Organisms Commons^™

Sea-Phages Research Opportunity, Sarah Ballarin

Trick to the Treat of Internships and Research

Research opportunity targeted for freshmen and sophomores through the SEA-PHAGES program. The goal of the research is to discover new bacteriophages (viruses that infect bacteria) to help combat antibiotic resistance. Phage therapy is a promising alternative to conventional antibiotics. Phages have also been widely used in the food industry to prevent microbial growth on certain foods and are currently being explored as a method for bioremediation of oil spills and wastewater treatment.

Last year, my research team discovered two new bacteriophages: Genamy16 and NovaSharks that were able to infect the bacteria Gordonia rubripertincta. These phages can possibly be used for …

Generation Of Mycobacterium Smegmatis Model Systems For Testing Inhibitors Of The Mycobactin Siderophore Of Mycobacterium Tuberculosis, Gabrielle A. Germain

Dissertations, Theses, and Capstone Projects

Mycobacterium tuberculosis (Mtb) is the pathogenic bacterium causative of tuberculosis. According to the 2021 World Health Organization (WHO) Global Tuberculosis (TB) Report, there were approximately 5.8 million TB cases in 2020, and 1.3 million TB deaths among HIV negative people in that year. The rise of multi-drug resistant Mtb strains has increased the need for more potent microbials against this pathogen. Biosynthesis of iron scavenging molecules, known as siderophores (e.g., mycobactin and carboxymycobactin), has been identified as a potential drug target candidate since iron acquisition has been directly linked to the survival and virulence of Mtb. Salicyl-AMS (Sal-AMS) is …

Holarctic Species In The Pluteus Romellii Clade Five New Species Described And Old Names Reassessed, Hana Ševčíková, Ekaterina Malysheva, Giuliano Ferisin, Francesco Dovana, Egon Horak, Jacob Kalichman, Oğuzhan Kaygusuz, Renée Lebeuf, Guillermo Muñoz González, Andrew M Minnis, Stephen D Russell, Michal Sochor, Bálint Dima, Vladimír Antonín, Alfredo Justo

Faculty, Staff and Students Publications

We studied the taxonomy of Pluteus romellii, and morphologically similar Holarctic species in the/romellii clade of section Celluloderma, using morphological and molecular data (nrITS, TEF1-α). Pluteus romellii is lectotypified and epitypified and accepted as an exclusively Eurasian species. Pluteus lutescens and P. pallescens are considered synonyms of P. romellii. Pluteus fulvibadius is accepted as a related, but separate, North American species. Five species in the/romellii clade are described as new to science: two from North America (P. austrofulvus and P. parvisporus), one from Asia (P. parvicarpus), one from Europe (P. siccus …

Pluteus Insidiosus Complex, Four New Species Described And Pluteus Reisneri Resurrected, Hana Ševčíková, Giuliano Ferisin, Ekaterina Malysheva, Alfredo Justo, Jacob Heilmann-Clausen, Egon Horak, Lyudmila Kalinina, Oğuzhan Kaygusuz, Henning Knudsen, Nelson Menolli, Pierre-Arthur Moreau, Guillermo Muñoz González, Irja Saar, İbrahim Türkekul, Francesco Dovana

Faculty, Staff and Students Publications

We studied the taxonomy of Pluteus insidiosus and similar species using morphological and molecular (nrITS, TEF1-α) data, including a detailed study of the type collection of P. insidiosus. Based on our results, we recognize five species in this group: P. insidiosus sensu stricto and four other taxa: P. assimilatus; P. farensis; P. flavostipitatus; and P. pseudoinsidiosus; described here as new. All these taxa are distinct from each other based on molecular data, but some of them are semi-cryptic based on morphology and co-occur in the Palaearctic region. An additional molecular lineage, phylogenetically separates from the P. …

Tick Transmission Of Borrelia Burgdorferi To The Murine Host Is Not Influenced By Environmentally Acquired Midgut Microbiota, Sukanya Narasimhan, Nallakkandi Rajeevan, Morven Graham, Ming-Jie Wu, Kathleen Deponte, Solenne Marion, Orlanne Masson, Anya J. O'Neal, Daniel E. Sonenshine, Erol Fikrig

Biological Sciences Faculty Publications

Background

Ixodes scapularis is the predominant tick vector of Borrelia burgdorferi, the agent of Lyme disease, in the USA. Molecular interactions between the tick and B. burgdorferi orchestrate the migration of spirochetes from the midgut to the salivary glands—critical steps that precede transmission to the vertebrate host. Over the last decade, research efforts have invoked a potential role for the tick microbiome in modulating tick-pathogen interactions.

