Biology Commons^™

Waracs: Wrappers To Automate The Reconstruction Of Ancestral Character States, Michael Gruenstaeudl

Biological Sciences Faculty Publications

Premise of the study: Reconstructions of ancestral character states are among the most widely used analyses for evaluating the morphological, cytological, or ecological evolution of an organismic lineage. The software application Mesquite remains the most popular application for such reconstructions among plant scientists, even though its support for automating complex analyses is limited. A software tool is needed that automates the reconstruction and visualization of ancestral character states with Mesquite and similar applications. Methods and Results: A set of command line–based Python scripts was developed that (a) communicates standardized input to and output from the software applications Mesquite, BayesTraits, and …

The Importance Of Having Two X Chromosomes, Jenny Link, Arthur P. Arnold, Karen Reue, Mansoureh Eghbali, Eric Vilain, Xuqi Chen, Negar Ghahramani, Yuichiro Itoh, Jingyuan Li, Tuck Ngun, Shayna M. Williams-Burris

Biology

Historically, it was thought that the number of X chromosomes plays little role in causing sex differences in traits. Recently, selected mouse models have been used increasingly to compare mice with the same type of gonad but with one versus two copies of the X chromosome. Study of these models demonstrates that mice with one X chromosome can be strikingly different from those with two X chromosomes, when the differences are not attributable to confounding group differences in gonadal hormones. The number of X chromosomes affects adiposity and metabolic disease, cardiovascular ischaemia/reperfusion injury and behaviour. The effects of X chromosome …

Role Of Soil Texture, Clay Mineralogy, Location, And Temperature In Coarse Wood Decomposition—A Mesocosm Experiment, Cinzia Fissore, Martin F. Jurgensen, James Pickens, Chris Miller, Deborah Page-Dumroese, Christian P. Giardina

Environmental Science

Of all the major pools of terrestrial carbon (C), the dynamics of coarse woody debris (CWD) are the least understood. In contrast to soils and living vegetation, the study of CWD has rarely relied on ex situ methods for elaborating controls on decomposition rates. In this study, we report on a mesocosm incubation experiment examining how clay amount (8%, 16%, and 24% clay), clay type (soil reconstructed with kaolinite vs. montmorillonite), wood placement (on litter layer surface, at the litter layer–soil interface, buried in the mineral soil), and laboratory incubation temperature (10°, 20°, or 30°C) control decomposition rates of highly …

Development Of Elisa Assay For D1327 Adenovirus, Christopher Peterson, Yohichi Kumaki, Dale L. Barnard

Biology Posters

Adenoviruses are a common cause of upper respiratory tract infections in children and the source of acute respiratory disease outbreaks among military recruits. Named after the human adenoid tissue it was first isolated in, the adenoviridae are non-enveloped, double-stranded DNA viruses with over 50 serotypes1. Yet to date vaccines have been developed for only two serotypes, and no adenovirus antiviral drugs have been approved by the FDA, highlighting the need for more research. In virus research, detection the presence of a particular virus is of especial interest when developing animal or cell models. As human pathogens often do not infect …

The Identification And Characterization Of Bacterial Endosymbionts In The Planthopper Family, Caliscelidae (Sternorrhyncha: Fulgoroidea, Ghazal Abu-Salim, Kathryn Weglarz

Biology Posters

Plant-sap sucking insects with deficient nutritional diets contain symbiotic microorganisms in a specific organ in the abdomen (bacteriome). Such symbionts were discovered to belong to various bacterial lineages. Ongoing genomic research concluded that these symbiotic organisms provide the essential nutrients that are absent in the insect’s diets such as amino acids and vitamins. While the identities and functions of several sap-sucking lineages have been studied, some lineages such as Fulgoroidea are not understood because recent results failed to confirm the presence of the symbiotic microbes even though older microscopy studies identified microbes in the bacteriomes. The objective of this research …

Effects Of Amniotic Fluid Mesenchymal Stem Cells In Carboxymethyl Cellulosegel On Healing Of Spontaneous Pressure Sores: Clinical Outcome In Sevenhospitalized Neonatal Foals, Eleonora Iacono, Aliai Lanci, Barbara Merlo, Francesca Ricci, Alessandro Pirrone, Carlotta Antonelli, Jole Mariella, Carolina Castagnetti

