DNA Analysis Research Articles

Serological Diagnosis and Molecular Detection of Varicella Zoster Virus in Patients with Suspected Meningoencephalitis

Background: Primary infection (chickenpox) or infection after reactivation (herpes zoster) of the herpesvirus Varicella-Zoster Virus (VZV) can lead to central nervous system complications, such as meningoencephalitis. This study aimed to determine the frequency of VZV infections in patients with meningoencephalitis. Methods: The serum and Cerebrospinal Fluid (CSF) sample data of 336 patients with meningoencephalitis, collected from the Health Surveillance Network, were analyzed. Immunoglobulin M (IgM) antibodies were detected in serum samples using Enzyme Immunoassay (EIA), and the CSF samples were used for molecular identification of VZV DNA via Polymerase Chain Reaction (PCR) using VM20 and VP22 primers. Results: Because of the lack of paired serum and CSF samples from all patients, samples from 101, 229, and 6 patients were tested using both PCR and EIA, only PCR, and only EIA, respectively. Among the paired and unpaired serum samples, 4.67% (5/107) were VZV-positive. Among these, 40% (2/5) and 60% (3/5) were obtained from male and female patients, respectively, belonging to different age groups ranging 6-66 years. Among the paired and unpaired CSF samples, 0.90% (3/330) were VZV-positive by PCR. Among these, one (33.4%) sample was obtained from a patient aged 10-19 years, while two (66.6%) samples were obtained from patients aged 0-10 years, of which one patient was male. The most frequent symptoms were dysphagia, headache, epileptic seizures, tremors, and cervical weakness. Muscle weakness was reported in all patients. Conclusions: Given the symptoms severity of the VZV, a rapid diagnosis is essentially needed to prevent mortality rate at all ages.

The identification of intact HIV proviral DNA from human cerebrospinal fluid

We evaluated the HIV-1 DNA reservoir in peripheral blood mononuclear cells (PBMC) and cerebrospinal fluid (CSF) in people with HIV (PWH) and associations to cognitive dysfunction. Using the intact proviral DNA assay (IPDA), an emerging technique to identify provirus that may be the source of viral rebound, we assessed HIV DNA in CSF and PBMC in PWH regardless of antiretroviral therapy (ART). CSF was used as a sampling surrogate for the central nervous system (CNS) as opposed to tissue. IDPA results (3′ defective, 5′ defective, and intact HIV DNA) were analyzed by compartment (Wilcoxon signed rank; matched and unmatched pairs). Cognitive performance, measured via a battery of nine neuropsychological (NP) tests, were analyzed for correlation to HIV DNA (Spearman's rho). 11 CSF and 8 PBMC samples from PWH were evaluated both unmatched and matched. Total CSF HIV DNA was detectable in all participants and was significantly higher than in matched PBMCs (p ​= ​0.0039). Intact CSF HIV DNA was detected in 7/11 participants and correlated closely with those in PBMCs but tended to be higher in CSF than in PBMC. CSF HIV DNA did not correlate with global NP performance, but higher values did correlate with worse executive function (p ​= ​0.0440). Intact HIV DNA is frequently present in the CSF of PWH regardless of ART. This further supports the presence of an HIV CNS reservoir and provides a method to study CNS reservoirs during HIV cure studies. Larger studies are needed to evaluate relationships with CNS clinical outcomes.

Genomic Profiling of Rare Undifferentiated Sarcomatoid Subtypes of Pancreatic Carcinomas: In Search of Therapeutic Targets

