Medical Genetics Commons^™

Functional Macroautophagy Induction By Influenza A Virus Without A Contribution To Major Histocompatibility Complex Class Ii-Restricted Presentation., Joseph D Comber, Tara M Robinson, Nicholas A Siciliano, Adam E Snook, Laurence C Eisenlohr

Department of Microbiology and Immunology Faculty Papers

Major histocompatibility complex (MHC) class II-presented peptides can be derived from both exogenous (extracellular) and endogenous (biosynthesized) sources of antigen. Although several endogenous antigen-processing pathways have been reported, little is known about their relative contributions to global CD4(+) T cell responses against complex antigens. Using influenza virus for this purpose, we assessed the role of macroautophagy, a process in which cytosolic proteins are delivered to the lysosome by de novo vesicle formation and membrane fusion. Influenza infection triggered productive macroautophagy, and autophagy-dependent presentation was readily observed with model antigens that naturally traffic to the autophagosome. Furthermore, treatments that enhance or …

Dna Repair Of 8-Oxo-7,8-Dihydroguanine Lesions In Porphyromonas Gingivalis, Leroy G. Henry Jr.

Loma Linda University Electronic Theses, Dissertations & Projects

The persistence of Porphyromonas gingivalis in the inflammatory environment of the periodontal pocket requires an ability to overcome oxidative stress. DNA damage is a major consequence of oxidative stress. Unlike other organisms, a non-base excision repair mechanism for the removal of 8-oxo-7,8-dihydroguanine (8-oxoG) in P. gingivalis was suggested. Because the uvrB gene is known to be important in nucleotide excision repair, the role of this gene in the repair of oxidative stress-induced DNA damage was investigated. A 3.1 kb fragment containing the uvrB gene was PCR-amplified from the chromosomal DNA of P. gingivalis W83. This gene was insertionally inactivated using …

Heat Shock Proteins As Novel Cancer Therapeutics: Targeting The Hallmarks Of Cancer, Chao Li

Theses and Dissertations

Molecular chaperones, commonly known as heat shock proteins (HSPs), are essential for mammalian cells to maintain homeostasis, and HSPs function by inducing an ATPase-coupled structural change, followed by interactions with diverse co-chaperones and over 200 client proteins implicated in many critical signaling networks. These highly expressed HSPs participate in the onset and progression of several human diseases including cancer, and their connection with tumorigenesis has facilitated research and clinical trials related to targeting HSPs as a novel anti-tumor therapy. The predominant mechanism of chaperone inhibition is through either disruption of the HSP association with client protein or an altered binding …

The Natural Polyphenol Resveratrol Potentiates The Lethality Of Hdac Inhibitors In Acute Myelogenous Leukemia Cells Through Multiple Mechanisms., Alae Abod Yaseen

Theses and Dissertations

This study examined the mechanisms underlying the interactions between the natural polyphenol Resveratrol and HDAC inhibitors in both U937 myelomonocytic leukemia cell line and blood samples from AML patients and normal cord blood. Simultaneous exposure to Resveratrol and HDAC inhibitors (Vorinostat-SAHA or Panobinostat-LBH589) resulted in potentiating the lethality caused by any single agent of the combination, this interaction found to be synergistic at multiple concentrations. Exposing U937 cells to minimal toxic doses of Resveratrol and HDACIs results in release of mitochondrial pro-apoptotic proteins AIF and cytochrome c, pro-apoptotic caspase activation especially caspase-8, and induction of DNA damage. These events were …

Microarray-Based Analysis Of Differential Gene Expression Between Infective And Noninfective Larvae Of Strongyloides Stercoralis., Roshan Ramanathan, Sudhir Varma, José M C Ribeiro, Timothy G Myers, Thomas J Nolan, David Abraham, James B Lok, Thomas B Nutman

Department of Microbiology and Immunology Faculty Papers

BACKGROUND: Differences between noninfective first-stage (L1) and infective third-stage (L3i) larvae of parasitic nematode Strongyloides stercoralis at the molecular level are relatively uncharacterized. DNA microarrays were developed and utilized for this purpose.

