Organisms Commons^™

Biophysical Interactions Control The Progression Of Harmful Algal Blooms In Chesapeake Bay: A Novel Lagrangian Particle Tracking Model With Mixotrophic Growth And Vertical Migration, Jilian Xiong, Jian Shen, Qubin Qin, Michelle C. Tomlinson, Yinglong J. Zhang, Xun Cai, Fei Yi, Linlin Cui, Margaret R. Mulholland

OES Faculty Publications

Climate change and nutrient pollution contribute to the expanding global footprint of harmful algal blooms. To better predict their spatial distributions and disentangle biophysical controls, a novel Lagrangian particle tracking and biological (LPT-Bio) model was developed with a high-resolution numerical model and remote sensing. The LPT-Bio model integrates the advantages of Lagrangian and Eulerian approaches by explicitly simulating algal bloom dynamics, algal biomass change, and diel vertical migrations along predicted trajectories. The model successfully captured the intensity and extent of the 2020 Margalefidinium polykrikoides bloom in the lower Chesapeake Bay and resolved fine-scale structures of bloom patchiness, demonstrating a reliable …

Doxypep, Angela E. Russo

Family Medicine Clerkship Student Projects

No abstract provided.

Covid-19 Vaccine Effectiveness In Preventing Severe Infections And Mortality Among Patients In Kerala, India., Surag Mk, Sarin S. M, Sarosh Kumar K K, Udaya A

Digital Journal of Clinical Medicine

ABSTRACT

Background:

India has a top status among world countries, related to the COVID-19 mortality that had crossed the 3-lakh level. The second wave of COVID19 had ravaged the world countries, created havoc of the highest order, leaving many hapless, thanks to the low availability of oxygen, ICU facilities, vaccines and counselling prospects.

There is a lack of information about how COVID-19 vaccines have affected mortality in specific geographic areas.

Method:

A Retrospective record-based design. Patients were matched for age, sex, ethnicity, co-morbidities and grouped into fully immunized, partially immunized and non-immunized.

The primary outcome was in-hospital deaths and secondary …

Difference In The Inhibitory Effects Of Violacein On Various Yeast Isolate Strains From The Hudson Valley Region, Lilah Dorothy Blaker

Senior Projects Spring 2023

Violacein is a purple pigmented compound produced by numerous bacterial species including Janthinobacterium lividum. Studies into violacein have found it to have a multitude of medicinal properties, from antifungal, antibiotic, to antitumor activity. Research has shown that violacein significantly inhibits both tumor and fungal growth and it has been shown to have higher cyotoxicity in pathogenic or cancerous cells than in healthy ones, giving it great potential as for use as a pharmaceutical drug in humans, alongside the fact that as a bacterial compound it’s easier and faster to produce than some other drugs. Violacein has also been shown to …

Amphisbaenian Head Movement And Burrowing Forces In Damp Granular Media, Jacob Newell

Williams Honors College, Honors Research Projects

Damp granular media is a difficult environment to study because it is both practically complex and it lacks equations which fully describe its behavior. In this study, an oscillatory lateral head movement and its effects while penetrating damp granular media were tested using a robophysical model. This experimental research was inspired by the burrowing behavior of the clade Amphisbaenia, a group of usually limbless squamates that employ a variety of different burrowing behaviors, but it can apply to a wide range of burrowers. This research could help with both human burrowing technologies and the further investigation of animal behaviors.

Knockout Of Endospanin 1 Via Crispr In Zebrafish, Danio Rerio, Jared Kittinger

Williams Honors College, Honors Research Projects

I made endospanin 1 knockout (KO) zebrafish to examine its effects on lipid and bone metabolism. Endospanin 1, or leptin receptor overlapping transcript (leprot), is a cytosolic protein linked to the protein hormone leptin that influences the trafficking of leptin receptors to the plasma membrane of cells. Genes for endospanin and tyrosinase (a pigmentation enzyme) were targeted via a microinjection of guide RNAs and CRISPR Cas9 into zebrafish embryos at 2-4 cell stages. I was able to disrupt the endospanin 1 gene (based upon the disruption of tyrosinase), but very few mutant zebrafish fully developed into adults. Only low KO …

A Global Comparison Of Marine Chlorophyll Variability Observed In Eulerian And Lagrangian Perspectives, Angela M. Kuhn, Matthew Mazloff, Stephanie Dutkiewicz, Oliver Jahn, Sophie Clayton, Tatiana Rynearson, Andrew D. Barton

