Biochemistry, Biophysics, and Structural Biology Commons^™

High-Resolution Cryo-Electron Microscopy Structure Of Photosystem Ii From The Mesophilic Cyanobacterium, Synechocystis Sp. Pcc 6803, Christopher J. Gisriel, Jimin Wang, Jinchan Liu, David A. Flesher, Krystle M. Reiss, Hao-Li Huang, Ke R. Yang, William H. Armstrong, M. R. Gunner, Victor S. Batista, Richard J. Debus, Gary W. Brudvig

Publications and Research

Photosystem II (PSII) enables global-scale, light-driven water oxidation. Genetic manipulation of PSII from the mesophilic cyanobacterium Synechocystis sp. PCC 6803 has provided insights into the mechanism of water oxidation; however, the lack of a highresolution structure of oxygen-evolving PSII from this organism has limited the interpretation of biophysical data to models based on structures of thermophilic cyanobacterial PSII. Here, we report the cryo-electron microscopy structure of PSII from Synechocystis sp. PCC 6803 at 1.93-Å resolution. A number of differences are observed relative to thermophilic PSII structures, including the following: the extrinsic subunit PsbQ is maintained, the C terminus of the …

A Temporal Analysis Of The Microbiota And Biofouling Development On Artificial Substrates In The Port Everglades Inlet, Florida, Denise Swack

All HCAS Student Capstones, Theses, and Dissertations

A pilot project was deployed in Port Everglades Inlet, Florida that aimed to evaluate the biofilm composing the microbiome on ecologically engineered artificial substrates used to build Coastal Marine Infrastructure. In April of 2017, an Articulated Concrete Block Mattress comprised of an ecological engineered concrete substrate and a standard smooth surface control substrates were compared. This study will provide a profile on the microbiome community on artificial substrates within Port Everglades Inlet on bio-enhancing concrete-based solutions in our Coastal Marine Infrastructure. To study the microbial community, the 16s rRNA technology was used in Illumina’s high-throughput DNA sequencing. Samples were collected …

Microbial Community Dynamics Of A Microcystis Bloom, Helena Pound

Doctoral Dissertations

Harmful algal bloom events are notoriously associated with massive economic and environmental consequences, causing wildlife and human health risks. As these blooms increase in occurrence, duration, and severity around the world, it is essential to understand conditions leading to bloom formation and why they persist. Abiotic factors such as nutrients are commonly considered in bloom dynamics, but biotic interactions with co-occurring microbial species and viruses must also be taken into account. Harmful algal blooms dominated by the cyanobacterial genus Microcystis occur in bodies of water around the world and provide an ideal system in which to study top-down controls on …

College Of Natural Sciences Newsletter, December 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 2, Issue 12

Page 1 Dean's Message
Page 2 Awards & Recognition
Page 2 Media Coverage of CNS
Page 3 Media Coverage Cont.
Page 4 Science as Art Competition
Page 5 Open PRAIRIE Data
Page 5 Grants Awarded in CNS

Deciphering The Role Of Hsp110 Chaperones In Diseases Of Protein Misfolding, Unekwu M. Yakubu

Dissertations & Theses (Open Access)

Molecular chaperones maintain protein homeostasis (proteostasis) by ensuring the proper folding of polypeptides. Loss of proteostasis has been linked to the onset of numerous neurodegenerative disorders including Alzheimer’s, Parkinson’s, and Huntington’s disease. Hsp110 is a member of the Hsp70 class of molecular chaperones and acts as a nucleotide exchange factor (NEF) for Hsp70, the preeminent Hsp70-family protein folding chaperone. Hsp110 promotes rapid cycling of ADP for ATP, allowing Hsp70 to properly fold nascent or unfolded polypeptides in iterative cycles. In addition to its NEF activity, Hsp110 possesses an Hsp70-like substrate binding domain (SBD) whose biological roles are undefined. Previous work …

