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https://www.readbyqxmd.com/read/28102322/size-selective-separation-and-overall-amplification-of-cell-free-fetal-dna-fragments-using-pcr-based-enrichment
#1
Qiwei Yang, Zhenwu Du, Yang Song, Sujie Gao, Shan Yu, He Zhu, Ming Ren, Guizhen Zhang
This study aimed to establish a method for the selective amplification of cell-free fetal DNA (cffDNA) in maternal plasma and preserve the integrity of DNA fragments during amplification, thereby providing a sufficient amount of cffDNA to meet the requirement of routine non-invasive prenatal testing. We amplified DNA molecules in a one-reaction system without considering their particular sequences and lengths (overall amplification) by using PCR-based enrichment. We then modified PCR conditions to verify the effect of denaturation temperature on DNA amplification on various lengths of DNA (selective overall amplification)...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28101463/development-of-a-novel-human-single-chain-antibody-against-egfrviii-antigen-by-phage-display-technology
#2
Leila Rahbarnia, Safar Farajnia, Hossein Babaei, Jafar Majidi, Bahman Akbari, Shiva Ahdi Khosroshahi
Purpose: EGFRvIII as the most common mutant variant of the epidermal growth factor receptor is resulting from deletion of exons 2-7 in the coding sequence and junction of exons 1 and 8 through a novel glycine residue. EGFRvIII is highly expressed in glioblastoma, carcinoma of the breast, ovary, and lung but not in normal cells. The aim of the present study was identification of a novel single chain antibody against EGFRvIII as a promising target for cancer therapy. Methods: In this study, a synthetic peptide corresponding to EGFRvIII protein was used for screening a naive human scFv phage library...
December 2016: Advanced Pharmaceutical Bulletin
https://www.readbyqxmd.com/read/28100584/umi-tools-modelling-sequencing-errors-in-unique-molecular-identifiers-to-improve-quantification-accuracy
#3
Tom Sean Smith, Andreas Heger, Ian Sudbery
Unique Molecular Identifiers (UMIs) are random oligonucleotide barcodes that are increasingly used in high-throughput sequencing experiments. Through a UMI, identical copies arising from distinct molecules can be distinguished from those arising through PCR-amplification of the same molecule. However, bioinformatic methods to leverage the information from UMIs have yet to be formalised. In particular, sequencing errors in the UMI sequence are often ignored, or else resolved in an ad-hoc manner. We show that errors in the UMI sequence are common and introduce network based methods to account for these errors when identifying PCR duplicates...
January 18, 2017: Genome Research
https://www.readbyqxmd.com/read/28097440/prevalence-of-nras-pten-and-akt1-gene-mutations-in-the-central-nervous-system-metastases-of-non-small-cell-lung-cancer
#4
Marcin Nicoś, Paweł Krawczyk, Bożena Jarosz, Marek Sawicki, Tomasz Trojanowski, Janusz Milanowski
Somatic mutations in NRAS, PTEN and AKT1 genes are rarely (~1%) reported in primary NSCLC, but their role in carcinogenesis have been proven. Therefore, we assessed the frequency of them in 145 FFPE tissue samples from CNS metastases of NSCLC using the real-time PCR technique. We identified four (two NRAS and single AKT1 and PTEN) mutations in CNS metastases of NSCLC. All mutations were observed in current male smokers (4% out of the male group; 4/100 and 4.25% out of smokers; 4/94). Three mutations have been detected in patients with SqCC (10...
January 17, 2017: Brain Tumor Pathology
https://www.readbyqxmd.com/read/28097405/role-of-exopolysaccharide-in-salt-stress-resistance-and-cell-motility-of-mesorhizobium-alhagi-ccnwxj12-2-t
#5
Xiaodong Liu, Yantao Luo, Zhefei Li, Jiamei Wang, Gehong Wei
Mesorhizobium alhagi, a legume-symbiont soil bacterium that forms nodules with the desert plant Alhagi sparsifolia, can produce large amounts of exopolysaccharide (EPS) using mannitol as carbon source. However, the role of EPS in M. alhagi CCNWXJ12-2(T), an EPS-producing rhizobium with high salt resistance, remains uncharacterized. Here, we studied the role of EPS in M. alhagi CCNWXJ12-2(T) using EPS-deficient mutants constructed by transposon mutagenesis. The insertion sites of six EPS-deficient mutants were analyzed using single primer PCR, and two putative gene clusters were found to be involved in EPS synthesis...
