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Lab Notes

Scientia

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Chemically Induced Phytoextraction Of Lead (Pb) Contaminated Soil By Switchgrass (Panicum Virgatum L.), Austin Gilly

Master of Science in Integrative Biology Theses

Soils contaminated with lead (Pb) from human activities including industrial byproducts create an environmental and human health risk. Phytoextraction through chemical acquisition of Pb in soils offer a potentially cost effective and ecologically driven approach to remediation. Switchgrass (Panicum virgatum L.) is known to have a tolerance for a wide range of heavy metals including Pb. Switchgrass is also able to grow in a wide range of climates. Soil chemistry manipulation, using chelates and plant growth promoters could provide an effective field method for phytoremediation using switchgrass. In this study chemically enhanced phytoextraction using the soil-fungicide Infuse (active ingredient …

Posttranslational Modification And Protein Disorder Regulate Protein-Protein Interactions And Dna Binding Specificity Of P53, Robin Levy

USF Tampa Graduate Theses and Dissertations

p53 is an intrinsically disordered transcription factor that suppresses tumor development by arresting the cell cycle and promoting DNA repair. p53 deletions or mutations can lead to cancer due to the inability of cells to respond to stress. The protein levels and post-translational modification state of p53 changes in response to cellular stress like DNA damage. Previous studies have shown that p53 can undergo coupled folding and binding with the E3 ubiquitin ligase, Mdm2, and the histone deacetylase, p300. In normal cells, p53 is kept at a low level by Mdm2, which marks it with ubiquitin, targeting p53 for proteasome …

Pyrococcus Horikoshii Rada Intein Site Selection, Noah Stallins

Honors College Theses

Inteins are protein segments interrupting polypeptides with the unique ability to excise from the host protein and link flanking protein fragments (exteins) to form a functional protein. Many of these proteins are involved in crucial processes such as DNA replication, DNA recombination, and DNA repair. The functionality of these elements in nature and applications in biotechnology necessitates the study of inteins. Pyrococcus horikoshii (Pho) provides an array of inteins to study, with a total of nine different proteins possessing inteins. Among the nine total inteins, the DNA repair and recombination protein RadA gained interest due to the speed …

Spatio-Temporal Dynamics Of Fungal Communities And Their Effects On Plants, Kel Cook

Biology ETDs

Fungi perform several critical functions in the environment. Spatiotemporal distributions of fungal communities will mediate when and where these functions happen and how they vary across the landscape. I first explored tropical tree canopy fungal community variation at small spatial scales and documented near total turnover of fungi across sub-meter distances and among adjacent substrates. The second chapter analyzed fungal turnover over the course of three years, where community stability was driven primarily by abundant fungi. In the third chapter, I tested effects of the environment, including host plant and habitat, on canopy fungal communities and found only small effects, …

Inoculum Potential Of Pinus Edulis-Associated Ectomycorrhizal Fungi Across A Forest Extirpation Chronosequence, Annie M. Montes

Biology ETDs

Few studies have examined inoculum potential of ectomycorrhizal fungi (EMF) in the absence of plant hosts, yet persistence of these fungi may be paramount to resilience of Pinus edulis and other mycorrhizal plant species. We conducted a study in which seven sites were selected in northwestern New Mexico with known dates of P. edulis extirpation and a lack of regeneration. Age classes included: two sites extirpated 10-20 years ago, two extirpated 55-65 years ago, two extirpated 500+ years ago, and one extirpated 11,000+ years ago. At each site, two plots were paired: an extirpated plot and the nearest live adult …

Milkfish (Chanos Chanos) Neurocranium, Golda Stewart, David Kerstetter

All Scans: Kerstetter Fisheries and Avian Ecology 3D Scan Series

Neurocranium from Milkfish (Chanos chanos), collected from Foodtown on 08/09/2020 by Golda Stewart.

