Microbiology Commons^™

Community Level Physiological Profiling Of The Longleaf Pine Savannah Microbiome, Gavin Treadaway

Symposium of Student Scholars

Soil microorganisms secrete chemicals into their surroundings, which the root system will uptake and in return release root exudates, which usually consist of low-molecular-weight organic compounds. These root exudates behave as signaling molecules and substrates for microorganisms to recruit beneficial soil bacteria to the plant root system, which will provide the plants with immunity to foliar diseases and pathogen infection. Studies have shown that bacteria on the root surface can protect aerial sections of the plant by promoting induced systemic resistance, a mechanism of increasing physical or chemical barriers of the plant.

The longleaf pine is an endangered species of …

Higher Entropy Observed In Sars-Cov-2 Genomes From The First Covid-19 Wave In Pakistan, Najia Karim Ghanchi, Asghar Nasir, Kiran I. Masood, Syed Hani Abidi, Syed Faisal Mahmood, Akber Kanji, Safina Abdul Razzak, Waqasuddin Khan, Saba Shahid, Maliha Yameen, Ali Raza, Javaria Ashraf, Zeeshan Ansar Ahmed, Mohammad Buksh Dharejo, Nazneen Islam, Zahra Hasan, Rumina Hasan

Department of Pathology and Laboratory Medicine

Background: We investigated the genome diversity of SARS-CoV-2 associated with the early COVID-19 period to investigate evolution of the virus in Pakistan.
Materials and methods: We studied ninety SARS-CoV-2 strains isolated between March and October 2020. Whole genome sequences from our laboratory and available genomes were used to investigate phylogeny, genetic variantion and mutation rates of SARS-CoV-2 strains in Pakistan. Site specific entropy analysis compared mutation rates between strains isolated before and after June 2020.
Results: In March, strains belonging to L, S, V and GH clades were observed but by October, only L and GH strains were present. The …

Synthesis And Antimicrobial Activities Of 1-((5-Chloro-1-Ethyl-2-Methyl-1h-Imidazol-4-Yl)Sulfonyl)-N-Ethylpyrrolidine-2-Carboxamide, Oluwaseyi B Ovonramwen, Bodunde J Owolabi, Abiodun Falodun

Tanzania Journal of Science

A new 1-((5-chloro-1-ethyl-2-methyl-1H-imidazol-4-yl)sulfonyl)-N-ethylpyrrolidine-2-carboxamide was synthesized from methyl-1-[(5-chloro-1-ethyl-2-methyl-1H-imidazol-4-yl)sulfonyl]pyrrolidine-2-carboxylate and ethylamine. The compound methyl-1-[(5-chloro-1-ethyl-2-methyl-1H-imidazol-4-yl)sulfonyl]pyrrolidine-2-carboxylate was synthesized from methyl pyrrolidine-2-carboxylate and 5-chloro-4-chlorosulfonyl-1-ethyl-2-methyl-imidazole. The compounds were characterized based on FTIR, 1H, 13C NMR, and DEPT 135 analysis. Antimicrobial activities of the 1-((5-chloro-1-ethyl-2-methyl-1H-imidazol-4-yl)sulfonyl)-N-ethylpyrrolidine-2-carboxamide against Gram-positive (methicillin-susceptible Staphylococcus aureus, methicillin-resistant Staphylococcus aureus, and Bacillus subtilis), Gram-negative (Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae), and Candida albicans were carried out using the standard microbiological method. The newly synthesized 1-((5-chloro-1-ethyl-2-methyl-1H-imidazol-4-yl)sulfonyl)-N-ethylpyrrolidine-2-carboxamide had no activities against the tested organisms. Keywords:    1-((5-chloro-1-ethyl-2-methyl-1H-imidazol-4-yl)sulfonyl)-N-ethylpyrrolidine-2-carboxamide; methyl-1-[(5-chloro-1-ethyl-2-methyl-1H-imidazol-4-yl)sulfonyl]pyrrolidine-2-carboxylate; L-proline; ethylamine.

