Deoxyribonucleic Acid Analysis Research Articles

HARDWARE ACCELERATION OF DNA READ ALIGNMENT PROGRAMS: CHALLENGES AND OPPORTUNITIES

The alignment or mapping of Deoxyribonucleic Acid (DNA) reads produced by the new massively parallel sequencing machines is a fundamental initial step in the DNA analysis process. DNA alignment consists of ordering millions of short nucleotide sequences called reads, using a previously sequenced genome as a reference, to reconstruct the genetic code of a species. Even with the efforts made in the development of new multi-stage alignment programs, based on sophisticated algorithms and new filtering heuristics, the execution times remain limiting for the development of various applications such as epigenetics and genomic medicine. This paper presents an overview of recent developments in the acceleration of DNA alignment programs, with special emphasis on those based on hardware, in particular Graphics Processing Units (GPUs), Field Programmable Gate Arrays (FPGAs), and Processing-in-Memory (PIM) devices. Unlike most of the works found in the literature, which review only the proposals that gradually emerged in some specific acceleration technology, this work analyzes the contemporary state of the subject in a more comprehensive way, covering from the conception of the problem, the modern sequencing technologies and the analysis of the structure of the new alignment programs, to the most innovative software and hardware acceleration techniques. The foregoing allows to clearly define, at the end of the paper, the trends, challenges and opportunities that still prevail in the field. We hope that this work will serve as a guide for the development of new and more sophisticated DNA alignment systems.

Use of serum Golgi protein 73 for screening chronic hepatitis B virus infection patients needing antiviral therapy in the community.

Use of serum Golgi protein 73 for screening chronic hepatitis B virus infection patients needing antiviral therapy in the community.

Cell-Free Fetal Deoxyribonucleic Acid (cffDNA) Analysis as a Remarkable Method of Non-Invasive Prenatal Screening

The cell-free fetal DNA (cffDNA) analysis for screening fetal genetic anomalies has increased dramatically since its commercialization in 2011 worldwide. In the early weeks of pregnancy, it offers a hassle-free, non-invasive procedure of antenatal screening. It guides and protects mothers from undergoing unwanted risk-laden invasive prenatal testing. cffDNA testing is accurate at detecting the abnormal fetus chromosome among a large pool population. Patau syndrome, Edward syndrome, and Down syndrome are currently being accurately screened by this method. Due to their sensitivity and specificity, they now have become the screening method of choice, approaching almost 100% in various studies with a large sample pool. The latest procedures to analyze cffDNA, like the new digital droplet polymerase chain reaction (ddPCR) and sophisticated next-generation sequencing (NGS), haveincreased detection rates with decreased analyzing time. The latest techniques make it possible to screen large numbers of the population with faster report generation. Screening for Rh incompatibility and its timely prevention is now more accessible and more accurate with the help of cffDNA analysis. The problem arises when we deviate from the primary disease and start testing for anomalies not intended to be screened by cffDNA in the first place. Fetal sex chromosome aneuploidy screening by cffDNA is one area where the test gives mixed results either due to differences in machinery, laboratory parameters, or human error. Other rare occurrences like trisomes, such as trisomy 7, trisomy 16, trisomy 22, and a few microdeletion syndromes are also being screened but with less accuracy. Like every technology, cffDNA analysis is not entirely free of criticism. Its high testing cost, potential to accurately prognosticate the gender of the developing fetus and absence of standard testing practices will become an issue as the test becomes routine worldwide.

Forensic Death Investigations of Dog Bite Injuries in 31 Cats.

