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Water Research Nov 2014Globally, denitrification is commonly employed in biological nitrogen removal processes to enhance water quality. However, substantial knowledge gaps remain concerning... (Review)
Review
Globally, denitrification is commonly employed in biological nitrogen removal processes to enhance water quality. However, substantial knowledge gaps remain concerning the overall community structure, population dynamics and metabolism of different organic carbon sources. This systematic review provides a summary of current findings pertaining to the microbial ecology of denitrification in biological wastewater treatment processes. DNA fingerprinting-based analysis has revealed a high level of microbial diversity in denitrification reactors and highlighted the impacts of carbon sources in determining overall denitrifying community composition. Stable isotope probing, fluorescence in situ hybridization, microarrays and meta-omics further link community structure with function by identifying the functional populations and their gene regulatory patterns at the transcriptional and translational levels. This review stresses the need to integrate microbial ecology information into conventional denitrification design and operation at full-scale. Some emerging questions, from physiological mechanisms to practical solutions, for example, eliminating nitrous oxide emissions and supplementing more sustainable carbon sources than methanol, are also discussed. A combination of high-throughput approaches is next in line for thorough assessment of wastewater denitrifying community structure and function. Though denitrification is used as an example here, this synergy between microbial ecology and process engineering is applicable to other biological wastewater treatment processes.
Topics: Bacteria; DNA, Bacterial; Denitrification; Environmental Microbiology; In Situ Hybridization, Fluorescence; Nitrogen; Sewage; Waste Disposal, Fluid
PubMed: 25078442
DOI: 10.1016/j.watres.2014.06.042 -
Biological Reviews of the Cambridge... Aug 2017The grey wolf (Canis lupus) is an iconic large carnivore that has increasingly been recognized as an apex predator with intrinsic value and a keystone species. However,... (Meta-Analysis)
Meta-Analysis Review
The grey wolf (Canis lupus) is an iconic large carnivore that has increasingly been recognized as an apex predator with intrinsic value and a keystone species. However, wolves have also long represented a primary source of human-carnivore conflict, which has led to long-term persecution of wolves, resulting in a significant decrease in their numbers, genetic diversity and gene flow between populations. For more effective protection and management of wolf populations in Europe, robust scientific evidence is crucial. This review serves as an analytical summary of the main findings from wolf population genetic studies in Europe, covering major studies from the 'pre-genomic era' and the first insights of the 'genomics era'. We analyse, summarize and discuss findings derived from analyses of three compartments of the mammalian genome with different inheritance modes: maternal (mitochondrial DNA), paternal (Y chromosome) and biparental [autosomal microsatellites and single nucleotide polymorphisms (SNPs)]. To describe large-scale trends and patterns of genetic variation in European wolf populations, we conducted a meta-analysis based on the results of previous microsatellite studies and also included new data, covering all 19 European countries for which wolf genetic information is available: Norway, Sweden, Finland, Estonia, Latvia, Lithuania, Poland, Czech Republic, Slovakia, Germany, Belarus, Russia, Italy, Croatia, Bulgaria, Bosnia and Herzegovina, Greece, Spain and Portugal. We compared different indices of genetic diversity in wolf populations and found a significant spatial trend in heterozygosity across Europe from south-west (lowest genetic diversity) to north-east (highest). The range of spatial autocorrelation calculated on the basis of three characteristics of genetic diversity was 650-850 km, suggesting that the genetic diversity of a given wolf population can be influenced by populations up to 850 km away. As an important outcome of this synthesis, we discuss the most pressing issues threatening wolf populations in Europe, highlight important gaps in current knowledge, suggest solutions to overcome these limitations, and provide recommendations for science-based wolf conservation and management at regional and Europe-wide scales.
Topics: Animals; Conservation of Natural Resources; Europe; Genetic Variation; Genetics, Population; Microsatellite Repeats; Wolves
PubMed: 27682639
DOI: 10.1111/brv.12298 -
Cancer Treatment Reviews Dec 2017The potential predictive value of genetic polymorphisms in ovarian cancer first-line treatment is inconsistently reported. We aimed to review ovarian cancer... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
The potential predictive value of genetic polymorphisms in ovarian cancer first-line treatment is inconsistently reported. We aimed to review ovarian cancer pharmacogenetic studies to update and summarize the available data and to provide directions for further research.
