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Search Results: 1 - 10 of 53025 matches for " David Danley "
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Targeted Deposition of Antibodies on a Multiplex CMOS Microarray and Optimization of a Sensitive Immunoassay Using Electrochemical Detection
John Cooper,Nina Yazvenko,Kia Peyvan,Karl Maurer,Chris R. Taitt,Wanda Lyon,David L. Danley
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0009781
Abstract: The CombiMatrix ElectraSense? microarray is a highly multiplex, complementary metal oxide semiconductor with 12,544 electrodes that are individually addressable. This platform is commercially available as a custom DNA microarray; and, in this configuration, it has also been used to tether antibodies (Abs) specifically on electrodes using complementary DNA sequences conjugated to the Abs.
Multiplexed Electrochemical Detection of Yersinia Pestis and Staphylococcal Enterotoxin B using an Antibody Microarray
Jason Wojciechowski,David Danley,John Cooper,Nina Yazvenko,Chris Rowe Taitt
Sensors , 2010, DOI: 10.3390/s100403351
Abstract: The CombiMatrix antibody microarray is a versatile, sensitive detection platform based on the generation and transduction of electrochemical signals following antigen binding to surface antibodies. The sensor chip described herein is comprised of microelectrodes coupled to an adjacent bio-friendly matrix coated with antibodies to the biological pathogens Yersinia pestis and Bacillus anthracis, and the bacterial toxin staphylococcal enterotoxin B (SEB). Using this system, we were able to detect SEB and inactivated Y. pestis individually as well as in two-plex assays at concentrations as low as 5 pg/mL and 106 CFU/mL, respectively. We also introduce super avidin-biotin system (SABS) as a viable and effective means to enhance assay signal responses and lower detection limits. Together these technologies represent substantial advances in point-of-care and point-of-use detection applications.
Use of a Multiplexed CMOS Microarray to Optimize and Compare Oligonucleotide Binding to DNA Probes Synthesized or Immobilized on Individual Electrodes
Karl Maurer,Nina Yazvenko,Jodi Wilmoth,John Cooper,Wanda Lyon,David Danley
Sensors , 2010, DOI: 10.3390/s100807371
Abstract: The CombiMatrix microarray with 12,544 electrodes supports in situ electrochemical synthesis of user-defined DNA probes. As an alternative, we immobilized commercially synthesized DNA probes on individual electrodes coated with electropolymerized polypyrrole (Ppy). Hybridization was measured using a biotinylated target oligonucleotide and either Cy5-streptavidin and fluorescence detection or horseradish peroxidase-streptavidin and enzyme-enhanced electrochemical detection. Detection efficiencies were optimized by varying the deposition of the Ppy, the terminal groups on the DNA probes, and other factors that impacted fluorescence quenching and electrical conductivity. Optimized results were compared against those obtained using a microarray with the same DNA sequences synthesized in situ. Immobilized probes produced higher fluorescence signals, possibly by providing a greater stand off between the Cy5 on the target oligonucleotide and the quenching effects of the Ppy and the platinum electrode.
Overview of Electrochemical DNA Biosensors: New Approaches to Detect the Expression of Life
Stefano Cagnin,Marcelo Caraballo,Carlotta Guiducci,Paolo Martini,Marty Ross,Mark SantaAna,David Danley,Todd West,Gerolamo Lanfranchi
Sensors , 2009, DOI: 10.3390/s90403122
Abstract: DNA microarrays are an important tool with a variety of applications in gene expression studies, genotyping, pharmacogenomics, pathogen classification, drug discovery, sequencing and molecular diagnostics. They are having a strong impact in medical diagnostics for cancer, toxicology and infectious disease applications. A series of papers have been published describing DNA biochips as alternative to conventional microarray platforms to facilitate and ameliorate the signal readout. In this review, we will consider the different methods proposed for biochip construction, focusing on electrochemical detection of DNA. We also introduce a novel single-stranded DNA platform performing high-throughput SNP detection and gene expression profiling.
Heart Is Active Citizenship: Reimagining Civic Education  [PDF]
Seungho Moon, Jenna Mortensen Nelson, Yeorim Hwang, Mary Danley
Creative Education (CE) , 2017, DOI: 10.4236/ce.2017.810113
Abstract: The ARtS (Aesthetic, Reflexive thoughts, & Sharing) Initiative is an innovative program for engaging children in reflexive thought about active citizenship in urban communities. This article explicates how children use art to imagine the alternatives in civic education. Using the heart metaphor as active citizenship, the authors illustrate how this organ connects citizens and pumps our desire for a better community through our veins, thus instigating social change. This article demonstrates the power of imagination to inspire students to conceptualize a more just society.