PURPOSE The highly aggressive undifferentiated sarcomatoid carcinoma (USC) subtype of pancreatic ductal adenocarcinoma (PDAC) remains poorly characterized because of its rarity. Previous case reports suggest that immune checkpoint inhibitors could be a promising treatment strategy, but the prevalence of established predictive biomarkers of response is largely unknown. The objective of this study was to leverage comprehensive genomic profiling of USC PDAC tumors to determine the prevalence of biomarkers associated with potential response to targeted therapies. METHODS USC tumors (n = 20) underwent central pathology review by a board-certified gastrointestinal pathologist to confirm the diagnosis. These samples were compared with non-USC PDAC tumors (N = 5,562). Retrospective analysis of DNA and RNA next-generation sequencing data was performed. RESULTS USC PDACs were more frequently PD-L1+ by immunohistochemistry than non-USC PDAC (63% v 16%, respectively, P < .001). Furthermore, USC PDAC had an increase in neutrophils (8.99% v 5.55%, P = .005) and dendritic cells (1.08% v 0.00%, q = 0.022) and an increased expression of PDCD1LG2 (4.6% v 1.3%, q = 0.001), PDCD1 (2.0% v 0.8%, q = 0.060), and HAVCR2 (45.9% v 21.7%, q = 0.107) than non-USC PDAC. Similar to non-USC PDAC, KRAS was the most commonly mutated gene (86% v 90%, respectively, P = 1). CONCLUSION To our knowledge, this work represents the largest molecular analysis of USC tumors to date and showed an increased expression of immune checkpoint genes in USC tumors. These findings provide evidence for further investigation into immune checkpoint inhibitors in USC tumors.

Impact of gamma rays on DNA quality and genetic traits in human blood samples

This research investigates the effects of gamma rays on DNA quality and genetic traits in eight participants from Saudi Arabia (4 males and 4 females). The study aims to understand changes in genetic fingerprint sites resulting from varying levels of radiation exposure. It addresses three key research questions related to DNA quantity, obtaining complete genetic fingerprint sites, and the reliability of genetic trait results from cancer patients undergoing radiation therapy. The study's significance lies in its potential applications in forensics, medical diagnostics, and public safety, providing insights into identifying victims and perpetrators in radiation-related incidents and enhancing treatment planning for cancer patients exposed to radiation therapies. The research contributes to a broader understanding of radiation's impact on genetic material, promotes scientific knowledge, and safeguards public health. This research investigated the impact of gamma radiation on DNA quality and genetic traits in human blood samples from Saudi Arabian volunteers. Exposure to gamma radiation at doses similar to therapeutic levels used in cancer treatment was found to cause DNA fragmentation, resulting in decreased concentrations of detectable genetic loci. The study revealed that higher radiation doses had a more pronounced effect on DNA content in blood cells.

Prevalence and Spectrum of AR Ligand-Binding Domain Mutations Detected in Circulating-Tumor DNA Across Disease States in Men With Metastatic Castration-Resistant Prostate Cancer.

Metastatic castration-resistant prostate cancer (mCRPC) is typically treated with agents directly or indirectly targeting the androgen receptor (AR) pathway. However, such treatment is limited by resistance mechanisms, including the development of activating mutations in the AR ligand-binding domain (AR-LBD). This study evaluated a database of over 15,000 patients with advanced prostate cancer (PC) undergoing comprehensive circulating-tumor DNA analysis (Guardant360, Redwood City, CA) between 2014 and 2021, with associated clinical information from administrative claims (GuardantINFORM database). Of 15,705 patients with PC included, 54% had mCRPC at the time of their blood draw. Of those, 49% had previous treatment with an AR pathway inhibitor (ARPi). AR-LBD mutation prevalence was 15% in patients with mCRPC who were untreated with a next-generation ARPi, 22% in those after one line of ARPi therapy, and 24% in those after two lines of ARPi treatment. Next-generation ARPi treatment yielded an increase in AR L702H and T878A/S mutations after abiraterone, and an increase in AR L702H and F877L mutations after enzalutamide. AR-LBD+ patients demonstrated unique biology, including increased concurrent mutations in the cell-cycle, wingless-related integration site, homologous recombination repair, and phospho-inositide 3-kinase pathways (all P < .0005), and greater low-level (copy number <10) AR amplifications (P = .0041). AR-LBD+ patients exhibited worse overall survival (OS) relative to a matched cohort of AR-LBD- patients (50.1 v 60.7 months, unadjusted log-rank P = .013). This large database analysis demonstrates that AR-LBD mutation prevalence increases after next-generation ARPi use. AR-LBD+ tumors demonstrate unique biology (more oncogenic pathway mutations and low-level AR amplification) and reduced OS. These findings inform the development of novel therapies designed to circumvent AR-mediated therapeutic resistance.

