scholarly journals In-silico Structural Annotation of Methylthioadenosine Nucleosidase Protein Zm00014a_031618 in Maize (Zea mays L.)

2019 ◽  
pp. 1-8
Author(s):  
Gali Adamu Ishaku
Keyword(s):  
Zea Mays ◽  
In Silico ◽  
3D Structure ◽  
Alpha Helix ◽  
Random Coil ◽  
Chemical Parameters ◽  
Structural Annotation ◽  
In Silico Studies ◽  
Physical And Chemical Parameters ◽  
Physical And Chemical

Aims: The aim of this study was In-Silico structural annotation of an amino acid sequence of Methylthioadenosine Nucleosidase Protein Zm00014a_031618 in Maize (Zea mays) retrieved from NCBI with the accession number PWZ58979. Study Design: The use of In-Silico studies for the structural annotation of Methylthioadenosine Nucleosidase protein. Place and Duration of Study: The research was conducted at the Bioinformatics Laboratory, Chevron Biotechnology Centre, Modibbo Adama University of Yola, Nigeria. Between June 2018 to July 2018. Methodology: The Methylthioadenosine Nucleosidase protein was retrieved from NCBI, physical and chemical parameters were calculated using ExPASy - ProtParam tool, the server SOPMA was used for secondary structure analysis (helix, sheets, and coils) and I-TASSER was used to obtain the 3D structure. Results: ExPASy - Prot Param tool computated the various physical and chemical parameters such as molecular weight (MW) 30117.97, total number of positively (+R) 27, negatively charged residues (-R) 30, theoretical isoelectric point (pI) 5.96, aliphatic index (AI) 103.67 and grand average hydropathy (GRAVY) 0.293. The SOPMA server was used for calculating the secondary structural features of protein sequences as Alpha helix 39.16%, Extended strand 14.69%, Beta turn 6.64% and Random coil 39.51%. I-Tasser was used for predicting the 3D structure where 2qttA from PDB was used as the template. Conclusion: This study helped in understanding the structural analysis of the Methylthioadenosine Nucleosidase Protein Zm00014a_031618 in maize (Z. mays).

scholarly journals In-silico characterization and structure-based functional annotation of a hypothetical protein from Campylobacter jejuni involved in propionate catabolism

2021 ◽  
Vol 19 (4) ◽  
pp. e43
Author(s):  
Lincon Mazumder ◽  
Mehedi Hasan ◽  
Ahmed Abu Rus'd ◽  
Mohammad Ariful Islam
Keyword(s):  
Campylobacter Jejuni ◽  
Protein Interactions ◽  
In Silico ◽  
Functional Annotation ◽  
3D Structure ◽  
Alpha Helix ◽  
Hypothetical Protein ◽  
Random Coil ◽  
Protein Protein Interactions ◽  
In Silico Characterization

Campylobacter jejuni is one of the most prevalent organisms associated with foodborne illness across the globe causing campylobacteriosis and gastritis. Many proteins of C. jejuni are still unidentified. The purpose of this study was to determine the structure and function of a non-annotated hypothetical protein (HP) from C. jejuni. A number of properties like physiochemical characteristics, 3D structure, and functional annotation of the HP (accession No. CAG2129885.1) were predicted using various bioinformatics tools followed by further validation and quality assessment. Moreover, the protein-protein interactions and active site were obtained from the STRING and CASTp server, respectively. The hypothesized protein possesses various characteristics including an acidic pH, thermal stability, water solubility, and cytoplasmic distribution. While alpha-helix and random coil structures are the most prominent structural components of this protein, most of it is formed of helices and coils. Along with expected quality, the 3D model has been found to be novel. This study has identified the potential role of the HP in 2-methylcitric acid cycle and propionate catabolism. Furthermore, protein-protein interactions revealed several significant functional partners. The in-silico characterization of this protein will assist to understand its molecular mechanism of action better. The methodology of this study would also serve as the basis for additional research into proteomic and genomic data for functional potential identification.

