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High-Throughput Nanoliter Dispensing Device For Biological Applications, Cole Reynolds, Euiwon Bae Dr., J Paul Robinson Dr. 2018 Purdue University

High-Throughput Nanoliter Dispensing Device For Biological Applications, Cole Reynolds, Euiwon Bae Dr., J Paul Robinson Dr.

The Summer Undergraduate Research Fellowship (SURF) Symposium

Pathogen identification is a field that can contribute largely to the prevention of the spreading of illness and disease. In the past, pathogen identification has been a long and arduous process due to the time-consuming processes and steps that requires technician’s time and effort. With new technologies emerging however, screening of bacteria colonies can be done in a quick and high-throughput way. The problem is that using the current methods, bacteria cannot be transferred to petri dishes fast enough to keep up with the new screening methods. The current study focuses on exploring different methods to create an ergonomic ...


Effect Of Carbohydrates On The Gut Microbiome, Maciej Filar, Mohit S. Verma 2018 Purdue University

Effect Of Carbohydrates On The Gut Microbiome, Maciej Filar, Mohit S. Verma

The Summer Undergraduate Research Fellowship (SURF) Symposium

The microbiome within the gut is directly linked to biological processes within a person, influencing factors such as metabolism, signaling pathways, and available nutrients. Long term dieting is known to alter ecological conditions within the gut, allowing certain types of microbes to flourish. Therefore, the overall health of an individual is ultimately influenced by shifts in the microbial community state caused by persistent dieting. This study investigates the connection between diet and the microbiome and draws an understanding of how common carbohydrates in food can affect bacterial composition. Using KBase software, anaerobic bacterial growth was investigated for bacteria subject to ...


Improving Biomanufacturing Production With Novel Elp-Based Transcriptional Regulators, Juya Jeon, Logan R. Readnour, Kevin V. Solomon 2018 Department of Agricultural and Biological Engineering, Purdue University

Improving Biomanufacturing Production With Novel Elp-Based Transcriptional Regulators, Juya Jeon, Logan R. Readnour, Kevin V. Solomon

The Summer Undergraduate Research Fellowship (SURF) Symposium

Microbes can be used to produce valuable drugs, chemicals, and biofuels, but their potential has not been fully realized due to low production yields. To improve biomanufacturing processes and yield, we are developing novel, transcriptional regulators using biosynthesis technology in order to improve cellular health and overall production. Our regulator contains elastin-like polypeptides (ELPs), which make ideal sensors since they exhibit a sharp, inverse phase transition to indicators of cell health such as intracellular pH and ionic strength, and external stimuli such as temperature. We hypothesize that ELP can be fused to transcription factors to control expression of target genes ...


Identification And Characterization Of Human Monoclonal Antibodies For Immunoprophylaxis Against Enterotoxigenic Escherichia Coli Infection, Serena Giuntini, Matteo Stoppato, Maja Sedic, Ejemel Monir, Jessica R. Pondish, Danielle Wisheart, Zachary Schiller, William D. Thomas Jr., Eileen M. Barry, Lisa Cavacini, mark S. klempner, Yan Wang 2018 University of Massachusetts Medical School

Identification And Characterization Of Human Monoclonal Antibodies For Immunoprophylaxis Against Enterotoxigenic Escherichia Coli Infection, Serena Giuntini, Matteo Stoppato, Maja Sedic, Ejemel Monir, Jessica R. Pondish, Danielle Wisheart, Zachary Schiller, William D. Thomas Jr., Eileen M. Barry, Lisa Cavacini, Mark S. Klempner, Yan Wang

Open Access Articles

Background. Enterotoxigenic Escherichia coli (ETEC) cause diarrheal illness in infants in the developing world and travelers to endemic countries including military personnel. ETEC infection of the host involves colonization of the small intestinal epithelium and toxin secretion leading to watery diarrhea. There is currently no vaccine licensed to prevent ETEC. CFA/I is one of the most common colonization factor antigens (CFAs). The CFA/I adhesin subunit, CfaE, is required for ETEC adhesion to host intestinal cells. Human antibodies against CfaE have potential to block colonization of ETEC and serve as an immunoprophylactic against ETEC-related diarrhea.

Methods. Mice transgenic for ...


