pcr sequencing and phylogenetic analysis

... sec, and one cycle of extension at 72 C for For second round nested -PCR, pmol of each primer, HE1 and HE3 (Genotech, Korea) and µl of first PCR product as template DNA were included in the PCR ... from Gyeonggi province (Table 1) The 396 bp PCR product o o o o o o o o o o o Cloning and sequence analysis PCR amplicons were purified using a GFX PCR DNA Purification Kit (Amersham, UK) according ... and adult ticks from cattle, horses, goats, dogs, cats, hedgehogs and wild rodents from Korean provinces [18] The ticks were identified and categorized with respect to developmental stages, and...

Ngày tải lên: 07/08/2014, 18:21

... Figure Phylogenetic analysis based on deduced amino acid sequence of complete B2L gene The phylogenetic tree was constructed by the neighbor-joining algorithm using MEGA 4.0, and bootstrap analysis ... most of the studies and drafted the manuscript JH and JY amplified the complete B2L gene HZ, ZL and YS provided consultation and preparation of the final report All authors read and approved the ... fragment obtained by PCR, stained with ethidium bromide Lane 1: DNA ladder markers 2000 bp; Lanes and 3: PCR products of complete B2L gene (1137 bp); Lane 4: negative control PCR using PBS as template...

Ngày tải lên: 12/08/2014, 04:20

... for cycle sequencing and subsequently run on an AB 3730 (Applied Biosystems, Foster City, CA) GenBank accession numbers are given in Table Phylogenetic and Sequence Analysis Phylogenetic analysis ... contributions MAA, ZA, LS and NS produced and analyzed the sequence data ES was involved in experimental design, performed the phylogenetic analysis and sequence analysis DES, KN, AH and SR were involved ... 23/Karachi-03 and 46/ Chakwal/03, were from the poultry flocks not vaccinated against AIV, while 35/Chakwal-01, 148/Chakwal-04 and 100/Karachi-04 were from vaccinated flocks Sequencing Sequencing and analysis...

Ngày tải lên: 12/08/2014, 04:20

... GenBank: Nucleotide sequence and position of the primers are listed in Table Table 1: Nucleotide sequences of the oligonucleotides used for PCR amplification and sequencing Primer set Primer ... http://www.virologyj.com/content/6/1/216 Table 2: Summary of sapovirus strains and representative strains for Lagovirus, Vesivirus, and Norovirus genera and NB-like viruses used in sequence analysis Strains Genus/genogroup GenBank ... TaKaRa RNA PCR kit (TaKaRa, Japan) in a 10 μL reaction volume The reaction condition was 40 at 42°C, then 15 sec at 86°C PCR and RACE amplifications of the full-length SaV genome PCR was carried...

Ngày tải lên: 12/08/2014, 04:21

... http://www.virologyj.com/content/6/1/47 Figure PPV phylogenetic analysis (A) and ORFV phylogenetic analysis (B) based on the B2L gene sequence PPV phylogenetic analysis (A) and ORFV phylogenetic analysis (B) based on the ... CB and EK participated in the planning of the project EK was the leader of the project ZL and CM collected the samples JA and RC, performed the PCR and phylogenetic analysis All authors read and ... for orthopoxviruses (OPV) using PCR and virus growth factor-specific primers [17] The PCR B2L product was purified using the QIAquick Gel Extraction Kit, (QIAGEN) and cloned into the pGEMTeasy...

Ngày tải lên: 12/08/2014, 04:21

... designed and coordinated the study and helped in draft correction SSH carried out the molecular studies, performed the RT -PCR assay and sequence analysis and drafted the manuscript MHB, ARO and NAZ ... Veterinaria Scandinavica 2010, 52:1 http://www.actavetscand.com/content/52/1/1 Page of Table List of feline coronavirus isolates and strains included in the sequence and phylogenetic analysis Table ... matrix and phylogenetic trees were constructed using Neighbor-Joining method (Bioedit) and TreeTop -Phylogenetic Tree Prediction (GeneBee-Molecular Biology Server Sharif et al Acta Veterinaria Scandinavica...

