Study of genetic variations of mitochondrial NADH dehydrogenase subunit 4 in Iranian women with breast cancer

Background: Breast cancer is the second reason of death in women population all around the world. One out of every eight women will be diagnosed with breast cancer in Iran. So, finding some clinical markers for prediction of cancer in the early stage is too important. There are many causes for cancer that mutation in the mitochondrial genome is one of the reasons, which had been observed in most breast cancer studies. The aim of this study was to evaluate the genetic region of ND4 in patients with breast cancer. Materials and Methods: This cross-sectional study was conducted on 60 women with breast cancer and 28 healthy women. DNA was extracted from paraffin blocks, the area mtND4 (11646-11860) was amplified by polymerase chain reaction, then the SSCP analysis was used to investigate different conformations between normal and cancer samples. Finally, each sample with different conformation was sequenced. Results: In this study, the sequence of mtND4 in 24 suspected patients was determined and 15 nucleotide changes were reported. the most variations was related to the G11719A polymorphism site. Other changes included 11803delT, G11717A, C11735T, C11716G, C11702T and A11812G. Conclusion: The findings of this study show new genetic changes in the mtND4. So, further studies are required to examine the role of these mutations to detect early breast cancer

Scale-up thermostable α-amylase production in lab-scale fermenter using rice husk as an elicitor by Bacillus licheniformis-AZ2 isolated from Qinarje Hot Spring (Ardebil Prov. of Iran)

Background and purpose: Amylases are commercially important enzymes with various biotechnological, clinical and medical applications. This study aimed at scaling up α-amylase production elicited by rice husk in stirred-fermenter using Bacillus lichneniformis-AZ2 isolated from Qinarje Hot Spring. Materials and methods: Effect of temperature, aeration rate and agitation speed on bacterial growth and ɑ-amylase production were investigated under batch fermentation process in a 3-Lit stirred-fermenter. OFAT method was followed to select optimum level of each parameter. Other factors were set upon the results of previous experiments carried out in shake-flask scale. Results: Maximum α-amylase production of 17.66 ± 0.87 U/mL (2.1 folds more than shake-flask cultures) was achieved in stirred-fermenter with optimized agitation speed of 100 rpm and 1 vvm aeration rate at 37ºC after 60 h of incubation. This time was shorter than the corresponding fermentation time obtained from shake-flask experiments by half. A comparison of kinetic parameters of fermentation in stirred-fermenter and shake-flask cultures revealed that B. licheniformis-AZ2 was more active to synthesize ɑ-amylase in fermenter. In shaken cultures Qx, Qp, Yp/x, µmax, qp and td, were 0.27 (g/L/h), 228.6 (U/L/h), 13.64 (U/g), 0.055 (h-1), 0.76 (U/g/h) and 12.48 h, whereas in stirred-fermenter the above values were 0.40 (g/L/h), 723.1 (U/L/h), 45.17 (U/g), 0.120 (h-1), 5.42 (U/g/h) and 5.78 h, respectively. Conclusions: SmF in stirred-fermenter is a potential strategy for ɑ-amylase production. Although for commercialization further studies are needed in pilot-scale. Rice husk as a low-cost agro-waste is preferable to use as the carbon and energy sources, which provides a great ɑ-amylase elicitation.</p

Production of thermostable extracellular α-amylase by a moderate thermophilic Bacillus licheniformis isolated from Qinarje Hot Spring (Ardebil prov. of Iran)