METHODS AND FINDINGS: Oligonucleotide hybridization probes for the array were designed to bind 3,571 putative mRNA transcripts predicted by analysis of 11,335 expressed sequence tags (ESTs) obtained as part of the Nematode EST project. RNA obtained from S. stercoralis L3i and L1 was co-hybridized to each array after labeling the individual samples with different fluorescent tags. Bioinformatic predictions of gene function were developed using a novel cDNA Annotation …

Comparison Of Human Memory Cd8 T Cell Responses To Adenoviral Early And Late Proteins In Peripheral Blood And Lymphoid Tissue., Amita Joshi, Biwei Zhao, Cara Romanowski, David Rosen, Phyllis Flomenberg

Department of Microbiology and Immunology Faculty Papers

Treatment of invasive adenovirus (Ad) disease in hematopoietic stem cell transplant (SCT) recipients with capsid protein hexon-specific donor T cells is under investigation. We propose that cytotoxic T cells (CTLs) targeted to the late protein hexon may be inefficient in vivo because the early Ad protein E3-19K downregulates HLA class I antigens in infected cells. In this study, CD8+ T cells targeted to highly conserved HLA A2-restricted epitopes from the early regulatory protein DNA polymerase (P-977) and late protein hexon (H-892) were compared in peripheral blood (PB) and tonsils of naturally infected adults. In tonsils, epitope-specific pentamers detected a significantly …

Prevalence Of Premature Ovarian Failure In Women With Tuberous Sclerosis, Emily Gabitzsch

Dissertations and Theses (Open Access)

Tuberous Sclerosis Complex (TSC) is an autosomal dominant tumor suppressor disorder characterized by hamartomas, or benign growths, in various organ systems. Inactivating mutations in either the TSC1 or the TSC2 gene cause most cases of TSC. Recently, the use of ovarian specific conditional knock-out mouse models has demonstrated a crucial role of the TSC genes in ovarian function. Mice with complete deletion of Tsc1 or Tsc2 showed accelerated ovarian follicle activation and subsequent premature follicular depletion, consistent with the human condition premature ovarian failure (POF). POF is defined in women as the cessation of menses before the age of 40 …

Natural History Study Of Arthrogryposis Multiplex Congenita, Amyoplasia Type, Trisha Nichols

Dissertations and Theses (Open Access)

Arthrogryposis or Arthrogrypsosis Multiplex Congenita (AMC) are terms used to describe the clinical finding of multiple congenital contractures. There are more than 300 distinct disorders associated with arthrogryposis. Amyoplasia is the most common type of arthrogryposis and is often referred to as the “classic” type. There is no known cause of amyoplasia and no risk factors have been identified. Moreover, there is no established diagnostic criteria, which has led to inconsistency and confusion in the medical literature. The purpose of this study was to describe the natural history of amyoplasia, to determine if there are any identifiable risk factors and …

The Association Between Hydroxyurea Treatment And Pain Intensity, Analgesic Use, And Utilization In Ambulatory Sickle Cell Anemia Patients., Wally R Smith, Samir K Ballas, William F Mccarthy, Robert L Bauserman, Paul S Swerdlow, Martin H Steinberg, Myron A Waclawiw, Investigators Of The Multicenter Study Of Hydroxyurea In Sickle Cell Anemia

Department of Medicine Faculty Papers

Background.  We compared daily pain, home analgesic use, and utilization among ambulatory adults in the randomized Multicenter Study of Hydroxyurea in Sickle Cell Anemia (MSH). We related the fetal hemoglobin (HbF) hydroxyurea response to these response variables. Methods.  Patients rated their sickle cell pain intensity (0-9), use of analgesics, and visits for pain daily. Diaries were collected biweekly, and intensity was collapsed into single interval ratings. The interval proportions of days of analgesic use and medical visits for pain were also calculated. Group comparisons were made by intention to treat as well as by HbF change levels from baseline to …

Health Needs Of Hiv-Infected Women In The United States: Insights From The Women Living Positive Survey., Kathleen E Squires, Sally L Hodder, Judith Feinberg, Dawn Averitt Bridge, Staats Abrams, Stephen P Storfer, Judith A Aberg

