Amount Of DNA Research Articles

A Comparative Study of Methyl-BEAMing and Droplet Digital PCR for MGMT Gene Promoter Hypermethylation Detection

Background: O-6-methylguanine-DNA methyltransferase is responsible for the direct repair of O6-methylguanine lesions induced by alkylating agents, including temozolomide. O-6-methylguanine-DNA methyltransferase promoter hypermethylation is a well-established biomarker for temozolomide response in glioblastoma patients, also correlated with therapeutic response in colorectal cancer. Objectives: The ARETHUSA clinical trial aims to stratify colorectal cancer patients based on their mismatch repair status. Mismatch repair-deficient patients are eligible for treatment with immune checkpoint inhibitors (anti-PDL-1), whereas mismatch repair-proficient samples are screened for O-6-methylguanine-DNA methyltransferase promoter methylation to identify those suitable for temozolomide treatment. Methods: In this context, a subset of ARETHUSA metastatic colorectal cancer samples was used to compare two different techniques for assessing O-6-methylguanine-DNA methyltransferase hypermethylation: Methyl-BEAMing, a highly sensitive digital PCR approach that combines emulsion PCR and flow cytometry, and droplet digital PCR, a more automated procedure that enables the rapid, operator-independent analysis of a large number of samples. Results: Our study clearly demonstrates that the results obtained using Methyl-BEAMing and droplet digital PCR are comparable, with both techniques showing similar accuracy, sensitivity, and reproducibility. Conclusions: Digital droplet PCR proved to be an efficient method for detecting gene promoter methylation. However, the Methyl-BEAMing method has proved more sensitive for detecting low quantities of DNA.

Comparison of Four Different DNA Isolation Methods from MGIT Culture for Long-Read Whole Genome Sequencing of Mycobacterium tuberculosis

Background: Tuberculosis (TB) remains a global health challenge, particularly due to drug resistance and limitations in rapid diagnosis. Next-generation sequencing (NGS), especially long-read whole genome sequencing (WGS), shows promise for rapidly detecting TB and drug resistance, but it requires high-quality DNA, which is difficult to extract from Mycobacterium tuberculosis due to its complex cell wall. Objectives: This study evaluated four DNA isolation methods for extracting pure DNA from M. tuberculosis, aiming to standardize protocols for long-read WGS. Methods: Mycobacterium tuberculosis H37RV colonies were grown in BACTEC MGIT liquid medium. Two pellets were prepared as the initial material for the DNA extraction protocol: Pellets from 1 mL McFarland 2 suspensions and all growing colonies from two MGIT liquid cultures. Four DNA extraction methods were used: The cetyltrimethylammonium bromide (CTAB) method, GeneJET Genomic DNA Purification Kit, Quick-DNA Fecal/Soil Microbe Kit, and Genematrix Tissue/Bacterial DNA Purification Kit, with some modifications. DNA quality was assessed based on concentration, purity, and integrity. Results: Among the tested methods, the Quick-DNA Fecal/Soil Kit yielded approximately 85 ng/mL of DNA and a purity of 1.9 at 260/280 nm from the colonial pellet of two MGIT tubes. However, lower intact DNA [DNA integrity number (DIN) ~ 6.8] was obtained with this kit. The CTAB method provided the highest intact DNA (DIN ~ 9.5), although the purity of the DNA was not sufficient. Conclusions: Based on three repetitions of McF-2 and colonial pellet extractions, the Quick-DNA Fecal/Soil Kit yielded the highest DNA quantity and purity but showed lower integrity compared to other methods, indicating the need for adjustments. A pellet from two MGIT cultures (~ 100 µL) is suitable for long-read WGS with this kit. However, a larger sample size is required to generalize these findings. For effective long-read sequencing of M. tuberculosis, DNA extraction protocols must be optimized to balance yield, fragment size, and purity for accurate sequencing and drug resistance analysis.

Characterization of Extracellular Matrix Derived From Porcine Organs Decellularized Using Different Methods.

