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DNA Sequencing

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https://www.readbyqxmd.com/read/28945026/-dna-marker-assisted-selection-of-medicinal-plants-%C3%A2-breeding-research-of-disease-resistant-cultivars-of-panax-notoginseng
#1
Qing Li, Biao Li, Shun-Xing Guo
SSR is one of the most important molecular markers used in molecular identification and genetic diversity research of Dendrobium nobile. In order to enrich the library of SSR and establish a method for rapid identification of D. nobile, the SSR information was analyzed in the transcriptome of D. nobile. A total of 32 709 SSRs were obtained from the transcriptome of D. nobile, distributed in 26 742 unigenes with the distribution frequency of 12.90%. SSR loci occurred every 3 748 bp. Mono-nucleotide repeat was the main type, account for as much as 72...
January 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28945025/-dna-marker-assisted-selection-of-medicinal-plants-%C3%A2-breeding-research-of-disease-resistant-cultivars-of-panax-notoginseng
#2
Lin-Lin Dong, Zhong-Jian Chen, Yong Wang, Fu-Gang Wei, Lian-Juan Zhang, Jiang Xu, Guang-Fei Wei, Rui Wang, Juan Yang, Wei-Lin Liu, Xi-Wen Li, Yu-Qi Yu, Shi-Lin Chen
DNA marker-assisted selection of medicinal plants is based on the DNA polymorphism, selects the DNA sequences related to the phenotypes such as high yields, superior quality, stress-resistance and so on according to the technologies of molecular hybridization, polymerase chain reaction and high-throughput sequencing, and assists the breeding of new cultivars. This study bred the first disease-resistant cultivar of notoginseng "Miaoxiang Kangqi 1" using the technology of DNA marker-assisted selection of medicinal plants and systematic breeding...
January 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28945022/-progress-of-gene-editing-technologies-and-prospect-in-traditional-chinese-medicine
#3
REVIEW
Yan-Yan Ma, Jing-Zhe Li, Er-Ning Gao, Dan Qian, Ju-Ying Zhong, Chang-Zhen Liu
Gene editing is a kind of technologies that makes precise modification to the genome. It can be used to knock out/in and replace the specific DNA fragment, and make accurate gene editing on the genome level. The essence of the technique is the DNA sequence change with use of non homologous end link repair and homologous recombination repair, combined with specific DNA target recognition and endonuclease.This technology has wide range of development prospects and high application value in terms of scientific research, agriculture, medical treatment and other fields...
January 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28944857/a-novel-fbn1-mutation-causes-autosomal-dominant-marfan-syndrome
#4
Ying Xiao, Xiaoqi Liu, Xiaoxin Guo, Liping Liu, Linxin Jiang, Qi Wang, Bo Gong
Marfan syndrome (MFS) is an inherited and systemic disorder. It has been reported that mutations in the fibrillin‑1 gene (FBN1) account for ~90% of autosomal dominant cases of MFS. This study was conducted to screen mutations of FBN1 in a Chinese family with autosomal dominant MFS; four individuals including two patients with MFS were recruited. The family members underwent complete physical, cardiovascular and ophthalmologic examinations. Genomic DNA samples were collected from the family along with 383 unrelated healthy subjects...
September 20, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28944824/efficient-gene-therapy-with-a-combination-of-ultrasound%C3%A2-targeted-microbubble-destruction-and-pei-dna-nls-complexes
#5
Yi-Jia Wang, Qing Zhou, Sheng Cao, Bo Hu, Qing Deng, Nan Jiang, Jingjing Cui
Current strategies of gene transfection are not efficient at achieving a notable therapeutic effect. The aim of the present study was to combine ultrasound‑targeted microbubble destruction (UTMD) with a polyethylenimine/pEGFP‑N3 plasmid/nuclear localization sequence (PEI/DNA/NLS) complex gene delivery system, and evaluate the transfection efficiency of enhanced green fluorescent protein (EGFP) gene delivery to 293T cells using this system. The formation of PEI/DNA/NLS complexes and the protective effects of PEI/NLS were verified by gel electrophoresis...
