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Glycyrrhizin, a bioactive constituent of Glycyrrhiza glabra has been reported to ameliorate diabetes. Here, the effects of liposome-encapsulated glycyrrhizin on STZ-induced diabetes and associated oxidative stress were investigated. Wistar rats were grouped as control (NC, received placebo), diabetic (DC, STZ-induced), diabetic treated with free glycyrrhizin (DTG, 3 i.v. doses, 1.6 mg/0.5 ml), empty liposomes (DTl, 3 i.v. doses), and liposome-encapsulated glycyrrhizin (DTbd, 3 i.v. doses, 1.6 mg/0.5 ml). Serum glucose, insulin, intraperitoneal glucose tolerance test and glycohemoglobin were estimated. Free iron and iron-mediated oxidative stress were examined. Histological examinations of the kidney and liver were performed. Liposomal-glycyrrhizin treatment caused significant improvement of hyperglycemia (DC vs. DTbd p <.05), glucose intolerance (DC vs. DTG p <.01 and DC vs. DTbd p <.05), insulin (DC vs. DTG p <.1, DTbd vs. DC p <.05 and DTbd vs. DTG p <.1) and glycohemoglobin (DC vs. DTG p <.1 and DC vs. DTbd p <.05) levels in the DTbd group. Alleviation of free iron release (DC vs. DTbd p <.05), lipid peroxidation (DC + H2O2 vs. DTbd + H2O2p <.05), deoxyribose (DC + H2O2 vs. DTbd + H2O2, p <.05), and DNA degradation occurred in the DTbd group. The abnormalities of the kidney and liver were abolished in the DTbd group. The inhibitory effects were more pronounced compared to free glycyrrhizin. Liposome-encapsulated glycyrrhizin treatment caused inhibition of diabetic complications through its antioxidant effects and can be exploited for effective treatment of diabetes. [ABSTRACT FROM AUTHOR]

Malaria remains a major public health issue for pregnant women. Côte d'Ivoire has adopted a series of measures aimed at combatting this plague, and these measures include administering Sulfadoxine-Pyrimethamine (SP) as an intermittent preventive treatment to pregnant women in the second and third terms. This cross-sectional study included a parturient population after informed written consent. We recruited women from the Terre Rouge maternity ward and the labor room of the Regional Medical Center of San-Pedro. Plasmodial DNA (desoxyribo nucleic acid) was extracted from Whatman filter papers with dried blood samples prepared from the venous, placental, and cord blood, utilizing Chelex 100. The extracts obtained were amplified by nested PCR. In all, 197 women were included, with an average age of 27-year-old (sd = 6.7 years old). The rates of the placental, venous and cord blood infections were 16, 2%, 15, 2% and 3, 6%, respectively. The women who took three doses of ITP were less infected at the cord (3, 2%), placental (10,6%) and venous level (13,8%). A statistically significant relationship between the number of doses and the rate of placental infection was established (p = 0.042). IPT reduces plasmodial infestation at the placental (OR = 0.4; CI = [0.2–1]), cord (OR = 0.8; CI = [0.2–3.7]) and venous (OR = 0.8; CI = [0.6–2.3]) level. In conclusion, the low frequency of placental, venous, and cord infestation in pregnant women who consistently followed a preventive treatment strategy clearly showed the efficiency of IPT against malaria during pregnancy. [ABSTRACT FROM AUTHOR]

Evidence suggests that the non-psychotropic phytocannabinoid cannabidiol (CBD) has anticancer activity on different cell lines and in animal models. The DNA-damaging drug epirubicin (EPI) is widely used for the treatment of malignant tumours. In this study we examined the effectiveness of CBD administered alone and in combination with EPI on HL-60, HL-60/Dox and MCF-7 cell-lines. We applied MTT reduction assay and the bioinformatics model of Chou-Talalay for experimental design of combination chemotherapy to evaluate the anticancer activity of several epirubicin-based combinations with CBD in various treatment regimens. In addition, we studied the efficacy of the co-treatment regimens to induce changes in two in-vitro model systems containing superoxide radical and 2-deoxyribose. We then evaluated the effectiveness of EPI plus CBD. The maximal growth cell inhibition ∼90% in leukemic and breast cancer cells was measured at the peak tested concentrations 2.5 EPI plus 25 CBD, µmol/L. The combination index (CI) value showed the presence of slightly expressed antagonism between EPI and CBD in most cases. The antiproliferative effect of the combination was reduced by only 8–10% vs. the inhibition induced by either EPI or CBD alone. We determined that the slight antagonism correlated positively to the registered dosage and decreased the extent of deoxyribose oxidative damage by using the enhanced chemiluminescent method with superoxide radicals. The therapeutic value of the combination of EPI plus CBD mainly consists of its high antiproliferative effect and the possibility to reduce the total dose on leukaemia-transformed cells by a factor of two. Supplemental data for this article is available online at https://doi.org/10.1080/13102818.2021.1996270. [ABSTRACT FROM AUTHOR]

Ubiquitous and ever increasing use of mobile phones led to the growing concern about the effects of radiofrequency radiation (RFR) emitted by cell phones on biological systems. The aim of this study is to explore whether long-term RFR exposure at different frequencies affects DNA damage and oxidant-antioxidant parameters in the blood and brain tissue of rats. 28 male Sprague Dawley rats were randomly divided into four equal groups (n = 7). They were identified as Group 1: sham-control, Group 2: 900 MHz, Group 3: 1800 MHz, and Group 4: 2100 MHz. Experimental groups of rats were exposed to RFR 2 h/day for 6 months. The sham-control group of rats was subjected to the same experimental condition but generator was turned off. Specific absorption rates (SARs) at brain with 1 g average were calculated as 0.0845 W/kg, 0.04563 W/kg, and 0.03957, at 900 MHz, 1800 MHz, and 2100 MHz, respectively. Additionally, malondialdehyde (MDA), 8-hydroxydeoxyguanosine (8-OHdG), total antioxidant status (TAS), and total oxidant status (TOS) analyses were conducted in the brain tissue samples. Results of the study showed that DNA damage and oxidative stress indicators were found higher in the RFR exposure groups than in the sham-control group. In conclusion, 900-, 1800-, and 2100-MHz RFR emitted from mobile phones may cause oxidative damage, induce increase in lipid peroxidation, and increase oxidative DNA damage formation in the frontal lobe of the rat brain tissues. Furthermore, 2100-MHz RFR may cause formation of DNA single-strand breaks. [ABSTRACT FROM AUTHOR]

