Biology Commons^™

Selective Mutation Accumulation: A Computational Model Of The Paternal Age Effect, Eoin C. Whelan, Alexander C. Nwala, Christopher Osgood, Stephan Olariu

Biological Sciences Faculty Publications

Motivation: As the mean age of parenthood grows, the effect of parental age on genetic disease and child health becomes ever more important. A number of autosomal dominant disorders show a dramatic paternal age effect due to selfish mutations: substitutions that grant spermatogonial stem cells (SSCs) a selective advantage in the testes of the father, but have a deleterious effect in offspring. In this paper we present a computational technique to model the SSC niche in order to examine the phenomenon and draw conclusions across different genes and disorders.

Results: We used a Markov chain to model the probabilities of …

Tick Genome Assembled: New Opportunities For Research On Tick-Host-Pathogen Interactions, Jose De La Fuente, Robert M. Waterhouse, Daniel E. Sonenshine, R. Michael Roe, Jose M. Ribeiro, David B. Sattelle, Catherine A. Hill

Biological Sciences Faculty Publications

As tick-borne diseases are on the rise, an international effort resulted in the sequence and assembly of the first genome of a tick vector. This result promotes research on comparative, functional and evolutionary genomics and the study of tick-host-pathogen interactions to improve human, animal and ecosystem health on a global scale.

Geospatial Approaches To Support Pelagic Conservation Planning And Adaptive Management, L. M. Wedding, Sara M. Maxwell, D. Hyrenbach, D. C. Dunn, J. J. Roberts, D. Briscoe, E. Hines, P. N. Halpin

Biological Sciences Faculty Publications

Place-based management in the open ocean faces unique challenges in delineating boundaries around temporally and spatially dynamic systems that span broad geographic scales and multiple management jurisdictions, especially in the 'high seas'. Geospatial technologies are critical for the successful design of pelagic conservation areas, because they provide information on the spatially and temporally dynamic oceanographic features responsible for driving species distribution and abundance in the open ocean, the movements of protected species, and the spatial patterns of distribution of potential threats. Nevertheless, there are major challenges to implementing these geospatial approaches in the open ocean. This Theme Section seeks to …

A Novel Method Of Microsatellite Genotyping-By-Sequencing Using Individual Combinatorial Barcoding, Salla Vartia, Jose L. Villanueva-Cañas, John Finarelli, Edward D. Farrell, Patrick C. Collins, Graham M. Hughes, Jeanette E.L. Carlson, David T. Gauthier, Philip Mcginnity, Thomas F. Cross, Richard D. Fitzgerald, Luca Mirimin, Fiona Crispie, Paul D. Cotter, Jens Carlsson

Biological Sciences Faculty Publications

This study examines the potential of next-generation sequencing based 'genotyping-by-sequencing' (GBS) of microsatellite loci for rapid and cost-effective genotyping in large-scale population genetic studies. The recovery of individual genotypes from large sequence pools was achieved by PCR-incorporated combinatorial barcoding using universal primers. Three experimental conditions were employed to explore the possibility of using this approach with existing and novel multiplex marker panels and weighted amplicon mixture. The GBS approach was validated against microsatellite data generated by capillary electrophoresis. GBS allows access to the underlying nucleotide sequences that can reveal homoplasy, even in large datasets and facilitates cross laboratory transfer. GBS …

A Missing Link In The Ionoregulatory Strategy Of Larval Sea Lamprey (Petromyzon Marinus) And African Lungfish (Protopterus Annectens): A Closer Look Into The Role Of The Non-Gastric H+/K+-Atpase, Justine E. Doherty

Theses and Dissertations (Comprehensive)

Fishes living in freshwater need to actively compensate for the diffusive loss of ions and osmotic gain of water. The gill is the primary organ of ion regulation and contains an array of ion transport proteins to help maintain homeostasis. Two of the more well studied ion pumps are the Na⁺/K⁺-ATPase (NKA) and vacuolar type proton ATPase (V-ATPase). This thesis focuses on another ion pump known as the non-gastric H⁺/K⁺-ATPase (ngHKA). The ngHKA (gene: atp12a) has not been found in any of the teleost fishes, indicating loss from that lineage. In …