Hyperhidrosis of Central Hypogonadism Leading to Diagnosis of Shapiro Syndrome: Temperature Dysregulation, Hypothermia and Agenesis of the Corpus Callosum  [PDF]
Megan A. Traxinger, Emily A. Beckett, Dana Danley, Udaya M. Kabadi
Open Journal of Endocrine and Metabolic Diseases (OJEMD) , 2019, DOI: 10.4236/ojemd.2019.91001
Abstract: Background: Central or hypothalamic hypogonadism as an initial manifestation of Shapiro Syndrome has not been described in the literature. Herein, we report first case in which initial presentation of central hypogonadism led to a confirmed diagnosis of Shapiro Syndrome during a casual evaluation of hypothalamic pituitary anatomy with MRI of brain. Case presentation: 53 year old Caucasian man was documented to manifest Central or hypogonadotropic hypogonadism following evaluation of excessive sweating episodes, lack of libido and erectile dysfunction for a duration of several years. Brain MRI performed for assessment of the etiology documented no pituitary abnormality. Instead agenesis of Corpus Callosum was noted. The subject had been hospitalized on many occasions at this and several other medical centers with hypothermia or hyperthermia without a documentation of a definite cause. Therefore, the diagnosis of Shapiro Syndrome was made. Conclusion: This report is the first documentation of subject manifesting central, more likely to be hypothalamic rather than hypogonadotropic hypogonadism in conjunction with Shapiro Syndrome.
Identification of Upper Respiratory Tract Pathogens Using Electrochemical Detection on an Oligonucleotide Microarray
Michael J. Lodes, Dominic Suciu, Jodi L. Wilmoth, Marty Ross, Sandra Munro, Kim Dix, Karen Bernards, Axel G. St?ver, Miguel Quintana, Naomi Iihoshi, Wanda J. Lyon, David L. Danley, Andrew McShea
PLOS ONE , 2007, DOI: 10.1371/journal.pone.0000924
Abstract: Bacterial and viral upper respiratory infections (URI) produce highly variable clinical symptoms that cannot be used to identify the etiologic agent. Proper treatment, however, depends on correct identification of the pathogen involved as antibiotics provide little or no benefit with viral infections. Here we describe a rapid and sensitive genotyping assay and microarray for URI identification using standard amplification and hybridization techniques, with electrochemical detection (ECD) on a semiconductor-based oligonucleotide microarray. The assay was developed to detect four bacterial pathogens (Bordetella pertussis, Streptococcus pyogenes, Chlamydia pneumoniae and Mycoplasma pneumoniae) and 9 viral pathogens (adenovirus 4, coronavirus OC43, 229E and HK, influenza A and B, parainfluinza types 1, 2, and 3 and respiratory syncytial virus. This new platform forms the basis for a fully automated diagnostics system that is very flexible and can be customized to suit different or additional pathogens. Multiple probes on a flexible platform allow one to test probes empirically and then select highly reactive probes for further iterative evaluation. Because ECD uses an enzymatic reaction to create electrical signals that can be read directly from the array, there is no need for image analysis or for expensive and delicate optical scanning equipment. We show assay sensitivity and specificity that are excellent for a multiplexed format.