Context:Clinical study of breast cancer patients in Chicago, IL, USA. Objective:Ascertain the utility of measurements of single-strand breaks (SSB) in DNA for assessment of breast cancer risk. Methods:Fine-needle aspirates of the breast, SSB by nick translation, percent breast density (PBD), Gail model risk, cumulative methylation index (CMI), enzymes of DNA repair and tissue antioxidants. Results:DNA repair enzymes and 4-hydroxyestradiol were negatively associated with SSB; CMI and PBD were positively associated. Conclusions:Quantitative measurement of SSBs by this procedure indicates the relative number of SSBs and is related to promoter methylation, antioxidant availability and percent breast density. [ABSTRACT FROM PUBLISHER]

The assimilation hypothesis dictates that knowledge of prior evidence makes legal decision makers assign more weight to subsequent evidence. For example, the evidentiary power of a line-up identification is perceived to be stronger if the decision maker knows that the suspect has confessed, compared to when knowledge of the confession is absent. In three studies, the assimilation hypothesis was tested. As expected, knowledge of DNA-evidence inflated the estimated strength of subsequent eyewitness identification evidence (Study 1), and also inflated overall conviction and conviction rate (Study 2). A similar assimilation effect was found with knowledge of the suspect's dangerous psychopathology (i.e. psychopathic and anti-social personality traits). Such knowledge inflated the estimated strength of fingerprint evidence. In conclusion, the assimilation effect is a threat to rational legal decision making in both lays (Study 2) and professional judges (Studies 1 and 3). [ABSTRACT FROM AUTHOR]

BackgroundThe correlation between genetics and geographical distance has already been examined through the study of the dispersion of human populations, especially in terms of uniparental genetic markers. AimThe present work characterises, at the level of the mitochondrial DNA (mtDNA), two new samples of Amhara and Oromo populations from Ethiopia to evaluate the possible pattern of distribution for mtDNA variation and to test the hypothesis of the Isolation-by-Distance (IBD) model among African, European and Middle-Eastern populations. Subjects and methodsThis study analysed 173 individuals belonging to two ethnic groups of Ethiopia, Amhara and Oromo, by assaying HVS-I and HVS-II of mtDNA D-loop and informative coding region SNPs of mtDNA. ResultsThe analysis suggests a relationship between genetic and geographic distances, affirming that the mtDNA pool of Africa, Europe and the Middle East might be coherent with the IBD model. Moreover, the mtDNA gene pools of the Sub-Saharan African and Mediterranean populations were very different. ConclusionIn this study the pattern of mtDNA distribution, beginning with the Ethiopian plateau, was tested in the IBD model. It could be affirmed that, on a continent scale, the mtDNA pool of Africa, Europe and the Middle East might fall under the IBD model. [ABSTRACT FROM PUBLISHER]

India has rich marine ornamental fish diversity with 400 fish species distributed in Gulf of Munnar/Palk Bay, Gulf of Kutch, and in reefs around Andaman & Nicobar and Lakshadweep Islands. Marine ornamental fish identification at the field level is very difficult because of their high diversity and profound changes in appearance during their developmental stages and camouflage. To facilitate ornamental fish trading with ease and in compliance with the biodiversity act, DNA barcoding technique could be used to accurately identify species. In this study, DNA barcodes were generated for 31 species of commercially important marine ornamental fishes from India. The average genetic distance (K2P model) within species, genus, and family was 0.446, 13.08, and 20.09%, respectively. Intraspecific variation has increased several folds (15–20 times) after including conspecific sequences from different geographical locations. The presence of allopatric lineages/cryptic species was observed in the Indo-pacific region. The NJ tree constructed based on K2P values showed distinct clusters shared by congeneric species specific to populations. [ABSTRACT FROM AUTHOR]

Norcantharidin (NCTD) is currently used in the treatment of several cancers such as leukemia, melanoma and hepatoma. The mechanism of action of NCTD is suggested to involve induction of apoptosis of cancer cells via production of reactive oxygen species. In this study, the genotoxic effect of different concentrations of NCTD (1, 10 and 20 μm) in human lymphocytes was investigated using sister chromatid exchanges (SCEs) and chromosomal aberrations (CAs) assays. The results revealed that NCTD significantly increased the rate of SCEs (p < 0.05) in a dose-dependent manner. In addition, NCTD significantly increased the number of high-frequency cells (SCEs ≥ 8,p < 0.05). However, NCTD did not have any significant effect on the rate of CAs (p > 0.05). In addition, no significant differences were detected in the mitotic index or proliferative index at examined doses (up to 20 μm). In conclusion, NCTD is genotoxic to human cultured lymphocytes as measured by SCE assay. [ABSTRACT FROM AUTHOR]

Gravesoil beneath decomposing cadavers undergoes substantial biochemical changes that have the potential to aid in PMI estimation and identification of clandestine gravesites. The use of DNA extraction methods is necessary for culture-independent downstream molecular applications such as PCR and next-generation sequencing. In this study, a comparison of four methods was performed for cadaver-soil collected beneath the heads and feet of 11 cadavers decaying in a natural setting. The four methods isolated 3.6–263 ng/μl of genomic DNA as determined by optical density analysis. The purity of the extracted DNA according to A260/280and A260/230ratios was determined. The A260/280and A260/230ratios were 1.24–1.97 and 0.27–2.12, respectively. The optical density at 320 nm was measured for humic acid quantification of the lysates from the method that provided the most efficient removal of humic acid. The results demonstrated that this method provided a 98% reduction of humic acid. PCR of 16S rRNA genes followed by gel electrophoresis was performed. The statistical analysis revealed a significant correlation between the yields and days on/in the soil using a phenol-chloroform method for soil collected at the head and feet. No earlier published work has extensively elucidated the efficacy of DNA extraction methods for DNA obtained from cadaver-soil. [ABSTRACT FROM PUBLISHER]

The aim of this work was to test a 52 SNP-plex in our laboratory in order to apply it in casework cases, namely in kinship involving relatives of the true father leading to low Parentage Index (PI) values, and in unusual cases such as paraffin-embedded tissue samples or in other cases involving severely degraded samples related to some identification cases. For this, a standard DNA was used, artificially degraded by digestion with DNase I and by different UV exposure times. STR previously-analysed cases were revisited and studied. All the samples were typed for the SNP for ID 52plex using the SNaPshotTM assay. In all the cases, a SNP profile was achieved. In two cases involving paraffin-embedded tissue samples, it was only possible to obtain results for 48% (11 out of 23) and 61% (14 out of 23) STR and mini-STR markers, respectively. Concerning SNPs, results were possible for all the SNPs (52) in one of the cases and for 50 SNPs (96%) in the other. The PI or LR calculated values suffered a minimum of a fourfold increment. Autosomal SNPs can be used as additional markers to the profiling of ‘difficult’ cases that emerge in the routine of many laboratories. [ABSTRACT FROM PUBLISHER]