Comparative Microbial Community Dynamics In A Karst Aquifer System And Proximal Surface Stream In Northwest Arkansas, Josue Rodriguez 2018 University of Arkansas, Fayetteville

Comparative Microbial Community Dynamics In A Karst Aquifer System And Proximal Surface Stream In Northwest Arkansas, Josue Rodriguez

Theses and Dissertations

Northwest Arkansas has well-developed karst systems, with numerous sinking streams and springs. Karst conduits make it easy for contaminants to enter groundwater systems, degrading the water quality and destroying fragile karst ecosystems. With the increase of urbanization, potential threats in the form of fecal contamination may prove to be more of a problem. The purpose of this research is to compare the difference between microbial communities within two different settings, a karst aquifer and a surface stream. The microbial communities within Blowing Spring Cave and Little Sugar Creek were detected and identified in water and sediment samples. Samples were also ...


Bacteriophages As Beneficial Regulators Of The Mammalian Microbiome, Joseph W. Francis, Matthew Ingle, Todd Charles Wood 2018 The Master's College

Bacteriophages As Beneficial Regulators Of The Mammalian Microbiome, Joseph W. Francis, Matthew Ingle, Todd Charles Wood

The Proceedings of the International Conference on Creationism

Much of the research on viruses has concentrated on their disease causing ability. The creation model biomatrix theory predicts that viruses play a beneficial role in cells and organisms. In this report we present a new theory which proposes that mammalian phages (bacteriophages), the most abundant organism associated with mammals, guard and regulate growth of the mammalian microbiome. We base this theory on nearly a century of published evidence that demonstrates that phage can insert into the bacterial genome and cover the surface of bacteria. We propose that this “cloaking” of the bacterial cell surface is an elegant mechanism whereby ...


Integrated Regulation Of Class Ii Human Endogenous Retroviruses In A Breast Cancer Cell Line, Yingguang Liu, Tam D. Nguyen 2018 Liberty University College of Osteopathic Medicine

Integrated Regulation Of Class Ii Human Endogenous Retroviruses In A Breast Cancer Cell Line, Yingguang Liu, Tam D. Nguyen

The Proceedings of the International Conference on Creationism

Endogenous retroviruses (ERVs) are still regarded as foreign invaders by most biologists. Because of structural and positional homology of ERVs in human and ape genomes, they have been considered molecular evidences of common ancestry. Using a breast cancer cell line, we analyzed the regulatory features of a group of human endogenous retroviruses (HERV-K), and found that they contain multiple sequence motifs subjecting them to regulation by sex hormones, a stem cell-specific transcription factor (OCT4), and DNA methylation. Mutation of the OCT4 motif abrogates their response to sex hormones, while methylation of a progesterone-response element enhances receptor-binding. We also found that ...


Whole Cell Cross-Linking To Discover Host-Microbe Protein Cognate Receptor/Ligand Pairs, Bart C. Weimer, Poyin Chen, Prerak T. Desai, Dong Chen, Jigna Shah 2018 University of California, Davis

Whole Cell Cross-Linking To Discover Host-Microbe Protein Cognate Receptor/Ligand Pairs, Bart C. Weimer, Poyin Chen, Prerak T. Desai, Dong Chen, Jigna Shah

Biological Engineering Faculty Publications

Bacterial surface ligands mediate interactions with the host cell during association that determines the specific outcome for the host–microbe association. The association begins with receptors on the host cell binding ligands on the microbial cell to form a partnership that initiates responses in both cells. Methods to determine the specific cognate partnerships are lacking. Determining these molecular interactions between the host and microbial surfaces are difficult, yet crucial in defining biologically important events that are triggered during association of the microbiome, and critical in defining the initiating signal from the host membrane that results in pathology or commensal association ...


General Microbiology (Dalton State), April Kay, Susan Burran, Leah Howell 2018 Dalton State College

General Microbiology (Dalton State), April Kay, Susan Burran, Leah Howell

Biological Sciences Grants Collections

This Grants Collection for General Microbiology was created under a Round Nine ALG Textbook Transformation Grant.

Affordable Learning Georgia Grants Collections are intended to provide faculty with the frameworks to quickly implement or revise the same materials as a Textbook Transformation Grants team, along with the aims and lessons learned from project teams during the implementation process.

