Vector NTI, a balanced all-in-one sequence analysis suite

Lu, Guoping

doi:10.1093/bib/5.4.378

Cited by 331 publications

(191 citation statements)

References 0 publications

Supporting

Mentioning

190

Contrasting

Unclassified

Order By: Relevance

“…The sequences obtained in the present study were compared with the previously published sequences deposited in GenBank using the BLAST program from the National Center for Biotechnology Information website. MseI RFLP analysis of the 5S-23S rRNA intergenic spacer was performed on the basis of the DNA sequences obtained using software Vector NTI 9.0 (Lu & Moriyama, 2004).The accession numbers of the 5S-23S rRNA intergenic spacer sequences obtained in this study are EU160458 and EU160459. (Balmelli & Piffaretti, 1995;van Dam et al, 1993).…”

mentioning

confidence: 99%

Presence of pathogenic Borrelia burgdorferi sensu lato in ticks and rodents in Zhejiang, south-east China

Chu

Jiang

Liu

et al. 2008

Journal of Medical Microbiology

View full text Add to dashboard Cite

A molecular epidemiological survey was conducted to investigate the presence of pathogenic Borrelia burgdorferi sensu lato (s.l.) species in the forest areas of Zhejiang province, south-east China. A total of 182 ticks of 6 species and 200 rodents of 8 species were collected and individually examined for the presence of B. burgdorferi s.l. DNA by nested PCR targeting the 5S-23S rRNA intergenic spacer. Forty-one ticks of four species, Haemaphysalis concinna, Haemaphysalis longicornis, Rhipicephalus microplus and Haemaphysalis warburconi, were infected with B. burgdorferi s.l., with an overall infection rate of 23 %. Sixteen rodents of four species, Nivivener confucianus, Nivivener coxingi, Apodemus sylvaticus and Rattus losea, were positive for B. burgdorferi s.l., with an overall prevalence of 8 %. MseI RFLP analysis and sequence analysis of the positive PCR products showed that Borrelia spirochaetes in specimens consisted of Borrelia garinii, Borrelia afzelii and Borrelia valaisiana-related group. Forty (98 %) of the B. burgdorferi s.l.-positive ticks were infected with B. garinii and one (2 %) was infected with B. afzelii. Twelve (75 %) of the positive rodents were infected with B. garinii and four (25 %) were infected with the Borrelia spirochaete belonging to B. valaisiana-related group. INTRODUCTIONLyme disease (LD) is a multi-organ infection caused by certain spirochaetes in the Borrelia burgdorferi sensu lato (s.l.) species complex (Steere et al., 1983;Hengge et al., 2003). The complex is considered to comprise at least 12 different genospecies to date (Masuzawa et al., 2001;Richter et al., 2006;Wang et al., 1999). Among them, Borrelia burgdorferi sensu stricto (s.s.), Borrelia garinii and Borrelia afzelii are the major aetological agents of human LD (Baranton et al., 1992;Wang et al., 1999). In addition, Borrelia bissettii (Picken et al., 1996), Borrelia valaisiana (Rijpkema et al., 1997), Borrelia lusitaniae (Collares-Pereira et al., 2004) and Borrelia spielmanii (Foldvari et al., 2005) are considered to be potentially pathogenic to humans. B. burgdorferi s.l. is mainly maintained in natural foci through the transmission cycles of competent tick vectors and vertebrate reservoirs Burgdorfer et al., 1991;Hengge et al., 2003). Humans accidentally enter this cycle and represent dead-end hosts for the agent (Hengge et al., 2003).LD was first documented in north-east China in 1986 (Ai et al., 1987). One typical case of human lyme borreliosis was reported in Zhejiang province of south-east China (Cheng et al., 1992), where a good many of the popular tourist destinations and the well-known tea gardens are located. Antibody to B. burgdorferi s.l. was also detected in serum samples from some residents living in the forest areas of this province (Zhang et al., 1997(Zhang et al., , 2001). However, only Borrelia sincica and B. valaisiana-related strains, which are not known to be pathogenic to humans, have been isolated in this area to date (Masuzawa et al., 2001). Furthermore, no information is available concerni...

show abstract

mentioning

confidence: 99%

Presence of pathogenic Borrelia burgdorferi sensu lato in ticks and rodents in Zhejiang, south-east China

Chu

Jiang

Liu

et al. 2008

Journal of Medical Microbiology

View full text Add to dashboard Cite

show abstract

“…After transformation into Escherichia coli, plasmid purifications from the overnight-grown colonies were performed and the cloned cDNA was sequenced by dideoxy-mediated chain termination sequencing at Takara Biotechnology, Inc. Sequence multiple alignments and comparisons to other GenBank entries were performed using CLUSTAL W software (http://genome.cs.mtu.edu/map.html). The secondary structure prediction was performed using NTI Vector 7.1 (Lu and Moriyama, 2004).…”

