Biotechnology Commons^™

Malate Dehydrogenase Allele Frequencies In Honeybee Populations And Its Correlation With Temperature, Thitipan Meemongkolkiat

Chulalongkorn University Theses and Dissertations (Chula ETD)

Temperature is one of the major factors that affect on the variation in honeybee in term of DNA and protein variants. The aim of this study is to investigate whether the three structural variants of the cytosolic malate dehydrogenase (cMDH) protein of the honeybee can explain clinal variation in allele frequencies. To test the hypothesis that there is a molecular basis to the temperature-dependent fitness of cMDH variation, the enzymic activity was determined across a range of temperatures in vitro. The F and S alleles have higher activity and are less sensitive to high temperatures than the M allele. Next, …

Enabling Precision Medicine Via Standard Communication Of Hts Provenance, Analysis, And Results, Gil Alterovitz, Dennis Dean, Carole Globe, Michael R. Crusoe, Stiam Soiland-Reyes, Amanda Bell, Anais Hayes, Anita Suresh, Anjan Purkkayastha, Charles H. King, Dan Taylor, Elaine Johanson, Elaine E. Thompson, Eric Donaldson, Hiroki Morizono, Hsinyi Tsang, Jeet K. Vora, Jeremy Goecks, Jianchao Yao, Jonas S. Almeida, Jonathon Keeney, Kanakadurga Addepalli, Konstantinos Krampis, Krista M. Smith, Lydia Guo, Mark Walderhaug, Marco Schito, Matthew Ezewudo, Nuria Guimera, Paul Walsh, Robel Kahsay, Srikanth Gottipati, Timothy C. Rodwell, Toby Bloom, Yuching Lai, Vahan Simonyan, Raja Mazumder

Publications and Research

A personalized approach based on a patient's or pathogen’s unique genomic sequence is the foundation of precision medicine. Genomic findings must be robust and reproducible, and experimental data capture should adhere to findable, accessible, interoperable, and reusable (FAIR) guiding principles. Moreover, effective precision medicine requires standardized reporting that extends beyond wet-lab procedures to computational methods. The BioCompute framework (https://w3id.org/biocompute/1.3.0) enables standardized reporting of genomic sequence data provenance, including provenance domain, usability domain, execution domain, verification kit, and error domain. This framework facilitates communication and promotes interoperability. Bioinformatics computation instances that employ the BioCompute framework are easily relayed, repeated …

Overview On Steady-State Nuclear Methods For Bwr Nuclear Core Design And Analysis, Chiang Ren-Tai

ASEAN Journal on Science and Technology for Development

An overview on nuclear methods for boiling water reactors (BWR) core design and analysis is provided based on the ANS Standard 19.3. The steady-state BWR nuclear methods, composed of neutron cross section library generation method, lattice physics method and core physics method, are systematically reviewed and associated computer codes in common use for BWR core design and analysis are listed. Verification and validation, the two complementary aspects in determining the range of applicability of the calculation system, are discussed extensively. The biases and uncertainties for the predictions from the calculation system over its demonstrated range of applicability are also discussed.

Overview Of Boron Neutron Capture Therapy: A Medical Aspect, Bangun Alan Anderson, Poedjomartono Bagaswoto

ASEAN Journal on Science and Technology for Development

Cancer is an abnormal growth of a cell due to the cell’s inability to control and maintain its proliferation, differentiation and apoptosis cycle. There are several methods to treat cancer; one of which is boron neutron capture therapy (BNCT). BNCT is a radiation modality by which a high radiation dose is delivered to tumor cells with lower damage to surrounding normal tissue. This modality has been used widely as a treatment for several cancer cases, such as head and neck cancer, breast cancer, and liver cancer. BNCT uses sodium borocaptate (BSH) or boronophenylalanine (BPA) as the delivery agent. Then, the …

