Microbiology Commons^™

Evaluation Of Archeal Growth On Complex Media And Antibiotic Regimes, Melanie Miller

Honors Program Theses

The first Archaea that were studied by scientists came from extreme environments such as fissures at the bottom of oceans where hydrothermal vents formed. It was perhaps surprising that later sampling of environmental DNA revealed Archaea inhabit normal environments as well, for example they are globally distributed in soils. These mesophilic soil species were only recently grown in laboratory pure cultures. In this study, we will expand on this work by feeding the community of soil microbes with various dilutions of tryptic soy broth and other complex media in combination with an antibiotic regime. This will allow us to compare …

The Search For Life In Extreme Environments: Measuring Diversity And Quantity Of Archaea In Wind Cave National Park, Nicole Geerdes

Honors Program Theses

Archaea have the potential to play an essential role in their environment at the base of the food chain. In particular, most of the known species in the phylum Thaumarchaea are autotrophs that can fix their own carbon using energy from ammonia oxidation, that is, they produce their own organic molecules from carbon dioxide by burning nitrogen-based fertilizer. Since their discovery, it has been difficult to learn more about these microbes because they do not grow well in pure laboratory culture. Therefore, much of what is known about them comes from analyzing environmental DNA samples. This allowed researchers to discover …

High Prevalence Of Pre-Existing Serological Cross-Reactivity Against Severe Acute Respiratory Syndrome Coronavirus-2 (Sars- Cov-2) In Sub-Saharan Africa, For Yue Tso, Salum Lidenge, Phoebe B. Peña, Ashley A. Clegg, John R. Ngowi, Julius Mwaiselage, Owen Ngalamika, Peter Julius, John T. West, Charles Wood

Nebraska Center for Virology: Faculty Publications

Objective: Significant morbidity and mortality have occurred in the USA, Europe, and Asia due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), whereas the numbers of infections and deaths in sub-Saharan Africa (SSA) have remained comparatively low. It has been hypothesized that exposure of the population in SSA to other coronaviruses prior to the COVID-19 pandemic resulted in some degree of cross-protection against SARS-CoV-2 infection and pathogenesis. We evaluated this hypothesis by comparing SARS-CoV-2 cross-reactive antibodies in pre-pandemic plasma samples collected from SSA and the USA.

Method: Pre-COVID-19 pandemic plasma samples from SSA and the USA were collected and tested by …

Chlorovirus Pbcv-1 Multidomain Protein A111/114r Has Three Glycosyltransferase Functions Involved In The Synthesis Of Atypical N-Glycans, Eric Noel, Anna Notaro, Immacolata Speciale, Garry A. Duncan, Cristina De Castro, James L. Van Etten

Nebraska Center for Virology: Faculty Publications

The structures of the four N-linked glycans from the prototype chlorovirus PBCV-1 major capsid protein do not resemble any other glycans in the three domains of life. All known chloroviruses and antigenic variants (or mutants) share a unique conserved central glycan core consisting of five sugars, except for antigenic mutant virus P1L6, which has four of the five sugars. A combination of ge- netic and structural analyses indicates that the protein coded by PBCV-1 gene a111/114r, conserved in all chloroviruses, is a glycosyltransferase with three putative domains of approximately 300 amino acids each. Here, in addition to in silico sequence …

Strategies Targeting Hemagglutinin As A Universal Influenza Vaccine, Brianna L. Bullard, Eric A. Weaver

Nebraska Center for Virology: Faculty Publications

Influenza virus has significant viral diversity, both through antigenic drift and shift, which makes development of a vaccine challenging. Current influenza vaccines are updated yearly to in- clude strains predicted to circulate in the upcoming influenza season, however this can lead to a mismatch which reduces vaccine efficacy. Several strategies targeting the most abundant and im- munogenic surface protein of influenza, the hemagglutinin (HA) protein, have been explored. These strategies include stalk-directed, consensus-based, and computationally derived HA immunogens. In this review, we explore vaccine strategies which utilize novel antigen design of the HA protein to improve cross-reactive immunity for development …

Zika Virus Infection Induces Endoplasmic Reticulum Stress And Apoptosis In Placental Trophoblasts, Philma Glora Muthuraj, Prakask K. Sahoo, Madison Kraus, Taylor Bruett, Arun S. Annamalai, Aryamav Pattnaik, Asit K. Pattnaik, Siddappa N. Byrareddy, Sathish Kumar Natarajan

