Biotechnology Commons^™

Multi-Material Mesh Representation Of Anatomical Structures For Deep Brain Stimulation Planning, Tanweer Rashid

Computational Modeling & Simulation Engineering Theses & Dissertations

The Dual Contouring algorithm (DC) is a grid-based process used to generate surface meshes from volumetric data. However, DC is unable to guarantee 2-manifold and watertight meshes due to the fact that it produces only one vertex for each grid cube. We present a modified Dual Contouring algorithm that is capable of overcoming this limitation. The proposed method decomposes an ambiguous grid cube into a set of tetrahedral cells and uses novel polygon generation rules that produce 2-manifold and watertight surface meshes with good-quality triangles. These meshes, being watertight and 2-manifold, are geometrically correct, and therefore can be used to …

Experience With The Quantitative Lyta Gene Real-Time Polymerase Chain Reaction For The Detection Of Streptococcus Pneumoniae From Pediatric Whole Blood In Pakistan, Furqan Kabir, Sahrish Muneer, Adil Kalam, Ana Sami, Shahida Qureshi, Aneeta Hotwani, Atif Riaz, Syed Mohiuddin, Mohammad Tahir Yousafzai, Sara Hussain, Syed Asad Ali, Sadia Shakoor

Department of Paediatrics and Child Health

Background: We present our experience with optimization and diagnostic use of quantitative real-time polymerase chain reaction (PCR) targeting the lytA gene of Streptococcus pneumoniae for the detection of S. pneumoniae in whole blood of children ≥5 CFU/10 μl or 1 copy of DNA/2 μl of blood.
Methods: This assay was applied on 1912 whole blood specimens collected from children pneumonia, of which 35 specimens were lytA positive. The bacterial loads were determined through categorization of load into five different categories, i.e., very high load, high load, moderate load, low load, and very low load.
Results: Of the 35 lytA-positive …

Bio-Docklets: Virtualization Containers For Single-Step Execution Of Ngs Pipelines, Baekdoo Kim, Thahmina Ali, Carlos Lijeron, Enis Afgan, Konstantinos Krampis

Publications and Research

Processing of next-generation sequencing (NGS) data requires significant technical skills, involving installation, configuration, and execution of bioinformatics data pipelines, in addition to specialized postanalysis visualization and data mining software. In order to address some of these challenges, developers have leveraged virtualization containers toward seamless deployment of preconfigured bioinformatics software and pipelines on any computational platform. We present an approach for abstracting the complex data operations of multistep, bioinformatics pipelines for NGS data analysis. As examples, we have deployed 2 pipelines for RNA sequencing and chromatin immunoprecipitation sequencing, preconfigured within Docker virtualization containers we call Bio-Docklets. Each Bio-Docklet exposes a single …

A Clinical Audit For Compliance On The Innovated Radiographic Technique At A Radiologic Unit, Ismanto S., Hassan C.H.

ASEAN Journal on Science and Technology for Development

This study identifed X-ray laboratory users’ compliance with the innovated radiographic technique and evaluated it’s effectiveness in decreasing risks of repeating unnecessary X-ray exposure. The use of various steps in the standard operating procedures of radiography, proper radiographic technique and critique, practical protection measures, and radiographic positioning practice in X-ray laboratory at a private radiographic academy in Indonesia were audited. Thirty participants were used as the simple random sample. The demographic distribution was divided into, gender, nationality, and practical experience. Generally, out of 30 participants, 20 (67%) complied, and 10 (33%) did not. Radiograph image results showed that proper radiographic …

Potential Application Of Enr/Epdm Blends, Chan B.L.

ASEAN Journal on Science and Technology for Development

Since the process and conversion of natural rubber into epoxidized natural rubber (ENR) was discovered and patented by I. R. Gelling of the Malaysian Rubber Product Research Association (or now known as the Tun Razak laboratory), Brickendonbury, Hertford, in the United Kingdom, there are more than 10 000 technical and technological papers cited in the internet. Information on ENR is available, not only in the the English language but also other languages like Chinese, Malay, French, Thai and even German languages are used.NR is the most versatile and reactive rubber/elastomer. It is an advanced natural rubber which could be potentially …

Editorial Board, Board Editorial

ASEAN Journal on Science and Technology for Development

No abstract provided.