OES Faculty Publications

The California Current System is a diatom‐dominated region characterized by seasonal coastal upwelling and additional elevated mesoscale activity. Cyclonic mesoscale eddies in the region trap productive coastal waters with their planktonic communities and transport them offshore with limited interaction with surrounding waters, effectively acting as natural mesocosms, where phytoplankton populations undergo ecological succession as eddies age. This study examines diatom community composition within two mesoscale cyclonic eddies that formed in the same region of the California Current System 2 months apart and in the California Current waters surrounding them. The diatom communities were analyzed in the context of shifting environmental …

Modeling The Production Of Microalgal Biomass In Large Water Resource Recovery Facilities And Its Processing Into Various Commodity Bioproducts, James Pierson, Gopi Raju Makkena, Sandeep Kumar, Vinod Kumar, Vivekanand Vivekanand, Hasan Husain, Muhammad Ayser, Venkatesh Balan

Civil & Environmental Engineering Faculty Publications

Algae are capable of sequestering nutrients such as nitrates and phosphates from wastewater in the presence of sunlight and carbon dioxide (CO₂) to build up their body mass and help combat climate change. In the current study, we carried out different case studies to estimate the volume of algal biomass that could be produced annually using the rotating algal biofilm (RAB) method in three large-scale water resource recovery facilities (WRRFs) in Texas: Fort Worth, Dallas, and Houston. We calculated the total amount of lipids, carbohydrates, and proteins that could be fractionated from the algal biomass while using the …

Extracting High-Molecular Weight Dna From Cyanobacteria Using Promega's Wizard® Hmw Dna Extraction Kit With A Modified Protocol, Metis, Megan A. Hept, Lesley H. Greene

Chemistry & Biochemistry Faculty Publications

Extraction of high molecular weight (HMW) DNA for long read sequencing with little to no fragmentation and high purity is difficult to acquire from cyanobacterial species. Here we describe a modified method of extraction using Promega's Wizard® HMW DNA Extraction Kit to acquire high molecular weight DNA from cyanobacterial species. The protocol used in the kit is the “3.D. Isolating HMW DNA from Gram-Positive and Gram-Negative Bacteria” protocol. During a key step in the protocol, the lingering remnants of the mucilage layer of the cyanobacterial species is removed, preventing it from sticking to the DNA pellet produced. This customized modification …

An Epidemiological And Pharmacokinetic-Pharmacodynamic Investigation Into The Impact Of Carbapenem-Resistant Enterobacterales, Justin Clark

Theses and Dissertations--Pharmacy

Background: According to the 2019 CDC Antibiotic Resistance Threats Report, more than 2.8 million antibiotic-resistant infections occur in the United States each year, leading to more than 35,000 deaths. Among the most urgent threats identified by the CDC are carbapenem-resistant Enterobacterales (CRE). Despite efforts to control the spread of these organisms, the number of estimated cases between 2012 and 2017 remained stable. In 2017, an estimated 13,100 hospitalized cases of CRE led to approximately 1,100 deaths and $130 million attributable healthcare costs. This dissertation seeks to address this issue from both a pharmacokinetic/pharmacodynamic and epidemiological perspective.

Methods: We evaluated the …

Alzheimer’S Disease Genetics And Short-Chain Fatty Acid Treatment In Studies Of The Murine Gut Microbiome, Diana Zajac

Theses and Dissertations--Physiology

Elucidating the relationship of the gut microbiome in Alzheimer's Disease (AD) risk and pathogenesis is an area of intense interest. Since 60 to 80% of AD risk is related to genetics and APOE alleles represent the most impactful genetic risk factors for AD, their mechanism(s) of action are under intense scrutiny.