Evaluation Of Anti-Cancer Function In Natural Killer Cells Generated From Rat Hematopoietic Stem Cells, Alireza Pirahmadian

Student Works (2020-2029)

Natural killer cells (NK) cells are lymphocytes and they are the most important key constituent of mammalian immune system against cancer tumour cells. The genome of NK cells is categorically divided to inhibitory and activator genes that code ligands on the surface of NK cells. Indeed, these ligands are cancer tumour cells destroyer arms of the NK cells. On the other hand, hematopoietic stem cells (HSCs) are the origin of all blood cells, derives from BM and mature to immune cells. NK cells cannot defeat CTCs on their own. The main reason is their population (numbers are low), they cannot …

Identification Of Novel Host Genes Required For Antiviral Immunity And Viral Genome Replication In C. Elegans, Fei Meng

LSU Doctoral Dissertations

RNA interference (RNAi) is a wide-spread gene silencing mechanism that control diverse biological functions and triggered by small interfering RNAs (siRNAs) processed from the viral genome or its replication intermediates. Mechanistic studies of antiviral RNAi in Caenorhabditis elegans has led to the identification of several critical factors involved in the process. As a result, whether antiviral RNAi requires additional novel genes remains to be an open question.

Viruses are intracellular parasites that rely on host products for reproduction. Disrupting their interaction with host factors can significantly compromise their replication and keep them under control. Thus, identification of host genes …

Using The Rdna Internal Transcribed Spacer 1 To Identify The Invasive Pest Rhagoletis Cerasi (Diptera: Tephritidae) In North America, Norman B. Barr, Daniel Garza, Lisa A. Ledezma, David A. Salinas

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

The cherry-infesting fruit fly Rhagoletis cerasi Loew is a significant commercial pest in Europe that has recently invaded North America. To date, it has been trapped only in Canada and northwestern counties of New York. It has the potential to spread further and threaten production and movement of cherry commodities. Timely diagnosis of the pest will facilitate surveys and quick response to new detections. Adult morphology of the pest is distinct from other flies in North America. However, when flies are significantly damaged on traps or the immature life stages are found in fruits, molecular methods of identification are important …

Mucosal Immune System Of African Lungfish, Ryan D. Heimroth

Biology ETDs

Conquering land was an apex moment in the evolution of vertebrates. Physiologically, the first vertebrates to transition to life on land had to adapt in order to survive in an oxygen-rich environment where gravitational forces and limited water prevailed. Several extant vertebrates including anurans and lungfish, survive droughts by undergoing aestivation. Unfavorable environmental conditions trigger lungfish to aestivate. Aestivation is a process of metabolic torpor wherein the fish will encase itself in a mucus cocoon and not move until favorable environmental conditions (food and water) are reintroduced. Aestivation can be reproduced in laboratory settings and, thus, lungfish can be used …

Aspergillus Niger Decreases Bioavailability Of Arsenic(V) Via Biotransformation Of Manganese Oxide Into Biogenic Oxalate Minerals, Bence Farkas, Marek Kolenčík, Miroslav Hain, Edmund Dobročka, Gabriela Kratošová, Marek Bujdoš, Huan Feng, Yang Deng, Qian Yu, Ramakanth Illa, B. Ratna Sunil, Hyunjung Kim, Peter Matúš, Martin Urík

Department of Earth and Environmental Studies Faculty Scholarship and Creative Works

The aim of this work was to evaluate the transformation of manganese oxide (hausmannite) by microscopic filamentous fungus Aspergillus niger and the effects of the transformation on mobility and bioavailability of arsenic. Our results showed that the A. niger strain CBS 140837 greatly affected the stability of hausmannite and induced its transformation into biogenic crystals of manganese oxalates—falottaite and lindbergite. The transformation was enabled by fungal acidolysis of hausmannite and subsequent release of manganese ions into the culture medium. While almost 45% of manganese was bioextracted, the arsenic content in manganese precipitates increased throughout the 25-day static cultivation of fungus. …

Climate-Related Geographical Variation In Performance Traits Across The Invasion Front Of A Widespread Non-Native Insect, Lily M. Thompson, Sean D. Powers, Ashley Appolon, Petra Hafker, Leila Milner, Dylan Parry, Salvatore J. Agosta, Kristine L. Grayson

Biology Faculty Publications

Aim

Invasive species are ideal systems for testing geographical differences in performance traits and measuring evolutionary responses as a species spreads across divergent climates and habitats. The European gypsy moth, Lymantria dispar dispar L. (Lepidoptera: Erebidae), is a generalist forest defoliator introduced to Medford, Massachusetts, USA in 1869. The invasion front extends from Minnesota to North Carolina and the ability of this species to adapt to local climate may contribute to its continuing spread. We evaluated the performance of populations along the climatic gradient of the invasion front to test for a relationship between climate and ecologically important performance traits. …

