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2023

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Articles 241 - 270 of 1823

Full-Text Articles in Biology

Md Anderson Internship: Targeting Il-27rα In Ovarian Cancer, Meghana Kavarthapu Oct 2023

Md Anderson Internship: Targeting Il-27rα In Ovarian Cancer, Meghana Kavarthapu

Trick to the Treat of Internships and Research

We utilized a novel explainable artificial intelligence (XAI) approach to identify Interleukin-27 Receptor α (IL-27Rα) as a potential therapeutic target for high grade serous ovarian cancer (HGSC) patients based on the Cancer Genome Atlas (TCGA) dataset. High expression of IL-27Rα was found to be significantly correlated with poorer survival in HGSC patients. To investigate its therapeutic potential, we silenced IL-27Rα in murine HGSC cells lines using siRNA and assessed its impact on tumor proliferation, migration, invasion, and angiogenesis. Our results demonstrated that IL-27Rα siRNA effectively reduced its expression, as confirmed by Western Blot analysis, and significantly attenuated proliferation by clonogenic …

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Florida's Summer Institute In Biostatistics And Data Science Program Experience, David Giordano Oct 2023

Florida's Summer Institute In Biostatistics And Data Science Program Experience, David Giordano

Trick to the Treat of Internships and Research

The Summer Institute in Biostatistics and Data Science, sponsored by the NHLBI and NIAID, offers a comprehensive six to seven-week training program. This program provides classroom instruction, career mentoring, and hands-on data analysis using clinical study data related to infectious, immune-mediated, and chronic diseases. It's designed to address the increasing demand for biostatisticians and data scientists, targeting undergraduates and early graduate students to consider graduate programs in these fields. The curriculum includes intensive biostatistical training, introducing students to statistical methods' principles and applications in biomedical and clinical research.

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Pre-Health Professional Volunteer, Divya Papaiya Oct 2023

Pre-Health Professional Volunteer, Divya Papaiya

Trick to the Treat of Internships and Research

I participated in the esteemed Pre-Health Professional Volunteer Program at Penn Medicine Princeton Health over this summer from May to August. Through this program, I was able to rotate through various departments in the hospital ranging from – but not limited to – Radiation Oncology to the Pathology/Blood Bank Lab. Along with completing my rotations, I was a part of a close-knit cohort that was able to attend special lectures dedicated to a variety of healthcare topics such as medical treatment inequality and disparity, EMS services, organ donation, and medical examiner (autopsy) recognition cases. Despite being part of a specialized …

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Big 5 Conservation Internship, Bernhard Riegl Oct 2023

Big 5 Conservation Internship, Bernhard Riegl

Trick to the Treat of Internships and Research

The Discover Eden Big 5 Ecology and Conservation course is located in South Africa. Through a series of first-hand experiences and lectures, one learns much about Conservation and what it really is. By working with Ecologists, Conservationists, and Veterinarians, you gain insight into these professions and what they entail

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Summer 2023 Graz Internship, Eleanor Wind, Alex Pope Oct 2023

Summer 2023 Graz Internship, Eleanor Wind, Alex Pope

Trick to the Treat of Internships and Research

The summer 2023 Graz Internship was a comprehensive medical internship which exposed us to both surgical and clinical sides of medicine. Over the course of 6 weeks we were able to observe a variety of operations and even scrub in and assist. Clinical skills acquired included IV placement, phlebotomy, laparoscopy, suturing and surgical knot tying. In addition to experience gained in the hospital, we learned the basics of international travel, citywide navigation in multiple cities, European culture, and ate quite a bit of good food. We were fortunate enough to meet a network of medical students and doctors from other …

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Science Alive, Adam Sadik, Pranav Madadi, Mahalaxmi Some, Lohita Sunkara, Ashley Abad, Lickchina Jeanlis Oct 2023

Science Alive, Adam Sadik, Pranav Madadi, Mahalaxmi Some, Lohita Sunkara, Ashley Abad, Lickchina Jeanlis

Trick to the Treat of Internships and Research

Through the Science Alive outreach program, we work to bring the excitement of hands-on learning to grade-school children and the entire community. Science Alive promotes science education and interaction between the college and grade school community as “science buddies”. Group leaders can earn Science Alive internship credit and serve as volunteers with Broward County public schools. There are a variety of ways NSU students are involved in this internship program. We have a regular schedule of leading students once per week on Friday afternoons at Nova Blanche Elementary through NSU student-led activities to explore science. We also have been building …

