scholarly journals Comparison ofMycobacterium tuberculosisGenomes Reveals Frequent Deletions in a 20 kb Variable Region in Clinical Isolates

Yeast ◽  
2000 ◽  
Vol 1 (4) ◽  
pp. 272-282 ◽  
Author(s):  
Timothy B. L. Ho ◽  
Brian D. Robertson ◽  
G. Michael Taylor ◽  
Rory J. Shaw ◽  
Douglas B. Young
Keyword(s):  
Genetic Diversity ◽  
Hot Spots ◽  
High Frequency ◽  
Biological Diversity ◽  
Variable Region ◽  
Clinical Isolates ◽  
Insertion Element ◽  
Genomic Deletions ◽  
Nucleotide Repeats ◽  
Strain H37rv

TheMycobacterium tuberculosiscomplex is associated with a remarkably low level of structural gene polymorphism. As part of a search for alternative forms of genetic variation that may act as a source of biological diversity inM. tuberculosis, we have identified a region of the genome that is highly variable amongst a panel of unrelated clinical isolates. Fifteen of 24 isolates examined contained one or more copies of theM. tuberculosis-specific IS6110insertion element within this 20 kb variable region. In nine of the isolates, including the laboratory-passaged strain H37Rv, genomic deletions were identified, resulting in loss of between two and 13 genes. In each case, deletions were associated with the presence of a copy of the IS6110element. Absence of flanking tri- or tetra-nucleotide repeats identified homologous recombination between adjacent IS6110elements as the most likely mechanism of the deletion events. IS6110insertion into hot-spots within the genome ofM. tuberculosisprovides a mechanism for generation of genetic diversity involving a high frequency of insertions and deletions.

scholarly journals Comparison of Mycobacterium tuberculosis Genomes Reveals Frequent Deletions in a 20 kb Variable Region in Clinical Isolates

Yeast ◽  
2000 ◽  
Vol 1 (4) ◽  
pp. 272-282
Author(s):  
Timothy B. L. Ho ◽  
Brian D. Robertson ◽  
G. Michael Taylor ◽  
Rory J. Shaw ◽  
Douglas B. Young
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Hot Spots ◽  
High Frequency ◽  
Biological Diversity ◽  
Variable Region ◽  
Clinical Isolates ◽  
Insertion Element ◽  
Genomic Deletions ◽  
Nucleotide Repeats ◽  
Strain H37rv

The Mycobacterium tuberculosis complex is associated with a remarkably low level of structural gene polymorphism. As part of a search for alternative forms of genetic variation that may act as a source of biological diversity in M. tuberculosis, we have identified a region of the genome that is highly variable amongst a panel of unrelated clinical isolates. Fifteen of 24 isolates examined contained one or more copies of the M. tuberculosis-specific IS6110 insertion element within this 20 kb variable region. In nine of the isolates, including the laboratory-passaged strain H37Rv, genomic deletions were identified, resulting in loss of between two and 13 genes. In each case, deletions were associated with the presence of a copy of the IS6110 element. Absence of flanking tri- or tetra-nucleotide repeats identified homologous recombination between adjacent IS6110 elements as the most likely mechanism of the deletion events. IS6110 insertion into hot-spots within the genome of M. tuberculosis provides a mechanism for generation of genetic diversity involving a high frequency of insertions and deletions.

Analysis of genetic polymorphisms affecting the four phospholipase C (plc) genes in Mycobacterium tuberculosis complex clinical isolates

Microbiology ◽  
2004 ◽  
Vol 150 (4) ◽  
pp. 967-978 ◽  
Author(s):  
C. Viana-Niero ◽  
P. E. de Haas ◽  
D. van Soolingen ◽  
S. C. Leão
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Phospholipase C ◽  
Genetic Polymorphisms ◽  
Blot Hybridization ◽  
Southern Blot Hybridization ◽  
Clinical Isolates ◽  
Significant Similarity ◽  
Genomic Deletions ◽  
Genes Encoding ◽  
Mycobacterium Africanum

