Hybrid Modeling of Biochemical Processes

2018 ◽  
pp. 89-127
Author(s):  
Vytautas Galvanauskas ◽  
Rimvydas Simutis ◽  
Andreas Lübbert
Author(s):  
Panagiotis Kouretas ◽  
Konstantinos Koutroumpas ◽  
John Lygeros ◽  
Zoi Lygerou

Author(s):  
Thomas M. Jovin ◽  
Michel Robert-Nicoud ◽  
Donna J. Arndt-Jovin ◽  
Thorsten Schormann

Light microscopic techniques for visualizing biomolecules and biochemical processes in situ have become indispensable in studies concerning the structural organization of supramolecular assemblies in cells and of processes during the cell cycle, transformation, differentiation, and development. Confocal laser scanning microscopy offers a number of advantages for the in situ localization and quantitation of fluorescence labeled targets and probes: (i) rejection of interfering signals emanating from out-of-focus and adjacent structures, allowing the “optical sectioning” of the specimen and 3-D reconstruction without time consuming deconvolution; (ii) increased spatial resolution; (iii) electronic control of contrast and magnification; (iv) simultanous imaging of the specimen by optical phenomena based on incident, scattered, emitted, and transmitted light; and (v) simultanous use of different fluorescent probes and types of detectors.We currently use a confocal laser scanning microscope CLSM (Zeiss, Oberkochen) equipped with 3-laser excitation (u.v - visible) and confocal optics in the fluorescence mode, as well as a computer-controlled X-Y-Z scanning stage with 0.1 μ resolution.


2014 ◽  
Vol 2 (2) ◽  
pp. 72-79 ◽  
Author(s):  
Mercedes Florez ◽  
Elvira Martinez ◽  
Victoria Carbonell

The main objective of this study is to determine the effects of 125 mT and 250mT magnetic treatment on the germination and initial growth of triticale seeds. This objective has a practical application in agriculture science: early growth of triticale. An increase in the percentage and rate of germination of seeds and a stimulation of growth of seedlings as positive response to magnetic field treatment in rice, wheat, maize and barley seeds have been found in previous studies. Germination tests were carried out under laboratory conditions by exposing triticale seeds to magnetic field for different times. The effect was studied by exposure of seeds prior sowing. The mean germination time were reduced for all the magnetic treatments applied. Most significant differences were obtained for time of exposure of 1 and 24 hours and maximum reductions was 12%. Furthermore, seedlings from magnetically treated seeds grew taller than control. The longest mean total length was obtained from seedlings exposed to 125 and 250 mT for 24 hours. External magnetic fields are assumed to enhance seed vigor by influencing the biochemical processes by stimulating activity of proteins and enzymes. Numerous studies suggested that magnetic field increases ions uptake and consequently improves nutrition value.


Author(s):  
A.D. Koval’ ◽  
◽  
A.V. Mironova ◽  
V.A. Pushkarev ◽  
K.E. Shevchenko ◽  
...  

2019 ◽  
Vol 20 (5) ◽  
pp. 540-550 ◽  
Author(s):  
Jiu-Xin Tan ◽  
Hao Lv ◽  
Fang Wang ◽  
Fu-Ying Dao ◽  
Wei Chen ◽  
...  

Enzymes are proteins that act as biological catalysts to speed up cellular biochemical processes. According to their main Enzyme Commission (EC) numbers, enzymes are divided into six categories: EC-1: oxidoreductase; EC-2: transferase; EC-3: hydrolase; EC-4: lyase; EC-5: isomerase and EC-6: synthetase. Different enzymes have different biological functions and acting objects. Therefore, knowing which family an enzyme belongs to can help infer its catalytic mechanism and provide information about the relevant biological function. With the large amount of protein sequences influxing into databanks in the post-genomics age, the annotation of the family for an enzyme is very important. Since the experimental methods are cost ineffective, bioinformatics tool will be a great help for accurately classifying the family of the enzymes. In this review, we summarized the application of machine learning methods in the prediction of enzyme family from different aspects. We hope that this review will provide insights and inspirations for the researches on enzyme family classification.


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