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Examining The Role Of Microglia In Diabetic Retinopathy: Phenotypes, Mechanisms, And Therapies, Charles W. Pfeifer Oct 2023

Examining The Role Of Microglia In Diabetic Retinopathy: Phenotypes, Mechanisms, And Therapies, Charles W. Pfeifer

Arts & Sciences Graduate Student Theses and Dissertations

Retinal microglia activation and function is a pivotal component of ocular disease pathology, but their involvement in diabetic retinopathy, a complex neurovascular complication of diabetes, remains unclear. The purpose of this thesis work is to thoroughly examine features of microglia activation in DR, identify mechanistic underpinnings of their contributions to neuroinflammatory features of disease pathogenesis, and assess immunotherapeutic targeting of microglia as a potential approach to treating early-stage DR. Here, we show that chronic hyperglycemia elicits morphological, ultrastructural, and transcriptional changes in retinal microglia during early-stage DR while other elements of the retinal neurovascular unit remain unperturbed. Through chronic ablation …

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Genome Sequences Of Six Cluster Ct And Two Cluster Dj Bacteriophages That Infect Gordonia Rubripertincta, Xavier F. Rodriguez, Daniel C. Williams, Catherine P. Chia Oct 2023

Genome Sequences Of Six Cluster Ct And Two Cluster Dj Bacteriophages That Infect Gordonia Rubripertincta, Xavier F. Rodriguez, Daniel C. Williams, Catherine P. Chia

School of Biological Sciences: Faculty Publications

We report the genome sequences of eight bacteriophages isolated using Gordonia rubripertincta NRRL B-16540-SEA. Based on gene content similarity to phages in the Actinobacteriophage database, six of the phages are assigned to phage cluster CT while two are assigned to cluster DJ.

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Effects Of A Major Hurricane On Dynamics, Structure, And Composition Of Mississippi River Delta Forests, Lance C. Umlang Oct 2023

Effects Of A Major Hurricane On Dynamics, Structure, And Composition Of Mississippi River Delta Forests, Lance C. Umlang

LSU Doctoral Dissertations

Tropical cyclones recurrently influence coastal forests worldwide. Tree survival (resistance) and post-cyclone recruitment (resilience) can vary with cyclone intensity, producing differences in composition, arboreal structure, and dynamics among affected forests. Studies of tropical cyclone wind effects on coastal forests typically emphasize damage more than post-cyclone responses. We hypothesized that intense cyclones might produce large, stratum-dependent effects that prevent affected forests from returning to pre-storm conditions. We explored direct effects of major Hurricane Katrina and post-hurricane changes in oak-dominated bottomland and cypress/tupelo-dominated swamp forests within the inactive portion of the Mississippi River deltaic plain. Overall mortality was high (14-25%) but concentrated …

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Evaluating The Utility Of S100a8/A9 As A Non-Invasive Biomarker, Leah Mellett Oct 2023

Evaluating The Utility Of S100a8/A9 As A Non-Invasive Biomarker, Leah Mellett

Arts & Sciences Graduate Student Theses and Dissertations

Biomarkers, a portmanteau of “biological markers”, are clinically relevant observations that can accurately and reproducibly indicate or predict patient outcomes. These objective measurements have vast clinical utility as they can aid clinicians with diagnoses, provide information about patient prognoses, and monitor changes in patient health statuses. While the discovery of several biomarkers are attributed to differential expression or concentration of genes or proteins within blood samples, biomarkers can be alternatively found in other bodily fluids or tissues depending on the associated condition. Recently, advances in urine proteomics have allowed for the identification of urine biomarkers that may eliminate the drawbacks …

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On The Origin Of Aids: Card8’S Role In Pathogenesis And Cure, Kolin Clark Oct 2023

On The Origin Of Aids: Card8’S Role In Pathogenesis And Cure, Kolin Clark

Arts & Sciences Graduate Student Theses and Dissertations

HIV infection remains a major global health burden with 1.7 million new acquisitions and 770,000 deaths in 2018 alone. While these numbers are declining due to antiretroviral therapy, only a handful of individuals have achieved complete remission from HIV. With the advent of antiretroviral therapy, HIV has turned a death sentence into a chronic, manageable condition. However, current antiretroviral therapies have only been studied on their ability to block infection and have not been able to clear the viral reservoir. Additionally, HIV cure strategies often rely upon sensing of highly variable epitopes such as the HIV envelope and have not …