Simple SummaryFatal dog bite injuries are common in free-ranging cats in Taiwan. The causes of death of these cats are sometimes speculated to be animal cruelty by the general public. To persuade the public and ease speculation, we document and summarize the features of dog bite injuries and further develop a method for canine DNA identification. Performing forensic necropsies on 31 cats with dog bite injuries, we found that puncture wounds, linear or small, round contusions/abrasions, and lacerations/avulsions are characteristic bite-related injuries. A preference for specific body regions was not observed. Using DNA samples from wound swabs and hair remains, we identified canine DNA in 27.3% of cases. This study provides an applicable method for canine DNA identification in cats and reference data for future veterinary forensic investigations of dog bite injuries.Animal bite injuries are common in free-ranging cats in Taiwan, and most fatal animal bite events are presumed to be caused by dogs. However, speculation regarding animal abuse may occur when carcasses with prominent injuries are found by members of the general public. Local animal protection offices and veterinary clinicians sometimes face difficulties in convincing these individuals by identifying specific features of dog bite injuries in cat carcasses. Therefore, the present study analyzed injury patterns and distribution in 31 necropsied cats with animal bite injuries, and applied deoxyribonucleic acid (DNA) analysis for canine DNA identification in 13 cats. The main necropsy findings included puncture wounds (26 (83.9%)), linear or small, round contusions/abrasions (20 (64.5%)), lacerations/avulsions (17 (54.8%)), abdominal wall rupture/laceration (19 (61.3%)), herniation (16 (51.6%)), fractures (21 (67.7%)), broken claws (16 (51.6%)), and hair tufts on the body surface (28 (90.3%)). The most-commonly injured regions were the ventral thorax and axilla (23 (74.2%)), hind limbs (22 (71.0%)), shoulder-to-dorsal thorax (21 (67.7%)), back and flank (20 (64.5%)), abdomen (19 (61.3%)), neck (19 (61.3%)), and hip/tail/perineum (17 (54.8%)). Canine mitochondrial DNA was identified in 3 out of 11 cases (27.3%) that were sampled using wound swabs and in 4 out of 5 cases that had hair entrapped in broken claws. In conclusion, this study determined the distribution and features of dog bite injuries in cats and developed an elemental method using trace evidence for DNA identification in animal bites.

Experiences in successive forensic analysis of GSR and DNA traces collected on a single tape lift stub.

Gunshot residue (GSR) and deoxyribonucleic acid (DNA) analyses are used in the reconstruction of shooting incidents involving firearms. In both fields, adhesive tapes are commonly applied to recover traces. Using a simultaneous sampling approach for retrieving both types of traces from objects related to a shooting can be powerful. We present the results for DNA testing and GSR analysis using "DNA stubs" to recover both types of traces in one sampling. The analyses are successive: stubs are first examined with scanning electron microscopy for the presence of GSR and next subjected to DNA extraction and short tandem repeat (STR) typing. The results show no negative effect on the DNA and GSR results. The risk of DNA contamination during GSR analysis is addressed, showing that it is negligible. Our experiences in casework show that the approach can be successfully implemented.

Peruvian Native Bacterial Strains as Potential Bioremediation Agents in Hg-Polluted Soils by Artisanal Mining Activities in Southern Peru

Bioremediation of soils and waters due to mercury (Hg) contamination represents one of the most critical environmental challenges. In addition, this challenge is even greater in arid soils due to the low economic interest in these regions. Such is the case of the Secocha Annex, located in the Arequipa province of Camaná in Southern Peru. In this region, the excessive use of Hg in artisanal and small-scale gold mining (ASGM) activities has seriously endangered the health of its inhabitants. Unfortunately, there are few projects aimed at improving the environmental and sanitary conditions of this locality. An alternative to conventional cleaning technology is the use of native microorganisms that allow the recovery of ecological environments with low-cost and low-tech techniques. This work aims to present two new Hg-resistant bacterial strains obtained from Hg-polluted soils of the Secocha Annex as potential bioremediation agents. Both strains showed growth capacity on Hg substrates and their adsorption behaviors and Hg removal capacities were evaluated. By deoxyribonucleic acid (DNA) analysis, both Gram-positive strains were identified as Kocuria sp. (99.35% similarity) and Zhihengliuella sp. (99.78% similarity). Spectrometry results showed elimination capacities with values close to 28.4 and 33.3 % in an incubation time period of 45 days, with the maximum elimination efficiency in the first 24 h. These results are encouraging and offer new possibilities for the use of native strains in the bioremediation of arid soils contaminated with Hg in the Secocha Annex. Furthermore, due to the low cost and minimization of negative impacts, this technique and our bacterial strains could be used in other regions of Peru.