METHODS
A systematic review followed by a meta-analysis was conducted on cohort studies assessing the involvement of genetic polymorphisms in ovarian cancer first-line treatment response retrieved through a MEDLINE database search by November 2016. Studies were pooled and summary estimates and 95% confidence intervals (CI) were calculated using random or fixed-effects models as appropriate.
RESULTS
One hundred and forty-two studies gathering 106871 patients were included. Combined data suggested that GSTM1-null genotype patients have a lower risk of death compared to GSTM1-wt carriers, specifically in advanced stages (hazard ratio (HR), 0.68; 95% CI, 0.48-0.97) and when submitted to platinum-based chemotherapy (aHR, 0.61; 95% CI, 0.39-0.94). ERCC1 rs11615 and rs3212886 might have also a significant impact in treatment outcome (aHR, 0.67; 95% CI, 0.51-0.89; aHR, 1.28; 95% CI, 1.01-1.63, respectively). Moreover, ERCC2 rs13181 and rs1799793 showed a distinct ethnic behavior (Asians: aHR, 1.41; 95% CI, 0.80-2.49; aHR, 1.07; 95% CI, 0.62-1.86; Caucasians: aHR, 0.10; 95% CI, 0.01-0.96; aHR, 0.18; 95% CI, 0.05-0.68, respectively).
CONCLUSION(S)
The definition of integrative predictive models should encompass genetic information, especially regarding GSTM1 homozygous deletion. Justifying additional pharmacogenetic investigation are variants in ERCC1 and ERCC2, which highlight the DNA Repair ability to ovarian cancer prognosis. Further knowledge could aid to understand platinum-treatment failure and to tailor chemotherapy strategies.
Topics: Antineoplastic Combined Chemotherapy Protocols; Cytoreduction Surgical Procedures; Female; Genetic Variation; Glutathione Transferase; Humans; Models, Genetic; Organoplatinum Compounds; Ovarian Neoplasms; Polymorphism, Single Nucleotide; Taxoids; Treatment Outcome
PubMed: 29100168
DOI: 10.1016/j.ctrv.2017.10.001 -
Environmental Toxicology and... Dec 2017Silica nanoparticles (SiNPs) have been found to pass through biological barriers and get distributed in the human body. They induce cell apoptosis via various mechanisms... (Review)
Review
Silica nanoparticles (SiNPs) have been found to pass through biological barriers and get distributed in the human body. They induce cell apoptosis via various mechanisms in body organs. To understand these mechanisms, we carried out systematic review of in vitro studies on SiNPs-induced cell apoptosis. Office of Health Assessment and Translation approach for Systematic Review and Evidence Integration was used to identify 14 studies dating from the year 2000 to current. Four studies showed an increase in DNA damage, cell cycle arrest, proapoptotic factors and decrease in antiapoptotic factors resulting to apoptosis. Eight studies showed induction of mitochondrial dysfunction, Bax upregulation, Bcl-2 downregulation, and caspase-3, -7, -9 activities increase. Increase in FADD, TNFR1 and Bid proteins was observed in one study, while the other NO production and caspase-3 activity was increased. These studies found the potency of SiNPs to induce cell apoptosis through DNA damage, mitochondrial, tumor necrosis factor, and nitric oxide related pathways.
Topics: Animals; Apoptosis; Apoptosis Regulatory Proteins; Cell Cycle Checkpoints; DNA Damage; Down-Regulation; Humans; In Vitro Techniques; Mitochondria; Nanoparticles; Signal Transduction; Silicon Dioxide
PubMed: 28957724
DOI: 10.1016/j.etap.2017.09.012 -
Applied and Environmental Microbiology Feb 2023Site-specific recombinases (integrases) can mediate the horizontal transfer of genomic islands. The ability to integrate large DNA sequences into target sites is very...