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Multiple Light Signaling Pathways Control Solar Tracking In Sunflowers, Christopher J. Brooks, Hagop S. Atamian, Stacey L. Harmer Oct 2023

Multiple Light Signaling Pathways Control Solar Tracking In Sunflowers, Christopher J. Brooks, Hagop S. Atamian, Stacey L. Harmer

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Sunflowers are famous for their ability to track the sun throughout the day and then reorient at night to face east the following morning. This occurs by differential growth patterns, with the east sides of stems growing more during the day and the west sides of stems growing more at night. This process, termed heliotropism, is generally believed to be a specialized form of phototropism; however, the underlying mechanism is unknown. To better understand heliotropism, we compared gene expression patterns in plants undergoing phototropism in a controlled environment and in plants initiating and maintaining heliotropic growth in the field. We …

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To What Extent Do Physiological Tolerances Determine Elevational Range Limits Of Mammals?, Jay F. Storz, Graham R. Scott Oct 2023

To What Extent Do Physiological Tolerances Determine Elevational Range Limits Of Mammals?, Jay F. Storz, Graham R. Scott

School of Biological Sciences: Faculty Publications

A key question in biology concerns the extent to which distributional range limits of species are determined by intrinsic limits of physiological tolerance. Here, we use common-garden data for wild rodents to assess whether species with higher elevational range limits typically have higher thermogenic capacities in comparison to closely related lowland species. Among South American leaf-eared mice (genus Phyllotis), mean thermogenic performance is higher in species with higher elevational range limits, but there is little among-species variation in the magnitude of plasticity in this trait. In the North American rodent genus Peromyscus, highland deer mice (Peromyscus maniculatus …

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A Computational Study On The Impact Of Anchoring Groups On The Optical And Electronic Properties Of Triphenylamine-Based Dyes For Dye-Sensitized Solar Cell Applications, Geradius Deogratias, Grace Kinunda Oct 2023

A Computational Study On The Impact Of Anchoring Groups On The Optical And Electronic Properties Of Triphenylamine-Based Dyes For Dye-Sensitized Solar Cell Applications, Geradius Deogratias, Grace Kinunda

Tanzania Journal of Science

Anchoring groups are crucial for enhancing the performance of dye-sensitized solar cells (DSSCs). For instance, cyanoacrylic acid serves as the primary anchoring group in DSSC due to its crucial elements required for effective electron transport. However, it suffers from degradation. To address this limitation, this study proposes alternative cyano-based anchoring groups for sensitizers. Density functional theory (DFT) and time-dependent DFT were used to investigate the optical and electronic properties of the dyes. The studied dyes (excluding the dye containing OH group) displayed three absorption bands within the visible and NIR regions. Low-energy peaks ranged from 498 to 576 nm, corresponding …

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Ecological Correlates For Endemic And Threatened Amphibians In The Uluguru Nature Forest Reserve, Tanzania, Joseph M. Christopher, Wilirk Ngalason, John V. Lyakurwa Oct 2023

Ecological Correlates For Endemic And Threatened Amphibians In The Uluguru Nature Forest Reserve, Tanzania, Joseph M. Christopher, Wilirk Ngalason, John V. Lyakurwa

Tanzania Journal of Science

Information on habitat characteristics for endemic and threatened amphibians along the altitudinal gradient in the Uluguru Nature Forest Reserve (UNFR) is limited. We assessed habitat characteristics associated with the occurrence of endemic and threatened amphibians in the Uluguru Nature Forest Reserve between April and June 2022. Bucket pitfall traps, time-constrained audio-visual surveys, plots and opportunistic searching were used to study amphibians in 6 sites along elevational gradient from 600 m to 2100 m a.s.l. Eighteen amphibian species were recorded, thirteen of them being endemic to the Eastern Arc Mountains, two near-endemic and three widely distributed. Among the species recorded, seven …

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Modification Of Chitosan Using Glycidyl Methacrylate-Grafted Cellulose (Gmagcell/ Chi) For Methylene Blue Adsorption, Haya Fathana, Rahmi Rahmi, Muhammad Adlim, Surya Lubis Oct 2023