Multidisciplinary lines of evidence reveal East/Northeast Asian origins of agriculturalist/pastoralist residents at a Han dynasty military outpost in ancient Xinjiang

Han/non-Han interactions were engrained among the border regions of ancient Imperial China. Yet, little is known about either the genetic origins or the lifeways of these border peoples. Our study applies tools from ancient deoxyribonucleic acid (DNA) and stable isotope analysis to the study of a Han dynasty population at the Shichengzi site in modern-day Xinjiang. Isotopic analysis (δ13C and δ15N) of human (n = 8), animal (n = 26), and crop remains (n = 23) from Shichengzi indicated that dietary patterns among site inhabitants could be split among agro-pastoral and agricultural groups based on differences in the collagen 15N ratios. DNA analysis divided the four Shichengzi samples into two groups, with one group primarily harboring the ancient Northeast Asian (ANA) related ancestry, while the other showed a dominant Late Neolithic Yellow River (YR_LN) related ancestry. Both ancient DNA and stable isotope evidence point to the Northeast Asian origins of pastoralists and East Asian origins of Han agriculturalists, who, nonetheless, shared a single burial space at Shichengzi. This study thus provides clear evidence for the multiple origins and identities of populations across the porous border represented by the Han Empire and surrounding regions and proposes a new model for the interpretation of border culture in early Imperial China.

Tooth as a Source of DNA in Forensic or Investigative Genetics: An Overview

Deoxyribonucleic acid (DNA) is the genetic code of most organisms including humans. In the last few years, DNA analysis methods are applied to forensic cases for human identification which is termed forensic or investigative genetics. It is often challenging to obtain and interpret DNA from routine samples like blood in severely decomposed or disfigured bodies recovered from incineration, immersion, trauma, mutilation, and decomposition as in incidents of fire, explosion, or murder. The tooth can survive any extreme environment with minimum risk of contamination making it a valuable alternative source of DNA in such cases. Tooth structures like the enamel (amelogenin protein), dentin, cementum, pulp, and adherent tissues like bone and periodontal fibers are sources from which DNA can be obtained. Various methods have been described for DNA extraction. There are numerous applications of DNA analysis like identification of the deceased or missing victim or the unknown culprit from a crime scene, solving paternity issues, determining the occurrence of any genetic disease, and determining the ancestry. This article briefly summarizes an overview of the tooth as a valuable DNA source and various methods and challenges related to DNA analysis.

Effect of Chronic Oral Exposure to Overdose of Cough Syrups on Rate of DNA Fragmentation in Liver and Brain of Wistar Rats

This study was designed to determine the effect of chronic oral exposure of overdose of cough syrups containing codeine (CSC) and dextromethorphan (DXM) on the rate of deoxyribonucleic acid (DNA) fragmentation in the liver and brain of Wistar rats. Forty-five rats divided into 9 groups of 5 rats were used. Groups 1, 2, 3, and 4 were treated with 0.1, 0.2, 0.4, and 0.6 mg/kg b/w of CSC, and Groups 5, 6, 7, and 8 were treated with the same doses of DXM, respectively for 21 days. Group 9 (control) received distilled water once daily and all the rats were sacrificed 24 hours after the last treatment. DNA analysis was done on the harvested liver and brain. Significant reductions (p < 0.05) in the rate of DNA fragmentation of the liver tissues were observed in all the groups treated with the overdose of cough syrups when compared to the control. However, there was no significant difference in the rate of DNA fragmentation of the brain in all the groups treated with cough syrup as compared to the control. The result indicated that overdose of cough syrup may cause suppressed DNA fragmentation of the liver thereby predisposing the organ to dysfunctions and untimely aging.

Differences in actionable genomic alterations between brain metastases and non‑brain metastases in patients with non‑small cell lung cancer.

Brain metastases (BM) have been closely associated with increased morbidity and poor survival outcomes in patients with non-small cell lung cancer (NSCLC). Excluding risk factors in histological subtypes, genomic alterations, including epidermal growth factor receptor mutations and anaplastic lymphoma kinase (ALK) rearrangements have been also regarded as greater risk factors for BM in the aspect of molecular subtypes. In the present study, 69 tumor tissues and 51 peripheral blood samples from patients with NSCLC were analyzed using a hybridization capture-based next-generation sequencing (NGS) panel, including 95 known cancer genes. Among the 90 patients with stage IV NSCLC, 26 cases suffered from BM and 64 cases did not. In total, 174 somatic mutations in 35 mutated genes were identified, and 12 of these genes were concurrently present in the BM group and the non-BM group. Importantly, five mutated genes including ALK, cytidine deaminase (CDA), SMAD family member 4 (SMAD4), superoxide dismutase 2 (SOD2) and Von Hippel-Lindau tumor suppressor (VHL) genes were uniquely detected in the BM group, and they were enriched in the Hippo signaling pathway, pyrimidine metabolism and pantothenate and co-enzyme A (CoA) biosynthesis, as demonstrated using Kyoto Encyclopedia of Genes and Genomes enrichment analysis. RNA polymerase II transcription regulator complex and promyelocytic leukemia nuclear body were the top functional categories according to the Gene Ontology enrichment analysis in the BM group and non-BM group, respectively. Furthermore, 43.33% (13/30) of mutated genes were detected by both tumor tissue deoxyribonucleic acid (DNA) and plasma-derived circulating tumor DNA (ctDNA) in the non-BM group, while this percentage was only limited to 29.41% (5/17) in the BM group. To summarize, significant differences in somatic mutations, somatic interactions, key signaling pathways, functional biological information, and clinical actionability for the therapy of targeted agents were founded between the BM group and the non-BM group, and ctDNA analysis may by applied as a more credible alternative for genomic profiling in patients with advanced NSCLC without BM, due to its higher consistency for genomic profiling between ctDNA analysis and tissue DNA analysis.