First, I conducted a study on APOE targeted replacement mice to investigate the impact of APOE alleles on the murine gut microbiome. The relative abundance of bacteria from the family Ruminococacceae and related genera increased with APOE2 status. The relative abundance of the class Erysipelotrichia increased with APOE4 status, …

Effects Of Red Light Intensity On Cultivation And Oxygen Production In Arthrospira Platensis, Abigail Roberts

Honors Theses

Maintaining life sustaining resources during long-term space travel has encouraged scientists to turn their attention to the potential benefits of a cyanobacteria named Arthrospira platensis, commonly known as Spirulina algae. This experiment measures the oxygen production and cell population growth of two structurally different Spirulina cultures under two different levels of red light intensities, 8 µmol/m2/s (high); 3 µmol/m2/s (low). The cell population, oxygen produced, and oxygen produced per cell measurements were observed and recorded at three 24 hour intervals. It was found there was not a significant difference between high and low light intensities when considering the cell concentration …

Effects Of Red Light Intensity On Cultivation & Oxygen Production In Arthrospira Plantensis, Abigail Roberts

Honors Theses

Maintaining life sustaining resources during long-term space travel has encouraged scientists to turn their attention to the potential benefits of a cyanobacteria named Arthrospira platensis, commonly known as Spirulina algae. This experiment measures the oxygen production and cell population growth of two structurally different Spirulina cultures under two different levels of red light intensities, 8 µmol/m 2Js (high); 3 µmol/m2/s (low). The cell population, oxygen produced, and oxygen produced per cell measurements were observed and recorded at three 24 hour intervals. It was found there was not a significant difference between high and low light intensities when considering the cell …

The Effects Of Light Intensity And Cell Structure On The Cultivation Of Arthrospira Platensis, Taylor Barnhart

Honors Theses

As scientists explore further into space, more cost-effective resources are needed for long-term space travel. An interesting solution is Arthrospira platensis, a filamentous cyanobacteria high in proteins and nutrients, and known for its helical structure. In unfavorable conditions, coiled spirulina cells become straight. Spirulina converts carbon dioxide gas into pure oxygen and the different cell structures stimulate different responses in oxygen production and cultivation. In these experiments, 2.3 L containers of pure coiled spirulina and mixed (coiled and straight) spirulina were placed into 3 incubators with different light intensities: 51µmol/m2/s, 25µmol/m2/s, 12µmol/m2/s. Each experiment length was 72 hours and the …

Sector Rural Colombiano, Salud Y Plaguicidas, Sandra Patricia Carmona Urueña, Maria Nieves Avila Avila, Claudia Del Rocío Contreras Rodríguez, Sindy Alejandro Cifuentes Guerrero, José Ever Ramírez Calderón

Ciencias de la Salud

La región del Sumapaz de Colombia es conocida como la despensa agrícola de Cundinamarca tiene una importante actividad económica en la producción de frutas y hortalizas, por lo que se debe conocer el estado sociocultural, demográfico, ambiental, laboral y de salud de los productores. Otro aspecto es la composición del suelo y el agua que se enfrenta a la degradación debido al abuso de plaguicidas, la deforestación, los monocultivos, la falta de cultura ambiental y presencia institucional, y los proyectos comunitarios ecoamigables. Los campesinos de la región se caracterizan por bajos niveles de educación, lo que afecta su capacidad para …

Electrochemical Inactivation Of Tobacco Mosaic Virus: A Novel Vaccine Method, Angelica Diaz

Undergraduate Research Symposium Posters

We tested the effectiveness of using electrochemistry to irreversibly damage Tobacco Mosaic Virus (TMV). Hypothesis: By utilizing the acidic properties of DNA and RNA, viral genetic material can be irreversibly and selectively damaged using electrochemical methods. Technique could assist in development of highly targeted and effective vaccines.

Poliovirus Detection In Las Vegas Wastewater, Sage Boss, Hayley Baker, Ching-Lan Chang

Undergraduate Research Symposium Posters

Wastewater surveillance for poliovirus is a useful tool for spatial surveillance and evaluation of immunization efficacy. Polio testing in wastewater has been conducted since the 1980s in Finland and Israel, and the virus was recently discovered in New York. With increasing concern regarding the vaccination of children against the virus, there has been worry that polio cases could once again present themselves in the Las Vegas Valley. By testing for the virus in wastewater, we can monitor any new cases or outbreaks that occur and inform authorities as to the location and viral count. The wastewater samples were collected at …

Exploring The Effects Of Fatty Acids (Pufas) On The Antimicrobial Resistance In Vibrio Cholerae, Naina Patel

Honors Theses

As antibiotic resistance becomes a major challenge for public health professionals, our research objectives aimed to investigate the potential for polyunsaturated fatty acids (PUFAs) to create membrane vulnerability in the gram-negative pathogen Vibrio cholerae to help improve the efficacy of several antibiotics. V. cholerae, normally residing in aquatic environments, is capable of altering its phospholipid composition through the uptake and assimilation of exogenous polyunsaturated fatty acids. The purpose of this study was to measure PUFA-mediated changes in the membrane permeability and antibiotic resistance of Vibrio cholerae. The three physiologically relevant PUFAs used were linoleic acid [18:2], arachidonic acid [20:4], and …