The Impact of the Geologic History and Paleoclimate on the Diversification of East African Cichlids
Patrick D. Danley,Martin Husemann,Baoqing Ding,Lyndsay M. DiPietro,Emily J. Beverly,Daniel J. Peppe
International Journal of Evolutionary Biology , 2012, DOI: 10.1155/2012/574851
Abstract: The cichlid fishes of the East African Great Lakes are the largest extant vertebrate radiation identified to date. These lakes and their surrounding waters support over 2,000 species of cichlid fish, many of which are descended from a single common ancestor within the past 10?Ma. The extraordinary East African cichlid diversity is intricately linked to the highly variable geologic and paleoclimatic history of this region. Greater than 10?Ma, the western arm of the East African rift system began to separate, thereby creating a series of rift basins that would come to contain several water bodies, including the extremely deep Lakes Tanganyika and Malawi. Uplifting associated with this rifting backponded many rivers and created the extremely large, but shallow Lake Victoria. Since their creation, the size, shape, and existence of these lakes have changed dramatically which has, in turn, significantly influenced the evolutionary history of the lakes' cichlids. This paper reviews the geologic history and paleoclimate of the East African Great Lakes and the impact of these forces on the region's endemic cichlid flocks. 1. Introduction East Africa had a highly dynamic geological and ecological history. Over the past 35 million years (Ma), tectonic plates have shifted, rifts in the landscape have opened, rivers have reversed course, and lakes have formed and desiccated. It is within this environment that the world’s largest extant vertebrate radiation has originated. Centered within the East African Great Lakes, over 2,000 species of cichlid fish have diversified to fill nearly every niche available to a freshwater fish. All of these fish are endemic to East Africa, many are single lake endemics, and several are microendemics found only at isolated areas within a given lake. Here, we examine the geologic and climatic history of East Africa and discuss how these forces have influenced this spectacular vertebrate radiation. 1.1. Geologic Setting and East African Climate The East Africa rift system (EARS) is the roughly north-south alignment of rift basins in East Africa (Figure 1) that defines the boundary between the Somalian and African plates [2, 3]. The EARS is divided into two structural branches that are also oriented roughly north-south (Figure 1). Rifting in the eastern branch began ~30–35?Ma in the Afar and Ethiopian Plateau and propagated north-south until it impinged on the strong Precambrian Tanzanian cratonic block, which is in the center of the East Africa Plateau [4]. The extensional stress associated with the rifting or with widespread
A cricket Gene Index: a genomic resource for studying neurobiology, speciation, and molecular evolution
Patrick D Danley, Sean P Mullen, Fenglong Liu, Vishvanath Nene, John Quackenbush, Kerry L Shaw
BMC Genomics , 2007, DOI: 10.1186/1471-2164-8-109
Abstract: We report the sequencing of 14,502 EST's from clones derived from a nerve cord cDNA library, and the subsequent construction of a Gene Index from these sequences, from the Hawaiian trigonidiine cricket Laupala kohalensis. The Gene Index contains 8607 unique sequences comprised of 2575 tentative consensus (TC) sequences and 6032 singletons. For each of the unique sequences, an attempt was made to assign a provisional annotation and to categorize its function using a Gene Ontology-based classification through a sequence-based comparison to known proteins. In addition, a set of unique 70 base pair oligomers that can be used for DNA microarrays was developed. All Gene Index information is posted at the DFCI Gene Indices web pageOrthopterans are models used to understand the neurophysiological basis of complex motor patterns such as flight and stridulation. The sequences presented in the cricket Gene Index will provide neurophysiologists with many genetic tools that have been largely absent in this field. The cricket Gene Index is one of only two gene indices to be developed in an evolutionary model system. Species within the genus Laupala have speciated recently, rapidly, and extensively. Therefore, the genes identified in the cricket Gene Index can be used to study the genomics of speciation. Furthermore, this gene index represents a significant EST resources for basal insects. As such, this resource is a valuable comparative tool for the understanding of invertebrate molecular evolution. The sequences presented here will provide much needed genomic resources for three distinct but overlapping fields of inquiry: neurobiology, speciation, and molecular evolution.Identifying the genetic basis of interesting phenotypic variation in non-model systems is often limited by the lack of sophisticated molecular resources, such as complete genome sequences and DNA microarrys, that are available in model genetic taxa such as Drosophila [1], Anopheles [2], Caenorhabditis [3] and Ap
The influence of the different elements of an organic molecule structure on the main kinetic parameters of its unimolecular reaction in the high-pressure region  [PDF]
David Krinkin
Natural Science (NS) , 2011, DOI: 10.4236/ns.2011.38090
Abstract: The most general dynamic tendencies of the energy redistribution in the high-pressure region are considered. Their influence on the possible deviations from the kinetic conceptions, which is now generally accepted, is examined. In this way, the structural elements of an organic molecule that promote internal energy mobilization in the high-pressure region and, conversely, hamper it, are defined. The first of these elements reduces both the Arrhenius parameters of the unimolecular reactions while the second leads to the opposite results. Some well-known exceptions to existing kinetic theories, which find an explanation in the framework of these proposed concepts, is considered. The proposed concept is very general as distinct from the existing dynamic studies, which investigate more particular details of the separate bond behaviors. The proposed general concept can broaden the study of chemical kinetics.
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