Nebraska Center for Virology: Faculty Publications

Zika virus (ZIKV) infection to a pregnant woman can be vertically transmitted to the fetus via the placenta leading to Congenital Zika syndrome. This is characterized by microcephaly, retinal defects, and intrauterine growth retardation. ZIKV induces placental trophoblast apoptosis leading to severe abnormalities in the growth and development of the fetus. However, the molecular mechanism behind ZIKV-induced apoptosis in placental trophoblasts remains unclear. We hypothesize that ZIKV infection induces endoplasmic reticulum (ER) stress in the trophoblasts, and sustained ER stress results in apoptosis. HTR-8 (HTR-8/SVneo), a human normal immortalized trophoblast cell and human choriocarcinoma-derived cell lines (JEG-3 and JAR) were …

Modeling Stromatolite Formation With Diffusion-Limited Aggregation, Laura E. Stevens

Graduate Student Theses, Dissertations, & Professional Papers

Stromatolites, microbialites, and other microbially induced sedimentary structures exist in the rock record as far back as 3.6 billion years ago and continue to form in the present day. Better characterizing these structures and better understanding how they form is crucial in distinguishing these biosignatures from similar, abiotic structures, which can help us to understand the conditions of early Earth and early Mars. To that end, I have modified DLA 3D EXT, an open-source stromatolite modeling program, to more closely reflect the process of microbial trapping-and-binding by filamentous microbes in a calcite-precipitating hot spring system. This modified program includes a …

การยับยั้งการติดไวรัสหัวเหลืองในกุ้งด้วยอนุภาคเสมือน Penaeus Stylirostris เดนโซไวรัสกับอาร์เอ็นเอสายคู่ของไวรัส, จารุวรรณ วรวิทยธาดา

Chulalongkorn University Theses and Dissertations (Chula ETD)