Documents are in .pdf format, with a separate .docx (Word) version available for download. Each collection contains the following materials:

  • Linked Syllabus
  • Initial Proposal
  • Final Report


Bacteriophages For Treating American Foulbrood And The Neutralization Of Paenibacillus Larvae Spores, Thomas Scott Brady 2018 Brigham Young University

Bacteriophages For Treating American Foulbrood And The Neutralization Of Paenibacillus Larvae Spores, Thomas Scott Brady

All Theses and Dissertations

The causative agent of the most devastating honeybee disease, American foulbrood (AFB), is the spore-forming bacterium Paenibacillus larvae. To prevent AFB outbreaks beekeepers prophylactically treat their hives with antibiotics even though it decreases the overall health of uninfected hives. A new treatment for AFB is needed due to recent legislation against using antibiotics, antibiotic resistance developing in P. larvae, and the resilience of P. larvae spores. Bacteriophages, or phages, are an attractive alternative to traditional antibiotics because of their specificity and ability to evolve alongside their target bacterium. In this study, two phage cocktails were developed for the treatment of ...


The Diversity Found Among Carbapenem-Resistant Bacteria, Galen Edward Card 2018 Brigham Young University

The Diversity Found Among Carbapenem-Resistant Bacteria, Galen Edward Card

All Theses and Dissertations

This work will look at two factors that add to the diversity of carbapenem resistant bacteria. First, it focuses on the diversity of carbapenemase resistance plasmids. 446 plasmids were characterized by size, gene content and replicon groups. We identified that on average, over 30% of the encoded proteins on each plasmid have an unknown function. Plasmid sizes ranged from 1.6kb to 500kb, with an average of around 100kb and median of 80kb. Additionally, six replicon groups account for 80% of all the carbapenemase resistance plasmids. We also highlight the lack of data available for carbapenemase carrying plasmids from bacterial ...


The Role Of Eukaryotic Abc-Transporters In Eliciting Neutrophil Infiltration During Streptococcus Pneumoniae Infection, Andrew Zukauskas 2018 University of Massachusetts Medical School

The Role Of Eukaryotic Abc-Transporters In Eliciting Neutrophil Infiltration During Streptococcus Pneumoniae Infection, Andrew Zukauskas

GSBS Dissertations and Theses

Streptococcus pneumoniae (S. pneumoniae) is a Gram-positive, encapsulated bacterium capable of causing significant morbidity and mortality throughout the world. A hallmark of S. pneumoniae infection is infiltration of neutrophils (PMNs) that assist in controlling the spread infection but may also contribute to pathology. Paradoxically, studies have shown that limiting PMN infiltration into the lumen of the lung during infection actually betters clinical outcome in experimental S. pneumoniae infection. The final step in PMN luminal trafficking is a Hepoxilin A3 (HXA3)-dependent migration across the pulmonary epithelium. HXA3 is a PMN chemoattractant that forms gradients along the polarized epithelial ...


Bacterial Diversity Associated With Mineral Substrates And Hot Springs From Caves And Tunnels Of The Naica Underground System (Chihuahua, Mexico), Adriana Espino del Castillo, Hugo Beraldi-Campesi, Patricia Amador-Lemus, Hiram Isaac Beltrán, Sylvie Le Borgne 2018 Universidad Autónoma Metropolitana

Bacterial Diversity Associated With Mineral Substrates And Hot Springs From Caves And Tunnels Of The Naica Underground System (Chihuahua, Mexico), Adriana Espino Del Castillo, Hugo Beraldi-Campesi, Patricia Amador-Lemus, Hiram Isaac Beltrán, Sylvie Le Borgne

International Journal of Speleology

The Naica Underground System (NUS) in Northern Mexico comprises a lead, zinc, and silver producing mine and displays the largest gypsum crystals ever found in natural caves. The caves are now closed to the public and mining activities have been suspended for an undefined period since October 2015. Besides its geological, economical, and tourist importance, the bacterial diversity in the NUS has not been fully explored yet. This study surveyed for bacteria present on different mineral substrates (gypsum crystals, iron oxide crusts) and hot spring samples collected before the NUS was inaccessible, using culture-dependent and culture–independent (PCR-DGGE) methods. This ...