Depth And Development Of The Sonic System In Deep-Sea Macrourid Fishes On The Continental Slope, Jonothan Wrenn

Theses and Dissertations

Work on sound production of deep-sea fishes has been limited to anatomy, and no sounds from identified species have been recorded on the continental slope. Here I examined the sonic muscles of six species in the family Macrouridae by depth (Coelorhincus carminatus, Nezumia bairdii, Coryphaenoides rupestris, Nezumia equalis, Coryphaenoides armatus, Coryphaenoides carapinus,). Due to increasingly limited food with depth, I hypothesized that sonic muscle development would decrease with depth. Sonic muscles were intrinsic and occurred in males and females. Swimbladder and sonic muscle dimensions increased linearly with fish size, but there were no clear differences with depth suggesting …

Seasonal Variation Of Fish And Macroinvertebrate Biomass Spectra In Southern West Virginia Streams, Andrew J. Kirk

Theses and Dissertations

The biomass size spectrum - the power-law scaling relationship between average individual size and total biomass - has often been studied in lake and marine ecosystems, but rarely in lotic systems. The objective of this study was to test for characteristic biomass spectra in small temperate streams. Seasonal fish and macroinvertebrate data, including population abundance and biomass estimates, were collected in three wadeable, southern West Virginia streams from October 2013 to May 2015. Fish abundances were estimated with 3-pass electrofishing (depletion) surveys and individuals were weighed in the field. Macroinvertebrates were collected with a Hess sampler and returned to the …

Roles Of Planar Cell Polarity Proteins In Copa Axon Pathfinding, Ashley Morgan Purdy

Theses and Dissertations

In zebrafish, CoPA (Commissural Primary Ascending) is the first among ascending commissural axons to pathfind anteriorly and form the spinal commissure. One pathway that guides their anterior growth is the planar cell polarity (PCP) signaling pathway, but it is not fully known how PCP signaling regulates anterior guidance. We examined CoPA pathfinding in various PCP mutants to determine if anterior-posterior (A-P) guidance of CoPAs is dependent on PCP signaling. We found that certain PCP mutants exhibited anterior pathfinding defects, with approximately half of all affected CoPAs migrating incorrectly posteriorly. By using a translation-blocking DCC (Deleted in …

Evaluation Of Redox Potential As A Novel Biomarker Of Oxidative Stress, Inflammatory Response, And Shock Using Nanoporous Gold Electrodes, Matthew C. Ellenberg

Theses and Dissertations

EVALUATION OF REDOX POTENTIAL AS A NOVEL BIOMARKER OF OXIDATIVE STRESS, INFLAMMATORY RESPONSE, AND SHOCK USING NANOPOROUS GOLD ELECTRODES

Background: Redox potential is a chemical species’ affinity for electrons. Increased oxidant concentration is associated with disease1,2, yet there is not a way to measure systemic redox status.3 Redox potentiometry uses metal electrodes that do not work in blood because protein molecules adhere on the metal surface, blocking electron exchange.

Methods: Nanoporous gold electrodes have large surface areas that allowed electron exchange to continue in blood.4 Redox potential was measured in blood with ascorbic acid, in cardiac bypass patients and pigs …

Plant Functional Trait And Hyperspectral Reflectance Responses To Comp B Exposure: Efficacy Of Plants As Landmine Detectors, Paul V. Manley Ii

Theses and Dissertations

At least 110 million landmines have been planted since the 1970s in about 70 nations, many of which remain in place today. Some risk of detection may be mitigated using currently available remote sensing techniques when vegetation is present. My study focused on using plants as phytosensors to detect buried explosives. I exposed three species representing different functional types (Cyperus esculentus (sedge), Ulmus alata (tree), Vitis labrusca (vine)) to 500 mg kg^-1 of Composition B (Comp B; 60/40 mixture of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) and 2,4,6-trinitrotoluene (TNT)), a commonly used explosive mixture, and measured functional traits and reflectance over …

The Effect Of Depth On Development And Sexual Dimorphism Of The Sonic System In Deep Sea Neobythitine Fishes: The Upper Continental Slope, Heba Ali

Theses and Dissertations

Abstract

Background: Cusk-eels from the subfamily Neobythiitinae are one of the major groups of sound-producing fishes on the continental slope. Sounds have never been recorded from a member of this subfamily, and sonic anatomy is considered a proxy for sound production. As the first part of a study on the effects of depth on sonic anatomy, we examined three relatively shallow species from the upper continental slope.

