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1

Profiling of regulatory microRNA transcriptomes in various biological processes: a review

100%
Shah A. A., Meese E., Blin N.
Journal of Applied Genetics
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2010
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vol. 51
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issue 4
501-507
EN
A class of small, non-coding ribonucleic acids, termed microRNA (miRNA), has recently emerged as a new key player in the cellular control of gene expression. By either blocking translation or inducing target mRNA degradation, miRNA not only participates in regular biological processes within cells and tissues but is also involved in pathological processes. Many human malignancies have been linked to specific miRNA expression patterns, raising hopes for new approaches to therapy. While such human disease-related mechanisms have been widely discussed and frequently reviewed, miRNA's general significance in animals has been less in editorial focus, despite its obvious role in basic physiological processes, e.g. neurosensory maturation, development of fertility, and hibernation. Using selected examples, this review highlights our current knowledge of miRNA's potential and its promise as a new tool for gene regulation.
2

Aberrant epigenetic patterns in the etiology of gastrointestinal cancers

100%
Karpinski P., Sasiadek M. M., Blin N.
Journal of Applied Genetics
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2008
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vol. 49
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issue 1
1-10
EN
A body of evidence accumulated over the past decade suggests that epigenetic mechanisms play an essential role in maintaining important cellular functions. Changes in epigenetic patterns (mainly DNA hyper- and hypomethylation and, more recently, histone modifications) may contribute to the development of cancer. Aberrant epigenetic events expand thorough tumor progression from the earliest to latest stages, therefore they can serve as convenient markers for detection and prognosis of cancer. The potential reversibility of epigenetic states in the tumor cell is an attractive target for cancer therapy. Much of our current knowledge on epigenetic alternations in cancer comes from studies on gastrointestinal malignancies, mainly on colorectal cancer, which currently serves as a model for epigenetic tumorigenesis. This review summarizes the current knowledge of epigenetic changes in gastrointestinal cancers and how this relates directly to disease progression and prognosis.
3

Molecular phylogenetics employing modern and ancient DNA

100%
Pusch C. M., Broghammer M., Blin N.
Journal of Applied Genetics
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2003
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vol. 44
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issue 3
269-290
EN
Comparative studies of DNA in recent populations and characterisation of ancient hereditary material have contributed very interesting facts to our understanding of evolution of modern mankind. Analysis of DNA homology in related species, assessment of mutations and polymorphisms in various populations and new DNA sequence data from prehistoric finds allowed ? via sophisticated DNA extraction techniques, PCR, sequencing and digitalised processing of genetic information ? insights into possible roots of Homo sapiens and related species, migration patterns and ancient cultural habits, thus enriching the palaeoanthropological discipline. However, a presentation of this development would not be complete without pointing towards the methodological limitations and manifold presentations burdened with artifacts, data misinterpretation and unjustified conclusions. Presently, this modern field of research is in its consolidation phase and new parameters for quality control and authentication are being implemented to avoid spectacular but unfounded reports. It is expected that most of the problems connected to old biomolecules may be closely related to fossilisation parameters. The future challenge will be the full understanding of the complex and multi-faceted processes underlying diagenesis, including the elucidation of nucleic acid ?postmortem damage?.
4

The intestinal trefoil factor (Tff3), also expressed in the inner ear, interacts with peptides contributing to apoptosis

