A bacterial strain 2H isolated from soil and identified as Thermoactinomyces vulgaris produce a potent Type II restriction endonuclease activity that has been extracted by a PEG/dextran aqueous two-phase system. Optimal temperature for the restriction endonuclease activity was 55-65°C. Specific DNA cleavage was obtained at pH range 7-10 and 10-20mM MgCl2. Restriction cleavage analysis followed by sequencing confirms GG^CC as the recognition sequence. This enzyme, named Tvu2HI, is a thermostable isoschizomer of the mesophilic prototype restriction endonuclease HaeIII. Sequencing of the complete Thermoactinomyces vulgaris 2H genome revealed the presence of two adjacent ORFs coding for the restriction endonuclease Tvu2HI and the corresponding methyltransferase; an ORF coding for a putative Vsr nicking enzyme was found close to those coding for the Tvu2HI restriction-modification system. Phylogenetic analysis based on sequence alignment suggests a common origin of Tvu2HI R-M system with HaeIII-like R-M systems. This is the first investigation dealing with a Type II restriction endonuclease identified in a natural isolate of the genus Thermoactinomyces.

Ochratoxin A (OTA) is a ubiquitous food toxin associated with chronic nephropathy in humans and renal carcinogenicity in rodents. The mutational spectra of cells exposed to OTA reveal that one-base deletions comprise the largest percentage (73%) of the total mutations that occur upon OTA exposure. To contribute toward understanding the prevalence of OTA-induced one-base deletion mutations, the present work uses molecular dynamics (MD) simulations to analyze the conformational preferences of one-base deletion duplexes containing OT-G, the major OTA adduct (addition product) at the C8-site of guanine. Specifically, the influence of OT-G in four possible ionization states and three sequence contexts (G1, G2 and G3 in the NarI (5\'-G1G2CG3CC-3\'), a prokaryotic mutational hotspot sequence) on the structure of the adducted DNA is investigated. Our data reveal that the damaged helices are stable in two (B-type (B) and stacked (S)) conformations that are structurally similar to those adopted by common N-linked C8-guanine lesions. However, the adduct ionization state and sequence context affect the degree of helical distortion and the B/S conformational heterogeneity, which will impact the lesion repair and replication outcomes. This finding correlates with the experimentally reported tissue-specific mutagenicity of OTA exposure. Furthermore, regardless of the adduct conformation, ionization state, or sequence context, more stable lesion-site interactions and lack of disruption of the flanking base pairs in the one-base deletion duplexes compared to the corresponding two-base deletion helices rationalize the greater abundance of OTA induced one-base deletions. Overall, our work provides valuable structural insights that help explain the experimentally observed mutagenicity associated with OTA.

Background: Gout arthritis is a common inflammatory arthritis and it poses a major threat to human health. Objective: A method of capillary electrophoresis with laser-induced fluorescence detection (CE-LIF) for the detection of HSP60 gene polymorphism has been developed and applied to the exploration of correlation between gouty arthritis and HSP60 gene polymorphism. Methods: The genomic deoxyribonucleic acid from 59 patients with gouty arthritis and 64 control subjects was extracted and the conservative fragment of HSP60 was amplified. The products were digested with restriction endonuclease NlaIII and then separated and detected by the proposed method. Results: In the case group, there were 7 cases of TT genotype, 29 cases of CC genotype, and 23 cases of CT genotype. In the control group, there were 4 cases of TT genotype, 6 cases of CC genotype, and 54 cases of CT genotype. The detection results of the samples were statistically analyzed by binary logistic regression and Spearman correlation analysis. After adjusting gender, age, and other compounding factors, the TT genotype and CT genotype of the HSP60 gene were found to affect gouty arthritis. Conclusions: When used for gene polymorphism research, the proposed CE-LIF method has the advantages of high efficiency, rapidity, sensitivity, and low sample consumption. A moderate correlation between gouty arthritis and HSP60 genotype distribution was discovered for the first time. Highlights: A new method using CE-LIF for the detection of HSP60 gene polymorphism of 59 patients with gouty arthritis and 64 control subjects in China. The correlation between gouty arthritis and HSP60 gene polymorphism was explored for the first time.

