Commercial DNA Isolation Kit Research Articles

An Investigation of Polymorphism on the FASN, SCD1, and SLC27A3 Genes in Sheep

Milk traits of sheep are affected by many environmental and genetic factors. These traits are quantitative traits and are determined by many genes. This study aimed to investigate polymorphisms of milk-related Fatty-acid synthase (FASN), Stearoyl-CoA desaturase (SCD1), and solute carrier 27A3 (SLC27A3) genes in cross-bred Hamdani sheep. Blood samples were collected from 100 healthy cross-bred Hamdani ewes from the jugular vein into K3-EDTA-containing tubes. Genomic DNA was extracted using a commercial DNA isolation kit. PCR products of FASN (275 bp), SCD1 (225 bp), SLC27A3-P1 (341 bp), and SLC27A3-P2 (319 bp) were subjected to restriction fragment length polymorphism (RFLP) analysis using SSil (AciI), Cfr13I, AluI, and Hpy188III the restriction enzyme, respectively. However, all gene regions were found to be monomorphic. In the study, only TT, AA, AA, and GG genotypes were detected for FASN, SCD1, SLC27A3-P1, and SLC27A3-P2, respectively. Allele and genotype frequencies were 1.00 for all genotypes and alleles. Although this study did not reveal favorable genotypes in FASN, SCD1, and SLC27A3 genes that can be used for milk traits, more comprehensive studies with larger sample sizes should be conducted to investigate polymorphisms in cross-bred Hamdani sheep.

Genetic Diversity and Relationship of Native Phalaenopsis Orchids: A Case Study of Indonesian Archipelago

The native Phalaenopsis is valuable germplasm for future orchid breeding programs and for its conservation because it provides many beneficial traits or genes. This study aimed to determine and analyze the molecular diversity and phylogeny of Indonesian native Phalaenopsis by a DNA barcoding (matK) marker. A total of 19 samples of Phalaenopsis orchids were used in this study. All leaf samples of orchid were extracted and purified using a commercial DNA isolation kit from Geneaid Biotech Ltd., Taiwan (GP100). The DNAs were then amplified by specific matK primers: Forward (5’-CGTACAGTACTTTTGTGTTTACGAG-3’) and Reverse (5’-ACCCAGTCCATCTGGAAATCTTGGTTC-3’). The DNA targets or products (matK) were purified and sequenced by the Sanger-bidirectional method at 1st Base Ltd., Malaysia. Before further analysis, the matK sequences of Phalaenopsis were edited, reconstructed, and aligned with the assistance of Clustal W in the MEGA 11 software. Its genetic diversity was determined using the nucleotide diversity index (π%), and the phylogenetic analysis was performed using the maximum likelihood (ML) method with a statistical bootstrap. The phylogenetic relationship was also assessed using principal component analysis (PCA). Based on this marker, the native Phalaenopsis has a high genetic diversity (π% = 1.70). In addition, the phylogenetic analysis revealed that this germplasm was separated into seven clades, where P. pantherina has the closest relation to P. cornu-cervi and P. gigantea. Conversely, the highest genetic distance was to P. amabilis from South Kalimantan and to P. celebensis from Sulawesi, at a coefficient divergence of 0.084. Our findings provide an essential foundation for supporting future orchid breeding practices, including conservation, on local and global scales.

Identification and classification of Eremogone species using DNA based Schottky diodes

The revelation of DNA's remarkable conducting characteristics provided a significant boost for the development of DNA-based electronics. These distinguishing characteristics can be used to identify or detect DNA. In this study, it was basically aimed to investigate the possibility of using Schottky barrier diodes in which semiconductor DNA is used as the interface from three endemic Eremogone species distributed in Turkey. We collected Eremogone ali-gulii, Eremogone armeniaca, and Eremogone scariosa endemic species and extracted the DNA via the QIAGEN commercial DNA isolation kit procedure. The DNA samples were deposited by drop casting on the thin film indium tin oxide substrate. Electrical characterization of DNA interlayered heterojunctions was investigated via a solar simulator. Electronic parameters such as ideality factor, barrier height, and series resistance were calculated from I to V characteristics. Electrical properties of DNA samples were investigated and compared to Colchicum triphyllum’s DNA which is completely from another genus. The results show that morphologically similar species have similar electrical properties. When compared to Colchicum triphyllum-DNA based device, genus Eremogone-DNA based devices have a lower ideality factor, barrier height, and series resistance. Via this technique, DNA samples can be identified, detected, and classified.

