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A Supermatrix Analysis Of Genomic, Morphological, And Paleontological Data From Crown Cetacea, Jonathan H. Geisler, Michael R. Mcgowen, Guang Yang, John Gatesy

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Cetacea (dolphins, porpoises, and whales) is a clade of aquatic species that includes the most massive, deepest diving, and largest brained mammals. Understanding the temporal pattern of diversification in the group as well as the evolution of cetacean anatomy and behavior requires a robust and well-resolved phylogenetic hypothesis. Although a large body of molecular data has accumulated over the past 20 years, DNA sequences of cetaceans have not been directly integrated with the rich, cetacean fossil record to reconcile discrepancies among molecular and morphological characters.

Results

We combined new nuclear DNA sequences, including segments of six genes (~2800 …

Bio::Phylo-Phyloinformatic Analysis Using Perl, Rutger A. Vos, Jason Caravas, Klaas Hartmann, Mark A. Jensen, Chase Miller

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Phyloinformatic analyses involve large amounts of data and metadata of complex structure. Collecting, processing, analyzing, visualizing and summarizing these data and metadata should be done in steps that can be automated and reproduced. This requires flexible, modular toolkits that can represent, manipulate and persist phylogenetic data and metadata as objects with programmable interfaces.

Results

This paper presents Bio::Phylo, a Perl5 toolkit for phyloinformatic analysis. It implements classes and methods that are compatible with the well-known BioPerl toolkit, but is independent from it (making it easy to install) and features a richer API and a data model that is …

Analysis Of Positional Candidate Genes In The Aaa1 Susceptibility Locus For Abdominal Aortic Aneurysms On Chromosome 19, John H. Lillvis, Yoshiki Kyo, Gerard Tromp, Guy M. Lenk, Ming Li, Qing Lu, Robert P. Igo Jr, Natzi Sakalihasan, Robert E. Ferrell, Charles M. Schworer, Zoran Gatalica, Susan Land, Helena Kuivaniemi

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Abdominal aortic aneurysm (AAA) is a complex disorder with multiple genetic risk factors. Using affected relative pair linkage analysis, we previously identified an AAA susceptibility locus on chromosome 19q13. This locus has been designated as the AAA1 susceptibility locus in the Online Mendelian Inheritance in Man (OMIM) database.

Methods

Nine candidate genes were selected from the AAA1 locus based on their function, as well as mRNA expression levels in the aorta. A sample of 394 cases and 419 controls was genotyped for 41 SNPs located in or around the selected nine candidate genes using the Illumina GoldenGate platform. …

A Protein Network-Guided Screen For Cell Cycle Regulators In Drosophila, Stephen T. Guest, Jingkai Yu, Dongmei Liu, Julie A. Hines, Maria A. Kashat, Russell L. Finley Jr

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Large-scale RNAi-based screens are playing a critical role in defining sets of genes that regulate specific cellular processes. Numerous screens have been completed and in some cases more than one screen has examined the same cellular process, enabling a direct comparison of the genes identified in separate screens. Surprisingly, the overlap observed between the results of similar screens is low, suggesting that RNAi screens have relatively high levels of false positives, false negatives, or both.

Results

We re-examined genes that were identified in two previous RNAi-based cell cycle screens to identify potential false positives and false negatives. We …

Hydrolysis Of Amelogenin By Matrix Metalloprotease-20 Accelerates Mineralization In Vitro, Vuk Uskoković, Feroz Khan, Haichuan Liu, Halina Ewa Witkowska, Li Zhu, Wu Li, Stefan Habelitz

Pharmacy Faculty Articles and Research

In the following respects, tooth enamel is a unique tissue in the mammalian body: (a) it is the most mineralized and hardest tissue in it comprising up to 95 wt% of apatite; (b) its microstructure is dominated by parallel rods composed of bundles of 40 – 60 nm wide apatite crystals with aspect ratios reaching up to 1:10,000 and (c) not only does the protein matrix that gives rise to enamel guides the crystal growth, but it also conducts its own degradation and removal in parallel. Hence, when mimicking the process of amelogenesis in vitro, crystal growth has to …

Stem Cell Biology And Strategies For Therapeutic Development In Degenerative Diseases And Cancer, Angel A. Alvarez

Electronic Theses and Dissertations

Stem cell biology is an exciting field that will lead to significant advancements in science and medicine. We hypothesize that inducing the expression of stem cell genes, using the embryonic stem cell gene nanog, will reprogram cells and dedifferentiate human mesenchymal stem cells into pluripotent stem cells capable of neural differentiation. The aims of initial studies are as follows: Aim 1: Demonstrate that forced expression of the embryonic stem cell gene nanog induces changes in human mesenchymal stem cells to an embryonic stem cell-like phenotype. Aim 2: Demonstrate that induced expression of nanog up-regulates the expression of multiple embryonic stem …

Table Of Contents

Journal of the South Carolina Academy of Science

No abstract provided.

