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In silico gene knockout prediction using a hybrid of Bat algorithm and minimization of metabolic adjustment

Mei Yen Man, Mohd Saberi Mohamad, Yee Wen Choon, Mohd Arfian Ismail
2021 Journal of Integrative Bioinformatics  
As a result, the aim of this paper is to propose a combination of the Bat algorithm and the minimization of metabolic adjustment (BATMOMA) to predict which genes to knock out in order to increase the succinate  ...  Metabolic engineering is the process of overcoming cellular regulation in order to achieve a desired product or to generate a new product that the host cells do not usually need to produce.  ...  A hybrid of Bat algorithm and minimization of metabolic adjustment (BATMOMA) This paper introduces a new hybrid algorithm, BATMOMA, and this section will explain the details of BAT-MOMA.  ... 
doi:10.1515/jib-2020-0037 pmid:34348418 pmcid:PMC8573224 fatcat:unp4frm6o5bojcg47ilhkublpi

Comparative Study of Harmony Search Algorithm and its Applications in China, Japan and Korea

Mohammad Nasir, Ali Sadollah, Jin Hee Yoon, Zong Woo Geem
2020 Applied Sciences  
Harmony Search (HS) is a music-inspired optimization algorithm for solving complex optimization problems that imitate the musical improvisational process.  ...  This paper reviews the potential of applying the HS algorithm in three countries, China, South Korea, and Japan.  ...  [51] , Bees Algorithm and Harmony Search (BAHS) were combined for Arabidopsis thaliana, the BAHS defined the functional parameters of critical amino acid production, calculated in the aspartate metabolism  ... 
doi:10.3390/app10113970 fatcat:3sqs2neqsfaclanvubh7rrjofa

Perfluorocarbon nanoemulsions create a beneficial O2 microenvironment in N2-fixing biological | inorganic hybrid

Shengtao Lu, Roselyn M. Rodrigues, Shuyuan Huang, Daniel A. Estabrook, John O. Chapman, Xun Guan, Ellen M. Sletten, Chong Liu
2021 Chem Catalysis  
The approach integrates the beauty of biocatalysis with the energy efficiency of inorganic materials for sustainable chemical production.  ...  Powered by renewable electricity, biological | inorganic hybrids employ water-splitting electrocatalysis and generate H2 as reducing equivalents for microbial catalysis.  ...  Giorgi Flow Cytometry Core Laboratory for flow-cytometry experiments, and the Molecular Instrumentation Center at the University of California, Los Angeles for sample characterizations.  ... 
doi:10.1016/j.checat.2021.06.002 pmid:34693393 pmcid:PMC8530205 fatcat:fnwy6lmrlbabrlismpgssq6wsq

Tailoring wine yeast for the new millennium: novel approaches to the ancient art of winemaking

Isak S. Pretorius
2000 Yeast  
However, due to the demanding nature of modern winemaking practices and sophisticated wine markets, there is an ever-growing quest for specialized wine yeast strains possessing a wide range of optimized  ...  The current status of genetically improved wine yeasts and potential targets for further strain development are outlined.  ...  Acknowledgements The author thanks Mr Terry Plantinga and Dr Maret du Toit for critical reading of this manuscript. Thanks are also due to Mr Yoshi Sho for his professional design of the graphics.  ... 
doi:10.1002/1097-0061(20000615)16:8<675::aid-yea585>3.3.co;2-2 pmid:10861899 fatcat:6aoksebkznctvjvtua6cpbk2fi

Tailoring wine yeast for the new millennium: novel approaches to the ancient art of winemaking

Isak S. Pretorius
2000 Yeast  
However, due to the demanding nature of modern winemaking practices and sophisticated wine markets, there is an ever-growing quest for specialized wine yeast strains possessing a wide range of optimized  ...  The current status of genetically improved wine yeasts and potential targets for further strain development are outlined.  ...  Acknowledgements The author thanks Mr Terry Plantinga and Dr Maret du Toit for critical reading of this manuscript. Thanks are also due to Mr Yoshi Sho for his professional design of the graphics.  ... 
doi:10.1002/1097-0061(20000615)16:8<675::aid-yea585>3.0.co;2-b pmid:10861899 fatcat:wecxb27fyrdh7lmwdahg2j6j3q

Fungal Genetics [chapter]

Malcolm Whiteway, Catherine Bachewich
2005 Fungi  
Maintenance of a low pH is essential for production; a pH below 2 is required for optimal fermentation.  ...  This type of system is optimal for maximizing biomass and is employed for the production of baker's yeast.  ...  For example, yeasts have been produced that (a) do not produce the organoleptic diacetyl, (b) contain genes for amylase and glucanse production and (c) flocculate at the end of the fermentation.  ... 
doi:10.1002/0470015330.ch2 fatcat:fswriirta5ds3gc2cm4q2afeze

A CRITICAL appraisal of the biochemical characteristics of morphologically separable cancers

1956 Cancer Research  
The dem- onstration of metabolic differences between differ- ent tissues lends optimism to the search for com- pounds having selective action on certain neo- plastic tissues.  ...  as an example of a common end-product of metabolism; the discovery that the very same amino acids, sugars, purines, py- rimidines, and, later, enzymes, vitamins, and various forms of energy-yielding reactions  ... 
pmid:13356289 fatcat:pdgpaqw3djchvhbuuw5eruz2pq

Detection of and Response to Signals Involved in Host-Microbe Interactions by Plant-Associated Bacteria