Regenerative medicine has extended the capacity of medicine to a point where tissues and organs could potentially be manufactured. This could resolve issues associated with organ transplantation. The extracellular matrix (ECM) provides a supportive scaffold and biochemical cues allowing cells to attach, proliferate, and differentiate. The ECM is composed of different fibrous proteins and proteoglycans. The extensive value of ECM lies in its dynamic microenvironment that aids in cell proliferation, differentiation, and regulation of intercellular communication. In this study, four methods were applied to decellularize porcine organs. The ECMs were characterized by histological methods illustrating the absence of nuclei and the presence of glycosaminoglycans (GAGs) and collagen. Hematoxylin and eosin analysis of native pancreas revealed necrosis by auto-digestion, also supported by a reduced dsDNA content, and could have led to the destruction of Type IV collagen, laminins, and other proteins in the resulting ECMs, as confirmed by mass spectrometry. DNA quantification of ECM revealed residual dsDNA contents lower than those of the native organs. Bicinchoninic acid (BCA) assay showed a difference in protein content between organs. Mass spectrometry coupled with proteomic analysis highlighted a significant difference in the protein composition. The number of different proteins, in some cases with more than 2700, in the produced ECM depended on the applied decellularization technique. Polarization microscopy indicated differences in the orientation of collagen fibers. This study provides a multimodal approach to characterize ECMs produced using different decellularization techniques, aiding in finding a balance between maintaining the ultrastructure and composition of ECM, while removing cellular components.

Impact of sample processing delays on plasma markers of inflammation, chemotaxis, cell death, and blood coagulation.

Biosampling studies in critically ill patients traditionally involve bedside collection of samples followed by local processing (ie. centrifugation, aliquotting, and freezing) and storage. However, community hospitals, which care for the majority of Canadian patients, often lack the infrastructure for local processing and storage of specimens. A potential solution is a "simplified" biosampling protocol whereby blood samples are collected at the bedside and then shipped to a central site for processing and storage. One potential limitation of this approach is that delayed processing may alter sample characteristics. To determine whether delays in blood sample processing affect the stability of cytokines (IL-6, TNF, IL-10, IFN-γ), chemokines (IL-8, IP-10, MCP-1, MCP-4, MIP-1α, MIP-1β), cell-free DNA (cfDNA) (released by dying cells), and blood clotting potential in human blood samples. Venous blood was collected into EDTA and citrate sample tubes and stored at room temperature (RT) or 4°C for progressive intervals up to 72 hours, prior to processing. Plasma cytokines and chemokines were quantified using single or multiplex immunoassays. cfDNA was measured using Picogreen DNA Quantification. Blood clotting potential was measured using a thrombin generation assay. Blood samples were collected from 9 intensive care unit (ICU) patients and 7 healthy volunteers. Admission diagnoses for the ICU patients included sepsis, trauma, ruptured abdominal aortic aneurysm, intracranial hemorrhage, gastrointestinal bleed, and hyperkalemia. After pre-processing delays of up to 72 hours at RT or 4°C, no significant changes were observed in plasma cytokines, chemokines, cfDNA, or thrombin formation. Delayed sample processing for up to 72 hours at either RT or 4°C did not significantly affect cytokines, chemokines, cfDNA, or blood clotting potential in plasma samples from healthy volunteers and ICU patients. A "simplified" biosampling protocol is a feasible solution for conducting biosampling research at hospitals without local processing capacity.

Beyond the mix: Advancements in simultaneous detection and quantification of human, dog, and cat DNA.

Animal-related crimes have increased with an increase in the number of pets worldwide, underscoring the importance of animal-related biological evidence at crime scenes. Evidence obtained in cases involving dogs and cats often includes a mixture of human and animal DNA. In this study, we developed a method using droplet digital polymerase chain reaction (ddPCR) to simultaneously identify and quantitatively detect human, dog, and cat DNA in mixed samples. HLA-DRA was chosen as a human-specific marker, OR6D7 as a dog-specific marker, and FLAI-K as a cat-specific marker. The species specificity of each target was confirmed using 14 control DNA samples from 11 mammals and 3 birds. Sensitivity tests determined the limit of detection to be 0.0008 ng/μL for human DNA and 0.00061 ng/μL for dog and cat DNA. In the mixture test, each DNA sample was independently and accurately detected in samples containing trace amounts of all three types of DNA. This study demonstrated the effectiveness of applying ddPCR to forensic case samples from dog- and cat-related incidents. We have presented a reliable method for the accurate identification and quantification of human, dog, and cat DNA simultaneously, offering possibilities for advancements in forensic DNA analysis and related fields.