Background and Purpose: Amylases are most important industrial enzymes that account for about 30% of the world’s food, feed, fermentation, textile, detergent and cellulosic industries. This study aimed at optimum production of thermostable α-amylase via moderate thermophilic bacterium (Bacillus licheniformis) which was recently isolated from Qinarje Hot spring.Material and Methods: Initially, ability of bacterium for amylase activity was determined by starch hydrolysis test using Gram’s iodine staining. Then bacterial growth pattern and amylase production curves in basal production medium were graphically determined at different time intervals. Finally, effect of different temperature, pH, carbon source, nitrogen source, minerals and inoculum size were studied on bacterial growth and amylase production using turbidimetric and DNS method, respectively.Results: Optimum enzyme production achieved after 84 hours of inoculation from cultures growing at 40 ˚C and pH 9.0 in a medium containing 0.03% (w/v) of CaCl2, compared to the basal medium, results showed that the best enzyme production happened with inoculum size of 4% (v/v). The addition of 1% (w/v) rice husk (as a Carbon source) enhanced enzyme productivity up to 160% and substitution of the peptone and yeast extract with 1% (w/v) of tryptone (as a Nitrogen source) increased the α-amylase production up to 160%.Conclusion: Our findings show that B. licheniformis-AZ2 strain has an ability to produce the thermostable α-amylase which is suitable in starch processing and food industries. To be commercialized, further investigation is required for enhancement of the enzyme production.Keywords: Bacillus licheniformis; Optimization; Basal medium; Agricultural by-products.</p

Structure and Function of a Mycobacterial NHEJ DNA Repair Polymerase

Non homologous end-joining (NHEJ)-mediated repair of DNA double-strand breaks in prokaryotes requires Ku and a specific multidomain DNA ligase (LigD). We present crystal structures of the primase/polymerisation domain (PolDom) of Mycobacterium tuberculosis LigD, alone and complexed with nucleotides. The PolDom structure combines the general fold of the archaeo-eukaryotic primase (AEP) superfamily with additional loops and domains that together form a deep cleft on the surface, likely used for DNA binding. Enzymatic analysis indicates that the PolDom of LigD, even in the absence of accessory domains and Ku proteins, has the potential to recognise DNA end-joining intermediates. Strikingly, one of the main signals for the specific and efficient binding of PolDom to DNA is the presence of a 5'-phosphate group, located at the single/double-stranded junction at both gapped and 3'-protruding DNA molecules. Although structurally unrelated, Pol lambda and Pol mu, the two eukaryotic DNA polymerases involved in NHEJ, are endowed with a similar capacity to bind a 5'-phosphate group. Other properties that are beneficial for NHEJ, such as the ability to generate template distortions and realignments of the primer, displayed by Pol lambda and Pol mu, are shared by the PolDom of bacterial LigD. In addition, PolDom can perform non-mutagenic translesion synthesis on termini containing modified bases. Significantly, ribonucleotide insertion appears to be a recurrent theme associated with NHEJ, maximised in this case by the deployment of a dedicated primase, although its in vivo relevance is unknown

Engineered split in Pfu DNA polymerase fingers domain improves incorporation of nucleotide γ-phosphate derivative

Using compartmentalized self-replication (CSR), we evolved a version of Pyrococcus furiosus (Pfu) DNA polymerase that tolerates modification of the γ-phosphate of an incoming nucleotide. A Q484R mutation in α-helix P of the fingers domain, coupled with an unintended translational termination-reinitiation (split) near the finger tip, dramatically improve incorporation of a bulky γ-phosphate-O-linker-dabcyl substituent. Whether synthesized by coupled translation from a bicistronic (−1 frameshift) clone, or reconstituted from separately expressed and purified fragments, split Pfu mutant behaves identically to wild-type DNA polymerase with respect to chromatographic behavior, steady-state kinetic parameters (for dCTP), and PCR performance. Although naturally-occurring splits have been identified previously in the finger tip region of T4 gp43 variants, this is the first time a split (in combination with a point mutation) has been shown to broaden substrate utilization. Moreover, this latest example of a split hyperthermophilic archaeal DNA polymerase further illustrates the modular nature of the Family B DNA polymerase structure

Novel mutations in Moloney Murine Leukemia Virus reverse transcriptase increase thermostability through tighter binding to template-primer

