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Domestication and Genome Evolution
Glazko,
Valeriy,
Zybaylov,
Boris,
Glazko,
Tatiana
Issue:
Volume 2, Issue 4, August 2014
Pages:
47-56
Received:
18 July 2014
Accepted:
30 July 2014
Published:
10 August 2014
Abstract: Background. Pressure on modern agriculture to increase production is rising with the increase in human population. To meet this demand it is important to effectively manage domesticated species. However, genetic mechanisms and genomic targets of domestication are still poorly understood. It is well known that phenotypic variability in domesticated animals is higher compared to the variability in the closest wild relatives. Indeed, there are many breeds clearly distinguishable from each other by their morphological and physiological traits. In this report we review some of available literature and present original data to define genomic targets of domestication. Results. Using both publically available data and results of our own research we demonstrate the existence of a well-defined genomic signature (also called “sub-genome”), which consists of the molecular targets of artificial selection. The genetic signatures of domestication are revealed by comparison of different mammalian species and breeds. As a result, we found that a wide repertoire of genes is involved in the domestication process. The vast majority of these genes either plays a role in the neuroendocrine regulation, immune response, or encodes the milk proteins. Comparison of cattle genome to wild relatives reveals higher degree of polymorphism within retrotransposons, enzymes of the exogenous substrate metabolism, and in the genetic elements associated with the immune system. Conclusions. Our data for first time challenges the current explanation of phenotypic variation in domesticated species as a consequence of inbreeding and concomitant increase in homozygosity. Instead, we clearly show that there is no difference in the bulk genetic variability, and other explanation for difference in phenotypic variability is needed. We discover different targets of natural and artificial selection: in the case of domesticated species systems that are responsible for exogenous substrate metabolism are the targets, while in the case of wild species, genetic systems that are responsible for energy metabolism are targeted. We further speculate that the hyperactivity of mobile genetic elements – as evident from the higher polymorphisms within retro transposons – could be the source of increased genetic variability in domesticated species.
Abstract: Background. Pressure on modern agriculture to increase production is rising with the increase in human population. To meet this demand it is important to effectively manage domesticated species. However, genetic mechanisms and genomic targets of domestication are still poorly understood. It is well known that phenotypic variability in domesticated ...
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Molecular Evolution of Key Receptor Genes in Primates and Non-Human Primates
Barbara Picone,
Alan Christoffels
Issue:
Volume 2, Issue 4, August 2014
Pages:
57-61
Received:
25 July 2014
Accepted:
6 August 2014
Published:
20 August 2014
Abstract: African primates remain an unexplored source of information required to complete the origin and evolution of many human pathogens. Current studies have shown the importance of several receptor human genes implicated in host resistance or susceptibility to tuberculosis. The validation of these genes in Mycobacterium tuberculosis infection makes them an excellent model system to investigate the mode of selective pressures that may act on pathogen defense genes. To trace the evolutionary history of these genes, the report describes preliminary results for eight receptors human genes having either a significant or a possible association with Tuberculosis (TB). By using a combination of maximum likelihood approaches, evidence of positive selection were detected for four genes. The analysis between species, nevertheless, shows a clear pattern of nucleotide variation mostly compatible with purifying selection.
Abstract: African primates remain an unexplored source of information required to complete the origin and evolution of many human pathogens. Current studies have shown the importance of several receptor human genes implicated in host resistance or susceptibility to tuberculosis. The validation of these genes in Mycobacterium tuberculosis infection makes them...
