keyword
MENU ▼
Read by QxMD icon Read
search

Novel dna extraction

keyword
https://www.readbyqxmd.com/read/29777738/establishment-of-an-efficient-genetic-transformation-method-in-dunaliella-tertiolecta-mediated-by-agrobacterium-tumefaciens
#1
Claudia D Norzagaray-Valenzuela, Lourdes J Germán-Báez, Marco A Valdez-Flores, Sergio Hernández-Verdugo, Luke M Shelton, Angel Valdez-Ortiz
Microalgae are photosynthetic microorganisms widely used for the production of highly valued compounds, and recently they have been shown to be promising as a system for the heterologous expression of proteins. Several transformation methods have been successfully developed, from which the Agrobacterium tumefaciens-mediated method remains the most promising. However, microalgae transformation efficiency by A. tumefaciens is shown to vary depending on several transformation conditions. The present study aimed to establish an efficient genetic transformation system in the green microalgae Dunaliella tertiolecta using the A...
May 16, 2018: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/29772771/a-novel-hepadnavirus-identified-in-an-immunocompromised-domestic-cat-in-australia
#2
Mahdis Aghazadeh, Mang Shi, Vanessa R Barrs, Alicia J McLuckie, Scott A Lindsay, Barbara Jameson, Bronte Hampson, Edward C Holmes, Julia A Beatty
High-throughput transcriptome sequencing allows for the unbiased detection of viruses in host tissues. The application of this technique to immunosuppressed animals facilitates the detection of viruses that might otherwise be excluded or contained in immunocompetent individuals. To identify potential viral pathogens infecting domestic cats we performed high-throughput transcriptome sequencing of tissues from cats infected with feline immunodeficiency virus (FIV). A novel member of the Hepadnaviridae , tentatively named domestic cat hepadnavirus, was discovered in a lymphoma sample and its complete 3187 bp genome characterized...
May 17, 2018: Viruses
https://www.readbyqxmd.com/read/29764378/grim-filter-fast-seed-location-filtering-in-dna-read-mapping-using-processing-in-memory-technologies
#3
Jeremie S Kim, Damla Senol Cali, Hongyi Xin, Donghyuk Lee, Saugata Ghose, Mohammed Alser, Hasan Hassan, Oguz Ergin, Can Alkan, Onur Mutlu
BACKGROUND: Seed location filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. State-of-the-art read mappers 1) quickly generate possible mapping locations for seeds (i.e., smaller segments) within each read, 2) extract reference sequences at each of the mapping locations, and 3) check similarity between each read and its associated reference sequences with a computationally-expensive algorithm (i...
May 9, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29764360/prediction-of-enhancer-promoter-interactions-via-natural-language-processing
#4
Wanwen Zeng, Mengmeng Wu, Rui Jiang
BACKGROUND: Precise identification of three-dimensional genome organization, especially enhancer-promoter interactions (EPIs), is important to deciphering gene regulation, cell differentiation and disease mechanisms. Currently, it is a challenging task to distinguish true interactions from other nearby non-interacting ones since the power of traditional experimental methods is limited due to low resolution or low throughput. RESULTS: We propose a novel computational framework EP2vec to assay three-dimensional genomic interactions...
May 9, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29755684/large-deletion-at-the-cdc73-gene-locus-and-search-for-predictive-markers-of-the-presence-of-a-cdc73-genetic-lesion
#5
Lucia Anna Muscarella, Daniela Turchetti, Andrea Fontana, Filomena Baorda, Orazio Palumbo, Annamaria la Torre, Danilo de Martino, Renato Franco, Nunzia Simona Losito, Andrea Repaci, Uberto Pagotto, Luigia Cinque, Massimiliano Copetti, Maria Grazia Chiofalo, Luciano Pezzullo, Paolo Graziano, Alfredo Scillitani, Vito Guarnieri
The Hyperparathyroidism with Jaw-Tumours syndrome is caused by mutations of the CDC73 gene: it has been suggested that early onset of the disease and high Ca2+ levels may predict the presence of a CDC73 mutation. We searched for large deletions at the CDC73 locus in patients with: HPT-JT (nr 2), atypical adenoma (nr 7) or sporadic parathyroid carcinoma (nr 11) with a specific MLPA and qRT-PCR assays applied on DNA extracted from whole blood. A Medline search in database for all the papers reporting a CDC73 gene mutation, clinical/histological diagnosis, age at onset, Ca2+ , PTH levels for familial/sporadic cases was conducted with the aim to possibly identify biochemical/clinical markers predictive, in first diagnosis, of the presence of a CDC73 gene mutation...