Ngày tải lên: 12/08/2014, 18:22

... one strand of DNA suitable for subsequent DNA sequencing Analysis, sequencing and in vitro expression of PCR products 99 Template DNA PCR with one biotinylated primer B Biotinylated PCR product ... ethidium bromidestained band with the marker bands A total of 30–90 ng of DNA is recommended for direct sequencing of PCR products Analysis, sequencing and in vitro expression of PCR products 109 Combine ... Nested PCR Nested PCR offers a quick and reliable way of verifying a PCR product It generally uses two primers that are internal to the product of the first PCR The PCR product from the first PCR...

Ngày tải lên: 25/10/2013, 22:20

... broad-range PCR and/ or reverse transcription PCR systems to search for bacterial DNA and RNA in synovial samples from patients with various forms of arthritis, including ReA [12,14,17] By cloning and sequencing ... DNA extraction and manipulation These included pipeting PCR components under a laminar flow of sterile air, using only sterile equipments, dedicated pre -PCR and post -PCR rooms, and dedicated sets ... procedures, and performed clinical and rheumatological data analyses AZ, CB and EC conducted assessment of Chlamydia trachomatis serology and DNA extraction BJ and JS participated in the design and coordination...

Ngày tải lên: 09/08/2014, 10:23

... lanes and versus and 4) Random hexamers (Rndm) were more efficient than B4R1, a primer specific to the 3'-UTR (lanes and versus and 6, or lanes and versus and 10) For amplicon 2, AMVRT and M-MLV ... in sequencing HCV genomes arise from three major sources: sequencing errors, enzymatic errors during RTPCR and primer bias during PCR Our sequencing depth averages over 4-fold and both strands ... source, and location of all PCR primers, sequencing primers, patient samples, RNAs, and PCR products The database is web-enabled to permit remote access, it is secured behind a fire-wall, and access...

Ngày tải lên: 19/06/2014, 08:20

... lanes and versus and 4) Random hexamers (Rndm) were more efficient than B4R1, a primer specific to the 3'-UTR (lanes and versus and 6, or lanes and versus and 10) For amplicon 2, AMVRT and M-MLV ... in sequencing HCV genomes arise from three major sources: sequencing errors, enzymatic errors during RTPCR and primer bias during PCR Our sequencing depth averages over 4-fold and both strands ... source, and location of all PCR primers, sequencing primers, patient samples, RNAs, and PCR products The database is web-enabled to permit remote access, it is secured behind a fire-wall, and access...

Ngày tải lên: 20/06/2014, 04:20

... AH and AS analyzed microbiological and sequencing data, and revised the manuscript All authors read and approved the final manuscript 15 16 17 Acknowledgements We thank Sebastien Chaussonneri and ... diagnosis, conducted sampling procedures, and performed clinical and rheumatological data analyses BJ and JS participated in the design and coordination of the study, and drafted the manuscript MR has ... broad-range PCR, cloning and sequencing the entire 16S rDNA and demonstrated the presence of a large number of bacterial DNA in the synovial tissue (ST) of patients with ReA, UA, and other arthropathies...

Ngày tải lên: 09/08/2014, 14:22

... density STRUCTURE [54,55] and principle components analyses of the Irish cohort both in comparison to similar cohorts from the UK, Netherlands, Denmark, Sweden and Finland [15], and in separate analyses ... Q32857) and QuantiT™ dsDNA HS Assay Kit (Invitrogen Q32851) Libraries were sequenced on Illumina GAII and latterly GAIIx Analyzer following the manufacturer’s standard clustering and sequencing ... Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, et al: Initial sequencing and analysis of the human genome Nature 2001, 409:860-921 Genome.gov | ENCODE and...

Ngày tải lên: 09/08/2014, 22:23

... [33,34], and identification of the convergent and divergent pathways between salinity and other abiotic stress responses and the nodes of signalling convergence may greatly enhance the understanding ... X-ray film at -70°C overnight, and developed Sequencing and analysis of the cloned ESTs The plasmid inserts of only the forward SSH cDNA library were considered for sequencing The plasmids purified ... functional catalogue and the genes were clustered under different functional categories Expression validation by Northern and real time PCR (qRT -PCR) Slot blot Northern analysis was done for...

