Molecular characterization of human enteroviruses in clinical samples: Comparison between VP2, VP1, and RNA polymerase regions using RT nested PCR assays and direct sequencing of products

2001 ◽  
Vol 65 (1) ◽  
pp. 138-148 ◽  
Author(s):  
I. Casas ◽  
G.F. Palacios ◽  
G. Trallero ◽  
D. Cisterna ◽  
M.C. Freire ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Molecular Characterization ◽  
Nested Pcr ◽  
Direct Sequencing ◽  
Clinical Samples ◽  
Pcr Assays ◽  
Nested Pcr Assays

scholarly journals Detection of Bovine and Porcine Adenoviruses for Tracing the Source of Fecal Contamination

2004 ◽  
Vol 70 (3) ◽  
pp. 1448-1454 ◽  
Author(s):  
Carlos Maluquer de Motes ◽  
Pilar Clemente-Casares ◽  
Ayalkibet Hundesa ◽  
Margarita Mart�n ◽  
Rosina Girones
Keyword(s):  
Nested Pcr ◽  
Fecal Contamination ◽  
Human Adenovirus ◽  
The Other ◽  
Animal Origin ◽  
Viral Contamination ◽  
Urban Sewage ◽  
Negative Results ◽  
Pcr Assays ◽  
Nested Pcr Assays

ABSTRACT In this study, a molecular procedure for the detection of adenoviruses of animal origin was developed to evaluate the level of excretion of these viruses by swine and cattle and to design a test to facilitate the tracing of specific sources of environmental viral contamination. Two sets of oligonucleotides were designed, one to detect porcine adenoviruses and the other to detect bovine and ovine adenoviruses. The specificity of the assays was assessed in 31 fecal samples and 12 sewage samples that were collected monthly during a 1-year period. The data also provided information on the environmental prevalence of animal adenoviruses. Porcine adenoviruses were detected in 17 of 24 (70%) pools of swine samples studied, with most isolates being closely related to serotype 3. Bovine adenoviruses were present in 6 of 8 (75%) pools studied, with strains belonging to the genera Mastadenovirus and Atadenovirus and being similar to bovine adenoviruses of types 2, 4, and 7. These sets of primers produced negative results in nested PCR assays when human adenovirus controls and urban-sewage samples were tested. Likewise, the sets of primers previously designed for detection of human adenovirus also produced negative results with animal adenoviruses. These results indicate the importance of further studies to evaluate the usefulness of these tests to trace the source of fecal contamination in water and food and for environmental studies.

scholarly journals Technical note: Development of multiplex PCR assays for the molecular characterization of Streptococcus uberis strains isolated from bovine mastitis

2020 ◽  
Vol 103 (1) ◽  
pp. 915-921
Author(s):  
Dario Calonzi ◽  
Alicia Romano ◽  
Valentina Monistero ◽  
Paolo Moroni ◽  
Mario Vittorio Luini ◽  
...  
Keyword(s):  
Multiplex Pcr ◽  
Molecular Characterization ◽  
Bovine Mastitis ◽  
Technical Note ◽  
Streptococcus Uberis ◽  
Pcr Assays

Molecular characterization of Candidatus Phytoplasma aurantifolia isolate infecting chickpea (Cicer arietinum) in Dharwad, Karnataka

2019 ◽  
Author(s):  
Gurupada Balol ◽  
C Channakeshava ◽  
M S Patil
Keyword(s):  
16S Rdna ◽  
Molecular Characterization ◽  
Cicer Arietinum ◽  
Nested Pcr ◽  
Rdna Sequences ◽  
Pcr Product ◽  
16S Rdna Sequences ◽  
Axillary Proliferation ◽  
Pale Green

Chickpea plants showing phytoplasma symptoms were observed in the research plots at University of Agricultural Sciences, Dharwad, Karnataka, India. The symptoms included phyllody, pale green leaves, bushy appearance and excessive axillary proliferation. The causal agent of the phyllody disease was identified based on symptoms, amplification of 16S rDNA of the phytoplasma by nested PCR with primers P1/P7 and R16F2n/R16R2 and 1,800 bp and 1,200 bp size products were amplified in first round PCR and nested-PCR respectively. The PCR product was sequenced and compared with the reference phytoplasma sequences collected from the database (NCBI). 16S rDNA sequences of Dharwad chickpea phytoplasma shared the highest nucleotide identity of (>98%) with Periwinkle phyllody16SrII-E (EU096500). This study indicated the association of ‘Candidatus Phytoplasma aurantifolia’ the 16SrII-E group infecting chickpea from Northern Karnataka.

Genotype characterization and prognosis of unknown primary melanoma patients with nodal metastases.

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. e19022-e19022
Author(s):  
Aleksandra Gos ◽  
Caroline Robert ◽  
Monika Jurkowska ◽  
Nyam Kamsu-Kom ◽  
Wanda Michej ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Direct Sequencing ◽  
Primary Melanoma ◽  
Genetic Alterations ◽  
Unknown Primary ◽  
Nodal Metastases ◽  
Multicentric Study ◽  
Molecular Features ◽  
Mutational Status

e19022 Background: Melanoma of unknown primary site (MUP) is unique, not completely understood entity with nodal metastases as the most common clinical manifestation. The aim of this multicentric study was to assess genetic alterations in MUP with clinically detected nodal metastases in terms of clinicopathological features and prognosis. Methods: We analyzed contemporary series of 37 MUP patients (median age 51 years) after therapeutic lymphadenectomy - LND (period: 1996-2010, 20 – axillary, 16 - inguinal, 1 – other basin) not treated with BRAF inhibitors and performed molecular characterization of BRAF/NRAS mutational status in nodal metastases using direct sequencing of respective coding sequences. Median follow-up time was 37 months. Results: BRAF mutations were detected in 23 (63%) cases (21 V600E - 91%, 2 others - 9%), and mutually exclusive NRAS mutations in 3 (8%) cases (Q61K, Q61R, Q13R). Presence of BRAF mutation correlated with younger age of patients (median 47 vs 60 years for BRAF+ vs. BRAF-, p<0.05). 3-year overall survival (OS) was 45%, median – 23 months (from date of lymph node dissection). We have not found any difference in terms of OS between BRAF mutated- and wild-type melanomas (p=0.99). Conclusions: This unique, comprehensive study on molecular characterization of MUP with nodal involvement stage showed that MUPs have similar molecular features as sporadic non-chronic-sun-damaged melanomas. BRAF mutational status has no prognostic value in this group of patients, what may have potential implications for adjuvant therapy.

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