Dpc29 Promotes Mitochondrial Translation Post-Initation In Saccharomyces Cerevisiae, Kyle Andrew Hubble

Graduate School of Biomedical Sciences Theses and Dissertations

Although the cytosolic and bacterial translation systems are well studied, much less is known about translation in mitochondria. In the yeast Saccharomyces cerevisiae, mitochondrial gene expression is predominately regulated by translational activators. These regulators are thought to promote translation by binding the elongated 5’-UTRs on their target mRNAs. Since mammalian mitochondrial mRNAs generally lack 5’-UTRs, they must regulate translation by other mechanisms. As expected, most yeast translational activators lack orthologues in mammals. Recently, a mitochondrial gene-specific translational activator, TACO1, was reported in mice and humans. To better define its role in mitochondrial translation I examined the yeast TACO1 orthologue, DPC29. …

Characterizing The Cutaneous Microbiome Of Eurycea Lucifuga As A Potential Defense Against Chytridiomycosis, Madeline Key

Senior Honors Theses

Chytridiomycosis is an emerging infectious disease that is significantly reducing global amphibian populations. The disease is caused by Batrachochytrium dendrobatidis (Bd), a fungus that lethally modifies amphibian skin. Recent research has suggested that the cutaneous microbiome of individual amphibians may play a role in susceptibility to the pathogen. In this study, twelve cave salamanders (Eurycea lucifuga) were collected. Cutaneous bacteria from each salamander were isolated and identified using Sanger Sequencing. Additionally, a Bd-challenge assay was performed to determine each isolate’s antifungal activity. Results indicated many microbial isolates possessed inhibitory capabilities against Bd, which may …

Knowledge, Attitudes, And Practices (Kap) Towards Covid-19 Pandemic Among Pregnant Women In A Tertiary Hospital In Karachi, Pakistan, Sumaira Naz, Syeda Dur E Shawar, Shamila Saleem, Ayesha Malik, Amir Raza

Department of Obstetrics & Gynaecology

Background: The aim of this study was to evaluate the knowledge, attitude, and practices (KAP) of the pregnant population during the COVID-19 pandemic in a tertiary care hospital.
Methods: This cross-sectional study was conducted at Aga Khan University Hospital, Karachi, Pakistan. KAP towards COVID-19 was assessed using 21-item questionnaires. A score for each category was calculated and points were summed. The outcome variables of KAP were compared with demographic characteristics. Data were analyzed by using SPSS 19.
Results: A total of 377 patients participated in the study. The majority of the patients were multiparous (36.8%) in the age group of …

Oxidative Stress Strongly Restricts The Effect Of Codon Choice On The Efficiency Of Protein Synthesis In Escherichia Coli, Lorenzo Eugenio Leiva, Sara Elgamal, Sebastian A. Leidel, Omar Orellana, Michael Ibba, Assaf Katz

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Introduction

The response of enterobacteria to oxidative stress is usually considered to be regulated by transcription factors such as OxyR and SoxR. Nevertheless, several reports have shown that under oxidative stress the levels, modification and aminoacylation of tRNAs may be altered suggesting a role of codon bias in regulation of gene expression under this condition.

Methods

In order to characterize the effects of oxidative stress on translation elongation we constructed a library of 61 plasmids, each coding for the green fluorescent protein (GFP) translationally fused to a different set of four identical codons.

Results

Using these reporters, we observed that …

Impact Of Alcohol On Bone Health In People Living With Hiv: Integrating Clinical Data From Serum Bone Markers With Morphometric Analysis In A Non-Human Primate Model, Alexandra Denys, Allison Norman, Daniel S. Perrien, Larry J. Suva, Liz Simon, Lee S. Mcdaniel, Tekeda Ferguson, Kim Pedersen, David Welsh, Patricia E. Molina, Martin J.J. Ronis

