DNA最新文献_第2页

Chromatin Organization during C. elegans Early Development 秀丽隐杆线虫早期发育过程中的染色质组织

DNA Pub Date : 2024-02-22 DOI: 10.3390/dna4010004

Eshna Jash, G. Csankovszki

引用次数: 1

Comparison of Reduced PCR Volume PowerPlex Fusion 6C Kit Validations on Manual and Automated Systems 减少 PCR 容量的 PowerPlex Fusion 6C 套件在手动和自动系统上的验证比较

DNA Pub Date : 2024-02-04 DOI: 10.3390/dna4010003

Eszter É. Lőrincz, Norbert Mátrai, Katalin A. Rádóczy, Tamás Cseppentő, Nóra M. Magonyi, Attila Heinrich

{"title":"Comparison of Reduced PCR Volume PowerPlex Fusion 6C Kit Validations on Manual and Automated Systems","authors":"Eszter É. Lőrincz, Norbert Mátrai, Katalin A. Rádóczy, Tamás Cseppentő, Nóra M. Magonyi, Attila Heinrich","doi":"10.3390/dna4010003","DOIUrl":"https://doi.org/10.3390/dna4010003","url":null,"abstract":"The PowerPlex Fusion 6C PCR™ amplification kit provides a strong discriminatory power for human identification. We have validated the kit with a reduced volume (12.5 µL) and as part of the validation we compared the efficiency of the polymerase chain reaction (PCR) prepared manually and on Hamilton Microlab® Autolys STAR Biorobot. Three years of casework data has been also included in the validation. Optimisation was carried out on different types of samples (blood, saliva, semen) and DNA was extracted robotically. Tests were conducted at two different cycle numbers (30;32), followed by analysis on both the Applied BiosystemsTM 3500 and 3500 xL Genetic Analyzer instruments (Applied Biosystems®, Foster City, CA, USA). When the PCR was prepared manually, no allele dropout was observed over 0.15 ng input DNA. Whereas when the PCR was prepared robotically, dropout already appeared at the level of 0.15 ng input DNA. In cases when increased cycle number was utilised, an increasing number of dropouts started to arise from 0.075 ng total input DNA. Despite the fact that robotically prepared PCR produced more missing alleles than the manually prepared PCR, using the optimal 0.5 ng input DNA, both methods proved to be reliable. Based on the results, our half-volume protocol is robust, and after three years of application it has proven to be effective with respect to a large number of casework samples.","PeriodicalId":72835,"journal":{"name":"DNA","volume":"2015 33","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139807155","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Comparison of Reduced PCR Volume PowerPlex Fusion 6C Kit Validations on Manual and Automated Systems 减少 PCR 容量的 PowerPlex Fusion 6C 套件在手动和自动系统上的验证比较

DNA Pub Date : 2024-02-04 DOI: 10.3390/dna4010003

Eszter É. Lőrincz, Norbert Mátrai, Katalin A. Rádóczy, Tamás Cseppentő, Nóra M. Magonyi, Attila Heinrich

{"title":"Comparison of Reduced PCR Volume PowerPlex Fusion 6C Kit Validations on Manual and Automated Systems","authors":"Eszter É. Lőrincz, Norbert Mátrai, Katalin A. Rádóczy, Tamás Cseppentő, Nóra M. Magonyi, Attila Heinrich","doi":"10.3390/dna4010003","DOIUrl":"https://doi.org/10.3390/dna4010003","url":null,"abstract":"The PowerPlex Fusion 6C PCR™ amplification kit provides a strong discriminatory power for human identification. We have validated the kit with a reduced volume (12.5 µL) and as part of the validation we compared the efficiency of the polymerase chain reaction (PCR) prepared manually and on Hamilton Microlab® Autolys STAR Biorobot. Three years of casework data has been also included in the validation. Optimisation was carried out on different types of samples (blood, saliva, semen) and DNA was extracted robotically. Tests were conducted at two different cycle numbers (30;32), followed by analysis on both the Applied BiosystemsTM 3500 and 3500 xL Genetic Analyzer instruments (Applied Biosystems®, Foster City, CA, USA). When the PCR was prepared manually, no allele dropout was observed over 0.15 ng input DNA. Whereas when the PCR was prepared robotically, dropout already appeared at the level of 0.15 ng input DNA. In cases when increased cycle number was utilised, an increasing number of dropouts started to arise from 0.075 ng total input DNA. Despite the fact that robotically prepared PCR produced more missing alleles than the manually prepared PCR, using the optimal 0.5 ng input DNA, both methods proved to be reliable. Based on the results, our half-volume protocol is robust, and after three years of application it has proven to be effective with respect to a large number of casework samples.","PeriodicalId":72835,"journal":{"name":"DNA","volume":"19 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139866998","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Effects of Particle LET and Fluence on the Complexity and Frequency of Clustered DNA Damage 粒子 LET 和通量对成簇 DNA 损伤的复杂性和频率的影响