Enzymatic Degradation Of Microcystin-Lr By Microcystinase (Mlra), Faisal Alqhtani

Graduate Theses and Dissertations

Microcystin-LR (MC-LR) is affecting the water supply worldwide. Hence, a way to eliminate this toxin is an essential target. In this study, successful cloning of the mlrA gene and producing MlrA enzyme that can degrade the cyclic MC-LR to linearized MC-LR was done. MlrA protein was expressed in Escherichia coli BL-21 (E. coli). Also, enhancing the MlrA yield by adding nickel to LB media was a success in producing more MlrA enzyme from the same volume. Even though the enzyme showed no activity after adding Ni, the enzyme was expressed at a higher yield. Furthermore, it was to investigate adding …

Genetically Engineered Thermosynechococcus Elongatus Bp1: Assessment Of Potential Biorisks And Biofuel Production, Thu Ho Anh Nguyen-Jones

Chemistry & Biochemistry Theses & Dissertations

According to the International Energy Outlook 2019, released by the U.S. Energy Information Administration, it is projected that the energy consumption will increase up to 50% between 2018 and 2050 worldwide. As fossil fuel being a finite source of energy with the risk of depletion, many countries are now facing an energy security crisis. Therefore, it is important to develop other renewable and sustainable energy sources that will allow countries to shift away from depending on fossil fuels. Among several types of renewable energy, biofuel production using genetically engineered cyanobacteria is capturing much interest due to its many advantages. Different …

Mechanisms Of Stress Survival In Gram Positive Bacterial Pathogens, Asia Poudel

Chemistry & Biochemistry Theses & Dissertations

Anaerobic Gram-positive bacteria are not a well-characterized group but include many human pathogens that are resilient against stresses caused by the human immune system or by antibiotic treatment. This dissertation investigated the survival mechanisms of two clinically relevant Gram-positive organisms, Clostridioides difficile and Cutibacterium acnes under extracellular stresses. The response of the opportunistic skin pathogen Cutibacterium acnes to nanosecond electric pulses is characterized and found that growth in a biofilm, which usually protects bacteria from stress, renders this species more killable by this treatment. In addition, the stringent response (SR), a conserved bacterial stress survival mechanism, is studied in the …

Unraveling The Role Of Novel G5 Peptidase Family Proteins In Virulence And Cell Envelope Biogenesis Of Staphylococcus Aureus, Stephanie M. Marroquin

USF Tampa Graduate Theses and Dissertations

Virulence factors and the bacterial cell envelope are two important components in S. aureus pathogenesis and survival. More importantly, understanding the regulation of these cellular processes is crucial to further understanding and combating this successful pathogen. To date, numerous factors have been identified as playing a role in the regulation of Agr activity in S. aureus, including transcription factors, antisense RNAs, and host elements. Herein we investigate the product of SAUSA300_1984 (termed MroQ), a transmembrane G5 peptidase family protein, as a novel effector of this system. Using a USA300 mroQ mutant we observed a drastic reduction in proteolysis, hemolysis, and …

College Of Natural Sciences Scholarship Brunch Program, November 6th 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

This is the program for the first annual College of Natural Sciences Scholarship Brunch, held on November 6th, 2021 at McCrory Gardens.

College Of Natural Sciences Newsletter, November 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 2, Issue 11

Page 1 Dean's Message
Page 2 Awards & Recognition
Page 3 Media Coverage of CNS
Page 4 2021 Day of Scholars
Page 5 Astronomy Outreach
Page 6 SDSU Faculty & Students Host American Society for Microbiology Annual Conference
Page 7 Scholarship Brunch
Page 8 Open PRAIRIE Data, SI Final Exam Review Sessions
Page 9 Aamlid Family Anatomy Lab Photos

Investigation Of An Alternative Protocol For The Production Of Sars-Cov-2 Antigenic Proteins, Nichole Ninaltowski

USF Tampa Graduate Theses and Dissertations

With the COVID-19 pandemic showing no signs of slowing down, large-scale antigenic protein production is still needed for surveillance using serologic assays. From screening to vaccines to biotherapeutics, being able to produce the proteins for these assays is essential; however, the current gold standard method for producing SARS-CoV-2 spike proteins is prohibitively expensive for most research groups.

