A Novel Partial Sequence Alignment Tool for Finding Large Deletions

Finding large deletions in genome sequences has become increasingly more useful in bioinformatics, such as in clinical research and diagnosis. Although there are a number of publically available next generation sequencing mapping and sequence alignment programs, these software packages do not correctly align fragments containing deletions larger than one kb. We present a fast alignment software package, BinaryPartialAlign, that can be used by wet lab scientists to find long structural variations in their experiments. For BinaryPartialAlign, we make use of the Smith-Waterman (SW) algorithm with a binary-search-based approach for alignment with large gaps that we called partial alignment. BinaryPartialAlign implementation is compared with other straight-forward applications of SW. Simulation results on mtDNA fragments demonstrate the effectiveness (runtime and accuracy) of the proposed method

Cloning of chimerical translocations as positive control for molecular genetic diagnosis of leukemia

The diagnosis of leukemia-specific mRNAs by polymerase chain reaction (PCR) and reverse transcription-PCR (RT-PCR) require well-known positive standard controls. In general, the positive controls are obtained from cell lines and leukemia patients who have been diagnosed at the molecular level by RT-PCR. These are expensive and restricted sources for standard positive controls. Thus, there is a need for less expensive and reproducible standard positive controls in this area. We have cloned the t (9: 22) p190, t (9: 22) p210, t (4: 11), t (1: 19), t (15: 17), t (12; 21) breakpoint junctions of fusion genes into the plasmids. Cloned fusion genes are suitable for testing PCR experiments of the molecular genetic diagnosis of leukemia samples. We cloned and optimized fusion gene junctions as a standard positive control to check PCR efficiency and as a standard positive marker for diagnosis

Relationship between Oral Anaerobic Bacteria and Otitis Media with Effusion

Objective: In this study hypothesing the translocation of oral bacteria from oropharynx into the middle ear cavity may be involved in the pathogenesis of otitis media with effusion (OME), we aimed to investigate the presence and similarity of Fusobacterium nucleatum and Treponema denticola in saliva, nasopharyngeal secretion and the middle ear effusion samples from the children with OME

Pendrin expression in nodular and non-nodular thyroid tissues

Introduction: Different mechanisms for the expression of pendrin which is an apical iodide transporter have been reported in nodular thyroid tissues compared to normal thyroid. The aim of the present study was to determine the alterations of pendrin expression in nodular and surrounding non-nodular thyroid tissues and clarify the role of pendrin in the functional behaviour of nodular lesions. Material and methods: Twenty-six nodular and paired non-nodular normal thyroid tissues were collected at the same centre. Patients were divided into two groups based on the function of the dominant thyroid nodule; hot nodules (n = 18) and cold nodules (n = 8). mRNA levels of pendrin were evaluated by quantitative RT-PCR. Pendrin protein expression was determined by immunohistochemical analysis. Results of dominant nodules were compared to non-nodular thyroid tissue of the same patient. Results: No statistically significant difference was found with respect to qualitative and quantitative measurements of pendrin expression between hot and cold nodules. However, percent immunohistochemical staining of pendrin was significantly higher in both hot and cold nodules compared to non-nodular thyroid tissue of the same patients. RT-PCR revealed comparable mRNA levels of pendrin gene between hot nodules and corresponding normal thyroid tissues. However, in cold nodules, significantly decreased mRNA levels of pendrin were observed compared to normal thyroid tissue. mRNA levels of pendrin showed significant positive correlation with TSH in corresponding non-nodular thyroid tissues. Conclusions: The present study demonstrates that expression of pendrin could not be influenced by TSH in thyroid nodules and expression level of pendrin seems not to have an effect on nodule function. (Endokrynol Pol 2013; 64 (3): 208–214)Wstęp: W guzkowej tkance tarczycowej opisano odmienny od pozaguzkowej tkanki tarczycowej mechanizm ekspresji pendryny — transportera jodu zlokalizowanego w części szczytowej komórki. Celem badania było ustalenie zmian w ekspresji pendryny w guzkowej tkance tarczycowej i otaczającej ją pozaguzkowej tkance tarczycowej, aby wyjaśnić rolę pendryny w zachowaniu czynnościowym zmian guzkowych. Materiał i metody: W tym samym ośrodku pobrano 26 wycinków guzkowej tkanki tarczycowej i sparowanych wycinków pozaguzkowej prawidłowej tkanki tarczycowej. Pacjentów podzielono na dwie grupy w zależności od statusu czynnościowego guzka dominującego: grupę z guzkami gorącymi (n = 18) i grupę z guzkami zimnymi (n = 8). Poziom mRNA i pendryny oznaczono ilościowo metodą RT-PCR. Ekspresję białka pendryny oznaczono metodą immunohistochemiczną. Wyniki dla guzków dominujących porównano z wynikami dla tkanki pozaguzkowej u tego samego pacjenta. Wyniki: Nie stwierdzono statystycznie znamiennych różnic pomiędzy guzkami gorącymi i zimnymi, jeżeli chodzi o wyniki oznaczenia ilościowego i jakościowego ekspresji pendryny. Procentowe barwienie immunohistochemiczne w kierunku pendryny było natomiast znamiennie większe zarówno w przypadku guzków gorących, jak i zimnych w porównaniu z tkanką pozaguzkową u tych samych pacjentów. RT-PCR wykazało porównywalne poziomy mRNA genu kodującego pendrynę w guzkach gorących i prawidłowej tkance tarczycowej u tych samych pacjentów. Z kolei w przypadku guzków zimnych stwierdzono znamiennie niższe poziomy pendryny w porównaniu z prawidłową tkanką tarczycową. Stwierdzono też korelację dodatnią poziomu mRNA pendryny i poziomu TSH w korespondujących tkankach pozaguzkowych. Wnioski: W przeprowadzonym badaniu wykazano, że na ekspresję pendryny nie może mieć wpływu TSH w guzkach tarczycy oraz że poziom ekspresji pendryny nie wydaje się wpływać na czynność guzków. (Endokrynol Pol 2013; 64 (3):208–214

