Comparative Insilco physiochemical and phylogenetic analysis of Insulin like growth factor 1 receptor (IGF-1R) in domestic animals

2018 ◽  
Author(s):  
P R. Sahoo ◽  
G. Sahoo ◽  
P. C. Behera
Keyword(s):  
Phylogenetic Analysis ◽  
Growth Factor ◽  
Evolutionary Genetics ◽  
Domestic Animals ◽  
Amino Acid Sequences ◽  
Insulin Like Growth Factor ◽  
Multiple Sequence ◽  
Lung Cancers ◽  
Physiochemical Parameters ◽  
Time Of Divergence

Insulin like growth factor 1receptors (IGF-1R) are the proteins which are expressed on the cell surface of almost all tissues in human as well as domestic animals with major involvement in growth, cancer, aging, production and in early embryonic development. Due to above importance, this protein needs to be characterized both in physiochemical and phylogenetically for further exploration in livestock research. In this study, the IGF1R amino acid sequences of selected domestic animals are retrieved from UniProt database and various physiochemical parameters were compared through ProtParam insilco tool. The multiple sequence alignment (MSA) and phylogenetic analysis was performed through Clustal omega and Molecular evolutionary genetics analysis (MEGA) application platform respectively. It was found that this protein is an unstable, hydrophilic in all domestic animals with amino acids varied from 1307 to 1412 in number. The phylogenetic analysis showed that highest time of divergence occurs in killer whale and rabbit, but least time of divergence occurs between goat and bovine. So this study will provide a better platform for the development of suitable anticancer therapeutics in domestic animals in nearest future as IGF-1R is implicated in several cancers, including breast, prostate, and lung cancers.

scholarly journals Molecular characterization and phylogenetic analysis of NBS-LRR genes in wild relatives of eggplant (Solanum melongena L

2018 ◽  
Author(s):  
Sona. S Dev ◽  
P. Poornima ◽  
Akhil Venu
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Sequence Similarity ◽  
Interleukin 1 ◽  
Preliminary Investigation ◽  
Solanum Melongena ◽  
Wild Relatives ◽  
Amino Acid Sequences ◽  
R Genes ◽  
Multiple Sequence

Eggplantor brinjal (Solanum melongena L.), is highly susceptible to various soil-borne diseases. The extensive use of chemical fungicides to combat these diseases can be minimized by identification of resistance gene analogs (RGAs) in wild species of cultivated plants.In the present study, degenerate PCR primers for the conserved regions ofnucleotide binding site-leucine rich repeat (NBS-LRR) were used to amplify RGAs from wild relatives of eggplant (Black nightshade (Solanum nigrum), Indian nightshade (Solanumviolaceum)and Solanu mincanum) which showed resistance to the bacterial wilt pathogen, Ralstonia solanacearumin the preliminary investigation. The amino acid sequence of the amplicons when compared to each other and to the amino acid sequences of known RGAs deposited in Gen Bank revealed significant sequence similarity. The phylogenetic analysis indicated that they belonged to the toll interleukin-1 receptors (TIR)-NBS-LRR type R-genes. Multiple sequence alignment with other known R genes showed significant homology with P-loop, Kinase 2 and GLPL domains of NBS-LRR class genes. There has been no report on R genes from these wild eggplants and hence the diversity analysis of these novel RGAs can lead to the identification of other novel R genes within the germplasm of different brinjal plants as well as other species of Solanum.

In silico structural and phylogenetic analysis of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in domestic animals

2019 ◽  
Author(s):  
P.R. Sahoo ◽  
S.R. Mishra ◽  
S. Mohapatra ◽  
Santoswini Sahu ◽  
G. Sahoo ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
In Silico ◽  
Tertiary Structure ◽  
Alpha Helix ◽  
Domestic Animals ◽  
Random Coil ◽  
Local Alignment ◽  
Physiochemical Properties ◽  
Gapdh Gene ◽  
Time Of Divergence

This study has been able to determine the physiochemical properties, secondary and tertiary structure, and phylogenetic analysis of GAPDH among domestic animals under in silico platform. Eighteen nucleotide and protein sequence of GAPDH gene of different mammalian species were retrieved from National Centre for Biotechnology information (NCBI). The percentage of identity and similarity was done by Basic Local Alignment Search Tool (BLAST), physiochemical properties were analyzed by ExPASy”s ProtParam tool, the secondary and 3-D structure was predicted by GOR IV and Swiss modeling respectively. Phylogenetic analysis among the animals was done by Molecular Evolutionary Genetics Analysis. It was found that the percentage of identity and similarity among all animals were almost more than 90%. The physiochemical analysis showed this protein is very stable, hydrophilic and intracytoplasmic in nature. The secondary structure analysis showed that GAPDH has more number of random coil (49.85%) Extended strand (27.93%), alpha helix (22.22%) of the protein. The QMEAN Z score was found 0.33 under protein modeling which interfered that this protein is of comparable quality. The phylogenetic analysis of this gene showed that the highest time of divergence occurred between sheep and common chimpanzee but least time of divergence observed between killer whale and dolphin. So it can be concluded that the GAPDH gene is highly conserved along all animal species.