Results

Using multiple strategies to perturb the microbiome composition of B. burgdorferi-infected nymphal ticks, we observe that changes in the microbiome composition do not significantly influence B. burgdorferi migration from the midgut, invasion of …

Sensory Descriptors For Three Edible Chilean Seaweeds And Their Relations To Umami Components And Instrumental Texture, Valentina Figueroa, Andrea Bunger, Jaime Ortiz, José Miguel Aguilera

Faculty, Staff and Students Publications

Although seaweeds exhibit many benefits as a food source, few studies have characterized their sensory attributes. An expert nine-member panel developed a vocabulary with 25 descriptors to describe the appearance, aroma, flavor, texture, and aftertaste of raw and cooked seaweeds consumed in Chile: Durvillaea antarctica, Pyropia spp., and Ulva lactuca. Subsequently, the vocabulary was used in a ranking descriptive analysis (RDA) to evaluate the sensory properties and relate them with physicochemical and physical data. Sensory attributes of the three seaweeds were very different from each other but similar between treatments (raw and cooked). Pyropia spp., both cooked and …

Identification Of A Rickettsial Endosymbiont In A Soft Tick Ornithodoros Turicata Americanus, Lichao Liu, Daniel E. Sonenshine, Hameeda Sultana, Girish Neelakanta

Biological Sciences Faculty Publications

Bacterial endosymbionts are abundantly found in both hard and soft ticks. Occidentia massiliensis, a rickettsial endosymbiont, was first identified in the soft tick Ornithodoros sonrai collected from Senegal and later was identified in a hard tick Africaniella transversale. In this study, we noted the presence of Occidentia species, designated as Occidentia-like species, in a soft tick O. turicata americanus. Sequencing and phylogenetic analyses of the two genetic markers, 16S rRNA and groEL confirmed the presence of Occidentia-like species in O. turicata americanus ticks. The Occidentia-like species was noted to be present in all developmental stages …

Antimicrobial Resistance: A Challenge Awaiting The Post-Covid-19 Era, Tekle Airgecho Lobie, Aklilu Abrham Roba, James Alexander Booth, Knut Ivan Kristiansen, Abraham Aseffa, Kirsten Skarstad, Magnar Bjørås

Research on Antimicrobial Resistance

Microbe exposure to pharmaceutical and non-pharmaceutical agents plays a role in the development of antibiotic resistance. The risks and consequences associated with extensive disinfectant use during the COVID-19 pandemic remain unclear. Some disinfectants, like sanitizers, contain genotoxic chemicals that damage microbial DNA, like phenol and hydrogen peroxide. This damage activates error-prone DNA repair enzymes, which can lead to mutations that induce antimicrobial resistance. Public health priority programs that have faced drug-resistance challenges associated with diseases, such as tuberculosis, HIV, and malaria, have given less attention to risks attributable to the COVID-19 pandemic. Pathogen-specific programs, like the directly observed treatment strategy …

Assesment Of Antibiotic Resistant Gene Expression In Clinical Isolates Of Pseudomonas Aeruginosa, Dustin Esmond

Biology Theses

Increasing prevalence of nosocomial infections by antimicrobial resistant pathogens resulting in higher mortality rates and financial burden is of great concern. Pseudomonas aeruginosa represents one of six highly virulent “ESKAPE” pathogens that exhibit considerable intrinsic drug resistance as well as mechanisms for acquiring further resistance. As many of these mechanisms are regulated through gene expression, we sought to identify regulatory strategies and patterns at play in 23 clinical isolates collected from Baku, Azerbaijan and Tyler, Texas, USA. Real-time quantitative polymerase chain reaction was performed on six gene targets implicated in resistance and contrasted with antibiotic phenotypes. We found AmpC cephalosporinase …

