Organisms Commons^™

Utilizing Biomimicry To Design Sustainable Architecture, Virginia Hammond

Architecture Undergraduate Honors Theses

Nature has an integral relationship with architecture and serves as a sustainable role model and inspiration for designers. The process of biomimicry in architecture has the potential to produce more sustainable design solutions and foster a connection between humans and nature. Existing biomimetic design projects have varying strengths and weaknesses as examples of the process. Utilizing guidelines and references from key leaders in biomimetic design consultancy (Biomimicry 3.8), selected case studies are assessed for their ability to demonstrate the benefits of this design strategy. Using these evaluations, the case studies are diagrammed and critiqued to determine how new projects could …

Reducing Food Scarcity: The Benefits Of Urban Farming, S.A. Claudell, Emilio Mejia

Journal of Nonprofit Innovation

Urban farming can enhance the lives of communities and help reduce food scarcity. This paper presents a conceptual prototype of an efficient urban farming community that can be scaled for a single apartment building or an entire community across all global geoeconomics regions, including densely populated cities and rural, developing towns and communities. When deployed in coordination with smart crop choices, local farm support, and efficient transportation then the result isn’t just sustainability, but also increasing fresh produce accessibility, optimizing nutritional value, eliminating the use of ‘forever chemicals’, reducing transportation costs, and fostering global environmental benefits.

Imagine Doris, who is …

Comparison Of The Humoral Immune Response Following Both Bacterial Challenge And Rnai Of Major Factors On Proliferation Of Bartonella Quintana In The Human Louse, Jake Zina

Masters Theses

Human body lice, Pediculus humanus humanus, and head lice, Pediculus humanus capitis, have been hematophagous ectoparasites of humans for thousands of years. Despite being ecotypes, only body lice are known to transmit bacterial diseases to humans, and it appears that lower humoral and cellular immune responses allow body lice to possess a higher vector competence. We previously observed that the transcription level of the defensin 1 gene was up-regulated only in head lice following oral challenge of Bartonella quintana, a causative agent of trench fever, and also that body lice excreted more viable B. quintana in their …

Diversity Of Bacteriophage In Burkholderia Species, Abigail Price

Honors Projects

Bacteriophages are viruses that infect and replicate within bacteria and offer the potential of a therapeutic alternative to chronic infections that do not respond to antibiotic-based therapies. B. vietnamiensis is one of a number of Burkholderia species involved with chronic drug resistant infections in the lungs of individuals with compromised respiratory systems, as found in those with chronic obstructive pulmonary disease and, most especially, are of particular significance in patients with cystic fibrosis. The diversity of the Burkholderia species is explored by using online databases and looking at bacteriophage or phage-encoding viruses found in B. vietnamiensis. The open reading frames …

Healthcare Simulation: A Key To The Future Of Medical Education - A Review, Omair Ayaz, Faisal Wasim Ismail

Medical College Documents

Aim: Simulation originates from its application in the military and aviation. It is implemented at various levels of healthcare education and certification today. However, its use remains unevenly distributed across the globe due to misconception regarding its cost and complexity and to lack of evidence for its consistency and validity. Implementation may also be hindered by an array of factors unique to the locale and its norms. Resource-poor settings may benefit from diverting external funds for short-term simulation projects towards collaboration with local experts and local material sourcing to reduce the overall cost and achieve long-term benefits. The recent shift …

Covid19 Disease Map, A Computational Knowledge Repository Of Virus–Host Interaction Mechanisms, Marek Ostaszewski, Tomáš Helikar, Bhanwar Lal Puniya, A Host Of Co-Authors, Covid-19 Disease Map Community

Department of Biochemistry: Faculty Publications

We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, …

Hexadecane Petroleum, And Biofuel Utilization In Marine Bacteria Isolated From Ballast Tanks, Alex Yashchenko

Graduate Theses

This study characterized the growth of bacteria isolated from ballast tank fluids in hexadecane, petroleum, plant, and algae-derived fuels. The study was performed to explore the capacity of ballast tank isolates to survive and grow within fuels that may be stored within ballast tanks. Results of the hexadecane analysis indicated that most isolates had higher viable cell counts in media supplemented with hexadecane. Members of Alteromonas, Pseudoalteromonas, and a single Brevundimonas species had viable cell counts that were one or several orders ofmagnitude greater than that of controls. Results offuel analysis indicated higher viable cell counts in pure JP-5 and …

Biotechnological Application In Aquaculture And Its Sustainability Constraints, Olaganathan Rajee, Tang Kar Mun Alicia

