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Micrat: A Novel Algorithm For Inferring Gene Regulatory Networks Using Time Series Gene Expression Data, Bei Yang, Yaohui Xu, Andrew Maxwell, Wonryull Koh, Ping Gong, Chaoyang Zhang 2018 Zhengzhou University

Micrat: A Novel Algorithm For Inferring Gene Regulatory Networks Using Time Series Gene Expression Data, Bei Yang, Yaohui Xu, Andrew Maxwell, Wonryull Koh, Ping Gong, Chaoyang Zhang

Faculty Publications

Background

Reconstruction of gene regulatory networks (GRNs), also known as reverse engineering of GRNs, aims to infer the potential regulation relationships between genes. With the development of biotechnology, such as gene chip microarray and RNA-sequencing, the high-throughput data generated provide us with more opportunities to infer the gene-gene interaction relationships using gene expression data and hence understand the underlying mechanism of biological processes. Gene regulatory networks are known to exhibit a multiplicity of interaction mechanisms which include functional and non-functional, and linear and non-linear relationships. Meanwhile, the regulatory interactions between genes and gene products are not spontaneous since various processes ...


Solvent Stable Microbial Lipases: Current Understanding And Biotechnological Applications, Barry Ryan, Priyanka Priyanka, Yeqi Tan, Gemma K Kinsella, Gary T. Henehan 2018 Technological University Dublin

Solvent Stable Microbial Lipases: Current Understanding And Biotechnological Applications, Barry Ryan, Priyanka Priyanka, Yeqi Tan, Gemma K Kinsella, Gary T. Henehan

Articles

Objective: This review examines on our current understanding of microbial lipase solvent tolerance, with a specific focus on the molecular strategies employed to improve lipase stability in a non-aqueous environment.

Results: It provides an overview of known solvent tolerant lipases and of approaches to improving solvent stability such as; enhancing stabilising interactions, modification of residue flexibility and surface charge alteration. It shows that judicious selection of lipase source supplemented by appropriate enzyme stabilisation, can lead to a wide application spectrum for lipases.

Conclusion: Organic solvent stable lipases are, and will continue to be, versatile and adaptable biocatalytic workhorses commonly employed ...


Quantification Of Voc Emissions From Carbonized Refuse-Derived Fuel Using Solid-Phase Microextraction And Gas Chromatography-Mass Spectrometry, Andrzej Białowiec, Monika Micuda, Antoni Szumny, Jacek Łyczko, Jacek A. Koziel 2018 Wrocław University of Environmental and Life Sciences

Quantification Of Voc Emissions From Carbonized Refuse-Derived Fuel Using Solid-Phase Microextraction And Gas Chromatography-Mass Spectrometry, Andrzej Białowiec, Monika Micuda, Antoni Szumny, Jacek Łyczko, Jacek A. Koziel

Agricultural and Biosystems Engineering Publications

In this work, for the first time, the volatile organic compound (VOC) emissions from carbonized refuse-derived fuel (CRDF) were quantified on a laboratory scale. The analyzed CRDF was generated from the torrefaction of municipal waste. Headspace solid-phase microextraction (SPME) and gas chromatography-mass spectrometry (GC-MS) was used to identify 84 VOCs, including many that are toxic, e.g., derivatives of benzene or toluene. The highest emissions were measured for nonanal, octanal, and heptanal. The top 10 most emitted VOCs contributed to almost 65% of the total emissions. The VOC mixture emitted from torrefied CRDF differed from that emitted by other types ...


A Generative Statistical Approach For Data Classification In A Biologically Inspired Design Tool, Marvin Manuel Arroyo Rujano 2018 University of Arkansas, Fayetteville

A Generative Statistical Approach For Data Classification In A Biologically Inspired Design Tool, Marvin Manuel Arroyo Rujano

Theses and Dissertations

The objective of the research this thesis describes is to find a way to classify text-based descriptions of biological adaption to support Biologically Inspired design. Biologically inspired design is a fairly new field with ongoing research. There are different tools to assist designers and biologists in bio-inspired design. Some of the most common are BioTRIZ and AskNature. In recent years, more tools have been proposed to aid and make research in the field easier, for example, the Biologically Inspired Adaptive System Design (BIASD) tool. This tool was designed with the goal of helping designers in early design stages generate more ...