Functional assessment of DNA extraction methods from frozen human blood samples for Sanger sequencing analysis.

The quality of input DNA is crucial for obtaining significant inferences from molecular techniques like Sanger sequencing and Next Generation Sequencing experiments. Many of the extraction methods are suitable for retrieving quality DNA from fresh blood and tissue samples, regardless of the isolation principle. However, while isolating DNA from frozen blood samples, processed tissue samples or low-quality samples, careful selection of suitable extraction methods is extremely important. Moreover, there is no standard protocol recommended for genomic DNA extraction from stored blood samples, particularly those stored in a Biobank, for applications like Sanger sequencing. Consequently, we have systematically compared different commercial DNA isolation kits with a modified manual extraction method for blood samples frozen for up to three years and assessed their quality, yield and suitability for PCR, Real-Time PCR and Sanger sequencing. The manual DNA extraction method was improved by incorporating a few modifications: a lower NaCl concentration was used for precipitatingDNA and excluded the use of phenol. The modified method provided the maximum DNA yield from stored blood. Although all the methods tested were suitable for recovering DNA from stored blood, the modified method described here may be preferred for large-scale applications as it provides cost-effective ways to obtain large quantities of quality DNA. Most importantly, the DNA isolated by the modified method appears to be more stable in long-term storage at -80°C.

Alteration of gut microbiota composition in patients with cholangiocarcinoma with non-responsiveness to first-line chemotherapy: A pilot study.

4104 Background: Gut microbiota established crucial roles in host metabolism and several diseases, particularly cancers. Distinct bacterial profiles from intestine are found to be a potential factor in carcinogenesis, while some of those are associated with detrimental treatment to the responsiveness in various types of cancer. Association of gut microbiota and treatment outcome has been thoroughly investigated in intrahepatic cholangiocarcinoma (ICCA). The present study aimed to compare gut microbiota profiles between chemotherapy responder and non-responder in ICCA patients. Methods: Unresectable or metastatic ICCA patients were recruited in the study. The criteria of all patients were naïve to chemotherapy. All patients received first line combination of cisplatin 25 mg/m2 and gemcitabine 1000 mg/m2 at day1 and day 8 in every 21-day cycle and were given up to 8 cycles. The primary endpoint was to evaluate the association between gut microbiota and the objective response rate. Bacterial genomic DNA samples were extracted from the stool using a commercial genomic DNA isolation kit (Qiagen, Hilden, Germany) and then underwent next-generation sequencing. Data analyses were conducted by using QIIME2 and Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC). Results: Seventeen ICCA patients were recruited. The objective response rate was 23.5% comparable to historical study. Chemotherapy responder group was defined as partial response patients (N = 4) and chemotherapy non-responder group included stable of disease and progressive disease (N = 13). Baseline characteristics were similar including age, sex, ECOG performance status, numbers of metastatic organ and CA 19-9 in two groups. Median Age were 63 years old (60-70) and 61 (45-73), respectively. Alpha-diversity and beta-diversity were not different between two groups. In chemotherapy non-responder group, some taxa were dominantly observed including Ruminococcaceae, Oribacterium, Oxalobacter, Peptostreptococcus, Aggregabacter, which had been previously reported increasing in ICCA patients. Interestingly, Ruminococcaceae, which was previously documented to be correlated with vascular invasion, was significantly increased abundance in non-responder group. Moreover, the median progression-free survival (PFS) was improved in chemotherapy responder group compared to non-responder group 11.8 and 6.6 month, respectively. Large sample sizes study to confirm this study result should be developed. Conclusions: Distinct bacteria from gut microbiota such as Ruminococcaceae has inversely associated with chemotherapy response in ICCA patients receiving first line cisplatin and gemcitabine combination, suggesting the possibility of the poorer PFS.

Rs10737680 polymorphism in complement factor H and neovascular age-related macular degeneration in Yogyakarta, Indonesia.

