using a full distance matrix. By providing a user-friendly interface (available online) that integrates the tasks of finding additional sequences, building and refining the divergent set, producing random divergent sets from the same sequences, and exporting identifiers, this software facilitates a wide range of bioinformatics analyses including finding significant motifs and covariations. As an example application of DivergentSet, we demonstrate that the motifs identified by the motif-finding package MEME (Motif Elicitation by Maximum Entropy) are highly unstable with respect to the specific choice of sequences. This instability suggests that the types of sensitivity analysis enabled by DivergentSet may be widely useful for identifying the motifs of biological significance.

Amino Acid Sequence↗
PubMed1992

Analysis of the immunodominant antigens of Corynebacterium pseudotuberculosis.

Antibodies to seven antigens in a whole cell lysate of Corynebacterium pseudotuberculosis ranging in molecular mass from 22 to 120 kilodaltons (kDa) were present in sera of 40 sheep and goats infected with C. pseudotuberculosis. Three antigens of about 120, 68, and 31.5 kDa in size were consistently detected with sera from all animals and twenty-two sera had antibodies to 64, 43, 40, and 22 kDa antigens. None of these antigens were detected by sera from 160 sheep in a C. pseudotuberculosis-free research flock. An NaCl extract of C. pseudotuberculosis cells contained one major protein of about 31.5 kDa and four minor proteins of 68, 64, 43, and 22 kDa in molecular mass as shown by Coomassie Blue staining. Immunoblot analysis demonstrated that the three immunodominant antigens identified in the whole cell extract were contained in the NaCl extract. The 31.5-kDa protein was purified from the NaCl extract by fast-protein liquid chromatography gel filtration to near homogeneity. The purified 31.5-kDa protein showed phospholipase D activity as indicated by synergistic hemolysis with Rhodococcus equi factors and sphingomyelinase activity. The 31.5-kDa protein reacted with antibodies in serum from a sheep naturally infected with C. pseudotuberculosis. This serum also had phospholipase D neutralizing activity. On the basis of its molecular mass, biological activity, N-terminal amino acid sequence analysis, and immunoreactivity, the 31.5-kDa protein was identified as the phospholipase D exotoxin of C. pseudotuberculosis.

Amino Acid Sequence↗
PubMed2004

Molecular evolution of the hepatitis delta virus antigen gene: recombination or positive selection?

We present the statistical analysis of diversifying selective pressures on the hepatitis D antigen gene (HDAg). Thirty-three distinct HDAg sequences from subtypes I, II, and III were tested for positive selection using maximum likelihood methods based on models of codon substitution that allow variable selective pressures across sites. Such methods have been shown to be sufficiently accurate and successful in detecting positive selection in a variety of viral and nonviral protein-coding genes. About 11% of codon sites in HDAg were estimated to be under diversifying selection. Remarkably, most of the residues predicted to evolve under positive selection were located in the immunogenic domain and the N-terminus region with reported antigenic activity. These sites are potential targets of the host's immune response. Identification of residues mutating to escape immune recognition may help to distinguish the most virulent strains and aid vaccine design. Possible interplay between positive selection and recombination on the gene is discussed but no significant evidence for recombination was found.

Amino Acid Sequence↗
PubMed2004

The anterior stomach of larval mosquitoes (Aedes aegypti): effects of neuropeptides on transepithelial ion transport and muscular motility.

The present investigation studied the influence of a number of neuropeptides on semi-open preparations of the isolated and perfused anterior stomach of larval Aedes aegypti. Effects of peptides were observed on the lumen negative transepithelial voltage (Vte) that is present with serotonin in the bath; this voltage most likely reflects active HCO3- secretion involved in alkalization of the larval anterior stomach. The five different A. aegypti allatostatins (allatostatin A 1-5) all affected Vte in almost identical ways, causing a 10-15% reduction of the voltage at 10(-7) mol l(-1). A. aegypti neuropeptide F and proctolin reduced Vte at submicromolar concentrations. At 10(-6) mol l(-1), neuropeptide F reduced Vte by 30% and proctolin reduced Vte by 50%. In contrast, A. aegypti allatotropin, A. aegypti head peptides I and III and A. aegypti short neuropeptide F were without effect on Vte. During the investigation it was observed that the peristaltic contractions of the preparations caused a dynamic component of Vte. Peristaltic contractions and the correlated voltage fluctuations depended on the presence of serotonin. Peristaltic activity and Vte deflections were progressively inhibited by A. aegypti head peptides I and III by A. aegypti short neuropeptide F and by A. aegypti neuropeptide F when the peptide concentrations were increased from 10(-8) to 10(-6) mol l(-1). These observations show that physiological concentrations of some of the tested neuropeptides affect two processes that require coordination: ion transport and motility of the larval anterior stomach.

Aedes↗
PubMed2005

APOBEC4, a new member of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases predicted by computational analysis.

Using iterative database searches, we identified a new subfamily of the AID/APOBEC family of RNA/DNA editing cytidine deaminases. The new subfamily, which is represented by readily identifiable orthologs in mammals, chicken, and frog, but not fishes, was designated APOBEC4. The zinc-coordinating motifs involved in catalysis and the secondary structure of the APOBEC4 deaminase domain are evolutionarily conserved, suggesting that APOBEC4 proteins are active polynucleotide (deoxy)cytidine deaminases. In reconstructed maximum likelihood phylogenetic trees, APOBEC4 forms a distinct clade with a high statistical support. APOBEC4 and APOBEC1 are joined in a moderately supported cluster clearly separated from AID, APOBEC2 and APOBEC3 subfamilies. In mammals, APOBEC4 is expressed primarily in testis which suggests the possibility that it is an editing enzyme for mRNAs involved in spermatogenesis.

APOBEC Deaminases↗