The Mycobacterium tuberculosis genome contains four highly related genes which present significant similarity to Pseudomonas aeruginosa genes encoding phospholipase C enzymes. Three of these genes, plcA, plcB and plcC, are organized in tandem (locus plcABC). The fourth gene, plcD, is located in a different region. This study investigates variations in plcABC and plcD genes in clinical isolates of M. tuberculosis, Mycobacterium africanum and ‘Mycobacterium canettii’. Genetic polymorphisms were examined by PCR, Southern blot hybridization, sequence analysis and RT-PCR. Seven M. tuberculosis isolates contain insertions of IS6110 elements within plcA, plcC or plcD. In 19 of 25 M. tuberculosis isolates examined, genomic deletions were identified, resulting in loss of parts of genes or complete genes from the plcABC and/or plcD loci. Partial plcD deletion was observed in one M. africanum isolate. In each case, deletions were associated with the presence of a copy of the IS6110 element and in all occurrences IS6110 was transposed in the same orientation. A mechanism of deletion resulting from homologous recombination of two copies of IS6110 was recognized in a group of genetically related M. tuberculosis isolates. Five M. tuberculosis isolates presented major polymorphisms in the plcABC and plcD regions, along with loss of expression competence that affected all four plc genes. Phospholipase C is a well-known bacterial virulence factor. The precise role of phospholipase C in the pathogenicity of M. tuberculosis is unknown, but considering the potential importance that the plc genes may have in the virulence of the tubercle bacillus, the study of isolates cultured from patients with active tuberculosis bearing genetic variations affecting these genes may provide insights into the significance of phospholipase C enzymes for tuberculosis pathogenicity.

High frequency of large genomic deletions in the PCCA gene causing propionic acidemia

2009 ◽  
Vol 96 (4) ◽  
pp. 171-176 ◽  
Author(s):  
Lourdes R. Desviat ◽  
Rocío Sanchez-Alcudia ◽  
Belén Pérez ◽  
Celia Pérez-Cerdá ◽  
Rosa Navarrete ◽  
...  
Keyword(s):  
High Frequency ◽  
Propionic Acidemia ◽  
Genomic Deletions

scholarly journals Genetic diversity of Plasmodium vivax clinical isolates from southern Pakistan using pvcsp and pvmsp1 genetic markers

2013 ◽  
Vol 12 (1) ◽  
pp. 16 ◽  
Author(s):  
Afsheen Raza ◽  
Najia K Ghanchi ◽  
Ali M Thaver ◽  
Sana Jafri ◽  
Mohammad A Beg
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Vivax ◽  
Genetic Markers ◽  
Clinical Isolates

scholarly journals UNCROSS: Filtering of high-frequency cross-talk in 16S amplicon reads

2016 ◽  
Author(s):  
Robert C. Edgar
Keyword(s):  
Ribosomal Rna ◽  
Cross Talk ◽  
High Frequency ◽  
Biological Diversity ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Illumina Gaiix ◽  
Microbial Metagenomics ◽  
Tumor Sequencing ◽  
Rna I

AbstractNext-generation amplicon sequencing is widely used for surveying biological diversity in applications such as microbial metagenomics, immune system repertoire analysis and targeted tumor sequencing of cancer-associated genes. In such studies, assignment of reads to incorrect samples (cross-talk) is a well-documented problem that is rarely considered in practice. By considering unexpected OTUs in artificial (mock) samples, I estimate that cross-talk occurred for ~2% of the reads in one Illumina GAIIx run and eleven Illumina MiSeq runs targeting 16S ribosomal RNA. I also describe UNCROSS, an algorithm for detecting and filtering cross-talk in OTU tables.

scholarly journals Primer Binding Site (PBS) Profiling of Genetic Diversity of Natural Populations of Endemic Species Allium ledebourianum Schult.

BioTech ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 23
Author(s):  
Oxana Khapilina ◽  
Ainur Turzhanova ◽  
Alevtina Danilova ◽  
Asem Tumenbayeva ◽  
Vladislav Shevtsov ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Endemic Species ◽  
Biological Diversity ◽  
Natural Populations ◽  
Subsequent Development ◽  
Dna Profiling ◽  
Primer Binding Site ◽  
Anthropogenic Factors ◽  
Habitat Specificity ◽  
Interspersed Repeats