Turkish Journal of Biology

In the present study, an innovative therapy for spontaneously arisen pressure sores in seven hospitalized neonatal foals is described, using mesenchymal stem cells obtained from equine amniotic fluid. Amniotic fluid mesenchymal stem cells (AFMSCs) were isolated from fluid samples recovered at delivery. Heterologous cells, at passage three of in vitro culture, were applied to sores twice a week for four consecutive times in a carboxymethylcellulose (CMC) gel. As a control, a commercial ointment was used. The results showed that the mean sore regression rate with AFMSCs in CMC gel was statistically higher than the mean value recorded in the control …

Direct Shoot Organogenesis And Agrobacterium Tumefaciens Mediated Transformation Of Solanum Trilobatum L., Jayabalan Shilpha, Manoharan Jayashre, Muthiah Joe Virgin Largia, Manikandan Ramesh

Turkish Journal of Biology

Solanum trilobatum L. İs one of the most valued medicinal plants of Indian Ayurveda and Siddha medicine. An efficient protocol for direct shoot organogenesis and Agrobacterium tumefaciens mediated transformation using in vitro derived leaf explants of S. Trilobatum was established for the first time. High frequency direct shoot regeneration (89%) was achieved in MS medium containing 2 mg/L 6-benzylaminopurine and 0.25 mg/L indole-3-acetic acid. The Agrobacterium strain EHA 105 harboring the binary vector pCAMBIA 1301, which contained hygromycin phosphotransferase (hpt) as a selectable marker gene and β-glucuronidase (gus) as a reporter gene, was used for the transformation. The factors that …

Analysis Of Rocky Mountain Snail (Oreohelix Sp.) Dietary Preference, Michael R. Bernard, Joseph S. Wilson

Biology Posters

Rocky Mountain snails in the genus Oreohelix go mostly unnoticed beneath layers of leaf litter in the western Mountain ranges. These snails are most common in rocky foothill habitat that consists of high-density deciduous groves of maple and oak. It is in this habitat where a great number of unobserved feeding behaviors occur. While some research indicates that terrestrial snails may prefer to feed on living plants, it is thought that Oreohelix are detritivores, feeding primarily on decomposing plant matter. In this study we investigated Oreohelix diet by designing a food preference experiment. We provided two food sources (Boxelder maple …

Use Of A Mouse Model To Evaluate The Effect Of Statins On The Immune Response To An Influenza Virus Vaccine, Calvin Olsen, Bart Tarbet

Biology Posters

Statins are cholesterol lowering drugs that have shown a profound effect on human health by reducing cardiovascular disease. However, two recent publications in the Journal of Infectious Diseases showed that statin use had a negative impact on the influenza vaccine response in elderly individuals [1, 2]. We propose to evaluate the immune response following vaccination in mice undergoing statin treatment. An initial study will determine the therapeutic window for statin treatment of mice fed a lipid-enriched diet. From the literature this window is expected to be between 21-28 days. That therapeutic window will be used for evaluation of the immune …

In Silico Identification Of Essential Proteins In Corynebacterium Pseudotuberculosis Based On Protein-Protein Interaction Networks, Edson Luiz Folador, Paulo Vinícius Sanches Daltro De Carvalho, Wanderson Marques Silva, Rafaela Salgado Ferreira, Artur Silva, Michael Gromiha, Preetam Ghosh, Debmalya Barh, Vasco Azevedo, Richard Röttger

Biology Publications

Background

Corynebacterium pseudotuberculosis (Cp) is a gram-positive bacterium that is classified into equi and ovis serovars. The serovar ovis is the etiological agent of caseous lymphadenitis, a chronic infection affecting sheep and goats, causing economic losses due to carcass condemnation and decreased production of meat, wool, and milk. Current diagnosis or treatment protocols are not fully effective and, thus, require further research of Cp pathogenesis.