Dosimetry Of In Vivo Experiment For Lung Cancer Based On Boron Neutron Capture Therapy On Radial Piercing Beam Port Kartini Nuclear Reactor By Mcnpx Simulation Method, Maysaroh Atika, Kusminarto Kusminarto, Palupi Dwi Satya, Sardjono Yohannes

ASEAN Journal on Science and Technology for Development

Cancer is one of the leading causes of death globally, with lung cancer being among the most prevalent. Boron Neutron Capture Therapy (BNCT) is a cancer therapy method that uses the interaction between thermal neutrons and boron-10 which produces a decaying boron-11 particle and emits alpha, lithium 7 and gamma particles. A study was carried out to model an in vivo experiment of rat organisms that have lung cancer. Dimensions of a rat’s body were used in Konijnenberg research. Modeling lung cancer type, non-small cell lung cancer, was used in Monte Carlo N Particle-X. Lung cancer was modeled with a …

Dose Analysis Of Gadolinium Neutron Capture Therapy (Gdnct) On Cancer Using Shield-Hit12a, Fasni Bagus Novrianto, Sardjono Yohannes, Lapanporo Boni Pahlanop

ASEAN Journal on Science and Technology for Development

This research aimed to determine the dose of radiation received in cancer therapy for each decay of Gadolinium atomic nuclei with isotope 157 (157Gd) in Gadolinium Neutron Capture Therapy using the SHIELD-HIT12A program. Knowing the amount of dose given to cancer tissue should aid in minimizing the damage that could occur in the healthy tissue around the cancer tissue, effectively killing only the cancer cells. The simulation employed in this research used the SHIELD-HIT12A program by providing input on beam.dat, mat.dat, detect.dat, and geo.dat files. The output data from the program comprised the value of recoil energy lost (energy absorbed …

Analysis Of Radiation Interactions And Biological Effects For Boron Neutron Capture Therapy, Chiang Ren-Tai

ASEAN Journal on Science and Technology for Development

The direct and indirect ionizing radiation sources for boron neutron capture therapy (BNCT)are identi?ed. The mechanisms of physical, chemical and biological radiation interactions for BNCT are systematically described and analyzed. The relationship between the effect of biological radiation and radiation dose are illustrated and analyzed for BNCT. If the DNAs in chromosomes are damaged by ion- izing radiations, the instructions that control the cell function and reproduction are also damaged. This radiation damage may be reparable, irreparable, or incorrectly repaired. The irreparable damage can result in cell death at next mitosis while incorrectly repaired damage can result in mutation. Cell …

Dose Analysis Of In Vitro And In Vivo Test For Boron Neutron Capture Therapy (Bnct), Faqqiyyah Hamidatul, Sunarno Sunarno, Akhlis Isa, Sardjono Yohannes

ASEAN Journal on Science and Technology for Development

The purpose of this study was to determine the in vitro and in vivo doses of boron neutron capture cancer therapy (BNCT) using the SHIELD-HIT12A program. To be able to determine the recoil energy, the research was conducted using the Monte Carlo method. Running data obtained the value of ionization activity and recoil lost. The results showed that in vitro and in vivo doses of BNCT for soft tissue irradiation had a value of 0.312 × 10-2 Sv, which is safe and does not harm healthy body tissue around the cancer cells because it is below the threshold of 1.5 …

Beam Shaping Assembly Optimization For Boron Neutron Capture Therapy Facility Based On Cyclotron 30 Mev As Neutron Source, Fauzi Arief, Tsurayya Afifah Hana, Harish Ahmad Faisal, Wijaya Gede Sutresna

ASEAN Journal on Science and Technology for Development

A design of beam shaping assembly (BSA) installed on cyclotron 30 MeV model neutron source for boron neutron capture therapy (BNCT) has been optimized using simulator software of Monte Carlo N-Particle Extended (MCNPX). The Beryllium target with thickness of 0.55 cm is simulated to be bombarded with 30 MeV of proton beam. In this design, the parameter regarding beam characteristics for BNCT treatment has been improved, which is ratio of fast neutron dose and epithermal neutron flux. TiF3 is replaced to 30 cm of 27Al as moderator, and 1.5 cm of 32S is combined with 28 cm of 60Ni as …