President's Message, Justin K. Wyatt

Journal of the South Carolina Academy of Science

No abstract provided.

Scas Officers And Council Members 2010 - 2011

Journal of the South Carolina Academy of Science

No abstract provided.

Properties And Uses Of Sodium Titanates And Peroxotitanates, David Hobbs

Journal of the South Carolina Academy of Science

No abstract provided.

Nanocarriers For Biomedical Applications, Shuyi Li, Lynsa Nguyen, Hairong Xion, Meiyao Wang, Tom C.-C. Hu, Jin-Xiong She, Steven M. Serkiz, George G. Wicks, William S. Dynan

Journal of the South Carolina Academy of Science

No abstract provided.

Removal And Sequestration Of Iodide From Alkaline Solutions Using Silver-Doped Carbon Nanotubes, Adrian L. Pishko, Steven M. Serkiz, Apparao M. Rao

Journal of the South Carolina Academy of Science

No abstract provided.

Table Of Contents

Journal of the South Carolina Academy of Science

No abstract provided.

Scas Officers And Council Members 2010-2011

Journal of the South Carolina Academy of Science

No abstract provided.

Gold Nanospheres As Inhibitors Of Amyloid- Β Protein Aggregation Involved In Alzheimer’S Disease, Mihyun Lim, Deborah Soto-Ortega, Rahina Mahtab, Melissa Moss

Journal of the South Carolina Academy of Science

No abstract provided.

Sirna-Mediated Inhibition Of The Hiv-1 Transactivator Of Transcription, Alexander Jureka, Pricilla Simon, William Jackson

Journal of the South Carolina Academy of Science

No abstract provided.

Physiological Markers Of Activity-Based Anorexia In Sprague Dawley Rats, Crystal Lange, Michelle Vieyra

Journal of the South Carolina Academy of Science

No abstract provided.

Inverse Correspondence Of Amh And Fsh Levels In Women Presenting For Infertility Treatments, Amara Iverson, Abdelmonium Younis, William Butler, William Roudebush

Journal of the South Carolina Academy of Science

No abstract provided.

In Vitro Efficacy Of Different Chemical Substances On Hydatid Cyst Components, Ömer Faruk Akinci, Mustafa Karaoğlanoğlu, Mustafa Sedat Bozkurt, Leyla Gözaydin, Sali̇h Zeki̇ Zi̇ylan

Turkish Journal of Medical Sciences

Cyst membrane, daughter cyst, and pericyst are the focal point of some problems related to the percutaneous treatment of hydatid disease. This study was planned to investigate the in vitro efficacy of sodium hypochlorite, hydrogen peroxide, some widely used scolicidal agents, and some chemical solvents on hydatid cyst components. Materials and methods: To investigate the effects of various pharmacological and chemical agents on hydatid cyst components, 5 mL each of 15 different agents was put into bottles. Tissue measuring 2 × 1 cm was cut from the pericyst and the cyst membrane was put into each bottle. Two undamaged daughter …

The Optimal Dose Of Vitamin D In Growing Girls During Academic Years: A Randomized Trial, Mehrdad Shakinba, Samane Tefagh, Zahra Nafei

Turkish Journal of Medical Sciences

Prevalence of vitamin D deficiency is remarkable during childhood and adolescence throughout the world. Sufficient intake of vitamin D contributes to a number of health outcomes. The aim of this study was to specify the optimal dose of vitamin D in growing girls in a Muslim country during an academic year. Materials and methods: This randomized clinical trial study was carried out in Yazd in the center of Iran in 2007;120 junior high school girls (aged 12-15 years) were randomly divided into 4 groups. Sixty students in groups I and II were treated for vitamin D deficiency with 300,000 IU …

Effects Of 50 Hz Electric Field On Malondyaldehide And Nitric Oxide Levels In Spinal Cord Of Rats At Prenatal Plus Postnatal Period, Ertuğrul Uzar, Haci Ramazan Yilmaz, Mustafa Yilmaz, Efkan Uz, Vedat Ali̇ Yürekli̇, Bumi̇n Dündar, Hasan Rifat Koyuncuoglu, Selçuk Çömlekçi̇