DNA extraction protocol from Myrciariacaerulescens J.M.A. Braga, M.T.C. Lacerda & Stadnik (MYRTACEAE)

Myrciaria caerulescens, a fruit-bearing species endemic to Bahia, Brazil, and recently described, has ecological and economic potential. The analysis of genetic diversity and the use of molecular techniques are essential for its conservation and genetic improvement of M. caerulescens.The objective of this work was to standardize the protocol for extracting total DNA from Myrciaria caerulescens in the municipalities of Caetité and Lagoa Real in Bahia. Young leaves were collected using three collection methods and added to aluminum foil stored on ice, aluminum foil with silica and silica in a 50 mL test tube, where they received alphanumeric identification.The material was taken to the Genetic Improvement and Biotechnology Center Laboratory at UFRB, the silica was removed from the samples and stored in an ultra freezer at -80°C. For genomic DNA extraction, the three collection and extraction methods of the 40 samples, three protocols were tested for each method. The protocols of Lodhi (1994), modified by Pereira (2005), Doyle and Doyle (1987) and Murray and Tompsom (1980).Liquid nitrogen was used for crushing, helping to break down the M.caerulescens material. The isolated DNA influenced the quality and quantity of the methods and protocols tested. Silica gel method in the test tube had a greater amount of DNA compared to the others.The best result in DNA bands was described in Lodhi (1994), modified by Pereira (2005), better quality and higher concentration of extracted DNA, the test tube with silica, greater presence of bands, following the aluminum foil with silica for both locations. CTAB protocols were efficient in extraction. The increase in the amount of NaCl (0.5 to 5M) made it possible to quantify DNA bands in the agarose gel with positive ions neutralizing the negative charge of the DNA phosphate group.

Multiplexed Methylated DNA Immunoprecipitation Sequencing (Mx-MeDIP-Seq) to Study DNA Methylation Using Low Amounts of DNA

Background/Objectives: DNA methylation is a key epigenetic mark involved in regulating gene expression. Aberrant DNA methylation contributes to various human diseases, including cancer, autoimmune disorders, atherosclerosis, and cardiovascular diseases. While whole-genome bisulfite sequencing and methylated DNA immunoprecipitation (MeDIP) are standard techniques for studying DNA methylation, they are typically limited to a few samples per run, making them expensive and low-throughput. Therefore, an automation-friendly method is needed to increase throughput and reduce costs without compromising data quality. Methods and Results: We developed a novel method called Multiplexed Methylated DNA Immunoprecipitation Sequencing (Mx-MeDIP-Seq), which can be used to analyze many DNA samples in parallel, requiring only small amounts of input DNA. In this method, 10 different DNA samples were fragmented, purified, barcoded, and pooled prior to immunoprecipitation. In a head-to-head comparison, we observed a 99% correlation between MeDIP-Seq performed individually or combined as Mx-MeDIP-Seq. Moreover, multiplexed MeDIP led to more than 95% normalized percent recovery and a 25-fold enrichment ratio by qPCR, like the enrichment of the conventional method. This technique was successfully performed with as little as 25 ng of DNA, equivalent to 3400 to 6200 cells. Up to 10 different samples were processed simultaneously in a single run. Overall, the Mx-MeDIP-Seq method is cost-effective with faster processing to analyze DNA methylome, making this technique more suitable for high-throughput DNA methylome analysis. Conclusions: Mx-MeDIP-Seq is a cost-effective and efficient method for high-throughput DNA methylation analysis, offering faster processing and reduced sample requirements. This technique makes DNA methylome analysis more accessible for large-scale studies.

Phytoplasma DNA Enrichment from Sugarcane White Leaves for Shotgun Sequencing Improvement

Sugarcane white leaf (SCWL) disease, caused by Candidatus Phytoplasma sacchari, poses a significant threat to sugarcane cultivation. An obligate parasite, phytoplasma is difficult to culture in laboratory conditions, making the isolation of its DNA from the massive amount of plant host DNA extremely challenging. Yet, the appropriate amount and quality of plant microbiome-derived DNA are key for high-quality DNA sequencing data. Here, a simple, cost-effective, alternative method for DNA isolation was applied using a guanidine-HCl-hydroxylated silica (GuHCl-Silica)-based method and microbiome DNA enrichment based on size-selective low-molecular-weight (LMW) DNA by PEG/NaCl precipitation. qPCR analysis revealed a significant enrichment of phytoplasma DNA in the LMW fraction. Additionally, the NEBNext Microbiome DNA enrichment kit was utilized to further enrich microbial DNA, demonstrating a remarkable increase in the relative abundance of phytoplasma DNA to host DNA. Shotgun sequencing of the isolated DNA gave high-quality data on the metagenome assembly genome (MAG) of Ca. Phytoplasma sacchari SCWL with completeness at 95.85 and 215× coverage. The results indicate that this combined approach of PEG/NaCl size selection and microbiome enrichment is effective for obtaining high-quality genomic data from phytoplasma, surpassing previous methods in efficiency and resource utilization. This low-cost method not only enhances the recovery of microbiome DNA from plant hosts but also provides a robust framework for studying plant pathogens in complex plant models.