Department of Medicine Faculty Papers

The objective of this study was to describe attitudes, opinions, and perceived health needs of HIV-infected women in the United States. In this cross-sectional study, women were invited to participate in the Women Living Positive survey, a structured interview instrument with 45 questions. Collected data were deidentified and the margin of error was calculated as four percentage points. Incoming toll-free phone interviews were conducted from December 21, 2006, through March 14, 2007 among subjects recruited from a U.S. national network of AIDS counseling centers. Seven hundred HIV-infected women (43% African American, 28.5% Hispanic, 28.5% Caucasian; median age, 42.5 years) receiving …

The Interplay Between Nf-Kappab And E2f1 Coordinately Regulates Inflammation And Metabolism In Human Cardiac Cells., Xavier Palomer, David Álvarez-Guardia, Mercy M Davidson, Tung O Chan, Arthur M Feldman, Manuel Vázquez-Carrera

Department of Medicine Faculty Papers

Pyruvate dehydrogenase kinase 4 (PDK4) inhibition by nuclear factor-κB (NF-κB) is related to a shift towards increased glycolysis during cardiac pathological processes such as cardiac hypertrophy and heart failure. The transcription factors estrogen-related receptor-α (ERRα) and peroxisome proliferator-activated receptor (PPAR) regulate PDK4 expression through the potent transcriptional coactivator PPARγ coactivator-1α (PGC-1α). NF-κB activation in AC16 cardiac cells inhibit ERRα and PPARβ/δ transcriptional activity, resulting in reduced PGC-1α and PDK4 expression, and an enhanced glucose oxidation rate. However, addition of the NF-κB inhibitor parthenolide to these cells prevents the downregulation of PDK4 expression but not ERRα and PPARβ/δ DNA binding activity, …

Hydrophobicity As A Driver Of Mhc Class I Antigen Processing., Lan Huang, Matthew C Kuhls, Laurence C. Eisenlohr

Department of Microbiology and Immunology Faculty Papers

The forces that drive conversion of nascent protein to major histocompatibility complex (MHC) class I-restricted peptides remain unknown. We explored the fundamental property of overt hydrophobicity as such a driver. Relocation of a membrane glycoprotein to the cytosol via signal sequence ablation resulted in rapid processing of nascent protein not because of the misfolded luminal domain but because of the unembedded transmembrane (TM) domain, which serves as a dose-dependent degradation motif. Dislocation of the TM domain during the natural process of endoplasmic reticulum-associated degradation (ERAD) similarly accelerated peptide production, but in the context of markedly prolonged processing that included nonnascent …

Epignetics And Allergic Disease, Jacob Sweeney '11

Honor Scholar Theses

In this thesis I will propose a novel framework for understanding allergy. I will argue that exposure to certain early-life environments lead to life-long allergic disease through epigenetic mechanisms. Although my argument currently exists as an unsubstantiated hypothesis, I will review indirect evidence that I have gathered throughout the immunologic and epigenetic literature to support my claim. | will then propose a set of experiments which will test my hypothesis. This thesis will address current scientific “hot topics” and their implications will challenge fundamental tenants of biology. Rather than jumping straight into the argument I will begin with some background …

Role Of Antiarrhythmic Drugs: Frequent Implantable Cardioverter-Defibrillator Shocks, Risk Of Proarrhythmia, And New Drug Therapy., Christopher Droogan, Chinmay Patel, Gan-Xin Yan, Peter R Kowey

Department of Medicine Faculty Papers

The implantable cardioverter-defibrillator (ICD) is the standard of care in patients with ischemic and nonischemic cardiomyopathy who are at high risk for arrhythmic events and sudden cardiac death. Although an ICD saves life, ICD shocks are emotionally and physically debilitating. Most patients receive adjuvant antiarrhythmic drug therapy to circumvent episodes of recurrent ventricular and supraventricular arrhythmias. Antiarrhythmic drugs including β-blockers, sotalol, amiodarone, and azimilide are effective at reducing the shock burden. This article describes data supporting the need for and potential risks and benefits of adjuvant antiarrhythmic drug therapy and examines the benefits and pitfalls of the same in ICD-implanted …

