Morphological and molecular identification of some species of nematode of the family Protostrongylidae Leiper, 1926

2016 ◽  
Vol 3 (4) ◽  
pp. 454-461
Author(s):  
Салахутдинов ◽  
I. Salakhutdinov ◽  
Рузиев ◽  
B. Ruziev ◽  
Каримова ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Trees ◽  
Molecular Genetic ◽  
Digital Camera ◽  
Molecular Genetic Analysis ◽  
Nucleotide Sequences ◽  
Genetic Identification ◽  
Mountain Area ◽  
Phylogenetic Relations ◽  
The Family

Objective of research: conducting morphological and molecular-genetic identification and studying phylogenetic relations between protostrongylids. Materials and methods: helminthological material was collected from wild (Capra sibirica, C. falconeri, Ovis vignei and O. ammon) and domestic hollow horned ruminants (C. hircus and O. aries), and land mollusks of the family Xeropicta in the piedmont and mountain area of Uzbekisan. The morphology of protostrongylids was studied using the methods of Boev (1975) and Anderson (1978). To identify the nematode type we used temporary preparations treated with glycerol. The first-stage larvae were investigated by examination of fecal samples from animals taking into account the length, tail form and body size. To study the morphology of the third-stage protostrongylid larvae the feet of infected mollusks Xeropicta candaсharica were separated and placed into the artificial gastric juice where the cap was destroyed and the infected larvae were eliminated. After determination of species belonging of mature and larval nematodes the material was stored in separate test-tubes with distilled water under the low temperature (- 20 ºС) or in 70 % Ethanol for the molecular analysis. We used microscopes ML 2000 with a digital camera and Olympus CX3. DNA extraction, amplification and sequencing were performed with an automated sequencer. Phylogenetic analysis was conducted using the software Clustal X 2.0. Phylogenetic trees were created by the Neighbor–Joining method. Nucleotide sequences ITS-2 regions of species Protostrongylus rufescens (EU018485), P. shiozawai (AB478249), Ortostrongylus macrotis (EU018483), Cystocaulus ocreatus (EU018481) and Umingmakstrongylus pallikuukensis (AY648409) received from the NCBI GenBank were used in phylogenetic analysis. Results and discussion: Four species of adult protostrongylid nematodes: Protostrongylus rufescens, P. hobmaieri, Spiculocaulus leuckarti and Cystocaulus ocreatus were determined. DNA from four species of mature protostrongylids and larvae was amplified by using ITS-2 regions. Amplificate dimension of nematodes P. rufescens and P. hobmaieri was 380 base pairs (b.p.), S. leuckarti – 388, C. ocreatus – 399 b.p. According to the results of phylogenetic analysis and comparison of nucleotide sequences, five protostrongylid species were found in animals of the Caprinae subfamily: P. rufescens, P. hobmaieri, Protostrongylus sp., S. leuckarti and C. ocreatus. The morphological and molecular-genetic analysis of detected nematodes enables the precise identification.

scholarly journals Use of the method of phylogenetic analysis in an epidemiological investigation in case of HIV infection in pediatric practice

2021 ◽  
Vol 13 (1) ◽  
pp. 106-114
Author(s):  
S. P. Kruglyak ◽  
V. O. Kotova ◽  
E. I. Miroshnichenko ◽  
O. A. Skaly ◽  
E. S. Makhno ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Nucleotide Sequence ◽  
Hiv Infection ◽  
Phylogenetic Trees ◽  
Comparison Group ◽  
Molecular Genetic ◽  
Molecular Genetic Analysis ◽  
Nucleotide Sequences ◽  
Likelihood Method ◽  
Epidemiological Investigation