Transcriptome amplification and fusion gene detection using ultra-trace cells derived from cytology specimens

Tumours are complex and despite scientific breakthroughs, there is much to be elucidated about cancer and its mechanisms. By personalising treatment, outcomes can be improved and genetic analysis is key to this as it allows genetic alterations to be identified and treatment to be precisely targeted. Dr Kenji Amemiya is a cytotechnologist and Chief Clinical Laboratory Technician at the Yamanashi Prefectural Central Hospital Genome Analysis Center (GAC). He is working to better understand the complex inner landscape of cancer and therefore improve cancer detection, diagnosis and treatment. Formalin‐fixed paraffin‐embedded (FFPE) specimens are typically used for genetic testing but there are drawbacks to this, including the FFPE DNA becoming damaged during the fixation process with formalin, resulting in low quality and quantity of DNA. Amemiya is collaborating closely with Chairman of the GAC, Professor Emeritus Masao Omata. They are interested in the use of cytology samples instead of tissue samples in genome analysis, as a less invasive method. Survival rates are increased when genomic analysis is utilised in non-small cell lung cancer (NSCLC). In one project, Amemiya, Omata and the team explored the potential of performing NGS analysis with archived cytological specimens (ACSs). They utilised an integrated NGS platform called the Oncomine Dx Target Test Multi-CDx system to compare the quantity and quality of extracted nucleic acids, the sequencing quality control (QC) and the detected variants between ACSs and FFPE tissues. They found that the RNA integrity was higher in ACSs and there was no difference in sequencing results, compared with FFPE tissues.

Leveraging AI to Automate Detection and Quantification of Extrachromosomal DNA (ecDNA) to Decode Drug Responses.

Traditional drug discovery efforts have largely focused on targeting rapid, reversible protein-mediated adaptations to undermine cancer cells' resistance to therapy. However, cancer cells also exploit DNA-based strategies, typically viewed as slow, irreversible, and unpredictable changes like point mutations or the selection of drug-resistant clones. Contrary to this perception, extrachromosomal DNA (ecDNA) represents a form of DNA alteration that is rapid, reversible, and predictable, playing a crucial role in cancer's adaptive response. In this study, we present a novel post-processing pipeline for the automated detection and quantification of ecDNA in Fluorescence in situ Hybridization (FISH) images using the Microscopy Image Analyzer (MIA) tool. Our approach is particularly designed to monitor ecDNA dynamics during drug treatment, providing a quantitative framework to understand how ecDNA enables cancer cells to swiftly and reversibly adapt to therapeutic pressure. This pipeline not only offers a valuable resource for researchers aiming to automate ecDNA detection in FISH images but also sheds light on the adaptive mechanisms of ecDNA in response to epigenetic remodeling agents like JQ1.

Effects of Lutein on the Body Weights, Hepato-renal DNA and Antioxidant Capacity Following Paraquat-induced Toxicity in Wistar Rats

Introduction: Paraquat is a leading cause of herbicide-related fatalities worldwide. Its high mortality rate is attributed to its inherent generation of ROS-mediated toxicity, and lack of effective treatment till date. Lutein is an antioxidant with free radical scavenging ability, which may contribute to its protective effects and possible DNA preservation. Objective: The study is evaluating the effects of lutein on body weights and hepato-renal antioxidant capacity with DNA quantification following paraquat toxicity in wistar rats. Methods: Thirty-five male Wistar rats (150-180g) rats were randomly divided into five equal groups (A-E). Paraquat toxicity was induced in Groups B-E with 5mg/kg for three days. Group A received normal saline only, while Group B was given paraquat only. Thereafter, Groups C-E received varying doses of lutein (50, 100, 150mg/kg) for 21 days. Their body weights were recorded twice weekly using a digital balance. The animals were sacrificed and their liver with kidneys were excised and processed. The photomicrographs were taken at various magnifications while Image J software was employed for DNA densities. The total antioxidant capacity (TAC) was assessed by Prieto method. Results: There was significant reductions in the body weights, (p=0.00) hepato-renal DNA densities (p=0.00, p=0.01) and antioxidant capacities of the PQ-only group relative to the positive control A in both liver and kidneys (p-0.01, p=0.02). However, the lutein-treated groups had dose-dependent similar features with the control, which had normal histo-morphological feature. The highest dose of lutein showed the best correlation with the control. Conclusion: This study showed significant alterations in body weights, hepato-renal DNA densities and antioxidant capacities especially in the PQ-only group. Meanwhile, the lutein-treated groups, especially at high dosages, showed significant improvements in the indices similar to the control. Hence, lutein may be a useful agent for attenuating paraquat toxicity.