scholarly journals Participation of Insulin-Like Growth Factor 1 in Articular Cartilage Remodeling

2021 ◽  
pp. 22-29
Author(s):  
Tatyana Ovcharova ◽  
◽  
Yuliya Zimina ◽  
Pavel Krylov ◽  
◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Growth Factor ◽  
Cartilage Damage ◽  
Cartilage Tissue ◽  
Laboratory Research ◽  
Insulin Like Growth Factor ◽  
Related Organism ◽  
Other Substances ◽  
Long Time ◽  
Further Development

Upon cartilage damage its natural recovery takes a long time. This is due to several reasons: the absence of blood vessels and low metabolic activity. In this regard, it is relevant to study the mechanism of operation of all components involved in the remodeling of cartilage tissue. For this purpose, protein insulin-like growth factor 1 (IGF-1) was taken as an object of research, since one of its main functions is regulation of cell proliferation, which is closely related to the process of cartilage tissue repair. It is known that in recent years, scientific studies have been conducted on the effect of IGF-1 on the remodeling of cartilage tissues, but in combination with other substances that stimulate more active cell regeneration. This review presents the features of the functional properties and protein structure and its main influence on chondrocyte proliferation for further development of accelerated and effective methods of IGF-1 action on cell growth and repair. The phylogenetic analysis of IGF-1 showed the most related organism for human IGF-1 and structural differences of its protein from human, which are inextricably linked with the functional characteristics of each of the organisms. The results of phylogenetic analysis in the future will identify the object for laboratory research in this question and the search for optimal ways to accelerate the process of remodeling of cartilage joints.

Physical mapping of human insulin-like growth factor-I using specific monoclonal antibodies

1997 ◽  
Vol 154 (2) ◽  
pp. 293-302 ◽  
Author(s):  
S Mañes ◽  
L Kremer ◽  
B Vangbo ◽  
A López ◽  
C Gómez-Mouton ◽  
...  
Keyword(s):  
Monoclonal Antibodies ◽  
Growth Factor ◽  
Growth Control ◽  
Amino Acid Sequences ◽  
Insulin Like Growth Factor ◽  
Factor I ◽  
Igf I ◽  
Growth Factor I ◽  
Α Helix ◽  
Cell Growth Control

Abstract The primary structure of recombinant human (h) insulin-like growth factor-I (IGF-I) epitopes recognized by a panel of 28 monoclonal antibodies (mAbs) is characterized. Pairwise mAb epitope mapping defines eight 'epitopic clusters' (I–VIII) which cover nearly the entire solvent-exposed IGF-I surface. Monoclonal antibody reactivity with 32 overlapping synthetic peptides and with IGF-I mutants is used to associate these epitopic clusters with the probable primary IGF-I sequences recognized. Epitopic cluster I involves residues in the C-domain and the first α-helix of the A-domain; clusters II, V and VII involve principally the B-domain; clusters III and IV map to amino acid sequences (55–70) and (1–13) respectively; cluster VI includes the A- and B-domains; and cluster VIII involves mainly the C-terminal part of the B-domain. Data indicate that this mAb panel defines 14 distinct IGF-I epitopes. The specific inhibition of HEL 92.1.7 IGF-I-promoted proliferation by these mAbs was explored. Direct correlation between mAb affinity and inhibitory activity was observed except in the case of clusters III- and VII-specific mAbs. Finally, the combination of epitopic cluster I and II mAbs detect 0·5–10 ng/ml hIGF-I in a sandwich immunoassay, with no IGF-II crossreactivity. These anti-IGF-I mAbs are, therefore, useful for both the inhibition of IGF-I mitogenic activity and for the quantification of this growth factor. The potential use of this mAb panel in tumor cell growth control is discussed. Journal of Endocrinology (1997) 154, 293–302

Genetic Diversity of Cryptosporidium Spp. in Njoro Sub County, Nakuru, Kenya

2021 ◽  
Author(s):  
Walter Miding'a Essendi ◽  
Charles Inyagwa Muleke ◽  
Miheso Manfred ◽  
Elick Onyango Otachi
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Sequence Alignment ◽  
Evolutionary Genetics ◽  
Domestic Animals ◽  
Local Alignment ◽  
Cryptosporidium Spp ◽  
Potential Source ◽  
Search Tool ◽  
Great Genetic Diversity

