Abstract: Tasks of the work were study the possible E.coli
contamination in red deer meat, identify pathogenic strains from
isolated E.coli, determine their incidence in red deer meat and
determine the presence of VT1, VT2 and eaeA genes for the
pathogenic E.coli. 8 (10%) samples were randomly selected from 80
analysed isolates of E.coli and PCR reaction was performed on them.
PCR was done both on initial materials – samples of red deer meat -
and for already isolated liqueurs. Two of analysed venison samples
contain verotoxin-producing strains of E. coli. It means that this meat
is not safe to consumer. It was proven by the sequestration reaction of
E. coli and by comparison of the obtained results with the database of
microorganism genome available on the internet that the isolated
culture corresponds to region 16S rDNS of E. coli thus presenting
correctness of the microbiological methods.
Abstract: During the last years, the genomes of more and more
species have been sequenced, providing data for phylogenetic recon-
struction based on genome rearrangement measures. A main task in
all phylogenetic reconstruction algorithms is to solve the median of
three problem. Although this problem is NP-hard even for the sim-
plest distance measures, there are exact algorithms for the breakpoint
median and the reversal median that are fast enough for practical use.
In this paper, this approach is extended to the transposition median as
well as to the weighted reversal and transposition median. Although
there is no exact polynomial algorithm known even for the pairwise
distances, we will show that it is in most cases possible to solve
these problems exactly within reasonable time by using a branch and
bound algorithm.
Abstract: In the paper, the relative performances on spectral
classification of short exon and intron sequences of the human and
eleven model organisms is studied. In the simulations, all
combinations of sixteen one-sequence numerical representations, four
threshold values, and four window lengths are considered. Sequences
of 150-base length are chosen and for each organism, a total of
16,000 sequences are used for training and testing. Results indicate
that an appropriate combination of one-sequence numerical
representation, threshold value, and window length is essential for
arriving at top spectral classification results. For fixed-length
sequences, the precisions on exon and intron classification obtained
for different organisms are not the same because of their genomic
differences. In general, precision increases as sequence length
increases.
Abstract: In recent years, there has been an increasing interest
toward the use of bovine genotyped embryos for commercial embryo
transfer programs. Biopsy of a few cells in morulla stage is essential
for preimplantation genetic diagnosis (PGD). Low amount of DNA
have limited performing the several molecular analyses within PGD
analyses. Whole genome amplification (WGA) promises to eliminate
this problem. We evaluated the possibility and performance of an
improved primer extension preamplification (I-PEP) method with a
range of starting bovine genomic DNA from 1-8 cells into the WGA
reaction. We optimized a short and simple I-PEP (ssI-PEP) procedure
(~3h). This optimized WGA method was assessed by 6 loci specific
polymerase chain reactions (PCRs), included restriction fragments
length polymorphism (RFLP). Optimized WGA procedure possesses
enough sensitivity for molecular genetic analyses through the few
input cells. This is a new era for generating characterized bovine
embryos in preimplantation stage.
Abstract: In this study, three subtypes of influenza A viruses (pH1N1, H5N1 and H3N2) which naturally infected human were analyzed by bioinformatic approaches to find candidate human cellular miRNAs targeting viral genomes. There were 76 miRNAs targeting influenza A viruses. Among these candidates, 70 miRNAs were subtypes specifically targeting each subtype of influenza A virus including 21 miRNAs targeted subtype H1N1, 27 miRNAs targeted subtype H5N1 and 22 miRNAs targeted subtype H3N2. The remaining 6 miRNAs target on multiple subtypes of influenza A viruses. Uniquely, hsa-miR-3145 is the only one candidate miRNA targeting PB1 gene of all three subtypes. Obviously, most of the candidate miRNAs are targeting on polymerase complex genes (PB2, PB1 and PA) of influenza A viruses. This study predicted potential human miRNAs targeting on different subtypes of influenza A viruses which might be useful for inhibition of viral replication and for better understanding of the interaction between virus and host cell.
Abstract: EcoDam is an adenine-N6 DNA methyltransferase
that methylates the GATC sites in the Escherichia coli genome.
DNA-adenine methylation is not present in higher eukaryotes
including humans. These observations raise the possibility that dam
inhibitors may be used as anti-microbial agents. Polyphosphate
(Poly(P)) is an important metabolite and signaling molecule in
prokaryotes and eukaryotes. Here, by using gel retardation
experiments to investigate the competition of DNA binding by
EcoDam in the presence of polyphosphate, we found that Poly (P)
strongly interferes with DNA binding by EcoDam, while same
concentration of monophosphate does not. In addition, we
demonstrated that Poly (P) binding inhibits the activity of EcoDam
and our results suggest that Poly (P) led to strong inhibition of the
EcoDam catalytic activity, while monophosphate had only moderate
effect.