A Novel Application Of Galleria Mellonella Larvae To Study Pathogenesis Of Rickettsia Rickettsii Infection, Jacob M. Jones

Honors College Theses

Rickettsia are obligate intracellular tick-borne bacteria that cause acute undifferentiated febrile illness accompanied by headache, malaise, myalgias, and disseminated endothelial infection. Immune responses to Rickettsia and pathogenesis of rickettsioses are not fully understood. Current work with Rickettsia is limited to vertebrate models that are strictly regulated and have low throughput. Since the innate immune system of vertebrates retains striking similarities with the immune response in insects, invertebrates are being used to study host responses to various pathogens. The purpose of this study was to evaluate if larvae of the greater wax moth Galleria mellonella (GML) can be used as an …

Functional Influence Of 14-3-3 (Ywha) Proteins In Mammals, Elizabeth Barley, Santanu De

Mako: NSU Undergraduate Student Journal

The 14-3-3 (YWHA) proteins are homologous, ubiquitous, and conserved in most organisms ranging from plants to animals and play important roles in regulating key cellular events such as cell signaling, development, apoptosis, etc. These proteins consist of seven isoforms in mammals, termed under Greek alphabetization: beta (β), gamma (γ), epsilon (ε), eta (η), tau/theta (τ), sigma (σ), and zeta (ζ). Each of these isoforms can interact with a plethora of binding partners and has been shown to serve a distinct role in molecular crosstalk, biological processes, and disease susceptibility. Protein 14-3-3 isoforms are scaffolding proteins capable of forming homodimers and …

A Microbiome Analysis Of The Relationship Among Crayfish Ectosymbionts And Their Environment, John Hoverson

Senior Honors Theses

The purpose of this project was to determine if there are differences present between the α-diversities of the crayfish microbiome and its surrounding water and sediment. Furthermore, this project sought to discover if these differences hold when microbiomes are evaluated between crayfish of first and second stream orders. Finally, this project sought to determine if the presence of branchiobdellidan ectosymbionts on the crayfish caused further differences in the crayfish microbiome. While the hypothesized patterns between crayfish, ectosymbionts, and stream order were not found to exist, a significantly different microbiome was observed between water, sediment, and crayfish, and the α-diversity of …

Wild Mice With Different Social Network Sizes Vary In Brain Gene Expression, Patricia C. Lopes, Barbara König

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Background

Appropriate social interactions influence animal fitness by impacting several processes, such as mating, territory defense, and offspring care. Many studies shedding light on the neurobiological underpinnings of social behavior have focused on nonapeptides (vasopressin, oxytocin, and homologues) and on sexual or parent-offspring interactions. Furthermore, animals have been studied under artificial laboratory conditions, where the consequences of behavioral responses may not be as critical as when expressed under natural environments, therefore obscuring certain physiological responses. We used automated recording of social interactions of wild house mice outside of the breeding season to detect individuals at both tails of a distribution …

Identifying Determinants Of Target Specificity In Two Related Bacterial Peptide Toxins, Andrew D. Holmes

Honors Thesis

Toxin-antitoxin (TA) systems were originally identified as two-component systems ensuring the stable inheritance of plasmids in bacterial populations. Recently, they have been identified on bacterial chromosomes where their functions remain mostly undefined. The par locus of E. faecalis plasmid pAD1 (par_pAD1) was the first TA system defined in a Gram-positive bacterium and a homolog encoded on the E. faecalis chromosome (par_EF0409) was later described. Related loci numbering in the hundreds have been identified throughout Gram-positive bacteria based on homology to the toxin of the system, Fst, and similarities in genetic organization and regulation. Despite …

Cell Type Composition And Circuit Organization Of Clonally Related Excitatory Neurons In The Juvenile Mouse Neocortex, Cathryn R Cadwell, Federico Scala, Paul G Fahey, Dmitry Kobak, Shalaka Mulherkar, Fabian H Sinz, Stelios Papadopoulos, Zheng H Tan, Per Johnsson, Leonard Hartmanis, Shuang Li, Ronald J Cotton, Kimberley F Tolias, Rickard Sandberg, Philipp Berens, Xiaolong Jiang, Andreas Savas Tolias