Occupational exposure as a painter is associated with DNA damage and development of cancer. Comet assay has been widely adopted as a sensitive and quantitative tool for DNA damage assessment at the individual cell level in populations exposed to genotoxics. The aim of this study was to assess the application of the high-throughput comet assay, to determine the DNA damage in car spray painters. The study population included 52 car spray painters and 52 unexposed subjects. A significant increase in the %TDNA median (p <  0.001) was observed in the exposed group in comparison to the unexposed group. Neither age (%TDNA:p =  0.913) nor time of exposure (%TDNA:p = 0.398) were significantly correlated with DNA damage. The car spray painters who consumed alcohol did not show a significant increase in DNA damage compared to nonalcohol consumers (p  > 0.05). The results showed an increase in DNA breaks in car spray painters exposed to organic solvents and paints; furthermore, they demonstrated the application of high-throughput comet assay in an occupational exposure study to genotoxic agents. [ABSTRACT FROM AUTHOR]

A series of six 2,5-disubstituted 1,3,4-thiadiazole derivatives was synthesized and examined for cytotoxic activity in MCF-7 and MDA-MB-231 breast cancer cells. MTT assay confirmed that 2-(3-fluorophenylamino)-5-(3-hydroxyphenyl)-1,3,4-thiadiazole (2), 2-(4-bromophenylamino)-5-(2,4-dichlorophenyl)-1,3,4-thiadiazole (3), 2-(4-fluorophenylamino)-5-(2,4-dichlorophenyl)-1,3,4-thiadiazole (4), had ability to inhibit MCF-7 and MDA-MB-231 cells proliferation. The IC50values for the mentioned compounds ranged between 120 and 160 μM (with respect to MCF-7 cells) and from 70 to 170 μM (with respect to MDA-MB-231 cells). It turned out, moreover, that compound2is a human topoisomerase II (topoII) catalytic inhibitor whereas the two other compounds (i.e.3and4) are capable of stabilizing DNA-topoII cleavage complex and thus are topoII poisons. [ABSTRACT FROM AUTHOR]

The carbonate radical anion CO3•−is a potent reactive oxygen species (ROS) producedin vivothrough enzymatic one-electron oxidation of bicarbonate or, mostly, via the reaction of CO2with peroxynitrite. Due to the vitally essential role of the carbon dioxide/bicarbonate buffer system in regulation of physiological pH, CO3•−is arguably one of the most important ROS in biological systems. So far, the studies of reactions of CO3•−with DNA have been focused on the pathways initiated by oxidation of guanines in DNA. In this study, low-molecular products of attack of CO3•−on the sugar–phosphate backbonein vitrowere analyzed by reversed phase HPLC. The selectivity of damage in double-stranded DNA (dsDNA) was found to follow the same pattern C4′ > C1′ > C5′ for both CO3•−and the hydroxyl radical, though the relative contribution of the C1′ damage induced by CO3•−is substantially higher. In single-stranded DNA (ssDNA) oxidation at C1′ by CO3•−prevails over all other sugar damages. An approximately 2000-fold preference for 8-oxoguanine (8oxoG) formation over sugar damage found in our study identifies CO3•−primarily as a one-electron oxidant with fairly low reactivity toward the sugar–phosphate backbone. [ABSTRACT FROM PUBLISHER]

Purpose: Radiation with high linear energy transfer (LET) produces clustering of DNA double-strand breaks (DSB) as well as non-DSB lesions. Heat-labile sites (HLS) are non-DSB lesions in irradiated cells that may convert into DSB at elevated temperature during preparation of naked DNA for electrophoretic assays and here we studied the initial formation and repair of these clustered damaged sites after irradiation with high LET ions. Materials and methods: Induction and repair of DSB were studied in normal human skin fibroblast (GM5758) after irradiation with accelerated carbon and nitrogen ions at an LET of 125 eV/nm. DNA fragmentation was analyzed by pulsed-field gel electrophoresis (PFGE) and by varying the lysis condition we could differentiate between prompt DSB and heat-released DSB. Results: Before repair (t = 0 h), the 125 eV/nm ions produced a significant fraction of heat-released DSB, which appeared clustered on DNA fragments with sizes of 1 Mbp or less. These heat-released DSB increased the total number of DSB by 30–40%. This increase is similar to what has been found in low-LET irradiated cells, suggesting that the relative biological effectiveness (RBE) for DSB induction will not be largely affected by the lysis temperature. After 1–2 hours repair, a large fraction of DSB was still unrejoined but there was essentially no heat-released DSB present. Conclusions: These results suggest that high LET radiation, as low LET gamma radiation, induces a significant fraction of heat-labile sites which can be converted into DSB, and these heat-released DSB may affect both induction yields and estimates of repair. [ABSTRACT FROM AUTHOR]

The concept of microbial content of the lung is still controversial. What make this more complicated are controversial results obtaining from different methodologies about lung microbiome and the definition of "lung sterility". Lungs may have very low bacteria but are not completely germ-free. Bacteria are constantly entering from the upper respiratory tract, but are then quickly being cleared. We can find bacterial DNA in the lungs, but it is much harder to ask about living bacteria. Here, we propose that if there is any trafficking of the microorganisms in the lung, it should be a 'Transient But Not Resident (TBNR)" model. So, we speculate a "Yin Yang model" for the lung immune system and TBNR. Despite beneficial roles of microbiome on the development of lung immune system, any disruption and alteration in the microbiota composition of upper and lower airways may trigger or lead to several diseases such as asthma, chronic obstructive pulmonary disease and mustard lung disease. [ABSTRACT FROM AUTHOR]

Neospora caninumis an intracellular protozoan parasite with a wide range of intermediate bird hosts. There is little information describing the prevalence and genetic characterization ofN. caninumin bird hosts worldwide and in Iran. In this study, a total of 217 brain samples of house sparrow (Passer domesticus) were examined forN. caninumpresence by nested polymerase chain reaction targeting theNc-5gene.N. caninumDNA was detected in 3.68% (8/217) of sparrows. Sequencing of theNc5genomic DNA revealed 97–99% of similarity withN. caninumsequences deposited in Genbank. To our knowledge, this study is the first molecular evidence ofN. caninumDNA in bird hosts in Iran. The results of this study highlight the role of the house sparrow (Passer domesticus) in maintaining and spreadingN. caninuminfection to canines in the feral and domestic environment. [ABSTRACT FROM PUBLISHER]