In an effort to increase the thermostability of Moloney Murine Leukemia Virus reverse transcriptase (MMLV RT), we screened random and site-saturation libraries for variants that show increased resistance to thermal inactivation. We discovered five mutations E69K, E302R, W313F, L435G and N454K that collectively increase the half-life of MMLV RT at 55°C from less than 5 min to ∼30 min in the presence of template-primer. In addition, these mutations alter the thermal profile by increasing specific activity of the pentuple mutant (M5) over a broad range of cDNA synthesis temperatures (25–70°C). We further show that M5 generates higher cDNA yields and exhibits better RT–PCR performance compared to wild-type RT when used at high temperature to amplify RNA targets containing secondary structure. Finally, we demonstrate that M5 exhibits tighter binding (lower Km) to template-primer, which likely protects against heat inactivation

A Recurrent Stop-Codon Mutation in Succinate Dehydrogenase Subunit B Gene in Normal Peripheral Blood and Childhood T-Cell Acute Leukemia

BACKGROUND: Somatic cytidine mutations in normal mammalian nuclear genes occur during antibody diversification in B lymphocytes and generate an isoform of apolipoprotein B in intestinal cells by RNA editing. Here, I describe that succinate dehydrogenase (SDH; mitochondrial complex II) subunit B gene (SDHB) is somatically mutated at a cytidine residue in normal peripheral blood mononuclear cells (PBMCs) and T-cell acute leukemia. Germ line mutations in the SDHB, SDHC or SDHD genes cause hereditary paraganglioma (PGL) tumors which show constitutive activation of homeostatic mechanisms induced by oxygen deprivation (hypoxia). PRINCIPAL FINDINGS: To determine the prevalence of a mutation identified in the SDHB mRNA, 180 samples are tested. An SDHB stop-codon mutation c.136C>T (R46X) is present in a significant fraction (average = 5.8%, range = less than 1 to 30%, n = 52) of the mRNAs obtained from PBMCs. In contrast, the R46X mutation is present in the genomic DNA of PBMCs at very low levels. Examination of the PBMC cell-type subsets identifies monocytes and natural killer (NK) cells as primary sources of the mutant transcript, although lesser contributions also come from B and T lymphocytes. Transcript sequence analyses in leukemic cell lines derived from monocyte, NK, T and B cells indicate that the mutational mechanism targeting SDHB is operational in T-cell acute leukemia. Accordingly, substantial levels (more than 3%) of the mutant SDHB transcripts are detected in five of 20 primary childhood T-cell acute lymphoblastic leukemia (T-ALL) bone marrow samples, but in none of 20 B-ALL samples. In addition, distinct heterozygous SDHB missense DNA mutations are identified in Jurkat and TALL-104 cell lines which are derived from T-ALLs. CONCLUSIONS: The identification of a recurrent, inactivating stop-codon mutation in the SDHB gene in normal blood cells suggests that SDHB is targeted by a cytidine deaminase enzyme. The SDHB mutations in normal PBMCs and leukemic T cells might play a role in cellular pre-adaptation to hypoxia

Quantitative Assessment of the Sensitivity of Various Commercial Reverse Transcriptases Based on Armored HIV RNA

The in-vitro reverse transcription of RNA to its complementary DNA, catalyzed by the enzyme reverse transcriptase, is the most fundamental step in the quantitative RNA detection in genomic studies. As such, this step should be as analytically sensitive, efficient and reproducible as possible, especially when dealing with degraded or low copy RNA samples. While there are many reverse transcriptases in the market, all claiming to be highly sensitive, there is need for a systematic independent comparison of their applicability in quantification of rare RNA transcripts or low copy RNA, such as those obtained from archival tissues.We performed RT-qPCR to assess the sensitivity and reproducibility of 11 commercially available reverse transcriptases in cDNA synthesis from low copy number RNA levels. As target RNA, we used a serially known number of Armored HIV RNA molecules, and observed that 9 enzymes we tested were consistently sensitive to ∼1,000 copies, seven of which were sensitive to ∼100 copies, while only 5 were sensitive to ∼10 RNA template copies across all replicates tested. Despite their demonstrated sensitivity, these five best performing enzymes (Accuscript, HIV-RT, M-MLV, Superscript III and Thermoscript) showed considerable variation in their reproducibility as well as their overall amplification efficiency. Accuscript and Superscript III were the most sensitive and consistent within runs, with Accuscript and Superscript II ranking as the most reproducible enzymes between assays.We therefore recommend the use of Accuscript or Superscript III when dealing with low copy number RNA levels, and suggest purification of the RT reactions prior to downstream applications (eg qPCR) to augment detection. Although the results presented in this study were based on a viral RNA surrogate, and applied to nucleic acid lysates derived from archival formalin-fixed paraffin embedded tissue, their relative performance on RNA obtained from other tissue types may vary, and needs future evaluation

