142 DESIGN OF ANTIBODIES SPECIFIC FOR PEPTIDES PRESENT EXCLUSIVELY IN DIFFERENT MEMBERS OF THE PREGNANCY ASSOCIATED GLYCOPROTEINS FAMILY

2010 ◽  
Vol 22 (1) ◽  
pp. 230
Author(s):  
J. I. Ruiz Álvarez ◽  
J. M. Teijeiro ◽  
A. R. Charmandarian ◽  
J. P. Haumüller ◽  
P. E. Marini
Keyword(s):  
Early Pregnancy ◽  
In Silico ◽  
Bovine Genome ◽  
In Silico Analysis ◽  
Immunological Methods ◽  
Santa Fe ◽  
Dot Blot ◽  
Essential Components ◽  
Silico Analysis ◽  
Peptide Antibodies

Accurate diagnosis of non-pregnancy and prompt re-enlistment of cattle into an appropriate breeding protocol are essential components of successful reproductive programs. The search for biochemical markers of early pregnancy has led to the characterization of the pregnancy-associated glycoproteins (PAG), a large family expressed exclusively in the placenta. In cattle, the PAG family is composed of at least 22 translated genes, with different spatiotemporal expression (Telugu B. et al. 2009 BMC Genomics 10, 185). The PAG may be detected in placenta and some members have been detected in serum by immunological methods (Garmo B et al. 2008 J. Dairy Sci. 91, 3025-3033). However, the lack of antibodies specific for different PAG has prevented the identification of any member of the family as being present in serum at early pregnancy and undetectable after parturition. The objective of this study was to develop a method that allows the preparation of antibodies specific for different PAG, as candidates of early pregnancy markers. The method employed was in silico analysis of the bovine PAG family members that have been reported as of early expression in placenta and in binucleated cells (which are fusion cells between maternal and embryonic tissues), searching for peptide regions that differ between them. Selected peptides were analyzed for localization in reported exposed regions, antigenicity in the protein context, lack of consensus sequences for post-translational modifications and of putative homologous peptides using the reported bovine genome, and feasibility of chemical synthesis with low rates of contamination. Chosen peptides were synthesized by a facility and coupled to rabbit albumin. Rabbits were immunized and the serum was analyzed for the presence of specific antibodies. After in silico analysis, 43 candidate peptides contained in 13 different PAG were considered suitable. Four of these were chosen for synthesis and coupled successfully to rabbit albumin. Rabbits were immunized with peptide-rabbit albumin, according to procedures used by Bioterio of Facultad de Ciencias Bioquímicas y Farmacéuticas, UNR. Analysis of the obtained serum by dot-blot showed the presence of anti-peptide antibodies only for one of the peptides. This result is in accordance with the efficiency of anti-peptide antibodies development in rabbits. In conclusion, we designed a method for selection of peptides specific for different members of the PAG family and with high chances of being exposed in the surface of the molecule, which would allow immunological detection of the native glycoprotein in cow serum. These antibodies are being used for analysis of serum from pregnant and non-pregnant cows. Fundación Nuevo Banco de Santa Fe Programa de fortalecimiento de las capacidades de investigación y desarrollo de la provincia de Santa Fe, Secretaria de Estado de Ciencia, Tecnología e Innovacón, Provincia de Santa Fe.

In Silico Analysis of HSP70 Gene Family in Bovine Genome

2020 ◽  
Author(s):  
Kabita Tripathy ◽  
Monika Sodhi ◽  
R. S. Kataria ◽  
Meenu Chopra ◽  
Manishi Mukesh
Keyword(s):  
Gene Family ◽  
In Silico ◽  
Bovine Genome ◽  
In Silico Analysis ◽  
Hsp70 Gene ◽  
Silico Analysis

A systematic review with in silico analysis on transcriptomic profile of gallbladder carcinoma

2020 ◽  
Vol 47 (6) ◽  
pp. 398-408
Author(s):  
Sonam Tulsyan ◽  
Showket Hussain ◽  
Balraj Mittal ◽  
Sundeep Singh Saluja ◽  
Pranay Tanwar ◽  
...  
Keyword(s):  
Systematic Review ◽  
Gallbladder Carcinoma ◽  
In Silico ◽  
In Silico Analysis ◽  
Transcriptomic Profile ◽  
Silico Analysis

Enalos Suite of Tools: Enhancing Cheminformatics and Nanoinfor - matics through KNIME