April 17, 2018: Oncotarget
https://www.readbyqxmd.com/read/29755665/increased-level-and-fragmentation-of-plasma-circulating-cell-free-dna-are-diagnostic-and-prognostic-markers-for-renal-cell-carcinoma
#6
Yoshiyuki Yamamoto, Motohide Uemura, Kosuke Nakano, Yujiro Hayashi, Cong Wang, Yu Ishizuya, Toshiro Kinouchi, Takuji Hayashi, Kyosuke Matsuzaki, Kentaro Jingushi, Taigo Kato, Atsunari Kawashima, Takeshi Ujike, Akira Nagahara, Kazutoshi Fujita, Ryoichi Imamura, Norio Nonomura
Background: Reliable biomarkers for renal cell carcinoma (RCC) have yet to be found. Circulating cell-free DNA (cfDNA) is an emerging resource for the diagnosis and prognosis of various cancers. This study aims to identify novel blood biomarkers for RCC. Materials And Methods: Plasma cfDNA was extracted from RCC patients ( n = 92) and healthy controls ( n = 41). Levels of cfDNA were determined using quantitative real-time PCR of ACTB as the target gene, and cfDNA fragment size was measured using a microfluidics-based platform...
April 17, 2018: Oncotarget
https://www.readbyqxmd.com/read/29752989/a-novel-pathogenic-variant-in-the-marveld2-gene-causes-autosomal-recessive-non-syndromic-hearing-loss-in-an-iranian-family
#7
Afsaneh Taghipour-Sheshdeh, Fatemeh Nemati-Zargaran, Narges Zarepour, Parisa Tahmasebi, Nader Saki, Mohammad Amin Tabatabaiefar, Javad Mohammadi-Asl, Morteza Hashemzadeh-Chaleshtori
BACKGROUND AND AIMS: Hearing loss (HL) is the most common sensorineural disorder and one of the most common human defects. HL can be classified according to main criteria, including: the site (conductive, sensorineural and mixed), onset (pre-lingual and post-lingual), accompanying signs and symptoms (syndromic and non-syndromic), severity (mild, moderate, severe and profound) and mode of inheritance (Autosomal recessive, autosomal dominant, X-linked and mitochondrial). Autosomal recessive non-syndromic HL (ARNSHL) forms constitute a major share of the HL cases...
May 9, 2018: Genomics
https://www.readbyqxmd.com/read/29752127/implementation-of-next-generation-sequencing-technology-for-somatic-mutation-detection-in-routine-laboratory-practice
#8
Tindaro Giardina, Cleo Robinson, Fabienne Grieu-Iacopetta, Michael Millward, Barry Iacopetta, Dominic Spagnolo, Benhur Amanuel
The introduction of next generation sequencing (NGS) in the routine diagnostic setting is still in the development phase and has been limited by its complexity. Targeted NGS offers an attractive alternative to performing multiple single target assays and is very useful in meeting the increasing clinical demand for testing of multiple genetic aberrations in cancer specimens. To this end, we carried out a blinded validation study on 113 tumours in a diagnostic laboratory and compared mutation results from targeted NGS with those from Sanger sequencing, pyrosequencing, competitive allele specific TaqMan polymerase chain reaction (CAST PCR) and Cobas assays...
May 8, 2018: Pathology
https://www.readbyqxmd.com/read/29750748/genetic-analysis-of-13-iranian-families-with-leukocyte-adhesion-deficiency-type-1
#9
Shahram Teimourian, Martin De Boer, Dirk Roos, Anna Isaian, Mohammad Hassan Bemanian, Sharhzad Lashkary, Mohammad Nabavi, Saba Arshi, Alireza Nateghian, Shirin Sayyahfar, Faezeh Sazgara, Gholamreza Taheripak, Elham Alipour Fayez
BACKGROUND AND AIM: Leukocyte adhesion deficiency type 1 is a rare, autosomal recessive disorder that results from mutations in the ITGB2 gene. This gene encodes the CD18 subunit of β2 integrin leukocyte adhesion cell molecules. Leukocyte adhesion deficiency type 1 is characterized by recurrent bacterial infections, impaired wound healing, inadequate pus formation, and delayed separation of the umbilical cord. MATERIALS AND METHODS: Blood samples were taken from 13 patients after written consent had been obtained...