Investigation Of Staphylococcus Aureus Bacteriophage Population At A South Carolina University: The Disappearance Of S. Aureus Bacteriophage Population Amidst The Covid-19 Pandemic, Korinne M. Swanson, Owen R. Smith, Madaline N. Plank, Paul E. Richardson

Journal of the South Carolina Academy of Science

Bacteriophages are naturally occurring, nonpathogenic viruses, which infect bacterial cells. Recently, bacteriophage research has increased with hopes of using them against antibiotic resistant bacterial infections in the future. This study aimed to determine a possible correlation between perceived stress and the Staphylococcus aureus bacteriophage population at Coastal Carolina University (CCU), Conway, South Carolina, using isolation and characterization techniques to further understand humans as a potential bacteriophage source. From October 2020 to March 2021, nasal and postauricular swab samples were collected from 12 participants on a monthly basis along with a perceived stress survey. Samples were subjected to filtration, amplification, plaque …

Structural Polymorphism Of Chitin And Chitosan In Fungal Cell Walls From Solid-State Nmr And Principal Component Analysis, Liyanage D. Fernando, Malitha C. Dickwella Widanage, Jackson Penfield, Andrew S. Lipton, Nancy Washton, Jean Paul Latgé, Ping Wang, Liqun Zhang, Tuo Wang

School of Graduate Studies Faculty Publications

Chitin is a major carbohydrate component of the fungal cell wall and a promising target for novel antifungal agents. However, it is technically challenging to characterize the structure of this polymer in native cell walls. Here, we recorded and compared 13C chemical shifts of chitin using isotopically enriched cells of six Aspergillus, Rhizopus, and Candida strains, with data interpretation assisted by principal component analysis (PCA) and linear discriminant analysis (LDA) methods. The structure of chitin is found to be intrinsically heterogeneous, with peak multiplicity detected in each sample and distinct fingerprints observed across fungal species. Fungal chitin exhibits partial similarity …

Insights Into Halophilic Microbial Adaptation: Analysis Of Integrons And Associated Genomic Structures And Characterization Of A Nitrilase In Hypersaline Environments, Sarah Sonbol

Theses and Dissertations

Hypersaline environments are extreme habitats that can be exploited as biotechnological resources. Here, we characterized a nitrilase (NitraS-ATII) isolated from Atlantis II Deep brine pool. It showed higher thermal stability and heavy metal tolerance compared to a closely related nitrilase.

We also studied integrons in halophiles and hypersaline environments. Integrons are genetic platforms in which an integron integrase (IntI) mediates the excision and integration of gene cassettes at specific recombination sites. In order to search for integrons in halophiles and hypersaline metagenomes, we used a PCR-based approach, in addition to different bioinformatics tools, mainly IntegronFinder.

We found that integrons and …

Comparative Microbiome Analysis Of The Funfus Gardening Ant Species Trachymyrmex Arizonensis, Chase D. Rowan

Biology Theses

Fungus-growing ants (Attini: Formicidae) and their fungal cultivars participate in ant-fungus mutualism that share a 50-million-year-old coevolutionary history. Fungal cultures are grown in gardens alongside ants and a diverse collection of microbes that interact with both species in mutualistic, commensal, and antagonistic relationships. These microbes aid in digestion and detoxification of food, provide essential nutrients, help in nest hygiene, and play a dominant role in defense against pathogens and disease. Microbial communities of many model species have been shown to change in a laboratory setting as compared to their natural environment. High-throughput 16s sequencing of the V4 variable region was …

Pulmonary Immune Cell Trafficking Promotes Host Defense Against Alcohol-Associated Klebsiella Pneumonia, Derrick R. Samuelson, Min Gu, Judd E. Shellito, Patricia E. Molina, Christopher M. Taylor, Meng Luo, David A. Welsh

School of Graduate Studies Faculty Publications

The intestinal microbiota generates many different metabolites which are critical for the regulation of host signaling pathways. In fact, a wide-range of diseases are associated with increased levels of local or systemic microbe-derived metabolites. In contrast, certain bacterial metabolites, such as tryptophan metabolites, are known to contribute to both local and systemic homeostasis. Chronic alcohol consumption is accompanied by alterations to intestinal microbial communities, and their functional capacities. However, little is known about the role of alcohol-associated dysbiosis on host defense against bacterial pneumonia. Our previous work using fecal transplantation demonstrated that alcohol-associated intestinal dysbiosis, independent of ethanol consumption, increased …

Phylogenetic And Drug-Resistance Analysis Of Hiv-1 Sequences From An Extensive Paediatric Hiv-1 Outbreak In Larkana, Pakistan, Syed Hani Abidi, George Makau Nduva, Dilsha Siddiqui, Wardah Rafaqat, Syed Faisal Mahmood, Amna Rehana Siddiqui, Apsara Ali, Aneeta Hotwani, Rashida Abbas Ferrand, Fatima Mir