Mir-21 Induced Angiogenesis Through Akt And Erk Activation And Hif-1Α Expression., Ling-Zhi Liu, Chongyong Li, Qi Chen, Yi Jing, Richard Carpenter, Yue Jiang, Hsiang-Fu Kung, Lihui Lai, Bing-Hua Jiang

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

MicroRNAs (miRNAs) are endogenous, small noncoding RNAs that play important roles in various cellular functions and tumor development. Recent studies have indicated that miR-21 is one of the important miRNAs associated with tumor growth and metastasis, but the role and molecular mechanism of miR-21 in regulating tumor angiogenesis remain to be elucidated. In this study, miR-21 was overexpressed by transfecting pre-miR-21 into human prostate cancer cells and tumor angiogenesis was assayed using chicken chorioallantoic membrane (CAM). We found that overexpression of miR-21 in DU145 cells increased the expression of HIF-1α and VEGF, and induced tumor angiogenesis. AKT and extracellular regulated …

Non-Identity-Mediated Crispr-Bacteriophage Interaction Mediated Via The Csy And Cas3 Proteins, Kyle C. Cady, George A. O'Toole

Dartmouth Scholarship

Studies of the Escherichia, Neisseria, Thermotoga, and Mycobacteria clustered regularly interspaced short palindromic repeat (CRISPR) subtypes have resulted in a model whereby CRISPRs function as a defense system against bacteriophage infection and conjugative plasmid transfer. In contrast, we previously showed that the Yersinia-subtype CRISPR region of Pseudomonas aeruginosa strain UCBPP-PA14 plays no detectable role in viral immunity but instead is required for bacteriophage DMS3-dependent inhibition of biofilm formation by P. aeruginosa. The goal of this study is to define the components of the Yersinia-subtype CRISPR region required to mediate this bacteriophage-host interaction. We show that the Yersinia-subtype-specific CRISPR-associated (Cas) proteins …

Igf2 Promotes Activation Of Estrogen Receptors In Basal-Like Breast Cancer Cells, Angelique Richardson

Loma Linda University Electronic Theses, Dissertations & Projects

The autocrine-paracrine effects of IGF2 are important in the growth and differentiation of normal breast. In breast cancer (BC), IGF2 is initially stimulated by estrogen, progesterone and prolactin to regulate proliferation and cancer progression. These actions are mediated by the IGF-1R and insulin receptor A (IR-A) both members of the tyrosine- kinase receptors family. The activation of Estrogen Receptor (ER) is also very important in BC growth and progression. As BC progresses to estrogen-independent growth, the IGF-1R and the estrogen receptor (ER) interact in crosstalk mechanisms that are synergistic and results in enhanced activation of both receptors signaling cascades. This …

Kidney Injury Molecule-1 (Kim-1) As An Early Detection Tool For Acute Kidney Injury And Other Renal Diseases, John Fontanilla, Md, Won K. Han, M.D

Department of Medicine Faculty Papers

Introduction: Although serum creatinine is the standard metric tool for the detection of renal injury, its lack of sensitivity has made the early diagnosis of acute kidney injury (AKI) very difficult.  In fact, the absence of sensitive AKI biomarkers has impaired progress in the nephrology field and had a detrimental effect on the design and outcome of AKI clinical trials.  Recently, several proteins have shown potential in the early detection of acute and chronic kidney injuries.

Areas covered: This review discusses the current status of kidney injury molecule-1 (KIM-1) as a potential diagnostic tool in patients with various acute …

Rho Activation Of Mdia Formins Is Modulated By An Interaction With Inverted Formin 2 (Inf2), Hua Sun, Johannes S. Schlondorff, Elizabeth J. Brown, Henry N. Higgs, Martin R. Pollak

Dartmouth Scholarship

Inverted formin 2 (INF2) encodes a member of the diaphanous subfamily of formin proteins. Mutations in INF2 cause human kidney disease characterized by focal and segmental glomerulosclerosis. Disease-causing mutations occur only in the diaphanous inhibitory domain (DID), suggesting specific roles for this domain in the pathogenesis of disease. In a yeast two-hybrid screen, we identified the diaphanous autoregulatory domains (DADs) of the mammalian diaphanous-related formins (mDias) mDia1, mDia2, and mDia 3 as INF2_DID-interacting partners. The mDias are Rho family effectors that regulate actin dynamics. We confirmed in vitro INF2_DID/mDia_DAD binding by biochemical assays, confirmed the in vivo interaction of these …