Optimization Of The Photochemical Degradation Of Textile Dye Industrial Wastewaters, Dang T.H., Mai T.P., Truong M.T., Dao L.T, Nguyen T.A.N

ASEAN Journal on Science and Technology for Development

In this study, the photochemical degradation via photo-Fenton process was carried out to degrade dyes in textile industrial wastewaters. Experimental design methodology was also applied for optimizing effects of factors which influencethe effective treatment such as ferric dose, hydroperoxide dosage, initial pH, reaction time and initial chemical oxygen demand (COD). Two independent variables namely colour and COD removal efficiencieswere used to evaluate the treatment yield. Under the optimal conditions, ca. 99% and ca. 88%, colour, and COD were removed, respectively.

Factors Influencing Iso 14001 Firm’S Perceived Environmental Performance In Malaysia, Rohati S., Norlida M.N., Syed Jamal A.N.S.M.

ASEAN Journal on Science and Technology for Development

The changes in the global environmental conditions have placed great challenges on governments, industries, and societies. Business organizations are often blamed for being the sources of theseenvironmental problems. This study aimed to examine the factors influencing the perceived environmental performance of firms certified under the ISO 14001 in Malaysia. A total of 268 manufacturing companies responded to the questionnaires. In this study, structural equation modeling was applied to test the hypotheses. It was found that the “environmental policy”, “environmental training”, “regulatory stakeholder’s pressures”, and “customer pressures”, influence the firm’s perceived environmental performance in which “customer pressures”, was found to be …

Efficient Dehydration And Recovery Of Ionic Liquid After Lignocellulosic Processing Using Pervaporation, Jian Sun, Jian Shi, N. V. S. N. Murthy Konda, Dan Campos, Dajiang Liu, Stuart Nemser, Julia Shamshina, Tanmoy Dutta, Paula Berton, Gabriela Gurau, Robin D. Rogers, Blake A. Simmons, Seema Singh

Biosystems and Agricultural Engineering Faculty Publications

Background: Biomass pretreatment using certain ionic liquids (ILs) is very efficient, generally producing a substrate that is amenable to saccharification with fermentable sugar yields approaching theoretical limits. Although promising, several challenges must be addressed before an IL pretreatment technology can become commercially viable. One of the most significant challenges is the affordable and scalable recovery and recycle of the IL itself. Pervaporation (PV) is a highly selective and scalable membrane separation process for quantitatively recovering volatile solutes or solvents directly from non-volatile solvents that could prove more versatile for IL dehydration.

Results: We evaluated a commercially available PV system for …

Mechanosensing Of Shear By Pseudomonas Aeruginosa Leads To Increased Levels Of The Cyclic-Di-Gmp Signal Initiating Biofilm Development, Christopher A. Rodesney, Brian Roman, Numa Dhamani, Benjamin J. Cooley, Ahmed Touhami, Vernita D. Gordon

Physics & Astronomy Faculty Publications

Biofilms are communities of sessile microbes that are phenotypically distinct from their genetically identical, free-swimming counterparts. Biofilms initiate when bacteria attach to a solid surface. Attachment triggers intracellular signaling to change gene expression from the planktonic to the biofilm phenotype. For Pseudomonas aeruginosa, it has long been known that intracellular levels of the signal cyclic-di-GMP increase upon surface adhesion and that this is required to begin biofilm development. However, what cue is sensed to notify bacteria that they are attached to the surface has not been known. Here, we show that mechanical shear acts as a cue for surface adhesion …

Marine Gastrobot Final Design Report, Wesley B. Williams, Eric Kane Dreischerf, Tommy Nicholas Yath