The Nature Of Genes Expressed Differently After Environmental Drug Exposure, Nicci Siffel

Scholars Week

The Nature of Genes Expressed Differently after Environmental Drug Exposure

N. Siffel, S. Anderson, B. Subedi, D.R. Hammond-Weinberger

Drug use, of prescription or illicit varieties, alter bodily functions in different ways, especially in the nervous system. These drugs are found in sources of drinking water because they are not removed by wastewater treatment facilities. To investigate the effects of these drugs as they appear in mixtures, we exposed groups of zebrafish embryos to cocktails of drugs and screened for genes that were differentially expressed between the experimental and control groups and could thus give more insight into their biological functions. …

Regulation Of Mpcs And Kat8 During Adipogenesis And Nutritional Regulation, Jasmine Burrell

LSU Doctoral Dissertations

Obesity is a global epidemic characterized by an expansion of adipose tissue. Adipose tissue, composed of adipocytes and a stromal vascular fraction, is an endocrine organ that regulates whole body homeostasis. Obesity leads to the dysregulation of adipocytes and is often associated with increased susceptibility to metabolic diseases such as Type II diabetes mellitus (T2DM). Understanding the mechanisms by which adipocyte function and development are regulated is crucial. Mitochondrial pyruvate carriers (MPCs) are transmembrane proteins that transport pyruvate from the cytosol into the mitochondrial matrix to generate acetyl CoA. Although MPCs have been studied extensively, their roles in adipocytes are …

Increasing Our Ability To Predict Contemporary Evolution, Patrik Nosil, Samuel M. Flaxman, Jeffrey L. Feder, Zachariah Gompert

Biology Faculty Publications

Classic debates concerning the extent to which scientists can predict evolution have gained new urgency as environmental changes force species to adapt or risk extinction. We highlight how our ability to predict evolution can be constrained by data limitations that cause poor understanding of deterministic natural selection. We then emphasize how such data limits can be reduced with feasible empirical effort involving a combination of approaches.

A Multi‑Disciplinary Comparison Of Great Ape Gut Microbiota In A Central African Forest And European Zoo, Victor Narat, Katherine R. Amato, Noémie Ranger, Maud Salmona, Séverine Mercier‑Delarue, Stephanie Rupp, Philippe Ambata, Richard Njouom, François Simon, Tamara Giles‑Vernick, Jérôme Legoff

Publications and Research

Comparisons of mammalian gut microbiota across different environmental conditions shed light on the diversity and composition of gut bacteriome and suggest consequences for human and animal health. Gut bacteriome comparisons across different environments diverge in their results, showing no generalizable patterns linking habitat and dietary degradation with bacterial diversity. The challenge in drawing general conclusions from such studies lies in the broad terms describing diverse habitats (“wild”, “captive”, “pristine”). We conducted 16S ribosomal RNA gene sequencing to characterize intestinal microbiota of free-ranging sympatric chimpanzees and gorillas in southeastern Cameroon and sympatric chimpanzees and gorillas in a European zoo. We conducted …

Tobacco Hornworm (Manduca Sexta) Oral Secretion Elicits Reactive Oxygen Species In Isolated Tomato Protoplasts, Akanksha Gandhi, Rupesh R. Kariyat, Cruz Chappa, Mandeep Tayal, Nirakar Sahoo

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

Plants are under constant attack by a suite of insect herbivores. Over millions of years of coexistence, plants have evolved the ability to sense insect feeding via herbivore-associated elicitors in oral secretions, which can mobilize defense responses. However, herbivore-associated elicitors and the intrinsic downstream modulator of such interactions remain less understood. In this study, we show that tobacco hornworm caterpillar (Manduca sexta) oral secretion (OS) induces reactive oxygen species (ROS) in tomato (Solanum lycopersicum) protoplasts. By using a dye-based ROS imaging approach, our study shows that application of plant-fed (PF) M. sexta OS generates significantly higher ROS while artificial diet-fed …