Publications

The valuable nutritional and biochemical properties have made fisheries products one of the most vital high-quality protein sources for human consumption. Aquaculture has become the great alternative to substitute wild catches when the yield from fishing are no longer sufficient to sustain the massive food demand of the human population which is constantly burgeoning. However, aquaculture requires multidisciplinary approaches with holistic and environmental-friendly management measures to ensure its long term success and sustainability. Biotechnological applications have enhanced the effectiveness and cost-efficiencies of aquaculture by augmenting the productivity of aquaculture to meet global needs. Despite the benefits, the biotechnological application in …

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

STAR Program Research 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 …

One-Step Hot Formamide Extraction Of Rna From Saccharomyces Cerevisiae, Daniel Shedlovskiy, Natalia Shcherbik, Dimitri G Pestov

Rowan-Virtua School of Osteopathic Medicine Faculty Scholarship

Current methods for isolating RNA from budding yeast require lengthy and laborious steps such as freezing and heating with phenol, homogenization with glass beads, or enzymatic digestion of the cell wall. Here, extraction with a solution of formamide and EDTA was adapted to isolate RNA from whole yeast cells through a rapid and easily scalable procedure that does not require mechanical cell lysis, phenol, or enzymes. RNA extracted with formamide-EDTA can be directly loaded on gels for electrophoretic analysis without alcohol precipitation. A simplified protocol for downstream DNase treatment and reverse transcription reaction is also included. The formamide-EDTA extraction of …

Emergence Of The L Phenotype In Group B Streptococci In The South Of Ireland, Katherine Hayes, Lesley Cotter, L. Barry, Fiona O'Halloran

Department of Biological Sciences Publications

Group B Streptococcal isolates (n = 235) from the South of Ireland were characterised by serotyping, antimicrobial susceptibility and determination of the phenotypic and genotypic mechanisms of resistance. Resistance to erythromycin and clindamycin was observed in 21·3% and 20·4% of the total population, respectively. The c-MLSB phenotype was the most common phenotype detected (62%), with ermB being the predominant genetic determinant, present in 84% of resistant isolates. The rare L phenotype was observed in 2·9% (n = 7) of isolates, four of which harboured the lsaC gene responsible for clindamycin resistance. Serotypes Ia, III and II were the most common …

Structure-Function Investigation Of Proteins Involved In Cellulose Biosynthesis By Escherichia Coli, Thomas Brenner

Theses and Dissertations (Comprehensive)

Bacteria thrive within multicellular communities called biofilms consisting of a self-produced matrix. Biofilm matrices improve bacterial adherence to surfaces while creating a barrier from host immune responses, disinfectants, antibiotics and other environmental factors. Persistent colonization by the widely distributed pathogens, Escherichia coli and Salmonella spp., has been linked to production of biofilms composed of the exopolysaccharide cellulose. Cellulose-containing biofilms are also important to Acetobacter, Sarcina, Rhizobium and Agrobacterium species to form symbiotic and pathogenic interactions. In Enterobacteriaceae, two operons (bcsABZC and bcsEFG) are proposed to encode for proteins that form a cellulose biosynthetic complex that spans the …

Comparative Genomic Analysis Of Two Serotype 1/2b Listeria Monocytogenes Isolates From Analogous Environmental Niches Demonstrates The Influence Of Hypervariable Hotspots In Defining Pathogenesis, Aidan Casey, Kieran Jordan, Aidan Coffey, Edward M. Fox, Olivia Mcauliffe

Department of Biological Sciences Publications

The vast majority of clinical human listeriosis cases are caused by serotype 1/2a, 1/2b, 1/2c, and 4b isolates of Listeria monocytogenes. The ability of L. monocytogenes to establish a systemic listeriosis infection within a host organism relies on a combination of genes that are involved in cell recognition, internalization, evasion of host defenses, and in vitro survival and growth. Recently, whole genome sequencing and comparative genomic analysis have proven to be powerful tools for the identification of these virulence-associated genes in L. monocytogenes. In this study, two serotype 1/2b strains of L. monocytogenes with analogous isolation sources, but …

Optimization Of A Genomic Editing System Using Crispr/Cas9-Induced Site-Specific Gene Integration, Jillian L. Mccool Ms., Nick Hum, Gabriela G. Loots

STAR Program Research Presentations

The CRISPR-Cas system is an adaptive immune system found in bacteria which helps protect against the invasion of other microorganisms. This system induces double stranded breaks at precise genomic loci (1) in which repairs are initiated and insertions of a target are completed in the process. This mechanism can be used in eukaryotic cells in combination with sgRNAs (1) as a tool for genome editing. By using this CRISPR-Cas system, in addition to the “safe harbor locus,” ROSAβ26, the incorporation of a target gene into a site that is not susceptible to gene silencing effects can be achieved through few …