Genome-wide association study identifies variants in the MHC class I, IL10, and IL23R-IL12RB2 regions associated with Behcet's disease

Behcet's disease is a genetically complex disease of unknown etiology characterized by recurrent inflammatory attacks affecting the orogenital mucosa, eyes and skin. We performed a genome-wide association study with 311,459 SNPs in 1,215 individuals with Behcet's disease (cases) and 1,278 healthy controls from Turkey. We confirmed the known association of Behcet's disease with HLA-B*51 and identified a second, independent association within the MHC Class I region. We also identified an association at IL10 (rs1518111, P = 1.88 x 10(-8)). Using a meta-analysis with an additional five cohorts from Turkey, the Middle East, Europe and Asia, comprising a total of 2,430 cases and 2,660 controls, we identified associations at IL10 (rs1518111, P = 3.54 x 10(-18), odds ratio = 1.45, 95% CI 1.34-1.58) and the IL23R-IL12RB2 locus (rs924080, P = 6.69 x 10(-9), OR = 1.28, 95% CI 1.18-1.39). The disease-associated IL10 variant (the rs1518111 A allele) was associated with diminished mRNA expression and low protein production

A novel ATP8 gene mutation in an infant with tetralogy of Fallot

We report the case of a novel mitochondrial DNA mutation in the MT-ATP8 gene in an infant with tetralogy of Fallot. Next-generation sequencing was applied to sequence whole mitochondrial DNA of the patient. A known Leber's hereditary optic neuropathy-associated mutation (G9804A), a heteroplasmic T7501C mutation (17%), and a novel C8481 T Pro > Leu missense mutation in the MT-ATP8 gene was identified

Designing of a novel dextransucrase efficient in acceptor reactions

Dextransucrase is produced by Leuconostoc, Streptococcus and Lactobacillus Species. The enzyme synthesizes dextran and acceptor products some of which act as prebiotics that are increasingly used in such industries as food, medicine, and cosmetics. B-512F Leuconostoc mesenteroides dextransucrase (DSR-S) is the preferred enzyme in commercial production of dextran and prebiotics. In the present work, a novel dextransucrase which is efficient in prebiotics production was designed. The enzyme was produced at optimal conditions in Escherichia coli by truncation and fusion to glutathione S-transferase (GST) in the gene from Leuconostoc mesenteroides B-512 FMC. The novel enzyme (MW: 119 kDa) was active and carried out dextran biosynthesis and acceptor reactions effectively. The novel dextransucrase (fTDSR-S) was produced by truncating signal, variable, and the glucan-binding regions in the gene and fusion of gst gene at the 50 end. fTDSR-S was characterized in detail and compared to the DSR-S. Truncation and fusion resulted in an increase in fTDSR-S biosynthesis in E. coli BL21 (DE3) by 35 fold. fTDSR-S leads to production of dextran as well as increased acceptor reactions. Due to GST fusion, it was possible to immobilize fTDSR-S covalently onto Eupergit C successfully. It was also found that the size of the active site of dextransucrase is 49 amino acids shorter than that reported previously in the literature. (C) 2014 Elsevier Ltd. All rights reserved

A novel method for covalent immobilization of dextransucrase

B-512F dextransucrase is an industrial enzyme used in commercial production of dextran and prebiotics. Several researchers have studied the covalent immobilization of this enzyme with little success due to dextran masking the reactive groups on the enzyme and inactivation of the enzyme during immobilization. A novel dextransucrase was designed and produced successfully to eliminate problems faced in covalent immobilization. In production of the novel enzyme, B-512F dextransucrase was truncated at N and C terminals and fused to glutathione S-transferase. The novel dextransucrase was fully active and carried out dextran biosynthesis and acceptor reactions effectively. The novel enzyme was immobilized covalently onto Eupergit C 250L, giving rise to 100% immobilization and 83.3% activity yields. Immobilized enzyme was used successfully for the production of acceptor products and low molecular weight dextran. The immobilized enzyme showed no decrease in activity for 15 batch reactions and retained its initial activity at storage (4 degrees C) for 35 days. Optimal conditions were not affected by the immobilization. The kinetic parameters for the free and immobilized enzyme were determined. The acceptor reactions using fructose, glucose, maltose, and lactose were also studied. The novel method developed could also be used in immobilization of some other biomolecules. (C) 2012 Elsevier B.V. All rights reserved

A Comparative Analysis of Smith-Waterman Based Partial Alignment

Finding large deletions in genome sequences have become increasingly more useful in bioinformatics, such as in clinical research and diagnosis. Several partial alignment approaches based on the Smith-Waterman (SW) algorithm has been proposed for alignment with large gaps. However, in the literature, no detailed comparisons of these three SW-based methods were given in terms of the runtimes and errors in estimated position of the start of the deletion in the query sequences. Our comparative simulations show that BinaryPartialAlign has the lowest error and very high speed