The influence of gelatin and starter culture on the physical and chemical parameters of cheeses with different fat content

2018 ◽  
Vol 6 (10) ◽  
pp. 123-130
Author(s):  
Yaroslava Zhukova ◽  
◽  
Pylyp Petrov ◽  
Olena Boloba ◽  
Tetiana Ohrimenko ◽  
...  
Keyword(s):  
Starter Culture ◽  
Fat Content ◽  
Chemical Parameters ◽  
Physical And Chemical Parameters ◽  
Physical And Chemical

In Silico Study of 1, 4 Alpha Glucan Branching Enzyme and Substrate Docking Studies

2020 ◽  
Vol 17 (1) ◽  
pp. 40-50
Author(s):  
Farzane Kargar ◽  
Amir Savardashtaki ◽  
Mojtaba Mortazavi ◽  
Masoud Torkzadeh Mahani ◽  
Ali Mohammad Amani ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
In Silico ◽  
Alpha Helix ◽  
In Silico Analysis ◽  
Glycogen Storage ◽  
Docking Studies ◽  
Random Coil ◽  
Special Topic ◽  
Industrial Biotechnology ◽  
In Silico Study

Background: The 1,4-alpha-glucan branching protein (GlgB) plays an important role in the glycogen biosynthesis and the deficiency in this enzyme has resulted in Glycogen storage disease and accumulation of an amylopectin-like polysaccharide. Consequently, this enzyme was considered a special topic in clinical and biotechnological research. One of the newly introduced GlgB belongs to the Neisseria sp. HMSC071A01 (Ref.Seq. WP_049335546). For in silico analysis, the 3D molecular modeling of this enzyme was conducted in the I-TASSER web server. Methods: For a better evaluation, the important characteristics of this enzyme such as functional properties, metabolic pathway and activity were investigated in the TargetP software. Additionally, the phylogenetic tree and secondary structure of this enzyme were studied by Mafft and Prabi software, respectively. Finally, the binding site properties (the maltoheptaose as substrate) were studied using the AutoDock Vina. Results: By drawing the phylogenetic tree, the closest species were the taxonomic group of Betaproteobacteria. The results showed that the structure of this enzyme had 34.45% of the alpha helix and 45.45% of the random coil. Our analysis predicted that this enzyme has a potential signal peptide in the protein sequence. Conclusion: By these analyses, a new understanding was developed related to the sequence and structure of this enzyme. Our findings can further be used in some fields of clinical and industrial biotechnology.

scholarly journals Analisis Kesesuaian Perairan untuk Keramba Jaring Apung di Kecamatan Sirah Pulau Padang Kabupaten Ogan Komering Ilir Provinsi Sumatera Selatan

2019 ◽  
Vol 8 (1) ◽  
pp. 20-30
Author(s):  
Rangga Bayu Kusuma Haris ◽  
Indah Anggraini Yusanti
Keyword(s):  
Water Quality ◽  
Current Velocity ◽  
Quality Parameters ◽  
Chemical Parameters ◽  
Chemical Laboratory ◽  
M Current ◽  
Bottom Substrate ◽  
A Value ◽  
Physical And Chemical Parameters ◽  
Physical And Chemical

Haris et al, 2019. The Analysis of Water Suitability for Floating Net Sprouts in Sirah Pulau Padang, Ogan Komering Ilir District, South Sumatra Province. JLSO 8(1):20-30.The purpose of this study is to analyze the level of water suitability of the floating net sprouts in sirah pulau padang, ogan komering river, Serdang Menang Village, OKI South Sumatra Regency based on water physical and chemical parameters. This study was conducted on July - August 2018 at the Komering River, Ulak Jermun village, Terusan Menang Village, and Mangun Jaya Village, OKI District, South Sumatra. The data of sampling was divided into 3 stations, they were; station 1 was Ulak Jermun Village (3 ° 18'45.48 "LS and 104 ° 53'5.32" BT), station 2 was Terusan Menang Village (3 ° 17'14.13 "LS and 104 ° 52'46.78 "BT), and station 3 was Mangun Jaya village (3 ° 18'14.92" LS and 104 ° 52'59.48 "BT). The data of Samples were tested at the chemical laboratory in Palembang Public Water Fisheries and Extension Research Institute directly. The results of the study was for Station 1, Station 2, and Station 3 with a value was  48% with a good feasibility information. The results of measurements of water quality parameters, the pH was about 6.6 - 6.7, temperature was about from 24., 53 - 26.93oC, DO 3.93 - 4.36 mg / l, ammonia was about 0.78 - 0.16 mg / l, water brightness was about from 34.67 - 43.33 cm, CO2 4.53 - 5.03 mg / l, depth 2.36 - 2.47 m, current velocity was about 0.38 - 0.44 m / s, nitrate was about 0.37 - 0.439 mg / l, phosphate was about 0.009 - 0.225 mg / l and the bottom substrate of water was mud.