Department of Biological & Biomedical Sciences

Introduction: In April 2019, an HIV-1 outbreak among children occurred in Larkana, Pakistan, affecting more than a thousand children. It was assumed that the outbreak originated from a single source, namely a doctor at a private health facility. In this study, we performed subtype distribution, phylogenetic and drug-resistance analysis of HIV-1 sequences from 2019 outbreak in Larkana, Pakistan.
Methods: A total of 401 blood samples were collected between April-June 2019, from children infected with HIV-1 aged 0-15 years recruited into a case-control study to investigate the risk factors for HIV-1 transmission. Partial HIV-1 pol sequences were generated from 344 blood …

Strainiq: An N-Gram-Based Method To Identify And Quantify Microbial Communities In Metagenomic Samples, Sanjit Pandey

Theses & Dissertations

Microbes are ubiquitous in nature, and they play vital roles in various processes associated with metabolism in the human body, photosynthesis in plants, or decomposition of waste in the environment. Hence, it is essential to understand how the composition of microbial communities affects the ecosystem of different environments ranging from ocean floors to hot springs to the human body. Microbial communities present in different human body sites are of particular importance due to their implications in the cause and prevention of human diseases. The traditional approaches limit microbial research to exclusively studying species that can be successfully cultured in the …

The Staphylococcus Aureus Lrgab Operon Encodes A Holin-Like Protein Involved In Pyruvate Transport, Jennifer L. Endres

Theses & Dissertations

The Staphylococcus aureus cidABC and lrgAB operons encode a well-conserved family of proteins involved in programmed cell death (PCD) during biofilm development. Based on the structural similarities that CidA and LrgA share with bacteriophage holins, we have hypothesized that these proteins function by forming pores within the cytoplasmic membrane. To test this, we utilized a “lysis cassette” system that demonstrated the abilities of the cidA and lrgA genes to support bacteriophage endolysin-induced cell lysis. In addition, the CidA and LrgA proteins were shown to localize to the surface of membrane vesicles and cause leakage of small molecules, providing direct evidence …

On The Relationship Of Diabetes And Sleep Apnea: Evolution And Epigenetics, Nancy Wilson

Undergraduate Honors Theses

This thesis gives an overview of the relationship between diabetes, sleep apnea, obesity, and heart disease. It then addresses evidence that the traditional understanding of this relationship is incomplete or misleading. In the process, there is a brief discussion of the evolutionary rationale for the development and retention of sleep apnea in light of blood sugar dysregulation, as an adaptive mechanism in response to environmental stressors, followed by a brief overview of the general concepts of epigenetics. Finally, this paper presents the results of a literature search on the epigenetic marks and changes in gene expression found in sleep apnea …

Role Of A Cryptic Trna Gene Operon In Survival Under Translational Stress, Javier Santamaría-Gómez, Miguel Ángel Rubio, Rocío López-Igual, Ana B. Romero-Losada, Fernando M. Delgado-Chaves, Roque Bru-Martínez, Francisco J. Romero-Campero, Antonio Herrero, Michael Ibba, Jesús A. G. Ochoa De Alda, Ignacio Luque

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

As compared to eukaryotes, bacteria have a reduced tRNA gene set encoding between 30 and 220 tRNAs. Although in most bacterial phyla tRNA genes are dispersed in the genome, many species from distinct phyla also show genes forming arrays. Here, we show that two types of arrays with distinct evolutionary origins exist. This work focuses on long tRNA gene arrays (L-arrays) that encompass up to 43 genes, which disseminate by horizontal gene transfer and contribute supernumerary tRNA genes to the host. Although in the few cases previously studied these arrays were reported to be poorly transcribed, here we show that …

You Are What You Eat — Exploring The Microbiome Through Inquiry-Based Labs. Microbiome Lesson Plans, Karla S. Fuller

Open Educational Resources

If these commonly used spices have the ability to inhibit pathogenic bacterial growth, could they also potentially inhibit the growth of normal, harmless bacteria that live in your body? In this lab, we will test common bacteria for resistance to food additives.