The mysteries of DNA preservation in bone: A comparative study of petrous bones and metacarpal epiphyses using ATR-FTIR spectroscopy

A comparative analysis of 26 petrous bones and epiphyses of metacarpals from the Second World War era revealed no significant differences in DNA yield or success in STR typing. This unexpected parity in DNA preservation between the petrous bone, a renowned source of endogenous DNA in skeletal remains, and the epiphyses of metacarpals, which are porous and susceptible to taphonomic changes, is surprising. In this study, we introduced ATR-FTIR spectroscopy as an approach to unravel the correlation between bone molecular structure and DNA preservation. Metacarpals and petrous bones with same taphonomic history were sampled and prepared for DNA analyses. While one portion of the sample was used for DNA analysis, the other underwent ATR-FTIR spectroscopic examination. The normalized spectra and FTIR indices between the epiphyses of metacarpals and petrous bones were compared. Because the taphonomic history of the remains used is relatively short and stable, the ATR-FTIR spectroscopy unveiled subtle structural differences between the two bone types. Petrous bones exhibited higher mineralization, whereas epiphyses contained more organic matter. The unexpected preservation of DNA in the epiphyses of metacarpals can likely be attributed to the presence of soft tissue remnants within the trabeculae. Here observed differences in the molecular structure of bones indicate there are different mechanisms enabling DNA preservation in skeletal tissues.

First report of Botrytis cinerea causing flower blight on macadamia in South Africa

AbstractMacadamia cultivation plays significant role in the economy of South Africa. Despite its importance, the industry grapples with disease‐related challenges, notably flower blight, which threatens substantial economic losses by affecting yield and nut quality. In 2022, diagnostic services at the Agricultural Research Council and the Forestry and Agricultural Biotechnology Institute received macadamia flowers displaying blight symptoms. Employing two methods for fungal isolation, 25 isolates were obtained which were classified into one group based on morphological characteristics. DNA analysis identified the isolates as Botrytis cinerea. The pathogenicity testing was conducted on macadamia flowers to confirm Koch's postulates. This is the first report of B. cinerea affecting Macadamia integrifolia Maiden &amp; Betche in South Africa, underlining its potential threat to the industry.

Culture time to optimize embryo cell-free DNA analysis for frozen-thawed blastocysts undergoing noninvasive preimplantation genetic testing for aneuploidy

To investigate the ideal time in culture to optimize embryo cell-free deoxyribonucleic acid (cfDNA) analysis in frozen-thawed blastocysts undergoing noninvasive preimplantation genetic testing for aneuploidy (PGT-A). Cell-free DNA is released into the spent blastocyst media (spent media) by the embryo. However, the optimal timing to determine maximal cfDNA in the case of frozen-thawed blastocysts undergoing noninvasive PGT-A remains to be elucidated. In this prospective observational study, 135 spent media and corresponding whole blastocysts were collected from January 2021 through March2022. Private fertility clinics. Day-5 frozen-thawed blastocysts were cultured for 8 hours (Day-5 Short) or 24 hours (Day-5 Long), whereas day-6 frozen-thawed blastocysts were cultured for 8 hours (Day-6 Short). The spent media and whole blastocysts were then collected for further analysis. Spent media and whole blastocysts were amplified using whole genome amplification and sequenced using next-generation sequencing. Informativity and concordance rates between cfDNA in spent media and whole blastocyst DNA were compared according to the different times in culture. When comparing time in culture, informativity rates for spent media were significantly higher for Day-5 Long and Day-6 Short (>91%) compared with the Day-5 Short group (<60%). A similar trend was observed for cases with and without a previous PGT-A. Regarding blastocyst expansion grade, informativity rates were lower on Day-5 Short compared with Day-5 Long and Day-6 Short, regardless of expansion degree. This decrease was significant for Gardner-grade expansion grades 3, 4, and 5-6. In addition, for a similar time in culture, the grade of expansion did not have an impact on the informativity rates. For concordance rates, no significant differences were observed among the 3 groups. In all cases, concordance rates were 90.5% for Day-5 Short, 93.6% for Day-5 Long, and 92.3% for Day-6 Short. No impact of the expansion grade was observed on concordance rates. Noninvasive PGT-A in frozen-thawed blastocysts yields very high concordance rates with whole blastocysts, possibly limiting the need for invasive PGT-A and making it available for a wider range of patients.