LiveMycoplasma gallisepticumvaccines are used for the control of respiratory disease, egg production losses and egg transmission associated withM. gallisepticuminfection in long-lived poultry. The first field case of apparent increased virulence and vertical transmission of ts-11, a liveM. gallisepticumvaccine, has been reported. In that study aM. gallisepticumisolate from the broiler progeny of ts-11-vaccinated breeders was genotyped as ts-11 by sequence analysis of four different genetic targets and Random Amplified Polymorphic DNA and found to be significantly more virulent than ts-11 vaccine. The objective of the current study was to evaluate the rate of egg transmission and pathogenicity of ts-11 vaccine and isolates recovered from ts-11-vaccinated breeders (K6222B) and their broiler progeny (K6216D) which had been genotyped as ts-11. Groups of 28-week-old specific pathogen-free chickens at 87% average weekly egg production were inoculated with sterile broth media (negative controls), ts-11 vaccine, K6222B, K6216D or R strain (positive controls) by eye-drop and aerosol. K6216D transmitted via the egg at an average rate of 4.0% in the third and fourth weeks post-infection, while egg transmission of K6222B and ts-11 vaccine was not detected.M. gallisepticumwas isolated from the air sacs, ovaries and oviducts of hens infected with K6216D and K6222B, but not from those infected with ts-11 vaccine. K6216D and K6222B both induced respiratory signs and significantly more tracheal colonization and more severe tracheal and air sac lesions than ts-11 vaccine (P≤ 0.05). There were no substantial differences in the egg production of ts-11, K6216D and K6222B infected groups. These results provide the first conclusive evidence of transovarian transmission of an isolate genotyped as ts-11 and indicate that isolates genotyed as ts-11 vary in their virulence and ability to transmit via the egg. [ABSTRACT FROM PUBLISHER]

Histones are the most abundant proteins associated with genomic DNA. Recent observations show that histones are quite susceptible to non-enzymatic glycation which results in the generation of free radicals causing structural perturbations. In this study, our aim is to define the role of deoxyribose-modified H2A histone in SLE initiation/progression. Glycation reaction was carried out by incubating H2A histone with 10 mM deoxyribose for 21 days at 37 °C. Structural changes in glycated-H2A were studied by various physico-chemical techniques. The antigen-antibody interaction was studied by direct binding, inhibition ELISA and mobility shift assay. Deoxyribose-modified-H2A histone showed increased hyperchromicity and increased fluorescence intensity. CD results demonstrated almost 50% loss in alpha helix conformation as a consequence of glycation. This was supported by an increase in Tm value vis-à-vis thermal stability. Glycated-H2A showed cross linking in SDS-PAGE. SLE sera positive for anti-nDNA autoantibodies showed preference for deoxyribose-modified-H2A histone compared to native H2A histone or native DNA. Inhibition ELISA supported the above findings. Band shift assay further reiterated the preferential recognition of glycated-H2A over native H2A by SLE IgG autoantibodies. Deoxyribose-modified-H2A histone exhibited damage as revealed by various physico-chemical studies. Glycation of H2A has resulted in the generation of neo-epitopes on H2A histone, which are preferably bound by SLE anti-nDNA autoantibodies. It implies that deoxyribose-modified-H2A may trigger immune response resulting in the generation of anti-glycated H2A antibodies with DNA cross reacting properties. [ABSTRACT FROM AUTHOR]

Objective: To determine the diagnostic accuracy, validity, current limitations of, and possible solutions to, fetal RhD genotyping from maternal blood based on existing studies written in English. Methods: A literature search was conducted that described fetal RhD determination from maternal blood. The number of samples tested, fetal RhD genotype, the source of cell-free fetal DNA, gestational age and fetal Rh type were examined in each study to calculate the accuracy, sensitivity and specificity of fetal RhD genotyping. Results: Forty-one publications, which included 11 129 samples with non-invasive Rh genotyping of cell-free fetal DNA from maternal blood, were selected. After the exclusion of 352 inconclusive samples, the overall diagnostic accuracy was 98.5% (10 611/10 777), and sensitivity and specificity were 99% and 98%, respectively. First trimester diagnosis showed an accuracy of 99%, higher than second and third trimester diagnosis. Thirty studies reported a 100% diagnostic accuracy of fetal RhD genotyping. Conclusion: Non-invasive fetal RhD genotyping from maternal blood has high accuracy, sensitivity and specificity. Methods reducing false results have been explored and applied in research. These achievements indicate that this technique will be widely used in routine clinical care. [ABSTRACT FROM AUTHOR]

Intraspecific competition for food is expected to increase the trophic niche width of consumers, defined here as their diet diversity, but this process has been little studied in herbivores. Population densities of small rodents fluctuate greatly, providing a good study model to evaluate effects of competition on trophic niche. We studied resource use in five arctic small rodent populations of four species combining DNA metabarcoding of stomach contents and stable isotope analysis (SIA). Our results suggest that for small rodents, the most pronounced effect of competition on trophic niche is due to increased use of secondary habitats and to habitat-specific diets, rather than an expansion of trophic niche in primary habitat. DNA metabarcoding and SIA provided complementary information about the composition and temporal variation of herbivore diets. Combing these two approaches requires caution, as the underlying processes causing observed patterns may differ between methodologies due to different spatiotemporal scales. [ABSTRACT FROM AUTHOR]

DNA typing of biological samples can be a challenging task due to the presence of small amounts of DNA and/or a high content of PCR inhibitors. Our aim is to develop a protocol to recover DNA suitable for DNA typing from blood-stained fabrics based on the DNA IQ System. Blood stains on different fabrics were buried in different types of soil and left for 1–7 days. The samples were then recovered and DNA was extracted with a modified DNA IQ System protocol, involving a modification in the preparation of the Wash Buffer. The samples extracted with the modified protocol showed a higher amount of recovered DNA compared with the recommended protocol. The removal of isopropanol from the Wash Buffer composition contributes to a higher amount of recovered DNA. [ABSTRACT FROM AUTHOR]

Purpose: This article reviews the early history of ionizing radiation-induced sugar damage in DNA in dedication to Prof. Clemens von Sonntag, who recently passed away. It covers the time between 1968 and 1978, during which most of the work on the ionizing radiation-induced damage to polyalcohols, carbohydrates and the 2'-deoxyribose moiety in DNA was performed. Methodologies using gas chromatography-mass spectrometry (GC-MS) were developed to identify and quantify the radiation-induced products that had previously remained elusive. Products were identified by GC-MS either directly or after reduction of samples with NaBH4 or NaBD4. Incorporation of deuterium atoms by NaBD4-reduction facilitated the identification of aldehyde, keto, carboxyi and deoxy groups in the molecules. Numerous products of a polyalcohol and carbohydrates were identified and quantified. Mechanisms of product formation were proposed. Several products of the 2'-deoxyribose moiety In DNA were identified, indicating that they were released from DNA strand, not bound to it. Alkali labile sites and products still remaining within DNA or bound to DNA as end groups were also elucidated by first reducing irradiated samples with NaBD4 followed by alkali treatment and GC-MS analysis. Conclusion:lhe knowledge of the products of the 2'-deoxyribose moiety in DNA led to the first mechanistic understanding of various pathways of hydroxyl radical-induced DNA strand breakage. To this date, some of these mechanisms still remain the most-widely studied mechanisms of DNA damage. Prof, von Sonntag's contributions to the understanding of the radiation chemistry of carbohydrates and DNA helped shape this field of science for years to come. [ABSTRACT FROM AUTHOR]