May 10, 2018: Journal of Pediatric Hematology/oncology
https://www.readbyqxmd.com/read/29749513/bioinformatics-analysis-of-key-differentially-expressed-genes-in-well-and-poorly-differentiated-endometrial-carcinoma
#10
Yuqin Zang, Mengting Dong, Kai Zhang, Wenyan Tian, Yingmei Wang, Fengxia Xue
Endometrial carcinoma (EC) is one of the most common gynecological malignancies. The malignant degree increases between grade (G)1 and G3, and EC of G3 usually presents a high recurrence rate and poor prognosis. Therefore, the present study aimed to examine the principal genes associated with the degree of differentiation in EC. The microarrays GSE17025, GSE24537 and GSE35784, representing data of Type I EC samples of G1 and G3, were downloaded from the Gene Expression Omnibus. The differentially expressed genes (DEGs) and differentially expressed micro (mi)RNAs (DEMs) were identified, followed by functional enrichment analyses and interaction network construction...
May 4, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29749129/plasma-cell-free-dna-as-a-predictive-marker-after-radiotherapy-for-hepatocellular-carcinoma
#11
Sangjoon Park, Eun Jung Lee, Chai Hong Rim, Jinsil Seong
PURPOSE: Cell-free DNA (cfDNA) is gaining attention as a novel biomarker for oncologic outcomes. We investigated the clinical significance of cfDNA in hepatocellular carcinoma (HCC) patients treated with radiotherapy (RT). MATERIALS AND METHODS: Fifty-five patients with HCC who received RT were recruited from two prospective study cohorts: one cohort of 34 patients who underwent conventionally fractionated RT and a second of 21 patients treated with stereotactic body radiation therapy...
June 2018: Yonsei Medical Journal
https://www.readbyqxmd.com/read/29745314/obesity-and-its-association-with-irisin-level-among-individuals-with-fndc5-irisin-gene-variants-rs16835198-and-rs726344
#12
Azza Abdu Allah, Eman Abd El Gayed, Sahar Hammoudah, Lama Mohamed El-Attar, Walid Shehab-Eldin
BACKGROUND: Irisin; a novel myokine/adipokine; encoded by FNDC5 gene have been suggested to play an important role in energy metabolism and obesity. However, the genetic variations at this locus and their effects on different metabolic parameters is still poorly understood. AIM: This study aimed to investigate the role of FNDC5/irisin gene polymorphisms (RS16835198 and RS726344) in obese individuals and their genotype phenotype correlation with circulating serum irisin level and other biochemical parameters like glucose, lipid metabolism and liver enzymes...
May 8, 2018: Protein and Peptide Letters
https://www.readbyqxmd.com/read/29742464/gastrointestinal-microbiota-and-mucosal-immune-gene-expression-in-neonatal-pigs-reared-in-a-cross-fostering-model
#13
Nidia Maradiaga, Brian Aldridge, Mohamed Zeineldin, James Lowe
Cross fostering is employed to equalize the number of piglet between litters ensuring colostrum intake for their survival and growth. However, little is known about the impact of cross fostering on the intestinal microbiota and mucosal immune gene expression of the neonatal pig. The objective of this study was to determine the influence of maternal microbial communities on the gastrointestinal (GI) microbiota and mucosal immune gene expression in young pigs reared in a cross-fostering model. Piglets were given high quality colostrum from birth dam or foster dam upon birth...
May 6, 2018: Microbial Pathogenesis
https://www.readbyqxmd.com/read/29740514/dna-metabarcoding-of-littoral-hard-bottom-communities-high-diversity-and-database-gaps-revealed-by-two-molecular-markers
#14
Owen S Wangensteen, Creu Palacín, Magdalena Guardiola, Xavier Turon
Biodiversity assessment of marine hard-bottom communities is hindered by the high diversity and size-ranges of the organisms present. We developed a DNA metabarcoding protocol for biodiversity characterization of structurally complex natural marine hard-bottom communities. We used two molecular markers: the "Leray fragment" of mitochondrial cytochrome c oxidase (COI), for which a novel primer set was developed, and the V7 region of the nuclear small subunit ribosomal RNA (18S). Eight different shallow marine littoral communities from two National Parks in Spain (one in the Atlantic Ocean and another in the Mediterranean Sea) were studied...
2018: PeerJ
https://www.readbyqxmd.com/read/29739076/quantitative-hepatitis-b-e-antigen-a-better-predictor-of-hepatitis-b-virus-dna-than-quantitative-hepatitis-b-surface-antigen
#15
Shuaibu A Hudu, Mohd T Niazlin, Syafinaz A Nordin, Mohammed I Saeed, Soek S Tan, Haniza Omar, Hamiza Shahar, Zamberi Sekawi
BACKGROUND: Hepatitis B surface antigen is usually secreted by infected hepatocytes in the form of subviral particles rather than infectious virions, while the hepatitis B e antigen originates from the core gene and is modified and secreted by hepatocytes into the circulation and functions as a marker of active viral replication. This study aimed to study the relationship between HBV DNA and quantitative hepatitis B surface and e antigen in Malaysian patients. METHODS: A total of 82 chronic hepatitis B patients were recruited for this study from the Hepatology Department of Selayang Hospital...
