Biology Commons^™

Tree Thinning And Fire Affect Ectomycorrhizal Fungal Communities And Enzyme Activities, Ann L. Rasmussen, J. Stephen Brewer, Colin R. Jackson, Jason D. Hoeksema

Faculty and Student Publications

Common ecological restoration treatments such as thinning trees and prescribed burning could result in changes to soil fungal communities and changes to the function of those communities. Ectomycorrhizal fungi are especially likely to be affected as they are symbionts on plant roots and exhibit host and niche preferences. Ectomycorrhizal fungi also produce extracellular enzymes that are important in soil nutrient cycling. We conducted a community survey of ectomycorrhizal fungi and assayed ectomycorrhizal root tip enzyme activity using substrate plugs in northern Mississippi upland oak–pine woodland plots differing in restoration history to explore the influence of woodland restoration on ectomycorrhizalfungal community …

Building Capacity For A Global Genome Editing Observatory: Institutional Design, Krishanu Saha, J. Benjamin Hurlbut, Sheila Jasanoff, Aziza Ahmed, Anthony Appiah, Elizabeth Bartholet, Francoise Baylis, Gaymon Bennett, George Church, I. Glenn Cohen, George Daley, Kevin Finneran, William Hurlbut, Rudolf Jaenisch, Laurence Lwoff, John Paul Kimes, Peter Mills, Jacob Moses, Buhm Soon Park, Erik Parens, Rachel Salzman, Abha Saxena, Hilton Simmet, Tania Simoncelli, O. Carter Snead, Kaushik Sunder Rajan, Robert D. Truog, Patricia Williams, Christiane Woopen

Journal Articles

A new infrastructure is urgently needed at the global level to facilitate exchange on key issues concerning genome editing. We advocate the establishment of a global observatory to serve as a center for international, interdisciplinary, and cosmopolitan reflection.

Characterizing The Effects Of Mutations In Stm And Ath1 On Floral Organ Development In Arabidopsis Thaliana, Hayden Malone

Honors Theses

Understanding the molecular controls involved in plant development is important in understanding plant physiology as a whole, and this knowledge in turn can lead to useful applications in agriculture and industry. This project investigates the roles of two transcription factors, SHOOT MERISTEMLESS (STM) and ARABIDOPSIS THALIANA HOMEOBOX GENE1 (ATH1) in the molecular pathway that creates boundaries between organs in flowers of Arabidopsis thaliana. Mutations in the STM and ATH1 genes prevent formation of basal boundaries between the floral organs and the stem, causing abscission defects in flowers. If the STM and ATH1 genes are also critical for establishing the boundaries …

The Effects Of Mutations In The Ath1 And Stm Genes On Sepal, Petal, And Stamen Abscission In Arabidopsis Thaliana Plants, Hunter L. Roth

Honors Theses

Floral organ boundaries are areas that allow distinct organs within a flower to differentiate from each other and the underlying stem. Boundary regions are also where abscission zones (AZs) can form, which allow floral organs to abscise, or detach, from the plant. This study takes a look into a pair of genes, ARABIDOPSIS THALIANA HOMEOBOX GENE1 (ATH1) and SHOOT MERISTEMLESS (STM), which code for transcription factors found in Arabidopsis thaliana that are responsible for proper boundary formation and AZ specification. Mutations in one or both of these genes affect AZ formation of specific floral organs. The ATH1 and STM transcription …

Determination Of The Chromosomal Position Of Three Mutations Using Recombination Mapping In Drosophila Melanogaster, Zane Bryant Coleman

Honors Theses

Genetic screens are performed in order to characterize genes and mutations, often relating to developmental processes. A previous genetic screen performed in Drosophila melanogaster found three mutations on the second chromosome affecting glial cell development: FF12, DD68, and D19. These mutations each disrupted the pattern and expression of reversed polarity (repo), a target gene of the glial fate master regulator, glial cells missing (gcm). Here, I use recombination mapping with phenotypically observable dominant markers to locate the genetic map position of each mutation. This method provides a rapid estimate of the mutations' locations that can then be tested against molecularly-defined …

Characterizing The Effects Of Stm And Ath1 Mutations On Floral Organ Development In Arabidopsis Thaliana, James Luke Leary