Mechanical Engineering

The Marine Gastrobot sponsored by Dr. Christopher Kitts of the Cal Poly Center for Applications in Biotechnology was a research and development effort intended to explore the use of microbial fuel cell technology as a power source for underwater robots. Our team Ocean Locomotion succeeded in developing a first iteration of an underwater robotic platform suitable for microbial fuel cell integration. The primary feature of the design is its sinusoidal fin propulsion intended for benthic exploration with limited risk of entanglement. During the course of development, Ocean Locomotion explored the use of low power actuation methods and determined their limited …

The 'Pseudomonas Aeruginosa' Psl Polysaccharide Is A Social But Noncheatable Trait In Biofilms, Yasuhiko Irie, Aled E. Roberts, Kasper N. Kragh, Vernita D. Gordon, Jaime B. Hutchison, Rosalind J. Allen, Gavin Melaugh, Thomas Bjarnsholt, Stuart A. West, Stephen P. Diggle

Biology Faculty Publications

Extracellular polysaccharides are compounds secreted by microorganisms into the surrounding environment, and they are important for surface attachment and maintaining structural integrity within biofilms. The social nature of many extracellular polysaccharides remains unclear, and it has been suggested that they could function as either cooperative public goods or as traits that provide a competitive advantage. Here, we empirically tested the cooperative nature of the PSL polysaccharide, which is crucial for the formation of biofilms in Pseudomonas aeruginosa. We show that (i) PSL is not metabolically costly to produce; (ii) PSL provides populationlevel benefits in biofilms, for both growth and antibiotic …

Characterization Of Genes Involved In Phycobiliprotein Biosynthesis In Fremyella Diplosiphon And Thermosynechococcus Elongatus, Christina M. Kronfel

LSU New Orleans Theses and Dissertations

Cyanobacteria are photosynthetic organisms that efficiently capture light by utilizing the light-harvesting complexes called phycobilisomes. In many cyanobacteria, phycobilisomes are composed of an allophycocyanin core with phycocyanin and phycoerythrin (PE) rods radiating from the core. These phycobiliproteins have multiple bilin chromophores, such as phycoerythrobilin (PEB), covalently attached to specific cysteine (Cys) residues for efficient photosynthetic light capture. Chromophore ligation on phycobiliprotein subunits occurs through bilin lyase catalyzed reactions.

This study mainly focuses on characterizing the roles of enzymes that are involved in the biosynthetic pathway of the phycobiliproteins within two cyanobacteria Thermosynechococcus elongatus and Fremyella diplosiphon. A combination of molecular …

B7h6: A Cancer Biomarker For The Development Of Novel Immunotherapy Approaches, Mariana Phillips

Seton Hall University Dissertations and Theses (ETDs)

Cancer-based immunotherapy has led the evolution of biologics that can stimulate immune responses towards tumor eradication. The synthesis of small to intermediate size molecules with the targeting and effector functions of mAb may represent a novel class of immunotherapeutics that may overcome the limitations of their biological counterparts.Towards this objective, B7H6 has been identified as a protein ligand localized on the cell surface of transformed tumor cells. B7H6 binds specifically to the activating receptor NKp30, constitutively expressed on all resting and active NK cells. Upon ligand:receptor binding, B7H6 triggers NK cell activation and release of chemokines and pro-inflammatory cytokines such …

Cloning, Purification, And Biochemical Characterization Of Human Prolyl Endopeptidase, Travis K. Moore

Electronic Theses and Dissertations

Eurygaster integriceps Puton, common name sunn Pest, is one of the primary sources of wheat crop wastes in North Africa, Middle East, and Eastern Europe. It feeds by injecting the wheat grain with an enzyme characterized as prolyl endoprotease (spPEP) that breaks down Gluten, the wheat’s main constitutive protein necessary for bread production (Darkoh et al., 2010). Previously, it has been shown that peptides isolated from Lactobacillus hydrolysates of caseins in bovine milk are able to inhibit mammalian PEP in colon cells, as well as bacterial PEP (Juillerat-Jeanneret et al., 2010). While recombinant versions of these peptides are also potential …

Survey Of Microbial Urea Degrader Diversity In Two Freshwater Ecosystems: Lake Shenandoah And The Shenandoah River, Naomi E. Gilbert