Modification Of Chitosan Using Glycidyl Methacrylate-Grafted Cellulose (Gmagcell/ Chi) For Methylene Blue Adsorption, Haya Fathana, Rahmi Rahmi, Muhammad Adlim, Surya Lubis

Karbala International Journal of Modern Science

In this study, a glycidyl methacrylate-grafted cellulose/chitosan (GMA-g-Cell/Chi) film was successfully prepared and characterized. GMA-g-Cell was obtained from the grafting process of cellulose derived from sugarcane bagasse using glycidyl methacrylate (GMA). The cellulose grafting process was obtained using 20% GMA for 4 hours at 60oC. The percentage of grafting (PG) and grafting efficiency (GE) values for these parameters were 516 and 60.28%, respectively. Chitosan was modified with GMA-g-Cell and has higher adsorption capacity and tensile strength than chitosan. The adsorption kinetics tend to follow the pseudo-first-order adsorption kinetics model, with Qe and k1 being 7 mg/g and 0.067 g/mg. minute. …

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Hurricanes And Tropical Storms’ Impact On Water Quality In Lake Okeechobee, Florida, Daniela Vasquez Diaz Oct 2023

Hurricanes And Tropical Storms’ Impact On Water Quality In Lake Okeechobee, Florida, Daniela Vasquez Diaz

USF Tampa Graduate Theses and Dissertations

Hurricanes are natural events with catastrophic outcomes, while climate change's effects on their intensity and frequency remain discussed. However, it is crucial to analyze these through models and statistics to understand their behavior and impact on the basins. Particularly in lakes on tropical coasts since disruptive events such as hurricanes tend to be highly affected. Lake Okeechobee is a unique lake located in Florida and one of the largest freshwater lakes. The lake and some of its significant stations are the locations chosen to perform the investigation. The main focus of the investigation is determining the effect that hurricanes have …

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Patterns In Biodiversity And Community Assemblage In Macrofaunal Fouling Communities On Tampa Bay Floating Docks, Cassidy C. Bell Oct 2023

Patterns In Biodiversity And Community Assemblage In Macrofaunal Fouling Communities On Tampa Bay Floating Docks, Cassidy C. Bell

USF Tampa Graduate Theses and Dissertations

Understanding biodiversity trends of highly disturbed urban landscapes is essential as anthropogenic factors continue to drive global biodiversity loss. Within marine ecosystems, macrofaunal fouling communities, aggregations of epibenthic invertebrates that colonize human-made structures, represent an ecologically important subset of urban coastlines. Tampa Bay is a highly urbanized estuary in Florida, USA, and is home to the state’s largest port, Port Tampa Bay. This makes the bay a prime site for the introduction of new species, with many organisms either considered invasive or cryptogenic, their origins left unclear. Many factors may contribute to the communities that form on urban structures including …

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Freshwater Macroinvertebrate Communities In Baldwin County, Georgia, Heath Michael Ghioto, Michelle K. Murdock, Nadya S. Gutierrez, Kristine N. White Ph.D. Oct 2023

Freshwater Macroinvertebrate Communities In Baldwin County, Georgia, Heath Michael Ghioto, Michelle K. Murdock, Nadya S. Gutierrez, Kristine N. White Ph.D.

Georgia Journal of Science

Freshwater ecosystems are critical habitats for maintaining biodiversity, often providing refuge for organisms especially in urban settings. Baldwin County, GA is home to many freshwater lakes that are part of the Oconee River watershed. Despite ongoing water quality monitoring, aquatic macroinvertebrates are under studied in the area. Aquatic macroinvertebrate diversity of one forested and one residential lake in Milledgeville, GA was documented for the first time. Despite low sample size, community composition was significantly different between lakes, with 27 families in Lake Laurel (forested), 44 families in Lake Oliver Hardy (residential), and only 19 families collected from both lakes. Seasonal …

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An Investigation Of Mitigation Measures On The Spread Of Covid-19 In A College Classroom Using Agent-Based Modeling, Saharsh Talwar, Anne E. Yust Oct 2023

An Investigation Of Mitigation Measures On The Spread Of Covid-19 In A College Classroom Using Agent-Based Modeling, Saharsh Talwar, Anne E. Yust

Spora: A Journal of Biomathematics

In this manuscript, we describe the process of using agent-based modeling in NetLogo to create a simulation of COVID-19 spread in a traditional college classroom. The model allows for an evaluation of different preventative measures implemented by the University of Pittsburgh, including the cohort classroom attendance model, mask and vaccine mandates, contact tracing, and classroom sanitation. Through the use of the model's interactive interface, the impact of adjusting specific measures by the institution could be visualized, providing a valuable tool for combating diseases that spread through droplet transmission.