Methods: Three species (Hoplobrotula armata, Neobythites longipes and Neobythites unimaculatus) were examined for sonic anatomy (skeleton, swimbladder and sonic muscles), and sonic and epaxial muscle fibers were measured for diameter. …

Current Status Of Stem Cell Therapy: Opportunities And Limitations, Elena Rusu, Laura Georgiana Necula, Ana Iulia Neagu, Mihail Alecu, Cristian Stan, Radu Albulescu, Cristiana Pistol Tanase

Turkish Journal of Biology

Over recent years stem cells have stood out as a promising tool for regenerative medicine, providing alternative therapeutic solutions for a large number of diseases. Many clinical trials using stem cells or induced pluripotent stem cells are focused on the repair and regeneration of various tissues and organs in degenerative diseases, whose current treatment only succeeds in slowing down the progression of the disease. Although the preliminary results are interesting, further studies are required in order to evaluate the safety and benefits of stem cell therapy, considering the teratoma development and ethical considerations in embryonic stem cell cases or reprogramming-induced …

The Heart Of The Matter: Cardiac Stem Cells, Esra Çağavi̇, Arzuhan Koç, Sevi̇lay Şahoğlu Göktaş

Turkish Journal of Biology

Cardiovascular diseases are the primary cause of death in the world. Pharmacological and surgical approaches are the main treatment options for heart disease; however, heart transplantation may be the only option for advanced heart failure patients despite its limited nature. Recent advances enabled stem cell-based therapies to become a promising treatment approach for injured or weakened cardiac tissue. With the identification of resident and heart-specific stem cells in early 2000, new avenues of research have been opened to understand heart development, disease, and regeneration. In this review article, different cardiac stem cell subpopulations are classified and defined based on the …

Glioblastoma Stem Cells: A Therapeutic Challenge, Erdoğan Pekcan Erkan, Ufuk Vurgun, Reşat Serhat Erbayraktar, Zübeyde Erbayraktar

Turkish Journal of Biology

The outcome for glioblastoma patients remains extremely poor, despite the advances in surgical and medical fields. It is hypothesized that glioblastoma progression, as well as tumor recurrence, is driven by a small number of cells called cancer stem cells (CSCs), which are characterized by their ability of self-renewal and proliferation, giving rise to progeny of transformation into multiple neuroepithelial lineages. Understanding the biology of CSCs is likely to explain why existing treatment strategies fail to affect the relatively quiescent and resistant CSC compartment. Here, we review the current knowledge on CSCs in glial tumors. In addition, we discuss the importance …

Induced Pluripotent Stem Cells: Methods, Disease Modeling, And Microenvironment For Drug Discovery And Screening, Suresh Palamadai Krishnan

Turkish Journal of Biology

The raging ethical, religious, moral, political, and safety issues pertaining to the use of embryonic stem cells for therapy and research have prompted researchers to develop possibly better alternatives that are more efficacious and serve multiple purposes. Induced pluripotent stem cells (iPSCs) developed by multiple methods provide an unparalleled source of cells that could be differentiated into progeny cells. In cell-based disease models the progeny cells mimic, at least in part, the pathology of the studied disease and are used to improve the mechanistic understanding of the pathology. Furthermore, these cells could be used to test the efficacy and safety …

Cancer Stem Cells: Lessons Learned From The Leukemic Stem Cells, Ayten Kandi̇lci̇