Identifying associations of human surfactant protein A SNPs and allelic variants with retinopathy of prematurity

Retinopathy of prematurity (ROP) is the primary cause of childhood blindness worldwide. Previous studies showed that allelic single nucleotide polymorphic (SNP) variants of the human surfactant protein A genes (SP-A1, SP-A2) are associated with the development of respiratory distress syndrome and bronchopulmonary dysplasia (BPD). In this work, we hypothesized that SP-A SNPs and allelic variants are associated with altered risk of ROP in prematurely born infants. To test this hypothesis, we used a modified PCR-based method to detect variants of the SP-A1 and SP-A2 genes in a cohort of preterm infants. Infants born at &lt;32 weeks’ gestation and/or&lt;1500 grams were enrolled. Scavenged blood samples or cheek swabs were collected and DNA was extracted using the QIAamp DNA Mini Kit. We measured SNPs in SP-A1 and SP-A2 using Taqman probes for allelic discrimination by PCR or PCR/RFLP/sequencing method. Associations of SP-A1 and SP-A2 SNP allele frequencies with ROP and BPD were determined using chi-square and logistic regression analyses. Our results show that, of the total patient cohort (n=59), 42 patients had a BPD diagnosis (23 with ROP and 36 without ROP). DNA analysis of these samples identified associations of SP-A1 and SP-A2 SNPs and variants with ROP. For SP-A1, the following SNP associations were found for ROP using chi-square: rs1059047 (p=0.44), rs1136450 (p=0.63), rs1136451 (p=0.21), rs1059057 (p=0.52). For SP-A2, the following SNPs associations were identified with ROP: rs1059046 (p=0.51), rs17886395 (p=0.050), rs1965707 (p=0.031), rs1965708 (p=0.46). Logistic regression analysis indicated an association of ROP with the SP-A1 6A2 variant (p-value = 0.47, OR (6A2/*)=0.8036, 95%CI [0.2299 - 2.8082], OR (6A2/6A2) = 0.4327, 95%CI [0.1063 - 1.7615]), which conferred protection, as well as an association of ROP with SP-A2 6A2 (p-value = 0.0055) with decreased risk when 1A2 variant is present. We conclude that SP-A1/SP-A2 polymorphisms are associated with the presence of ROP in infants with BPD. The 6A4 SP-A1 and SP-A2 1A2 appear to confer protection in babies against ROP. Further studies will determine the mechanisms of this protective effect. Indiana University, University of Chicago Metcalf Internship Program Grant, The University of Oklahoma Health Sciences Center. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Evaluation of post-PCR purification methods and subsequent optimisation of the MinElute® PCR Purification Kit for low input DNA samples amplified with PowerPlex® 21