Site-specific recombinases (integrases) can mediate the horizontal transfer of genomic islands. The ability to integrate large DNA sequences into target sites is very important for genetic engineering in prokaryotic and eukaryotic cells. Here, we characterized an unprecedented catalogue of 530 tyrosine-type integrases by examining genes potentially encoding tyrosine integrases in bacterial genomic islands. The phylogeny of putative tyrosine integrases revealed that these integrases form an evolutionary clade that is distinct from those already known and are affiliated with novel integrase groups. We systematically searched for candidate integrase genes, and their integration activities were validated in a bacterial model. We verified the integration functions of six representative novel integrases by using a two-plasmid integration system consisting of a donor plasmid carrying the integrase gene and site and a recipient plasmid harboring an site in -deficient Escherichia coli. Further quantitative reverse transcription-PCR (qRT-PCR) assays validated that the six selected integrases can be expressed with their native promoters in E. coli. The region reductions showed that the extent of sites of integrases is approximately 200 bp for integration capacity. In addition, mutational analysis showed that the conserved tyrosine at the C terminus is essential for catalysis, confirming that these candidate proteins belong to the tyrosine-type recombinase superfamily, i.e., tyrosine integrases. This study revealed that the novel integrases from bacterial genomic islands have site-specific recombination functions, which is of physiological significance for their genomic islands in bacterial chromosomes. More importantly, our discovery expands the toolbox for genetic engineering, especially for efficient integration activity. Site-specific recombinases or integrases have high specificity for DNA large fragment integration, which is urgently needed for gene editing. However, known integrases are not sufficient for meeting multiple integrations. In this work, we discovered an array of integrases through bioinformatics analysis in bacterial genomes. Phylogeny and functional assays revealed that these new integrases belong to tyrosine-type integrases and have the ability to conduct site-specific recombination. Moreover, region extent and catalysis site analysis were characterized. Our study provides the methodology for discovery of novel integrases and increases the capacity of weapon pool for genetic engineering in bacteria.
Topics: Integrases; Genomic Islands; Escherichia coli; Tyrosine; Plasmids; Bacteriophages; Attachment Sites, Microbiological
PubMed: 36719242
DOI: 10.1128/aem.01738-22 -
Neural Regeneration Research Dec 2024The search for reliable and easily accessible biomarkers in Parkinson's disease is receiving a growing emphasis, to detect neurodegeneration from the prodromal phase and...
The search for reliable and easily accessible biomarkers in Parkinson's disease is receiving a growing emphasis, to detect neurodegeneration from the prodromal phase and to enforce disease-modifying therapies. Despite the need for non-invasively accessible biomarkers, the majority of the studies have pointed to cerebrospinal fluid or peripheral biopsies biomarkers, which require invasive collection procedures. Saliva represents an easily accessible biofluid and an incredibly wide source of molecular biomarkers. In the present study, after presenting the morphological and biological bases for looking at saliva in the search of biomarkers for Parkinson's disease, we systematically reviewed the results achieved so far in the saliva of different cohorts of Parkinson's disease patients. A comprehensive literature search on PubMed and SCOPUS led to the discovery of 289 articles. After screening and exclusion, 34 relevant articles were derived for systematic review. Alpha-synuclein, the histopathological hallmark of Parkinson's disease, has been the most investigated Parkinson's disease biomarker in saliva, with oligomeric alpha-synuclein consistently found increased in Parkinson's disease patients in comparison to healthy controls, while conflicting results have been reported regarding the levels of total alpha-synuclein and phosphorylated alpha-synuclein, and few studies described an increased oligomeric alpha-synuclein/total alpha-synuclein ratio in Parkinson's disease. Beyond alpha-synuclein, other biomarkers targeting different molecular pathways have been explored in the saliva of Parkinson's disease patients: total tau, phosphorylated tau, amyloid-β1-42 (pathological protein aggregation biomarkers); DJ-1, heme-oxygenase-1, metabolites (altered energy homeostasis biomarkers); MAPLC-3beta (aberrant proteostasis biomarker); cortisol, tumor necrosis factor-alpha (inflammation biomarkers); DNA methylation, miRNA (DNA/RNA defects biomarkers); acetylcholinesterase activity (synaptic and neuronal network dysfunction biomarkers); Raman spectra, proteome, and caffeine. Despite a few studies investigating biomarkers targeting molecular pathways different from alpha-synuclein in Parkinson's disease, these results should be replicated and observed in studies on larger cohorts, considering the potential role of these biomarkers in determining the molecular variance among Parkinson's disease subtypes. Although the need for standardization in sample collection and processing, salivary-based biomarkers studies have reported encouraging results, calling for large-scale longitudinal studies and multicentric assessments, given the great molecular potentials and the non-invasive accessibility of saliva.