100%
Lubka M., Shah A. A., Blin N., Baus-Loncar M.
Journal of Applied Genetics
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2009
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vol. 50
|
issue 2
167-171
EN
The 3 members of the mammalian trefoil factor family (TFF) are expressed and secreted as cytoprotective peptides along the entire length of the normal gastrointestinal tract. More recently, they were shown to display multifunctional properties. Goblet cells of the small and large intestine constitute a major source for the synthesis of the third family member, TFF3 (formerly intestinal trefoil factor, ITF). TFF3, like the other family members, is rapidly up-regulated in response to physical wounding of the digestive tract. In addition, Tff3 was also detected in the posterior pituitary gland. Apart from this Tff3 function as a neuropeptide, also presence of Tff3 in the mouse cochlea was noted and Tff3-deficient animals display hearing impairment and accelerated presbyacusis. To elucidate Tff3's mode of function and its unexpected contribution to the hearing process, we strived to determine Tff3's interacting partners and to establish the functional network. To this end, we used a protein-protein binding assay based on a specific transcriptional regulation in yeast cells (the yeast-two-hybrid assay). We looked for interacting partners of Tff3 in a mouse cochlea cDNA library (from donors aged 3?15 days, P3-P15). Our data show that several binding candidates exist and that they could contribute to the known involvement of the trefoil peptides to apoptosis.
5

Unidirectional orientation of twelve expressed tagged sites within 40 kb of human chromosomal region 22q13.1

100%
Pusch C., Wang Z., Roe B., Blin N.
Journal of Applied Genetics
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1998
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vol. 39
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issue 2
199-204
EN
. The single copy sequence D22S16 from human chromosomal region 22q13.1 that carries a putative conserved gene, was used to probe a chromosome 22-specific cosmid library. Genomic sequencing of one positive, 40 kb long cosmid (C1155) revealed a hereto unmapped gene (a subunit of DNA-dependent RNA polymerase II, POLR2F), a SOX9-related sequence and 12 expressed sequence tags. Although not parts of one consecutive gene, all 12 ESTs and, in addition, the polymerase gene are oriented in the same transcriptional direction within the genomic sequence represented by cosmid C1155.
6

Documenting ancient DNA quality via alpha satellite amplification and assessment of clone sequence diversity

76%
Pusch C. M., Kayademir T., Prangenberg K., Conard N. J., Czarnetzki A., Blin N.
Journal of Applied Genetics
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2002
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vol. 43
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issue 3
351-363
EN
C/GT/A nucleotide alterations have been shown to hamper the straightforward interpretation of mitochondrial DNA sequence data derived from ancient tissues. Attempting to characterise this finding with respect to nuclear DNA, we contrasted two established protocols: (i) an enzymatic repair of damaged DNA, thereby translating and closing nicks in the DNA, and (ii) the application of N-phenacylthiazolium bromide, which cleaves glucose-derived protein crosslinks, presumably derived from Maillard reactions. We used medieval human bones that were refractory to standard PCR procedures. Due to negligible presence of short tandem repeat loci and also mitochondrial sequences, the extracted ancient DNA needed a higher copy PCR system to yield amplification products. The chosen PCR target was specific alphoid repetitive DNA with an experimentally determined minimum of 1000 copies per haploid genome. Alphoid repeat segments were generated from both contemporary DNA and DNA extracts of two human skeletons dating from 450-600 AD (omitting uracil N-glycosylase pre-treatment of the extracted samples), and were subsequently cloned and sequenced. The sequences were evaluated for the number and type of nucleotide alterations noted after the different pre-treatments, and were compared to our alphoid consensus sequence generated from modern DNA. Both methods failed to reflect the expected 32% variability among single alphoid repeats (accounting for locus-specific differences and polymerase errors) as well as to display the actual 2.88 ratio of transitions to transversions. Our data obtained from high-copy-number nuclear DNA mirror the phenomenon of sequence deviations observed in mitochondrial DNA extracted from old specimens.
7

Frequent D-loop polymorphism in mtDNA enables genotyping of 1400-year-old human remains from Merowingian graves