Weak and partial DNA profiles are commonly encountered within forensic casework due to amplification of low DNA input samples. One option for increasing allelic detection in such samples is the purification of amplified PCR product using commercially available column-based methods. In this study, four commercially available post-PCR purification methods, QIAGEN MinElute®, Independent Forensics Amplicon™ Rx, Millipore Microcon® and Thermo Fisher Scientific ExoSAP-IT™ were evaluated, comparing the quality of PowerPlex® 21 DNA profiles produced to the standard DNA profile generated prior to purification. An increased detection of alleles above the analytical threshold was observed following purification with the MinElute®, Amplicon™ Rx and Microcon® methods, allowing informative DNA profiles to be recovered using as little as 8 pg DNA. However, post-PCR purification using the ExoSAP-IT™ kit was unsuccessful, with no alleles detected above analytical threshold in samples with ≤16 pg DNA. The MinElute® kit was selected for optimisation on the basis of DNA profile quality, including increased detection of alleles and minimal artefacts. The MinElute® method was optimised by evaluating the number of washes and final elution buffer volume, resulting in a further increase in detection of alleles by reducing the elution buffer volume. Overall, this study showed that PowerPlex® 21 DNA profiles from low input DNA can be successfully enhanced by employing the MinElute® post-PCR purification method.

Recovery of DNA from acetaminophen exploring physical state and sampling methods

Research into the recovery of DNA from illicit drug samples has shown it is possible to get forensically useful profiles from such substrates. However, it is not yet known if the different physical states that drugs can be found in influences the quantity and quality of DNA that can be recovered or what is the best sampling method to adopt for powdered samples. This research used acetaminophen in four different states – large crystalline, powder, in solution, or residue – to determine the efficacy of current DNA technology in recovery and analysis of the resulting sample. Five replicates of each were prepared. Human blood was deposited on or mixed with the drug and left for 1 hour. The surface of the drug was sampled by wet/dry swabbing (where appropriate), or the entire sample was deposited in a tube, and the DNA then extracted using DNA-IQ™. The amount of DNA recovered (ng), degradation index, number of PCR cycles (Ct) required for the IPC to reach threshold, number of alleles in the DNA profile and average peak height (APH) were assessed. All samples, irrespective of the physical state they were collected from, returned full DNA profiles that corresponded to the DNA profile of the blood donor, with no degradation or inhibition detected. It was also found the wet/dry swabbing method returned higher levels of DNA than inclusion of the entire sample into the tube for powdered acetaminophen and the appropriate method to use will be dependent on casework circumstances. The findings of this research further develops our understanding of the recovery of DNA from drugs, and supports the need for further investigation to understand under what conditions DNA can be recovered from illicit substances.

Developments in DNA analysis and forensic procedures legislation: comparisons across Australian jurisdictions

ABSTRACT Forensic procedures legislation guides the collection and analysis of forensic material, including DNA, and the establishment of DNA databases. It requires the balancing of several competing interests, such as identifying and convicting those who commit criminal offences, ensuring that individuals in Australian society are not subjected to unlawful or unfair treatment, and preserving individual privacy and civil liberties. With increased data-sharing arrangements across jurisdictions, harmonising forensic procedures legislation becomes pivotal. Reviews published in 2003 and 2010 established the existence of discrepancies and inadequacies in the forensic procedures legislation of Australian jurisdictions. Since then, jurisdictions have made amendments to their own legislation that may further reduce the extent to which harmonisation exists across jurisdictions. This study, therefore, aimed to examine the legislative amendments made between 2010 and 2022 to the forensic procedures legislation of Australia’s Commonwealth, States and Territories and compare current legislation with that of the Commonwealth. The findings from the comparative analysis highlight key elements of current legislation that represent a significant departure from the protection of individual rights to privacy and civil liberties. The article then discusses the potential implications of these departures and suggests some directions for further research, legislative review, and critical analysis.

Harnessing the intragenomic variability of rRNA operons to improve differentiation of Vibrio species

Although the 16S rRNA gene is frequently used as a phylogenetic marker in analysis of environmental DNA, this marker often fails to distinguish closely related species, including those in the genus Vibrio. Here, we investigate whether inclusion and analysis of 23S rRNA sequence can help overcome the intrinsic weaknesses of 16S rRNA analyses for the differentiation of Vibrio species. We construct a maximum likelihood 16S rRNA gene tree to assess the use of this gene to identify clades of Vibrio species. Within the 16S rRNA tree, we identify the putative informative bases responsible for polyphyly, and demonstrate the association of these positions with tree topology. We demonstrate that concatenation of 16S and 23S rRNA genes increases the number of informative nucleotide positions, thereby overcoming ambiguities in 16S rRNA-based phylogenetic reconstructions. Finally, we experimentally demonstrate that this approach considerably improves the differentiation and identification of Vibrio species in environmental samples.