Neovascular age-related macular degeneration (nAMD) is one of the main causes of blindness in developed countries. Complement factor H (CFH) is one of the genes involved in the pathogenesis of nAMD. This study investigated the rs10737680 polymorphism in CFH and its conferred susceptibility to nAMD in Yogyakarta, Indonesia. This case-control hospital-based study recruited participants consisting of 96 patients with nAMD and 101 controls without nAMD from the Eye Polyclinic of Sardjito Hospital, YAP Eye Hospital, and Hardjolukito Hospital Yogyakarta. nAMD was diagnosed when fundus examination, fundus photographs, and optical coherence tomography revealed hard or soft drusen in the macular area measuring > 63 µm that appeared below the retinal pigment epithelium, with or without macular hypo- or hyperpigmentation, and was accompanied by choroidal neovascularization. Genomic DNA was extracted using a commercial DNA isolation kit. The restriction fragment length polymorphism technique was used to identify the rs10737680 polymorphism in CFH. The mean (standard deviation [SD]) age of the nAMD group was not homogeneous with that of the control group (P < 0.05); 65.41 (9.74) years versus 68.24 (7.82) years. The number of patients with hypertension in the nAMD group was significantly higher than in the control group (P < 0.05). In the nAMD group, the genotype distribution indicated homozygous risk allele in 34.38%, heterozygous risk allele in 57.29%, and homozygous non-risk allele in 8.33%. In the control group, the genotype distribution indicated homozygous risk allele in 21.78%, heterozygous risk allele in 36.63%, and homozygous non-risk allele in 41.58%. Statistical analysis between the two study groups according to homozygous risk allele genotype (odds ratio [OR], 7.87; 95% confidence interval [CI], 2.88-22.79) and heterozygous genotype (OR, 7.80; 95% CI, 3.11-21.19) showed a significant difference (both P < 0.01). Homozygous risk allele was less frequent than heterogeneous risk allele in patients with nAMD; however, both increased the risk for nAMD. Although the homozygous or heterozygous risk-alleles were detected in most patients, yet other important genetic or environmental factors could be involved in the pathogenesis of nAMD. Overall, we found a significant association between rs10737680 polymorphism in CFH and the susceptibility to nAMD in Yogyakarta, Indonesia; however, future studies are needed to fully delineate the mechanism.

Comparative Evaluation of an Easy Laboratory Method for the Concentration of Oocysts and Commercial DNA Isolation Kits for the Molecular Detection of Cyclospora cayetanensis in Silt Loam Soil Samples.

Cyclospora cayetanensis is a protozoan parasite that causes foodborne outbreaks of diarrheal illness (cyclosporiasis) worldwide. Contact with soil may be an important mode of transmission for C. cayetanensis and could play a role in the contamination of foods. However, there is a scarcity of detection methods and studies for C. cayetanensis in soil. Traditional parasitology concentration methods can be useful for the detection of C. cayetanensis, as found for other protozoa parasites of similar size. The present study evaluated a concentration method using flotation in saturated sucrose solution, subsequent DNA template preparation and qPCR following the Bacteriological Analytical Manual (BAM) Chapter 19b method. The proposed flotation method was compared to three commercial DNA isolation kits (Fast DNATM 50 mL SPIN kit for soil (MP Biomedicals, Irvine, CA, USA), Quick-DNATM Fecal/Soil Microbe Midiprep kit (Zymo Research, Irvine, CA, USA) and DNeasy® PowerMax® Soil Kit (Qiagen, Hilden, Germany)) for the isolation and detection of DNA from experimentally seeded C. cayetanensis soil samples (5–10 g with 100 oocysts). Control unseeded samples were all negative in all methods. Significantly lower cycle threshold values (CT) were observed in the 100 oocyst C. cayetanensis samples processed via the flotation method than those processed with each of the commercial DNA isolation kits evaluated (p < 0.05), indicating higher recovery of the target DNA with flotation. All samples seeded with 100 oocysts (n = 5) were positive to the presence of the parasite by the flotation method, and no inhibition was observed in any of the processed samples. Linearity of detection of the flotation method was observed in samples seeded with different levels of oocysts, and the method was able to detect as few as 10 oocysts in 10 g of soil samples (limit of detection 1 oocyst/g). This comparative study showed that the concentration of oocysts in soil samples by flotation in high-density sucrose solutions is an easy, low-cost, and sensitive method that could be implemented for the detection of C. cayetanensis in environmental soil samples. The flotation method would be useful to identify environmental sources of C. cayetanensis contamination, persistence of the parasite in the soil and the role of soil in the transmission of C. cayetanensis.