Turkish Journal of Medical Sciences

The effect of 50 Hz electric field (EF) on developing neural tissues is not known. We aimed to determine whether there would be any oxidative stress effect of 50 Hz EF on developing spinal cord tissues of pup rats by evaluating malondialdehyde (MDA), nitric oxide (NO) levels, and antioxidant enzyme activities such as superoxide dismutase (SOD) and catalase (CAT) measurement. Materials and methods: In the prenatal+postnatal group, the pregnant rat was exposed to continuous EF at 50 Hz 10 kV/s until delivery. Then the female pups of this group (n = 7) were exposed to EF at the same doses …

Efficacy Of Hyaluronic Acid - Carboxymethyl Cellulose Membrane (Seprafilm®) And Polylactic Acid Barrier Film (Surgiwrap™) For The Prevention Of Adhesions After Thyroid Surgery: An Experimental Model, Gökhan Çi̇pe, Hakan Mustafa Köksal, Sadik Yildirim, Mustafa Fevzi̇ Celayi̇r, Adi̇l Baykan

Turkish Journal of Medical Sciences

Adhesions occurring after initial surgery increase complications in secondary thyroid operations. Therefore use of anti-adhesive barriers may reduce complication rates of secondary thyroid operations. In this study, we investigated the efficacy of hyaluronic acid-carboxymethyl cellulose membrane (HA-CMC, Seprafilm®) and polylactic acid barrier film (PLA, Surgiwrap™) in reducing adhesions after thyroid surgery. Materials and methods: A randomized-controlled experimental animal model was utilized. Forty-eight male Wistar Albino rats were randomly divided into 3 equal groups, forming study and control groups. Thyroid surgery was performed in all subjects. HA-CMC and PLA were applied between the thyroid zone and strap muscles after thyroid surgery …

Urginea Maritima (L.) Baker (Liliaceae) Extract Induces More Cytotoxicity Than Standard Chemotherapeutics In The A549 Non-Small Cell Lung Cancer (Nsclc) Cell Line, Hakan Bozcuk, Mustafa Özdoğan, Oktay Aykurt, Fati̇h Topçuoğlu, Hasan Öztürk, Deni̇z Eki̇nci̇, Asuman Karadeni̇z, Ayli̇n Mutlu, Durmuş Burgucu

Turkish Journal of Medical Sciences

Urginea maritima (Um) is a plant native to especially Turkey and the Mediterranean area. In this study, we investigated whether Um extract exerted cytotoxicity on cancer cells. Materials and methods: We made various extracts of Um. These extracts in varying concentrations were added to an A549 NSCLC cell culture, alone or with gemcitabine and/or cisplatin. Growth inhibition was tested by the MTT assay and an Annexin V-FITC apoptosis detection kit Results: The onion Um extract (1 µg/mL) was more cytotoxic than cisplatin (1 µg/mL), gemcitabine (1 nm/mL), and leaf Um extract (1 µg/mL) with P < 0.001, P = 0.097, and P < 0.001, respectively. The efficacy of Um extract was further improved by the addition of an antioxidant cocktail to an IC_{50} value of 0.02 µg/mL. Conclusion: Um extract has been shown for the first time to be a strong candidate for drug development in solid tumors. Our studies continue to further define the specific antitumor compound(s) in this extract.

Ex Vivo Produced Oral Mucosa Equivalent Preliminary Report: A Technical Note, Gürkan Raşi̇t Bayar

Turkish Journal of Medical Sciences

The aim of this study was to produce of ex vivo oral mucosal equivalent. The continuous stratified layer of human oral keratinocytes was grown on a cadaveric human dermal matrix in a defined culture medium without a feeder layer. Materials and methods: Human oral keratinocytes from a keratinized oral mucosa biopsy specimen were enzymatically dissociated and cultured in a serum-free defined culture medium, "EpiLife" (Cascade Biologics, Portland, OR, USA), containing a low calcium concentration of 0.06 mM. Oral keratinocytes were expanded one passage. Once a sufficient population of keratinocytes was reached, they were seeded onto the type IV collagen coated …

Relationship Between Pon1 Phenotype And Headache Duration In Migraine Patients, Şahbetti̇n Selek, Recep Alp, Selen İlhan Alp, Abdullah Taşkin

Turkish Journal of Medical Sciences

The available data on the activity of paraoxonase-1 (PON1) in patients suffering from migraine without aura (MWoA) is scarce. The present study was conducted to fulfill the objective of investigating the probability of an association between PON1 phenotype distribution and headache duration in patients suffering from MWoA. Materials and methods: Seventy-six patients who suffer from MWoA and were not experiencing attacks at the time and 65 healthy volunteers were enrolled for the purpose of evaluation in the present study. Results: The levels of serum paraoxonase, arylesterase activities, and lipid hydroperoxide (LOOH) were determined for these subjects. The results obtained revealed …