Developmental validation of the ForenSeq® Kintelligence kit, MiSeq FGx® sequencing system and ForenSeq Universal Analysis Software

Forensic Investigative Genetic Genealogy, a recent sub discipline of forensic genomics, leverages the high throughput and sensitivity of detection of next generation sequencing and established genetic and genealogical approaches to support the identification of human remains from missing persons investigations and investigative lead generation in violent crimes. To facilitate forensic DNA evidence analysis, the ForenSeq® Kintelligence multiplex, consisting of 10,230 SNPs, was developed. Design of the ForenSeq Kintelligence Kit, the MiSeq FGx® Sequencing System and the ForenSeq Universal Analysis Software is described. Developmental validation in accordance with SWGDAM guidelines and forensic quality assurance standards, using single source samples, is reported for the end-to-end workflow from library preparation to data interpretation. Performance metrics support the conclusion that more genetic information can be obtained from challenging samples compared to other commercially available forensic targeted DNA assays developed for capillary electrophoresis (CE) or other current next generation sequencing (NGS) kits due to the higher number of markers, the overall shorter amplicon sizes (97.8% <150 bp), and kit design. Data indicate that the multiplex is robust and fit for purpose for a wide range of quantity and quality samples. The ForenSeq Kintelligence Kit and the Universal Analysis Software allow transfer of the genetic component of forensic investigative genetic genealogy to the operational forensic laboratory.

Optimizing Bangkaew dog breed identification using DNA technology.

The Bangkaew dog is an indigenous dog breed in the Phitsanulok province of Thailand. This breed is recognized by the Fédération Cynologique Internationale (FCI), a global canine organization. The unique traits of the Bangkaew breed lead to purebred selection for breeding, while only their traits and pedigree from parental history are recorded. Determination of the risk of inbreeding depression and the origin of unknown DNA profiles is essential due to the challenges in predicting puppy characteristics, which are crucial for breed management and conservation. This study aimed to emphasize that current allelic frequency data for the Bangkaew dog breed must be considered for precise individual identification. Approximately 82 Bangkaew dogs from various Thai localities were studied using 15 microsatellite markers for genotypic monitoring and individual identification. Maternal genetic inheritance was assessed via mtDNA D-loop analysis. The results revealed high genetic diversity in the Bangkaew breed, indicating low potential for inbreeding. We also found that using a 15 loci microsatellite panel was effective for the identification of Bangkaew dogs. The optimized 10 loci microsatellite genotyping panel developed in this study presents improved identification testing efficiency, promoting both time- and cost-effectiveness. Analysis of microsatellite DNA markers in Bangkaew dogs using an optimized panel of 10 loci selected from 15 loci effectively facilitated individual identification. This approach not only enhances time and cost efficiency, but also provides accurate allelic frequency estimates, which are crucial for the realistic evaluation of DNA evidence.