Results

Here, we mapped known protein-protein interactions (PPI) from various species to nine Cp strains to reconstruct parts of the potential Cp interactome and to identify potentially essential proteins serving as putative drug …

Regulation Of Mitotic Progression By Btf And Trap150, Divya Cheedu

Browse all Theses and Dissertations

Serine-arginine-rich (SR) or SR-like splicing factors interact with exon junction complex proteins during pre-mRNA processing to promote mRNA packaging into mature messenger ribonucleoproteins (mRNPs) and to dictate mRNA stability, nuclear export, and translation. In this thesis, I examined if depletion of two homologous non-classical serine-arginine-rich (SR) splicing factors, Btf (BCLAF1) and TRAP150, impacts regulation of cell cycle regulator transcripts and mitosis. Previous work showed that depletion of these proteins by RNAi causes mitotic defects including chromosome misalignment in metaphase. However, since Btf and/or TRAP150 did not co-localize with mitotic structures during mitosis, I hypothesized that Btf and/or TRAP150 depletion affect …

Determining Protein-Protein Interactions Of Als-Associated Sod1, Leah A. Shurte

Browse all Theses and Dissertations

Amyotrophic Lateral Sclerosis (ALS) is a neurodegenerative disorder that occurs due to the death of motor neurons and leads to paralysis and death within three to five years after symptoms present (Byrne et al., 2013). Superoxide Dismutase 1 (SOD1) was first identified to be associated with ALS in 1993. The objective of this study is to determine which proteins interact with wild type and mutant SOD1 and find any similarities or differences between them. ALS is attributed to a gain of toxicity, therefore abnormal protein interactions in mutant SOD1 are important. The results of this study will provide insight on …

Biochemical Characterization Of Wild-Type And Mutant (Q9f And S21y/V22d)Iron Oxidases Isolated From Acidithiobacillus Ferrooxidans M1, Di̇lşat Ni̇gar Çolak, Hali̇l İbrahi̇m Güler, Sabri̇ye Çanakçi, Ali̇ Osman Beldüz

Turkish Journal of Biology

Iron oxidase, a member of the high potential iron-sulfur protein (HiPIP) family within the iron-sulfur cluster, was thought to be involved in the iron respiratory electron transport chain in Acidithiobacillus ferrooxidans. A. ferrooxidans M1 strain was isolated from Murgul copper mine. The iro gene of this bacterium encoding iron oxidase was cloned, and the complete nucleotide sequence was disclosed. The gene was cloned and overexpressed successfully. The highly conserved amino acid residues within the iron oxidase enzyme sequence were determined, and their Q9F and S21Y/V22D recombinants were created through site-directed mutagenesis. Wild-type and recombinant iron oxidase enzymes were purified and …

The Aggregatibacter Actinomycetemcomitans Heat Shock Protein Groel Interacts Directly With Human Peripheral Blood T Cells, Ayten Nalbant, Tahsi̇n Saygili

Turkish Journal of Biology

Heat shock family protein GroEL of Aggregatibacter actinomycetemcomitans (Aa) has antigenic properties. We previously demonstrated that A. actinomycetemcomitans GroEL-like protein affects human CD4 T cells by converting them into IL-10 and IFNg double cytokine producing Tbet+ Th1 cells. The objective of this study was to investigate whether or not AaGroEL communicates with T cells directly. To do this, sorted cells from peripheral blood mononuclear cells were stimulated with AaGroEL for 48 h. Flow cytometry was used to measure soluble and intracellular cytokine expression in the cell cultures and detect TLR2 expression on the surface of T cells. Expression of six …

Reforestation In Southern China: Revisiting Soil N Mineralization And Nitrification After 8 Years Restoration, Qifeng F. Mo, Zhi'an A. Li, Weixing X. Zhu, Bi Zou, Yingwen W. Li, Shiqin Q. Yu, Yongzhen Z. Ding, Yao Chen, Xiaobo B. Li, Faming M. Wang

Biological Sciences Faculty Scholarship

Nitrogen availability and tree species selection play important roles in reforestation. However, long-term field studies on the effects and mechanisms of tree species composition on N transformation are very limited. Eight years after tree seedlings were planted in a field experiment, we revisited the site and tested how tree species composition affects the dynamics of N mineralization and nitrification. Both tree species composition and season significantly influenced the soil dissolved organic carbon (DOC) and nitrogen (DON). N-fixing Acacia crassicarpa monoculture had the highest DON, and 10-mixed species plantation had the highest DOC. The lowest DOC and DON concentrations were both …