2020 ◽  
Vol 27 (38) ◽  
pp. 6523-6535 ◽  
Author(s):  
Antreas Afantitis ◽  
Andreas Tsoumanis ◽  
Georgia Melagraki
Keyword(s):  
Data Analysis ◽  
Virtual Screening ◽  
In Silico ◽  
Model Development ◽  
In Silico Analysis ◽  
Material Design ◽  
Efficient Solutions ◽  
Biological Data ◽  
Cost Efficient ◽  
Silico Analysis

Drug discovery as well as (nano)material design projects demand the in silico analysis of large datasets of compounds with their corresponding properties/activities, as well as the retrieval and virtual screening of more structures in an effort to identify new potent hits. This is a demanding procedure for which various tools must be combined with different input and output formats. To automate the data analysis required we have developed the necessary tools to facilitate a variety of important tasks to construct workflows that will simplify the handling, processing and modeling of cheminformatics data and will provide time and cost efficient solutions, reproducible and easier to maintain. We therefore develop and present a toolbox of >25 processing modules, Enalos+ nodes, that provide very useful operations within KNIME platform for users interested in the nanoinformatics and cheminformatics analysis of chemical and biological data. With a user-friendly interface, Enalos+ Nodes provide a broad range of important functionalities including data mining and retrieval from large available databases and tools for robust and predictive model development and validation. Enalos+ Nodes are available through KNIME as add-ins and offer valuable tools for extracting useful information and analyzing experimental and virtual screening results in a chem- or nano- informatics framework. On top of that, in an effort to: (i) allow big data analysis through Enalos+ KNIME nodes, (ii) accelerate time demanding computations performed within Enalos+ KNIME nodes and (iii) propose new time and cost efficient nodes integrated within Enalos+ toolbox we have investigated and verified the advantage of GPU calculations within the Enalos+ nodes. Demonstration data sets, tutorial and educational videos allow the user to easily apprehend the functions of the nodes that can be applied for in silico analysis of data.

In-Silico Analysis of Chromone Containing Sulfonamide Derivatives as Human Carbonic Anhydrase Inhibitors

2013 ◽  
Vol 9 (4) ◽  
pp. 608-616 ◽  
Author(s):  
Zaheer Ul-Haq ◽  
Saman Usmani ◽  
Uzma Mahmood ◽  
Mariya al-Rashida ◽  
Ghulam Abbas
Keyword(s):  
Carbonic Anhydrase ◽  
In Silico ◽  
In Silico Analysis ◽  
Carbonic Anhydrase Inhibitors ◽  
Human Carbonic Anhydrase ◽  
Silico Analysis

In-Vitro and In-Silico Characterization of Xylose Reductase from Emericella nidulans

2019 ◽  
Vol 13 (2) ◽  
pp. 159-170 ◽  
Author(s):  
Vishal Ahuja ◽  
Aashima Sharma ◽  
Ranju Kumari Rathour ◽  
Vaishali Sharma ◽  
Nidhi Rana ◽  
...  
Keyword(s):  
Production Process ◽  
In Silico ◽  
Xylose Reductase ◽  
In Silico Analysis ◽  
Emericella Nidulans ◽  
Higher Temperature ◽  
In Silico Characterization ◽  
Silico Analysis

Background: Lignocellulosic residues generated by various anthropogenic activities can be a potential raw material for many commercial products such as biofuels, organic acids and nutraceuticals including xylitol. Xylitol is a low-calorie nutritive sweetener for diabetic patients. Microbial production of xylitol can be helpful in overcoming the drawbacks of traditional chemical production process and lowring cost of production. Objective: Designing efficient production process needs the characterization of required enzyme/s. Hence current work was focused on in-vitro and in-silico characterization of xylose reductase from Emericella nidulans. Methods: Xylose reductase from one of the hyper-producer isolates, Emericella nidulans Xlt-11 was used for in-vitro characterization. For in-silico characterization, XR sequence (Accession No: Q5BGA7) was used. Results: Xylose reductase from various microorganisms has been studied but the quest for better enzymes, their stability at higher temperature and pH still continues. Xylose reductase from Emericella nidulans Xlt-11 was found NADH dependent and utilizes xylose as its sole substrate for xylitol production. In comparison to whole cells, enzyme exhibited higher enzyme activity at lower cofactor concentration and could tolerate higher substrate concentration. Thermal deactivation profile showed that whole cell catalysts were more stable than enzyme at higher temperature. In-silico analysis of XR sequence from Emericella nidulans (Accession No: Q5BGA7) suggested that the structure was dominated by random coiling. Enzyme sequences have conserved active site with net negative charge and PI value in acidic pH range. Conclusion: Current investigation supported the enzyme’s specific application i.e. bioconversion of xylose to xylitol due to its higher selectivity. In-silico analysis may provide significant structural and physiological information for modifications and improved stability.

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