낙태죄 비범죄화 이후

Access to safe abortion is a key aspect of sexual and reproductive rights. However, even after the decriminalization of abortion in 2021, abortion care has not been normalized in South Korea. This study analyzes the current state of medical assistance and access to abortion after decriminalization, with a focus on abortion due to sexual violence, keeping in mind that abortion, even before decriminalization, was not punished and it was included in the government’s medical expenses subsidy. In-depth interviews with sexual violence victim support workers and healthcare providers revealed that while decriminalization has improved access to care and information, many interviewees did not see any significant changes in medical support for abortion for sexual violence victims. Both support organizations and providers often felt that “abortion has not been legal yet” and as a result, they felt that they were under pressure to make sure that a pregnancy was the result of sexual violence in order to justify providing assistance to victims. As a result they tend to impose strict requirements on victims for providing medical assistance for them. In some cases, support organizations required a complaint of sexual violence, DNA matching of the perpetrator and the fetus, a case conference decision by an external advisor, or parental consent for adolescent victims as prerequisites for medical assistance, which made it impossible for victims to receive assistance. In addition, the Ministry of Gender Equality and Family’s guidelines discourage supporting organizations to apply for assistance as the guidelines stress the possibility of being accused of false accusation and redeeming of support money. It was also pointed out that the guidelines do not specify whether to support medical expenses for pregnancies resulting from prostitution, so the possibility of support is ambiguous. The most difficult thing with regard to supporting abortion was to find a medical professional who would provide medical care ad abortion to victims. Despite being a victim of sexual violence, women were frequently rejected by healthcare providers and were not officially provided with information on which hospitals could provide abortion care. The experiences of being rejected by medical professionals or support organizations in itself caused worse stigma and pain of abortion for victims. Even at hardly found hospitals, it was often the case that hospitals refuse abortion operation expenses be covered by medical insurance and charged high fees while abortions were mostly performed surgically. Parental consent was required for all processes of investigation and medical assistance, leading adolescent victims to abandon their requests for assistance because they were unable to inform their guardians about their problems. There were also challenges in ensuring the right to self-determination for victims with developmental disabilities. Secondary victimization has been found occurred during the medical assistance, investigation, and victim assistance processes. Post-abortion support for contraception was limited, and counseling and follow-up support were scarce. Since the decriminalization of abortion, amendments to the abortion law were submitted to the National Assembly which maintain the punishment of abortion but limiting them based on respective of reasons. The Ministry of Women and Family Affairs’ policy regarding abortion is that it will only fund abortions in some cases of sexual violence. However, the results of the in-depth interviews show that no support for abortion is possible while criminalizing or stigmatizing it in principle. Given the above-mentioned interview results, this study recommends the measures to ensure the right to abortion for sexual violence victims.

Exploration of genetic variability in Garcinia [&lt;i&gt;Garcinia gummi-gutta&lt;/i&gt; L.(Robson)] germplasm based on growth, yield and quality traits

Eleven Garcinia germplasm along with local check of Pechiparai were evaluated and underwent principal component analysis to assess genetic divergence and variation patterns during 2019 to 2022. The first two principal components, contributing significant Eigen values, explained 71.20% of the total variability. The Acc. Gg 9 was the top performer, exhibiting favourable yield and growth traits with lower pest and disease incidence, high biochemical compounds viz., hydroxy citric acid and tartaric acid compared to local check. Cluster analysis revealed four major clusters, offering diversity for breeding programs. Correlation studies highlighted traits such as number of fruits per tree, rind thickness, and tartaric acid showing significant positive correlations with yield per tree. Selection based on identified key traits was deemed crucial for enhancing effectiveness. Additionally, DNA fingerprinting analysis indicated the potential use of RAPD markers (OPA03570) for differentiating Kudampuli cultivar PPI (K) 1 from the local check. Overall, the present investigation provides insights into optimizing Garcinia breeding programs, emphasizing trait-based selection and DNA fingerprinting for varietal differentiation.

Studying the Role of Soil Factors on Degree of Degradation of DNA of Human Remains

