Demystified ... DNA nucleotide sequencing

AbstractSeveral routine procedures are available for diagnosis of diseases caused by an alteration in a single gene. These techniques include Southern analysis, the polymerase chain reaction, allele-specific oligonucleotide screening, automated DNA nucleotide sequencing, and linkage analysis. DNA testing procedures can be used for diagnosis of disease, determination of carrier status in affected families, or general screening of the population. Some of the more commonly used techniques and their applications are described in this article.

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Sequencing Analysis and Phylogenetic Tree of HPV Isolated from Breast Cancer Patients at Thi-Qar Province/Iraq

10.32792/utq/utjsci/vol7/2/10 ◽

2020 ◽

pp. 37-40

Keyword(s):

Nucleotide Sequence ◽

Phylogenetic Tree ◽

Evolutionary Relationship ◽

Nucleotide Sequencing ◽

Sequencing Analysis ◽

Breast Cancer Patients ◽

The North ◽

Formalin Fixed Paraffin ◽

Formalin Fixed Paraffin Embedded ◽

History Of

Genetic variety examination has demonstrated fundamental to the understanding of the epidemiological and developmental history of Papillomavirus (HPV), for the development of accurate diagnostic tests and for efficient vaccine design. The HPV nucleotide diversity has been investigated widely among high-risk HPV types. To make the nucleotide sequence of HPV and do the virus database in Thi-Qar province, and compare sequences of our isolates with previously described isolates from around the world and then draw its phylogenetic tree, this study done. A total of 6 breast formalin-fixed paraffin-embedded (FFPE) of the female patients were included in the study, divided as 4 FFPE malignant tumor and 2 FFPE of benign tumor. The PCR technique was implemented to detect the presence of HPV in breast tissue, and the real-time PCR used to determinant HPV genotypes, then determined a complete nucleotide sequence of HPV of L1 capsid gene, and draw its phylogenetic tree. The nucleotide sequencing finding detects a number of substitution mutation (SNPs) in (L1) gene, which have not been designated before, were identified once in this study population, and revealed that the HPV16 strains have the evolutionary relationship with the South African race, while, the HPV33 and HPV6 showing the evolutionary association with the North American and East Asian race, respectively.

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Children's Hospital of Pittsburgh Histocompatibility Center Nucleotide Sequencing for Detection of Alleles at HLA Class I and Class II Loci on Ethnic Minorities

10.21236/ada371509 ◽

1999 ◽

Author(s):

Massimo Trucco

Keyword(s):

Ethnic Minorities ◽

Hla Class I ◽

Class Ii ◽

Class I ◽

Nucleotide Sequencing ◽

Children's Hospital ◽

Children’S Hospital

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Circulation and Molecular Epidemiology of Enteroviruses in Paralyzed, Immunodeficient and Healthy Individuals in Tunisia, a Country with a Polio-Free Status for Decades

Viruses ◽

10.3390/v13030380 ◽

2021 ◽

Vol 13 (3) ◽

pp. 380

Author(s):

Anissa Chouikha ◽

Dorra Rezig ◽

Nadia Driss ◽

Ichrak Abdelkhalek ◽

Ahlem Ben Yahia ◽

...

Keyword(s):

Detection Rate ◽

Warning System ◽

World Health ◽

Clinical Samples ◽

Nucleotide Sequencing ◽

Comprehensive Picture ◽

Set Up ◽

Health Organization ◽

Type 3

This report is an overview of enterovirus (EV) detection in Tunisian polio-suspected paralytic cases (acute flaccid paralysis (AFP) cases), healthy contacts and patients with primary immunodeficiencies (PID) during an 11-year period. A total of 2735 clinical samples were analyzed for EV isolation and type identification, according to the recommended protocols of the World Health Organization. Three poliovirus (PV) serotypes and 28 different nonpolio enteroviruses (NPEVs) were detected. The NPEV detection rate was 4.3%, 2.8% and 12.4% in AFP cases, healthy contacts and PID patients, respectively. The predominant species was EV-B, and the circulation of viruses from species EV-A was noted since 2011. All PVs detected were of Sabin origin. The PV detection rate was higher in PID patients compared to AFP cases and contacts (6.8%, 1.5% and 1.3% respectively). PV2 was not detected since 2015. Using nucleotide sequencing of the entire VP1 region, 61 strains were characterized as Sabin-like. Among them, six strains of types 1 and 3 PV were identified as pre-vaccine-derived polioviruses (VDPVs). Five type 2 PV, four strains belonging to type 1 PV and two strains belonging to type 3 PV, were classified as iVDPVs. The data presented provide a comprehensive picture of EVs circulating in Tunisia over an 11-year period, reveal changes in their epidemiology as compared to previous studies and highlight the need to set up a warning system to avoid unnoticed PVs.