Identification And Sequence Analysis Of Alkaloid Biosynthesisgenes In Papaver Section Oxytona, Yağiz Alagöz, Tuğba Gürkök, İskender Parmaksiz, Turgay Ünver

Turkish Journal of Biology

The benzylisoquinoline alkaloids (BIA) are secondary metabolites that are produced by many of the Papaver species including Papaver bracteatum, Papaver pseudo-orientale, and Papaver orientale, three representative members of the section Oxytona Bernh. The sequences and expression levels of the genes positioned on the BIA biosynthesis pathway were previously defined in opium poppy (Papaver somniferum), one of the mostly studied species of the same genus. Nevertheless, the majority of predicted BIA-related gene sequences in the section Oxytona have not been specified. Here we are presenting new cDNA sequences that belong to the Oxytona species. In this study, partial sequences of norcoclaurine-6-O-methyltransferase …

Chondroitin Sulfate-Based Biomaterials For Tissue Engineering, Hyuck Joon Kwon, Youngbae Han

Turkish Journal of Biology

Chondroitin sulfate (CS) is a sulfated glycosaminoglycan (GAG) that is usually found attached to proteins as part of a proteoglycan. The use of CS-based biomaterials in the field of tissue engineering applications has been intensively growing over the past decades because CS is a biopolymer with the major advantages of being biodegradable, biocompatible, easily available, and highly versatile. In vitro and in vivo studies have shown that CS-based biomaterials upregulate cartilage-specific gene expression in chondrocytes and mesenchymal stem cells and also support osteogenic differentiation by increasing the effectiveness of bone anabolic growth factors. Chondroitin sulfate proteoglycan plays a key role …

Antisenescence Activity Of G9a Inhibitor Bix01294 On Human Bone Marrow Mesenchymal Stromal Cells, Min-Ji Ahn, Sin-Gu Jeong, Goang Won Cho

Turkish Journal of Biology

Alterations in epigenomic patterns are associated with diverse physiological functions and pathological mechanisms causing aging-related diseases, such as degenerative disorders and cancers. We investigated the senescent effects of BIX01294, a G9a (histone methyltransferase) inhibitor, in human bone marrow mesenchymal stromal cells (hBM-MSCs). We determined the optimal dose and time of BIX01294 treatment in hBM-MSCs to be 1 μM and 12 h, respectively. Under these conditions, the expression of the antisenescent genes TERT, bFGF, VEGF, and Oct-4 increased, whereas the expression of the senescent factors p16, p21, and p53 decreased. The number of β-galactosidase-positive cells decreased significantly, and the rates of …

Rejuvenation Of Mature Lentisk By Micrografting And Evaluation Of Genetic Stability, Ahmet Onay, Engi̇n Ti̇lkat, Veysel Süzerer, Özge Karakaş Meti̇n, Yelda Özden Çi̇ftçi̇, Fati̇h Mehmet Kilinç, İbrahi̇m Koç, Muhammet Şaki̇roğlu, Hakan Yildirim, Ahu Altinkut Uncuoğlu, Nazan Çalar, Ömer Faruk Akdemi̇r

Turkish Journal of Biology

An in vitro propagation method was established for both male and female genotypes of lentisk using actively growing shoot tips derived from forcefully lignified shoots. The effects of growth regulators on in vitro morphogenesis were investigated. Since rooting of the regenerated shoots for both genotypes was not achieved, an in vitro micrografting method was developed for the production of plantlets. Moreover, genetic stability of 3-, 6-, and 24-times subcultured clones of both genotypes was assessed and compared with the mother plants using fluorescent-based amplified fragment length polymorphism (AFLP) analysis. The set of main plants and the different subcultured clones were …

Cloning, Expression, And In Silico Analysis Of A Novel Annexin Gene Ftanx1from Tartary Buckwheat (Fagopyrum Tataricum (L.) Gaertn.), Lingli Hou, Xueni Dong, Mengqi Ding, Xuemei Zhu, Jirong Shao