Comparative Gender Analysis Of The Efficacy And Safety Of Atazanavir/Ritonavir And Lopinavir/Ritonavir At 96 Weeks In The Castle Study., Kathleen E Squires, Margaret Johnson, Rong Yang, Jonathan Uy, Louise Sheppard, Judith Absalon, Donnie Mcgrath

Department of Medicine Faculty Papers

OBJECTIVES: To examine whether the overall results of the CASTLE study pertain to both genders, we analysed the efficacy and safety of atazanavir/ritonavir and lopinavir/ritonavir in 277 female and 606 male patients in the open-label, multinational trial over 96 weeks. The trial is registered with ClinicalTrials.gov, number NCT00272779.

METHODS: Treatment-naive patients aged ≥ 18 years with HIV-1 RNA ≥ 5000 copies/mL were randomized to receive either atazanavir/ritonavir 300/100 mg once daily or lopinavir/ritonavir 400/100 mg twice daily, with fixed-dose tenofovir/emtricitabine 300/200 mg once daily.

RESULTS: At week 96, confirmed virological response rates (HIV RNA <50 copies>/mL; intent-to-treat analysis) were higher in …

Evidence-Based Genomic Diagnosis Characterized Chromosomal And Cryptic Imbalances In 30 Elderly Patients With Myelodysplastic Syndrome And Acute Myeloid Leukemia., Renu Bajaj, Fang Xu, Bixia Xiang, Katherine Wilcox, Autumn J Diadamo, Rachana Kumar, Alexandra Pietraszkiewicz, Stephanie Halene, Peining Li

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

BACKGROUND: To evaluate the clinical validity of genome-wide oligonucleotide array comparative genomic hybridization (aCGH) for detecting somatic abnormalities, we have applied this genomic analysis to 30 cases (13 MDS and 17 AML) with clonal chromosomal abnormalities detected in more than 50% of analyzed metaphase cells.

RESULTS: The aCGH detected all numerical chromosomal gains and losses from the mainline clones and 113 copy number alterations (CNAs) ranging from 0.257 to 102.519 megabases (Mb). Clinically significant recurrent deletions of 5q (involving the RPS14 gene), 12p12.3 (ETV6 gene), 17p13 (TP53 gene), 17q11.2 (NF1 gene) and 20q, double minutes containing the MYC gene and …

The Pax Gene Eyegone Facilitates Repression Of Eye Development In Tribolium, Nazanin Zarinkamar, Xiaoyun Yang, Riyue Bao, Frank Friedrich, Rolf Beutel, Markus Friedrich

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

The Pax transcription factor gene eyegone (eyg) participates in many developmental processes in Drosophila, including the Notch signaling activated postembryonic growth of the eye primordium, global development of the adult head and the development of the antenna. In contrast to other Pax genes, the functional conservation of eyg in species other than Drosophila has not yet been explored.

Results

We investigated the role of eyg during the postembryonic development of the red flour beetle Tribolium castaneum. Our results indicate conserved roles in antennal but not in eye development. Besides segmentation defects in the antenna, Tribolium eyg knockdown animals …

Δ-Aminolevulinic Acid Dehydratase Single Nucleotide Polymorphism 2 And Peptide Transporter 2*2 Haplotype May Differentially Mediate Lead Exposure In Male Children, Christina Sobin, Natali Parisi, Tanner Schaub, Marisela Gutierrez, Alma Ortega

Selected Works Temporary Series

Child low-level lead (Pb) exposure is an unresolved public health problem and an unaddressed child health disparity. Particularly in cases of low-level exposure, source removal can be impossible to accomplish, and the only practical strategy for reducing risk may be primary prevention. Genetic biomarkers of increased neurotoxic risk could help to identify small subgroups of children for early intervention. Previous studies have suggested that, by way of a distinct mechanism, d-aminolevulinic acid dehydratase single nucleotide polymorphism 2 (ALAD2) and/or peptide transporter 2*2 haplotype (hPEPT2*2) increase Pb blood burden in children. Studies have not yet examined whether sex mediates the effects …