Alternative methods of transfecting mammalian cells to produce recombinant proteins that are relatively inexpensive have been used for years. Unlike the expensive, commercially available lipid-based methods, other established methods such as polyethyleneimine (PEI), are considerably easier, and cheaper to meet the needs of …

A Nosy Neighbor: Purification And Functional Characterization Of Lpg2149, Ashley M. Holahan

The Journal of Purdue Undergraduate Research

Ubiquitination is a process that marks proteins for various cell-signaling pathways, namely protein degradation and other processes. Th ese pathways are essential in a wide array of cellular processes, including defense mechanisms against invading pathogens. Th e ubiquitination process is universally found in all eukaryotic organisms, including plants and animals, and thus plays a vital role in cellular homeostasis. Recently, more discoveries have been made on prokaryotic effector proteins that hijack the ubiquitination system even when they do not possess a ubiquitin system of their own. MavC, also known as lpg2147 (Gan, Nakayasu, Hollenbeck, & Luo, 2019; Puvar et al., …

Structure-Function Studies Of The Trypanosome Mitochondrial Replication Protein Polib, Raveen Armstrong

Masters Theses

Trypanosoma brucei and related protists are distinguished from all other eukaryotes by an unusual mitochondrial genome known as kinetoplast DNA (kDNA) that is a catenated network composed of minicircles and maxicircles. Replication of this single nucleoid involves a release, replicate, and reattach mechanism for the thousands of catenated minicircles and requires at least three DNA polymerase (POLIB, POLIC and POLID) with similarity to E. coli DNA polymerase I. Like other proofreading replicative DNA polymerases, POLIB has both an annotated polymerase domain and an exonuclease domain. Predictive modelling of POLIB indicates that it has the canonical right hand …

A Bioinformatic And Biochemical Analysis Of Cruciviruses, George William Kasun

Dissertations and Theses

Cruciviruses are novel ssDNA viruses discovered through metagenomics and direct environmental DNA amplification and cloning. The genomes of cruciviruses suggest that gene transfer between RNA and DNA viruses occurred due to the presence of putative protein-encoding genes that are homologous to both ssRNA and ssDNA viruses. In order to gain a better understanding of this group of viruses both bioinformatic analyses and in vitro biochemical experiments were employed. The results of the bioinformatic analyses show that cruciviruses are a highly diverse group of ssDNA viruses. Their placement within established ssDNA phylogenies is difficult due to heterogeneity in their putative replication-associated …

College Of Natural Sciences Newsletter, October 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 2, Issue 10

Page 1 Dean's Message
Page 2 Awards and Recognition; Introducing Natural Sciences Student Ambassadors
Page 3 Media Coverage of CNS
Page 4 Spooky Science Outreach
Page 5 The BIG Event Outreach
Page 6 Geography Club Road Trip
Page 7 Aamlid Family Anatomy Lab
Page 8 Hobo Day Recap
Page 10 Open PRAIRIE Data; Grants Awarded in CNS

A Conserved Structural Role For The Walker-A Lysine In P-Loop Containing Kinases, Fatlum Hajredini, Ranajeet Ghose

Publications and Research

Bacterial tyrosine kinases (BY-kinases) and shikimate kinases (SKs) comprise two structurally divergent P-loop containing enzyme families that share similar catalytic site geometries, most notably with respect to their Walker-A, Walker-B, and DxD motifs. We had previously demonstrated that in BY-kinases, a specific interaction between the Walker-A and Walker-B motifs, driven by the conserved “catalytic” lysine housed on the former, leads to a conformation that is unable to efficiently coordinate Mg²⁺•ATP and is therefore incapable of chemistry. Here, using enhanced sampling molecular dynamics simulations, we demonstrate that structurally similar interactions between the Walker-A and Walker-B motifs, also mediated by …