January 17, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28093679/effect-of-single-nucleotide-polymorphisms-of-toll-like-receptor-4-tlr-4-on-reproductive-performance-and-immune-function-in-dairy-cows
#6
Takashi Shimizu, Yurie Kawasaki, Yuka Aoki, Fumie Magata, Chiho Kawashima, Akio Miyamoto
In dairy cows, inflammatory diseases caused by infection with pathogenic bacteria post calving affect ovarian functions. This study examined the relationship between single-nucleotide polymorphisms (SNPs) of Toll-like receptor 4 (TLR4), reproductive performances [the number of artificial insemination (AI) application and days open], and immune cell functions (apoptosis and migration). Two hundred Holstein cows from the Obihiro University farm were included. The SNPs of TLR4 were genotyped by PCR-restriction fragment length polymorphism (PCR-RFLP) method...
January 16, 2017: Biochemical Genetics
https://www.readbyqxmd.com/read/28092604/replication-kinetics-of-neuropathogenic-and-non-neuropathogenic-equine-herpesvirus-type-1-ehv-1-strains-in-primary-murine-neurons-and-ed-cell-line
#7
J Cymerys, A Słońska, J Brzezicka, A Tucholska, A Chmielewska, J Rola, P Malik, M W Bańbura
Equine herpesvirus type 1 (EHV-1) causes respiratory infections, abortion and neurological disorders in horses. Molecular epidemiology studies have demonstrated that a single-point mutation in DNA polymerase gene, resulting in an amino acid variation (N752/D752), is significantly associated with the neuropathogenic potential of EHV-1 strains. The aim of the study was to elucidate if there are any differences between neuropathogenic (EHV-1 26) and non-neuropathogenic (Jan-E and Rac-H) EHV-1 strains in their ability to infect neuronal cells...
December 1, 2016: Polish Journal of Veterinary Sciences
https://www.readbyqxmd.com/read/28090143/acute-exercise-regulates-adipogenic-gene-expression-in-white-adipose-tissue
#8
Y Shen, H Zhou, W Jin, H J Lee
White adipose tissue expansion is associated with both hypertrophy and hyperplasia of adipocytes. Exercise training results in adipocyte hypotrophy by activating lipolysis, but it is poorly understood whether exercise regulates adipogenesis by altering adipogenic gene expression. The purpose of this study was to evaluate the effect of a single bout of swimming exercise on adipogenic gene expression in white adipose tissue (WAT). Male C57BL/6J mice were divided into two groups: a sedentary control group and a 120-minute swimming exercise group...
December 2016: Biology of Sport
https://www.readbyqxmd.com/read/28089546/expression-of-interleukin-6-by-a-recombinant-rabies-virus-enhances-its-immunogenicity-as-a-potential-vaccine
#9
Jun Luo, Boyue Zhang, Yuting Wu, Qin Tian, Jing Zhao, Ziyu Lyu, Qiong Zhang, Mingzhu Mei, Yongwen Luo, Xiaofeng Guo
Several studies have confirmed that interleukin-6 (IL6) mediates multiple biological effects that enhance immune responses when used as an adjuvant. In the present study, recombinant rabies virus (RABV) expressing canine IL6 (rHEP-CaIL6) was rescued and its pathogenicity and immunogenicity were investigated in mice. We demonstrated that mice received a single intramuscular immunization with rHEP-CaIL6 showed an earlier increase and higher maximum titres of virus-neutralizing antibody (VNA) as well as anti-RABV antibodies compared with mice immunized with the parent strain...
January 12, 2017: Vaccine
https://www.readbyqxmd.com/read/28088972/-critical-roles-of-matrix-metalloproteinases-secreted-by-leukemic-cells-in-the-pathogenesis-of-central-nervous-system-leukemia
#10
S R Feng, Z X Chen, J N Cen, H J Shen, Y Y Wang, L Yao
Objective: To observe the effects of matrix metalloproteinases (MMP)-2 and MMP-9 secreted by leukemic cells on tight junction proteins ZO-1, claudin-5 and occluding and the permeability of the blood-brain barrier (BBB) and explore the mechanisms of MMP-2 and MMP-9 in leukemic cell infiltration of the central nervous system (CNS). Methods: The mRNA expressions of MMP-2 and MMP-9 in leukemic cell lines SHI-1, HL-60 and U937 were detected by quantitative RT-PCR. The MMP inhibitor GM6001 was used to inhibit the secretion of MMP-2 and MMP-9...