The aim of the study is to study the main pathways and risk factors for HIV infection in a child, to establish a probable source of infection for a child, as well as to exclude the possibility of criminal or nosocomial infection.Materials and methods. At the first stage, an epidemiological investigation was conducted. Next, a molecular genetic analysis of two blood plasma samples studied (child and mother) and a comparison group were used, in which 18 nucleotide sequences of HIV-1 variants were used, obtained from patients living in the Primorsky Region, and 8 characterized nucleotide sequences additionally taken from GenBank international database. Distance calculation and phylogenetic analysis were performed by constructing phylogenetic trees using the Maximum Likelihood method using the GTR evolution model.Research results. The data obtained indicate that the nucleotide sequence from the child is most similar to the nucleotide sequence from the mother (potential source) and reliably grouped on the phylogenetic tree, forming a common cluster that is different from the samples of the comparison group. This indicates the likelihood of an epidemiological link between HIV infections in the mother and her child.Conclusion. According to the results of this study, we can conclude that the child is infected from an HIV-infected mother, approximately at the age of a child older than 4 years old, when he received the last negative test result for HIV markers.

scholarly journals Waterborne Outbreak of Acute Gastroenteritis Caused by Recombinant Norovirus GII.P7–GII.6 in Khabarovsk in 2019

2020 ◽  
pp. 50-54
Author(s):  
LV Butakova ◽  
EYu Sapega ◽  
OE Trotsenko ◽  
TA Zaytseva ◽  
TN Karavyanskaya ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Acute Gastroenteritis ◽  
Molecular Genetic ◽  
Disease Onset ◽  
Molecular Genetic Analysis ◽  
Nucleotide Sequences ◽  
Contaminated Water ◽  
Rt Pcr ◽  
Waterborne Outbreak ◽  
Causative Agents

Background: Noroviruses are common causative agents of acute gastroenteritis worldwide. Person-to-person transmission is the dominant transmission route for norovirus infection but contaminated water also often leads to outbreaks. Objectives: Our purpose was to do epidemiologic and molecular genetic analyses of waterborne norovirus infection outbreak among children in Khabarovsk in 2019. Materials and methods: Clinical and water samples were screened for the presence of norovirus RNA using real-time RT-PCR detection kit. The norovirus nucleotide sequences were determined by Sanger sequencing. The obtained sequences were subjected to a phylogenetic analysis. Results: In July 2019, 34 children developed acute gastroenteritis in Khabarovsk. The epidemiologic investigation showed that on the eve of the disease onset all patients played and bathed in a pedestrian fountain complex. A molecular genetic analysis of 18 biological samples from children with acute gastroenteritis and a water sample from the fountain revealed a recombinant norovirus GII.P7-GII.6. We established a 100.0% identity of all obtained nucleotide sequences to each other. A phylogenetic analysis of ORF2 partial sequences showed that the capsid protein of the Khabarovsk GII.P7-GII.6 strains belonged to the variant GII.6a. Conclusions: Contaminated water in the pedestrian interactive fountain complex was the most likely cause of the norovirus infection outbreak among children in Khabarovsk in 2019 associated with the lack of proper maintenance and regular disinfection measures.

scholarly journals Extensive Phylogenetic Analysis of Piscine Orthoreovirus Genomic Sequences Shows the Robustness of Subgenotype Classification

Pathogens ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 41
Author(s):  
Marcos Godoy ◽  
Daniel A. Medina ◽  
Rudy Suarez ◽  
Sandro Valenzuela ◽  
Jaime Romero ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Variation ◽  
Sequence Analysis ◽  
Molecular Phylogeny ◽  
Phylogenetic Trees ◽  
Genomic Segment ◽  
Double Stranded Rna ◽  
The Family ◽  
Original Classification

Piscine orthoreovirus (PRV) belongs to the family Reoviridae and has been described mainly in association with salmonid infections. The genome of PRV consists of about 23,600 bp, with 10 segments of double-stranded RNA, classified as small (S1 to S4), medium (M1, M2 and M3) and large (L1, L2 and L3); these range approximately from 1000 bp (segment S4) to 4000 bp (segment L1). How the genetic variation among PRV strains affects the virulence for salmonids is still poorly understood. The aim of this study was to describe the molecular phylogeny of PRV based on an extensive sequence analysis of the S1 and M2 segments of PRV available in the GenBank database to date (May 2020). The analysis was extended to include new PRV sequences for S1 and M2 segments. In addition, subgenotype classifications were assigned to previously published unclassified sequences. It was concluded that the phylogenetic trees are consistent with the original classification using the PRV genomic segment S1, which differentiates PRV into two major genotypes, I and II, and each of these into two subgenotypes, designated as Ia and Ib, and IIa and IIb, respectively. Moreover, some clusters of country- and host-specific PRV subgenotypes were observed in the subset of sequences used. This work strengthens the subgenotype classification of PRV based on the S1 segment and can be used to enhance research on the virulence of PRV.