A Recombinant Herpesviral Vector Containing A Near-Full-Length Sivmac239 Genome Produces Siv Particles And Elicits Immune Responses To All Nine Siv Gene Products, Young C. Shin, Georg F. Bischof, William A. Lauer, Lucas Gonzalez-Nieto, Eva G. Rakasz, Gregory M. Hendricks, David I. Watkins, Mauricio A. Martins, Ronald C. Desrosiers 2018 University of Miami

A Recombinant Herpesviral Vector Containing A Near-Full-Length Sivmac239 Genome Produces Siv Particles And Elicits Immune Responses To All Nine Siv Gene Products, Young C. Shin, Georg F. Bischof, William A. Lauer, Lucas Gonzalez-Nieto, Eva G. Rakasz, Gregory M. Hendricks, David I. Watkins, Mauricio A. Martins, Ronald C. Desrosiers

Radiology Publications and Presentations

The properties of the human immunodeficiency virus (HIV) pose serious difficulties for the development of an effective prophylactic vaccine. Here we describe the construction and characterization of recombinant (r), replication-competent forms of rhesus monkey rhadinovirus (RRV), a gamma-2 herpesvirus, containing a near-full-length (nfl) genome of the simian immunodeficiency virus (SIV). A 306-nucleotide deletion in the pol gene rendered this nfl genome replication-incompetent as a consequence of deletion of the active site of the essential reverse transcriptase enzyme. Three variations were constructed to drive expression of the SIV proteins: one with SIV's own promoter region, one with a cytomegalovirus (cmv ...


The Comparative Genomics Of Bifidobacterium Callitrichos Reflects Dietary Carbohydrate Utilization Within The Common Marmoset Gut, Korin Albert, Asha Rani, David A. Sela 2018 University of Massachusetts Amherst

The Comparative Genomics Of Bifidobacterium Callitrichos Reflects Dietary Carbohydrate Utilization Within The Common Marmoset Gut, Korin Albert, Asha Rani, David A. Sela

Open Access Articles

Bifidobacterium is a diverse genus of anaerobic, saccharolytic bacteria that colonize many animals, notably humans and other mammals. The presence of these bacteria in the gastrointestinal tract represents a potential coevolution between the gut microbiome and its mammalian host mediated by diet. To study the relationship between bifidobacterial gut symbionts and host nutrition, we analyzed the genome of two bifidobacteria strains isolated from the feces of a common marmoset (Callithrix jacchus), a primate species studied for its ability to subsist on host-indigestible carbohydrates. Whole genome sequencing identified these isolates as unique strains of Bifidobacterium callitrichos. All three strains, including these ...


Investigating The Viral Ecology Of Global Bee Communities With High-Throughput Metagenomics, David A. Galbraith, Zachary L. Fuller, Allyson M. Ray, Axel Brockmann, Maryann Frazier, Mary W. Gikungu, J. Francisco Iturralde Martinez, Karen M. Kapheim, Jeffrey T. Kerby, Sarah D. Kocher, Oleksiy Losyev, Elliud Muli, Harland M. Patch, Cristina Rosa, Joyce M. Sakamoto, Scott Stanley, Anthony D. Vaudo, Christina M. Grozinger 2018 Pennsylvania State University

Investigating The Viral Ecology Of Global Bee Communities With High-Throughput Metagenomics, David A. Galbraith, Zachary L. Fuller, Allyson M. Ray, Axel Brockmann, Maryann Frazier, Mary W. Gikungu, J. Francisco Iturralde Martinez, Karen M. Kapheim, Jeffrey T. Kerby, Sarah D. Kocher, Oleksiy Losyev, Elliud Muli, Harland M. Patch, Cristina Rosa, Joyce M. Sakamoto, Scott Stanley, Anthony D. Vaudo, Christina M. Grozinger

Biology Faculty Publications

Bee viral ecology is a fascinating emerging area of research: viruses exert a range of effects on their hosts, exacerbate the impacts of other environmental stressors, and, importantly, are readily shared across multiple bee species in a community. However, our understanding of bee viral communities is limited, as it is primarily derived from studies of North American and European Apis mellifera populations. Here, we examined viruses in populations of A. mellifera and 11 other bee species from 9 countries, across 5 continents and Oceania. We developed a novel pipeline to rapidly, inexpensively, and robustly screen for bee viruses. This pipeline ...