Pediatrician Perceptions Of The Patient-Centered Medical Home Model, Christopher Ray

Theses and Dissertations

The Patient-Centered Medical Home (PCMH) is an emerging model of health care designed to provide a simpler, more effective health care experience. The model places heavy emphasis on the concept of every patient having a "personal physician" who is the point of access for all health care needs and concerns. The personal physician integrates all relevant health care information to provide the patient with a holistic picture of his health. The supposed benefits of the PCMH model include an improved patient experience, increased effectiveness of care, increased efficiency of care, greater access to care, among others. Only now is evidence …

Mir-27b*, An Oxidative Stress-Responsive Microrna Modulates Nuclear Factor-Kb Pathway In Raw 264.7 Cells, Sivasubramani Thulasingam, Chandirasegaran Massilamany, Arunakumar Gangaplara, Hongjiu Dai, Shahlo Yarbaeva, Sakthivel Subramaniam, Jean-Jack Riethoven, James Eudy, Marjorie F. Lou, Jay Reddy

Jay Reddy Publications

Reactive oxygen species (ROS) produced in macrophages is critical for microbial killing, but they also take part in inflammation and antigen presentation functions. MicroRNAs (miRNAs) are endogenous regulators of gene expression, and they can control immune responses. To dissect the complex nature of ROS-mediated effects in macrophages, we sought to characterize miRNAs that are responsive to oxidative stress-induced with hydrogen peroxide (H₂O₂) in the mouse macrophage cell line, RAW 264.7. We have identified a set of unique miRNAs that are differentially expressed in response to H₂O₂. These include miR-27a*, miR-27b*, miR-29b*, miR-24-2*, …

Histone Deacetylases (Hdacs) In Xpc Gene Silencing And Bladder Cancer, Xiaoxin S. Xu, Le Wang, Judith Abrams, Gan Wang

Wayne State University Associated BioMed Central Scholarship

Abstract

Bladder cancer is one of the most common malignancies and causes hundreds of thousands of deaths worldwide each year. Bladder cancer is strongly associated with exposure to environmental carcinogens. It is believed that DNA damage generated by environmental carcinogens and their metabolites causes development of bladder cancer. Nucleotide excision repair (NER) is the major DNA repair pathway for repairing bulk DNA damage generated by most environmental carcinogens, and XPC is a DNA damage recognition protein required for initiation of the NER process. Recent studies demonstrate reduced levels of XPC protein in tumors for a majority of bladder cancer patients. …

Phylogeny And Adaptive Evolution Of The Brain-Development Gene Microcephalin (Mcph1) In Cetaceans, Michael R. Mcgowen, Stephen H. Montgomery, Clay Clark, John Gatesy

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Representatives of Cetacea have the greatest absolute brain size among animals, and the largest relative brain size aside from humans. Despite this, genes implicated in the evolution of large brain size in primates have yet to be surveyed in cetaceans.

Results

We sequenced ~1240 basepairs of the brain development gene microcephalin (MCPH1) in 38 cetacean species. Alignments of these data and a published complete sequence from Tursiops truncatus with primate MCPH1 were utilized in phylogenetic analyses and to estimate ω (rate of nonsynonymous substitution/rate of synonymous substitution) using site and branch models of molecular evolution. We also tested …

Unfolded Protein Response In Cancer: The Physician's Perspective, Xuemei Li, Kezhong Zhang, Zihai Li

Wayne State University Associated BioMed Central Scholarship

Abstract

The unfolded protein response (UPR) is a cascade of intracellular stress signaling events in response to an accumulation of unfolded or misfolded proteins in the lumen of the endoplasmic reticulum (ER). Cancer cells are often exposed to hypoxia, nutrient starvation, oxidative stress and other metabolic dysregulation that cause ER stress and activation of the UPR. Depending on the duration and degree of ER stress, the UPR can provide either survival signals by activating adaptive and antiapoptotic pathways, or death signals by inducing cell death programs. Sustained induction or repression of UPR pharmacologically may thus have beneficial and therapeutic …

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 …