Turkish Journal of Biology

Cancer is the second cause of death in Turkey and the frequency of cancer deaths increased from 12% in 2002 to 21% in 2009 ( Özkan et al., 2013). To win the war on cancer, we certainly need to apply well-planned prevention policies, given that it is caused mostly by environmental factors, and to develop more effective therapies. To achieve a cure for the disease, it is crucial to understand the cellular and molecular mechanisms leading to cancer and to therapeutically target all the factors playing a role in the initiation, progression, maintenance, and relapse of the disease, preferably in …

Epigenetics: The Guardian Of Pluripotency And Differentiation, Marta Gladych, Aleksandra Nijak, Paula Lota, Urszula Oleksiewicz

Turkish Journal of Biology

Multicellular organisms comprise a variety of cell types that have the same genotype but distinct phenotypes. This diversity is possible because of the establishment of a specific epigenetic landscape that stabilizes gene expression profiles that are exclusive for a particular cell type. Accumulating data indicate that the maintenance, loss, and reacquisition of pluripotency are dynamically regulated by epigenetic alterations evoked by a subset of cellular factors. A better understanding of the epigenetic mechanisms involved in stem cell biology and differentiation will improve our ability to use these cells in the clinical context. Here we review current insights into the epigenetic …

Epigenetic Regulation Of Specific Transcription Factors In Osteogenicdifferentiation Of Mesenchymal Stem Cells, Milad Zadi Heydarabad, Mousa Vatanmakanian, Mina Nikasa, Majid Farshdousti Hagh

Turkish Journal of Biology

An abundance of experiments have been performed to clarify the differentiation process of mesenchymal stem cells (MSCs). Osteogenic differentiation and in vitro conditions favoring these cell lineages have attracted the attention of many researchers. Moreover, the gene expression profile during MSC differentiation toward its main specialized cells (bone, cartilage, and adipose cells) has been mostly understood. In the last decades another layer of investigation has attempted to clarify the epigenetic mechanisms underlying MSC differentiation into its specialized cells. It has been shown that as MSCs progress through the differentiation process, more nonspecific genes undergo DNA methylation to prevent differentiation into …

Human Embryonic Stem Cell N-Glycan Features Relevant To Pluripotency, Sabi̇re Karaçali

Turkish Journal of Biology

Human embryonic stem cells (hESCs) and reprogrammed human induced pluripotent stem cells (hiPSCs) proliferate indefinitely in the undifferentiated state (self-renewal) and differentiate into the three germ layers (and ultimately into all cell types) (pluripotency). Branching in the N-glycan core of hESCs/hiPSCs is limited. hESCs/hiPSCs have high mannose-type and biantennary complex-type core structures, indicating immature stages of N-glycoproteins. The two branches on the core consist of type 2 N-acetyllactosamine (LacNAc), completed mainly with α 2,6-linked sialic acid. Complex terminal fucosylation, particularly α 1,2-linked fucosylation, is another characteristic N-glycosylation feature of hESCs/hiPSCs. All of these structural features are probably associated with the …

Limbal Stem Cell Deficiency: Special Focus On Tracking Limbal Stem Cells, Santhosh Kacham, Bhaskar Birru, Sreenivasa Rao Parcha, Ramaraju Baadhe

Turkish Journal of Biology

The cornea, the transparent part of the eye that helps in the formation of images, has multiple layers. Among them, the superficial epithelial layer is protected and maintained homeostatically by the limbus, located in the periphery of the cornea. Limbal stem cells are located at the basal layer of the limbus and the loss of these cells is called limbal stem cell deficiency (LSCD). LSCD is characterized by corneal vascularization, inflammation, and conjunctivalization, which ultimately lead to blindness. Several clinical transplantation procedures used for the treatment of LSCD are cultivated limbal epithelial transplantation, simple limbal epithelial transplantation, and cultured oral …

Comparison Of The Osteogenic Differentiation Capacity Of Adipose Tissuederived Mesenchymal Stem Cells From Humans And Rats, Seçi̇l Erden Tayhan, Şeyma Taşdemi̇r, Sai̇me İsmet Deli̇loğlu Gürhan, Erol Mi̇r