Serum Paraoxonase And Arylesterase Activities In Iron Deficiency Anemia During Pregnancy, Hakan Camuzcuoğlu, Harun Toy, Mehmet Vural, Aysun Camuzcuoğlu, Abdullah Taşkin, Haki̇m Çeli̇k

Turkish Journal of Medical Sciences

To investigate serum paraoxonase and arylesterase activities, and lipid hydroperoxide levels in pregnant women with iron deficiency anemia. Materials and methods: Paraoxonase and arylesterase activities, and lipid hydroperoxide levels were assessed for pregnant women with iron deficiency anemia (n = 50) and controls (n = 70). Serum basal and salt-stimulated paraoxonase, and arylesterase activities were measured spectrophotometrically. The lipid hydroperoxide levels were measured by ferrous ion oxidation xylenol orange assay. In addition, lipid parameters were determined by routine laboratory methods. Results: Basal and salt-stimulated paraoxonase, and arylesterase activities were significantly lower (P = 0.026, P = 0.031, and P = …

The Cytomorphological Analysis Of Buccal Mucosa Cells In Smokers, Mustafa Göregen, Hayati̇ Murat Akgül, Cemal Gündoğdu

Turkish Journal of Medical Sciences

To examine the effect of smoking on normal buccal mucosa cytomorphologically. Materials and methods: Forty individuals aged between 40 and 60, comprising 23 smokers (14 male, 9 female) and 17 and non-smokers (10 male, 7 female), were included in the study. The buccal epithelial cells of these individuals were collected with a brush and the cells were measured cytomorphometrically using software. Results: The average nuclear area (NA), nuclear perimeter (NP), minimal nuclear diameter (D-min), and maximal nuclear diameter (D-max) were 46.00 ± 11.31, 28.18 ± 2.43, 6.18 ± 0.88, and 10.00 ± 0.94, respectively, in the control group, and 53.61 …

In Vitro Effect Of Resveratrol Against Oxidative Injury Of Human Coronary Artery Endothelial Cells, Oya Sayin, Nur Arslan, Zeki̇ye Sultan Altun, Gül Akdoğan

Turkish Journal of Medical Sciences

Reactive oxygen species induce oxidative stress that may contribute to endothelial dysfunction. In addition to endogen antioxidants, adding antioxidants to diet has been used to reduce oxidative-stress-induced endothelial dysfunction. Resveratrol is a natural phytoalexin which has many effects including antioxidant activity. The aim of this study was to investigate whether resveratrol could protect human coronary artery endothelial cells against in vitro oxidative-stress-mediated injury. Materials and methods: Human coronary artery endothelial cells were treated with varying concentrations of hydrogen peroxide for different durations and hydrogen peroxide plus varying concentrations of resveratrol. Then cell death was measured using lactate dehydrogenase release. Human …

Immunomodulatory Role Of Leptin Treatment In Experimental Sepsis Caused By Gram Negative Bacteria, Cemi̇le Koca, Havva Şahi̇n Kavakli, Özlem Alici

Turkish Journal of Medical Sciences

To investigate the effect of leptin treatment on circulating inflammatory cytokines and on tissue damage in experimental rat model of gram-negative sepsis. Materials and methods: Adult male Wistar rats, 28 in total, were randomly divided into 4 groups (n = 7): sham, leptin, sepsis, and sepsis group treated with leptin (sepsis+leptin). Sepsis was induced by intraperitoneal (ip) injection of 2 × 10^{10} CFU of Escherichia coli ATCC 25922. Leptin and sepsis+leptin groups received a single dose ip 0.1 mg/kg leptin, while sham group received 1 mL of ip saline. Rats were sacrificed 24 h after the induction of sepsis. Blood …

Glutamate Dehydrogenase And Triose-Phosphate-Isomerase Coding Genes For Detection And Genetic Characterization Of Giardia Lamblia In Human Feces By Pcr And Pcr-Rflp*, Kareem Hatam Nahavandi, Esmaeel Fallah, Mohammad Asgharzadeh, Nasrin Mirsamadi, Behroz Mahdavipour

Turkish Journal of Medical Sciences

The purpose of this study was comparison of the glutamate dehydrogenase (gdh) and triose phosphate isomerase (tpi) genes for detection and genetic characterization of Giardia lamblia (G. lamblia) in human stool by polymerase chain reaction (PCR) and PCR-restriction fragment length polymorphism (RFLP). Our assay was specific and distinguished between G. lamblia assemblages A and B. Materials and methods: Among the 325 stool samples obtained from patients with acute gastroenteritis hospitalized in the Pediatric Hospital and infected humans referred to the Tabriz Reference Laboratory (TRL), 34 Giardia-positive stool samples were identified by conventional techniques. Two assays-PCR and PCR-RFLP-targeting the tpi and …