BACKGROUND: Acne vulgaris (AV) pathogenesis is multifactorial. Vitamin D (VitD) plays an important role in sebocytes\' differentiation and function. Most VitD functions are mediated by the nuclear VitD receptor (VDR) following binding of its biologically active form (1,25 dihydroxyvitamin D3). Genetic variations in VDR gene may cause significant receptor dysfunction and have been found to be associated with many inflammatory skin diseases. Two adjacent single nucleotide polymorphisms of VDR, ApaI (rs7975232) and TaqI (rs731236), were commonly studied.
OBJECTIVE: To evaluate the association between VDR ApaI and TaqI gene polymorphism and AV.
METHODS: This case control study included 30 Egyptian acne patients who attended Dermatology Outpatient Clinic of Al-Zahraa University and Misr University for Science and Technology Hospitals. Thirty age- and sex-matched healthy individuals participated as controls. VDR gene ApaI and TaqI polymorphisms were examined by polymerase chain reaction restriction fragment length polymorphism. Serum 25(OH)D was measured in all participants.
RESULTS: Patients had significant decrease in ApaI A allele and AATT combined genotype (60%, 3.3%) than controls (78.3%, 20%), respectively, and significant increase in TaqI tt genotype and t allele (46.7%, 63.3%) than controls (13.3%, 41.7%), respectively. Patients showed significantly lower serum 25(OH)D3 concentration than controls.
CONCLUSIONS: Polymorphisms of ApaI and TaqI may have a role in the pathogenesis of AV as A allele and AATT combined genotype could be considered protective against acne development and tt genotype and t allele may increase the risk of AV development. VitD deficiency can be considered as a risk factor for AV development.

Community-acquired pneumonia (CAP) is the leading cause of child deaths around the world. Recently, the vitamin D receptor (VDR) gene has emerged as a susceptibility gene for CAP.
To evaluate the association of the VDR gene Fok I polymorphism with susceptibility to CAP in Egyptian children.
This was a multicenter case-control study of 300 patients diagnosed with CAP, and 300 well-matched healthy control children. The VDR Fok I (rs2228570) polymorphism was genotyped by PCR-restriction fragment length polymorphism (RFLP), meanwhile serum 25-hydroxy vitamin D (25D) level was assessed using ELISA method.
The frequencies of the VDR FF genotype and F allele were more common in patients with CAP than in our control group (OR = 3.6; (95% CI: 1.9-6.7) for the FF genotype; P = 0.001) and (OR: 1.8; (95% CI: 1.4-2.3) for the F allele; P = 0.01). Patients carrying the VDR FF genotype had lower serum (25D) level (mean; 14.8 ± 3.6 ng/ml) than Ff genotype (20.6 ± 4.5 ng/ml) and the ff genotype (24.5 ± 3.7 ng/ml); P < 0.01.
The VDR gene Fok I (rs2228570) polymorphism confers susceptibility to CAP in Egyptian children.

Sickle cell haemoglobinopathy is a genetic disorder caused by the presence of haemoglobin S (HbS) including sickle cell disease (SCD) (sickle cell anemia, HbS/β -thalassaemia and HbSC disease) and sickle cell trait. In Siwa Oasis, most remote oasis town in Egypt, the prevalence rate of sickle cell haemoglobinopathy is approaching 20%. The Xmn1 polymorphism was reported to increase the HbF level ameliorating the severity of the SCD. The present study aims mainly to investigate the genotype frequency of -158Gγ (C→T) Xmn1 polymorphism in Siwa Oasis, Egypt and to study, if possible, any association with increased HbF expression. This study was performed on 62 sickle cell carriers (AS), three cases of sickle cell anaemia (SS) detected during a screening programme conducted on primary school children in Siwa Oasis by Alexandria Faculty of Medicine in 2011-2012. Sixty-five age-matched and sex-matched healthy controls (AA) were included. All enrolled children were subjected to PCR-RFLP for the detection of -158Gγ (C→T) Xmn1 polymorphism using the Xmn1 restriction enzyme. Genotyping of the -158Gγ (CvT) Xmn1 polymorphism revealed that among AS, 85.5% were homozygous for the wild-type allele (CC) and 14.5% were heterozygous (CT). However, among SS, two cases were homozygous for the wild-type allele (CC) and one case was heterozygous (CT). The genotype frequencies among AA were 83.1% homozygous for the wild-type allele (CC) and 16.9% heterozygous (CT). None of the studied cases or controls was homozygous for the mutant allele (TT). Among both AS and AA, there was no significant difference between the wild-type and heterozygous genotypes regarding HbF level. Studying genotype frequency of the Xmn1 γG globin polymorphism (-158C>T ) in Siwa Oasis, Egypt can be considered as a starting point for further research targeting this community sector. However, in our studied cohort, there were only three sickle cell anaemia patients. Further, none of the tested cases or controls was found to be homozygous for the mutant allele (TT). In the absence of any homozygous genotype for the mutant allele (TT) in the studied cohort, any reasonable conclusion on the effect of polymorphism on increase in HbF could not be established. Further studies with a larger sample size are needed for better understanding of the possible association.

