scholarly journals Sequence Characterization of Glutamate Receptor Genes of Rat a Vertebrate and Arabidopsis Thaliana a Plant

2018 ◽  
Author(s):  
Antara Sengupta ◽  
Pabitra Pal Choudhury ◽  
Subhadip Chakraborty
Keyword(s):  
Amino Acids ◽  
Arabidopsis Thaliana ◽  
Gene Family ◽  
Phylogenetic Trees ◽  
Chemical Properties ◽  
Protein Sequences ◽  
Data Set ◽  
Sequence Characterization ◽  
Conserved Regions ◽  
Long Course

AbstractiGluR gene family of a vertebrate, Rat and AtGLR gene family of a plant, Arabidopsis thaliana [4] perform some common functionalities in neuro-transmission, which have been compared quantitatively. Our attempt is based on the chemical properties of amino acids [6, 7, 8] comprising the primary protein sequences of the aforesaid genes. 19 AtGLR genes of length varying from 808 amino acid (aa) to 1039 aa and 16 iGluR genes length varying from 902aa to 1482 aa have been taken as data sets. Thus, we detected the commonalities (conserved elements) during the long evolution of plants and animals from a common ancestor [4]. Eight different conserved regions have been found based on individual amino acids. Two different conserved regions are also found, which are based on chemical groups of amino acids. We have tried too to find different possible patterns which are common throughout the data set taken. 9 such patterns have been found with size varying from 2 to 5 amino acids at different regions in each primary protein sequences. Phylogenetic trees of AtGLR and iGluR families have also been constructed. This approach is likely to shed light on the long course of evolution.

scholarly journals Chemical characterizations of Neurotransmission Receptors of human and plant to unfold the evolutionary relationships among them

2021 ◽  
Author(s):  
ANTARA SENGUPTA ◽  
SUBHADIP CHAKRABORTY ◽  
PABITRA PAL CHOUDHURY
Keyword(s):  
Amino Acids ◽  
Nervous System ◽  
Comparative Study ◽  
Phylogenetic Trees ◽  
Chemical Properties ◽  
Protein Sequences ◽  
Close Relation ◽  
Receptor Protein ◽  
Evolutionary Relationships ◽  
Numerical Representation

Abstract Vertebrates have very well defined nervous system. It is established that plant also has an alternative sort of sensitive nervous system. Researchers find a close relationship of the neurotransmission mechanism of animal with the plant and suspects close relation in amino acid transport mechanism among both the organisms. Along with the abilities of determining protein structure and various functions, the chemical properties of amino acids also have great contribution in molecular evolution. Hence, in this present work it is aimed at making comparative study on the distribution of amino acids in the neurotransmission receptors associated to animals and plants, based on the chemical properties the amino acids contain. It is possible to classify 20 amino acids into 8 chemical groups and are identified by specific numeric value. The common pattern finding procedure in numerical representation of protein sequences find some conserved regions in the receptor protein sequences of both the species. The comparative study has been made on distributions of chemical properties in protein sequences of ionotropic glutamate receptor protein sequences and GABA receptor protein sequences of two species namely human, a vertebrate and Arabidopsis thaliana, a plant. Experiments have been carried out to calculate proximity between protein sequences based on the distribution of each chemical group (in percentage) in them and phylogenetic trees have been constructed to find evolutionary relationships of neurotransmission receptors of both the spices.

scholarly journals NeoCoV Is Closer to MERS-CoV than SARS-CoV

2020 ◽  
Vol 13 ◽  
pp. 117863372093071
Author(s):  
Mohamed M Hassan ◽  
Mohamed A Hussain ◽  
Sumaya Kambal ◽  
Ahmed A Elshikh ◽  
Osama R Gendeel ◽  
...  
Keyword(s):  
Amino Acids ◽  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Chemical Properties ◽  
Structural Formula ◽  
Likelihood Method ◽  
Evolutionary Changes ◽  
Whole Genomes ◽  
Physical And Chemical ◽  
The Relationship