PubMed: 38595280
DOI: 10.4103/NRR.NRR-D-23-01677 -
Mutation Research. Reviews in Mutation... 2016Airborne particles are small, solid particles projected into the air either by natural forces, or by mechanical or man-made processes, and include fibers and dusts.... (Review)
Review
Airborne particles are small, solid particles projected into the air either by natural forces, or by mechanical or man-made processes, and include fibers and dusts. Their toxicity is usually subsequent to inhalation and can lead to pulmonary dysfunctions and diseases, including cancer. Cytochalasin B blocked micronucleus assay in lymphocytes (L-CBMN) has been shown as a sensitive and reliable technique in assessing genotoxic exposure, An extensive search of the PubMed and Web of Science databases allowed retrieval of 18 articles on occupational or environmental exposure evaluating L-CBMN in subjects exposed to fibers or dusts (asbestos, silica, rockwool, beryllium, tobacco, and wood). For each study, mean L-CBMN levels were compared in exposed subjects vs. unexposed controls providing a point estimate, the Mean Ratio (MR). The high heterogeneity among retrieved studies and their relatively limited number did not allow a quantitative meta-analysis. However, the inter-quartile range of all MRs fell within the interval between 1.25 and 2.23, supporting the hypothesis that exposure to airborne particles increases DNA damage, although mechanisms of genotoxicity should be further investigated. A borderline significant correlation was found with SCE, but not with chromosome aberrations or comet assay. Future research should focus on exposure assessment, in order to perform proper dose-response studies and disentangle the effect of different compounds in mixed exposures. To fully exploit the cytome assay, L-CBMN frequency should be integrated with other endpoints, such as nucleoplasmic bridges and nuclear buds. The use of alternative tissues, such as nasal and buccal mucosa, and the implementation of other cytogenetic assay, may help to understand the effects of this exposure.
Topics: Asbestos; Biomarkers; Dust; Environmental Exposure; Humans; Micronucleus Tests
PubMed: 27894680
DOI: 10.1016/j.mrrev.2016.05.004 -
Fertility and Sterility Jan 2024Because analytic technologies improve, increasing amounts of data on methylation differences between assisted reproductive technology (ART) and unassisted conceptions... (Review)
Review
IMPORTANCE
Because analytic technologies improve, increasing amounts of data on methylation differences between assisted reproductive technology (ART) and unassisted conceptions are available. However, various studies use different tissue types and different populations in their analyses, making data comparison and integration difficult.
OBJECTIVE
To compare and integrate data on genome-wide analyses of methylation differences due to ART, allowing exposure of overarching themes.
EVIDENCE REVIEW
All studies undertaking genome-wide analysis of human methylation differences due to ART or infertility in any tissue type across the lifespan were assessed for inclusion.
FINDINGS
Seventeen studies were identified that met the inclusion criteria. One study assessed trophectoderm biopsies, 2 first-trimester placenta, 1 first-trimester fetal tissue, 2 term placenta, 7 cord blood, 3 newborn dried blood spots, 1 childhood buccal smears, 1 childhood peripheral blood, and 2 adult peripheral blood. Eleven studies compared tissues from in vitro fertilization (IVF) conceptions with those of unassisted conceptions, 4 compared intracytoplasmic sperm injection with unassisted conceptions, 4 compared non-IVF fertility treatment (NIFT) with unassisted conceptions, 4 compared NIFT with IVF, and 5 compared an infertile population (conceiving via various methods) with an unassisted presumably fertile population. In studies assessing placental tissue, 1 gene with potential methylation changes due to IVF when compared with unassisted conceptions was identified by 2 studies. In blood, 11 potential genes with methylation changes due to IVF compared with unassisted conceptions were identified by 2 studies, 1 of which was identified by 3 studies. Three potentially affected genes were identified by 2 studies involving blood between intracytoplasmic sperm injection and unassisted populations. There were no overlapping genes identified in any tissue type between NIFT and unassisted populations, between NIFT and IVF, or the infertility combined population when compared with the unassisted fertile population.
CONCLUSIONS
Comparing studies is challenging due to differing variables between analyses. However, even in similar tissue types and populations, overlapping methylation changes are limited, suggesting that differences due to ART are minimal.
RELEVANCE
Information from this systematic review is significant for providers and patients who provide and use ART to understand methylation risks that may be associated with the technology.