Turkish Journal of Biology

Mesenchymal stem cells (MSCs) can be found in many types of adult tissues such as the bone marrow, adipose, placenta, liver, and periosteum. Recently, adipose tissue-derived MSCs (ADMSCs) have become one the most preferred MSC types because of their fast proliferation rate, abundance, and high plasticity for variable cell types. It is known that ADMSCs are able to differentiate into various cells, including osteoblasts, so they are quite promising for orthopedic clinical trials. The present study aimed to compare the osteogenic differentiation conditions of MSCs from human adipose tissue (hADMSC) and those of MSCs from rat adipose tissue (rADMSC). Therefore, …

Analysis Of Global Micrornaome Profiles Of Caenorhabditis Elegans Oocytes And Early Embryos, Selen Güçlü Durgun, Ahmet Raşi̇t Öztürk, Arzu Atalay

Turkish Journal of Biology

One of the most complex cell transformations in biology is the remodeling of a fertilized oocyte into a totipotent zygote. There is no transcription during this event, and therefore mRNAs and proteins accumulated in the oocyte during oogenesis are utilized until zygotic genome activation. In order to differentiate into somatic cells, the embryo must erase the totipotency signature coming from the oocyte cytoplasm in the somatic blastomeres. In this study, the microRNAome profiles of oocytes and early embryos before and after zygotic genome activation were identified. By using next-generation high-throughput pyrosequencing and miRNA microarray techniques, miRNAome profiles of Caenorhabditis elegans …

Human Adipose-Derived Stem Cells Differentiation Into Epidermal Cells And Interaction With Human Keratinocytes In Coculture, Alexandra Gaspar, Daniel Constantin, Ana-Maria Seciu, Lucia Moldovan, Oana Craciunescu, Elena Ganea

Turkish Journal of Biology

Current procedures used for skin injury reepithelization have yet to improve. At present, stem cell-based therapies provide great potential in repairing different damaged tissues due to the multipotent character of these cells. This study aimed to investigate the in vitro differentiation capacity of human adipose-derived stem cells (ASCs) into epidermal cells and to evaluate their interaction with HaCaT keratinocytes in coculture experimental models that mimicked the living environment of human skin. The mesenchymal phenotype of isolated stem cells was indicated by their spindle-shaped morphology and the expression of specific surface markers CD73, CD90, and CD105. After 21 days of cultivation …

Baculoviral Vector Loaded Mesenchymal Stem Cells As Efficient Gene Therapy Tools For Cancer Treatment, Sedef Hande Aktaş, Hakan Akbulut, Ayşe Eser Elçi̇n, Mahmut Parmaksiz, Arzu Keski̇n Aktan, Arzu Çöleri̇ Ci̇han, Yaşar Murat Elçi̇n, Fi̇kri̇ İçli̇

Turkish Journal of Biology

Insufficient targeting of the therapeutic genes to tumor cells is one of the major reasons for failure in cancer gene therapy. Mesenchymal stem cells (MSCs) seem to be a good candidate as a carrier for gene therapy because of its selective tumor tissue-homing properties. In the current study, we constructed baculoviral vectors (BVs) carrying cytosine deaminase (CD) (BV-CD) or green fluorescence protein (GFP) genes (BV-GFP) and tested the transduction efficiency of the vectors in tumor and mesenchymal stem cells. We also tested the in vivo efficacy of the BV-CD vector in a colon cancer model. Our results showed that the …

Weighing The Relative Potential Impacts Of Climate Change And Land-Use Change On An Endangered Bird, Betsy A. Bancroft, Joshua J. Lawler, Nathan H. Schumaker

Biology Faculty Scholarship

Climate change and land-use change are projected to be the two greatest drivers of biodiversity loss over the coming century. Land-use change has resulted in extensive habitat loss for many species. Likewise, climate change has affected many species resulting in range shifts, changes in phenology, and altered interactions. We used a spatially explicit, individual-based model to explore the effects of land-use change and climate change on a population of the endangered Red-cockaded Woodpecker (RCW; Picoides borealis). We modeled the effects of land-use change using multiple scenarios representing different spatial arrangements of new training areas for troops across Fort Benning. …