Distribution Of Dengue And Zika Virus Igg Immunoglobulin, Madison Smith, Awadalkareem Adam, Anuja Mathew 2018 University of Rhode Island

Distribution Of Dengue And Zika Virus Igg Immunoglobulin, Madison Smith, Awadalkareem Adam, Anuja Mathew

Senior Honors Projects

Introduction. Dengue Virus (DENV) and Zika Virus (ZIKV) are viruses that belong to the Flavivirus family. They are transmitted by the Aedes aegypti species of mosquitoes. Infection with DENV can result in no symptoms, mild symptoms which include fever, rash, and headache (dengue fever) or more severe symptoms which include hemorrhage, dengue hemorrhagic fever (DHF) and shock, dengue shock syndrome (DSS). ZIKV, until recently caused mild disease but an outbreak in Brazil was associated with fetal complications such as microcephaly or Guillain-Barré syndrome in adults. Due to the similarity between ZIKV and DENV, antibodies (Abs) generated in humans to these ...


The Goldilocks Approach: A Review Of Employing Design Of Experiments In Prokaryotic Recombinant Protein Production, Barry Ryan, Albert Uhoraningoga, Gemma K. Kinsella, Gary T. .. Henehan 2018 Technological University Dublin

The Goldilocks Approach: A Review Of Employing Design Of Experiments In Prokaryotic Recombinant Protein Production, Barry Ryan, Albert Uhoraningoga, Gemma K. Kinsella, Gary T. .. Henehan

Articles

The production of high yields of soluble recombinant protein is one of the main objectives of protein biotechnology. Several factors, such as expression system, vector, host, media composition and induction conditions can influence recombinant protein yield. Identifying the most important factors for optimum protein expression may involve significant investment of time and considerable cost. To address this problem statistical models, such as Design of Experiments (DoE), have been used to optimise recombinant protein production. This review explores the application of DoE in the production of recombinant proteins, focusing on prokaryotic expression systems with a specific emphasis on media composition and ...


Cellulose-Specific Type B Carbohydrate Binding Modules: Understanding Oligomeric And Non-Crystalline Substrate Recognition Mechanisms, Abhishek A. Kognole, Christina M. Payne 2018 University of Kentucky

Cellulose-Specific Type B Carbohydrate Binding Modules: Understanding Oligomeric And Non-Crystalline Substrate Recognition Mechanisms, Abhishek A. Kognole, Christina M. Payne

Chemical and Materials Engineering Faculty Publications

Background: Effective enzymatic degradation of crystalline polysaccharides requires a synergistic cocktail of hydrolytic enzymes tailored to the wide-ranging degree of substrate crystallinity. To accomplish this type of targeted carbohydrate recognition, nature produces multi-modular enzymes, having at least one catalytic domain appended to one or more carbohydrate binding modules (CBMs). The Type B CBM categorization encompasses several families (i.e., protein folds) of CBMs that are generally thought to selectively bind oligomeric polysaccharides; however, a subset of cellulose-specific CBM families (17 and 28) appear to bind non-crystalline cellulose more tightly than oligomers and in a manner that discriminates between surface topology ...


The Pharmaceutical Industry: A Pharmacy Student's Guide, Christian Egly, Yaman Kaakeh 2018 Purdue University

The Pharmaceutical Industry: A Pharmacy Student's Guide, Christian Egly, Yaman Kaakeh

Purdue Journal of Service-Learning and International Engagement

Christian Egly is a fourth-year (P4) pharmacy student in the Purdue University College of Pharmacy. During his years at Purdue, he worked in labs performing bench research in clinical pharmacology and biochemistry. He plans to work in the pharmaceutical industry after graduation. During his fourth year, he completed rotations in business development at Kashiv Pharma, LLC, and was hired there for an internship in 2017. In the article, Christian describes his personal experiences at Kashiv Pharma, LLC, and how industry can positively affect patient communities.