September 18, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28944240/novel-compound-heterozygous-mutations-in-telo2-in-a-patient-with-severe-expression-of-you-hoover-fong-syndrome
#6
Shahida Moosa, Janine Altmüller, Troels Lyngbye, Rikke Christensen, Yun Li, Peter Nürnberg, Gökhan Yigit, Ida Vogel, Bernd Wollnik
BACKGROUND: Very recently, compound heterozygous loss-of-function mutations in TELO2 were shown to underlie the newly-described You-Hoover-Fong syndrome. TELO2 forms part of the co-chaperone triple T complex (TTT complex), which plays an important role in the maturation and stabilization of the phosphatidylinositol 3-kinase-related protein kinases (PIKKs). Patients with mutations in TELO2 present with microcephaly and associated intellectual disability, postnatal growth retardation and dysmorphic features...
September 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28944019/utility-of-dna-barcoding-to-identify-rare-endemic-vascular-plant-species-in-trinidad
#7
Fazeeda N Hosein, Nigel Austin, Shobha Maharaj, Winston Johnson, Luke Rostant, Amanda C Ramdass, Sephra N Rampersad
The islands of the Caribbean are considered to be a "biodiversity hotspot." Collectively, a high level of endemism for several plant groups has been reported for this region. Biodiversity conservation should, in part, be informed by taxonomy, population status, and distribution of flora. One taxonomic impediment to species inventory and management is correct identification as conventional morphology-based assessment is subject to several caveats. DNA barcoding can be a useful tool to quickly and accurately identify species and has the potential to prompt the discovery of new species...
September 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28944006/regulation-of-gene-expression-is-associated-with-tolerance-of-the-arctic-copepod-calanus-glacialis-to-co2-acidified-sea-water
#8
Allison Bailey, Pierre De Wit, Peter Thor, Howard I Browman, Reidun Bjelland, Steven Shema, David M Fields, Jeffrey A Runge, Cameron Thompson, Haakon Hop
Ocean acidification is the increase in seawater pCO 2 due to the uptake of atmospheric anthropogenic CO 2, with the largest changes predicted to occur in the Arctic seas. For some marine organisms, this change in pCO 2, and associated decrease in pH, represents a climate change-related stressor. In this study, we investigated the gene expression patterns of nauplii of the Arctic copepod Calanus glacialis cultured at low pH levels. We have previously shown that organismal-level performance (development, growth, respiration) of C...
September 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28943971/genome-comparison-of-pseudomonas-fluorescens-um270-with-related-fluorescent-strains-unveils-genes-involved-in-rhizosphere-competence-and-colonization
#9
Julie E Hernández-Salmerón, Gabriel Moreno-Hagelsieb, Gustavo Santoyo
Pseudomonas fluorescens UM270 is a rhizosphere-colonizing bacterium that produces multiple diffusible and volatile compounds involved in plant growth-promoting activities. Strain UM270 exhibits excellent biocontrol capacities against diverse fungal pathogens . In a previous study, the general UM270 genome characteristics were published. Here, we report a deeper analysis of its gene content and compare it to other P. fluorescens strains to unveil the genetic elements that might explain UM270's great colonizing and plant growth-promoting capabilities...
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28943934/l-securinine-inhibits-the-proliferation-of-a549-lung-cancer-cells-and-promotes-dkk1-promoter-methylation
#10
Shuwen Han, Xi Yang, Yuefen Pan, Quan Qi, Junjun Shen, Huifen Fang, Zhaoning Ji
L-securinine is a natural product extracted and isolated from the leaf of dried Securinega suffruticosa. The aim of the present study was to explore the effects of L-securinine on proliferation, and the methylation profile of the dickkopf-related protein 1 (DKK1) gene in human lung cancer cells and fibroblasts. L-securinine was extracted, isolated and the structure was identified. The cytotoxicity of L-securinine in A549 cells was evaluated by Cell Counting Kit-8 assays. The expression and DNA methylation profile of DKK genes was analyzed by reverse transcription-quantitative polymerase chain reaction and bisulfite sequencing polymerase chain reaction, respectively...