Rt-Qpcr Demonstrates Light-Dependent Atrbcs1a And Atrbcs3b Mrna Expressions In Arabidopsis Thaliana Leaves, Ming-Mei Chang, Anna Li, Robert Feissner, Talal Ahmad

Biology

Reverse transcription quantitative polymerase chain reaction (RT-qPCR) is widely used in diagnosis and research to determine specific mRNA expressions in cells. As RT-qPCR applications increase, it’s necessary to provide undergraduates hands-on experience of this modern technique. Here, we report a 3-week laboratory exercise using RT-qPCR to demonstrate the light-dependent expressions of AtRBCS1A and AtRBCS3B genes encoding two Arabidopsis thaliana small subunits of the ribulose 1,5-bisphosphate carboxylase/ oxygenase (Rubisco). In the first week, students purified and quantified total RNA from leaves of A. thaliana pretreated in the dark for 96 hr and untreated controls. In the second week, RNA samples were …

Expression And Function Of A Putative Cox-Like Gene In D. Melanogaster, Michelle S. Batchu

Dissertations and Theses

Cyclooxygenases (COX) are the enzymes that catalyze the conversion of arachidonic acid into prostaglandins. In mammals, isoform COX-1 is constitutively expressed, whereas the isoform COX-2 gene expression is induced, primarily at sites of inflammation. While eicosanoids play a major role in inflammation in insects, their existence in fruit flies has not been reported. Recent computational analyses by Qi and Singh (2014) have identified putative COX-like enzymes in the fruit fly Drosophila melanogaster. Here we compare the expression patterns of these enzymes and the effects of their knockdown in immune cells of D. melanogaster third instar larvae. Because of high genetic …

"Molecular Analysis Of Virulence Factors Unique To Leptopilina Heterotoma-A Parasitic Wasp Of Drosophila Spp.", Noelle Dziedzic

Dissertations and Theses

Endoparasitioid wasps of Drosophila spp. frequently avoid or overcome the immune defense mechanisms of their fly hosts. Leptopilina heterotoma (Lh) is a generalist wasp species, successful on many Drosophila spp. world-wide. During oviposition, the female wasp introduces venom proteins and virus-like particles (VLPs) into developing fly larvae. VLPs are endocytosed by plasmatocytes, a macrophage-like blood cell that is the most abundant hemocyte present in the circulating hemolymph. Once internalized, VLPs destroy plasmatocytes by programmed cell death. To understand the contributions of VLP proteins in VLP trafficking within host cells, we took advantage of proteomic data from purified Lh VLPs. Two …

Revised Distributional Estimates For The Recently Discovered Olinguito (Bassaricyon Neblina), Using Museum And Science Records, Beth E. Gerstner

Dissertations and Theses

In the context of global change, a necessary first step for the conservation of species is gaining a good understanding of their distributional limits. This is especially important for biodiversity hotspots with high endemism such as the Northern Andes. The olinguito (Procyonidae: Bassaricyon neblina) is a recently described, medium-sized carnivoran found in Northern Andean cloud forests. A preliminary distributional model was published along with the original description, and I here provide revised distributional estimates using updated locality records and more current ENM methods. I build ecological niche models in Maxent using occurrence data (georeferenced museum records and citizen science-derived photo-vouchers) …

Evaluating The Evolutionary And Genetic Relationships Of The Andean Orchids Of Northwestern Ecuador, Kylie Bucalo

Theses and Dissertations

DNA barcoding is a molecular based technique used to separate and identify individual species. Here we establish a DNA Barcode library for the orchid flora of an Andean cloud forest in Northwestern Ecuador. The library contains 135 matK and 136 rbcL DNA Barcodes representing over 33 Orchidaceae genera. Sequence analysis shows percent species resolution was higher for matK (98.8%) than rbcL (70.24%), with a large portion of the unresolved species for the rbcL loci coming from taxonomically complex genera in the subtribe Pleurothallidinae. Neighbor Joining (NJ) trees revealed that the orchid flora of Siempre Verde is divided taxonomically into …