DNA Pub Date : 2024-01-05 DOI: 10.3390/dna4010002

M. Rezaee, A. Adhikary

{"title":"The Effects of Particle LET and Fluence on the Complexity and Frequency of Clustered DNA Damage","authors":"M. Rezaee, A. Adhikary","doi":"10.3390/dna4010002","DOIUrl":"https://doi.org/10.3390/dna4010002","url":null,"abstract":"Motivation: Clustered DNA-lesions are predominantly induced by ionizing radiation, particularly by high-LET particles, and considered as lethal damage. Quantification of this specific type of damage as a function of radiation parameters such as LET, dose rate, dose, and particle type can be informative for the prediction of biological outcome in radiobiological studies. This study investigated the induction and complexity of clustered DNA damage for three different types of particles at an LET range of 0.5–250 keV/µm. Methods: Nanometric volumes (36.0 nm3) of 15 base-pair DNA with its hydration shell was modeled. Electron, proton, and alpha particles at various energies were simulated to irradiate the nanometric volumes. The number of ionization events, low-energy electron spectra, and chemical yields for the formation of °OH, H°, eaq−, and H2O2 were calculated for each particle as a function of LET. Single- and double-strand breaks (SSB and DSB), base release, and clustered DNA-lesions were computed from the Monte-Carlo based quantification of the reactive species and measured yields of the species responsible for the DNA lesion formation. Results: The total amount of DNA damage depends on particle type and LET. The number of ionization events underestimates the quantity of DNA damage at LETs higher than 10 keV/µm. Minimum LETs of 9.4 and 11.5 keV/µm are required to induce clustered damage by a single track of proton and alpha particles, respectively. For a given radiation dose, an increase in LET reduces the number of particle tracks, leading to more complex clustered DNA damage, but a smaller number of separated clustered damage sites. Conclusions: The dependency of the number and the complexity of clustered DNA damage on LET and fluence suggests that the quantification of this damage can be a useful method for the estimation of the biological effectiveness of radiation. These results also suggest that medium-LET particles are more appropriate for the treatment of bulk targets, whereas high-LET particles can be more effective for small targets.","PeriodicalId":72835,"journal":{"name":"DNA","volume":"34 41","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139382671","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Evaluating Metabarcoding Markers for Identifying Zooplankton and Ichthyoplankton Communities to Species in the Salish Sea: Morphological Comparisons and Rare, Threatened or Invasive Species 评估用于识别咸海浮游动物和浮游鱼类群落物种的元标码标记：形态比较和稀有、濒危或入侵物种

DNA Pub Date : 2023-12-22 DOI: 10.3390/dna4010001

Carol A. Stepien, Haila K. Schultz, Sean M. McAllister, Emily L. Norton, J. Keister

{"title":"Evaluating Metabarcoding Markers for Identifying Zooplankton and Ichthyoplankton Communities to Species in the Salish Sea: Morphological Comparisons and Rare, Threatened or Invasive Species","authors":"Carol A. Stepien, Haila K. Schultz, Sean M. McAllister, Emily L. Norton, J. Keister","doi":"10.3390/dna4010001","DOIUrl":"https://doi.org/10.3390/dna4010001","url":null,"abstract":"Zooplankton and ichthyoplankton community assessments depend on species diagnostics, yet morphological identifications are time-consuming, require taxonomic expertise, and are hampered by a lack of diagnostic characters, particularly for larval stages. Metabarcoding can identify multiple species in communities from short DNA sequences in comparison to reference databases. To evaluate species resolution across phylogenetic groups and food webs of zooplankton and ichthyoplankton, we compare five metabarcode mitochondrial (mt)DNA markers from gene regions of (a) cytochrome c oxidase subunit I, (b) cytochrome b, (c) 16S ribosomal RNA, and (d) 12S ribosomal RNA for DNA extracted from net tows in the Northeastern Pacific Ocean’s Salish Sea across seven sites and two seasons. Species resolved by metabarcoding are compared to invertebrate morphological identifications and biomass estimates. Results indicate that species resolution for different zooplankton and ichthyoplankton taxa can markedly vary among gene regions and markers in comparison to morphological identifications. Thus, researchers seeking “universal” metabarcoding should take caution that several markers and gene regions likely will be needed; all will miss some taxa and yield incomplete overlap. Species resolution requires careful attention to taxon marker selection and coverage in reference sequence repositories. In summary, combined multi-marker metabarcoding and morphological approaches improve broadscale zooplankton diagnostics.","PeriodicalId":72835,"journal":{"name":"DNA","volume":"42 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138945633","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Expression of Cowpea VuWRKY21 and VuWRKY87 Genes in Arabidopsis thaliana Confers Plant Tolerance to Salt Stress 豇豆VuWRKY21和VuWRKY87基因在拟南芥中的表达使植物具有耐盐性