A Tail Of Two Phages: Genomic And Functional Analysis Of Listeria Monocytogenes Phages Vb_Lmos_188 And Vb_Lmos_293 Reveal The Receptor-Binding Proteins Involved In Host Specificity, Aidan Casey, Kieran Jordan, Horst Neve, Aidan Coffey, Olivia Mcauliffe

Department of Biological Sciences Publications

The physical characteristics of bacteriophages establish them as viable candidates for downstream development of pathogen detection assays and biocontrol measures. To utilize phages for such purposes, a detailed knowledge of their host interaction mechanisms is a prerequisite. There is currently a wealth of knowledge available concerning Gram-negative phage-host interaction, but little by comparison for Gram-positive phages and Listeria phages in particular. In this research, the lytic spectrum of two recently isolated Listeria monocytogenes phages (vB_LmoS_188 and vB_LmoS_293) was determined, and the genomic basis for their observed serotype 4b/4e host-specificity was investigated using comparative genomics. The late tail genes of these …

Draft Genome Sequences Of Six Different Staphylococcus Epidermidis Clones, Isolated Individually From Preterm Neonates Presenting With Sepsis At Edinburgh's Royal Infirmary, Paul Walsh, M. Bekaert, J. Carroll, T. Manning, B. Kelly, A. O'Driscoll, X. Lu, C. Smith, P. Dickinson, K. Templeton, P. Ghazal, Roy D. Sleator

Department of Biological Sciences Publications

Herein, we report the draft genome sequences of six individual Staphylococcus epidermidis clones, cultivated from blood taken from different preterm neonatal sepsis patients at the Royal Infirmary, Edinburgh, Scotland, United Kingdom.

Examining Phage Infection Utilizing Mycobacterium Smegmatis, Tanya L. Riddick

Undergraduate Research

Bacteriophages, also known as phages, are viruses that are ubiquitous and survive and replicate within the host of the bacterial cell, Mycobacterium smegmatis. They are considered one of the most abundant organisms on earth (10³¹). Structurally, they are 100-200nm in size and consist of a protein encapsulated head that contains DNA or RNA, a tail sheath and tail fibers. This research consisted of examining phage infection, by re-isolating a novel phage, Tango. Tango was originally isolated genetically in 2013 by a previous ISBT student, Anna Maccarrone. The phage was sent to genetic sequencing but two phages were discovered, …

First Proof Of Concept Of Sustainable Metabolite Production From High Solids Fermentation Of Lignocellulosic Biomass Using A Bacterial Co-Culture And Cycling Flush System, Wanying Yao, Sue E. Nokes

Biosystems and Agricultural Engineering Faculty Publications

To improve the lignocellulose conversion for ABE in high solids fermentation, this study explored the feasibility of cycling the process through the cellulolytic or/and solventogenic phases via intermittent flushing of the fermentation media. Five different flushing strategies (varying medium ingredients, inoculum supplement and cycling through phases) were investigated. Flushing regularly throughout the cellulolytic phase is necessary because re-incubation at 65 °C significantly improved glucose availability by at least 6-fold. The solvents accumulation was increased by 4-fold using corn stover (3-fold using miscanthus) over that produced by flushing only through the solventogenic phase. In addition, cycling process was simplified by re-incubating …

Enhanced Expression Of Codon Optimized Mycobacterium Avium Subsp. Paratuberculosis Antigens In Lactobacillus Salivarius, Christopher D. Johnston, John P. Bannatine, Rodney Govender, Lorraine Endersen, Daniel Pletzer, Helge Weingart, Aidan Coffey, Jim O'Mahony, Roy D. Sleator

Department of Biological Sciences Publications

It is well documented that open reading frames containing high GC content show poor expression in A+T rich hosts. Specifically, G+C-rich codon usage is a limiting factor in heterologous expression of Mycobacterium avium subsp. paratuberculosis (MAP) proteins using Lactobacillus salivarius. However, re-engineering opening reading frames through synonymous substitutions can offset codon bias and greatly enhance MAP protein production in this host. In this report, we demonstrate that codon-usage manipulation of MAP2121c can enhance the heterologous expression of the major membrane protein (MMP), analogous to the form in which it is produced natively by MAP bacilli. When heterologously over-expressed, antigenic determinants …

Trait Selection And Welfare Of Genetically Engineered Animals In Agriculture, Michael Greger

Michael Greger, MD, FACLM

The release of the Final Guidance from the US Food and Drug Administration on the commercialization of genetically engineered animals has sparked renewed discussion over the ethical, consumer, and regulatory implications of transgenesis in animal agriculture. Animal welfare critiques have focused on unexpected phenotypic effects in animals used in transgenic research, rather than on the health and welfare implications of the intended productivity enhancement. Unless breeding goals are redefined to reflect social concerns, the occurrence and magnitude of undesirable side effects may increase and consumer confidence in the nascent technology may be undermined.