Ngày tải lên: 12/08/2014, 03:20

... brachyantha and/ or O granulata, L perrieri and P parviflora) Putative functions were verified by BLASTX alignment against Viridiplantae proteins Figures 2, and and Additional files and show phylogenetic ... performed the phylogenetic, comparative genomic and statistical analysis, and drafted the manuscript ML participated in the design of the study and acquisition of sequence data RC conceived the analysis, ... in the MONOCULM1 region were also low [25] dS and dN ratios between O minuta copies and (BB) were slightly lower than between copies and and copies and We postulate that if there was divergence...

Ngày tải lên: 12/08/2014, 03:21

... Genotype A and D strains of HBV On the other hand, despite being costly or technically demanding, LiPA and direct DNA sequencing yielded accurate identification of all genotype A and genotype D and ... SA and WAN designed the study and FH collected the specimens MMA carried out the DNA Extraction, INNO-LiPA genotyping assay, Direct DNA Sequencing, PCR- RFLP studies, sequence alignments and analysis ... procedure [12] and sequenced by using quick start cycle DNA sequencing kit (Beckman-Coulter) The DNA sequencing was performed as described in detail previously [13,14] The LiPA identified 63 and four...

Ngày tải lên: 12/08/2014, 04:20

... and phylogenetic studies and drafted the manuscript ND and ALW participated in the design of the study, analyses and interpretation of data and revision of the manuscript All authors read and ... previously analysed at these loci [14] The analysis involved MUSCLE [15] amino acid and nucleotide alignments and construction of UPGMA and Neighbour-Joining [16] phylogenetic trees based on these alignments ... albatross and falcon in both N-J and UPGMA trees PEPV was found to have 99% nucleotide identity with both TKPV isolates in subclade A2, compared to 95% identity with ABPV and FLPV and 94% with...

Ngày tải lên: 12/08/2014, 04:21

... albicans and fission yeast Schizosaccharomyces pombe, plants such as Arabidopsis thaliana, and metazoans such as Drosophila melanogaster and Homo sapiens, are longer and more complex and exhibit ... with 46%, 87% and 33% similarity and hsChl4R shares conserved blocks of 20 and 50 amino acids with 45% and 40% similarity (Figure 5) The potential human orthologs of S pombe Fta1 and Sim4 were ... Microspora Sp Apicomplexa 0.1 Phylogenetic analysis of kinetochore protein conserved domains Figure Phylogenetic analysis of kinetochore protein conserved domains Radial phylogenetic trees were assembled...

Ngày tải lên: 14/08/2014, 16:21

... 28.95 Volume 8, Issue 2, Article R19 comment Sample Standard1 Standard1 Standard2 Standard2 Standard3 Standard3 Standard4 Standard4 Standard5 Standard5 Genome Biology 2007, R19.4 Genome Biology 2007, ... related variation (PCR block, lamp, filters, detectors, and so on), data analysis settings (baseline correction and threshold), reagents (polymerase, fluorophores, and so on) and optical properties ... transformed ratio and the standard deviation Virc for all runs l and a given IRC combination (m, m') and a given gene j Vsample and Vrun are calculated similarly from Asample and Arun, respectively:...

Ngày tải lên: 14/08/2014, 17:22

... cases, superposition files and influence lines 3.64 Version 8.38.03 • • • • Use of combination codes “SupOrX” and “SupAndX” for superposition files corrected New command “PLSCFAC” in plot file ... Önorm Standard 4700, British Standard 5400 and Honk Kong Standard 5400 3.81 Version 8.34.02 • Minor changes 3.82 Version 8.34.01 • • • • • • Tendon results (primary and secondary forces) can be ... • • • • Width and height of composite section for wind load corrected Extended printout for shear check (AAHSTO) Minor changes and error corrections in import/export with non-standard units LIST:GEN...

Ngày tải lên: 06/09/2012, 15:18

... Disclaimer and Copyright Disclaimer Much time and effort have gone into the development and documentation of RM2000 and GP2000 The programs have been thoroughly tested and used The user accepts and ... Supposition: Main Girder Axis and segment, Cross Section for the girder plus the cross section for the piers plus the Segment numbering and assignment and Part numbering and assignment for the main ... –10 and top is at height in steps of metres Select the ‘Edit’ icon and assign the pier cross section to the segment points Choose ‘Parts’ and then the ‘Edit’ icon Enter the material type, and...

Ngày tải lên: 06/09/2012, 15:55