Abstract: The PRAF family of proteins is a plant specific family of proteins with distinct domain architecture and various unique sequence/structure traits. We have carried out an extensive search of the Arabidopsis genome using an automated pipeline and manual methods to verify previously known and identify unknown instances of PRAF proteins, characterize their sequence and build 3D structures of their individual domains. Integrating the sequence, structure and whatever little known experimental details for each of these proteins and their domains, we present a comprehensive characterization of the different domains in these proteins and their variant properties.
Abstract: Eukaryotic protein-coding genes are interrupted by spliceosomal introns, which are removed from the RNA transcripts before translation into a protein. The exon-intron structures of different eukaryotic species are quite different from each other, and the evolution of such structures raises many questions. We try to address some of these questions using statistical analysis of whole genomes. We go through all the protein-coding genes in a genome and study correlations between the net length of all the exons in a gene, the number of the exons, and the average length of an exon. We also take average values of these features for each chromosome and study correlations between those averages on the chromosomal level. Our data show universal features of exon-intron structures common to animals, plants, and protists (specifically, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Cryptococcus neoformans, Homo sapiens, Mus musculus, Oryza sativa, and Plasmodium falciparum). We have verified linear correlation between the number of exons in a gene and the length of a protein coded by the gene, while the protein length increases in proportion to the number of exons. On the other hand, the average length of an exon always decreases with the number of exons. Finally, chromosome clustering based on average chromosome properties and parameters of linear regression between the number of exons in a gene and the net length of those exons demonstrates that these average chromosome properties are genome-specific features.
Abstract: In molecular biology, microarray technology is widely and successfully utilized to efficiently measure gene activity. If working with less studied organisms, methods to design custom-made microarray probes are available. One design criterion is to select probes with minimal melting temperature variances thus ensuring similar hybridization properties. If the microarray application focuses on the investigation of metabolic pathways, it is not necessary to cover the whole genome. It is more efficient to cover each metabolic pathway with a limited number of genes. Firstly, an approach is presented which minimizes the overall melting temperature variance of selected probes for all genes of interest. Secondly, the approach is extended to include the additional constraints of covering all pathways with a limited number of genes while minimizing the overall variance. The new optimization problem is solved by a bottom-up programming approach which reduces the complexity to make it computationally feasible. The new method is exemplary applied for the selection of microarray probes in order to cover all fungal secondary metabolite gene clusters for Aspergillus terreus.
Abstract: The National Agricultural Biotechnology Information
Center (NABIC) plays a leading role in the biotechnology information
database for agricultural plants in Korea. Since 2002, we have
concentrated on functional genomics of major crops, building an
integrated biotechnology database for agro-biotech information that
focuses on bioinformatics of major agricultural resources such as rice,
Chinese cabbage, and microorganisms. In the NABIC,
integration-based biotechnology database provides useful information
through a user-friendly web interface that allows analysis of genome
infrastructure, multiple plants, microbial resources, and living
modified organisms.
Abstract: The Block Sorting problem is to sort a given
permutation moving blocks. A block is defined as a substring
of the given permutation, which is also a substring of the
identity permutation. Block Sorting has been proved to be
NP-Hard. Until now two different 2-Approximation algorithms
have been presented for block sorting. These are the best known
algorithms for Block Sorting till date. In this work we present
a different characterization of Block Sorting in terms of a
transposition cycle graph. Then we suggest a heuristic,
which we show to exhibit a 2-approximation performance
guarantee for most permutations.
Abstract: Whole genome duplication (WGD) increased the
number of yeast Saccharomyces cerevisiae chromosomes from 8 to
16. In spite of retention the number of chromosomes in the genome
of this organism after WGD to date, chromosomal rearrangement
events have caused an evolutionary distance between current genome
and its ancestor. Studies under evolutionary-based approaches on
eukaryotic genomes have shown that the rearrangement distance is an
approximable problem. In the case of S. cerevisiae, we describe that
rearrangement distance is accessible by using dedoubled adjacency
graph drawn for 55 large paired chromosomal regions originated
from WGD. Then, we provide a program extracted from a C program
database to draw a dedoubled genome adjacency graph for S.
cerevisiae. From a bioinformatical perspective, using the duplicated
blocks of current genome in S. cerevisiae, we infer that genomic
organization of eukaryotes has the potential to provide valuable
detailed information about their ancestrygenome.
Abstract: Sense-antisense gene pair (SAGP) is a pair of two oppositely transcribed genes sharing a common region on a chromosome. In the mammalian genomes, SAGPs can be organized in more complex sense-antisense gene architectures (CSAGA) in which at least one gene could share loci with two or more antisense partners. Many dozens of CSAGAs can be found in the human genome. However, CSAGAs have not been systematically identified and characterized in context of their role in human diseases including cancers. In this work we characterize the structural-functional properties of a cluster of 5 genes –TMEM97, IFT20, TNFAIP1, POLDIP2 and TMEM199, termed TNFAIP1 / POLDIP2 module. This cluster is organized as CSAGA in cytoband 17q11.2. Affymetrix U133A&B expression data of two large cohorts (410 atients, in total) of breast cancer patients and patient survival data were used. For the both studied cohorts, we demonstrate (i) strong and reproducible transcriptional co-regulatory patterns of genes of TNFAIP1/POLDIP2 module in breast cancer cell subtypes and (ii) significant associations of TNFAIP1/POLDIP2 CSAGA with amplification of the CSAGA region in breast cancer, (ii) cancer aggressiveness (e.g. genetic grades) and (iv) disease free patient-s survival. Moreover, gene pairs of this module demonstrate strong synergetic effect in the prognosis of time of breast cancer relapse. We suggest that TNFAIP1/ POLDIP2 cluster can be considered as a novel type of structural-functional gene modules in the human genome.