Classification Of Planetary Craters Using Outline-Based Morphometrics, Thomas J. Slezak, Jani Radebaugh, Eric H. Christiansen, Mark C. Belk

Faculty Publications

The morphologies of craters on planetary surfaces reveal clues about the geologic mechanisms by which they originate and subsequently evolve, as well as the materials and physical variables inherent to the environment in which they formed. We carried out a quantitative multivariate analysis of shape descriptors derived from the outlines of craters formed by volcanic processes on Mars, Io, and Earth and by impact cratering on the Moon using elliptic Fourier analysis (EFA) and the Zahn-Roskies (Z-R) shape function. Canonical variate analysis (CVA) was used to construct a statistical model of differences between the crater groups to classify …

Trophic Cascades Alter Eco-Evolutionary Dynamics And Body Size Evolution, Thomas M. Luhring, John Delong

School of Biological Sciences: Faculty Publications

Trait evolution in predator–prey systems can feed back to the dynamics of interacting species as well as cascade to impact the dynamics of indirectly linked species (eco-evolutionary trophic cascades; EETCs). A key mediator of trophic cascades is body mass, as it both strongly influences and evolves in response to predator–prey interactions. Here, we use Gillespie ecoevolutionary models to explore EETCs resulting from top predator loss and mediated by body mass evolution. Our four-trophic-level food chain model uses allometric scaling to link body mass to different functions (ecological pleiotropy) and is realistically parameterized from the FORAGE database to mimic the parameter …

Contributions To The Knowledge Of Water Bugs In Mindoro Island, Philippines, With A Species Checklist Of Nepomorpha And Gerromorpha (Insecta, Hemiptera, Heteroptera), Arthien Lovell Pelingen, Herbert Zettel, Clister V. Pangantihon, Kyra Mari Dominique Aldaba, Earl Kevin Fatallo, Jemillie Madonna De Leon, Hendrik Freitag

Biology Faculty Publications

This survey aims to provide an updated species checklist of aquatic and semi-aquatic bugs in the intra-Philippine biogeographic Region of Mindoro. An assessment survey of water bugs (Hemiptera, Heteroptera) was conducted mostly by manual collection in selected areas of Oriental Mindoro from 2017 to 2018, in which some of the collecting activities were undertaken by graduate students of Ateneo de Manila University. Twenty-nine aquatic and semi-aquatic heteropteran species were documented and some are known island-endemic species or subspecies, including Enithares martini mindoroensis Nieser & Zettel, 1999, Hydrotrephes stereoides mindoroensis Zettel, 2003, Aphelocheirus freitagi Zettel & Pangantihon, 2010, Rhagovelia mindoroensis Zettel, …

The Tissues Of Adult Female Reproductive System Of The Pipistrellus Kuhlii Bat: Comparative Study With Other Mammals, Muna Rashid

Journal of the Arab American University مجلة الجامعة العربية الامريكية للبحوث

This study is attempt for investigating the tissues, which comprise the female reproductive system of the bat. Then, compare it with the same system of other mammals. The bat has been anatomized and the organs of female reproductive system was taken away. They include: ovary, ovarian duct and uterus, where they have been studied histological.

The results of the microscopic investigation of the tissue of the female bat, showed that the ovary has two parts; an outer cortex and an inner medulla. The cortex consists of follicles, different growth stages and the proper tissues have net of connective tissue fibers. …

Antibacterial Activity Of Selected Plant Extracts On Methicillin Resistant Staphylococcus Aureus, Lubna Abdallah

Journal of the Arab American University مجلة الجامعة العربية الامريكية للبحوث

Based on the importance of herbal plants in medicine, this study was conducted to evaluate the antibacterial efficacy of aqueous, ethanol and methanol extracts of Thymbra spicata, Nepeta curviflora, and Verbascum fruticulosum against two clinical isolates (I and II) of the gram positive methicillin resistant Staphylococcus aureus (MRSA). Agar well diffusion method was performed to examine the antibacterial activity of all studied plant extracts. Micro-broth dilution method was used to measure the minimum inhibitory concentration (MIC) then the minimum bacteriocidal concentration (MBC) for all active extracts. The examined isolates were susceptible to the prepared plant extracts. Ethanol and methanol extracts …