Roles Of A Bradykinin Storm And A Cytokine Storm In Covid-19 Cases, Nouha H. Odeh

Honors College Theses

In the light of recent events, it is imperative to understand the key inflammatory response elements that appear to be the source of more severe ailments resulting from a SARS-CoV-2 viral infection known as Covid-19 The more severe cases of Covid-19 are characterized by a severe inflammatory response resulting in tissue damage. My research proposal aims to investigate the two possible culprits of this response: a bradykinin (BK) storm and an interleukin-6 (IL-6) mediated cytokine storm. In both systems respectively, the excess release of these signals subsequently signals the production of even more of the same response element, resulting in …

Respons Pertumbuhan Pakcoy Terhadap Asam Humat Dan Trichoderma Dalam Media Tanam Pelepah Kelapa Sawit, Ratih Rahhutami, Aline Sisi Handini, Dwi Astutik

Jurnal Kultivasi

Pemanfaatan limbah organik dari perkebunan sebagai media tanam pakcoy (Brassica chinensis L.) diharapkan dapat ditingkatkan dengan penggunaan pupuk organik serta pupuk hayati. Penelitian disusun menggunakan Rancangan Acak Kelompok (RAK) pola faktorial. Faktor pertama adalah dosis asam humat meliputi 1, 3, dan 5 g. Faktor kedua adalah dosis Trichoderma sp., meliputi 50, 100, dan 150 mL. Data yang diperoleh kemudian dianalisis ragam pada taraf nyata 5%. apabila terdapat pengaruh nyata, dilanjutkan dengan uji DMRT. Hasil penelitian menunjukkan bahwa aplikasi asam humat dan Trichoderma sp. memiliki pengaruh mandiri dan tidak terdapat interaksi. Dosis asam humat 3 g per tanaman menghasilkan jumlah daun, …

Antibacterial Properties Of Citric Acid/Β-Alanine Carbon Dots Against Gram-Negative Bacteria, Anju Pandey, Asmita Devkota, Zeinab Yadegari, C. Korsi Dumenyo, Ali Taheri

Agricultural and Environmental Sciences Faculty Research

While multi-drug resistance in bacteria is an emerging concern in public health, using carbon dots (CDs) as a new source of antimicrobial activity is gaining popularity due to their antimicrobial and non-toxic properties. Here we prepared carbon dots from citric acid and β-alanine and demonstrated their ability to inhibit the growth of diverse groups of Gram-negative bacteria, including E. coli, Salmonella, Pseudomonas, Agrobacterium, and Pectobacterium species. Carbon dots were prepared using a one-pot, three-minute synthesis process in a commercial microwave oven (700 W). The antibacterial activity of these CDs was studied using the well-diffusion method, and their minimal inhibitory concentration …

Microbes On The Mountain: Plant-Microbe Associations And Interactions On Mount St. Helens, Emily Rose Wolfe

Dissertations and Theses

Plant-microbe associations and interactions provide critical context to studies in both community and ecosystem ecology, especially in systems that are relatively new and still undergoing early successional processes. Microbes can colonize the surfaces and interiors of all plant tissues, and these assemblages vary in composition both spatially and temporally, even within the same plant. Endophytes are bacteria or fungi that spend most of their lifecycles living within plant tissues asymptomatically--typically, "endophyte" refers specifically to aboveground tissues such as leaves and stems, and therefore may have direct influences on defenses against herbivory, pathogen or pest tolerance, and even afterlife effects on …

Unbiased Automated Quantitation Of Ros Signals In Live Retinal Neurons Of Drosophila Using Fiji/Imagej, Prajakta Deshpande, Neha Gogia, Anuradha Venkatakrishnan Chimata, Amit Singh

Biology Faculty Publications

Numerous imaging modules are utilized to study changes that occur during cellular processes. Besides qualitative (immunohistochemical) or semiquantitative (Western blot) approaches, direct quantitation method(s) for detecting and analyzing signal intensities for disease(s) biomarkers are lacking. Thus, there is a need to develop method(s) to quantitate specific signals and eliminate noise during live tissue imaging. An increase in reactive oxygen species (ROS) such as superoxide (O2•-) radicals results in oxidative damage of biomolecules, which leads to oxidative stress. This can be detected by dihydroethidium staining in live tissue(s), which does not rely on fixation and helps prevent stress on tissues. However, …

A Review Of Novel Coronavirus: Cross-Disciplinal Perspective, Iram Asim, Hafsa Rehman, Rabeea Anwar, Humaira Yasmeen

Journal of Bioresource Management

The whole world is under the influence of coronavirus after its first report from Wuhan, China in December 2019. The virus is from coronaviridae family which has zoonotic viruses that can spread from animals to humans. The coronavirus like other viruses of this family produces mild flu-like symptoms within 2-14 days in the human host which progresses to death in severe cases. Unlikely coronavirus spread fast among humans-infectious diseases. Up till now (27/04/2020) around 2.97M cases and 207K deaths have been reported. The presence of a virus in respiratory secretions is diagnosed through molecular methods and chest scans. For this …