Amplification of cestode DNA from the peri-anal region of naturally infected foxes by PCR and LAMP: proof of concept for a potential sampling strategy for diagnosing human taeniosis

The diagnosis of human taeniosis can be achieved through coproscopy, ELISA or PCR. An important limitation of these methods is the high turnaround time for stool sample collection and preparation, indicating the need for a straightforward sampling strategy. Due to the high metabolic activity and reproductive potential of Taenia spp., we hypothesise that parasite DNA (cells and eggs) present in the peri-anal region of the host can be exploited as a target for molecular diagnosis. We evaluated the feasibility of recovering parasite DNA from the peri-anal area of foxes naturally infected with Taenia spp. Before necropsy, cotton swabs were rubbed at the peri-anal region of foxes. DNA was extracted using alkaline lysis coupled with a commercial DNA isolation kit (method A) or alkaline lysis alone (method B). DNA was used in the multiplex-PCR assay (previously described and called here swab-PCR) and a novel LAMP assay detecting Taenia spp. commonly found in foxes (swab-LAMP). The results of these assays from 105 foxes were compared with the presence of intestinal helminths determined at necropsy and by the sedimentation and counting technique (SCT). The sensitivity of swab-PCR for detecting Taenia (n = 68) was 89.8% (95% CI, 77.7–96.6) and 89.5% (66.9–98.7) using methods A and B, respectively. The sensitivity of the swab-LAMP assay was 83.7% (70.3–92.7) using method A and 89.5% (66.9–98.7) with method B. We postulate that peri-anal swab sampling followed by simplified DNA extraction and LAMP might be a suitable strategy for surveillance of human taeniosis in resource-limited settings in the future.

Relationship between postmenopausal osteoporosis and glucocorticoid receptor gene (NR3C1) polymorphism in a Turkish population

IntroductionGlucocorticoids (GCs) are used in the treatment of numerous diseases, and long-term use of GCs causes bone loss. GC receptor activation decreases Bone Mineral Density (BMD) by inhibiting and stimulating osteoblasts and osteoclasts, respectively. GC receptor gene polymorphisms are also associated with increased susceptibility to GCs. The purpose of this study was to assess the relationship between osteoporosis and Glucocorticoid receptor gene (NR3C1) polymorphism in Turkish population.Material and methodsThe study group consisted of 232 unrelated patients with osteoporosis and 150 unrelated healthy controls. All participants, patients and healthy controls, were of Turkish origin, from the central region of Turkey. Genomic DNA was isolated from whole venous blood samples using a commercial DNA isolation kit. The NR3C1 BclI gene C/G polymorphism was analyzed by polymerase chain reaction.ResultsThe frequencies of CC, CG and GG genotypes in the patients were 34.5%, 48.3%, and 17.2% and in the controls were 48.0%, 42.0%, and 10.0%. A statistically significant difference was observed between patients and controls according to genotype frequencies (p=0.01). C and G allele frequencies of C/G polymorphism were 58.6% and 41.4% in patient group and 69.0% and 31.0% in control group (p=0.005).ConclusionsThe NR3C1 BclI gene C/G polymorphism could be one of the genetic factors causing osteoporosis.

Optimizing DNA Extraction from Cave Microorganisms

Wind Cave near Hot Springs, South Dakota has over 150 miles of surveyed area and is yet to be completely mapped. Identifying the types of microorganisms living in the cave will provide insights into understanding what types of organisms could be found in other extreme environments. The main question to be answered in this work is which commercial DNA isolation kits provide the best yield of purified DNA from microorganisms collected at Wind Cave. Samples from the cave were collected and grown on culture media. Taking an unbiased approach, seven commercially available DNA isolation kits were evaluated using the manufacturers’ recommended protocols. Kits from Omega Bio-tek and Qiagen exhibited optimal performance and were most effective at isolating DNA from the samples collected in Wind Cave. The DNA obtained from the samples will be used to perform PCR-based sequencing analysis using primers targeting either a specific region of the 16S small ribosomal subunit of prokaryotes for bacteria and archaea or an internal transcribed spacer (ITS) for identifying fungal microbial eukaryotic lineages.