December 14, 2016: Zhonghua Xue Ye Xue za Zhi, Zhonghua Xueyexue Zazhi
https://www.readbyqxmd.com/read/28088362/molecular-characterization-of-a-novel-orthomyxovirus-from-rainbow-and-steelhead-trout-oncorhynchus-mykiss
#11
William N Batts, Scott E LaPatra, Ryan Katona, Eric Leis, Terry Fei Fan Ng, Marine S O Brieuc, Rachel B Breyta, Maureen K Purcell, Carla M Conway, Thomas B Waltzek, Eric Delwart, James R Winton
A novel virus, rainbow trout orthomyxovirus (RbtOV), was isolated in 1997 and again in 2000 from commercially-reared rainbow trout (Oncorhynchus mykiss) in Idaho, USA. The virus grew optimally in the CHSE-214 cell line at 15°C producing a diffuse cytopathic effect; however, juvenile rainbow trout exposed to cell culture-grown virus showed no mortality or gross pathology. Electron microscopy of preparations from infected cell cultures revealed the presence of typical orthomyxovirus particles. The complete genome of RbtOV is comprised of eight linear segments of single-stranded, negative-sense RNA having highly conserved 5' and 3'-terminal nucleotide sequences...
January 11, 2017: Virus Research
https://www.readbyqxmd.com/read/28086908/hiv-integration-sites-in-latently-infected-cell-lines-evidence-of-ongoing-replication
#12
Jori Symons, Abha Chopra, Eva Malantinkova, Ward De Spiegelaere, Shay Leary, Don Cooper, Chike O Abana, Ajantha Rhodes, Simin D Rezaei, Linos Vandekerckhove, Simon Mallal, Sharon R Lewin, Paul U Cameron
BACKGROUND: Assessing the location and frequency of HIV integration sites in latently infected cells can potentially inform our understanding of how HIV persists during combination antiretroviral therapy. We developed a novel high throughput sequencing method to evaluate HIV integration sites in latently infected cell lines to determine whether there was virus replication or clonal expansion in these cell lines observed as multiple integration events at the same position. RESULTS: We modified a previously reported method using random DNA shearing and PCR to allow for high throughput robotic processing to identify the site and frequency of HIV integration in latently infected cell lines...
January 13, 2017: Retrovirology
https://www.readbyqxmd.com/read/28086804/comparative-analysis-of-the-root-transcriptomes-of-cultivated-sweetpotato-ipomoea-batatas-l-lam-and-its-wild-ancestor-ipomoea-trifida-kunth-g-don
#13
Sathish K Ponniah, Jyothi Thimmapuram, Ketaki Bhide, Venu Kal Kalavacharla, Muthusamy Manoharan
BACKGROUND: The complex process of formation of storage roots (SRs) from adventitious roots affects sweetpotato yield. Identifying the genes that are uniquely expressed in the SR forming cultivated species, Ipomoea batatas (Ib), and its immediate ancestral species, Ipomoea trifida (It), which does not form SRs, may provide insights into the molecular mechanisms underlying SR formation in sweetpotato. RESULTS: Illumina paired-end sequencing generated ~208 and ~200 million reads for Ib and It, respectively...
January 13, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28077243/effective-use-of-oral-ribavirin-for-respiratory-syncytial-viral-infections-in-allogeneic-haematopoietic-stem-cell-transplant-recipients
#14
C M Gorcea, E Tholouli, A Turner, M Saif, E Davies, E Battersby, F L Dignan
BACKGROUND: Respiratory syncytial virus (RSV) is a frequent cause of respiratory viral infections, increasing the morbidity and mortality in allogeneic haematopoietic stem cell transplantation (HSCT) recipients. Little is known about the best management strategy in this immunocompromised group and there are very few data on oral ribavirin treatment. AIM: To evaluate the effectiveness of oral ribavirin in allogeneic HSCT patients with RSV infection. METHODS: Twenty-three RSV cases treated with oral ribavirin were analysed retrospectively...
November 25, 2016: Journal of Hospital Infection
https://www.readbyqxmd.com/read/28073899/paper-based-microrna-expression-profiling-from-plasma-and-circulating-tumor-cells
#15
Sai Mun Leong, Karen Mei-Ling Tan, Hui Wen Chua, Mo-Chao Huang, Wai Chye Cheong, Mo-Huang Li, Steven Tucker, Evelyn Siew-Chuan Koay
BACKGROUND: Molecular characterization of circulating tumor cells (CTCs) holds great promise for monitoring metastatic progression and characterizing metastatic disease. However, leukocyte and red blood cell contamination of routinely isolated CTCs makes CTC-specific molecular characterization extremely challenging. METHODS: Here we report the use of a paper-based medium for efficient extraction of microRNAs (miRNAs) from limited amounts of biological samples such as rare CTCs harvested from cancer patient blood...