Preparation and characterization of bovine dental pulp-derived extracellular matrix hydrogel for regenerative endodontic applications: an in vitro study

BackgroundThe use of biological scaffolds in regenerative endodontics has gained much attention in recent years. The search for a new biomimetic scaffold that contains tissue-specific cell homing factors could lead to more predictable tissue regeneration. The aim of this study was to prepare and characterize decellularized bovine dental pulp-derived extracellular matrix (P-ECM) hydrogels for regenerative endodontic applications.MethodsFreshly extracted bovine molar teeth were collected. Bovine dental pulp tissues were harvested, and stored at -40º C. For decellularization, a 5-day protocol was implemented incorporating trypsin/EDTA, deionized water and DNase treatment. Decellularization was evaluated by DNA quantification and histological examination to assess collagen and glycosaminoglycans (GAGs) content. This was followed by the preparation of P-ECM hydrogel alone or combined with hyaluronic acid gel (P-ECM + HA). The fabricated scaffolds were then characterized using protein quantification, hydrogel topology and porosity, biodegradability, and growth factor content using Enzyme-linked immunosorbent assay (ELISA): transforming growth factor beta-1(TGF-β1), basic fibroblast growth factor (bFGF), bone morphogenetic protein 2 (BMP-2) and vascular endothelial growth factor (VEGF).ResultsDecellularization was histologically confirmed, and DNA content was below (50 ng/mg tissue). P-ECM hydrogel was prepared with a final ECM concentration of 3.00 mg/ml while P-ECM + HA hydrogel was prepared with a final ECM concentration of 1.5 mg/ml. Total protein content in P-ECM hydrogel was found to be (439.0 ± 123.4 µg/µl). P-ECM + HA showed sustained protein release while the P-ECM group showed gradual decreasing release. Degradation was higher in P-ECM + HA which had a significantly larger fiber diameter, while P-ECM had a larger pore area percentage. ELISA confirmed the retention and release of growth factors where P-ECM hydrogel had higher BMP-2 release, while P-ECM + HA had higher release of TGF-β1, bFGF, and VEGF.ConclusionsBoth P-ECM and P-ECM + HA retained their bioactive properties demonstrating a potential role as functionalized scaffolds for regenerative endodontic procedures.

Bovine pulp extracellular matrix hydrogel for regenerative endodontic applications: in vitro characterization and in vivo analysis in a necrotic tooth model

BackgroundRegenerative endodontic procedures (REPs) offer the promise of restoring vitality and function to a previously necrotic and infected tooth. However, the nature of regenerated tissues following REPs remains unpredictable and uncontrollable. Decellularized extracellular matrix scaffolds have gained recent attention as scaffolds for regenerative endodontics.ObjectivesPreparation and characterization of a bovine dental pulp-derived extracellular matrix (P-ECM) hydrogel for regenerative endodontic applications. Biocompatibility and regenerative capacity of the prepared scaffold were evaluated in vivo in a canine animal model.MethodsFifteen freshly extracted bovine molar teeth were used to prepare P-ECM hydrogels following approval of the institutional review board of the faculty of dentistry, Alexandria University. Decellularization and lyophilization of the extracted pulp tissues, DNA quantification and histological examination of decellularized P-ECM were done. P-ECM hydrogel was prepared by digestion of decellularized pulps. Prepared scaffolds were evaluated for protein content and release as well as release of VEGF, bFGF, TGF-β1 and BMP2 using ELISA. Rabbit dental pulp stem cells’ (rDPSCs) viability in response to P-ECM hydrogels was performed. Finally, proof-of-concept of the regenerative capacity of P-ECM scaffolds was assessed in an infected mature canine tooth model following REPs versus blood clot (BC), injectable platelet-rich fibrin (i-PRF) or hyaluronic acid (HA). Statistical analysis was done using independent t test, the Friedman test and chi-square tests (p value ≤ 0.05).ResultsDNA was found to be below the cut-off point (50 ng/mg tissue). Histological evaluation revealed absence of nuclei, retention of glycosaminoglycans (GAGs) and collagen content, respectively. P-ECM hydrogel had a total protein content of (493.12 µg/µl) and protein release was detected up to 14 days. P-ECM hydrogel also retained VEGF, bFGF, TGF-β1 and BMP2. P-ECM hydrogel maintained the viability of rDPSCs as compared to cells cultured under control conditions. P-ECM hydrogel triggered more organized tissues compared to BC, i-PRF and HA when used in REPs for necrotic mature teeth in dogs. Periapical inflammation was significantly less in HA and P-ECM groups compared to blood-derived scaffolds.ConclusionBovine dental pulp-derived extracellular matrix (P-ECM) hydrogel scaffold retained its bioactive properties and demonstrated a promising potential in regenerative endodontic procedures compared to conventional blood-derived scaffolds.