Fractionation And Characterization Of Lignin Streams From Unique High-Lignin Content Endocarp Feedstocks, Wenqi Li, Kirtley Amos, Mi Li, Yunqiao Pu, Seth DeBolt, Arthur J. Ragauskas, Jian Shi 2018 University of Kentucky

Fractionation And Characterization Of Lignin Streams From Unique High-Lignin Content Endocarp Feedstocks, Wenqi Li, Kirtley Amos, Mi Li, Yunqiao Pu, Seth Debolt, Arthur J. Ragauskas, Jian Shi

Biosystems and Agricultural Engineering Faculty Publications

Background: Lignin is a promising source of building blocks for upgrading to valuable aromatic chemicals and materials. Endocarp biomass represents a non-edible crop residue in an existing agricultural setting which cannot be used as animal feed nor soil amendment. With significantly higher lignin content and bulk energy density, endo-carps have significant advantages to be converted into both biofuel and bioproducts as compared to other biomass resources. Deep eutectic solvent (DES) is highly effective in fractionating lignin from a variety of biomass feedstocks with high yield and purity while at lower cost comparing to certain ionic liquids.

Results: In the present ...


33 - Identification Of Proteins That Regulate Crispr Dna Uptake Of Pyrococcus Furiosus, Landon Clark 2018 University of Georgia

33 - Identification Of Proteins That Regulate Crispr Dna Uptake Of Pyrococcus Furiosus, Landon Clark

Georgia Undergraduate Research Conference (GURC)

The CRISPR-Cas (Clustered Regularly Interspace Short Palindromic Repeats-CRISPR associated) system is a prokaryotic, adaptive immune system used by bacterial and archaeal organism to fight infections by viruses and other harmful invasive DNAs. These prokaryotic CRISPR-Cas immune systems have been exploited as powerful genome editing tools that work many different organisms and cells including humans. The newly developed CRISPR-based technologies are transforming medicine and science and have been used in research applications for developing cures for certain cancers, HIV, hemophilia, etc. The function of the CRISPR-Cas systems follow three basis steps: (1) adaptation (invading DNA is integrated into the host genome ...


Identification Of Pathogens Associated With Mango Dieback Disease On Mango In The United Arab Emirates, Fatima Ali Hassan Kamil 2018 United Arab Emirates University

Identification Of Pathogens Associated With Mango Dieback Disease On Mango In The United Arab Emirates, Fatima Ali Hassan Kamil

Biology Theses

Dieback caused by the fungus Lasiodiplodia theobromae is an important disease on mango plantations in the United Arab Emirates (UAE). In this study, 53 actinobacterial isolates were obtained from mango rhizosphere soil in the UAE, of which 35 (66%) were classified as streptomycetes (SA) and 18 (34%) as non-streptomycetes (NSA). Among these isolates, 19 (12 SA and 7 NSA) showed antagonistic activities against L. theobromae associated with either the production of diffusible antifungal metabolites, extracellular cell-wall-degrading enzymes (CWDEs), or both. Using a “novel” mango fruit bioassay, all isolates were screened in vivo for their abilities to reduce lesion severity on ...


Mouse Genome-Wide Association Studies And Systems Genetics Uncover The Genetic Architecture Associated With Hepatic Pharmacokinetic And Pharmacodynamic Properties Of A Constrained Ethyl Antisense Oligonucleotide Targeting Malat1, Elaine Pirie, Shayoni Ray, Calvin Pan, Wuxia Fu, Andrew F. Powers, Danielle Polikoff, Colton M. Miller, Katrina M. Kudrna, Edward N. Harris, Aldons J. Lusis, Rosanne M. Crooke, Richard G. Lee 2018 Carlsbad, California

Mouse Genome-Wide Association Studies And Systems Genetics Uncover The Genetic Architecture Associated With Hepatic Pharmacokinetic And Pharmacodynamic Properties Of A Constrained Ethyl Antisense Oligonucleotide Targeting Malat1, Elaine Pirie, Shayoni Ray, Calvin Pan, Wuxia Fu, Andrew F. Powers, Danielle Polikoff, Colton M. Miller, Katrina M. Kudrna, Edward N. Harris, Aldons J. Lusis, Rosanne M. Crooke, Richard G. Lee

Biochemistry -- Faculty Publications

Antisense oligonucleotides (ASOs) have demonstrated variation of efficacy in patient populations. This has prompted our investigation into the contribution of genetic architecture to ASO pharmacokinetics (PK) and pharmacodynamics (PD). Genome wide association (GWA) and transcriptomic analysis in a hybrid mouse diversity panel (HMDP) were used to identify and validate novel genes involved in the uptake and efficacy of a single dose of a Malat1 constrained ethyl (cEt) modified ASO. The GWA of the HMDP identified two significant associations on chromosomes 4 and 10 with hepatic Malat1 ASO concentrations. Stabilin 2 (Stab2) and vesicle associated membrane protein 3 (Vamp3) were identified ...