January 10, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28073467/quantitative-pcr-assay-for-detection-and-enumeration-of-ciguatera-causing-dinoflagellate-gambierdiscus-spp-gonyaulacales-in-coastal-areas-of-japan
#16
Tomohiro Nishimura, Naohito Hariganeya, Wittaya Tawong, Hiroshi Sakanari, Haruo Yamaguchi, Masao Adachi
In Japan, ciguatera fish poisoning (CFP) has been increasingly reported not only in subtropical areas but also in temperate areas in recent years, causing a serious threat to human health. Ciguatera fish poisoning is caused by the consumption of fish that have accumulated toxins produced by an epiphytic/benthic dinoflagellate, genus Gambierdiscus. Previous studies revealed the existence of five Gambierdiscus species/phylotypes in Japan: Gambierdiscus australes, Gambierdiscus scabrosus, Gambierdiscus sp. type 2, Gambierdiscus sp...
February 2016: Harmful Algae
https://www.readbyqxmd.com/read/28069692/genes-involved-in-development-and-differentiation-are-commonly-methylated-in-cancers-derived-from-multiple-organs-a-single-institutional-methylome-analysis-using-1007-tissue-specimens
#17
Kentaro Ohara, Eri Arai, Yoriko Takahashi, Nanako Ito, Ayako Shibuya, Koji Tsuta, Ryoji Kushima, Hitoshi Tsuda, Hidenori Ojima, Hiroyuki Fujimoto, Shun-Ichi Watanabe, Hitoshi Katai, Takayuki Kinoshita, Tatsuhiro Shibata, Takashi Kohno, Yae Kanai
The aim of this study was to clarify the significance of DNA methylation alterations shared by cancers derived from multiple organs. We analyzed single-institutional methylome data by single-CpG-resolution Infinium assay for 1,007 samples of non-cancerous tissue (N) and corresponding cancerous tissue (T) obtained from lung, stomach, kidney, breast and liver. Principal component analysis revealed that N samples of each organ showed distinct DNA methylation profiles, DNA methylation profiles of N samples of each organ being inherited by the corresponding T samples and DNA methylation profiles of T samples being more similar to those of N samples in the same organ than those of T samples in other organs...
January 9, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28068587/quantitative-assessment-of-viable-cells-of-lactobacillus-plantarum-strains-in-single-dual-and-multi-strain-biofilms
#18
Mónica D Fernández Ramírez, Ioannis Kostopoulos, Eddy J Smid, Masja N Nierop Groot, Tjakko Abee
Biofilms of Lactobacillus plantarum are a potential source for contamination and recontamination of food products. Although biofilms have been mostly studied using single species or even single strains, it is conceivable that in a range of environmental settings including food processing areas, biofilms are composed of multiple species with each species represented by multiple strains. In this study six spoilage related L. plantarum strains FBR1-FBR6 and the model strain L. plantarum WCFS1 were characterised in single, dual and multiple strain competition models...
December 29, 2016: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28068321/analysis-of-dna-methylation-in-single-circulating-tumor-cells
#19
C F Pixberg, K Raba, F Müller, B Behrens, E Honisch, D Niederacher, H Neubauer, T Fehm, W Goering, W A Schulz, P Flohr, G Boysen, M Lambros, J S De Bono, W T Knoefel, C Sproll, N H Stoecklein, R P L Neves
Direct analysis of circulating tumor cells (CTCs) can inform on molecular mechanisms underlying systemic spread. Here we investigated promoter methylation of three genes regulating epithelial-to-mesenchymal transition (EMT), a key mechanism enabling epithelial tumor cells to disseminate and metastasize. For this, we developed a single-cell protocol based on agarose-embedded bisulfite treatment, which allows investigating DNA methylation of multiple loci via a multiplex PCR (multiplexed-scAEBS). We established our assay for the simultaneous analysis of three EMT-associated genes miR-200c/141, miR-200b/a/429 and CDH1 in single cells...
January 9, 2017: Oncogene
https://www.readbyqxmd.com/read/28062830/dissecting-inherent-intratumor-heterogeneity-in-patient-derived-glioblastoma-culture-models
#20
Jian Teng, Cintia Carla da Hora, Rami S Kantar, Ichiro Nakano, Hiroaki Wakimoto, Tracy T Batchelor, E Antonio Chiocca, Christian E Badr, Bakhos A Tannous
BACKGROUND: Molecular profile of glioblastoma multiforme (GBM) revealed 4 subtypes, 2 of which, proneural and mesenchymal, have been predominantly observed, with the latter displaying a more aggressive phenotype and increased therapeutic resistance. Single-cell RNA sequencing revealed that multiple subtypes actually reside within the same tumor, suggesting cellular heterogeneity in GBM. Further, plasticity between these 2 subtypes is observed during tumor recurrence and in response to radiation therapy...
January 6, 2017: Neuro-oncology
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