Polymorphisms in the glucocerebrosidase gene and pseudogene urge caution in clinical analysis of Gaucher disease allele c.1448T>C (L444P)

BACKGROUND: Gaucher disease is a potentially severe lysosomal storage disorder caused by mutations in the human glucocerebrosidase gene (GBA). We have developed a multiplexed genetic assay for eight diseases prevalent in the Ashkenazi population: Tay-Sachs, Gaucher type I, Niemann-Pick types A and B, mucolipidosis type IV, familial dysautonomia, Canavan, Bloom syndrome, and Fanconi anemia type C. This assay includes an allelic determination for GBA allele c.1448T>C (L444P). The goal of this study was to clinically evaluate this assay. METHODS: Biotinylated, multiplex PCR products were directly hybridized to capture probes immobilized on fluorescently addressed microspheres. After incubation with streptavidin-conjugated fluorophore, the reactions were analyzed by Luminex IS100. Clinical evaluations were conducted using de-identified patient DNA samples. RESULTS: We evaluated a multiplexed suspension array assay that includes wild-type and mutant genetic determinations for Gaucher disease allele c.1448T>C. Two percent of samples reported to be wild-type by conventional methods were observed to be c.1448T>C heterozygous using our assay. Sequence analysis suggested that this phenomenon was due to co-amplification of the functional gene and a paralogous pseudogene (ΨGBA) due to a polymorphism in the primer-binding site of the latter. Primers for the amplification of this allele were then repositioned to span an upstream deletion in the pseudogene, yielding a much longer amplicon. Although it is widely reported that long amplicons negatively impact amplification or detection efficiency in recently adopted multiplex techniques, this assay design functioned properly and resolved the occurrence of false heterozygosity. CONCLUSION: Although previously available sequence information suggested GBA gene/pseudogene discrimination capabilities with a short amplified product, we identified common single-nucleotide polymorphisms in the pseudogene that required amplification of a larger region for effective discrimination

Identification of Sequence Variants in Genetic Disease-Causing Genes Using Targeted Next-Generation Sequencing

Identification of gene variants plays an important role in research on and diagnosis of genetic diseases. A combination of enrichment of targeted genes and next-generation sequencing (targeted DNA-HiSeq) results in both high efficiency and low cost for targeted sequencing of genes of interest.To identify mutations associated with genetic diseases, we designed an array-based gene chip to capture all of the exons of 193 genes involved in 103 genetic diseases. To evaluate this technology, we selected 7 samples from seven patients with six different genetic diseases resulting from six disease-causing genes and 100 samples from normal human adults as controls. The data obtained showed that on average, 99.14% of 3,382 exons with more than 30-fold coverage were successfully detected using Targeted DNA-HiSeq technology, and we found six known variants in four disease-causing genes and two novel mutations in two other disease-causing genes (the STS gene for XLI and the FBN1 gene for MFS) as well as one exon deletion mutation in the DMD gene. These results were confirmed in their entirety using either the Sanger sequencing method or real-time PCR.Targeted DNA-HiSeq combines next-generation sequencing with the capture of sequences from a relevant subset of high-interest genes. This method was tested by capturing sequences from a DNA library through hybridization to oligonucleotide probes specific for genetic disorder-related genes and was found to show high selectivity, improve the detection of mutations, enabling the discovery of novel variants, and provide additional indel data. Thus, targeted DNA-HiSeq can be used to analyze the gene variant profiles of monogenic diseases with high sensitivity, fidelity, throughput and speed