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In Silico Identification of Novel Candidate Drug Targets in Haemophilus Influenzae Rd KW20
Ranjith Kumavath,
Swaraj Prasad,
Pratap Devarapalli,
Debmalya Barh
Issue:
Volume 2, Issue 4, August 2014
Pages:
62-67
Received:
21 July 2014
Accepted:
7 August 2014
Published:
20 August 2014
Abstract: Background: Globally, respiratory diseases cause an estimated 1.9 million deaths per year. One of the most important aetiological organisms of both adult and childhood respiratory disease is Non-Typeable Haemophilus influenzae (NTHi). NTHi is frequently isolated from the respiratory tract during episodes of sinusitis, Otitis Media and pneumonia and is the most common cause of Chronic Obstructive Pulmonary Disease (COPD) and bronchiectasis exacerbations. Methods: The work has been effectively complemented with the compilation of the Database of Essential Genes (DEG) of H. influenzae Rd KW20. Each protein is subjected to BLASTP in NCBI server http://www.ncbi.nlm.nih.gov/blastp. The candidate drug targets are determined by KAAS (KEGG Automatic Annotation Server), KEGG ORTHOLOGY and KEGG GENES. Results: The given gram negative bacteria H. influenzae Rd KW20 has six distinguished domains i.e., cytoplasmic, cytoplasmic membrane, periplasmic, outer membrane, extracellular and unknown domains. Out of 642 essential genes, the predicted non-human Homologous are 412 in the different domain of given bacteria. With the help of KAAS (KEGG Automatic Annotation Server), KEGG ORTHOLOGY and KEGG GENES, we successfully identified 35 novel drug targets which have common metabolic pathways both in host and pathogen & pathogen specific metabolic pathways. Conclusion: The novel drug targets suggest those genes which are active in both the host and pathogen metabolic pathway and should be a pathogen specific metabolic pathway. The important drug target regions are vacJ, lepB, emrB, MurG & dgkA. vacJ is present in outer membrane while lepB, emrB, MurG&dgkA are present in cytoplasmic membrane. All these genes are fully sequenced and specifically annotated in KEGG PATHWAY.
Abstract: Background: Globally, respiratory diseases cause an estimated 1.9 million deaths per year. One of the most important aetiological organisms of both adult and childhood respiratory disease is Non-Typeable Haemophilus influenzae (NTHi). NTHi is frequently isolated from the respiratory tract during episodes of sinusitis, Otitis Media and pneumonia and...
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Linkage Disequilibrium and the Mapping of Human Disease Genes
Nahid Askari,
Amin Baghizadeh
Issue:
Volume 2, Issue 4, August 2014
Pages:
68-76
Received:
30 June 2014
Accepted:
15 July 2014
Published:
20 August 2014
Abstract: Identification of human disease genes can be accomplished by two strategies: functional cloning and positional cloning. Genetic mapping is the localization of genes underlying phenotypes on the basis of correlation with DNA variation, without the need for prior hypotheses about biological function and the simplest form, called linkage analysis. The ability to clone and sequence DNA made it possible to tie genetic linkage maps in model organisms to the underlying DNA sequence. In conclusion particular alleles at neighboring loci tend to be co-inherited. For tightly linked loci, this might lead to associations between alleles known as linkage disequilibrium (LD). Considerable effort and expense have been expended in whole-genome screens aimed at detection of genetic loci contributing to the susceptibility to complex human diseases.
Abstract: Identification of human disease genes can be accomplished by two strategies: functional cloning and positional cloning. Genetic mapping is the localization of genes underlying phenotypes on the basis of correlation with DNA variation, without the need for prior hypotheses about biological function and the simplest form, called linkage analysis. The...
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Trisomy 19 as the Sole Chromosomal Abnormality in CML
Salil N. Vaniawala,
Pankaj K. Gadhia
Issue:
Volume 2, Issue 4, August 2014
Pages:
77-79
Received:
4 August 2014
Accepted:
19 August 2014
Published:
30 August 2014
Abstract: Presence of trisomy 19 in chronic myeloid leukemia (CML) normally considered as secondary abnormality but trisomy 19 rarely occur as sole abnormality. In the present study a total of 2312 Ph positive CML were screened from year2004 to 2014 and we found 2 cases of trisomy 19 as sole karyotype abnormalities. Both karyotype showed 47,XY,t(9;22)(q34;q11.2),+19,complements. It is not known that which gene(s) present on chromosome 19 plays important role in development of this condition.
Abstract: Presence of trisomy 19 in chronic myeloid leukemia (CML) normally considered as secondary abnormality but trisomy 19 rarely occur as sole abnormality. In the present study a total of 2312 Ph positive CML were screened from year2004 to 2014 and we found 2 cases of trisomy 19 as sole karyotype abnormalities. Both karyotype showed 47,XY,t(9;22)(q34;q1...
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