scholarly journals A Novel Mutation of ATP7B Gene in a Case of Wilson Disease

Medicina ◽  
2021 ◽  
Vol 57 (2) ◽  
pp. 123
Author(s):  
Cigdem Yuce Kahraman ◽  
Ali Islek ◽  
Abdulgani Tatar ◽  
Özlem Özdemir ◽  
Adil Mardinglu ◽  
...  
Keyword(s):  
Wilson Disease ◽  
Novel Mutation ◽  
Molecular Genetic ◽  
Molecular Genetic Analysis ◽  
Compound Heterozygous ◽  
Atp7b Gene ◽  
Loss Of Function ◽  
Clinical Presentations ◽  
The Family ◽  
The Brain

Wilson disease (WD) (OMIM# 277900) is an autosomal recessive inherited disorder characterized by excess copper (Cu) storage in different human tissues, such as the brain, liver, and the corneas of the eyes. It is a rare disorder that occurs in approximately 1 in 30,000 individuals. The clinical presentations of WD are highly varied, primarily consisting of hepatic and neurological conditions. WD is caused by homozygous or compound heterozygous mutations in the ATP7B gene. The diagnosis of the disease is complicated because of its heterogeneous phenotypes. The molecular genetic analysis encourages early diagnosis, treatment, and the opportunity to screen individuals at risk in the family. In this paper, we reported a case with a novel, hotspot-located mutation in WD. We have suggested that this mutation in the ATP7B gene might contribute to liver findings, progressing to liver failure with a loss of function effect. Besides this, if patients have liver symptoms in childhood and/or are children of consanguineous parents, WD should be considered during the evaluation of the patients.

scholarly journals Genetic identification of bovine leukaemia virus

2018 ◽  
Vol 6 (2) ◽  
pp. 314-324 ◽  
Author(s):  
Irina Donnik ◽  
Irina Donnik ◽  
Ramil Vafin ◽  
Ramil Vafin ◽  
Aram Galstyan ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Research Methods ◽  
Bovine Leukemia Virus ◽  
Leukemia Virus ◽  
Molecular Genetic ◽  
Genetic Research ◽  
Genetic Identification ◽  
Gene Fragment ◽  
Phylogenetic Classification ◽  
Pcr Rflp

Molecular genetic research methods make it possible to evaluate the genetic diversity of bovine leukemia virus (BLV) and are the most informative approaches to its genetic identification. Molecular genetic research methods work well for the phylogenetic analysis of sequenced nucleotide DNA sequences of the provirus, as well as for the polymerase chain reaction-restriction fragment length polymorphism analysis (PCR-RFLP) according to the phylogenetic classification of the pathogen. The purpose of the research was to study the scientific and methodological approaches to the genetic identification of bovine leukemia virus, integrated into the molecular monitoring of infection of cattle with BLV genotypes. The authors used PCR-RFLP-genotyping and comparative phylogenetic analysis of aligned nucleotide sequences of the env gene fragment of the BLV provirus isolates to detect the genotypic affiliation of the cattle from twenty-one livestock farms of the Republic of Tatarstan. As a result, isolates of four out of ten BLV genotypes were found in the Tatarstani cattle, namely genotypes 1, 4, 7, and 8. The research involved a comparative analysis of 505 nucleotide sequences of a fragment of the BLV env gene, including those deposited in GenBank NCBI. The analysis confirms the inconsistency of several earlier PCR-RFLP typing strategies with the current approach in assessing the genotypic diversity by phylogenetic analysis. The improved strategy of PCR-RFLP genotyping of BLV corresponds with its modern phylogenetic classification. The strategy makes it possible to identify all the known genotypes of the viral pathogen. Its validity has been proved by in silico modelling of restrictogrammes and a phylogenetic analysis of the env gene fragment of 57 reference isolates of ten BLV genotypes that generate 57 genotype-associated combinations of diagnostically significant PCR-RFLP profiles.