ไวรัสหัวเหลืองเป็นไวรัสก่อโรคที่ทำให้กุ้งหลายชนิดตายเป็นจำนวนมากในระยะเวลาสั้น ส่งผลให้อุตสาหกรรมการเพาะเลี้ยงและส่งออกกุ้งของไทยเกิดความเสียหายเป็นอย่างมาก ในปัจจุบันมีการใช้เทคโนโลยีทางอณูชีววิทยา นำอาร์เอ็นเอสายคู่ (dsRNA) มากระตุ้นให้เกิดกระบวนการ RNA interference (RNAi) เพื่อควบคุมและยับยั้งการติดไวรัสในกุ้ง โดยยีนเป้าหมายที่มีประสิทธิภาพในการยับยั้งไวรัสหัวเหลือง คือ ยีน protease (pro) อย่างไรก็ตามการขนส่งอาร์เอ็นเอสายคู่ก็ยังคงมีข้อจำกัด เปลือกหุ้มไวรัสบางชนิดสามารถรวมตัวเกิดเป็นอนุภาค-เสมือนไวรัส (Virus-like particle) สามารถใช้เป็นตัวขนส่งที่มีประสิทธิภาพและเข้าจับกับเซลล์เจ้าบ้านอย่างจำเพาะเจาะจงได้ โดยก่อนหน้านี้ได้มีการแสดงออกร่วมกันของยีนโปรตีนเปลือกหุ้มไวรัสของ Penaeus stylirostris เดนโซไวรัส (PstDNV) และอาร์เอ็นเอสายคู่ที่จำเพาะต่อยีนของไวรัสภายในเซลล์แบคทีเรียเดียวกัน พบว่าสามารถยับยั้งการเพิ่มจำนวนของไวรัสหัวเหลืองในกุ้งได้ แต่ทว่ากระบวนการแสดงออกร่วมกันนี้ ไม่สามารถควบคุมระดับการแสดงออกของยีนทั้งสองได้ ดังนั้นวัตถุประสงค์ของงานวิจัยนี้ คือ สร้างอนุภาคเสมือนไวรัส PstDNV กับอาร์เอ็นเอสายคู่ที่จำเพาะต่อยีน pro ของไวรัสหัวเหลือง (PstDNV VLPs-dspro) ให้อยู่ภายใต้โปรโมเตอร์เดียวกัน เพื่อนำไปประยุกต์ใช้และเพิ่มประสิทธิภาพในการป้องกันการติดเชื้อไวรัสหัวเหลืองในกุ้ง โดยการโคลนอาร์เอ็นเอสายคู่ที่จำเพาะต่อยีน pro ของไวรัสหัวเหลืองเข้าสู่เวกเตอร์สำหรับการแสดงออกที่มียีนโปรตีนเปลือกหุ้มไวรัส PstDNV เพื่อควบคุมการแสดงออกของยีนทั้งสองภายใต้โปรโมเตอร์ต่อ T7 RNA polymerase จากนั้นแสดงออกใน E. coli Rosetta-gami โดยผ่านการชักนำด้วย IPTG ที่ความเข้มข้นสุดท้าย 0.4 มิลลิโมลาร์ ที่อุณหภูมิ 30 องศาเซลเซียส เป็นเวลา 3 ชั่วโมง จากผลการวิเคราะห์พบทั้งรีคอมบิแนนท์โปรตีนขนาดประมาณ 37 กิโลดาลตัน ที่เข้าจับกับแอนติบอดีที่จำเพาะต่อ Histidine ได้ และพบอาร์เอ็นเอสายคู่ที่จำเพาะต่อยีน pro ของไวรัสหัวเหลือง ขนาดประมาณ 400 คู่เบส จากนั้นรีคอมบิแนนท์โปรตีนถูกทำให้บริสุทธิ์ด้วย Affinity chromatography และตรวจสอบภายใต้กล้องจุลทรรศน์อิเล็กตรอนแบบส่องผ่าน (TEM) พบอนุภาค-เสมือนไวรัส PstDNV ที่มีการกระจายตัวเป็นอนุภาคเสมือนไวรัสเดี่ยว คล้ายกับอนุภาคเสมือนไวรัส PstDNV ที่พบในธรรมชาติ ซึ่งต่างจากอนุภาคเสมือนไวรัส PstDNV ที่ได้จากการแสดงออกร่วมกันของยีนโปรตีนเปลือกหุ้มไวรัส PstDNV กับอาร์เอ็นเอสายคู่ที่จำเพาะต่อยีนของไวรัสหัวเหลืองภายในเซลล์แบคทีเรียเดียวกัน (PstDNV VLPs-dspro co-expression) เกิดการจับกันของอนุภาคเสมือนไวรัส เมื่อตรวจสอบอาร์เอ็น-เอสายคู่จากอนุภาคเสมือนไวรัส PstDNV พบว่าอาร์เอ็นเอสายคู่นั้นถูกห่อหุ้มอยู่ทั้งภายในและอยู่ล้อมรอบอนุภาคเสมือนไวรัส PstDNV โดยพบว่ามีปริมาณอาร์เอ็นสายคู่ต่อไมโครกรัมของรีคอมบิแนนท์โปรตีนของ …

Expression Of Programmed Cell Death 1 (Pd-1) In Human Monocytic Cell Line Thp-1 And Its Regulatory Mechanism, Kittitach Sri-Ngern-Ngam

Chulalongkorn University Theses and Dissertations (Chula ETD)

Cancer is the leading cause of death worldwide. Immune system defends the host against foreign antigens, not only pathogens or their products, but also cancer cells via coordinated complex responses. The immune response against cancer; however, often poorly control the cancer growth because tumors can effectively escape the immune defense mechanisms by various immune evasion strategies. Programmed cell death 1 (PD-1) is a co-inhibitory immune checkpoint receptor expressed on various immune cells, especially in activated T cells. Engagement of PD-1 with its ligand, PD-L1 or PD-L2, leads to the negative regulation of T cell functions, resulting in impaired antitumor immunity. …

Advancing Cyanobacteria Biomass Estimation From Hyperspectral Observations: Demonstrations With Hico And Prisma Imagery, Ryan E. O'Shea, Nima Pahlevan, Brandon Smith, Mariano Bresciani, Todd Egerton, Claudia Giardino, Lin Li, Tim Moore, Antonio Ruiz-Verdu, Steve Ruberg, Stefan G.H. Simis, Richard Stumpf, Diana Vaičiūtė