76%
Zeller M., Mirghomizadeh M. F., Mirghomizadeh F., Wehner W. H.-D., Wehner H.-D., Blin B. N., Blin N.
Journal of Applied Genetics
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2000
|
vol. 41
|
issue 4
285-292
EN
Improvements of DNA extraction and amplification techniques presently enable DNA analysis of ancient DNA (aDNA) from samples which range from several hundred years of age up to possibly 5000 years. Taking advantage of the abundance of mitochondrial DNA and its polymorphic D-loop sequence, ten individuals from multiple burial sites of the Merowingian culture (South Germany), estimated to be about 1400 years old, were genotyped to determine possible kinship. Moreover, gonosomal DNA markers from the X- and Y-chromosome were applied for sex determination of the remains. In all individuals investigated, deviations from the Anderson mtDNA consensus sequence were observed, all representing substitutions (7 transitions and 3 transversions). Although such mutations have been reported from recent populations, our study constitutes the first description of these mtDNA mutations from numerous aDNA samples recovered from multiple burial sites. The results obtained by molecular anthropology can aid in describing kinship relations and burial customs of ancient remains.
8

Adaptor-mediated amplification of minute amounts of severely fragmented ancient nucleic acids

64%
Pusch C. M., Blin B. N., Blin N., Broghammer B. M., Broghammer M., Nicholson N. G. J., Nicholson G. J., Scholz S. M., Scholz M.
Journal of Applied Genetics
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2000
|
vol. 41
|
issue 4
303-315
EN
It has been repeatedly shown that high copy number mitochondrial DNA sequences can be recovered from ancient samples. A significant increase in the volume of information available to researchers will be observed when the amplification of nuclear DNA becomes commonplace and reproducible. To this end we established a modification of the Rapid Amplification of cDNA Ends (RACE) procedure normally used for the generation of cDNA ends from adaptor-ligated expressed sequence tag libraries. The modifications were designed to specifically address the problems associated with the highly damaged nucleic acids extracted from palaeontological specimens. For this study we used 6 human samples dating to 450 AD and ~6.500 BP that were refractory to reliable amplification of single copy loci by PCR. Racemate contents (ratio of D/L enantiomers) of aspartic acid, alanine, and leucine also indicated that no amplifiable DNA is present in 5 of the 6 samples. The proposed technique allowed us (i) to amplify four X-chromosomal loci from 5 human specimens, and (ii) to correct allelic drop-out phenomena at the amelogenin locus in one individual, thus showing that the threshold of 80 ? 10?3 for D/Lasp as a borderline for the presence/absence of amplifiable aDNA requires reassessment. Reliability of the proposed technique (i.e. amplification of DNA sequences endogenous to the find) was validated by the application of ?ancient RACE? (aRACE) to prehistoric animal samples.
9

Analysis of candidate genes for genotypic diagnosis in the long QT syndrome

64%
Haack B., Kupka S., Ebauer M., Siemiatkowska A., Pfister M., Kwiatkowska J., Erecinski J., Limon J., Ochman K., Blin N.
Journal of Applied Genetics
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2004
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vol. 45
|
issue 3
375-381
EN
Patients with the long QT syndrome (LQTS) suffer from cardiac arrhythmias that can lead to abrupt loss of consciousness and sudden death, already in young individuals. Thus, an early diagnosis of LQTS is essential for patients and their family members. So far, six genes (KCNQ1, HERG, SCN5A, ANK2, KCNE1, KCNE2) have been demonstrated to be involved in the development of LQTS. Since this syndrome is genetically heterogeneous and large-sized families are often not available for linkage analysis, alternative tools are required for a genetic diagnosis. To investigate genes with numerous exons, like KCNQ1, HERG, SCN5A and ANK2, segregation analysis of a Polish Romano-Ward family with eight members was performed as a reliable method faster than linkage analysis or direct sequencing. To test these four LQT loci, an appropriate selection of microsatellite markers covering different chromosomal regions was applied. Furthermore, two small genes KCNE1 and KCNE2 (at the LQT5 and LQT6 loci), and the SGK1 gene (encoding a kinase regulating KCNE1 and SCN5A channels) were sequenced. All six LQT loci and the SGK1 gene were excluded by these analyses, thus a different pathogenic mechanism of LQT syndromes can be presumed.
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