A Review On Bioconversion Of Agro-Industrial Wastes To Industrially Important Enzymes, Rajeev Ravindran, Shady S. Hassan, Gwilym A. Williams, Amit K, Jaiswal 2018 Dublin Institute of Technology

A Review On Bioconversion Of Agro-Industrial Wastes To Industrially Important Enzymes, Rajeev Ravindran, Shady S. Hassan, Gwilym A. Williams, Amit K, Jaiswal

Articles

Agro-industrial waste is highly nutritious in nature and facilitates microbial growth. Most agricultural wastes are lignocellulosic in nature; a large fraction of it is composed of carbohydrates. Agricultural residues can thus be used for the production of various value-added products, such as industrially important enzymes. Agro-industrial wastes, such as sugar cane bagasse, corn cob and rice bran, have been widely investigated via different fermentation strategies for the production of enzymes. Solid-state fermentation holds much potential compared with submerged fermentation methods for the utilization of agro-based wastes for enzyme production. This is because the physical–chemical nature of many lignocellulosic substrates ...


Adapting Cell-Free Protein Synthesis As A Platform Technology For Education, Grace W. Chu, Max Z. Levine, Nicole E. Gregorio, Javin P. Oza 2018 California State University, Los Angeles

Adapting Cell-Free Protein Synthesis As A Platform Technology For Education, Grace W. Chu, Max Z. Levine, Nicole E. Gregorio, Javin P. Oza

STAR (STEM Teacher and Researcher) Presentations

Cell-free protein synthesis (CFPS) has emerged as an enabling biotechnology for research and biomanufacturing as it allows for the production of protein without the need for a living cell. Applications of CFPS include the construction of libraries for functional genomics and structural biology, the production of personalized medicine, and the expression of virus-like particles. The absence of a cell wall provides an open platform for direct manipulation of the reaction conditions and biological machinery. This project focuses on adapting the CFPS biotechnology to the classroom, making a hands-on bioengineering approach to learning protein synthesis accessible to students grades K-16 through ...


Consistent And Reproducible Cultures Of Large-Scale 3d Mammary Epithelial Structures Using An Accessible Bioprinting Platform, John A. Reid, Peter M. Mollica, Robert D. Bruno, Patrick C. Sachs 2018 Old Dominion University

Consistent And Reproducible Cultures Of Large-Scale 3d Mammary Epithelial Structures Using An Accessible Bioprinting Platform, John A. Reid, Peter M. Mollica, Robert D. Bruno, Patrick C. Sachs

Medical Diagnostics & Translational Sciences Faculty Publications

Background: Standard three-dimensional (3D) in vitro culture techniques, such as those used for mammary epithelial cells, rely on random distribution of cells within hydrogels. Although these systems offer advantages over traditional 2D models, limitations persist owing to the lack of control over cellular placement within the hydrogel. This results in experimental inconsistencies and random organoid morphology. Robust, high-throughput experimentation requires greater standardization of 3D epithelial culture techniques.

Methods: Here, we detail the use of a 3D bioprinting platform as an investigative tool to control the 3D formation of organoids through the "self-assembly" of human mammary epithelial cells. Experimental bioprinting procedures ...


Theobromine And Related Methylxanthines As Inhibitors Of Primary Amine Oxidase, Padraig Shanahan, Jeffrey O’Sullivan, Keith Tipton, Gemma Kinsella, Barry Ryan, Gary Henehan 2018 Technological University Dublin

Theobromine And Related Methylxanthines As Inhibitors Of Primary Amine Oxidase, Padraig Shanahan, Jeffrey O’Sullivan, Keith Tipton, Gemma Kinsella, Barry Ryan, Gary Henehan

Articles

Methylxanthines are the most widely consumed drugs in the world and evidence of their health benefits has been growing in recent years. Primary Amine Oxidase (PrAO) has been recognised as a therapeutic target for amelioration of inflammatory, vascular and neurodegenerative diseases. Previous work in our laboratories showed that caffeine inhibited Bovine PrAO with a Ki of 1.0mM using benzylamine as substrate.

This study aimed to extend our previous work and explore the possibility that related methylxanthines might influence PrAO activity. While paraxanthine, theophylline and 7-methylxanthine had little effect on PrAO, theobromine was a noncompetitive inhibitor with a Ki of ...