Recently, Coronavirus has been given considerable attention from the biomedical community based on the emergence and isolation of a deadly coronavirus infecting human. To understand the behavior of the newly emerging MERS-CoV requires knowledge at different levels (epidemiologic, antigenic, and pathogenic), and this knowledge can be generated from the most related viruses. In this study, we aimed to compare between 3 species of Coronavirus, namely Middle East Respiratory Syndrome (MERS-CoV), Severe Acute Respiratory Syndrome (SARS-CoV), and NeoCoV regarding whole genomes and 6 similar proteins (E, M, N, S, ORF1a, and ORF1ab) using different bioinformatics tools to provide a better understanding of the relationship between the 3 viruses at the nucleotide and amino acids levels. All sequences have been retrieved from National Center for Biotechnology Information (NCBI). Regards to target genomes’ phylogenetic analysis showed that MERS and SARS-CoVs were closer to each other compared with NeoCoV, and the last has the longest relative time. We found that all phylogenetic methods in addition to all parameters (physical and chemical properties of amino acids such as the number of amino acid, molecular weight, atomic composition, theoretical pI, and structural formula) indicated that NeoCoV proteins were the most related to MERS-CoV one. All phylogenetic trees (by both maximum-likelihood and neighbor-joining methods) indicated that NeoCoV proteins have less evolutionary changes except for ORF1a by just maximum-likelihood method. Our results indicated high similarity between viral structural proteins which are responsible for viral infectivity; therefore, we expect that NeoCoV sooner may appear in human-related infection.

scholarly journals Protein sequence comparison under a new complex representation of amino acids based on their physio-chemical properties

2018 ◽  
Vol 7 (1.8) ◽  
pp. 181
Author(s):  
Jayanta Pal ◽  
Soumen Ghosh ◽  
Bansibadan Maji ◽  
Dilip Kumar Bhattacharya
Keyword(s):  
Amino Acids ◽  
Protein Sequence ◽  
Sequence Comparison ◽  
Phylogenetic Trees ◽  
Protein Sequences ◽  
Complex Representation ◽  
Hydrophobic Property ◽  
The Real ◽  
Pair Wise Comparison ◽  
Protein Sequence Comparison

The paper first considers a new complex representation of amino acids of which the real parts and imaginary parts are taken respectively from hydrophilic properties and residue volumes of amino acids. Then it applies complex Fourier transform on the represented sequence of complex numbers to obtain the spectrum in the frequency domain. By using the method of ‘Inter coefficient distances’ on the spectrum obtained, it constructs phylogenetic trees of different Protein sequences. Finally on the basis of such phylogenetic trees pair wise comparison is made for such Protein sequences. The paper also obtains pair wise comparison of the same protein sequences following the same method but based on a known complex representation of amino acids, where the real and imaginary parts refer to hydrophobicity properties and residue volumes of the amino acids respectively. The results of the two methods are now compared with those of the same sequences obtained earlier by other methods. It is found that both the methods are workable, further the new complex representation is better compared to the earlier one. This shows that the hydrophilic property (polarity) is a better choice than hydrophobic property of amino acids especially in protein sequence comparison.

scholarly journals The gene annotated by the locus tag At3g08860 encodes a β-alanine/L-alanine aminotransferase in Arabidopsis thaliana

2019 ◽  
Author(s):  
Anutthaman Parthasarathy ◽  
Francisco C. Savka ◽  
André O. Hudson
Keyword(s):  
Amino Acids ◽  
Arabidopsis Thaliana ◽  
Gene Family ◽  
Alanine Aminotransferase ◽  
Nitrogen Utilization ◽  
Utilization Efficiency ◽  
E Coli ◽  
Model Plant ◽  
Nitrogen Utilization Efficiency ◽  
Vitamin B5

AbstractThe aminotransferase gene family in the model plant Arabidopsis thaliana consists of 44 genes some of which remain uncharacterized. This study elucidates the function of an uninvestigated aminotransferase annotated by the locus tag At3g08860. The cDNA was shown to functionally complement two E. coli mutants auxotrophic for the amino acids β-alanine (non-proteogenic) and L-alanine (proteogenic). The elucidation of At3g08860 activity has the potential to facilitate experiments for the optimization of plant lines involved in nitrogen utilization efficiency, response to hypoxia, osmo-protection, vitamin B5 and coenzyme A metabolism.

scholarly journals Molecular characterization of duplicate cytosolic phosphoglucose isomerase genes in Clarkia and comparison to the single gene in Arabidopsis.