Benchmarking DNA isolation kits used in analyses of the urinary microbiome

The urinary microbiome has been increasingly characterized using next-generation sequencing. However, many of the technical methods have not yet been specifically optimized for urine. We sought to compare the performance of several DNA isolation kits used in urinary microbiome studies. A total of 11 voided urine samples and one buffer control were divided into 5 equal aliquots and processed in parallel using five commercial DNA isolation kits. DNA was quantified and the V4 segment of the 16S rRNA gene was sequenced. Data were processed to identify the microbial composition and to assess alpha and beta diversity of the samples. Tested DNA isolation kits result in significantly different DNA yields from urine samples. DNA extracted with the Qiagen Biostic Bacteremia and DNeasy Blood & Tissue kits showed the fewest technical issues in downstream analyses, with the DNeasy Blood & Tissue kit also demonstrating the highest DNA yield. Nevertheless, all five kits provided good quality DNA for high throughput sequencing with non-significant differences in the number of reads recovered, alpha, or beta diversity.

Оптимизация выделения мтДНК из клубней картофеля с использованием различных сорбционных носителей и разной степени очистки митохондрий

В настоящее время существует интерес к оценке повреждений мтДНК как к маркеру окисли-тельного стресса, при этом данный вопрос недостаточно изучен для мтДНК растений. Однако мито-хондриальный геном растений обладает рядом особенностей, которые могут существенно затруднять проведение ПЦР. При недостаточной очистке митохондрий пробы всё ещё могут быть контаминиро-ваны ядерной и пластидной ДНК, что может привести к неспецифичному отжигу праймеров. Целью данной работы является оптимизация процесса выделения мтДНК из картофеля (Solanum tube- rosum L.) при использовании различных сорбционных носителей. Применение методов сорбции на твердофазных носителях является наиболее эффективным для крупных по размерам молекул мтДНК. Нами было проведено сравнение эффективности трёх коммерческих наборов для выделения ДНК: diaGene (Диа-М, Россия), Проба-ГС (ДНК-Технология, Россия) и Plasmid miniPrep (Evrogen, Россия). Эти методы подразумевают связывание ДНК с поверхностью сорбционных колонок (diaGene, Plasmid miniPrep), либо на силикатном сорбенте (Проба-ГС). Для оценки эффективности рассмотренных ме-тодов с помощью количественной ПЦР был измерен уровень обогащения мтДНК. Также приведено сравнение эффективности выделения ДНК при разных степенях очистки исходного материала – при использовании гомогената картофеля, при очистке дифференциальным и центрифугированием в гра-диенте Перколла. Низкий уровень насыщенности мтДНК наблюдался при выделении из гомогената, высокий – при выделении митохондрий градиентным центрифугированием. При использовании гра-диентного центрифугирования высокий уровень обогащения мтДНК наблюдался только при выделе-нии ДНК набором Проба-ГС. Нами было обнаружено, что наибольшим насыщение материала мтДНК будет при использовании набора Plasmid miniPrep при предварительной очистке митохондрий гради-ентным центрифугированием. Только градиентное центрифугирование способно максимально очи-стить митохондрии от примесей. Использование набора Plasmid miniPrep, предназначенного для вы-деления плазмидной ДНК, показывает свою эффективность и для мтДНК, которые аналогично пла-стидным ДНК являются преимущественно кольцевыми. В результате удалось разработать оптимизи-рованный процесс выделения мтДНК картофеля, пригодного для проведения дальнейших молекуляр-но-генетических исследований. Этот метод может быть использован для любых научных изысканий, связанных с изучением митохондриального генома растений.

Level of Microparticles in Patients with Essential Thrombocythemia and Its Relation with JAK2V617F Mutation