Biological Sciences Faculty Publications

Retrieval of the phycocyanin concentration (PC), a characteristic pigment of, and proxy for, cyanobacteria biomass, from hyperspectral satellite remote sensing measurements is challenging due to uncertainties in the remote sensing reflectance (∆R_rs) resulting from atmospheric correction and instrument radiometric noise. Although several individual algorithms have been proven to capture local variations in cyanobacteria biomass in specific regions, their performance has not been assessed on hyperspectral images from satellite sensors. Our work leverages a machine-learning model, Mixture Density Networks (MDNs), trained on a large (N = 939) dataset of collocated in situ chlorophyll-a concentrations (Chla), …

Biology And Molecular Biology Of Ixodes Scapularis, Daniel E. Sonenshine, Ladislav Šimo, Justin D. Radolf (Ed.), D. Scott Samuels (Ed.)

Biological Sciences Faculty Publications

This chapter describes the biology of the tick Ixodes scapularis in relation to its role as the vector of the Lyme disease agent, Borrelia burgdorferi. Following a review of the internal anatomy of the tick, we review basic molecular processes that contribute to an understanding of the dynamics of the tick's specialized parasitic processes, including attachment behavior, salivation; silencing of host anti-inflammatory responses to enable blood ingestion at the dermal feeding site; hemoglobin digestion and reproduction. The chapter is divided into three parts: 1) systematic and anatomical characteristics of ticks; 2) host finding, attachment, salivary disruption of host defenses, blood …

Why Do Antibiotics Exist?, Fabrizio Spagnolo, Monica Trujillo, John J. Dennehy

Publications and Research

In the struggle with antibiotic resistance, we are losing. There is now a serious threat of moving into a postantibiotic world. High levels of resistance, in terms of both frequency and strength, have evolved against all clinically approved antibiotics worldwide. The usable life span of new clinically approved antibiotics is typically less than a decade before resistance reaches frequencies so high as to require only guarded usage. However, microbes have produced antibiotics for millennia without resistance becoming an existential issue. If resistance is the inevitable consequence of antibiotic usage, as has been the human experience, why has it not become …

Rotavirus A Genome Segments Show Distinct Segregation And Codon Usage Patterns, Irene Hoxie, John J. Dennehy

Publications and Research

Reassortment of the Rotavirus A (RVA) 11-segment dsRNA genome may generate new genome constellations that allow RVA to expand its host range or evade immune responses. Reassortment may also produce phylogenetic incongruities and weakly linked evolutionary histories across the 11 segments, obscuring reassortment-specific epistasis and changes in substitution rates. To determine the co-segregation patterns of RVA segments, we generated time-scaled phylogenetic trees for each of the 11 segments of 789 complete RVA genomes isolated from mammalian hosts and compared the segments’ geodesic distances. We found that segments 4 (VP4) and 9 (VP7) occupied significantly different tree spaces from each other …

Narratives On The Academic Resilience Of Former Homeless Students, Alia Aboulhosn

Walden Dissertations and Doctoral Studies

The number of homeless students in U.S public schools continues to rise. Although many homeless students drop out due to challenges they face, lacking is research on how some homeless students overcome challenges and graduate high school, referred to as academically resilient. The purpose of this qualitative narrative study was to gain a deeper understanding of the experiences that promoted former students who were homeless during their senior year of high school to graduate despite adversity, using Resiliency Theory as the theoretical framework. Semi-structured interviews with five participants provided insight into the broader sociopolitical and personal contexts in their stories, …

Pseudomonas Aeruginosa Vaccine Development Using Dual-Species Whole Cell And Subunit Vaccines, Catherine Bell Blackwood

Graduate Theses, Dissertations, and Problem Reports (ETD)

Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen which can cause severe, recurrent, and chronic infections. The pathogen is highly adaptable, and pneumonia caused by it is associated with high morbidity and mortality, especially in individuals with the genetic disorder cystic fibrosis. Antibiotic resistance amongst clinical isolates of P. aeruginosa is steadily increasing, and multi-drug resistant strains are prevalent. There is currently no vaccine available for commercial use against P. aeruginosa. For these reasons, we sought to understand the immunity to P. aeruginosa induced by whole cell vaccination and identify antigens for development of future subunit vaccines. In this dissertation, …

A Snapshot Of Ancient Microbial Life: Microorganisms And Organic Compounds In Primary Fluid Inclusions In Bedded Halite, Neoproterozoic Browne Formation Of Central Australia, Sara I. Schreder-Gomes

Graduate Theses, Dissertations, and Problem Reports (ETD)

Modern shallow brine environments contain an abundance of microorganisms. Microorganisms, mineral crystals, and air bubbles can be trapped with those brines in primary fluid inclusions in bedded halite as it grows in shallow saline surface waters. Primary fluid inclusions and their contents can be preserved, unaltered, for millions of years.