Section: Methodsmentioning

confidence: 99%

Molecular cloning, tissue distribution and ontogenetic expression of sodium proton exchanger isoform 2 (NHE-2) mRNA in the small intestine of pigs

Feng

AiMin

Zou

et al. 2009

Animal

View full text Add to dashboard Cite

Molecular cloning, tissue distribution and ontogenetic regulation of sodium/proton exchanger isoform 2 (NHE-2) mRNA expression were evaluated in the pig small intestine during postnatal development. The 2872-bp porcine full cDNA sequence of the NHE-2 (EF672046) cloned in this study showed 80% and 70% homology with known human and mouse gene sequence, respectively. Hydrophobic prediction suggests 13 putative membrane-spanning domains within porcine NHE-2. The porcine NHE-2 mRNA was detected in the brain, liver, kidney, heart, lung, small intestine and muscle. The small intestine had the highest NHE-2 mRNA abundance and the brain, lung and liver had the lowest NHE-2 mRNA abundance ( P , 0.05). Along the longitudinal axis, the duodenum had the highest NHE-2 mRNA abundance and the ileum and colon had the lowest NHE-2 mRNA abundance ( P , 0.05). The NHE-2 mRNA level was increased from day 1 to day 26 in the duodenum ( P , 0.05) and dropped dramatically on day 30 ( P , 0.05). There is no difference between day 1 and day 7 ( P . 0.05). After day 30, the NHE-2 mRNA level remained the same except on day 90 ( P . 0.05). The mRNA expression of NHE-2 was not only differentially regulated by age but also differentially distributed along the small intestine of piglets at early stages and growing stages of life, which may contribute to changes in NHE activity.

show abstract

“…Contiguous sequences were assembled and edited using VectorNTI advance 10 ( Lu and Moriyama, 2004), and the resultant sequence identities were checked using the Basic Local Alignment Search Tool (BLAST) available from GenBank (Benson et al, 2005). The eight most complete new sequences generated in this work (GenBank accession numbers KP294376 -KP294383) and a previously published sequence of L. cephali from Blasco-Costa et al (2012) (GenBank accession number JN996865) were aligned for comparison using MUSCLE (Edgar, 2004) implemented in MEGA v5.1 (Tamura et al, 2011).…”

Section: Molecular Datamentioning

confidence: 99%

Phenotypic plasticity in haptoral structures of Ligophorus cephali (Monogenea: Dactylogyridae) on the flathead mullet (Mugil cephalus): a geometric morphometric approach

Rodríguez-González

Míguez-Lozano

Llopis‐Belenguer

et al. 2015

International Journal for Parasitology

View full text Add to dashboard Cite

Evaluating phenotypic plasticity in attachment organs of parasites can provide information on the capacity to colonize new hosts and illuminate evolutionary processes driving host specificity.We analysed the variability in shape and size of the dorsal and ventral anchors of Ligophorus cephali from Mugil cephalus by means of geometric morphometrics and multivariate statistics. We also assessed the morphological integration between anchors and between the roots and points in order to gain insight into their functional morphology. Dorsal and ventral anchors showed a similar gradient of overall shape variation, but the amount of localized changes was much higher in the former. Statistical models describing variations in shape and size revealed clear differences between anchors. The dorsal anchor/bar complex seems more mobile than the ventral one in Ligophorus, and these differences may reflect different functional roles in attachment to the gills. The lower residual variation associated with the ventral anchor models suggests a tighter control of their shape and size, perhaps because these anchors seem to be responsible for firmer attachment and their size and shape would allow more effective responses to characteristics of the microenvironment within the individual host. Despite these putative functional differences, the high level of morphological integration indicates a concerted action between anchors. In addition, we found a slight, although significant, morphological integration between roots and points in both anchors, which suggests that a large fraction of the observed phenotypic variation does not compromise the functional role of anchors as levers. Given the low level of genetic variation in our sample, it is likely that much of the morphological variation reflects host-driven plastic responses. This supports the hypothesis of monogenean specificity through host-switching and rapid speciation. The present study demonstrates the potential of geometric morphometrics to provide new and previously unexplored insights into the functional morphology of attachment and evolutionary processes of host-parasite coevolution.4

show abstract

Vector NTI, a balanced all-in-one sequence analysis suite

Cited by 331 publications

References 0 publications

Presence of pathogenic Borrelia burgdorferi sensu lato in ticks and rodents in Zhejiang, south-east China

Presence of pathogenic Borrelia burgdorferi sensu lato in ticks and rodents in Zhejiang, south-east China

Molecular cloning, tissue distribution and ontogenetic expression of sodium proton exchanger isoform 2 (NHE-2) mRNA in the small intestine of pigs

Phenotypic plasticity in haptoral structures of Ligophorus cephali (Monogenea: Dactylogyridae) on the flathead mullet (Mugil cephalus): a geometric morphometric approach

Contact Info

Product

Resources

About