DNA Pub Date : 2023-11-08 DOI: 10.3390/dna3040014

Joelson Germano Crispim, Elenilson dos Santos Souza, Marina Ferreira Kitazono Antunes, Hai Liu, Valesca Pandolfi, Marciana Bizerra de Morais, Lili Sun, Cláudia Ulisses, Roel Collamat Rabara, José Ribamar Costa Ferreira-Neto, Ana Maria Benko-Iseppon, Michael P. Timko, Ana Christina Brasileiro-Vidal

{"title":"Expression of Cowpea VuWRKY21 and VuWRKY87 Genes in Arabidopsis thaliana Confers Plant Tolerance to Salt Stress","authors":"Joelson Germano Crispim, Elenilson dos Santos Souza, Marina Ferreira Kitazono Antunes, Hai Liu, Valesca Pandolfi, Marciana Bizerra de Morais, Lili Sun, Cláudia Ulisses, Roel Collamat Rabara, José Ribamar Costa Ferreira-Neto, Ana Maria Benko-Iseppon, Michael P. Timko, Ana Christina Brasileiro-Vidal","doi":"10.3390/dna3040014","DOIUrl":"https://doi.org/10.3390/dna3040014","url":null,"abstract":"WRKY transcription factors play a pivotal role in regulating stress signaling pathways, including those associated with salt stress response. The present work characterized the effects of two WRKY genes from Vigna unguiculata, namely VuWRKY21 and VuWRKY87, on enhancing plant salinity tolerance. Under salt stress conditions, Arabidopsis lines expressing VuWRKY21 or VuWRKY87 showed elevated expression of genes participating in saline stress response pathways and reduced oxidative stress induced by reactive oxygen species (ROS). Among the salt-responsive genes in Arabidopsis, AtP5CS1, AtNHX1, AtRD29A, AtSOS3, AtSOS2, and AtSOS1 exhibited modulated expression levels after stress imposition. Furthermore, compared to wild-type plants, at most evaluated times, transgenic lines, on average, presented lower H2O2 content while displaying higher content of SOD (EC: 1.15.1.1) and CAT (EC: 1.11.1.6) at early stages of salt stress. These findings suggest that the expression of both VuWRKY genes in Arabidopsis, particularly VuWRKY21, activated genes involved in salinity tolerance.","PeriodicalId":72835,"journal":{"name":"DNA","volume":"21 4","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135391215","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genetic Insights into Teratozoospermia: A Comprehensive Computational Study of UTR Variants in AURKC, SPATA16, and SUN5 畸形精子症的遗传洞察:AURKC、SPATA16和SUN5中UTR变异的综合计算研究

DNA Pub Date : 2023-10-26 DOI: 10.3390/dna3040013

Maria-Anna Kyrgiafini, Zissis Mamuris

{"title":"Genetic Insights into Teratozoospermia: A Comprehensive Computational Study of UTR Variants in AURKC, SPATA16, and SUN5","authors":"Maria-Anna Kyrgiafini, Zissis Mamuris","doi":"10.3390/dna3040013","DOIUrl":"https://doi.org/10.3390/dna3040013","url":null,"abstract":"Teratozoospermia, a complex male fertility disorder affecting sperm morphology, has been linked to AURKC, SPATA16, and SUN5 gene defects. However, the sheer volume of SNPs in these genes necessitates prioritization for comprehensive analysis. This study focuses on the often-overlooked untranslated region (UTR) variants in these genes, aiming to assess their association with teratozoospermia and prioritize them. We employed a multi-step filtering process, including functional significance assessment (RegulomeDB, 3DSNP v2.0, SNPinfo (FuncPred)), evaluation of gene expression impacts in testis tissue using GTEx, and assessment of miRNA binding site effects (PolymiRTS Database 3.0, miRNASNP v3). Additionally, we used SNPnexus to evaluate their conservation and association with diseases. In AURKC, we identified six UTR SNPs (rs11084490, rs58264281, rs35582299, rs533889458, rs2361127, rs55710619), two of which influenced gene expression in testis, while others affected the binding sites of 29 miRNAs or were located in transcription-factor binding sites. Three of these SNPs were also found to be associated with spermatogenic failure according to previous studies indicating a potential regulatory role in teratozoospermia, too. For SPATA16, two 3′ UTR variants, rs146640459 and rs148085657, were prioritized, with the latter impacting miRNA binding sites. In SUN5, three 3′ UTR variants (rs1485087675, rs762026146, rs1478197315) affected miRNA binding sites. It should be noted that none of the above variants was identified in a conserved region. Our findings shed light on the potential regulatory roles of these SNPs in teratozoospermia and lay the foundation for future research directions in this area.","PeriodicalId":72835,"journal":{"name":"DNA","volume":"42 8-9","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134908664","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Inka Child Mummy Found in Cerro Aconcagua (Argentina) Traced Back to Populations of the Northern Peruvian Coast through Y-Chromosome Analysis 在阿根廷阿空加瓜发现的印卡儿童木乃伊通过y染色体分析可追溯到秘鲁北部海岸的人群