First Record of the Goby Lentipes armatus Sakai and Nakamura, 1979 (Teleostei: Gobiidae) in the Amburayan River in Benguet, Luzon Island, Philippines

A species of goby, Lentipes armatus Sakai and Nakamura 1979, described as endemic to the Ryukyu Islands in Japan was recently discovered in the Amburayan River in Benguet, Luzon Island, Philippines. Lentipes armatus has been identified based on photographic and actual specimens from landed catch surveys in Atok, Kapangan, and Kibungan in the Province of Benguet. Morphological features, morphometric characters, and meristic counts of the collected specimens of the local population match those reported in the Ryukyu Islands in Japan. Moreover, genetic studies of the species confirmed its identification as L. armatus. Samples for the Deoxyribonucleic Acid (DNA) analysis and identification of this species were collected from the Amburayan River traversing the Municipalities of Atok, Kapangan, and Kibungan in the Province of Benguet. Therefore, the specimen described herein constitutes the first record of the species in the Cordillera. Furthermore, the occurrence of the L. armatus in the Amburayan River in the Cordillera, northern part of the Philippines, suggests its possible range expansion. The first record of the L. armatus in the Philippines was reported from the Taguibao River upstream of Sitio Bongodman (proper), in the east end of Ancicala, Province of Agusan del Norte, Mindanao Island. With this, it may also propose that the L. armatus is an indigenous fish species in the country, particularly thriving in the Amburayan River, Benguet and Taguibao River, Agusan del Norte, Philippines.

Theoretical simulation of DNA hybridization based on cascaded plasmonic V-shaped channel biosensor

A compact biosensor based on specially designed Cascaded V-shaped Channels (CVSChs) for the analysis and detection of Deoxyribonucleic Acid (DNA) hybridization is presented in this paper. The proposed biosensor employs a Gold (Au) nanowire in then CVSChs sensing region and provides more flexibility as far as tailoring the detection range and sensitivity as compared to the single V-shaped channel (VSC). It has been numerically demonstrated that the detection sensitivity of DNA hybridization is significantly dependent on the number of the V shaped channels. A two – dimensional Finite Difference Time Domain (FDTD) analysis with Perfectly Matched Layers (PMLs) is employed to evaluate the sensor performance with different structural parameters. Simulation results indicate that the proposed biosensor can achieve a high sensitivity of 2541 nm / RIU by optimizing the structural parameters. We demonstrate a proof-of-concept hybrid biosensor by monitoring the resonance shift due to the hybridization event. The proposed biosensor will have great impact on early stage detection of infected cells.

Severe Congenital Myopathy and Neuropathy with Congenital Cataracts due to GFER Variant: A Neuropathological Study

We describe the clinical, muscle and nerve biopsy, and genetic findings in a 10-year-old girl with a profound and rapid global regression. She presented during neonatal period with hypotonia, followed by weakness in the facial, bulbar, respiratory, and neck flexor muscles. She developed bilateral cataracts at 4 months of age and started to regress. Quadriceps muscle biopsy revealed extensive fiber atrophy but sparing of some, predominantly type 1, fibers. Sural nerve biopsy showed depletion of myelinated and unmyelinated fibers; most remaining myelinated fibers were of small caliber. Neuroimaging revealed global brain atrophy. Although the investigations indicated a multisystem disorder, extensive genetic and metabolic investigations were negative. She was tracheostomy- and ventilator-dependent for most of her life. The child died at 10 years of age. Further deoxyribonucleic acid analysis undertaken via whole genome sequencing revealed a novel pathogenic GFER sequence variant consistent with the patient's clinical presentation.