Influence Of Media Composition On The Growth Rate Of Chlorella Vulgaris And Scenedesmus Acutus Utilized For Co2 Mitigation, Czarena L. Crofcheck, Xinyi E, Aubrey Shea, Michael D. Montross, Mark Crocker, Rodney Andrews

Biosystems and Agricultural Engineering Faculty Publications

Atmospheric carbon dioxide levels have increased since the industrial revolution due to increasing combustion of fossil fuels. One possible CO₂ mitigation strategy is the use of microalgae for mitigation of CO₂. This paper focuses on the influence of media composition on the growth rate of two microalgae strains, Chlorella vulgaris and Scenedesmus actus. A KNO₃ based medium was found to work better for Chlorella, while a urea based equivalent worked better for Scenedesmus. The urea based media investigated here resulted in growth similar to that found with previously reported KNO₃ based media. …

Development Of Pyrf-Based Genetic System For Targeted Gene Deletion In Clostridium Thermocellum And Creation Of A Pta Mutant, Shital A. Tripathi, Daniel G. Olson, D. Aaron Argyros, Bethany B. Miller, Trisha F. Barrett, Daniel M. Murphy, Jesse D. Mccool, Anne K. Warner, Vineet B. Rajgarhia, Lee R. Lynd, David A. Hogsett, Nicky C. Caiazza

Dartmouth Scholarship

We report development of a genetic system for making targeted gene knockouts in Clostridium thermocellum, a thermophilic anaerobic bacterium that rapidly solubilizes cellulose. A toxic uracil analog, 5-fluoroorotic acid (5-FOA), was used to select for deletion of the pyrF gene. The ΔpyrF strain is a uracil auxotroph that could be restored to a prototroph via ectopic expression of pyrF from a plasmid, providing a positive genetic selection. Furthermore, 5-FOA was used to select against plasmid-expressed pyrF, creating a negative selection for plasmid loss. This technology was used to delete a gene involved in organic acid production, namely pta, which encodes …

A New Laser Pointer Driven Optical Microheater For Precise Local Heat Shock, Mike Placinta

Masters Theses 1911 - February 2014

The zebrafish has emerged as an important genetic model system for the study of vertebrate development. However, while genetics is a powerful tool for the study of early gene functions, the approach is more limited when it comes to understanding later functions of genes that have essential roles in early embryogenesis. There is thus a need to manipulate gene expression at different times, and ideally only in some regions of the developing embryo. Methods for conditional gene regulation have been established in Drosophila, C.elegans and the mouse, utilizing conditional gene activation systems such as the Gal4-UAS system (fly) and the …

N-Glycan Modification In Aspergillus Species, Elke Kainz, Andreas Gallmetzer, Christian Hatzl, Juergen H. Nett, Huijuan Li, Thorsten Schinko, Robert Pachlinger, Harald Berger, Yazmid Reyes-Dominguez, Andreas Bernreiter, Tillmann Gerngross, Stefan Wildt, Joseph Strauss

Dartmouth Scholarship

The production by filamentous fungi of therapeutic glycoproteins intended for use in mammals is held back by the inherent difference in protein N-glycosylation and by the inability of the fungal cell to modify proteins with mammalian glycosylation structures. Here, we report protein N-glycan engineering in two Aspergillus species. We functionally expressed in the fungal hosts heterologous chimeric fusion proteins containing different localization peptides and catalytic domains. . This strategy allowed the isolation of a strain with a functional -1,2-mannosidase producing increased amounts of N-glycans of the Man 5 GlcNAc 2 type. This strain was further engineered by the introduction of …

Metal-Resistance Genetically Engineered Bacteria, Sylvia Daunert, Donna Scott, Sridhar Ramanathan

KWRRI Research Reports

Bacterial-based electrochemical and optical sensing systems that respond in a highly selective and sensitive manner to antimonite and arsenite have been developed. This was accomplished by using genetically engineered bacteria bearing one of two plasmids constructed for our studies. The first plasmid, pBGD23, contains the operator/promoter region (O/P) and the gene of the ArsR protein from the ars operon upstream from the β-galactosidase gene. In the absence of antimonite/arsenite, ArsR binds to the 0/P site and prevents the transcription of the genes for ArsR and β-galactosidase, thus blocking expression of these proteins. When antimonite or arsenite is present in the …