Senior Honors Projects, 2010-2019

One of the primary drivers of cyanobacterial harmful algal blooms (cHABs) in freshwater systems is nutrient loading, particularly of nitrogen and phosphorus. There has been an increased focus on assessing the role of nitrogen (N) in freshwater lakes and rivers that suffer cHABs. Urea, a widely-used, N-rich fertilizer, is a source of interest due to its abundance in freshwater ecosystems, primarily caused by anthropogenic nutrient loading. While recent work has shown that cHAB population succession may favor the toxic cyanobacterium Microcystis in urea-rich waters, the diversity of the associated bacterial community capable of degrading urea has yet to be determined. …

Construction Of A Heterologous Vaccine Against Bordetella Avium And Campylobacter Jejuni Utilizing The B. Avium Transporter, Baa1, Rachel Korba

Senior Honors Projects, 2010-2019

A Gram negative species of bacteria, Campylobacter jejuni, is the leading cause of food poisoning worldwide. Humans often contract food poisoning after ingesting contaminated poultry. Detecting the presence of C. jejuni in poultry is difficult because it is part of the natural flora and does not cause symptomatic infection. In a related manner, Bordetella avium is a Gram negative species of bacteria that causes bordetellosis in poultry. This disease is similar to whooping cough caused by the related pathogen of humans, B. pertussis. Though the mortality rate for bordetellosis is low, it weakens the birds’ immune systems, often …

Topical Administration Of Lacritin Peptide For The Treatment Of Canine Keratoconjunctivitis Sicca, Eliza A. Gaylord

Senior Honors Projects, 2010-2019

Keratoconjunctivitis sicca (KCS), also known as dry-eye disease, causes a deficiency of tears in both humans and canines. Due to the lack of effective therapeutics for the treatment of dry-eye disease, there is a market potential for a novel secretion enhancing factor. Lacritin, a naturally occurring tear glycoprotein, increases basal tearing in rabbits when topically applied to the ocular surface and shows potential as a dry-eye therapeutic. This study aims to characterize Lacritin as a biomarker of dry-eye disease in canines with KCS. A total of 46 canine tear samples, 24 normal and 22 diagnosed with KCS, were obtained through …

Impact Of Burkholderia Phytofirmans Strain Psjn On The Ex Vitro Acclimatization And In Vitro Propagation Of Tissue Cultured Dionaea Muscipula (Venus Fly Trap), Peter L. Riley

Masters Theses, 2010-2019

Dionaea muscipula, Venus fly trap, is an endangered plant that is propagated primarily through tissue culture. Tissue cultured plants must be acclimatized to their new environments when removed from their test tubes and the ensuing stress can result in plant mortality. A plant growth promoting rhizobacterium, Burkholderia phytofirmans strain PsJN, has been utilized in biotic hardening of tissue cultured plants and in the amelioration of stresses, particularly drought stress in potted plants. We investigated whether this bacterium could improve either propagation or acclimatization of tissue cultured Venus fly traps. Standardized inoculations were performed by adjusting cell density of inoculant …

Development Of A Core Clostridium Thermocellum Kinetic Metabolic Model Consistent With Multiple Genetic Perturbations, Satyakam Dash, Ali Khodayari, Jilai Zhou, Evert K. Holwerda, Daniel Olson, Lee Lynd, Costas Maranas

Dartmouth Scholarship

Clostridium thermocellum is a Gram-positive anaerobe with the ability to hydrolyze and metabolize cellulose into biofuels such as ethanol, making it an attractive candidate for consolidated bioprocessing (CBP). At present, metabolic engineering in C. thermocellum is hindered due to the incomplete description of its metabolic repertoire and regulation within a predictive metabolic model. Genome-scale metabolic (GSM) models augmented with kinetic models of metabolism have been shown to be effective at recapitulating perturbed metabolic phenotypes.

In this effort, we first update a second-generation genome-scale metabolic model (iCth446) for C. thermocellum by correcting cofactor dependencies, restoring elemental and charge balances, …