Faculty, Staff and Students Publications

Clones of excitatory neurons derived from a common progenitor have been proposed to serve as elementary information processing modules in the neocortex. To characterize the cell types and circuit diagram of clonally related excitatory neurons, we performed multi-cell patch clamp recordings and Patch-seq on neurons derived from Nestin-positive progenitors labeled by tamoxifen induction at embryonic day 10.5. The resulting clones are derived from two radial glia on average, span cortical layers 2–6, and are composed of a random sampling of transcriptomic cell types. We find an interaction between shared lineage and connection type: related neurons are more likely to …

Immune-Endocrine Links To Gregariousness In Wild House Mice, Patricia C. Lopes, Esther H. D. Carlitz, Morgan Kindel, Barbara König

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Social interactions are critically important for survival and impact overall-health, but also impose costs on animals, such as exposure to contagious agents. The immune system can play a critical role in modulating social behavior when animals are sick, as has been demonstrated within the context of “sickness behaviors.” Can immune molecules affect or be affected by social interactions even when animals are not sick, therefore serving a role in mediating pathogen exposure? We tested whether markers of immune function in both the blood and the brain are associated with gregariousness, quantified as number of animals interacted with per day. To …

Neuroanatomy Of The Blackspotted Rockskipper, Entomacrodus Striatus, Pooja Dayal

Williams Honors College, Honors Research Projects

Here I characterized the central neuroanatomy of the Blackspotted Rockskipper, Entomacrodus striatus, native to French Polynesia. The neuroanatomy of E. striatus has not been studied prior to this paper. I used several histology and antibody staining techniques to accomplish this, including Crystal Violet, immunohistochemistry, immunofluorescence, and Bielschowsky’s Silver Nitrate staining. This paper describes the most successful techniques used, identifies major structures in the species’ neuroanatomy, and also explains why studying E. striatus is important in the future of vertebrate research.

Assessing Morphology Of Iprgcs After Traumatic Brain Injury, Brian Foresi, Matt Smith

Williams Honors College, Honors Research Projects

ipRGCs are retinal ganglion cells that project to visual processing centers of the brain for nonimage forming visual functions. The relation of ipRGCs to tramatic brain injury (TBI) is emerging as data has been published describing ipRGC functional changes in TBI affected military veterans. Major symptomologies of concussions, a mild form of TBI, also overlap with the function governed by sites in the brain with major ipRGC projection percentages. Assesing if a morphological change is occuring in the ipRGCs after a TBI could support the idea of a pathological mechanism of the injury. This study could also indicate further relevance …

The Biosorption Of Lead From Aqueous Solutions By A Wood-Immobilized Fungal Biosorbent, Zomesh A N Maini, Niña Therese B. Flores, Enrico P. Muñoz

Biology Faculty Publications

Lead [Pb(II)] biosorption capacities of immobilized Talaromyces macrosporus on Moringa oleifera L. wood were compared against pure fungal and pure M. oleifera biomass. A Pb(II) contact test of 1000 ug/mL show similar Pb(II) removal of non-immobilized fungal biomass (F) and powdered wood colonized with fungi (WP+F), with WP+F producing more biomass. Powdered sorbents had higher Pb(II) uptake compared to whole sorbents analyzed through ICP-AES, possibly due to increased surface area for Pb(II) binding. FTIR analysis of the F, WP, and WP+F identified hydroxyl, amino, carbonyl, and sulfhydryl functional groups which constitute probable Pb(II)-affinitive binding sites. The biosorbents tested in a …

The Relationship Between Biofilm Production And Human Respiratory Cell Attachment And Invasion By Acinetobacter Baumannii, Rachel A. Pearson

Theses and Dissertations

Acinetobacter baumannii is an opportunistic gram-negative bacterial pathogen that causes many nosocomial infections in immunocompromised individuals. Common infections include catheter-associated urinary tract infections, ventilator-associated pneumonia, skin and soft tissue infections, and bloodstream infections that often lead to septicemia. Increasing multidrug resistance (MDR) in A. baumannii warrants new approaches to understanding its virulence mechanisms and pathogenicity. As a first step in infection, A. baumannii can attach to host cells, providing a surface for the bacteria to grow and perhaps facilitating biofilm formation and subsequent tissue invasion. In this study, we evaluated antibiotic resistance and characterized biofilm formation, attachment, invasion, and surface …