Methanogens: Pushing The Boundaries Of Biology, Nicole R. Buan

Department of Biochemistry: Faculty Publications

Methanogens are anaerobic archaea that grow by producing methane gas. These microbes and their exotic metabolism have inspired decades of microbial physiology research that continues to push the boundary of what we know about how microbes conserve energy to grow. The study of methanogens has helped to elucidate the thermodynamic and bioenergetics basis of life, contributed our understanding of evolution and biodiversity, and has garnered an appreciation for the societal utility of studying trophic interactions between environmental microbes, as methanogens are important in microbial conversion of biogenic carbon into methane, a high-energy fuel. This review discusses the theoretical basis for …

Methanogens: Pushing The Boundaries Of Biology, Nicole R. Buan

Department of Biochemistry: Faculty Publications

Methanogens are anaerobic archaea that grow by producing methane gas. These microbes and their exotic metabolism have inspired decades of microbial physiology research that continues to push the boundary of what we know about how microbes conserve energy to grow. The study of methanogens has helped to elucidate the thermodynamic and bioenergetics basis of life, contributed our understanding of evolution and biodiversity, and has garnered an appreciation for the societal utility of studying trophic interactions between environmental microbes, as methanogens are important in microbial conversion of biogenic carbon into methane, a high-energy fuel. This review discusses the theoretical basis for …

Use Of Co-Immunoprecipitations And 2d Gel Electrophoresis To Identify Protein-Protein Interactions Of Maturase K, Lauren Angello

Honors Theses

Maturase K (MatK) is the only group II intron encoded protein in the chloroplast of land plants. Maturases are prokaryotic enzymes that catalyze formation of the lariat structure needed for intron removal from precursor RNAs. The chloroplast maturase MatK, is a descendant of prokaryotic maturases, however, unlike its prokaryotic relatives, MatK is thought to catalyze excision of, not only its own intron, but also the introns of other group II introns in the plastome. Similar to the multiprotein and snRNA spliceosomal complex of the nucleus, it is postulated that MatK is not working alone to excise these introns but most …

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 …

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

Graduate 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 …

Engineering Yeast To Evaluate Human Proteins Involved In Selective Rna Packaging During Hiv Particle Production, Ryan M. Bitter

Master's Theses

Despite recent advances in antiretroviral therapy, nearly 37 million people continue to live with human immunodeficiency virus (HIV). Basic and applied research on the assembly of HIV could be enhanced by using a genetically tractable organism, such as yeast, rather than mammalian cells. While previous studies showed that expression of the HIV Gag polyprotein in Saccharomyces cerevisiae spheroplasts resulted in the production of virus-like particles (VLPs), many questions regarding the utility of yeast in HIV assembly remain uninvestigated. Here, we report use of S. cerevisiae for both the production of VLPs with selectively packaged RNA and to evaluate the human …

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 …

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 …

Comprehensive Sequencing With Surface Tagmentation Based Technology, Kuan Feng

Biomedical Sciences ETDs

Next-generation sequencing technologies (NGS) have undergone extensive improvements since the invention of the 454 sequencing system in 2005. With tremendous progress in throughput, speed and a dramatic reduction in per-base cost, DNA sequencing is widely used in basic science as well as translational research. However, it is still a challenge to acquire a complete human genome. The long-range information is often missing due to the short length of NGS reads, which leaves many gaps in between scaffolds rather than an entire piece for each chromosome. Moreover, without the long-range information, haplotype-resolved genome sequencing and structural variant detection can be difficult, …

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.

Results: …

Bs In Biotechnology, Joanna Burkhardt

Library Impact Statements

No abstract provided.