Antimicrobial Activities Of Culturable Microorganisms (Actinomycetes And Fungi) Isolated From Chaabe Cave, Algeria, Larbi Belyagoubi, Nabila Belyagoubi-Benhammou, Valme Jurado, Joëlle Dupont, Sandrine Lacoste, Fatima Djebbah, Fatima Z. Ounadjela, Souad Benaissa, Salim Habi, Djamel E. Abdelouahid, Cesareo Saiz-Jimenez 2018 Université Abou Bekr Belkaid

Antimicrobial Activities Of Culturable Microorganisms (Actinomycetes And Fungi) Isolated From Chaabe Cave, Algeria, Larbi Belyagoubi, Nabila Belyagoubi-Benhammou, Valme Jurado, Joëlle Dupont, Sandrine Lacoste, Fatima Djebbah, Fatima Z. Ounadjela, Souad Benaissa, Salim Habi, Djamel E. Abdelouahid, Cesareo Saiz-Jimenez

International Journal of Speleology

The discovery of new antibiotics and other bioactive microbial metabolites is a priority given the frequency of the emerging multi-drug resistant pathogenic microorganisms. Thus, scientists are searching for new antibiotics in microorganisms isolated from extreme habitats such as caves. In the present study, we aimed to perform the first analysis on culturable microorganisms in the Chaabe Cave (Algeria), and to test the antimicrobial activities of the isolates (Streptomyces spp. and Penicillium spp.). The potential for antimicrobial activity of 47 strains of actinomycetes and 23 strains of fungi were tested on Candida albicans, Staphylococcus aureus, Micrococcus luteus, Listeria monocytogenes, Bacillus subtilis ...


Biomarker Analysis And Clinical Relevance Of Thymidine Kinase 1 In Solid And Hematological Malignancies, Evita Giraldez Weagel 2018 Brigham Young University

Biomarker Analysis And Clinical Relevance Of Thymidine Kinase 1 In Solid And Hematological Malignancies, Evita Giraldez Weagel

All Theses and Dissertations

Despite the global effort to discover and improve ways to detect, treat, and monitor cancer, it still remains the second leading cause of death in the United States and poses a major health and economic burden worldwide. While traditional treatments like surgery, chemotherapy, radiation therapy, and hormone therapy have been successful and have decreased cancer mortality, cancer incidence in all sites continues to rise. Consequently, there is an immediate need to find new therapeutics for the treatment of cancer. In recent years, and with the continuing push towards personalized medicine, cancer biomarkers have become crucial to detect, treat, and monitor ...


Ms Analysis Of A Dilution Series Of Bacteria: Phytoplankton To Improve Detection Of Low Abundance Bacterial Peptides, Emma Timmins-Schiffman, Molly P. Mikan, Ying Sonia Ting, H. Rodger Harvey, Brook L. Nunn 2018 Old Dominion University

Ms Analysis Of A Dilution Series Of Bacteria: Phytoplankton To Improve Detection Of Low Abundance Bacterial Peptides, Emma Timmins-Schiffman, Molly P. Mikan, Ying Sonia Ting, H. Rodger Harvey, Brook L. Nunn

OEAS Faculty Publications

Assigning links between microbial activity and biogeochemical cycles in the ocean is a primary objective for ecologists and oceanographers. Bacteria represent a small ecosystem component by mass, but act as the nexus for both nutrient transformation and organic matter recycling. There are limited methods to explore the full suite of active bacterial proteins largely responsible for degradation. Mass spectrometry (MS)-based proteomics now has the potential to document bacterial physiology within these complex systems. Global proteome profiling using MS, known as data dependent acquisition (DDA), is limited by the stochastic nature of ion selection, decreasing the detection of low abundance ...


Characterizing The Role Of N Terminus Of Influenza A Nucleoprotein For Location And Viral Rnp Activity, Jared Lin 2018 California State University - San Bernardino

Characterizing The Role Of N Terminus Of Influenza A Nucleoprotein For Location And Viral Rnp Activity, Jared Lin

Electronic Theses, Projects, and Dissertations

The influenza viral ribonucleoprotein complexes (vRNPs) are responsible for viral RNA synthesis. Each vRNP is comprised of one vRNA segment, the viral RNA dependent RNA polymerase complex (RdRP), and multiple copies of nucleoprotein (NP). NP serves as scaffold in formation of vRNPs, but also regulates vRNP activity. The N-terminus of NP contains a nonconventional nuclear localization signal (NLS1) essential for initial vRNP nuclear import, but also interacts with host RNA helicases to enhance viral RNA replication in the nucleus. NP contains at least one additional NLS sequence, with bioinformatics revealing a third NLS in some NP proteins.

Published yeast-two hybrid ...


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