Complex History Of Codiversification And Host Switching Of A Newfound Soricid-Borne Orthohantavirus In North America, Schuyler W. Liphardt, Hae Ji Kang, Laurie J. Dizney, Luis A. Ruedas, Joseph A. Cook, Richard Yanagihara

Biology Faculty Publications and Presentations

Orthohantaviruses are tightly linked to the ecology and evolutionary history of their mammalian hosts. We hypothesized that in regions with dramatic climate shifts throughout the Quaternary, orthohantavirus diversity and evolution are shaped by dynamic host responses to environmental change through processes such as host isolation, host switching, and reassortment. Jemez Springs virus (JMSV), an orthohantavirus harbored by the dusky shrew (Sorex monticola) and five close relatives distributed widely in western North America, was used to test this hypothesis. Total RNAs, extracted from liver or lung tissue from 164 shrews collected from western North America during 1983–2007, were analyzed for orthohantavirus …

A Rapid Viability And Drug‑Susceptibility Assay Utilizing Mycobacteriophage As An Indicator Of Drug Susceptibilities Of Anti‑Tb Drugs Against Mycobacterium Smegmatis Mc2 155, Gillian Catherine Crowley, Jim O'Mahony, Aidan Coffey, Riona G. Sayers, Paul D. Cotter

Department of Biological Sciences Publications

Background: A rapid in-house TM4 mycobacteriophage-based assay, to identify multidrug resistance against various anti-tuberculosis drugs, using the fast-growing Mycobacterium smegmatis mc² 155 in a microtiter plate format was evaluated, based on phage viability assays. Methods: A variety of parameters were optimized before the study including the minimum incubation time for the drugs, phage and M. smegmatis mc² 155 to be in contact. An increase in phage numbers over 2 h was indicative that M. smegmatis mc² 155 is resistant to the drugs under investigation, however when phage numbers remained static, M. smegmatis mc² 155 found to …

Crispr/Cas9 In Yeast: A Multi-Week Laboratory Exercise For Undergraduate Students, Randi J. Ulbricht

Open Educational Resources

Providing undergraduate life-science students with a course-based research experience that utilizes cutting-edge technology, is tractable for students, and is manageable as an instructor is a challenge. Here, I describe a multi-week lesson plan for a laboratory-based course with the goal of editing the genome of budding yeast, Saccharomyces cerevisiae. Students apply knowledge regarding advanced topics such as: CRISPR/Cas9 gene editing, DNA repair, genetics, and cloning. The lesson requires students to master skills such as bioinformatics analysis, restriction enzyme digestion, ligation, basic microbiology skills, polymerase chain reaction, and plasmid purification. Instructors are led through the technical aspects of the protocols, …

The Association Between Herpes Simplex Virus Type 1 Reactivation And Alzheimer’S Disease, Andrew Allee

BIO 410 Spring 2019 Research Papers

This review will focus on the interaction of herpes simplex virus type 1 (HSV-1) and its causative role in pathogenesis of Alzheimer’s disease (AD) noting specifically, the epidemiological relevance of addressing this problem, as well as the molecular pathways associated. HSV-1 reactivation tends to be one of the primary causative events that is responsible for many of the pathologies associated with AD, such as: amyloid beta (Aβ) accumulation caused by malfunctioning cleavage of amyloid precursor protein (APP) as well as tau hyperphosphorylation. HSV-1 reactivation is a primary causative event in downstream dysfunction and is also shown to be directed by …

The Effects Of Bacterial Endotoxin Lps On Synaptic Transmission At The Neuromuscular Junction, Robin L. Cooper, Micaiah Mcnabb, Jeremy Nadolski

Biology Faculty Publications

The direct action of bacterial lipopolysaccharides (LPS) endotoxin was shown to enhance synaptic transmission and hyperpolarize the membrane potential at low doses, but block glutamatergic receptors and decrease observable spontaneous events at a high dosage. The dosage effects are LPS type specific. The hyperpolarization is not due to voltage-gated potassium channels or to activation of nitric oxide synthase (NOS). The effects are induced directly by LPS, independent of an immune response.