Purpose: To understand the degradation processes and role of secondary species on deoxyribonucleic acid (DNA)-damaged fragments as a result of irradiation with energetic ions. Materials and methods: Damage caused to DNA thin films as a result of exposure to 4 keV carbon ions beam was accessed by analyzing the infrared spectra, obtained in situ for different irradiation times, with both bi-dimensional (2D) correlation spectroscopy and independent component analysis (ICA). Results: Results indicated that deoxyribose, phosphate and base groups of the DNA molecule were being damaged and new reaction products as oxime and furfural groups are being formed. Conclusions: Damage on DNA bases is consistent with the formation of oxime products which react with DNA deoxyribose products forming furfural groups and confirming that DNA damage is caused by direct and indirect processes. [ABSTRACT FROM AUTHOR]

Aldehydes produced from carbohydrates by oxidation or acid hydrolysis may be visualized by application of aqueous thiosemicarbazide followed by Schmorl's ferricyanide reduction. The thiosemicarbazide reacts with the aldehydes by its hydrazine group, while its thiocarbamyl group remains active. The thiocarbamyl moiety is a strong reducing group that converts ferricyanide to ferrocyanide in Schmorl's reaction. The ferrocyanide is trapped immediately by the ferric salt, which deposits Prussian blue at the site of the aldehydes thereby demonstrating the location of the original substance. [ABSTRACT FROM AUTHOR]

To control the spread of tick-borne diseases, there is an urgent need to develop a reliable technique that can distinguish different species of ticks. DNA barcoding has been proved to be a powerful tool to identify species of arthropods, but this technique has not yet been developed for identifying ticks. Here, we screened and analyzed 1082 sequences of ticks from BOLD system and GenBank, consisting of 647 16S, 325 COI, and 110 18S. These sequences are reported in previous studies and considered to be correctly identified at the species level. Through the analyses of genetic divergences and neighbor-joining (NJ) phylogenetic relationships between the species of ticks, our results show that COI and 16S are reliable in discriminating species of ticks and the 18S could discriminate ticks at the genera level. New universal primers for 16S, 18S, and COI of ticks were designed and a DNA barcoding system for the Ixodida was developed. To assess the performance of this system, 57 specimens of ticks were collected within China. Our results show that DNA barcoding system could correctly identify the species of specimens in adult and subadult stages. This system would assist non-taxonomists to conveniently identify the species of Ixodida based on DNA sequences rather than morphological traits. However, there are still serious deficiencies in the information of 16S and COI of some species of ticks, and additional research is needed to resolve this problem. [ABSTRACT FROM AUTHOR]

Two colonial ascidians Didemnum granulatum and D. psammathodes were collected from Tuticorin coastal waters. These ascidians were sequenced at 603 and 576 bp region of the mitochondrial cytochrome oxidase subunit I gene (COI) for phylogenetic analysis. Barcode sequences were extracted via FASTA format from NCBI. The genetic distances of submitted DNA sequences were compared with related ascidian species. Didemnum granulatum (JQ013198) sequence shows maximum identical 99% with D. vexillum. Didemnum psammathodes (JN624758) sequence submitted at present shows maximum identical 100% with another D. psammathodes sequence which was already submitted in NCBI. The sequence also shows maximum identical 90-89% with D. vexillum. From the present study it is concluded that precise and accurate identification of ascidians could be performed using the barcode sequences of the mitochondrial DNA (in the COI gene). [ABSTRACT FROM AUTHOR]

We previously showed that BCL6B acts as a tumor suppressor in gastric cancer and up to 66% gastric cancer patients have promoter hypermethylation in tumor tissues. We aimed to evaluate the feasibility of detecting BCL6B methylation in plasma DNA as a potential biomarker for gastric cancer. Hypermethylation of the CpG islands in BCL6B promoter was detected in 42.5% (17/40) plasma DNA samples from gastric cancer patients, while no methylation was found in the plasma DNA of healthy controls ( p < 0.001). BCL6B methylation may serve as a novel potential non-invasive plasma biomarker for the detection of gastric cancer. [ABSTRACT FROM AUTHOR]

The aim of this study is to prepare supermacroporous cryogels embedded with Fe3+-attached sporopollenin particles (Fe3++-ASPs) having large surface area for high DNA adsorption capacity. Supermacroporous poly(2-hydroxyethyl methacrylate) (PHEMA)-based monolithic cryogel column embedded with Fe3++-ASPs was prepared by radical cryo-copolymerization of 2-hydroxyethyl methacrylate (HEMA) with N,N´-methylene- bis-acrylamide (MBAAm) as cross-linker directly in a plastic syringe for DNA adsorption studies. Firstly, Fe3++ ions were attached to the sporopollenin particles (SPs), then the supermacroporous PHEMA cryogel with embedded Fe3++-ASPs was produced by free radical polymerization using N,N,N´, N´-Tetramethylethylenediamine (TEMED) and ammonium persulfate (APS) as initiator/activator pair in an ice bath. Optimum conditions of adsorption experiments were performed at pH 6.0 (0.02 M Tris buffer containing 0.2 M NaCl), with flow rate of 0.5 mL/min, and at 5°C. The maximum amount of DNA adsorption from aqueous solution was very high (109 mg/g SPs) with initial concentration of 3 mg/mL. It was observed that DNA could be repeatedly adsorbed and desorbed with this composite cryogel without significant loss of adsorption capacity. As a result, higher amounts of DNA adsorbed these composite cryogels are expected to be good candidate for achieving higher removal of anti-DNA antibodies from systemic lupus erythematosus (SLE) patients plasma. [ABSTRACT FROM AUTHOR]

Topoisomerase IIβ (Top2β)-DNA cleavage complexes are known to arrest elongating RNA polymerase II (RNAPII), triggering a proteasomal degradation of the RNAPII large subunit (RNAPII LS) and Top2β itself as a prelude to DNA repair. Here, we demonstrate that the degradation of Top2β occurs through a novel ubiquitin-independent mechanism that requires only 19S AAA ATPases and 20S proteasome. Our results suggest that 19S AAA ATPases play a dual role in sensing the Top2β cleavage complex and coordinating its degradation by 20S proteasome when RNAPII is persistently stalled by the Top2β protein roadblock. Clarification of this transcription-associated proteasome pathway could shed light on a general role of 19S AAA ATPases in processing tight protein-DNA complexes during transcription elongation. [ABSTRACT FROM AUTHOR]