School of Medicine Faculty Publications

People living with HIV (PLWH) represent a vulnerable population to adverse musculoskeletal outcomes due to HIV infection, antiretroviral therapy (ART), and at-risk alcohol use. Developing measures to prevent skeletal degeneration in this group requires a grasp of the relationship between alcohol use and low bone mass in both the PLWH population and its constituents as defined by sex, age, and race. We examined the association of alcohol use with serum biochemical markers of bone health in a diverse cohort of PLWH enrolled in the New Orleans Alcohol Use in HIV (NOAH) study. To explore the effects of alcohol on bone …

Metagenomics Next Generation Sequencing (Mngs): An Exciting Tool For Early And Accurate Diagnostic Of Fungal Pathogens In Plants, Fatma Seyma Gökdemir, Özlem Darcansoy Iseri, Abhishek Sharma, Premila Achar, Füsun Eyidogan

Faculty and Research Publications

Crop output is directly impacted by infections, with fungi as the major plant pathogens, making accurate diagnosis of these threats crucial. Developing technology and multidisciplinary approaches are turning to genomic analyses in addition to traditional culture methods in diagnostics of fungal plant pathogens. The metagenomic next-generation sequencing (mNGS) method is preferred for genotyping identification of organisms, identification at the species level, illumination of metabolic pathways, and determination of microbiota. Moreover, the data obtained so far show that this new approach is promising as an emerging new trend in fungal disease detection. Another approach covered by mNGS technologies, known as metabarcoding, …

Comparison Of The Humoral Immune Response Following Both Bacterial Challenge And Rnai Of Major Factors On Proliferation Of Bartonella Quintana In The Human Louse, Jake Zina

Masters Theses

Human body lice, Pediculus humanus humanus, and head lice, Pediculus humanus capitis, have been hematophagous ectoparasites of humans for thousands of years. Despite being ecotypes, only body lice are known to transmit bacterial diseases to humans, and it appears that lower humoral and cellular immune responses allow body lice to possess a higher vector competence. We previously observed that the transcription level of the defensin 1 gene was up-regulated only in head lice following oral challenge of Bartonella quintana, a causative agent of trench fever, and also that body lice excreted more viable B. quintana in their …

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 …

Osteomyelitis Of The Clivus Secondary To Mucormycosis: A Rare Case Study, Davin Evanson, Ramiz Ahmad, Michael Romeo Do

Tower Health Research Day

No abstract provided.

Genomic Data Mining Reveals Abundant Uncharacterized Transporters In Coccidioides Immitis And Coccidioides Posadasii, Hong Cai, Hao Zhang, Daniel H. Guo, Yufeng Wang, Jianying Gu

Publications and Research

Coccidioides immitis and Coccidioides posadasii are causative agents of coccidioidomycosis, commonly known as Valley Fever. The increasing Valley Fever cases in the past decades, the expansion of endemic regions, and the rising azole drug-resistant strains have underscored an urgent need for a better understanding of Coccidioides biology and new antifungal strategies. Transporters play essential roles in pathogen survival, growth, infection, and adaptation, and are considered as potential drug targets. However, the composition and roles of transport machinery in Coccidioides remain largely unknown. In this study, genomic data mining revealed an abundant, uncharacterized repertoire of transporters in Coccidioides genomes. The catalog …

What? Is Epstein–Barr Virus Infection Linked To Multiple Sclerosis?, Asha Mahajan, Steven B Lippmann

The University of Louisville Journal of Respiratory Infections

No abstract provided.

Emergence Of A Multidrug-Resistant And Virulent Streptococcus Pneumoniae Lineage Mediates Serotype Replacement After Pcv13: An International Whole-Genome Sequencing Study, Stephanie W. Lo, Kate Mellor, Robert Cohen, Alba Redin Alonso, Sophie Belman, Narender Kumar, Paulina A. Hawkins, Rebecca A. Gladstone, Sadia Shakoor, Muhammad Imran Nisar

Department of Pathology and Laboratory Medicine

Background: Serotype 24F is one of the emerging pneumococcal serotypes after the introduction of pneumococcal conjugate vaccine (PCV). We aimed to identify lineages driving the increase of serotype 24F in France and place these findings into a global context.
Methods: Whole-genome sequencing was performed on a collection of serotype 24F pneumococci from asymptomatic colonisation (n=229) and invasive disease (n=190) isolates among individuals younger than 18 years in France, from 2003 to 2018. To provide a global context, we included an additional collection of 24F isolates in the Global Pneumococcal Sequencing (GPS) project database for analysis. A Global Pneumococcal Sequence Cluster …