To detect the levels of microparticles (MP) in plasma of patients with esseutial thrombo-cythermia(ET) and analyze the relationship between the JAK2V617F mutant and MP in ET patients. The numerical values of MPs were analysed by using flow cytometry. Venous blood of 56 ET patients and 28 healthy persons was collected in the morning and anticoagulated with sodium citrate (1∶9). The RMP, PMP, TF+MP and EMP were detected by FCM using phycoerythrin (PE)-conjugated monoclonal antibodies to CD235a for red blood cells, CD61 for platelets, CD142 for tissue factor (TF) and CD62E for endothelial cells, respectively. Forward scatter was set in scale using fluorescent microspheres of 0.8 μm. Standard fluorescent microbeads (0-0.8 μm) in diameter were used to set the microparticles gate. Genomic DNA was extracted from mononuclear cells by using a commercial DNA isolation kit and amplified by allele specific polymerase chain reaction (PCR). According to the size of molecular weight, the amplified products were separated by electrophoresis on a 2% agarose gel to screen 26 JAK2V617F mutations. The detection results showed that the MP levels in ET group were higher than those in normal control group: RMP (157.2±304.9/μl vs 21.3±18.4/μl), PMP (1378.9±2454/μl vs 113.8±97.1/μl), TF+MP (123±354.6/μl vs 21±15.7/μl) and EMP (1434.7±2601.9/μl vs 291.7±297.7/μl) (P<0.05). In 8 patients with thrombus, the levels of these four kinds of MP were higher than those of controls without thrombus: RMP (258.2±327.7/μl vs 55.6±63.8/μl), PMP (1853±1874.7/μl vs 444.7±712/μl), TF+MP (120.4±112.5/μl vs 60.3±128.3/μl) and EMP (1637.1±1563.5/μl vs 629.4±1000.2/μl) (P<0.05). The levels of those 4 kinds of MP in 17 patients with splenomegaly were significantly higher than those in 11 patients without splenomegaly: RMP (306.8±491.1/μl vs 59.3±51/μl), PMP (2944.8±3767.6/μl vs 334.8±420.2/μl), TF+MP (162.9±166.8/μl vs 31.0±28.7/μl) and EMP (3031.8±4048.8/μl vs 701.5±729.2/μl) (P<0.05). The level of other MP showed no difference between MPN patients with JAK2V617F mutation and without JAK2V617F mutation (P>0.05), except TF+MP (154.7±516.3/μl vs 100.5±126.6/μl) (P<0.05). The numerical values of MP detected are more in ET patients than those in healthy controls. The number of MP is higher in patients with thrombus than that without thrombus, so do in patients with splenomegaly and without splenomegaly. Patients with JAK2V617F mutation show higher number of TF+MP than that without JAK2V617F mutation. But the other three kinds of MP show no this difference.

A Simple and Cost-Effective DNA Preparation Method Suitable for High-Throughput PCR Quantification of Hepatitis B Virus Genomes.

Hepatitis B virus (HBV) is a para-retrovirus that reverse transcribes its pregenomic RNA into relaxed circular DNA inside viral nucleocapsids. The number of HBV genomes produced in vitro is typically quantified using commercial silica-membrane-based nucleic acid purification kits to isolate total DNA followed by HBV-specific quantitative PCR (qPCR). However, despite the convenience of commercial kits, this procedure is costly and time-consuming due to multiple centrifugation steps, which produce unnecessary waste. Here, we report a rapid, cost-effective, and environmentally friendly total DNA preparation method. The assay is based on the simple incubation of detergent and proteinase K with cells or cell-free supernatants to permeabilize cells and disrupt viral particles. After heat inactivation and subsequent centrifugation to clear the lysates, DNA samples are directly subjected to qPCR to quantify HBV genomes. As a proof of concept, the assay was developed in 12-well plates to assess intra- and extracellular HBV genome equivalents (GEqs) of stably viral-replicating cell lines (e.g., HepAD38) and HBV-infected HepG2-NTCP cells, both treated with lamivudine (LMV), an HBV replication inhibitor. Viral DNA was also prepared from the serum of patients chronically infected with HBV. To validate the assay, a representative commercial DNA isolation kit was used side-by-side to isolate intra- and extracellular HBV DNA. Both methods yielded comparable amounts of HBV GEqs with comparable LMV 50% efficient concentration (EC50) values. The assay was subsequently adapted to 96- and 384-well microtiter plates using HepAD38 cells. The EC50 values were comparable to those obtained in 12-well plates. In addition, the calculated coefficient of variation, Z’ values, and assay window demonstrated high reproducibility and quality. We devised a novel, robust, reproducible, high-throughput microtiter plate DNA preparation method suitable for quantifying HBV GEqs by qPCR analysis. This strategy enables rapid and convenient quantitative analysis of multiple viral DNA samples in parallel to investigate intracellular HBV replication and the secretion of DNA-containing viral particles.

The effects of humic substances on DNA isolation from soils.