Forensic Science in The Nigerian Criminal Justice System

Abstract This research aimed at assessing the application and impact of forensic science in the Nigerian criminal justice system by making reference to certain components of forensics that are relevant to the criminal justice system. Such components include, Deoxyribonucleic Acid (DNA) analysis, Fingerprint analysis, Polygraph test, Ballistics, Forensic anthropology, Forensic pathology and Computer forensics. In the course of this research, it was found that establishing certain types of evidence such as fingerprint impressions and DNA, against accused persons was difficult due to the absence of sophisticated forensic laboratories and this hindered conviction of such persons. In view of this problem, this research recommends for proper training of law enforcement agencies in terms of how crimes and crime scenes are handled and also the establishment of sophisticated forensic labs where evidence and accused persons can be tested in order to determine their guilt or innocence, thereby easing the administration of justice in Nigeria. Keywords: forensic science, Nigerian criminal justice

Latent, genetic, and molecular genetic structure of the Wisconsin Card Sorting Test.

The main goal of this study was to explore the latent structure and genetic basis of cognitive processes involved in the Wisconsin Card Sorting Task (WCST) within phenotypic, behavioral genetic, and molecular genetic research paradigms. The sample used in phenotypic and behavioral genetic analyses comprised 468 twins (154 monozygotic and 80 dizygotic twin pairs), while molecular genetic analyses were performed on 404 twins from the same sample. The zygosity of most twin pairs (96.8%) was determined via deoxyribonucleic acid (DNA) analysis of buccal swabs. Trained researchers administered the Wisconsin Card Sorting Test (WCST; Heaton et al., 1993) to the entire sample. A phenotypic factor analysis of WCST variables suggested a single-factor solution. Overall heritability ranged from 0.19 to 0.23 across different measures of the WCST. The presence of a single general genetic factor, which could be identified from different measures of the WCST, indicated the unity of various WCST indicators and the existence of a common basic ability. Performance on the WCST did not reveal significant differences between the three genotypes on catechol-O-methyltransferase (COMT) and dopamine receptor D2 (DRD2). Carriers of the brain-derived neurotrophic factor (BDNF) Met + genotype exhibited better performance in cognitive functions in comparison to the BDNF Met- genotype. This study highlighted similarities in the phenotypic and genetic structures of the WCST, suggesting one general factor underlying different cognitive functions. The BDNF Met + genotype showed significant main effects on different WCST measures. (PsycInfo Database Record (c) 2022 APA, all rights reserved).

Analysis of Cocoa Clonal Seedlings Purity Through Deoxyribonucleic Acid (DNA) Barcoding and Random Amplification of Polymorphic DNA (RAPD) Fingerprinting

The genetic purity of a plant indicates the similarity properties between seedlings in the field and the description of the plant in the database. Identifying plant purity through a morphological approach has several drawbacks, including time efficiency and environmental factors, and the diversity is limited and inconsistent. This condition encourages the development of detection methods using DNA molecular markers. Plant identification through fingerprinting or the use of molecular markers has not been widely carried out on a commercial scale, considering the investment costs for this analysis are still quite expensive. Another method used for plant identification through DNA Barcoding by comparing variations between DNA sequences. The primers used to identify barcodes on cocoa were derived from the chloroplast genome, including rbcL and matK. This research aims to see the consistency of the rbcL primer when applied to other cocoa clones, and the analysis of the polymorphic diversity of each cocoa clone using DNA fingerprinting RAPD. This method will be tested on clones of Sulawesi 1, Sulawesi 2, ICCRI 03, and ICCRI 09, which were propagated by SE and mother plants in the field using cocoa leaf samples. The stages include DNA extraction, sequencing, and analysis of the sequencing results. The results of seedlings uniformity analysis using DNA barcoding on cocoa plants produced from in vitro propagation showed that the multiplied seeds did not show any difference in sequence with the parent plant (DR2, Sulawesi 1, Sulawesi 2, and ICCRI 09). The analysis of the diversity of cocoa clones DR 2, MCC 2, Sulawesi 1, Sulawesi 2, and ICCRI 09 through DNA Fingerprinting RAPD showed that the OPA 15 primer produced a more apparent polymorphic band than the other three primers (OPP 08, OPW 11, and M 29).

Fabrication of an Oscillating Thermocycler to Analyze the Canine Distemper Virus by Utilizing Reverse Transcription Polymerase Chain Reaction.