Genetics ◽  
1993 ◽  
Vol 135 (3) ◽  
pp. 895-905 ◽  
Author(s):  
B R Thomas ◽  
V S Ford ◽  
E Pichersky ◽  
L D Gottlieb
Keyword(s):  
Amino Acids ◽  
Arabidopsis Thaliana ◽  
Nucleotide Sequence ◽  
Fragment Length Polymorphism ◽  
Single Gene ◽  
Protein Sequences ◽  
Phosphoglucose Isomerase ◽  
A Site ◽  
Restriction Fragment Length

Abstract The nucleotide sequence of PgiC1-a which encodes a cytosolic isozymes of phosphoglucose isomerase (PGIC; EC 5.3.1.9) in Clarkia lewisii, a wildflower native to California, is described and compared to the previously published sequence of the duplicate PgiC2-a from the same genome. Both genes have the same structure of 23 exons and 22 introns located in identical positions, and they encode proteins of 569 amino acids. Exon and inferred protein sequences of the two genes are 96.4% and 97.2% identical, respectively. Intron sequences are 88.2% identical. The high nucleotide similarity of the two genes is consistent with previous genetic and biosystematic findings that suggest the duplication arose within Clarkia. A partial sequence of PgiC2-b was also obtained. It is 99.5% identical to PgiC2-a in exons and 99.7% in introns. The nucleotide sequence of the single PgiC from Arabidopsis thaliana was also determined for comparison to the Clarkia genes. The A. thaliana PgiC has 21 introns located at positions identical to those in Clarkia PgiC1 and PgiC2, but lacks the intron that divides Clarkia exons 21 and 22. The A. thaliana PGIC protein is shorter, with 560 amino acids, and differs by about 17% from the Clarkia PGICs. The PgiC in A. thaliana was mapped to a site 20 cM from restriction fragment length polymorphism marker 331 on chromosome 5.

ADAPTIVE CAPACITY OF EINKORN HUSKLESS IN THE SECOND, THIRD AND SEVENTH RUSSIAN FEDERATION REGIONS

1970 ◽  
pp. 34-38
Author(s):  
S. K. Temirbekova ◽  
M. Sh. Begeulov ◽  
Yu. V. Afanaseva ◽  
I. M. Kulikov ◽  
N. E. Ionova
Keyword(s):  
Amino Acids ◽  
Biochemical Analysis ◽  
Chemical Properties ◽  
First Grade ◽  
Essential Amino Acids ◽  
Wheat Grain ◽  
Volume Yield ◽  
Class 1 ◽  
Group B ◽  
Field And Laboratory Conditions

Biochemical, immunological and physico-chemical properties of an ancient wheat grain – hulless spelt cultivar Gremme are investigated. Biochemical analysis of grain revealed a high content of protein, fiber, macro-and microelements, a rich composition of essential amino acids, which is characteristic of ancient wheat species. Evaluated milling and baking properties of spelt flour. Physical and chemical parameters of spelt grain met the requirements for soft wheat grain class 1: the mass fraction of gluten-38.7 %, the nature of the grain-795 g / l, the number of drops-416 C, the total vitreousness-70 %. However, gluten had an increased stickiness, which is obviously due to the increased content of fiber and gliadin fraction. Grinding of spelt grain was carried out on the aggregate mill installation "Miller 100 Lux" to obtain baking flour of various cultivars. The overall yield of flour of the first grinding was 59.7 %. The highest volume yield (359 cm3) and the best organoleptic properties (total baking score – 3.6 points) were observed in a sample of bread baked from spelt flour that meets the requirements for wheat baking flour of the first grade. Studies have confirmed the possibility of using flour produced from the spelt grain of the Gremme variety for the production of bakery products of increased biological, therapeutic and prophylactic, nutritional value and with a high organoleptic rating. Cereals and flour are very rich in trace elements-manganese, selenium, zinc, potassium, iron, phosphorus, vitamins from group B and B, essential amino acids (biochemical analysis was carried out by the Cherkizovo Center). The cultivar is resistant to drought, heat, excessive moisture. Proved immunological properties to several diseases in the field and laboratory conditions-resistant to enzyme-mycotic seed depletion (EMIS), various types of rust, powdery mildew.

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