Oxidation Alters The Architecture Of The Phenylalanyl-Trna Synthetase Editing Domain To Confer Hyperaccuracy, Pooja Srinivas, Rebecca E. Steiner, Ian J. Pavelich, Ricardo Guerrera-Ferreira, Puneet Juneja, Michael Ibba, Christine M. Dunham

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

High fidelity during protein synthesis is accomplished by aminoacyl-tRNA synthetases (aaRSs). These enzymes ligate an amino acid to a cognate tRNA and have proofreading and editing capabilities that ensure high fidelity. Phenylalanyl-tRNA synthetase (PheRS) preferentially ligates a phenylalanine to a tRNA^Phe over the chemically similar tyrosine, which differs from phenylalanine by a single hydroxyl group. In bacteria that undergo exposure to oxidative stress such as Salmonella enterica serovar Typhimurium, tyrosine isomer levels increase due to phenylalanine oxidation. Several residues are oxidized in PheRS and contribute to hyperactive editing, including against mischarged Tyr-tRNA^Phe, despite these oxidized residues not …

A Novel Approach For Characterizing The Ultra-Micro Size-Fraction Community, Abdullah Ahmed Salim, Priscilla Nicole Pineda, Isabella Alamilla, Andrew Dean Putt

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

A Novel Approach for Characterizing the Ultra-Micro Size-Fraction Community

Students: Abdullah Salim, Priscilla Pineda, Isabella Alamilla

Mentors/Supervisors: Andrew Putt, Terry C. Hazen

ABSTRACT

The ultra-micro size-fraction (UMSF) are bacteria that can pass through the 0.2 µm pore membrane filters employed in environmental surveys. Despite being ubiquitous and having high metabolic activity, UMSF remain elusive and largely uncultured. Investigations of UMSF are skewed by difficulties in culturing and a lack of techniques for measuring UMSF biogeochemical signatures. This study measures surface stream UMSF community diversity, and community response to the addition of the synthetic pharmaceutical and cosmetic carbon product cyclodextrin which …

College Of Natural Sciences Newsletter, September 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 2, Issue 9.

Page 1 Dean's Message
Page 2 Awards and Recognition
Page 3 Student Clubs in Natural Science
Page 4 Media Coverage of CNS
Page 5 Hobo Day Festivities
Page 6 Open PRAIRIE Data; Grants Awarded in CNS
Page 7 One Day for State Recap

Don't Sell Them Short, There's More To Bacterial Natural Products Than Antibiotics, Alison Clare Domzalski

Dissertations, Theses, and Capstone Projects

Recent genomic studies of microbiomes have revealed an overwhelming number of biosynthetic genes of unknown function. Most of these “cryptic” biosynthetic genes are not expressed in laboratory monocultures of individual microbes. Thus, there remains tremendous untapped potential for natural products discovery. Here we employ mixed microbial culture (MMC) as a simple yet powerful approach to awaken cryptic biosynthetic gene clusters. Our preliminary studies demonstrated that arrays of metabolites could be induced in MMCs upon environmental cues, such as surface adhesion. Using this system, we have screened, identified, and isolated bioactive bacterial metabolites, which were characterized structurally and biologically. Of the …

Oxydifficidin-Producing Bacillus Presents Novel Antimicrobial Activity Against Neisseria Gonorrhoeae Involving The Deda Protein, Jingbo Kan

Dissertations, Theses, and Capstone Projects

Bacterial human pathogens cause severe infectious diseases which are the second most common cause of death next to cancer and cardiovascular diseases in the world, especially in developing countries. Gonorrhea particularly, is the second most common sexually transmitted infection (STI) which is caused by the microorganism Neisseria gonorrhoeae (GC). Centers for Disease Control and Prevention (CDC) estimates that more than 1.6 million new gonorrhea cases emerged in USA in 2018 (“Detailed STD Facts - Gonorrhea” n.d.). Also, the WHO (World Health Organization) shows that gonorrhea is the most antibiotic resistant STI (“PAHO/WHO | Gonorrhea” n.d.), highlighting the shortage of efficient …

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 …

Assessing Selective Plasmids For Bradyrhizobium Sp. Doa9 And Mesorhizobium Loti, Aiden J. Wilcox, Rebecca Meaney, Bogumil Karas

Undergraduate Student Research Internships Conference

No abstract provided.