Fungal Endophytes In A Seed-Free Host: New Species That Demonstrate Unique Community Dynamics, Brett Steven Younginger

Dissertations and Theses

Fungal endophytes are highly diverse, cryptic plant endosymbionts that form asymptomatic infections within host tissue. They represent a large fraction of the millions of undescribed fungal taxa on our planet with some demonstrating mutualistic benefits to their hosts including herbivore and pathogen defense and abiotic stress tolerance. Other endophytes are latent saprotrophs or pathogens, awaiting host plant senescence to begin alternative stages of their life cycles. Most, however, are likely plant commensals with no observable benefits to their hosts while under study. Yet, when considering the context-dependence that may determine plant resistance to pathogen attack, the consortium of endophytes present …

A Time Course Study Of Rotavirus-Infected Intestinal Cells Treated With Stilbenoids And The Regulation Of Apoptosis, Rebecca D. Parr, Caleb M. Witcher, Rebekah Napier-Jameson, Hannah L. Wilson, Stormey Wisdom, Macie N. Mattila, Essence B. Strange, Josephine Taylor, Beatrice Clack, Fabricio Medina-Bolivar, Judith M. Ball

Faculty Publications

This is a time course study of virus –host interactions that are modified with the addition of two small natural products. They appear to effect virus replication and the host response to the infection.

In Vivo Structures Of The Helicobacter Pylori Cag Type Iv Secretion System, Yi-Wei Chang, Carrie L. Shaffer, Lee A. Rettberg, Debnath Ghosal, Grant J. Jensen

Veterinary Science Faculty Publications

The type IV secretion system (T4SS) is a versatile nanomachine that translocates diverse effector molecules between microbes and into eukaryotic cells. Here, using electron cryotomography, we reveal the molecular architecture of the Helicobacter pylori cag T4SS. Although most components are unique to H. pylori, the cag T4SS exhibits remarkable architectural similarity to other T4SSs. Our images revealed that, when H. pylori encounters host cells, the bacterium elaborates membranous tubes perforated by lateral ports. Sub-tomogram averaging of the cag T4SS machinery revealed periplasmic densities associated with the outer membrane, a central stalk, and peripheral wing-like densities. Additionally, we resolved pilus-like …

Characterization Of The Interaction Between R. Conorii And Human Host Vitronectin In Rickettsial Pathogenesis, Abigail Inez Fish

LSU Doctoral Dissertations

Spotted Fever Group Rickettsia are inoculated into the mammalian host during hematophagous arthropod feeding. Once in the bloodstream and during dissemination, the survival of these pathogens is dependent upon their ability to evade innate host defenses until a proper cellular target is reached. The establishment of a successful infection also relies on the ability of the bacteria to attach and invade target cells, as failure to do so results in destruction of the bacterium. Rickettsia conorii expresses an outer membrane protein, Adr1, which binds the multifunctional human glycoprotein, vitronectin, to promote resistance to complement mediated killing. Homologs of Adr1 are …

Mrub_1199 & Mrub_2272 Of Meiothermus Ruber Are Orthologous Genes To The B0262 Gene In Escherichia Coli While Mrub_1200, Mrub_1201, Mrub_2015 & Mrub_2271 Are Not Orthologous To The B0262 Gene Coding For The Iron (Fe3+) Abc Transport System, Kumail Hussain, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

In this project we investigated the biological function of the genes Mrub_1199, Mrub_1200, Mrub_1201, Mrub_2015, Mrub_2271 and Mrub_2272 (KEGG map number 02010). We predict these genes encode components of an Iron (Fe3+) ATP Binding Cassette (ABC) transporter: 1) Mrub_1199 (DNA coordinates [1211595-1212572] on the reverse strand) encodes the permease component (aka transmembrane domain); and 2) Mrub_1200 (DNA coordinates [1212612-1214093] on the reverse strand) encodes the ATP-binding domain (aka nucleotide binding domain); and 3) Mrub_1201 (DNA coordinates [1214347-1215309] on the reverse strand) encodes the substrate binding protein (aka the periplasmic component); and Mrub_2015 ( DNA coordinates [2053963-2054949] on the reverse strand) …