October 2017: Oncology Letters
https://www.readbyqxmd.com/read/28943896/a-large-chinese-pedigree-of-multiple-endocrine-neoplasia-type-2a-with-a-novel-c634y-d707e-germline-mutation-in-ret-exon-11
#11
Fanqian Lu, Xiaohong Chen, Yunlong Bai, Yaru Feng, Jian Wu
The present study identified the clinical features of the largest multiple endocrine neoplasia type 2 (MEN2) A pedigree from China, with a novel double missense rearranged during transfection (RET) mutation (C634Y/D707E). To the best of our knowledge, the D707E mutation has not been identified to date. In the present study, a total of 101 family members who originated from a large pedigree (134 members in total) underwent RET mutation screening by next-generation sequencing and polymerase chain reaction (PCR) amplification, followed by direct bidirectional DNA sequencing...
September 2017: Oncology Letters
https://www.readbyqxmd.com/read/28943871/global-screening-of-salmonella-enterica-serovar-typhimurium-genes-for-desiccation-survival
#12
Rabindra K Mandal, Young M Kwon
Salmonella spp., one of the most common foodborne bacterial pathogens, has the ability to survive under desiccation conditions in foods and food processing facilities for years. This raises the concerns of Salmonella infection in humans associated with low water activity foods. Salmonella responds to desiccation stress via complex pathways involving immediate physiological actions as well as coordinated genetic responses. However, the exact mechanisms of Salmonella to resist desiccation stress remain to be fully elucidated...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28943773/detection-of-korean-native-honey-and-european-honey-by-using-duplex-polymerase-chain-reaction-and-immunochromatographic-assay
#13
Chang-Kyu Kim, Deug-Chan Lee, Suk-Ho Choi
Korean native honey (KNH) is much more expensive than European honey (EH) in Korea, because KNH is a favored honey which is produced less than EH. Food fraud of KNH has drawn attention of the government office concerned, which is in need of a method to differentiate between KNH and EH which are produced by the Asiatic honeybee, Apis cerana and the European honeybee, Apis mellifera, respectively. A method to discriminate KNH and EH was established by using duplex polymerase chain reaction (PCR) in this study...
2017: Korean Journal for Food Science of Animal Resources
https://www.readbyqxmd.com/read/28943766/characterization-of-the-biodiversity-of-the-spoilage-microbiota-in-chicken-meat-using-next-generation-sequencing-and-culture-dependent-approach
#14
Hee Soo Lee, Mirae Kwon, Sunhak Heo, Min Gon Kim, Geun-Bae Kim
This study investigated the psychrotrophic bacteria isolated from chicken meat to characterize their microbial composition during refrigerated storage. The bacterial community was identified by the Illumina MiSeq method based on bacterial DNA extracted from spoiled chicken meat. Molecular identification of the isolated psychrotrophic bacteria was carried out using 16S rDNA sequencing and their putrefactive potential was investigated by the growth at low temperature as well as their proteolytic activities in chicken meat...
2017: Korean Journal for Food Science of Animal Resources
https://www.readbyqxmd.com/read/28943408/epidemiology-of-transmissible-diseases-array-hybridization-and-next-generation-sequencing-as-universal-nucleic-acid-mediated-typing-tools
#15
W Michael Dunne, Hannes Pouseele, Stefan Monecke, Ralf Ehricht, Alex van Belkum
The magnitude of interest in the epidemiology of transmissible human diseases is reflected in the vast number of tools and methods developed recently with the expressed purpose to characterize and track evolutionary changes that occur in agents of these diseases over time. Within the past decade a new suite of such tools has become available with the emergence of the so-called "omics" technologies. Among these, two are exponents of the ongoing genomic revolution. Firstly, high-density nucleic acid probe arrays have been proposed and developed using various chemical and physical approaches...