Host cytokine genetic polymorphisms in a selected population of persons living with hepatitis B virus infection in the central region of Ghana.

Hepatitis B virus (HBV) infection is a public health concern in resource limited settings like Ghana. Over the past decades, it is noted that the natural course of HBV in persons infected are taking a worse turn leading to liver cirrhosis and cancer. The outcome of HBV infection is influenced by viral and host factors including genetics. Cytokine variations affect virus survival and progression and may even influence associated complications. Cytokines such as tumor necrosis factor alpha (TNF-α), interleukins (IL-4, IL-6, IL-8, IL-10, IL-18), interferon gamma (IFN)-γ, and tumor growth factor-beta (TGF-β) have key roles in HBV infection and modulation. In this study, polymorphisms occurring in five cytokines were analysed to understand how they can influence prognosis of HBV infection. The study is a single centre cross-sectional study involving 227 participants made up of HBV infected participants and HBV-negative controls. Recruitment was from March 2021 to April 2022. Blood samples were taken for full blood count, HBV antigen profile, liver function tests, HBV DNA quantification and cytokine genotyping. FIB score was calculated using available tools. Statistical analysis was undertaken with p < 0.05 set as statistically significant. The 20-39-year-old group formed majority of the HBV infected participants with 60% of all participants being classified as healthy HBsAg carriers. IL2 rs1479920 GG carriers ((1258.93; 0.00-5011.87) IU/mL had reduced HBV DNA in comparison to IL2 rs1479920 AA ((5011.87; 2113.49-5956.62) /AG (3548.13; 0.00-6309.57) IU/mL carriers. TNF-α rs1800629 AA carriers (1258.93; 0.00-3981.07) IU/mL had a reduction in HBV DNA levels in comparison to TNF-α rs1800629 GG carriers (1584.89; 0.00-5011.87) IU/mL. The results of univariate (OR = 0.08, 0.00-0.93; p = 0.043) and multivariate (OR = 0.02, 0.00-0.67; p = 0.029) analysis, showed that carrying TNF-α rs1800629 AA genotype reduce susceptibility to high FIB score compared with GG genotypes. In univariate analysis, subjects aged 20-39years (OR = 5.00, 1.13-6.10; p = 0.034) and 40-59years (OR = 41.99, 3.74-47.21; p = 0.0002) were more susceptible to high FIB score compared to subjects aged 1-19years. Being female (OR = 2.42, 1.03-5.71; p = 0.043) in the univariate models showed higher odds of having high levels of HBV DNA in the multivariate model. There was a reduced likelihood of herbal medicine usage influencing HBV DNA levels significantly (OR = 0.29, 0.10-0.86; p = 0.025). In conclusion, variations in IL2 rs1479920 GG and IL2 rs1479921 AA could offer protective effects by reducing HBV DNA. TNF-α rs179924CT may also cause elevation in HBV DNA levels whiles TNF-α -308A/G, showed a potential protective effect on liver scarring in HBV infected participants. It is therefore important to take a further look at such variations for understanding of HBV modulation in the Ghanaian population.