Endemic species are especially vulnerable to biodiversity loss caused by isolation or habitat specificity, small population size, and anthropogenic factors. Endemic species biodiversity analysis has a critically important global value for the development of conservation strategies. The rare onion Allium ledebourianum is a narrow-lined endemic species, with natural populations located in the extreme climatic conditions of the Kazakh Altai. A. ledebourianum populations are decreasing everywhere due to anthropogenic impact, and therefore, this species requires preservation and protection. Conservation of this rare species is associated with monitoring studies to investigate the genetic diversity of natural populations. Fundamental components of eukaryote genome include multiple classes of interspersed repeats. Various PCR-based DNA fingerprinting methods are used to detect chromosomal changes related to recombination processes of these interspersed elements. These methods are based on interspersed repeat sequences and are an effective approach for assessing the biological diversity of plants and their variability. We applied DNA profiling approaches based on conservative sequences of interspersed repeats to assess the genetic diversity of natural A. ledebourianum populations located in the territory of Kazakhstan Altai. The analysis of natural A. ledebourianum populations, carried out using the DNA profiling approach, allowed the effective differentiation of the populations and assessment of their genetic diversity. We used conservative sequences of tRNA primer binding sites (PBS) of the long-terminal repeat (LTR) retrotransposons as PCR primers. Amplification using the three most effective PBS primers generated 628 PCR amplicons, with an average of 209 amplicons. The average polymorphism level varied from 34% to 40% for all studied samples. Resolution analysis of the PBS primers showed all of them to have high or medium polymorphism levels, which varied from 0.763 to 0.965. Results of the molecular analysis of variance showed that the general biodiversity of A. ledebourianum populations is due to interpopulation (67%) and intrapopulation (33%) differences. The revealed genetic diversity was higher in the most distant population of A. ledebourianum LD64, located on the Sarymsakty ridge of Southern Altai. This is the first genetic diversity study of the endemic species A. ledebourianum using DNA profiling approaches. This work allowed us to collect new genetic data on the structure of A. ledebourianum populations in the Altai for subsequent development of preservation strategies to enhance the reproduction of this relict species. The results will be useful for the conservation and exploitation of this species, serving as the basis for further studies of its evolution and ecology.

scholarly journals Bibliometric Analysis of Studies on Tumor Organoids

2021 ◽  
Author(s):  
Qiwei Chen ◽  
Yu Zhang ◽  
Kun Li ◽  
Zhikai Zhang ◽  
Ya Wang ◽  
...  
Keyword(s):  
Future Development ◽  
Hot Spots ◽  
High Frequency ◽  
Visual Analysis ◽  
Drug Effects ◽  
Research Field ◽  
The Matrix ◽  
Genetic Mechanisms ◽  
Double Clustering ◽  
High Frequency Words

Abstract Background: Organoid is an artificially grown mass of cells or tissues, which is similar to an organ. It can replicate the complexity of an organ and can be used for gaining a better understanding of diseases. In this study, the hot spots of “organoids” were classified into 6 categories and 10 aspects, and organoids used for studying genetic mechanisms, drug effect, and metabolism of tumors showed the greatest potential for future development.Methods: A total of 1550 articles relevant to organoid in tumor research field were recruited as research samples. High-frequency words and text/co-word matrix were constructed by BICOMB software. gCLUTO software was applied to analyze the matrix by double-clustering and visual analysis subsequently to identify the hotspot in this area.Results: We constructed a text and co-word matrix composed of 21 high-frequency words and 1550 articles and generated a hotspot “peak map” based on double-clustering analysis. The strategic coordinates approach was used to assess the research prospects of each hotspot and the connections between these hotspots.Conclusions: In this study, we classified the hot-spots of “organoid” into 6 categories and 10 aspects. Calculation and analysis revealed that the field of tumor organoid shows a slight trend of polarization, and organoid for studying the genetic mechanisms, drug effects and metabolism of tumor shows the greatest potential for future development.

scholarly journals AUTOCHTHONOUS BREEDS OF DOMESTIC ANIMALS AND CONSERVATION MEASURES

AGROFOR ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Zoran MALETIC
Keyword(s):  
Genetic Diversity ◽  
Biological Diversity ◽  
Domestic Animals ◽  
Conservation Strategy ◽  
Ex Situ ◽  
Animal Genetic Resources ◽  
Diversity Preservation ◽  
The Republic ◽  
International Conventions

Recently, highly productive breeds of various species of domestic animals have been used in livestock production, which has resulted in the destruction of indigenous breeds of domestic animals around the world, even in our area. This is the first reason why indigenous races and strains have been endangered. Another reason is that domestic, indigenous breeds were crossed with specialized breeds, which were imported, and in that way their genetic diversity was negatively affected. Resistance is lost, adaptation to the conditions in which they were created, the ability to survive in nature. Indigenous breeds of different species of domestic animals, which are recognized in the Republic of Srpska (BiH) are gatačko cattle and buša (cattle), Vlašić pramenka, Podveleška pramenka, Kupres pramenka (sheep), domestic Balkan horned goat (goats), Bosnian mountain horse (horses), mangulica (pigs) and pogrmuša hen or živičarka hen (poultry). By acceding to international conventions, BiH /Republic of Srpska has committed itself to establishing a system of measures that will enable the conservation of biological diversity and the protection of indigenous and endangered breeds of domestic animals. The choice of a strategy for the conservation of diversity, the establishment of an adequate conservation scheme, and the implementation of a conservation strategy are some of the key elements of any process for the conservation of genetic diversity. Preservation of autochthonous and protected breeds of domestic animals is possible through preservation in the original environment (in situ) and preservation outside the original environment (ex situ). There is a possibility of combining these models of conservation of animal genetic resources.

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