The reverse transcription-polymerase chain reaction (RT-PCR) has been utilized as an effective tool to diagnose the infectious diseases of viruses. In the present work, the oscillating thermocycler is fabricated and performed to carry out the one-step RT-PCR process successfully. The ribonucleic acid (RNA) mixture is pipetted into the fixed sample volume inside an aluminum reaction block. The sample oscillates the pathway onto the linear motion control system and through the specific RT-PCR heating zones with individual homemade thermal control modules. The present oscillating thermocycler combines the merits of the chamber type and the CF type systems. Before PCR, the reaction chamber moves to the low-temperature zone to complete the RT stage and synthesize the complementary deoxyribonucleic acid (DNA). Next, the low-temperature zone is regulated to the annealing zone. Furthermore, the reactive sample is moved back and forth among three isothermal zones to complete PCR. No extra heating zone is required for the RT stage. The total length of the moving displacement of the chamber is within 100 mm. The miniaturization of the oscillating thermocycler can be expected. In our oscillatory device, the denaturation zone located between the annealing and extension zones is suggested as the appropriate arrangement of the heating blocks. Heat management without thermal cross-talk is easy. Finally, an improved oscillating device is demonstrated to execute the RT-PCR process directly, utilized to amplify the canine distemper virus templates successfully, which could be well applied to a low-cost DNA analysis system in the future.

In Situ Bioremediation of a Chlorinated Hydrocarbon Plume: A Superfund Site Field Pilot Test

The North Railroad Avenue Plume, discovered in 1989, contained chlorinated solvent groundwater plumes extending over 23.5 hectares (58 acres) and three hydrostratigraphic units. The source contaminant, tetrachloroethene, stemmed from release at a dry cleaner/laundromat business. The anaerobic biodegradation byproducts trichloroethene, isomers of dichloroethene (DCE), and vinyl chloride were detected in groundwater samples collected prior to remedial action. The impacted aquifers are the sole source drinking water aquifers for the communities near the site. Following the remedial investigation and feasibility study, the selected alternative for full-scale remedial action at the site was enhanced reductive dichlorination (ERD) focused on four treatment areas: the shallow source zone, the shallow hotspot area, the shallow downgradient area, and the deep zone. Pilot testing, which was conducted in the source zone and hotspot areas, is the subject of this paper. The primary objectives of the pilot test were to obtain the necessary information to select an ERD treatment formulation, dose, and frequency of dosing for use during full-scale remedial action, as well as to refine the site’s hydrogeologic conceptual site model and design parameters. Four (4) test cells, each of which contained well pairs of injection and downgradient extraction wells, were used to test ERD bio-amendment formulations: ethyl lactate, dairy whey, emulsified vegetable oil (EVO), and a combination of EVO and a hydrogen gas infusion. A conservative tracer, bromide, was added to the recirculation flow to record tracer breakthrough, peak, and dissipation at extraction wells. The results of these dipole tracer tests were used to reassess the hydraulic conductivity and hydrodynamic dispersity used in the remedial design. In addition to water quality analyses of contaminants and substrates, groundwater samples were also analyzed for biological analyses before, during, and after the addition of bioamendment. Analyses of phospholipid fatty acids and deoxyribonucleic acid (DNA) extracts from fresh groundwater samples informed decisions on the capacity for complete ERD without DCE stalling and tracked the shifts in the bacterial and archaeal taxonomy and phylogeny stemming from the addition of bioamendments. The pilot test concluded that EVO was the most suitable, considering (1) support of the native microbial consortia for ERD, (2) mechanics and hydraulics of the remediation system, and (3) sustainability/retention of the substrate in the subsurface. Along with EVO, the addition of a nutrient broth derived from brewery waste accelerated and sustained the desired conditions and microbial diversity and population levels. The pilot test results were also used to assess the utilization kinetics of the injected substrates based on total organic carbon (TOC) concentrations measured in the groundwater. After determining that substrate utilization followed Monod kinetics, a TOC threshold at 300 milligrams per liter, equivalent to approximately twice its half-saturation constant was established. Full scale treatment dosing and dose frequency were designed around this threshold, assuming the maximum substrate utilization would yield optimum ERD.

Presence of Specific Periodontal Pathogens in Prostate Gland Diagnosed With Chronic Inflammation and Adenocarcinoma.