Who threw that stone? A study on DNA transfer

Contact or touch DNA traces from stones account for around 5 % of all crime scene-related swab samples analysed in our department. These traces are often used to identify perpetrators in cases such as burglary, when a stone is used as a tool to break a window or in cases of property damage during riots. Provided that a DNA profile can be obtained in such a case, questions may arise in court regarding the possibilities of DNA transfer onto the stone. Was the subject's DNA indeed transferred onto the stone while it was being used for the crime, or was it already present as background DNA? Alternatively, could it have been transferred by other means, such as by handing over the stone to someone else who then threw it, or by touching it during an attempt to prevent someone else from throwing it? This study focused on two scenarios: experiments involving different participants throwing various stones and a handover scenario where one person touched the stone and another person threw it. We observed that the amount of DNA transferred/detected on the stone is mainly dependent on the individual handling it rather than on the properties of the stone itself or on the order in which the stones are thrown. In the handover scenario, the person who first touched the stone was found to be the main contributor to the trace as often as the person who eventually threw the stone. Our findings therefore confirm that no conclusions can be drawn about the way of interaction with the stones based solely on the obtained DNA profiles.

IL-6 and INF-γ Mediated Immune Responses in Mice Induced by Campylobacter jejuni Bacterial Ghosts

Background: Bacterial ghosts (BGs) a growing interest in their potential medical and pharmacological uses in recent years which is just. The empty bacterial envelopes Absent its internal substance .in this study using BGs for campylobacter jejuni which is curved, non- spore -forming, gram -negative rods that measure approximately 0.2 to 0.9µ₥×0.5 to 5.0 µ₥. Enteric campylobacter may appear as long spirals or S-or seagull -wing shapes. these organisms may appear as coccobacilli in smears prepared older cultures. Methods: On gram stained smears, these organisms stain poorly for better visualization carbol- fuchsin is recommended as a counterstain, if safranin is used, counterstaining should be extended to 2 to 3 minutes campylobacter spp. is motil. There are two methods for preparation of (BGs) either by E-lysis gene creating a lysis tunnel structure inside the active bacteria's envelope. Or by using minimum inhibition concentration and minimum growth concentration for chemical compounds (MIC), (MGC) in a row. The ideal circumstances for the generation of BGs were mapped using the Plackett-Burman experimental design using two experimental. Results: A spectrophotometer was used to measure the amount of DNA and protein released. The whole experiment was divided into three steps: in the first step all the chemical reagents except H2O2 were added to bacterial suspension, in the second step only H2O2, and in the third step, the cell pellets reconstituted in 60% ethanol and kept at room temperature for thirty minutes with gentle swirl of the cells for thirty seconds every five minutes. Cell pellets were gathered and cleaned again using the same procedure as mentioned. It was assured that no living cells were left behind in the bacterial spoon by cultivation using N.B. after the experiment. The lab animal Mic injected with BG from Campylobacter jejuni as a vaccine 28 days from the last immunization, which used the qPCR technique for the immune test, has been chosen. IL-6 and INF-G for this test. Conclusion: The immune responses accorded as a result of giving the vaccine was obtained from this the results of this research.

Internal validation of the Precision ID GlobalFiler NGS STR panel v2 kit with locus-specific analytical threshold, and with special regard to mixtures and low template DNA detection

We performed an internal laboratory validation of the Precision ID GlobalFiler NGS STR panel v2 kit to assist the introduction of the technology into the routine forensic casework practice. The study was designed and evaluated based not only on the key validation standards like sensitivity, stability, reproducibility, repeatability, mixture, and concordance, but we also tested the effect of reduced input DNA, we measured and applied locus-specific analytical threshold values, tested two different PCR cycle conditions, sequence artifacts and stutters were also analysed. During the study we also tested the new method on real casework samples. The sensitivity study confirmed that adding 500 pg template DNA for library preparation can be optimal at base PCR cycle number (that was 24), because the measured average heterozygote balance was not lower than 0.82, and each allele was detected above the analytical threshold. However, contrary to previous communications, increasing the PCR cycle numbers up to 28 has not resulted the significant elevation of the heterozygote imbalance. According to our results, raised PCR cycle condition (i.e. 28) is appropriate at or below 150 pg total input DNA. For most loci, the calculated AT was lower than the manufacturer’s recommended. Applying the newly established ATs with raised PCR cycle conditions the allele detection sensitivity and reliability increased. We observed allele dropouts only at the 15 pg template DNA experiments with 5 % frequency, that is better to previously published studies. This result indicates that this low amount of DNA (i.e. 15 pg) could be a minimum limit of template input for a potentially successful analysis. In the mixture study the minor contributor could be detected up to 1:19 mixture ratio. We detected minor alleles in all measurements and concentrations above the threshold if the template DNA were fixed and only SNP differences were observed between the same alleles of the contributors. To test concordance between the new method and traditional STR genotyping we analysed 58 Hungarian individual samples in parallel. Nearby the detected 248 different length-based alleles on the 31 loci in the sample pool we revealed additional 75 sequence variant alleles, that represent an approximately 23 % increase in the total number of observed alleles. The casework study confirmed that the Precision ID GlobalFiler NGS STR panel v2 kit is effective even in genotyping degraded samples with extremely low levels of DNA, if we apply elevated cycle number for library preparation and use locus-specific analytical thresholds.