BACKGROUND: The aim of this study is to evaluate the association of TGFA TaqI polymorphism with nonsyndromic cleft lip and/or palate (NSCLP) in an Iranian population.
METHODS: In this case-control study, 113 children with NSCLP and 209 controls were included. Genotyping of the TaqI polymorphism was performed by polymerase chain reaction and restriction fragment length polymorphism methods. A p-value of <0.05 was considered statistically significant.
RESULTS: For the TGFA TaqI polymorphism, the distributions of genotypes in the NSCLP (p = 0.810) and control group (p = 0.422) were in Hardy-Weinberg equilibrium. There was no statistically significant difference in the genotype distribution (p = 0.059) and allele frequency (p = 0.065) of the TGFA TaqI polymorphism in the NSCLP and control groups.
CONCLUSIONS: TGFA TaqI polymorphism was not associated with the risk of NSCLP in Iranian children. Birth Defects Research 109:1386-1389, 2017.© 2017 Wiley Periodicals, Inc.

Background Childhood-onset systemic lupus erythematosus (cSLE) is a lifelong autoimmune disorder. The vitamin D receptor (VDR) gene is a potential candidate gene for cSLE susceptibility. In this study, we aimed to investigate the FokI polymorphism in the VDR gene in Egyptian children and adolescents with SLE, to determine whether this polymorphism could be a genetic marker for cSLE susceptibility or disease activity and we also measured the serum level of 25-hydroxyvitamin D [25(OH) D] to assess its relation to such polymorphism. Methods This was a case-control study, which included 300 patients with cSLE and 300 age, sex, and ethnicity-matched healthy controls. All participants were genotyped for the VDR gene FokI (rs2228570) polymorphism by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), while the serum [25(OH) D] levels were measured by enzyme-linked immunosorbent assay (ELISA). Results The VDR FokI FF genotype and F allele were overrepresented among cSLE patients compared with the controls, [odds ratio (OR) = 2.7; 95% confidence interval (CI): 1.6-4.4 for the FF genotype; p = 0.000; and OR = 1.6; 95% CI: 1.27-2.05 for the F allele; p = 0.000, respectively]. We found a significant association between VDR FokI FF genotype with lupus nephritis (OR: 4.8; 95% CI: 2.2-10.6; p = 0.002); and high disease activity index score ( p = 0.01). Conclusions The FokI polymorphism in the VDR gene may contribute to susceptibility to SLE in Egyptian children and adolescents. Moreover, the FF genotype constituted a risk factor for the development of lupus nephritis and was associated with low serum [25(OH) D] levels as well as higher disease activity index score among studied patients with cSLE.

Great advances in biotechnology have allowed the construction of a computer from DNA. One of the proposed solutions is a biomolecular finite automaton, a simple two-state DNA computer without memory, which was presented by Ehud Shapiro\'s group at the Weizmann Institute of Science. The main problem with this computer, in which biomolecules carry out logical operations, is its complexity - increasing the number of states of biomolecular automata. In this study, we constructed (in laboratory conditions) a six-state DNA computer that uses two endonucleases (e.g. AcuI and BbvI) and a ligase. We have presented a detailed experimental verification of its feasibility. We described the effect of the number of states, the length of input data, and the nondeterminism on the computing process. We also tested different automata (with three, four, and six states) running on various accepted input words of different lengths such as ab, aab, aaab, ababa, and of an unaccepted word ba. Moreover, this article presents the reaction optimization and the methods of eliminating certain biochemical problems occurring in the implementation of a biomolecular DNA automaton based on two endonucleases.

We studied the relationship between lipoprotein lipase (LPL) gene HindIII polymorphism and the development of acute pancreatitis in the Russian population. Whole blood samples were collected from 145 patients with acute non-biliary pancreatitis and 191 healthy individuals. Genotyping of LPL gene HindIII (rs320) polymorphism was performed by PCR with TaqMan assay. It was found that allele H+ (OR=0.63, 95%CI 0.41-0.96, p=0.03) and genotype H+/H+ (OR=1.79, 95%CI 1.06-3.04, p=0.03) were associated with the risk of acute non-biliary pancreatitis only in males. In this study, the relationship between HindIII polymorphism of LPL gene with the risk of acute non-biliary pancreatitis was revealed.