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Phenotypic Plasticity Of Male Calls In Two Populations Of The Katydid Neoconocephalus Triops (Insecta: Tettigoniidae), Oliver M. Beckers, Teiya Kijimoto, Johannes Schul Oct 2023

Phenotypic Plasticity Of Male Calls In Two Populations Of The Katydid Neoconocephalus Triops (Insecta: Tettigoniidae), Oliver M. Beckers, Teiya Kijimoto, Johannes Schul

Faculty & Staff Research and Creative Activity

The ability to respond to environmental changes plays a crucial role for coping with environmental stressors related to climate change. Substantial changes in environmental conditions can overcome developmental homeostasis, exposing cryptic genetic variation. The katydid Neoconocephalus triops is a tropical species that extended its range to the more seasonal environment of North America where it has two reproductive generations per year. The harsher winter conditions required adults to diapause which resulted in substantially different mating calls of the diapausing winter animals compared to the non-overwintering summer animals in northern Florida. The summer call corresponds to that of tropical populations, whereas …

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Essential Role Of The Amino-Terminal Region Of Drosha For The Microprocessor Function, Amit Prabhakar, Song Hu, Jin Tang, Prajakta Ghatpande, Giorgio Lagna, Xuan Jiang, Akiko Hata Oct 2023

Essential Role Of The Amino-Terminal Region Of Drosha For The Microprocessor Function, Amit Prabhakar, Song Hu, Jin Tang, Prajakta Ghatpande, Giorgio Lagna, Xuan Jiang, Akiko Hata

Biology

Drosha is a core component of the Microprocessor complex that cleaves primary-microRNAs (pri-miRNAs) to generate precursor-miRNA and regulates the expression of ∼80 ribosomal protein (RP) genes. Despite the fact that mutations in the amino-terminal region of Drosha (Drosha-NTR) are associated with a vascular disorder, hereditary hemorrhagic telangiectasia, the precise function of Drosha-NTR remains unclear. By deleting exon 5 from the Drosha gene and generating a Drosha mutant lacking the NTR (ΔN), we demonstrate that ΔN is unable to process pri-miRNAs, which leads to a global miRNA depletion, except for the miR-183/96/182 cluster. We find that Argonaute 2 facilitates the processing …

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Spatial Structure Of Germination And Seed-Associated Fungi In Tropical Pioneer Seeds, Daniela Varon Garcia Oct 2023

Spatial Structure Of Germination And Seed-Associated Fungi In Tropical Pioneer Seeds, Daniela Varon Garcia

USF Tampa Graduate Theses and Dissertations

Negative density-dependent regulation is the process by which host-specific natural enemies reduce the survival of seeds and seedlings of conspecifics near adult trees, favoring heterospecific recruitment, and ultimately increasing local diversity. Negative density-dependent regulation by fungal pathogens has been consistently reported to promote plant diversity in the tropics, even though they tend to be multi-host and host-specificity is rarely reported. Nevertheless, evidence suggests that host-generalist fungi can have host-specific effects that produce disproportionate negative effects on some plant species but not others, promoting regional diversity. However, such studies have not tested for both host-specificity and distance-dependent effects in fully replicated …

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Domoic Acid In Canadian Pacific Waters, From 2016 To 2021, And Relationships With Physical And Chemical Conditions, R. Ian Perry, Nina Nemcek, Melissa Hennekes, Akash Sastri, Andrew R.S. Ross, Hayleigh Shannon, Ryan B. Shartau Oct 2023

Domoic Acid In Canadian Pacific Waters, From 2016 To 2021, And Relationships With Physical And Chemical Conditions, R. Ian Perry, Nina Nemcek, Melissa Hennekes, Akash Sastri, Andrew R.S. Ross, Hayleigh Shannon, Ryan B. Shartau

Biology Faculty Publications and Presentations

Domoic acid, a phycotoxin produced by species of the marine diatom Pseudo-nitzschia, can cause deleterious impacts to marine food webs and human health. Domoic acid and Pseudo-nitzschia spp. were surveyed from 2016 to 2021 in the Pacific waters of Canada to assess their occurrences, concentrations, and relationships with physical and chemical conditions. Domoic acid was common, occurring in measurable concentrations in 73% of the 454 samples. It occurred in all regions (west coast of Vancouver Island, Salish Sea, Queen Charlotte Sound /Hecate Strait, deep oceanic NE Pacific), in all years and all seasons. Median concentrations were highest along the west …