Honors Theses

The purpose of this project was to explore the function of SHOOTMERISTEMLESS (STM) and ARABIDOPSIS THALIANA HOMEOBOX GENE1 (ATH1), two transcription factors in Arabidopsis thaliana that play a role in the molecular pathways that establish organ boundaries in flowers. Prior research has shownthat mutations in the STM and ATH1 genes cause defects in the boundaries formed between floral organs and the stem of the plant. My study was designed to investigate whether ATH1 and STM also control the boundaries found between adjacent floral organs. I predicted that stm ath1-3 double mutant flowers would display a significant number of stamen-stamen and …

The Construction And Characterization Of Vaccines Expressing The Pre-Membrane And Glycoprotein E Antigens Of The West Nile Virus, Ryan Johnson

Honors Theses

The West Nile Virus (WNV) is a positive polarity, single-stranded RNA virus belonging to the family Flaviviridae. In this family, there are several globally relevant human pathogens including dengue fever virus (DENV), Japanese encephalitis virus (JEV), yellow fever virus (YFV), the newly emerging Zika virus, and the West Nile Virus (WNV). WNV, like other Flaviviruses, is spread by an arthropod vector, and can cause West Nile fever and West Nile encephalitis and meningitis, and is now considered to be endemic in Africa, Asia, Europe, the Middle East, and the United States. No vaccine is currently available to prevent WNV infection, …

Development Of A Novel Salivary Cortisol Laboratory Experiment For Undergraduate Physiology Students, Charmin C. Guy

Honors Theses

Developing an endocrine-based laboratory exercise for undergraduate students is challenging because of the limitations that are characteristic of endocrine processes. These laboratory exercises often involve invasive methods and expensive biochemical analysis. They are also time consuming because of the slow-acting endocrine responses. A potential endocrine-based exercise that can be completed in 2-3 hours, is non-invasive, and at a low cost is a salivary assay. This assay is not without drawbacks, however, including sample collection outside the laboratory classroom. Cortisol is a hormone that is accessible in saliva and provides some insight into the Hypothalamic-Pituitary-Adrenal Axis (HPA Axis), also known as …

Constitutive Map-Kinase Activation Suppresses Germline Apoptosis In Nth-1 Dna Glycosylase Deficient C. Elegans, Henok Kassahun, Tamina Sengupta, Alfonso Schiavi, Suzanne Estes, Silvia Maglioni, Hanne K. Skjeldam, Katarzyna Arczewska, Nicole L. Brockway, Lars Eide, Natascia Ventura, Hilde Nilsen

Biology Faculty Publications and Presentations

Oxidation of DNA bases, an inevitable consequence of oxidative stress, requires the base excision repair (BER) pathway for repair. Caenorhabditis elegans is a well-established model to study phenotypic consequences and cellular responses to oxidative stress. To better understand how BER affects phenotypes associated with oxidative stress, we characterised the C. elegans nth-1 mutant, which lack the only DNA glycosylase dedicated to repair of oxidative DNA base damage, the NTH-1 DNA glycosylase. We show that nth-1 mutants have mitochondrial dysfunction characterised by lower mitochondrial DNA copy number, reduced mitochondrial membrane potential, and increased steady-state levels of reactive oxygen species. Consistently, nth-1 …

Jeweled Spider Flies (Eulonchus Tristis) Are Important Pollinators Of Iris Bracteata, A Rare Siskiyou Mountain Endemic, Jean-Paul E. Ponte

Cal Poly Humboldt theses and projects

Little is known about the pollination biology of the Pacific Coast Irises (Iris: series Californicae, hereafter PCI), especially who visits and pollinates their flowers. In general, Iris flowers are considered bee-pollinated, however, flies in the genus Eulonchus (Acroceridae) are known to visit some PCI members. Therefore, I assessed the relative importance of Eulonchus and other insect visitors to the pollination of a rare PCI species native to the Siskiyou Mountains, I. bracteata.

Methods. I quantified pollinator importance for all flower visitors at sites in northern California and southern Oregon as the product of average visit rate and …

Is Detection Of Preclinical Alzheimer’S Disease Possible?, Shana Brawer

The Science Journal of the Lander College of Arts and Sciences

No abstract provided.

Possible Causes Of Preeclampsia And Potential Treatments, Helene Weinreb

The Science Journal of the Lander College of Arts and Sciences

Preeclampsia is a common complication of pregnancy characterized by hypertension and proteinuria. Its symptoms are well-defined, but the pathophysiology is not fully understood. This paper analyzes several of the most credible causes of this syndrome and attempts to relate these to the known risk factors. Current preeclampsia treatments are examined, and special focus is given to novel experimental treatments which offer hope of ending preeclampsia and eclampsia.