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Impact of Subclinical Haemoproteus columbae Infection on Farmed Domestic Pigeons from Central Java (Yogyakarta), Indonesia, with Special Reference to Changes in the Hemogram

Pathogens ◽

10.3390/pathogens10040440 ◽

2021 ◽

Vol 10 (4) ◽

pp. 440

Author(s):

Imron Rosyadi ◽

Siti Isrina Oktavia Salasia ◽

Bayanzul Argamjav ◽

Hiroshi Sato

Keyword(s):

Chronic Phase ◽

Hypochromic Anemia ◽

Hemoglobin Concentration ◽

Columba Livia ◽

Nucleotide Sequencing ◽

Mean Corpuscular Hemoglobin ◽

Haemoproteus Columbae ◽

Central Java ◽

Mitochondrial Cytochrome B ◽

Domestic Pigeons

Pigeon haemoproteosis caused by Haemoproteus columbae (Apicomplexa: Haemosporida: Haemoproteidae) is globally prevalent in rock doves (Columba livia), although little is known regarding this disease in pigeons and doves in Indonesia. Blood samples of 35 farmed domestic pigeons (C. livia f. domestica) from four localities in Yogyakarta Special Region, Central Java, Indonesia, were collected from March to June, 2016, subjected to a hemogram, and analyzed for the presence of hemoprotozoan infections. Microscopic examination of blood smears revealed a prevalence of 62.5–100% of H. columbae at the four localities (n = 8–10 for each locality), and geometric means of 3.0–5.6% of erythrocytes were parasitized by young and mature gametocytes, suggesting that all infected pigeons were in the chronic phase of infection with repeated recurrences and/or reinfections. Nucleotide sequencing of mitochondrial cytochrome b gene (cytb) for haemosporidian species demonstrated the distribution of four major cytb lineages of H. columbae (mainly HAECOL1, accompanied by COLIV03, COQUI05, and CXNEA02 according to the MalAvi database). Hemogram analysis, involving the estimation of packed cell volume, erythrocyte counts, mean corpuscular volume, mean corpuscular hemoglobin concentration, and plasma protein and fibrinogen levels of 20 parasitized pigeons and five non-infected pigeons demonstrated significant macrocytic hypochromic anemia with hypoproteinemia and hyperfibrinogenemia in the infected pigeons. This study shows the profound impact of long-lasting subclinical pigeon haemoproteosis caused by H. columbae on the health of farmed domestic pigeons.

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Dominant Mutations of Drosophila MAP Kinase Kinase and Their Activities in Drosophila and Yeast MAP Kinase Cascades

Genetics ◽

10.1093/genetics/146.1.263 ◽

1997 ◽

Vol 146 (1) ◽

pp. 263-273 ◽

Cited By ~ 3

Author(s):

Young-Mi Lim ◽

Leo Tsuda ◽

Yoshihiro H Inoue ◽

Kenji Irie ◽

Takashi Adachi-Yamada ◽

...

Keyword(s):

Map Kinase ◽

Tyrosine Kinases ◽

Egf Receptor ◽

Kinase Domain ◽

Nucleotide Sequencing ◽

Gain Of Function ◽

Highly Sensitive ◽

Mitogen Activated Protein ◽

Signal Specificity ◽

Map Kinase Kinase

Eight alleles of Dsor1 encoding a Drosophila homologue of mitogen-activated protein (MAP) kinase kinase were obtained as dominant suppressors of the MAP kinase kinase kinase D-raf. These Dsor1 alleles themselves showed no obvious phenotypic consequences nor any effect on the viability of the flies, although they were highly sensitive to upstream signals and strongly interacted with gain-of-function mutations of upstream factors. They suppressed mutations for receptor tyrosine kinases (RTKs); torso (tor), sevenless (sev) and to a lesser extent Drosophila EGF receptor (DER). Furthermore, the Dsor1 alleles showed no significant interaction with gain-of-function mutations of DER. The observed difference in activity of the Dsor1 alleles among the RTK pathways suggests Dsor1 is one of the components of the pathway that regulates signal specificity. Expression of Dsor1 in budding yeast demonstrated that Dsor1 can activate yeast MAP kinase homologues if a proper activator of Dsor1 is coexpressed. Nucleotide sequencing of the Dsor1 mutant genes revealed that most of the mutations are associated with amino acid changes at highly conserved residues in the kinase domain. The results suggest that they function as suppressors due to increased reactivity to upstream factors.

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Streptococcus pluranimalium meningoencephalitis in a horse

Journal of Veterinary Diagnostic Investigation ◽

10.1177/10406387211023465 ◽

2021 ◽

pp. 104063872110234

Author(s):

Dah-Jiun Fu ◽

Akhilesh Ramachandran ◽

Craig Miller

Keyword(s):

Ribosomal Rna ◽

Cross Sections ◽

Nucleotide Sequencing ◽

Formalin Fixed Paraffin ◽

Quarter Horse ◽

Formalin Fixed Paraffin Embedded ◽

History Of ◽

The Brain ◽

Gram Positive Cocci ◽

Formalin Fixed

A 3-y-old, female Quarter Horse with a history of acute neurologic signs was found dead and was submitted for postmortem examination. Areas of petechial and ecchymotic hemorrhage were present on cross-sections of the cerebrum, cerebellum, and brainstem. Histologic examination of the brain revealed severe, purulent meningoencephalitis and vasculitis with a myriad of intralesional gram-positive cocci. Streptococcus pluranimalium was identified from formalin-fixed, paraffin-embedded tissue obtained from sites with active lesions by PCR and nucleotide sequencing of bacterial 16S ribosomal RNA. S. pluranimalium should be considered as a cause of meningoencephalitis in a horse.

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