Conventional and SYBR Green Q Rti-PCR assays using primers targeting the12S rRNAof chicken mitochondrial genes were employed for the detection and quantification of chicken used in food stuffs. The assays were recruited to amplify different known concentrations of DNA in the mixtures. Different kinds of processed meats were prepared using various amounts of chicken that were heated at different temperatures in order to detect the chicken in the mixtures. The PCR amplification of DNA revealed that the assay can amplify the species-specific amplicons as little as 0.01 ng of DNA in PCR reactions. Different concentrations of raw chicken were detected based on the threshold cycle. The technique was able to detect from 5% to 90% ratios of the chicken materials in sausages. Analysis of the experimental meat mixtures revealed the usefulness of the assays in detecting and quantifying chicken mitochondrial DNA in the mixtures. [ABSTRACT FROM AUTHOR]

Nascent untranslated transcripts in bacteria are prone to generating RNA-DNA hybrids (R-loops); Rho-dependent transcription termination acts to reduce their prevalence. Here we discuss the mechanisms of R-loop formation and growth inhibition in bacteria. [ABSTRACT FROM AUTHOR]

The article focuses on researchers L. Hill and Lyn Turner's stand on DNA identification. It states that problem with their exchange is that between orientation of forensic science to production of legally authorized identification and perception of those who seek to know fate of their relative. It mentions that there is failure to come up with a form of analysis in which nature and consequences of occupying each position become important topics for inquiry than resources for arguments.

Punica granatum L. (Family: Punicaceae), commonly known as pomegranate (Anar) has been used traditionally as medicine to treat a number of diseases and disorders. Various parts of the plant and their active constituents are known to possess diverse biological activity. However, little is known about the antioxidant potential of pomegranate fruit peel, which is otherwise considered as waste. Therefore, the concentration-dependent hydroxyl radical scavenging ability of Punica granatum seed and peel extracts (alcoholic and aqueous) using deoxyribose degradation assay were analyzed and compared. The hydroxyl radical scavenging activity at different concentrations of extract (10 to 250 μg/mL) both in presence and/or absence of ascorbic acid and ethylenediamine tetra acetic acid was determined. It was observed that a higher concentration of extract suppresses scavenging activity and lower promotes antioxidant property. Based on the observations, it may be inferred that pomegranate extract, especially from the spent/waste prt, has a strong antioxidant property as assessed by its property of scavenging hydroxyl radical formation. [ABSTRACT FROM AUTHOR]

The aim of this study was to evaluate the anti-oxidant activities of petroleum ether, methanol, ethyl acetate, and aqueous extracts of the aerial parts and inflorescences of the herb, Artemisia amygdalina Decne. Methanolic extracts of the aerial parts and aqueous extracts of the inflorescences gave the maximum levels of inhibition (90.6% and 76.4%, respectively) in the 1, 1-diphenyl-2-picrylhydrazyl (DPPH) assay when compared to ascorbic acid, which showed 77.9% inhibition. The superoxide radical scavenging activity was highest in methanolic extracts of the aerial parts and in methanolic extracts of inflorescences (94.3% and 88.5%, respectively).These values were comparable to the reference standard, ascorbic acid, which showed 92.8% superoxide radical scavenging activity. In the deoxyribose assay, α-tocopherol showed 50.1% inhibition, while methanolic extracts of the aerial parts and inflorescences showed 46.2% and 46.4% inhibitory activity, respectively, against hydroxyl radicals. In the ferric thiocyanate assay, petroleum ether extracts of the aerial parts showed 78.7% inhibition, while ethyl acetate extracts of inflorescences showed 80.2% inhibition. The commercial standard, alpha-tocopherol, showed 79.7% scavenging activity. Extracts of A. amygdalina may provide an alternative source of natural anti-oxidant activity. [ABSTRACT FROM AUTHOR]

A total of 91 lactic acid bacteria (LAB) were isolated from 50 beef samples, 25 packaged by traditional vacuum packaging and 25 packaged using advanced vacuum skin packaging. The isolated LAB were identified using 16S rRNA sequencing, whereas randomly amplified polymorphic DNA (RAPD-PCR) and cluster analysis were used for typing the LABs. Ten different species of LAB were identified and assigned to the following species: Enterococcus gilvus (22 isolates), Enterococcus faecium (9 isolates), Enterococcus casseliflavus (8 isolates), Enterococcus faecalis (4 isolates), Enterococcus malodoratus (3 isolates), Enterococcus devriessei (3 isolates), Lactobacillus sakei (15 isolates), Carnobacterium divergens (12 isolates), Carnobacterium maltaromaticum (5 isolates), and Leuconostoc mesenteroides (8 isolates). The RAPD profile bands observed were not significantly discriminatory, with exceptions of E. casseliflavus, E. faecalis, and E. faecium, which suggests that the type of packaging system used had no specific effect on the selection of most microbiota in the meat after packaging. Un total de 91 bacterias ácido-lácticas (LAB) fueron aisladas a partir de 50 muestras de carne de ternera, de las cuales 25 fueron envasadas al vacío de modo tradicional y 25 fueron envasadas mediante un sistema de vacío avanzado. Los aislamientos fueron identificados a través de la secuenciación del ADN ribosomal 16S, mientras que la caracterización de las LAB se realizó mediante la amplificación al azar del ADN polimórfico (RAPD-PCR) y su posterior análisis cluster. Fueron identificadas cepas pertenecientes a diez especies bacterianas diferentes, en concreto: Enterococcus gilvus (22 aislamientos), E. faecium (9 aislamientos), E. casseliflavus (8 aislamientos), E. faecalis (4 aislamientos), E. malodoratus (3 aislamientos), E. devriessei (3 aislamientos), Lactobacillus sakei (15 aislamientos), Carnobacterium divergens (12 aislamientos), C. maltaromaticum (5 aislamientos) y Leuconostoc mesenteroides (8 aislamientos). Los perfiles de bandas de ADN obtenidas no revelaron diferencias significativas, con las excepciones de E. casseliflavus, E. faecalis y E. faecium, sugiriendo que el tipo de envasado no tiene un efecto específico en la selección de la mayor parte de la microbiota presente en la carne envasada. [ABSTRACT FROM AUTHOR]