The complete description of larval stages of the lobster shrimpLeonardsaxius amurensis(Kobjakova, 1937) (Decapoda: Axiidea: Axiidae) identified by DNA barcoding

2017 ◽  
Vol 98 (6) ◽  
pp. 1435-1453 ◽  
Author(s):  
Elena S. Kornienko ◽  
Darya D. Golubinskaya ◽  
Olga M. Korn ◽  
Svetlana N. Sharina
Keyword(s):  
Larval Development ◽  
Sequence Data ◽  
Molecular Genetic ◽  
Sympatric Species ◽  
Molecular Genetic Analysis ◽  
Mitochondrial Coi ◽  
Larval Stages ◽  
The Family ◽  
Rdna Sequence Data ◽  
First Time

The complete larval development of the lobster shrimpLeonardsaxius amurensis(Kobjakova, 1937) (Decapoda: Axiidea: Axiidae) is described and illustrated for the first time. The first zoeae of this species were collected from the plankton samples and reared in the laboratory before moulting to the megalopa. A molecular genetic analysis based on comparison of partial mitochondrial COI, 12S rDNA and 16S rDNA sequence data confirmed the identity of axiid larvae found in the plankton andL. amurensisadults collected in the same area. The larval development ofL. amurensisincludes five zoeal stages and a single megalopa. Zoeae I ofL. amurensisare characterized by the presence of one short posterodorsal spine on the fifth pleonite in contrast to the larvae of related sympatric speciesBoasaxius princepshaving four posterodorsal spines on the pleonites 2–5.Leonardsaxius amurensisoccupies an intermediate position between lobster shrimps with abbreviated pelagic development (2–3 zoeal stages) and species with long development (up to eight zoeal stages). Thus, the number of zoeal stages in the family Axiidae varies widely, similarly to that in the families Callianassidae and Upogebiidae.

scholarly journals HUMAN BEING AS THE BEARER OF IDENTIFYING BIOLOGICAL INFORMATION

2021 ◽  
Author(s):  
L. Кotliarenko ◽  
А. Коfanov ◽  
O. Коfаnоvа ◽  
V. Zherebak
Keyword(s):  
Genetic Analysis ◽  
Dna Analysis ◽  
Molecular Genetic ◽  
Genetic Research ◽  
Molecular Genetic Analysis ◽  
Genetic Identification ◽  
Criminal Proceedings ◽  
Genetic Traits ◽  
Criminal Offenses ◽  
Genetic Examination

In forensic practice, biological traces of a person are very often used as material evidence - blood, hair, saliva, semen, urine, sweat, as well as parts of organs and tissues. Establishing the origin of these traces from a specific person is very important for the investigation of criminal offenses. The current level of development of molecular genetic research indicates the need to use DNA analysis in the detection and investigation of criminal offenses against a person. Today, molecular genetic identification reveal reliable prospects for solving identification problems in the criminal proceedings and developing the evidence base, and also has a number of advantages over traditional serological methods for studying human biological traces. It should be noted that along with the traditional method of nuclear DNA research, mitochondrial DNA research is also being carried out, which allows solving the problem of molecular genetic examination to establish biological affinity. The value of this method lies in its effectiveness in the study of a small amount of degraded DNA, secretions and heavily damaged objects, the study of which is impossible by traditional methods. When performing a forensic molecular genetic examination for the full identification of the detected traces when examining the places of committed criminal offenses, comparative samples are important, as well as the selection of appropriate biological samples to establish paternity and family ties. Molecular genetic analysis of DNA is only one of the stages of identification, and in order to arrive at the final result, a statistical analysis of the data obtained is necessary, which is especially important when the genotypes of the criminal and the suspect in mixed tracks coincide. For a probable-statistical assessment of the results of the identification significance of the set of established genetic traits, the frequencies of the distribution of the studied alleles in the population are required. Today, the DNA analysis method has become one of the most demanded directions in the development of forensic examinations, and its results are quite reliable evidence of the involvement of a specific person in a crime. Due to its unique capabilities, molecular genetic analysis of DNA is a powerful tool in the investigation of criminal proceedings.