Generating a DNA profile using autosomal Short Tandem Repeat (STR) DNA allele from skeletal remains is a crucial step in the identification process for mass disaster and unidentified person situations. The capacity to extract substantial amounts of relevant DNA from bones, which were highly durable biological components that can withstand soil elements and climatic conditions over long periods of time, would be advantageous. 70 femur male bone samples were collected from two different environmental mass graves (Al-Mahaweel massgrave) in Babil governorate and (Al-Saqlawiya massgrave) in Al-Anbar governorate in Iraq. The DNA from bone samples extracts were assessed by capillary electrophoresis and a standardized set of short tandem repeat (STR) loci are analyzed using Mutiplex 21 STR loci System to allow human identification by matching the profile of the dead individuals with their relatives. From these two different sites; soil samples were collected to analyze and study the different environmental factors and find a relation between the degree of preservation or degradation with these factors like temperature, humidity, salinity, PH and texture of soil and find how these factors can affect on pattern of degradation of DNA profiles. The average of the percentage of the detected alleles in each locus in the two sites; were 87\% for Al-Mahaweel site and 32\% for Al- Saqlawiya site. we found that clay soil, low salt concentration, PH slightly alkaline and low humidity for Al-Mahaweel site; all participate in DNA preservation while the chalky and very high salt concentration of Al- Saqlawiya site soil; all participate in DNA degradation. Predicting the effect of these factors on the quality of the DNA profiles can be helpful in finding better solutions for many complications that may face the process of analyzing samples and finding sufficient informative profiles.

Cutibacterium acnes-derived extracellular vesicles promote tumor growth in renal cell carcinoma.

Bacterial flora are present in various parts of the human body, including the intestine, and are thought to be involved in the etiology of various diseases such as multiple sclerosis, intestinal diseases, cancer, and uterine diseases. In recent years, the presence of bacterial 16S rRNA genes has been revealed in blood, which was previously thought to be a sterile environment, and characteristic blood microbiomes have been detected in various diseases. However, the mechanism and the origin of the bacterial information are unknown. In this study, we performed 16S rRNA metagenomic analysis of bacterial DNA in serum extracellular vesicles from five healthy donors and seven patients with renal cell carcinoma and detected Cutibacterium acnes DNA as a characteristic bacterial DNA in the serum extracellular vesicles of patients with renal cell carcinoma. In addition, C. acnes DNA was significantly reduced in postoperative serum extracellular vesicles from patients with renal cell carcinoma compared with that in preoperative serum extracellular vesicles from these patients and was also detected in tumor tissue and extracellular vesicles from tumor tissue-associated microbiota, suggesting an association between C. acnes extracellular vesicles and renal cell carcinoma. C. acnes extracellular vesicles were taken up by renal carcinoma cells to enhance their proliferative potential. C. acnes extracellular vesicles also exhibited tumor-promoting activity in a mouse model of renal cancer allografts with enhanced angiogenesis. These results suggest that extracellular vesicles released by C. acnes localized in renal cell carcinoma tissues act in a tumor-promoting manner.

Exploration of Genome-Wide Recombination Rate Variation Patterns at Different Scales in Pigs.

Meiotic recombination is a prevalent process in eukaryotic sexual reproduction organisms that plays key roles in genetic diversity, breed selection, and species evolution. However, the recombination events differ across breeds and even within breeds. In this study, we initially computed large-scale population recombination rates of both sexes using approximately 52 K SNP genotypes in a total of 3279 pigs from four different Chinese and Western breeds. We then constructed a high-resolution historical recombination map using approximately 16 million SNPs from a sample of unrelated individuals. Comparative analysis of porcine recombination events from different breeds and at different resolutions revealed the following observations: Firstly, the 1Mb-scale pig recombination maps of the same sex are moderately conserved among different breeds, with the similarity of recombination events between Western pigs and Chinese indigenous pigs being lower than within their respective groups. Secondly, we identified 3861 recombination hotspots in the genome and observed medium- to high-level correlation between historical recombination rates (0.542~0.683) and estimates of meiotic recombination rates. Third, we observed that recombination hotspots are significantly far from the transcription start sites of pig genes, and the silico-predicted PRDM9 zinc finger domain DNA recognition motif is significantly enriched in the regions of recombination hotspots compared to recombination coldspots, highlighting the potential role of PRDM9 in regulating recombination hotspots in pigs. Our study analyzed the variation patterns of the pig recombination map at broad and fine scales, providing a valuable reference for genomic selection breeding and laying a crucial foundation for further understanding the molecular mechanisms of pig genome recombination.