By What Mechanism Does Stress Affect Ovulation?, Chana Minkowicz

The Science Journal of the Lander College of Arts and Sciences

This paper explores the many mechanisms of how stress influences ovulation. For ovulation to occur, there needs to be a series of hormones released in a specific order, and in a specific amount. This paper will discuss the various type of stress a person can experience, and which specific reproductive hormone each different type of stress disrupts. This paper will also bring proof as to how each hormone is disturbed, and by which mechanism it is disrupted. There has not been one main mechanism that has been found thus far, therefore, it is important to take into consideration the various …

Full Issue: Volume 12, Number 1

The Science Journal of the Lander College of Arts and Sciences

No abstract provided.

What Are The Mechanisms And Effects Of Age-Related Shortening Of The Spine?, Joseph Weingarten

The Science Journal of the Lander College of Arts and Sciences

Osteoporosis and Degenerative Disc Disease can cause a loss of height in the spine. This paper focuses on the mechanisms that cause age-related loss of height and its effects. Possible relationships between receptor activator nuclear factor kappa-B ligand (RANKL) and estrogen with osteoporosis are discussed, as well as possible genetic causes. Exercise may prevent osteoporosis. Osteoporosis may cause a loss of height, vertebral fracture, a decrease in maximum lung capacity, and hip fracture. Degenerative disc disease may cause shortening of the spine. Disc height loss can result in a reduction in the range of motion and stiffness at the affected …

Pathogenic Mechanisms Of Takotsubo Cardiomyopathy Or Broken Heart Syndrome, Devorah Leah Borisute

The Science Journal of the Lander College of Arts and Sciences

Takotsubo Cardiomyopathy (TTC) is a temporary heart-wall motion abnormality with the clinical presentation of a myocardial infarction. Found predominantly in postmenopausal women, TTC most often appears with apical ballooning and mid-ventricle hypokinesis. Often induced by an emotional or physical stress, TTC is reversible and excluded as a diagnosis in patients with acute plaque rupture and obstructive coronary disease. The transient nature and positive prognosis of this cardiomyopathy leaves a dilemma as to what precipitates it. This paper explores the theories of the pathogenesis of TTC including coronary artery spasm, microvascular dysfunction, and catecholamine excess. A thorough analysis of the pathogenesis …

New Medical Indications For Thalidomide And Its Derivatives, Chaya Newfield

The Science Journal of the Lander College of Arts and Sciences

Thalidomide is an anti-inflammatory and an anti-angiogenesis drug that is being used around the world for a variety of malignant and inflammatory diseases. Is it justified to continue prescribing and developing thalidomide given the discovery of many well-known side effects including catastrophic birth defects? To answer this question, this paper will discuss the pharmacology and history of thalidomide, as well as many of its proposed mechanisms of action.The medical indications for the current use of thalidomide as well as for several newer and more potent derivatives are mentioned for their therapeutic results, as well as their adverse side effects.

Can Somatic Cell Nuclear Transfer Produce Human Pluripotent Stem Cells For Regenerative Medicine?, Alexandra Iskhakov

The Science Journal of the Lander College of Arts and Sciences

In the last half a century, researchers and scientists discovered the application of somatic cell nuclear transfer (SCNT) to clone mammalian embryos to produce a line of pluripotent stem cells for medical and laboratory use. This is a breakthrough technology that is applied to stem cell research, regenerative medicine, and cloning. Somatic cells are non-germ cells that are differentiated but provide the nuclei that are transferred to enucleated oocytes. The replacement of the nuclei results in a developing embryo that contains the genetic information of the donated nucleus, which can either be transplanted into a surrogate mother to produce a …

Relaxin As A Cure For Fibrosis, Sarah Akilov

The Science Journal of the Lander College of Arts and Sciences

Until recently, relaxin has been known as a hormone that pertained to the female reproductive system. Its ability to remodel the extracellular matrix is responsible for its known reproductive effects. Current research has indicated that it may be useful as a drug to combat fibrosis. Relaxin has been proposed as an antifibrotic drug to target a variety of organs, including the skin, lung, kidney, liver, and heart. Studies done using the relaxin null knockout mouse have given scientists insight into the workings of this hormone. Human studies have also been done to test the efficacy of relaxin in its reversal …