Induction Of Oil Accumulation By Heat Stress Is Metabolically Distinct From N Stress In The Green Microalgae Coccomyxa Subellipsoidea C169, James W. Allen, Rahul Tevatia, Yaşar Demirel, Concetta C. DiRusso, Paul N. Black 2018 University of Nebraska-Lincoln

Induction Of Oil Accumulation By Heat Stress Is Metabolically Distinct From N Stress In The Green Microalgae Coccomyxa Subellipsoidea C169, James W. Allen, Rahul Tevatia, Yaşar Demirel, Concetta C. Dirusso, Paul N. Black

Biochemistry -- Faculty Publications

Algae are often promoted as feedstock organisms to produce a sustainable petroleum fossil fuel alternative. However, to induce lipid accumulation most often requires a severe stress that is difficult to induce in large batch cultures. The objective of this study is to analyze and mathematically model heat stress on growth, chlorophyll content, triacylglyceride, and starch synthesis in algae. We initially screened 30 algal species for the most pronounced induction of lipid droplets from heat stress using confocal microscopy and mass spectroscopy techniques. One species, Coccomyxa subellipsoidea C169, was selected and subjected to further biochemical analyses using a jacketed bioreactor amended ...


Nanoparticles As Multimodal Photon Transducers Of Ionizing Radiation, Edwin C. Pratt, Travis M. Shaffer, Qize Zhang, Charles Michael Drain, Jan Grimm 2018 Weill Cornell Medical College

Nanoparticles As Multimodal Photon Transducers Of Ionizing Radiation, Edwin C. Pratt, Travis M. Shaffer, Qize Zhang, Charles Michael Drain, Jan Grimm

Publications and Research

In biomedical imaging, nanoparticles combined with radionuclides that generate Cerenkov luminescence are used in diagnostic imaging, photon-induced therapies, and as activatable probes. In these applications, the nanoparticle is often viewed as a carrier inert to ionizing radiation from the radionuclide. However, certain phenomena such as enhanced nanoparticle luminescence and generation of reactive oxygen species cannot be explained by only Cerenkov luminescence interactions with nanoparticles. Herein, we report methods to examine the mechanisms of nanoparticle excitation by radionuclides, including interactions with Cerenkov luminescence, β particles, and γ radiation. We demonstrate that β scintillation contributes appreciably to excitation and reactivity in certain ...


Developing A Sustainable Insect Pest Management System By Manipulating Plant Volatile Emissions, Scott R. Hughes 2018 The University of Western Ontario

Developing A Sustainable Insect Pest Management System By Manipulating Plant Volatile Emissions, Scott R. Hughes

Electronic Thesis and Dissertation Repository

Herbivorous insects are a constant problem for farmers and growers globally, who rely on insecticides to control pest populations. Alternative measures are required due to insects developing resistance to chemical insecticides, along with increasing pressure from consumers. Integrated pest management (IPM) programs are a popular alternative. IPM uses a multifaceted approach to reduce pest populations below economic injury thresholds. Many plant-insect interactions are modulated by plant volatile organic compound (VOC) emissions. Manipulating this communication channel by producing transgenic plants with modified VOC emissions could provide another tool for use in IPM programs. I developed tomato Solanum lycopersicum (L.) plants expressing ...


Phenotypic Screening Identifies Brefeldin A/Ascotoxin As An Inducer Of Lipid Storage In The Algae Chlamydomonas Reinhardtii, Nishikant Wase, Boqiang Tu, Paul N. Black, Concetta C. DiRusso 2018 University of Nebraska-Lincoln

Phenotypic Screening Identifies Brefeldin A/Ascotoxin As An Inducer Of Lipid Storage In The Algae Chlamydomonas Reinhardtii, Nishikant Wase, Boqiang Tu, Paul N. Black, Concetta C. Dirusso

Nishikant Wase

The use of microalgae as a biofuel feedstock is highly desired, but current methods to induce lipid accumulation cause severe stress responses that limit biomass and, thus oil yield. To address these issues, a high throughput screening (HTS) method was devised to identify chemical inducers of growth and lipid accumulation. Optimization was performed to determine the most effective cell density, DMSO and Nile Red (NR) concentrations to monitor growth and lipid accumulation. The method was tested using 1717 compounds from National Cancer Institute (NCI) Diversity Set III and Natural Products Set II in Chlamydomonas reinhardtii. Cells were inoculated at low ...


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