BackgroundHumic substances (HS) are compounds with a complicated structure, present in the humus soil layer, water, lake sediments, peat, brown coal and shales. Due to their similar physicochemical properties to DNA, they may have an adverse effect on the subsequent use of the isolated material. The main aim of this research was to examine the effect of HS on DNA isolation depending on the soil type and land use, taking into account the spectroscopic full characteristics of HS fractions.MethodsThe research was conducted on eight types of soil sample. Soils represented the most important Soil Reference Groups for temperate climates: Fluvisols, Regosols, Cambisols, Arenosols, Histosols and Luvisols. Soil samples were also collected from areas diversified in terms of use: arable land, grassland and forest. The extraction of HS fractions was performed using the procedure recommended by the International HS Society. The fractional composition of HS was characterized by UV–Vis and fluorescence methods. Soil DNA is extracted by direct cell lysis in the using a CTAB-based method with a commonly-used commercial soil DNA isolation kit. The basis for assessing the quantity and quality of extracted DNA was the Polymerase chain reaction (PCR) reaction since the analysis of soil DNA often relies on the use of PCR to study soil microorganisms.ResultsBased on the results, it can be concluded that in the presence of a high concentration of HS, the isolated DNA was low quality and the additional purification procedure was necessary. Despite the differentiation of the internal structure of HS fractions, the decisive factor in the efficiency of DNA isolation from soil samples was the total carbon content in HS. Reduced DNA yields can significantly constrain PCR detection limits to levels inadequate for metagenomic analysis, especially from humus-rich soils.

Improved genetic identification of acipenseriform embryos with application to the endangered pallid sturgeon Scaphirhynchus albus.

We produced pallid sturgeon Scaphirhynchus albus embryos at five pre-hatch developmental stages and isolated and quantified genomic DNA from four of the stages using four commercial DNA isolation kits. Genomic DNA prepared using the kit that produced the largest yields and concentrations were used for microsatellite DNA analyses of 10-20 embryos at each of the five developmental stages. We attempted to genotype the hatchery-produced embryos at 19 microsatellite loci and confirmed reliable genotyping by comparing the microsatellite genotypes to those of known parents. Embryos at stages 5 and 8 did not produce reliable genotyping while those at stages 14, 24 and 33 did. We used the same DNA isolation method on 262 wild-caught acipenseriform embryos collected from the lower Yellowstone River. A total of 200 of the wild embryos were successfully identified to stages 8 to 34 and the rest could not be staged. Using a combination of single nucleotide polymorphism and microsatellite markers, 249 of the wild-caught embryos were genetically identified as paddlefish Polyodon spathula, five were identified as shovelnose sturgeon Scaphirhynchus platorynchus and eight failed to amplify. None were identified as pallid sturgeon. This study demonstrates that early-stage wild-spawned acipenseriform embryos can be genetically identified less than 24 h post-spawn. This methodology will be useful for recovery efforts for endangered pallid sturgeon and can be applied to other acipenseriform species.

Gelatin-coated magnetic nanoparticles-based DNA isolation method: A comparison with commercial DNA isolation kits from whole blood

DNA isolation is the first step for most molecular tests, thus indicating the importance of using a reliable and suitable method for this procedure. The use of magnetic nanoparticles for blood DNA isolation offers several advantages including subjecting little mechanical stress to your sample, obtaining higher quality and quantity of DNA, and non-laborious procedures. In this study, we isolated genomic DNA using gelatin-coated magnetic nanoparticles from blood samples and test its use compare with three commercial blood DNA isolation kits. DNA purity and yield were assessed by measuring absorbance at A260/A280 and by agarose gel electrophoresis. The suitability of the isolated DNA for downstream applications was analyzed by end-point PCR and Sanger sequencing. In this study, gelatin-coated magnetite particles for genomic DNA isolation provide an efficient, simple, and inexpensive method that does not require the use of commercial blood DNA Isolation Kit.

A Look Back at 2018

A Look Back at 2018

Impact of JAK2V617F Mutation Burden on Clinial Presentation and Survival in ET Patients