Xenotransplantation:The Science, The Advantages, The Ethics, Chana Erlbaum

The Science Journal of the Lander College of Arts and Sciences

Xenotransplantation is a breakthrough medicinal technology that is an attempt to change the lives of millions of people. The problems in the current organ transplant system risk the lives of patients each and every day. Intense waiting periods and extremely costly procedures exemplify the stress and pressure that these patients face as an attempt to save their own lives. Xenotransplantation is the idea of growing human organs in a different species, using incredible stem-cell and CRISPR technology. This can introduce an answer to some of the issues in the current transplant system. Many technical and ethical issues are becoming relevant …

Music And The Brain, Maddie Nierman

The Science Journal of the Lander College of Arts and Sciences

Music is an important part of cultures worldwide. It has been used throughout the ages as a method of conveying emotions to the listener. However, there is some confusion about exactly which areas of the brain are affected by music. This study shows the general areas of the brain stimulated by music, explaining how these sections influence emotion and learning capability. In addition, this paper demonstrates that music therapy may be helpful in relieving stress or some neurological disorders, based on the areas activated by music. Training in music has cognitive and motor coordination benefits, as well, because this training …

The Potential Of Cold Plasma For Safe And Sustainable Food Production, Paula Bourke, Dana Ziuzina, Daniela Boehm, Patrick J. Cullen, Kevin Keener

Articles

In-package decontamination of foods using cold plasma has advanced this technology as a unit process for fresh foods decontamination and shelf-life extension.

Chemical residues of agricultural pesticides of varying structure can be degraded to safe or less-toxic structures using cold plasma.

Cold-plasma-mediated control of contaminants, along with the promotion of seed germination and plant growth, offers alternatives to current pesticides and fertilizers for agriculture.

Controlling plasma reactive species formulations in dry and liquid delivery formats advances the potential for understanding and successful translation to multiple points along the agriculture and food sectors.

Employing predictive microbiology, process optimization tools and a …

Microbial Community Response To Light And Heavy Crude Oil In Freshwater Systems, Timothy M. Butler

Dissertations, Master's Theses and Master's Reports

With increased demand for oil, there is an increased risk for oil spills in many environments. A number of pipelines transport oil near or across freshwater systems including the Great Lakes. Microbes are capable of breaking down oil and have thus been proposed as tools for oil spill response through bioremediation. There is a need to understand the microbial response to diverse oil types in freshwater environments due to the lack of research into this topic. This study’s main objectives are to understand how the freshwater microbial communities respond to oil, and how the bacterial communities may respond to different …

Combined Extract Of Moringa Oleifera And Centella Asiatica Modulates Oxidative Stress And Senescence In Hydrogen Peroxide-Induced Human Dermal Fibroblasts, Elly Ezlinda Abdul Hisam, Mohd Salleh Rofiee, Aina Mardhia Khalid, Ahmad Firdaus Jalaluddin, Mohd Izwan Muhammad Yusof, Muhd Hanis Idris, Salfarina Ramli, Richard Johari James, Wee Jack Yoeng, Teh Lay Kek, Mohd Zaki Salleh

Turkish Journal of Biology

Moringa oleifera Lam. and Centella asiatica (L.) Urb. leaves have been previously reported to exhibit antioxidant activity. The objective of the present study is to determine the in vitro antioxidant activity of the combined extracts of M. oleifera and C. asiatica (TGT-PRIMAAGE) and its effect on hydrogen peroxide (H$_{2}$O$_{2}$)-induced oxidative stress in human dermal fibroblasts. TGT-PRIMAAGE acted on the mechanism of hydrogen transfer as it showed scavenging activity in the DPPH assay. This is due to the presence of phenolics and flavonoids in TGT-PRIMAAGE. TGT-PRIMAAGE effectively reduced cellular generation of reactive oxygen species induced by H$_{2}$O$_{2}$. The activities of superoxide …

Crm1 Knockdown By Specific Small Interfering Rna Reduces Cell Proliferation And Induces Apoptosis In Head And Neck Cancer Cell Lines, Si̇bel Özdaş, Tali̇h Özdaş