DNA Pub Date : 2023-10-11 DOI: 10.3390/dna3040012

José R. Sandoval, Ricardo Fujita, Marilza S. Jota, Thomaz Pinotti, Fabrício R. Santos

{"title":"Inka Child Mummy Found in Cerro Aconcagua (Argentina) Traced Back to Populations of the Northern Peruvian Coast through Y-Chromosome Analysis","authors":"José R. Sandoval, Ricardo Fujita, Marilza S. Jota, Thomaz Pinotti, Fabrício R. Santos","doi":"10.3390/dna3040012","DOIUrl":"https://doi.org/10.3390/dna3040012","url":null,"abstract":"The mummy of a seven-year-old child that was discovered in 1985 in Cerro Aconcagua (Mendoza, Argentina) was likely part of an Inka sacrificial religious practice known as capacocha. Previous uniparental DNA marker studies conducted by some scholars have suggested that the mummified child may be related to the southern Andean population of Peru. However, autosome genome-wide analysis performed by others has indicated that the child was more closely related to the population along the northern Peruvian coast than to that of the southern Andes. In this study, we aimed to determine possible genealogical connections in the male lineage of the mummified child. To achieve this, we compared the genetic profile of the mummy with an extensive database of contemporary individuals from the northern Peruvian coastal and southern Andean regions. We used single nucleotide polymorphisms and short tandem repeats from the nonrecombining region of the Y-chromosome for our analysis. Our results confirmed that the Inka child mummy was closely related to individuals from the north coast of Peru. This suggests that the child was likely descended from the Muchik–Chimor-speaking people.","PeriodicalId":72835,"journal":{"name":"DNA","volume":"26 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136212138","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Disease-Associated Mutation A554V Disrupts Normal Autoinhibition of DNMT1. 疾病相关突变A554V破坏DNMT1的正常自抑制

DNA Pub Date : 2023-09-01 DOI: 10.3390/dna3030010

Rebecca L Switzer, Zach J Hartman, Geoffrey R Hewett, Clara F Carroll

{"title":"Disease-Associated Mutation A554V Disrupts Normal Autoinhibition of DNMT1.","authors":"Rebecca L Switzer, Zach J Hartman, Geoffrey R Hewett, Clara F Carroll","doi":"10.3390/dna3030010","DOIUrl":"https://doi.org/10.3390/dna3030010","url":null,"abstract":"<p><p>DNA methyltransferase 1 (DNMT1) is the enzyme primarily responsible for propagation of the methylation pattern in cells. Mutations in DNMT1 have been linked to the development of adult-onset neurodegenerative disorders; these disease-associated mutations occur in the regulatory replication foci-targeting sequence (RFTS) domain of the protein. The RFTS domain is an endogenous inhibitor of DNMT1 activity that binds to the active site and prevents DNA binding. Here, we examine the impact of the disease-associated mutation A554V on normal RFTS-mediated inhibition of DNMT1. Wild-type and mutant proteins were expressed and purified to homogeneity for biochemical characterization. The mutation increased DNA binding affinity ~8-fold. In addition, the mutant enzyme exhibited increased DNA methylation activity. Circular dichroism (CD) spectroscopy revealed that the mutation does not significantly impact the secondary structure or relative thermal stability of the isolated RFTS domain. However, the mutation resulted in changes in the CD spectrum in the context of the larger protein; a decrease in relative thermal stability was also observed. Collectively, this evidence suggests that A554V disrupts normal RFTS-mediated autoinhibition of DNMT1, resulting in a hyperactive mutant enzyme. While the disease-associated mutation does not significantly impact the isolated RFTS domain, the mutation results in a weakening of the interdomain stabilizing interactions generating a more open, active conformation of DNMT1. Hyperactive mutant DNMT1 could be responsible for the increased DNA methylation observed in affected individuals.</p>","PeriodicalId":72835,"journal":{"name":"DNA","volume":"3 3","pages":"119-133"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10470860/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10149865","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

TFAM in mtDNA Homeostasis: Open Questions. 线粒体DNA稳态中的TFAM：悬而未决的问题。

DNA Pub Date : 2023-09-01 Epub Date: 2023-08-07 DOI: 10.3390/dna3030011

Mikhail Alexeyev

引用次数: 1