Assessment of Genomic Integrity of Vitex negundoL., An Important Indian Medicinal Plant, Using RAPD Markers

Vitex negundo is an Indian medicinal plant containing steroids, flavonoids, lignans and terpenoids that can be used as a precursor for commercial production. An efficient marker system such as Random Amplified Polymorphic DNA (RAPD) was used to assess the genetic integrity of V. negundo. The straightforward method RAPD can be used to evaluate genomic integrity because it uses a small amount of DNA for PCR amplification. Six out of thirteen RAPD primers generated 150 distinct bands, of which 31 were polymorphic, with an average of 5.16 polymorphic bands per primer. A maximum of up to 32 fragments were amplified, and an average of 25 per primer, and the amplicons varied in size between 100 and 2000bp. The percentage of polymorphism ranges from 12.9 to 22.5, with an average of 16.6. The PIC values ranged from 0.11 to 0.63 for RAPD primers. The study pointed out that RAPD markers evaluate the genetic fidelity in Vitex negundo. The UPGMA cluster analysis grouped all in vitro raised plantlets treated with different growth regulators such as BAP, DPU, TDZ, and mT. The principal component analysis also substantiates this clustering pattern. Thus, the phylogenetic relationship and a high genetic variation revealed in the present study could provide baseline data for the conservation and improvement of this plant in future. Also, the molecular marker identified in this study will be helpful in the authentication of this species to prevent adulteration in herbal medicine.

DNA: Novel Crystallization Regulator for Solid Polymer Electrolytes in High-Performance Lithium-Ion Batteries.

In this work, we designed a novel polyvinylidene fluoride (PVDF)@DNA solid polymer electrolyte, wherein DNA, as a plasticizer-like additive, reduced the crystallinity of the solid polymer electrolyte and improved its ionic conductivity. At the same time, due to its Lewis acid effect, DNA promotes the dissociation of lithium salts when interacting with lithium salt anions and can also fix the anions, creating more free lithium ions in the electrolyte and thus improving its ionic conductivity. However, owing to hydrogen bonding between DNA and PVDF, excess DNA occupies the lone pairs of electrons of the fluorine atoms on the PVDF molecular chains, affecting the conduction of lithium ions and the conductivity of the solid electrolyte. Hence, in this study, we investigated the effects of adding different DNA amounts to solid polymer electrolytes. The results show that 1% DNA addition resulted in the best improvement in the electrochemical performance of the electrolyte, demonstrating a high ionic conductivity of 3.74 × 10-5 S/cm (25 °C). The initial capacity reached 120 mAh/g; moreover, after 500 cycles, the all-solid-state batteries exhibited a capacity retention of approximately 71%, showing an outstanding cycling performance.

Comparison of Two Different DNA Isolation Methods (Quick &amp; Dirty vs. Commercial Kit) in Small Insects

The COI gene region is the most commonly employed method for species identification in insects, as in all animals. The importance of DNA isolation methods is increasing, and they are of great importance for identifying insects. Unlike other large animals, DNA isolation from insects, especially from agricultural pests with very small structures, is possible with expensive commercial kits. In this study, an expensive commercial kit and a fast and economical method were compared in terms of time, cost, DNA quantity and quality. It was found that the success of commercial kits in terms of DNA quality and quantity is unquestionable. However, it was determined that the modified ‘quick and dirty’ method can be successfully used to extract DNA from insects and insect parts of all sizes, especially in studies that do not require long-term storage of DNA. Average isolation time for Q&amp;D was 45 minutes, compared to 4 hours or more for commercial kits. Finally, cost is the most important factor in today’s global economy. The unit cost of DNA isolation using the Q&amp;D method is approximately 88% lower.