Abstract: De novo genome assembly is always fragmented. Assembly fragmentation is more serious using the popular next generation sequencing (NGS) data because NGS sequences are shorter than the traditional Sanger sequences. As the data throughput of NGS is high, the fragmentations in assemblies are usually not the result of missing data. On the contrary, the assembled sequences, called contigs, are often connected to more than one other contigs in a complicated manner, leading to the fragmentations. False connections in such complicated connections between contigs, named a contig graph, are inevitable because of repeats and sequencing/assembly errors. Simplifying a contig graph by removing false connections directly improves genome assembly. In this work, we have developed a tool, SIMGraph, to resolve ambiguous connections between contigs using NGS data. Applying SIMGraph to the assembly of a fungus and a fish genome, we resolved 27.6% and 60.3% ambiguous contig connections, respectively. These results can reduce the experimental efforts in resolving contig connections.
Abstract: We have developed a database for membrane protein functions, which has more than 3000 experimental data on functionally important amino acid residues in membrane proteins along with sequence, structure and literature information. Further, we have proposed different methods for identifying membrane proteins based on their functions: (i) discrimination of membrane transport proteins from other globular and membrane proteins and classifying them into channels/pores, electrochemical and active transporters, and (ii) β-signal for the insertion of mitochondrial β-barrel outer membrane proteins and potential targets. Our method showed an accuracy of 82% in discriminating transport proteins and 68% to classify them into three different transporters. In addition, we have identified a motif for targeting β-signal and potential candidates for mitochondrial β-barrel membrane proteins. Our methods can be used as effective tools for genome-wide annotations.
Abstract: As part of national epidemiological survey on bovine
viral diarrhea virus (BVDV), a total of 274 dejecta samples were
collected from 14 cattle farms in 8 areas of Xinjiang Uygur
Autonomous Region in northwestern China. Total RNA was extracted
from each sample, and 5--untranslated region (UTR) of BVDV
genome was amplified by using two-step reverse
transcriptase-polymerase chain reaction (RT-PCR). The PCR products
were subsequently sequenced to study the genetic variations of BVDV
in these areas. Among the 274 samples, 33 samples were found
virus-positive. According to sequence analysis of the PCR products,
the 33 samples could be arranged into 16 groups. All the sequences,
however, were highly conserved with BVDV Osloss strains. The virus
possessed theses sequences belonged to BVDV-1b subtype by
phylogenetic analysis. Based on these data, we established a typing
tree for BVDV in these areas. Our results suggested that BVDV-1b
was a predominant subgenotype in northwestern China and no
correlation between the genetic and geographical distances could be
observed above the farm level.
Abstract: Tofurther advance research on immune-related genes
from T. molitor, we constructed acDNA library and analyzed
expressed sequence taq (EST) sequences from 1,056 clones. After
removing vector sequence and quality checkingthrough thePhred
program (trim_alt 0.05 (P-score>20), 1039 sequences were generated.
The average length of insert was 792 bp. In addition, we identified 162
clusters, 167 contigs and 391 contigs after clustering and assembling
process using a TGICL package. EST sequences were searchedagainst
NCBI nr database by local BLAST (blastx, E
Abstract: Bioinformatics and computational biology involve
the use of techniques including applied mathematics,
informatics, statistics, computer science, artificial intelligence,
chemistry, and biochemistry to solve biological problems
usually on the molecular level. Research in computational
biology often overlaps with systems biology. Major research
efforts in the field include sequence alignment, gene finding,
genome assembly, protein structure alignment, protein structure
prediction, prediction of gene expression and proteinprotein
interactions, and the modeling of evolution. Various
global rearrangements of permutations, such as reversals and
transpositions,have recently become of interest because of their
applications in computational molecular biology. A reversal is
an operation that reverses the order of a substring of a permutation.
A transposition is an operation that swaps two adjacent
substrings of a permutation. The problem of determining the
smallest number of reversals required to transform a given
permutation into the identity permutation is called sorting by
reversals. Similar problems can be defined for transpositions
and other global rearrangements. In this work we perform a
study about some genome rearrangement primitives. We show
how a genome is modelled by a permutation, introduce some
of the existing primitives and the lower and upper bounds
on them. We then provide a comparison of the introduced
primitives.