The ~830 million-year-old Browne Formation of central Australia contains intervals of bedded halite with unaltered primary fluid inclusions. Intervals of bedded halite were sampled in the Empress 1A core from ~1480 m – 1520 m depths. Here, I used petrography to describe suspect microorganisms and organic compounds that were trapped …

The 20th Anniversary Meeting Of The Rocky Mountain Virology Association, Joel Rovnak, Laura A. St Clair, Carley Mcalister, Chinemerem P. Ogbu, Jessica Smolenske, Randall J. Cohrs, Rushika Perera

Nebraska Center for Virology: Faculty Publications

Due to the COVID-19 pandemic and multiple devastating forest fires, the 2020 meeting of the Rocky Mountain Virology Association was held virtually. The three-day gathering featured talks describing recent advances in virology and prion research. The keynote presentation described the measles virus paradox of immune suppression and life-long immunity. Special invited speakers presented information concerning visualizing antiviral effector cell biology in mucosal tissues, uncovering the T-cell tropism of Epstein-Barr virus type 2, a history and current survey of coronavirus spike proteins, a summary of Zika virus vaccination and immunity, the innate immune response to flavivirus infections, a discussion concerning prion …

Identification Of Blda As A Major Regulator Of Virulence In The Sweetpotato Soil Rot Pathogen Streptomyces Ipomoeae And Characterization Of Distinct Clostridium Sweetpotato Soft Rot Isolates, Kuei-Ting Yang

LSU Doctoral Dissertations

Streptomyces ipomoeae is the causative agent of Streptomyces soil rot on sweetpotato, a disease characterized by extensive necrosis of both adventitious and storage roots. While Streptomyces potato scab pathogens produce a phytotoxin (thaxtomin A), which is induced in the presence of cellobiose and suberin, S. ipomoeae produces a less-modified, phytotoxin (thaxtomin C), whose inducer has not been identified. To investigate transcriptional regulation of thaxtomin C production, we inserted a promoter involved in thaxtomin C synthesis upstream of the gusA reporter in an S. ipomoeae strain. Reporter gene expression was significantly upregulated in the presence of size-fractionated sweetpotato extract (SPE). The …

A Cophylogenetic Analysis Of Fungus Gardening Ants And Their Symbiotic Fungi, Katherine Beigel

Biology Theses

Fungus-growing ants (Tribe Attini) and their fungal cultivars share a 50-million-year coevolutionary history. Large scale phylogenetic analyses depict a strong co-phyletic signal among ants and their farmed fungi yet fungus sharing among unrelated ant lineages is somewhat widespread. An overview of sharing has been hampered by a lack of genetic markers that exhibit intraspecific variation and surveys across geographic regions. For example, previous studies have shown similar sequences of the internal transcribed spacer (ITS) region of fungus in different species of Trachymyrmex, suggesting that these ant species are farming the same fungal clone. To examine whether this was a …

Multistrain Hiv-1 Elimination: A Crispr-Cas9 And Theranostics-Based Approach, Jonathan Herskovitz

Theses & Dissertations

A critical barrier to achieving a functional cure for infection by human immunodeficiency virus type one (HIV-1) rests in the presence of latent proviral DNA integrated in the nuclei of host CD4+ T cells and mononuclear phagocytes. Accordingly, HIV-1-infected patients must adhere to lifelong regimens of antiretroviral therapy (ART) to prevent viral rebound, CD4+ T cell decline, and progression to acquired immunodeficiency syndrome (AIDS). Gene editing using clustered regularly interspersed short palindromic repeat (CRISPR)-Cas9 technology stands as one means to inactivate integrated proviral DNA. We devised a mosaic gRNA CRISPR-Cas9 system- TatDE- that targets viral transcriptional regulator genes tat / …