scholarly journals Molecular genetic analysis of variant phenotypes of the ABO blood group system

Blood ◽  
1996 ◽  
Vol 88 (7) ◽  
pp. 2732-2737 ◽  
Author(s):  
K Ogasawara ◽  
R Yabe ◽  
M Uchikawa ◽  
N Saitou ◽  
M Bannai ◽  
...  
Keyword(s):  
Blood Group ◽  
Molecular Genetic ◽  
Nonsynonymous Substitution ◽  
Single Strand Conformation Polymorphism ◽  
Molecular Genetic Analysis ◽  
Nucleotide Sequences ◽  
Activity Level ◽  
Blood Group System ◽  
Nucleotide Substitutions ◽  
Group System

ABO is clinically the most important blood group system in transfusion medicine and includes many variant phenotypes. To understand the molecular genetic basis of this polymorphic system, we have analyzed genomic DNAs obtained from Japanese individuals possessing variant ABO phenotypes including A2, Ax, Ael, cis-AB, Bx, and Bel. By polymerase chain reaction-single-strand conformation polymorphism (SSCP) and nucleotide sequence analyses, we identified 11 different alleles. These alleles had nucleotide sequences different from those of the previously described 13 different alleles responsible for the common ABO phenotypes. Analysis of the nucleotide sequences of the alleles responsible for those variant phenotypes showed that the amino acid residues at position 266 and 268 may be crucial for transferase specificity, whereas those at positions 214, 216, 223, 291, and 352 may be critical for the activity level. Nine of the 11 alleles, responsible for the A2, Ax, Ael, cis-AB, Bx, and Bel phenotypes, were presumed to be generated from common ABO alleles by single nucleotide mutations such as nonsynonymous substitution, deletion, or insertion. Two other alleles, responsible for the A2 and Ael phenotypes, may have originated by recombination, gene conversionlike events or accumulation of nucleotide substitutions. Our data indicate that different alleles could cause the same ABO variant phenotypes, and that these alleles do not necessarily belong to a single evolutionary lineage.

scholarly journals Morphological and molecular genetic analysis of Synhimantus (Synhimantus) laticeps (Rudolphi, 1819) (Nematoda, Acuariidae) from the barn owl (Tyto alba) and the common kestrel (Falco tinnunculus) in Austria

2017 ◽  
Vol 54 (3) ◽  
pp. 262-269 ◽  
Author(s):  
D. Ebmer ◽  
H.-P. Fuehrer ◽  
B. Eigner ◽  
H. Sattmann ◽  
A. Joachim
Keyword(s):  
Molecular Genetic ◽  
First Record ◽  
Barn Owl ◽  
Molecular Genetic Analysis ◽  
Genetic Identification ◽  
Coi Gene ◽  
Tyto Alba ◽  
Electron Microscopic ◽  
Barn Owls ◽  
The Common

SummaryIn the framework of the biodiversity initiative and barcoding project “Austrian Barcode of Life” (ABOL) post mortem examinations of the gastro-intestinal tracts of different species of wild birds were carried out and several adult helminths were retrieved. In the gizzard of two barn owls (Tyto alba) and one common kestrel (Falco tinnuculus) acuariid nematodes belonging to the species Synhimantus (Synhimantus) laticeps (Rudolphi, 1819) were discovered. This report illustrates the identification of this parasitic nematode by morphometric comparison and scanning electron microscopic photographs. Furthermore, genetic identification of individual parasites based on a fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene and the nuclear 18S ribosomal RNA gene was carried out. This report constitutes the first COI-based DNA barcoding of S. (S.) laticeps and its first record in the barn owl (Tyto alba) in Austria.

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