Turkish Journal of Biology

Head and neck squamous cell carcinoma (HNSCC) is the most common and most aggressive type of head and neck cancer. Current approaches for the treatment of HNSCC are not sufficient to increase the patient survival or to reduce the high recurrence rate. Consequently, there is a need to explore the molecular characteristics of this cancer in order to discover potential therapeutic target molecules. The overexpression of chromosome region maintenance 1 (Crm1), responsible for the transport of different classes of macromolecules from the nuclear membrane to the cytoplasm, in various cancer cells has made it an attractive target molecule in cancer …

Journey To The Center Of The Protein: Allostery From Multitemperature Multiconformer X-Ray Crystallography, Daniel A. Keedy

Advanced Science Research Center

Proteins inherently fluctuate between conformations to perform functions in the cell. For example, they sample product-binding, transition-state-stabilizing and product-release states during catalysis, and they integrate signals from remote regions of the structure for allosteric regulation. However, there is a lack of understanding of how these dynamic processes occur at the basic atomic level. This gap can be at least partially addressed by combining variable-temperature (instead of traditional cryogenic temperature) X-ray crystallography with algorithms for modeling alternative conformations based on electron-density maps, in an approach called multitemperature multiconformer X-ray crystallography (MMX). Here, the use of MMX to reveal alternative conformations at …

Quantitative Acoustic Differentiation Of Cryptic Species Illustrated With King And Clapper Rails, Lydia L. Stiffler, Katie M. Schroeder, James T. Anderson, Susan B. Mcrae, Todd E. Katzner

Faculty & Staff Scholarship

Reliable species identification is vital for survey and monitoring programs. Recently, the development of digital technology for recording and analyzing vocalizations has assisted in acoustic surveying for cryptic, rare, or elusive species. However, the quan- titative tools that exist for species differentiation are still being refined. Using vocali- zations recorded in the course of ecological studies of a King Rail (Rallus elegans) and a Clapper Rail (Rallus crepitans) population, we assessed the accuracy and effective- ness of three parametric (logistic regression, discriminant function analysis, quadratic discriminant function analysis) and six nonparametric (support vector machine, CART, Random Forest, k-nearest neighbor, weighted …

Parasitaemia Data And Molecular Characterization Of Haemoproteus Catharti From New World Vultures (Cathartidae) Reveals A Novel Clade Of Haemosporida, Michael J. Yabsley, Ralph E.T. Vanstreels, Ellen S. Martinsen, Alexandra G. Wickson, Amanda E. Holland, Sonia M. Hernandez, Alec T. Thompson, Susan L. Perkins, Christopher A. Lawrence Bryan, Christopher A. Cleveland, Emily Jolly, Justin D. Brown, Dave Mcruer, Shannon Behmke, James C. Beasley

Faculty & Staff Scholarship

Background: New World vultures (Cathartiformes: Cathartidae) are obligate scavengers comprised of seven species in five genera throughout the Americas. Of these, turkey vultures (Cathartes aura) and black vultures (Coragyps atratus) are the most widespread and, although ecologically similar, have evolved differences in morphology, physiology, and behaviour. Three species of haemosporidians have been reported in New World vultures to date: Haemoproteus catharti, Leucocytozoon toddi and Plasmodium elongatum, although few studies have investigated haemosporidian parasites in this important group of species. In this study, morphological and molecular methods were used to investi- gate the epidemiology and molecular biology of haemosporidian parasites of …

The Effects Of Aqueous Nitrate On Freshwater Crayfish, Erik Hartman

Williams Honors College, Honors Research Projects

Globalization and a rising need for greater production from the agricultural system have increased the use of fertilizer by farms across the entire country. The purpose of this experiment was to observe the effects of aqueous nitrate (commonly found in many fertilizers) on the metabolic rate and hemolymph lactate concentration of freshwater crayfish. After exposure, there was no observed change in metabolic rate, but there was a significant decrease in hemolymph lactate concentration in the groups exposed to nitrate.

Quantifying Cortical And Cancellous Bone Volume: A Computed Tomography Approach, Hannah Rutkowski

Williams Honors College, Honors Research Projects

Human identification primarily uses long bones of the body such as femora and tibiae which have a high cortical bone amount, these are thought to contain the highest amount of DNA. However, current research shows this is not the case, cancellous bone could contain more DNA in the porous spaces than dense cortical bone. This study aims to measure the variation in the amount of cortical and cancellous bone taken from sampling sites of seven individuals from ten different skeletal elements: femur, tibia, middle rib, calcaneus, first cuneiform, patella, third metacarpal, third metatarsal, first distal phalanx, and cervical vertebra. This …