BackgroundIntraprostatic inflammation is frequently observed in the prostate and linked to prostatic diseases, including prostatitis, benign prostatic hyperplasia (BPH), and cancer. The etiology of prostate diseases is unclear. Periodontal diseases are associated with an increased risk of prostate diseases. In men, chronic prostatitis and moderate/severe periodontitis have significantly elevated serum prostate-specific antigen (PSA) levels. Treatment of periodontal disease reduced PSA levels in men. The presence of periodontal pathogens deoxyribonucleic acid (DNA) was identified in the prostate fluid of prostatitis patients. These pathogenic bacteria might have the potential to trigger prostatitis progressing to prostatic adenocarcinoma. The mechanism(s) explaining the etiology of association between periodontal disease and prostate cancer remains unclear. However, the presence of periodontal pathogens has not been analyzed in the prostate gland.ObjectiveTo identify and compare the presence of specific periodontal pathogens in the areas of BPH, inflammation, and cancer of the prostate glands diagnosed with malignancy.Materials and methodsWhole-mount radical prostatectomy sections from men (n=30) were identified for BPH, inflammation, and cancer areas and marked for tissue procurement. The tissues were subjected to DNA isolation and analysis of microbial DNA and total bacterial load for the following pathogens, including Porphyromonas gingivalis strain ATCC 33277, Prevotella intermedia strain B422, Treponema denticola strain 35405, Fusobacterium nucleatum subsp. fusiform strain, Tannerella forsythia strain ATCC 43037, and Campylobacter​​​​​​​ rectus strain ATCC 33238performed real-time PCR. The universal bacterial primer pairs were used to detect genomic DNA (gDNA) from the total bacteria present in the samples. All species-specific primers were designed to target the variable regions of the 16S ribosomal RNA (rRNA). Data were analyzed using the 2-ΔΔCT method, statistically validated using unpaired t-test and ANOVA test.ResultsA total of 90 samples of prostate tissue specimens were analyzed for periodontal pathogens; only one pathogen (F. nucleatum subsp. fusiform strain ATCC 51190) showed a significant difference compared to the expression of S. epidermidis (internal control). In particular, F. nucleatum expression was 9, 11.9, and 10.3-fold higher in BPH, inflammation, and cancer, respectively, at p-value <0.05. Moreover, the bacterial load abundance/expression was almost similar in BPH (46.8-fold), inflammation (40.9 fold), and cancer (41.5 fold) higher. There was no significant difference in bacterial load (folder change) among the three areas of BPH, inflammation, and cancer (p-valve>0.05). Similarly, there was no significant difference between F. nucleatum (folder change) among the three areas (p-valve>0.05).Conclusion Fusobacterium nucleatum is identified in the prostates that harbor cancer, chronic inflammation, and BPH.

Epigenome-wide association study of mitochondrial genome copy number.

We conducted cohort- and race-specific epigenome-wide association analyses of mitochondrial deoxyribonucleic acid (mtDNA) copy number (mtDNA CN) measured in whole blood from participants of African and European origins in five cohorts (n = 6182, mean age = 57-67years, 65% women). In the meta-analysis of all the participants, we discovered 21 mtDNA CN-associated DNA methylation sites (CpG) (P < 1 × 10-7), with a 0.7-3.0 standard deviation increase (3 CpGs) or decrease (18 CpGs) in mtDNA CN corresponding to a 1% increase in DNA methylation. Several significant CpGs have been reported to be associated with at least two risk factors (e.g. chronological age or smoking) for cardiovascular disease (CVD). Five genes [PR/SET domain 16, nuclear receptor subfamily 1 group H member 3 (NR1H3), DNA repair protein, DNA polymerase kappa and decaprenyl-diphosphate synthase subunit 2], which harbor nine significant CpGs, are known to be involved in mitochondrial biosynthesis and functions. For example, NR1H3 encodes a transcription factor that is differentially expressed during an adipose tissue transition. The methylation level of cg09548275 in NR1H3 was negatively associated with mtDNA CN (effect size = -1.71, P = 4 × 10-8) and was positively associated with the NR1H3 expression level (effect size = 0.43, P = 0.0003), which indicates that the methylation level in NR1H3 may underlie the relationship between mtDNA CN, the NR1H3 transcription factor and energy expenditure. In summary, the study results suggest that mtDNA CN variation in whole blood is associated with DNA methylation levels in genes that are involved in a wide range of mitochondrial activities. These findings will help reveal molecular mechanisms between mtDNA CN and CVD.