A. Brencic, S. C. Winans
2005 Microbiology and Molecular Biology Reviews  
ACKNOWLEDGMENTS We thank Alan Collmer and John Helmann for critical reading of the manuscript. Research in our laboratory is supported by grants from the NIH (GM42893) and NSF (MCB-9904917).  ...  It involves a highly coordinated exchange of signals between the plant and the bacteria and leads to a gradual and coordinated differentiation and adjustment of physiology and metabolism in both partners  ...  Metabolism of phenolic compounds. Phenolic compounds, the major signal required for induction of virulence genes, are metabolized by the product of one of the vir genes, namely, VirH2 (50, 256).  ... 
doi:10.1128/mmbr.69.1.155-194.2005 pmid:15755957 pmcid:PMC1082791 fatcat:r4z5ibbbkbdpzd62oijchkiloq

Prospective of 68Ga-Radiopharmaceutical Development

Irina Velikyan
2014 Theranostics  
and corresponding ligands, production and availability of 68 Ga, automation of the radiopharmaceutical production, progress of positron emission tomography technologies and image analysis methodologies  ...  Development and availability of new radiopharmaceuticals specific for particular diseases is one of the driving forces of the expansion of clinical PET.  ...  rat model of A. fumigatus infection while [ 68 Ga]Ga-FC showed prolonged retention in blood and rapid metabolism.  ... 
doi:10.7150/thno.7447 pmid:24396515 pmcid:PMC3881227 fatcat:h56dtt75szgwfnjqwi43vmfc4u

Lysosomal damage drives mitochondrial proteome remodelling and reprograms macrophage immunometabolism [article]

Claudio Bussi, Tiaan Heunis, Enrica Pellegrino, Elliott M. Bernard, Nourdine Bah, Mariana Silva dos Santos, Pierre Santucci, Beren Aylan, Angela Rodgers, Antony Fearns, Julia Mitschke, Christopher Moore (+5 others)
2022 bioRxiv   pre-print
In a mouse model of endomembrane damage, metabolic analysis confirmed that in vivo, live lung macrophages that internalised crystals displayed impaired mitochondrial function and increased glycolytic and  ...  Mitochondrial metabolic reprogramming required lysosomal leakage of Cathepsin B and Cathepsin L and was independent of proteasome degradation and mitophagy.  ...  For the purpose of Open Access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.  ... 
doi:10.1101/2022.08.09.503288 fatcat:m7miqtv2cnd3dfk7zbdr26k4ju

Currents in Biochemical Research

1947 Archives of Pediatrics & Adolescent Medicine  
23 the dark" or "light per se is not essential for photosynthesis."  ...  Before we analyze these attempts we must say a few words about intermediates.  ...  Here w^e have to search for a direct interrelation, an intermediate metabolic link. We may sum up as follows.  ... 
doi:10.1001/archpedi.1947.02020410096011 fatcat:zwwsij4j65cwvb36smfulyn3ii

Abstracts of Presentations at the 2016 APS Annual Meeting

2016 Phytopathology  
Treatments for Phytophthora diseases are limited, therefore optimization of available products is of great importance.  ...  screen hybrid chestnut for resistance to pathogens A.  ...  Collectively, higher sugar accumulation, a lower rate of energy metabolism, and elevated lipid and nucleic acid turnover was observed in B73.  ... 
doi:10.1094/phyto-106-12-s4.1 pmid:27922801 fatcat:vztse3dj7rhkdkcokeku2sbqrq

Abstracts of Papers for Presentation at the 51st Annual National Meeting of the American Society of Animal Production

1959 Journal of Animal Science  
Analysis of the 3000 x G sediment fermentations for end-products revealed primarily propionic and acetic acids, along with lesser amounts of succinic acid.  ...  Volatile fatty acid pro- duction was used as a criterion of digestion for cellulose, starch, casein and hay, in addition to the production of ammonia nitrogen for the last two substrates.  ... 
doi:10.2527/jas1959.1841460x fatcat:zyo4kupkqbhq5b2ohclvi4md4a

Abstracts

1972 American Zoologist  
late pregnancy i.e. day 15 for lactic dehydrogenase and alkaline phosphatase and on day 18 for succinic dehydrogenase and acid phosphatase.  ...  data, and the use of a night-vision "Starlight Scope" for observing the behavior of prey animals through the night in search of a behavioral explanation for prey preferences.  ...  The optimal wave pattern of a species should be a balance between the demand for speed with the least expenditure of energy, favored by a pattern of many large waves at one time, and the demand for tenacity  ... 
doi:10.1093/icb/12.4.641 fatcat:pyvogckbqvcu3pdyh4e66bl54u

A bacterial bioreporter panel to assay the cytotoxicity of atmospheric particulate matter

Nivi Kessler, James J. Schauer, Sharon Yagur-Kroll, Sahar Melamed, Ofir Tirosh, Shimshon Belkin, Yigal Erel
2012 Atmospheric Environment  
In order to minimize the adverse public health effects of atmospheric PM by exposure management, there is a need for a greater understanding of the toxic mechanisms and the components that are liable for  ...  A linear programming optimization model was developed to minimize the mean error between simulated and monitored PM10 concentrations in different counties.  ...  Then it realizes the source identification by a global searching of the optimal values with the objective function of the maximum location probability considering the sensor noise.  ... 
doi:10.1016/j.atmosenv.2012.09.048 fatcat:io4k5yahovcgvgzpnrxd6mynym
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