Thymidine phosphorylase (TPase) is also known as the platelet-derived endothelial cell growth factor (PD-ECGF) and plays a role in angiogenesis. Deoxyribose (dR; a downstream TPase-product) addition to endothelial cells may stimulate FAK and p70/S6k signaling, which can be inhibited by rapamycin. Rapamycin is a specific mammalian target of the rapamycin (mTOR) inhibitor, a kinase that lies directly upstream of p70/S6k. This suggests a role for TPase in the mTOR/p70/S6k pathway. In order to study this in more detail, we exposed cells with and without TPase expression to dR and rapamycin and determined the effect on cell growth. We observed protection in cytotoxicity in Colo320 cells, but not Colo320 TP1 cells. This was in part mediated by activation of p70/S6k and inhibition of autophagy. Further studies are recommended to elucidate the mechanism behind the protective effect of dR. [ABSTRACT FROM PUBLISHER]

Objectives Flavonoids are ubiquitous phenolic plant metabolites. Many of them are well known for their pro- and antioxidant properties. Myricetin has been reported to be either a potent antioxidant or a pro-oxidant depending on the conditions. The reaction conditions for the pro- and antioxidant activities were therefore investigated using variations of the deoxyribose degradation assay systems. Methods The deoxyribose degradation assay systems were conducted as follows; H2O2/FeIII/ascorbic acid, H2O2/FeIII, FeIII/ascorbic acid, and FeIII. Each system was carried out in two variants, FeCl3 (iron ions added as FeCl3) and FeEDTA (iron added in complex with ethylenediaminetetraacetic acid). Results When ascorbic acid was present, myricetin showed antioxidant properties, especially when it occurred in complex with iron. In ascorbic acid-free systems, pro-oxidant activities prevailed, which where enhanced if iron was in complex with EDTA. Discussion Myricetin's antioxidant activity depends on both the reactive oxygen species (ROS) scavenging and iron ions chelation properties. The pro-oxidative properties are caused by reduction of molecular oxygen to ROS and iron(III) to iron(II). Myricetin is able to substitute for ascorbic acid albeit less efficiently. [ABSTRACT FROM AUTHOR]

To evaluate germplasm variability and to identify DNA profiles useful for tracing the genetic identity of olive oil, we used six Simple Sequence Repeats (SSRs) in 47 cultivated olive varieties from Central and Southern Italy. A total of 80 polymorphic SSR markers were scored and both the observed heterozygosity and the polymorphic index content were, on average, high. Genetic similarities were investigated by agglomerative hierarchical clustering and principal component analysis. The results implied that most of the olive accessions from the Campania region were genetically different from those of other Italian regions. This finding was further supported by partitioning the genetic variability using analysis of molecular variance. Furthermore, we analysed the DNA isolated from the fruit and mono-varietal oils of three cultivars. Comparative analysis of the SSR profiles revealed that these were conserved in the agro-food chain, although our data also suggested that some issues, such as the sensitivity and performance of the assay in complex mixtures, may pose limitations. Our findings extend current knowledge of Italian olive germplasm and highlight the richness and specificity of the genetic resource of olives in some regions of Southern Italy. They also provide molecular information that can be exploited for the protection of genetic material and mono-varietal oils. [ABSTRACT FROM AUTHOR]

The present study was conducted to determine the antimicrobial, antifungal and antioxidant activity of the ethanol extract of Hypericum scabrum L (HSm), Hypericum lysimachioides var. lysimachioides (HL), and Hypericum retusum Aucher (HR) and ethanol extracts of Achillea aleppica D.C. subsp. aleppica (AA), Achillea aleppica D.C. subsp. zederbaueri (Hayek) Hub.-Mor (AZ), and Achillea biebersteinii Afan. (AB). The antioxidant properties of extracts were evaluated using different antioxidants tests, including reducing power, free radical scavenging, deoxyribose assay, metal chelating activities and determination of total phenolic compounds. The extracts obtained from Hypericum and Achillea species showed high antioxidant properties. The protective effects of plant extracts were compared with a well known antioxidant, Butilated Hydroxytoluen (BHT) and α-tocopherol. Total antioxidant activity of ethanol extracts of plants were also tested by using ferric thiocyanate (FTC) and thiobarbituric acid (TBA) methods. Antioxidative activities of plant extracts were found to be comparable with Vitamin E. The results showed that the ethanol extracts of all tested plant exhibited different activity against tested microorganisms. Since most of the studied extracts have good antimicrobial and antioxidant activity, it might be possible to use them as natural food additives that act both as antioxidants and as spices. [ABSTRACT FROM AUTHOR]

The article highlights the efforts of researchers to tap the potential of G-quadruplex DNA motifs as specific molecular targets for anti-cancer therapies. It cites a study that shows how the pentacyclic acridinium derivative RHPS4 selectively targets G-quadruplex motifs to impede the replication of cancer cells. Another study reveals how the compound pyridostatin induces DNA damage at telomeric and non-telomeric regions of the genome in a panel of human cancer cells.

In 2003, two different approaches-DNA taxonomy and DNA barcoding-were simultaneously proposed to overcome some of the perceived intrinsic weaknesses of the traditional morphology-based taxonomical system, and to help non-taxonomists to resolve their crucial need for accurate and rapid species identification tools. After 7 years, it seems unlikely that a completely new taxonomical system based on molecular characters only (DNA taxonomy) will develop in the future. It is more likely that both morphological and molecular data will be simultaneously analyzed, developing what has been coined as 'integrative taxonomy'. Concerning DNA barcoding, it is now clear that it does not focus on building a tree-of-life nor to perform DNA taxonomy, but rather to produce a universal molecular identification key based on strong taxonomic knowledge that is collated in the barcode reference library. The indisputable success of the DNA barcoding project is chiefly due to the fact that DNA barcoding standards considerably enhance current practices in the molecular identification field, and standardization offers virtually endless applications for various users. [ABSTRACT FROM AUTHOR]

The present study was undertaken to investigate the effect of extracts of Schleichera oleosa (Sapindaceae) for its cytotoxic and hydroxyl radical-scavenging activities. The bark of the tree was used to prepare extracts with different solvents (i.e., hexane, chloroform, ethyl acetate, methanol, and water). The extracts were initially assessed for their in vitro cytotoxicity potential in the sulforhodamine B dye assay against cell lines, such as 502713 (colon), SW-620 (colon), HCT-15 (colon), A-549 (lung), HEP-2 (liver), SK-NS-H (central nervous system), and IMR-32 (neuroblastoma). It was observed that the water extract was effective against all the three colon cancer cell lines, while only methanol and water extracts were effective against A-549 (lung) and HEP-2 (liver), respectively. As DNA damage is one of the hallmarks of cell death, so the extracts were assessed for their ability to scavenge hydroxyl radicals, in the deoxyribose degradation assay (site- and nonsite specific) as well as their protective effect against the hydroxyl radical–induced DNA damage in the plasmid nicking assay, using pBR322. It was observed that all the extracts, except chloroform and hexane, exhibited relatively greater antioxidant activity in the nonsite-specific than in the site-specific assay. Similarly, the extracts were also found to be effective in inhibiting the hydroxyl radical–induced unwinding of supercoiled DNA, which further confirmed the hydroxyl radical–scavenging ability of the extracts in the deoxyribose degradation method. [ABSTRACT FROM AUTHOR]