Copper-Mediated Regulation Of A Traditional Iron Uptake System In Uropathogenic Escherichia Coli., George Lwanga Katumba

Arts & Sciences Electronic Theses and Dissertations

Transition metals constitute an important part of the host-pathogen interface. Iron is an essential nutrient that functions as a cofactor for numerous bacterial and host proteins, as either a ligand for oxygen in carrier proteins or an enzyme catalytic site due to its natural redox properties. As part of the innate immune response, infected hosts sequester iron from pathogens to limit their growth, a phenomenon known as nutritional immunity. On the other hand, copper ions are deployed at infection sites as a potent antimicrobial agent to kill bacteria. The ability to survive within multiple, often harsh, microenvironments is fundamental to …

The Regulation Of Plasmodium Falciparum Metabolism By Haloacid Dehalogenase Proteins, Philip Frasse

Arts & Sciences Electronic Theses and Dissertations

Malaria is an enormous financial and public health burden for much of the world, infecting over 200 million and killing over 400,000 people every year. While much progress has been made combating malaria in the past few decades, those advances have slowed in recent years, partially due to the emergence of resistance to all known antimalarials used to date. To achieve the goal of eliminating malaria as a major global health problem, new therapeutics need to be developed, targeting novel categories of parasite biology. One poorly understood area of parasite biology is the regulation of various metabolic pathways. We have …

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 …

College Of Natural Sciences Newsletter, August 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 2, Issue 8.

Page 1 Dean's Message
Page 2 Awards and Recognition
Page 3 Student Summer Research
Page 4 Media Coverage of CNS
Page 5 Wintrode Student Success Center
Page 6-7 Welcome to our new Faculty & Staff!
Page 8 One Day for State: Thursday, Sept. 2nd
Page 7 Open PRAIRIE Data; Fall Faculty Retreat 2021

The Role Of Calcium Ions In Signaling And Regulation Of Efflux Pump Genes In Staphylococcus Aureus, Amy Rebecca Nava

Open Access Theses & Dissertations

Calcium ions (Ca2+) play an important role in eukaryote cell signaling and regulation of physiological functions. Although evidence of a similar role for Ca2+ in prokaryotes has been difficult to demonstrate, there is mounting evidence that Ca2+ acts as a cell regulator in bacteria. The purpose of this study was to investigate Ca2+ signaling and the effect of Ca2+ on gene expression of various multidrug resistant (MDR) efflux pumps and their regulator MgrA in Staphylococcus aureus and clinically isolated MRSA. We hypothesized that the presence of Ca2+ increased gene expression of multidrug resistance pumps, LmrS, NorA, and the regulator, MgrA. …

Roles Of Secreted Proteins And Iron Utilization Proteins In Virulence Of The Fish Pathogen Flavobacterium Columnare, Rachel Conrad

Theses and Dissertations

The Gram-negative bacterium Flavobacterium columnare is the causative agent of columnaris disease and is responsible for significant economic losses in aquaculture. Little is known regarding the virulence factors produced by F. columnare, and control measures are limited. Like many members of the phylum Bacteroidetes, F. columnare uses the type IX secretion system (T9SS) to secrete enzymes, adhesins, and proteins involved in gliding motility. When a core component of this system was deleted in the wild type strain, the resulting mutant was avirulent in zebrafish, rainbow trout, and channel catfish infection studies. This suggests that the individual secreted proteins may function …