Turkish Journal of Biology

Annexins are generally thought to play an essential role in the regulation of plant growth, development, and stress responses. Here we describe an annexin gene from Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.), designated as FtANX1. The full-length coding sequence of FtANX1 is 942 bp in size, encoding a polypeptide of 313 amino acids with a theoretical molecular mass of 36.0 kDa and pI 5.94. In silico analysis of the sequence revealed that FtANX1 contains four repeats, with a type-II Ca2+-binding site in repeat I. Expression pattern analysis provided evidence that FtANX1 was predominantly expressed in immature achenes, while its level …

Simba: A Web Tool For Managing Bacterial Genome Assembly Generated By Ion Pgm Sequencing Technology, Diego C. B. Mariano, Felipe L. Pereira, Edgar L. Aguiar, Letícia C. Oliveira, Leandro Benevides, Luís C. Guimarães, Edson L. Folador, Thiago J. Sousa, Preetam Ghosh, Debmalya Barh, Henrique C. P. Figueiredo, Artur Silva, Rommel T. J. Ramos, Vasco A. C. Azevedo

Biology Publications

Background

The evolution of Next-Generation Sequencing (NGS) has considerably reduced the cost per sequenced-base, allowing a significant rise of sequencing projects, mainly in prokaryotes. However, the range of available NGS platforms requires different strategies and software to correctly assemble genomes. Different strategies are necessary to properly complete an assembly project, in addition to the installation or modification of various software. This requires users to have significant expertise in these software and command line scripting experience on Unix platforms, besides possessing the basic expertise on methodologies and techniques for genome assembly. These difficulties often delay the complete genome assembly projects.

Results …

Apoptotic Induction Via Membrane/Dna Damage And Metabolic Inactivation By Synthetic Food Colorants In Allium Cepa Root Meristem, Prajitha Vazhangat, John Ernest Thoppil

Turkish Journal of Biology

The present study investigates the cytotoxic and genotoxic effects of two frequently employed synthetic food colorants, lemon yellow and orange red, using an Allium cepa assay. Uptake of food colorants by root cells at different concentrations and varied exposures significantly altered the cytogenetic system, membrane integrity, mitochondrial function, root growth, and cell division. The food colorants induced significant DNA damage, micronucleus formation, and other severe chromosomal aberrations at genetic level and inhibited cell division as well as root growth. Severe DNA damage, membrane damage, and metabolic inactivation observed in the result are indicative of apoptotic cell death. These results confirm …

Alternate Method Of Phycocyanin Extraction, Will Higham, Matthew Agiro, Jon Y. Takemoto

Biology Posters

Phycocyanin is an abundant protein-pigment complex in many photosynthetic microbes and the feedstock for several emerging products in the food and pharmaceutical industries. The purpose of this project was to research the effectiveness of sonication technology to improve the efficiency and yields of phycocyanin production from the cyanobacterium Spirulina platensis. Sonication is the application of sound energy to agitate and break particles or cells. When used to augment the current methods of phycocyanin production, it has the potential benefit of reducing cell extraction volumes and increasing the yield of phycocyanin. Experiments were conducted to determine the effects of sonication time …

Wolbachia And Sex, Ian J. Aper, Katie Weglarz, Carol Von Dohlen

Biology Posters

Insects with complex life cycles provide an ideal system for investigating the relationship between sex-skewing bacterial symbionts and the secondary loss of sexual reproduction. This research utilized the insect family Adelgidae, a group notorious for having peculiar and complex life cycles. In this family, some species have lost their sexual generation entirely, trapping them in asexual reproduction. Additionally, these insects are known to harbor multiple symbionts, both obligate and facultative. The array of facultative symbionts that have been detected includes the infamous sex-skewing symbiont Wolbachia. This symbiont is known to induce male killing, cytoplasmic incompatibility, and parthenogenesis in insects. Additionally, …

The Identification And Characterization Of Bacterial Endosymbionts In The Planthopper Family, Issidae (Sternorrhyncha:Fulgoroidea), Lina Ghabayen