Multi-Scale 3d Cryo-Correlative Microscopy For Vitrified Cells, Gong-Her Wu, Patrick G. Mitchell, Jesus G. Galaz-Montoya, Corey W. Hecksel, Emily M. Sontag, Vimal Gangadharan, Jeffrey Marshman, David Mankus, Margaret E. Bisher, Abigail K.R. Lytton-Jean, Judith Frydman, Kirk Czymmek, Wah Chiu

Biological Sciences Faculty Research and Publications

Three-dimensional (3D) visualization of vitrified cells can uncover structures of subcellular complexes without chemical fixation or staining. Here, we present a pipeline integrating three imaging modalities to visualize the same specimen at cryogenic temperature at different scales: cryo-fluorescence confocal microscopy, volume cryo-focused ion beam scanning electron microscopy, and transmission cryo-electron tomography. Our proof-of-concept benchmark revealed the 3D distribution of organelles and subcellular structures in whole heat-shocked yeast cells, including the ultrastructure of protein inclusions that recruit fluorescently-labeled chaperone Hsp104. Since our workflow efficiently integrates imaging at three different scales and can be applied to other types of cells, it could …

A Genomic Analysis Of Osmotolerance In Staphylococcus Aureus, Dylan Casey, Roy D. Sleator

Department of Biological Sciences Publications

A key phenotypic characteristic of the Gram-positive bacterial pathogen, Staphylococcus aureus, is its ability to grow in low aw environments. A homology transfer based approach, using the well characterised osmotic stress response systems of Bacillus subtilis and Escherichia coli, was used to identify putative osmotolerance loci in Staphylococcus aureus ST772-MRSA-V. A total of 17 distinct putative hyper and hypo-osmotic stress response systems, comprising 78 genes, were identified. The ST772-MRSA-V genome exhibits significant degeneracy in terms of the osmotic stress response; with three copies of opuD, two copies each of nhaK and mrp/mnh, and five copies of opp. Furthermore, regulation of …

The Use Of Spanish Moss As A Biological Indicator To Examine Relationships Between Metal Air Pollution, Vegetation Cover, And Environmental Equity In Tampa, Florida, Yousif Abdullah

USF Tampa Graduate Theses and Dissertations

Studies of inequality in exposure to less common air pollutants, like metals, are often limited by the costs of high spatial resolution measurements. Spanish moss (Tillandsia usneoides) is a promising bioindicator for measuring air pollution due to its lower cost, enabling capture of time-average environmental concentrations at high spatial resolution. This study had three major aims. First, I aimed to use Spanish moss as a bioindicator to characterize ambient concentrations of selected metals (Ti, Cr, Mn, Co, Ni, Cd, Hg, Pb, As, and Sb) in Tampa, Florida. My second goal was to determine the impact of vegetation cover on metals …

Shoot Extracts From Two Low Nodulation Mutants Significantly Reduce Nodule Number In Pea, Christian A. Huynh, Frédérique Guinel

Biology Faculty Publications

E107 and E132 are pea mutants that nodulate poorly. Because they have a shoot-controlled nodulation phenotype, we asked if their mutated genes were implicated in the autoregulation of nodulation (AON), a mechanism which consists of two systemic circuits, the positive CEP/CRA2 and the negative CLE/SUNN, coordinated via NIN and miR2111. We further characterized the mutants’ phenotype by studying nodule distribution and nodulation efficiency. E107 was similar to wild-type (WT) in its nodule distribution, but E132 had an extended nodulation zone with nodules forming distally on its lateral roots. Moreover, we tested whether their shoots produced a compound inhibitory to nodulation. …

Blue Swimmer Crab Resource Of South-West Western Australia Harvest Strategy : 2020-2025 : Version 1.0, Department Of Fisheries

Fisheries Management Papers

No abstract provided.

Estuarine And Nearshore Finfish Resource Of South-West Western Australia Harvest Strategy : 2020-2025 : Version 1.0, Department Of Fisheries

Fisheries Management Papers

No abstract provided.

West Coast Deep Sea Crustacean Resource Harvest Strategy 2020-2025, Department Of Fisheries

Fisheries Management Papers

No abstract provided.