Abstract Cryptosporidium spp. cause Cryptosporidiosis in humans through zoonotic and anthroponotic transmission. Previous studies have illustrated the significance of domestic animals as reservoirs of this parasite. However, there is no information on the Cryptosporidium spp. and genotypes circulating in Njoro Sub County. A total of 2174 samples from humans, cattle, chicken, sheep and goats were assessed for presence of Cryptosporidium spp. Thirty-three positive samples were successfully sequenced. The sequences obtained were compared to Cryptosporidium sequences in the GenBank using NCBI’s (National Center for Biotechnology Information) online BLAST (Basic Local Alignment Search Tool) algorithmic program. Sequence alignment was done using the Clustal W program and phylogenetic analysis was executed in MEGA 6 (Molecular Evolutionary Genetics Analysis version 6.0). The Cryptosporidium spp. present in the watershed showed great genetic diversity with nine (9) Cryptosporidium spp. namely: C. parvum, C. hominis, C. ubiquitum, C. meleagridis, C. andersoni, C. baileyi, C. muris, C. xiaoi and C. viatorum. Cattle were the biggest reservoirs of zoonotic Cryptosporidium spp. hence a potential source of zoonosis in humans while goats had the least species. This is the first study that reported presence of C. viatorum in Kenya.

Purification, amino acid sequences and assay cross-reactivities of porcine insulin-like growth factor-I and -II

1989 ◽  
Vol 122 (3) ◽  
pp. 681-687 ◽  
Author(s):  
G. L. Francis ◽  
P. C. Owens ◽  
K. A. McNeil ◽  
J. C. Wallace ◽  
F. J. Ballard
Keyword(s):  
Amino Acid ◽  
Growth Factor ◽  
Mammalian Species ◽  
Cross Reactivity ◽  
Porcine Insulin ◽  
Amino Acid Sequences ◽  
Insulin Like Growth Factor ◽  
Factor I ◽  
Igf I ◽  
Growth Factor I

ABSTRACT Porcine insulin-like growth factor-I (IGF-I) and IGF-II have been characterized to help define the roles of these peptides in the growth process. The amino acid sequence of porcine IGF-I was found to be identical to the human and bovine peptides. Porcine IGF-II was more similar to human IGF-II than to forms of this growth factor in other mammalian species, differing only in the replacement of asparagine for serine at residue 36. In a biological assay that measures the stimulation of protein synthesis in rat L6 myoblasts, porcine IGF-I was approximately ninefold more potent than porcine IGF-II or bovine IGF-II, while recombinant human IGF-I and IGF-II had half the potency of the respective natural peptides. Porcine and recombinant human IGF-I showed essentially equal competition for binding in a human IGF-I radioimmunoassay while between 0·6 and 1·5% cross-reactivity was observed with human, bovine or porcine IGF-II. A receptor assay for IGF-II demonstrated similar potencies for the three IGF-II peptides, while the cross-reactivity of recombinant human IGF-I was only 0·05%. Porcine IGF-I exhibited a higher cross-reactivity, presumably due to very slight contamination with IGF-II. Journal of Endocrinology (1989) 122, 681–687

scholarly journals Measuring Historical and Compositional Signals in Phylogenetic Data

2020 ◽  
Author(s):  
Lars S Jermiin ◽  
Bernhard Misof
Keyword(s):  
Phylogenetic Analysis ◽  
Model Selection ◽  
Simulated Data ◽  
Evolutionary Processes ◽  
Multiple Sequence ◽  
Phylogenetic Methods ◽  
Phylogenetic Data ◽  
Molecular Phylogenetic ◽  
Full Symmetry ◽  
Time Of Divergence

AbstractMost commonly-used molecular phylogenetic methods assume that the sequences evolved on a single bifurcating tree and that the evolutionary processes operating at the variable sites are Markovian. Typically, it is also assumed that these evolutionary processes were stationary, reversible and homogenous across the edges of the tree and that the multiple substitutions at variable sites occurred so infrequently that the historical signal (i.e., the signal in DNA that is due to the order and time of divergence event) in phylogenetic data has been retained, allowing for accurate phylogenetic estimates to be obtained from the data. Here, we present two metrics, λ and δCFS, to quantify the strength of the historical and compositional signals in phylogenetic data. λ quantifies loss of historical signal, with λ = 0.0 indicating evidence of a strong historical signal and λ = 1.0 indicating evidence of a fully eroded historical signal. δCFS quantifies compositional distance from full symmetry of a divergence matrix generated by comparing two sequences, with δCFS = 0.0 indicating no evidence of evolution under dissimilar conditions and δCFS > 0.0 indicating increasing evidence of lineages diverging under different conditions. The metrics are implemented in methods intended for use after multiple sequence alignment and before model selection and phylogenetic analysis. Results generated using these methods allow users of phylogenetic tools to select phylogenetic data more wisely than it previously was possible. The merits of these metrics and methods are illustrated using simulated data and multi-gene alignments obtained from 144 insect genomes.

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