scholarly journals The first report of ants (Formicidae: Hymenoptera) in salt marshes and salt pans in central parts of Iran

2019 ◽  
Vol 20 (9) ◽  
Author(s):  
MOHAMMAD REZA MOHSENI ◽  
SHAHROKH PASHAEI RAD
Keyword(s):  
Salt Marshes ◽  
Dominant Species ◽  
Salt Lake ◽  
Vegetation Density ◽  
Chemical Parameters ◽  
Salt Pans ◽  
Mountain Station ◽  
Physical And Chemical Parameters ◽  
Physical And Chemical ◽  
First Time

The present study was conducted in Salt marshes and Salt pans in central parts of Iran. 121 specimens of ants were collected by trapping and hand during spring, summer and autumn 2017 to 2019. Nine species belong to two subfamilies of Myrmicinae and Formicinae were identified. The vegetation, physical and chemical parameters of soil such as salinity, Ph, and other factors were investigated. Darband Shoor Mountain station with five species had the highest diversity and vegetation density and the lowest salinity of soil (72.14 ds/m) whereas Salt Lake station had only one species, with no vegetation and the highest salinity of soil (153.15 ds/m). Cataglyphis lividus (André, 1881) was the dominant species in all the stations except in Darband Shoor Mountain station. All the species were reported for the first time from salt marshes and salt pans in the central parts of Iran and were approved by Prof. Brian Taylor, in Royal Entomological Society of London, England.

scholarly journals Bioecology of Manggabai Fish (Glossogobius giuris) in Limboto Lake

2020 ◽  
Vol 4 (2) ◽  
pp. 89
Author(s):  
Dewi Nuryanti Fazrin ◽  
Hasim Hasim ◽  
Juliana Juliana
Keyword(s):  
Fishing Gear ◽  
Residential Areas ◽  
Chemical Parameters ◽  
Fish Traps ◽  
Physical And Chemical Parameters ◽  
Glossogobius Giuris ◽  
Net Cages ◽  
Physical And Chemical ◽  
Traditional Fishing ◽  
The Relationship

The purpose of this study was to determine the relationship between the length and weight of Manggabai fish (Glossogobius giuris) and to know the relationship between the presence of Manggabai fish (Glossogobius giuris) and water quality in Limboto Lake. This research was conducted in February 2019, located in the waters of Lake Limboto, Gorontalo Province. The method used in determining the location of sampling is Purposive Sampling. Fish sampling is determined by considering fishing locations, litoral areas, the presence of residential areas, agricultural and plantation areas, the existence of floating net cages and in the middle of the lake. The study was conducted at 20 observation stations using fish traps in the form of bamboo and used motorcycle tires that have been modified and become traditional fishing gear. The results showed that the physical and chemical parameters in Lake Limboto and showed temperature values ​​ranged from 29.77 to 31.630C, dissolved oxygen levels ranged from 2.1 to 5.48 ppm, pH ranged from 7.09 to 8.94, TDS ranging from 0.251 to 0.369, Nitrite Levels 0.04-0.08 ppm, Nitrate Levels 1.2-4.7 ppm, BOD ranges from 2.5-57 ppm and phosphate levels 0.1-1.14 ppm. The relationship between length and body weight of fish are allometric, where W = 0.8769 L10,023 and constant b (10,023)> 3.

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