Biology Posters

Many insects live on nutrient-poor diets; to compensate, they have evolved obligate associations with microorganisms that are transmitted directly between generations. The bacterial associates of some Hemiptera insects have been identified and understood, but several remain unknown. Our objective is to identify the diversity of bacterial endosymbionts in Issidae using modern microscopy and molecular methods, and compare their identities to known symbionts from related insects. To do so, we will extract DNA from insect samples, amplify bacterial symbiont 16S genes, sub-clone PCR products, sequence the products, and determine their phylogenetic relationships to other insect symbionts and free-living bacteria. Our study …

Effectiveness Of Seed Treatments In Reducing Tmv Infection, Tanner A. Robison

Biology Posters

Tobacco mosaic virus (TMV), named for the plant it was first discovered in, can infect hundreds of different species. It has no known invertebrate vectors, but TMV is spread mechanically through contact with other plants, clothes, tools, contaminated soil and seed borne. While TMV is known to be exceptionally stable, it has been reported that treatment of tools with powdered milk can significantly reduce the infection rate of the virus. While there is a seed treatment available for conventional agriculture, there is no seed treatment available for organic production. Organic growers, who grow heirloom tomatoes experience the highest rates of …

Arenavirus Glycoprotein-Host Cell Receptor Interactions, Brayden L. Stembridge, Jonna B. Westover, Brady T. Hickerson, Brian B. Gowen

Biology Posters

Pichinde virus (PICV) is an enveloped single-stranded RNA New World arenavirus. The new world arenaviruses are divided into three separate clades designated as A, B, and C. The clade B arenaviruses are known to cause severe viral hemorrhagic fever. The clade A PICV is prevalent in the rodent population of Colombia. PICV is currently designated as a biosafety level-2 (BSL 2) pathogen due to its low pathogenicity in humans. Efforts have been made to identify the cellular receptors utilized by the virus glycoproteins to enter the host cell. Clade B arenaviruses utilize various species-specific forms of Transferrin Receptor 1 to …

Development Of Archaeal And Algalytic Bacteria Detection Systems, Andrew Walters, Anna Doloman, Charles Miller

Biology Posters

Natural gas (methane) is emerging as a viable power source for many industrial, commercial, and domestic applications. Bio-methane provides a promising replacement for mined natural gas. Methanogenic bacteria produce this bio-methane. These anaerobic bacteria pertain to the Domain Archaea, and are found in extreme environments where few other bacteria survive. They are employed by Up-Flow Anaerobic Sludge Blanket (UASB) reactors in the digestion of wastes to a marketable product (methane). The genome of methanogenic bacteria can be amplified using polymerase chain reaction (PCR), a synthetic DNA replication system. This system employs specific sequences of DNA called primers. The primers employed …

Floral Developmental Stages And Stress-Induced Reversions From Asexual To Sexual Seed Formation In Boechera (Brassiccaceae), Devin Wright

Biology Posters

In the apomictic process, plants produce a genetic copy of themselves by forming genetically-unreduced eggs (2n instead of 1n) that produce embryos parthenogenically, i.e., without fusion of egg and sperm nuclei.

• In some plants such as the Boechera species studies have shown that stressing the apomictic plants caused a reversion from apomeiosis to meiosis1.

• The object of my study is to more fully understand the stage of floral development at which an apomictic plant must be exposed to a stress signal in order to revert from apomictic to sexual reproduction or vice versa.

• Apomixis could be used …

Resistive Behaviors Of Spider Silk Nanofibers In Humidity Controlled Environments, Jesse Steadman, Nader Shehata, Ishac Kandas, Ibrahim Hassounah, Randolph V. Lewis

Biology Posters

Spider silk is becoming more useful for its desired properties as more information about the nanostructure is discovered. Due to the fact that this protein is nearly impossible to mass produce directly from the spider, the protein coding gene has been duplicated from the spider genome and inserted into the E. coli, goat, alfalfa, and silkworm genomes. This has allowed us to extract the produced protein from the transgenic hosts at a larger scale than the spiders offer. Spider silk is one of the strongest and most elastic fibers found in nature and these two characteristics, along with others others, …