September 21, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28943406/microbial-sequence-typing-in-the-genomic-era
#16
Marcos Pérez-Losada, Miguel Arenas, Eduardo Castro-Nallar
Next-generation sequencing (NGS), also known as high-throughput sequencing, is changing the field of microbial genomics research. NGS allows for a more comprehensive analysis of the diversity, structure and composition of microbial genes and genomes compared to the traditional automated Sanger capillary sequencing at a lower cost. NGS strategies have expanded the versatility of standard and widely used typing approaches based on nucleotide variation in several hundred DNA sequences and a few gene fragments (MLST, MLVA, rMLST and cgMLST)...
September 21, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28943336/the-origins-of-specificity-in-the-microcin-processing-protease-tldd-e
#17
Dmitry Ghilarov, Marina Serebryakova, Clare E M Stevenson, Stephen J Hearnshaw, Dmitry Volkov, Anthony Maxwell, David M Lawson, Konstantin Severinov
TldD and TldE proteins are involved in the biosynthesis of microcin B17 (MccB17), an Escherichia coli thiazole/oxazole-modified peptide toxin targeting DNA gyrase. Using a combination of biochemical and crystallographic methods we show that E. coli TldD and TldE interact to form a heterodimeric metalloprotease. TldD/E cleaves the N-terminal leader sequence from the modified MccB17 precursor peptide, to yield mature antibiotic, while it has no effect on the unmodified peptide. Both proteins are essential for the activity; however, only the TldD subunit forms a novel metal-containing active site within the hollow core of the heterodimer...
September 11, 2017: Structure
https://www.readbyqxmd.com/read/28942823/novel-pcr-primers-to-diagnose-visceral-leishmaniasis-using-peripheral-blood-spleen-or-bone-marrow-aspirates
#18
Mahbuba Khatun, S M Sabbir Alam, Abed Hussain Khan, M Anwar Hossain, Jalaluddin Ashraful Haq, Md Shariful Alam Jilani, Mohammad Tariqur Rahman, Muhammad Manjurul Karim
OBJECTIVE: To establish a suitable method of diagnosis of visceral leishmaniasis (VL) using peripheral blood, spleen or bone marrow aspirates. METHODS: Peripheral blood, bone marrow and spleen aspirate samples were collected from clinically suspected VL patients (n = 26). A new PCR primer pair (MK1F/R) was designed targeting kinetoplast mini circle DNA sequences of Leishmania donovani, and Leishmania infantum, and was used to diagnose VL along with some other established primers for VL in polymerase chain reactions...
August 2017: Asian Pacific Journal of Tropical Medicine
https://www.readbyqxmd.com/read/28942795/genetics-of-mitochondrial-disease
#19
Russell P Saneto
Mitochondria are intracellular organelles responsible for adenosine triphosphate production. The strict control of intracellular energy needs require proper mitochondrial functioning. The mitochondria are under dual controls of mitochondrial DNA (mtDNA) and nuclear DNA (nDNA). Mitochondrial dysfunction can arise from changes in either mtDNA or nDNA genes regulating function. There are an estimated ∼1500 proteins in the mitoproteome, whereas the mtDNA genome has 37 proteins. There are, to date, ∼275 genes shown to give rise to disease...
2017: Advances in Genetics
https://www.readbyqxmd.com/read/28942733/dna-methylation-dynamics-during-early-plant-life
#20
Daniel Bouyer, Amira Kramdi, Mohamed Kassam, Maren Heese, Arp Schnittger, François Roudier, Vincent Colot
BACKGROUND: Cytosine methylation is crucial for gene regulation and silencing of transposable elements in mammals and plants. While this epigenetic mark is extensively reprogrammed in the germline and early embryos of mammals, the extent to which DNA methylation is reset between generations in plants remains largely unknown. RESULTS: Using Arabidopsis as a model, we uncovered distinct DNA methylation dynamics over transposable element sequences during the early stages of plant development...
September 25, 2017: Genome Biology
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