To better define the effect of JAK2V617F mutant allele burden on clinical presentation of patients with essential thrombo cythamia (ET), especially thrombosis. Two ml of heparin anti-coagulated bone marrow was collected from 229 ET cases, who were diagnosed and treated in the First People's Hospital of Yunnan Province during 2013.10 to 2016.12. and then the mononuclear cells were separated by Red Blood Cell Lysis Buffer, genomic DNA was extracted from mononuclear cells by using a commercial DNA isolation kit and amplified by allele specific polymerase chain reaction (PCR). According to the size of molecular weight, the amplified products were separated by electrophoresis on a 2% agarose gel to screen the JAK2V617F mutation, then the JAK2V617F mutation burden was detected by real-time polymerase chain reaction (RT-PCR) in 120 patients with JAK2V617F mutation. Meanwhile, these samples were sequenced in order to verify the accuracy of the PCR screewing. ET patients with thrombotic events had significantly higher JAK2V617F allele burden than those without thrombosis (23.2% vs 14.2%) ( P<0.05). Meanwhile, ET patients showed increased JAK2V617F allele burden in the group with higher leukocytosis (WBC > 10×109/L) (P<0.001) and hemoglobin (> 150 g/L) (P<0.05). JAK2V617F mutation burden in 17 patients with splenomegaly was higher than that in 45 patients without splenomegaly (28.1% vs 11.8%) (P<0.05). but the JAK2V617F mutation burden was regatively correlated with platelet count (P<0.05). On the other hand, no correlation was found between JAK2V617F mutation burden and sex (P > 0.05). Univariate analysis showed that the JAK2V617F allele burden did not affect survival. Multivariable analysis showed that prognostic variable including WBC counts, hemoglobin level, age, sex, and splenomegaly not affected survival, (P > 0.05). The clinical presentations of ET patients, such as WBC counts, hemoglobin level and splenomegaly, are influenced by the JAK2V617F mutation burden. ET patients with thrombotic events has significantly higher JAK2V617F allele burden than those in ET palients without thrombosis.JAK2V617F mutation burden has no relations with sex and age..

Investigation of Streptococcus pyogenes virulence factors and typing by multiple locus variable number tandem repeat fingerprinting (MLVF) method

Streptococcus pyogenes is an important bacterial pathogen that colonizes the throat and skin of human beings and causes a wide variety of diseases ranging from mild infections like pharyngitis, tonsillitis and impetigo to severe invasive infections such streptococcal toxic shock syndrome, septicemia, and necrotizing fasciitis, and produces a wide variety of virulence factors. The aim of this study was to investigate the antibiotic resistance, virulence genes; [pyrogenic exotoxin genes (speA, C, G, H, I, J, K, L, M, smeZ and ssa), deoxyribonuclease genes (sdaB, spd3, sdc ve sdaD), protease genes (speB, spyCEP ve scpA) and inhibitor genes (mac and sic)] of S.pyogenes strains isolated from throat cultures of patients with symptomatic tonsillo-pharyngitis and typing by multiple locus variable number tandem repeat fingerprinting (MLVF) method. One hundred and fifty S.pyogenes isolates were identified by conventional methods and streptococcus group A latex kit (Biomerieux, France). Antibiotic susceptibility tests were performed by Kirby-Bauer disk diffusion method as recommended by Clinical and Laboratory Standards Institute. DNA isolation was performed by using a commercial DNA isolation kit (Qiagen, Germany) in accordance with manufacturer's recommendations. The virulence genes were determined by multiplex PCR. MLVF method was performed with multiplex PCR using specific primers for repeated sequences within bacterial genome. All of the S.pyogenes isolates were susceptible to penicillin G, cefotaxime, ceftriaxone, chloramphenicol, clindamycin, erythromycin, levofloxacin, vancomycin and linezolid. Among streptococcal pyrogenic exotoxin genes the most frequent gene was smeZ (90.0%) followed by speG (88.0%), speC (58.7%), ssa (42.7%), speA (33.3%), speJ (24.0%), speK (18.7%), speH (14.0%), speI (13.3%), speL and speM (9.3%). Of the DNase genes, sdaB was detected in all strains (100%), spd3, sdc, sdaD genes were determined as 64.7%, 36.0%, 24.7% respectively. Protease genes (speB, spyCEP, scpA) and mac gene from the inhibitor genes were positive in all strains, and sic gene was positive in only 3 (2.0%) of the isolates. Thirty-two different patterns that contained two or more isolates were determined by MLVF analysis. Ninety one isolates were included in any of the 32 different patterns, while 59 isolates were defined as sporadic isolates. In conclusion, S.pyogenes isolates collected from throat cultures of patients with symptomatic tonsillo-pharyngitis in Konya/Turkey were susceptible to all antibiotics studied and have carried a very high rate of virulence factors. However the isolates were mostly clonally unrelated and sporadic. This study is the first report in Turkey, in which S.pyogenes isolates were typed by the MLVF method and a large number of virulence factors were investigated.