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Biofilm Formation In Bath Toys, Kelsey Daniels Oct 2023

Biofilm Formation In Bath Toys, Kelsey Daniels

Harrisburg University Research Symposium: Highlighting Research, Innovation, & Creativity

Biofilms are a collective of microorganisms and matrixes that can grow on a variety of surfaces. Depending on the environment, the growth of biofilm formation can vary. These environmental factors may include temperature or access to nutrients. Overtime unkept bath toys can form a biofilm layer, which can be hard to remove and hazardous to children. It is important to understand biofilms so that a variety of methods can be successfully used against them.

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The Effects Of Vaping Coil Temperature On The Viability Of Veillonella Parvula And Streptococcus Mutans, Marvelous O. Aluko Oct 2023

The Effects Of Vaping Coil Temperature On The Viability Of Veillonella Parvula And Streptococcus Mutans, Marvelous O. Aluko

Harrisburg University Research Symposium: Highlighting Research, Innovation, & Creativity

No abstract provided.

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Effects Of Micro-Plastic Exposure On Growth Rate Of Lactuca Sativa Var. Capitata, Cassie Morris Oct 2023

Effects Of Micro-Plastic Exposure On Growth Rate Of Lactuca Sativa Var. Capitata, Cassie Morris

Harrisburg University Research Symposium: Highlighting Research, Innovation, & Creativity

No abstract provided.

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Effects Of Growth Rate On Peptidoglycan Crosslink Density Of E. Coli Using Fluorescent Labeling, Morgan Olszewski Oct 2023

Effects Of Growth Rate On Peptidoglycan Crosslink Density Of E. Coli Using Fluorescent Labeling, Morgan Olszewski

Harrisburg University Research Symposium: Highlighting Research, Innovation, & Creativity

Peptidoglycan (PG) is a polymer composed of polysaccharides and crosslinked peptide chains found in bacterial cell walls. It helps to protect the cell from environmental stress and maintain cell morphology throughout its life cycle and further generations. The PG is made up of two sugars, N-acetyl muramic acid (NAM) and N-acetyl glucosamine (NAG). NAM and NAG are connected by glycosidic linkages to form repeated chains. The chains are formed in layers, which are interconnected via a polypeptide stem linked by a peptide bridge. During cell growth, continuous turnover of existing PG occurs by severing existing crosslinks, inserting new PG into …

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Southern California Marine Protected Areas Promote Bolder Fish Populations, Lucian Himes, Florybeth F. La Valle Oct 2023

Southern California Marine Protected Areas Promote Bolder Fish Populations, Lucian Himes, Florybeth F. La Valle

Summer Undergraduate Research in Biology Program

Marine protected areas (MPAs) aim to protect habitats and ecosystems to promote the diversity and health of marine populations. To evaluate the health of fish populations within and outside of MPAs in Southern California, we used flight initiation distance (FID). FID is the distance at which an individual will flee from a perceived predator and is a direct measure of boldness. Lower FIDs are indicative of bolder populations. Lower FID values indicate that fish will have the opportunity to dedicate less energy to fleeing from predators which could then be used for increased foraging. Data was collected from eight locations …

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Unraveling The Functional Dark Matter Through Global Metagenomics, Georgios A. Pavlopoulos, Fotis A. Baltoumas, Sirui Liu, Oguz Selvitopi, Antonio Pedro Camargo, Stephen Nayfach, Ariful Azad, Simon Roux, Lee Call, Natalia N. Ivanova, Min I. Chen, David Paez-Espino, Evangelos Karatzas, Nathan Ahlgren Oct 2023

Unraveling The Functional Dark Matter Through Global Metagenomics, Georgios A. Pavlopoulos, Fotis A. Baltoumas, Sirui Liu, Oguz Selvitopi, Antonio Pedro Camargo, Stephen Nayfach, Ariful Azad, Simon Roux, Lee Call, Natalia N. Ivanova, Min I. Chen, David Paez-Espino, Evangelos Karatzas, Nathan Ahlgren

Biology

Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities1,2. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 …

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