The asialoglycoprotein receptor, which is abundantly and near exclusively expressed on hepatocytes, has received much attention in the design of non-viral hepatotropic DNA delivery systems. Thus, asialoglycoproteins and hexopyranosyl ligands have been coupled to DNA-binding cationic polymers and liposomes in the assembly of complexes intended for uptake by liver parenchymal cells. The aim of the study was to construct a hepatocyte-targeted multimodular liposome-based transfecting complex, in which the biotin-streptavidin interaction provides the cohesive force between the ligand asialorosomucoid and the liposome bilayer, and to evaluate its transfection capabilities in the hepatocyte-derived human transformed cell line HepG2. Dibiotinylated asialoorosomucoid was attached to cationic liposomes constructed from 3 β[N-(N’,N’-dimethylaminopropane)-carbamoyl] cholesterol (Chol-T):dioleoylphosphatidylethanolamine:biotinylcholesterylformylhydrazide (MSB1) (48:50:2 mole ratio) through streptavidin interposition. Liposome-pGL3 DNA interactions were studied by gel band shift and ethidium displacement assays. The cytotoxicity of assemblies was evaluated in the HepG2 cell line and transfection capabilities determined by measuring the activity of the transgene luciferase. Binding assays showed that all DNA was liposome associated at a DNA (negative):liposome (positive) charge ratio of 1:1. Accommodation of a streptavidin dibiotinylated asialoorosomucoid assembly was achieved at a DNA:liposome:streptavidin dibiotinylated asialoorosomucoid ratio of 1:4:9 (weight basis). Complexes showed optimal transfection activity at this ratio, which was reduced 10-fold by the presence of the competing ligand asialofetuin. The streptavidin-biotin interaction has been applied for the first time to the assembly of hepatocyte-targeted lipoplexes that display asialoorosomucoid and that are well tolerated by a human hepatoma cell line in which transfection is demonstrably achieved by receptor mediation. Favorable size and charge ratio characteristics suggest that this system may be suitable for in vivo application. [ABSTRACT FROM AUTHOR]

The aim of this project was to explore the views of young people, in particular those whose details are held on the National DNA Database (NDNAD), about some of the social and ethical issues surrounding the NDNAD. Ten focus groups revealed the majority of participants supported a universal DNA database; many thought taking a DNA sample should depend on the seriousness of the crime rather than the age of the person and that profiles of innocent people should be kept on the NDNAD. Participants' main concern regarding their information being held on the NDNAD was that the police might be able to frame them for a crime because they had access to their DNA. We suggest that policymakers hold further public debates regarding the NDNAD, with a greater variety of people, in order to ensure that the views of all members of society are addressed and protected and that there is greater understanding about the regulation of the NDNAD. [ABSTRACT FROM AUTHOR]

This study examined metal levels (especially U and Ni) in the tail tissues of water snakes from contaminated (Tim's Branch) and reference areas on the Department of Energy's Savannah River Site (SRS). Home ranges of snakes were quantified to determine the ratio of the habitat that they use in relation to the contaminated areas to better estimate exposure Compared to conventional methods that do not. The exposure assessment indicated that water snakes in the contaminated areas could expect U exposure at 3-4 orders of magnitude greater than the Agency for Toxic Substances and Disease Registry's Minimum Risk Level (MRL) from ingestion of amphibians and fish. Ni and U, in addition to Se, Mn, and Cu, were related to increased DNA double-strand breakage (DDSB) in water snakes. We report burdens for each metal individually, but the results of the DDSB indicated that these metals did not behave independently, but as a suite. If we did not have a secondary endpoint (DDSB), we might have assumed from the exposure predictions and tissue burden analyses that U was the sole metal of concern to water snakes in Tim's Branch. These data also imply that these toxicants do not biomagnify at the spatial and temporal scale of this study. [ABSTRACT FROM AUTHOR]

Based on the convolutional code model of error-correction coding theory, we propose an approach to characterize and compare DNA sequences with consideration of the effect of codon context. We construct an 8-component vector whose components are the normalized leading eigenvalues of the L/L and M/M matrices associated with the original DNA sequences and the transformed sequences. The utility of our approach is illustrated by the examination of the similarities/dissimilarities among the coding sequences of the first exon of β-globin gene of 11 species, and the efficiency of error-correction coding theory in analysis of similarity/dissimilarity of DNA sequences is represented. [ABSTRACT FROM AUTHOR]

The development of a new methodology to achieve electrophilic fluorination of triisopropylsilyl-protected 2-deoxyribonolactone has been employed to synthesize clofarabine and gemcitabine with improved synthetic efficiency versus prior synthetic methods. These studies highlight the versatility of this new methodology to obtain medically relevant 2'-fluoronucleosides. [ABSTRACT FROM AUTHOR]

A modified version of this project was used during the final seven days of a year-long calculus sequence at the United States Military Academy to introduce students to the nature of integrative learning. Students from different majors were brought together in groups and spent the first few days going over the mathematics material presented here. They then spent a day separated into their respective departments to learn how their chosen fields viewed and contributed to issues related to DNA and gene technologies. Afterwards, the students reconvened in their groups to develop and give presentations advising a hypothetical candidate for public office on the many diverse viewpoints associated with this topic. While the coursework in calculus is essential for this project as presented here, some level of biology coursework will also greatly assist student understanding. In the absence of biology coursework, additional reading material can be provided to introduce the relevant concepts. [ABSTRACT FROM AUTHOR]

Tert-butyldiphenylsilyl (TBDPS) was found to be an effective orthogonal protecting strategy for the 5-substituted hydroxyl groups of de novo synthesized deoxyuridine analogues 1-3 and 7-(3-hydroxypropynyl)- of 8-aza-7-deazadeoxyadenosine 4 for their incorporation into oligodeoxynucleotides by phosphoramidite chemistry. It could be completely cleaved under normal and ultra-mild deprotection conditions applied to DNA synthesis, without extra cleaving operation. The new phosphoramidites were coupled as usual with high yields. The new modified oligodeoxynucleotides were characterized by MALDI-TOF and enzymatic cleavage analysis. The thermal stability and conformation of these hydroxyl-functionalized DNA duplexes were evaluated. [ABSTRACT FROM AUTHOR]