April 1, 2018: Clinical Laboratory
https://www.readbyqxmd.com/read/29733880/identification-of-a-novel-antimicrobial-peptide-from-the-sea-star-patiria-pectinifera
#16
Chan-Hee Kim, Hey-Jin Go, Hye Young Oh, Ji Been Park, Tae Kwan Lee, Jung-Kil Seo, Maurice R Elphick, Nam Gyu Park
Antimicrobial peptides (AMPs) are components of innate immunity found in many forms of life. However, there have been no reports of AMPs in sea star (Phylum Echinodermata). Here we report the isolation and characterization of a novel antimicrobial peptide from a coelomic epithelium extract of the sea star Patiria pectinifera. The isolated peptide comprises 38 amino acid residues, is cationic (pI 9.2), has four cysteine residues that form two disulfide bonds (C1-C3 and C2-C4) and is amidated at the C-terminus and is designated P...
May 4, 2018: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/29731767/whole-exome-sequencing-identified-a-novel-heterozygous-mutation-in-hmbs-gene-in-a-chinese-patient-with-acute-intermittent-porphyria-with-rare-type-of-mild-anemia
#17
Yongjiang Zheng, Jiehua Xu, Shengran Liang, Dongjun Lin, Santasree Banerjee
Acute intermittent porphyria (AIP) is a rare hereditary metabolic disease with an autosomal dominant mode of inheritance. Germline mutations of HMBS gene causes AIP. Mutation of HMBS gene results into the partial deficiency of the heme biosynthetic enzyme hydroxymethylbilane synthase. AIP is clinically manifested with abdominal pain, vomiting, and neurological complaints. Additionally, an extreme phenotypic heterogeneity has been reported in AIP patients with mutations in HMBS gene. Here, we investigated a Chinese patient with AIP...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29730989/identification-of-tick-borne-pathogen-diversity-by-metagenomic-analysis-in-haemaphysalis-longicornis-from-xinyang-china
#18
Lu Zhuang, Juan Du, Xiao-Ming Cui, Hao Li, Fang Tang, Pan-He Zhang, Jian-Gong Hu, Yi-Gang Tong, Zhi-Chun Feng, Wei Liu
BACKGROUND: A wide variety of pathogens could be maintained and transmitted by Haemaphysalis longicornis. The aim of this study is to systematically examine the variety of pathogens carried by Haemaphysalis longicornis, an importnatn vector, in tick-borne diseases epidemic area, and to estimate the risk of human infection imposed by tick bites. METHODS: Adult questing ticks were collected in Xinyang, central China. Genomic DNA and RNA were extracted from 144 H. longicornis ticks individually, and sequenced respectively as the templates for high-throughput sequencing...
May 7, 2018: Infectious Diseases of Poverty
https://www.readbyqxmd.com/read/29726742/isolation-and-characterization-of-novel-bacterial-strain-present-in-a-lab-scale-hybrid-uasb-reactor-treating-distillery-spent-wash
#19
R Thiyagu, P Sivarajan
Recalcitrant compounds degrading novel bacteria was isolated from lab scale hybrid UASB reactor treating distillery spent wash, enriched with biomass activity. The granules were subjected to SEM analysis to classify and isolate the bacterial strains. The strain was ubiquitous, mesophilic, gram-negative, motile, non-spore forming and cultivable optimally at 30°C at pH 7. Most potential isolates from the strains were subjected to 16S rRNA sequencing and branded as a member of diverse genera, gamma-proteobacteria, Stenotrophomonas sp...
May 4, 2018: Environmental Technology
https://www.readbyqxmd.com/read/29721947/whole-exome-sequencing-identifies-novel-variants-that-co-segregates-with-autosomal-recessive-retinal-degeneration-in-a-pakistani-pedigree
#20
Pooja Biswas, Muhammad Asif Naeem, Muhammad Hassaan Ali, Muhammad Zaman Assir, Shaheen N Khan, Sheikh Riazuddin, J Fielding Hejtmancik, S Amer Riazuddin, Radha Ayyagari
PURPOSE: To identify the molecular basis of inherited retinal degeneration (IRD) in a familial case of Pakistani origin using whole-exome sequencing. METHODS: A thorough ophthalmic examination was completed, and genomic DNA was extracted using standard protocols. Whole exome(s) were captured with Agilent V5 + UTRs probes and sequenced on Illumina HiSeq genome analyzer. The exomeSuite software was used to filter variants, and the candidate causal variants were prioritized, examining their allele frequency and PolyPhen2, SIFT, and MutationTaster predictions...
2018: Advances in Experimental Medicine and Biology
keyword
keyword
23207
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"