Topics: Adult; Child; Female; Humans; Infant, Newborn; Male; Pregnancy; DNA Methylation; Fertilization in Vitro; Genome-Wide Association Study; Infertility; Placenta; Reproductive Techniques, Assisted; Semen
PubMed: 37827482
DOI: 10.1016/j.fertnstert.2023.10.007 -
Clinical Epigenetics 2016Epigenetic mechanisms are important for the regulation of gene expression and differentiation in the fetus and the newborn child. Symptoms of maternal depression and... (Review)
Review
INTRODUCTION
Epigenetic mechanisms are important for the regulation of gene expression and differentiation in the fetus and the newborn child. Symptoms of maternal depression and antidepressant use affects up to 20 % of pregnant women, and may lead to epigenetic changes with life-long impact on child health. The aim of this review is to investigate whether there is an association between exposure to maternal antidepressants during pregnancy and epigenetic changes in the newborn.
MATERIAL AND METHODS
Systematic literature searches were performed in MEDLINE and EMBASE combining MeSH terms covering epigenetic changes, use of antidepressant medication, pregnancy and newborns. A keyword search was also performed. We included studies on pregnant women and their children where there was a history of maternal depressed mood or anxiety, a reported use of antidepressant medication, and measurements of epigenetic changes in umbilical cord blood. Studies using genome-wide or candidate-based epigenetic analyses were included. Citations and references from the included articles were investigated to locate further relevant articles. The completeness of reporting as well as the risk of bias and confounding was assessed.
RESULTS
Six studies were included. They all investigated methylation changes. Genome-wide methylation changes were examined in 184 children and methylation status in specific genes was examined in 96 children exposed to antidepressant medication. Three of the studies found an association between use of antidepressant medication during pregnancy and methylation status at various CpG sites measured in cord blood of the newborn. One of these studies found an association in African-Americans, but not Caucasians. The remaining three studies found associations between maternal mood and epigenetic changes in umbilical cord blood but no association between epigenetic changes and maternal use of antidepressant medication.
CONCLUSION
The included studies have not established a clear association between use of antidepressant medication during pregnancy and epigenetic changes in the cord blood. Future studies using newer, more wide-ranging epigenetic methods could discover possible new differentially methylated sites. Larger sample sizes and good validity of exposures are warranted in order to adjust for level of maternal depression, other maternal illness, maternal use of other types of medication, and maternal ethnicity. PROSPERO registration number: CRD42015026575.
Topics: Antidepressive Agents; DNA Methylation; Depression; Epigenesis, Genetic; Female; Fetal Blood; Humans; Maternal Exposure; Pregnancy; Pregnancy Complications
PubMed: 27610205
DOI: 10.1186/s13148-016-0262-x -
Scandinavian Journal of Medicine &... Oct 2022The aim of this systematic review and meta-analysis was to identify the genetic variants of (inter)national competing long-distance runners and road cyclists compared... (Meta-Analysis)
Meta-Analysis
The aim of this systematic review and meta-analysis was to identify the genetic variants of (inter)national competing long-distance runners and road cyclists compared with controls. The Medline and Embase databases were searched until 15 November 2021. Eligible articles included genetic epidemiological studies published in English. A homogenous group of endurance athletes competing at (inter)national level and sedentary controls were included. Pooled odds ratios based on the genotype frequency with corresponding 95% confidence intervals (95%CI) were calculated using random effects models. Heterogeneity was addressed by Q-statistics, and I . Sources of heterogeneity were examined by meta-regression and risk of bias was assessed with the Clark Baudouin scale. This systematic review comprised of 43 studies including a total of 3938 athletes and 10 752 controls in the pooled analysis. Of the 42 identified genetic variants, 13 were investigated in independent studies. Significant associations were found for five polymorphisms. Pooled odds ratio [95%CI] favoring athletes compared with controls was 1.42 [1.12-1.81] for ACE II (I/D), 1.66 [1.26-2.19] for ACTN3 TT (rs1815739), 1.75 [1.34-2.29] for PPARGC1A GG (rs8192678), 2.23 [1.42-3.51] for AMPD1 CC (rs17602729), and 2.85 [1.27-6.39] for HFE GG + CG (rs1799945). Risk of bias was low in 25 (58%) and unclear in 18 (42%) articles. Heterogeneity of the results was low (0%-20%) except for HFE (71%), GNB3 (80%), and NOS3 (76%). (Inter)national competing runners and cyclists have a higher probability to carry specific genetic variants compared with controls. This study confirms that (inter)national competing endurance athletes constitute a unique genetic make-up, which likely contributes to their performance level.
Topics: Humans; Actinin; Athletes; Genotype; Odds Ratio; Polymorphism, Genetic; Running; Bicycling
PubMed: 35839336
DOI: 10.1111/sms.14212