Integration of Antibody Array Technology into Drug Discovery and Development.

PubMed

Huang, Wei; Whittaker, Kelly; Zhang, Huihua; Wu, Jian; Zhu, Si-Wei; Huang, Ruo-Pan

Antibody arrays represent a high-throughput technique that enables the parallel detection of multiple proteins with minimal sample volume requirements. In recent years, antibody arrays have been widely used to identify new biomarkers for disease diagnosis or prognosis. Moreover, many academic research laboratories and commercial biotechnology companies are starting to apply antibody arrays in the field of drug discovery. In this review, some technical aspects of antibody array development and the various platforms currently available will be addressed; however, the main focus will be on the discussion of antibody array technologies and their applications in drug discovery. Aspects of the drug discovery process, including target identification, mechanisms of drug resistance, molecular mechanisms of drug action, drug side effects, and the application in clinical trials and in managing patient care, which have been investigated using antibody arrays in recent literature will be examined and the relevance of this technology in progressing this process will be discussed. Protein profiling with antibody array technology, in addition to other applications, has emerged as a successful, novel approach for drug discovery because of the well-known importance of proteins in cell events and disease development.

Nanostructured aligned CNT platforms enhance the controlled release of a neurotrophic protein from polypyrrole

NASA Astrophysics Data System (ADS)

Thompson, Brianna C.; Chen, Jun; Moulton, Simon E.; Wallace, Gordon G.

2010-04-01

An aligned CNT array membrane electrode has been used as a nanostructured supporting platform for polypyrrole (PPy) films, exhibiting significant improvement in the controlled release of neurotrophin. In terms of linearity of release, stimulated to unstimulated control of NT-3 release and increased mass and % release of incorporated NT-3, the nanostructured material performed more favourably than the flat PPy film.

Reverse phase protein arrays in signaling pathways: a data integration perspective

PubMed Central

Creighton, Chad J; Huang, Shixia

2015-01-01

The reverse phase protein array (RPPA) data platform provides expression data for a prespecified set of proteins, across a set of tissue or cell line samples. Being able to measure either total proteins or posttranslationally modified proteins, even ones present at lower abundances, RPPA represents an excellent way to capture the state of key signaling transduction pathways in normal or diseased cells. RPPA data can be combined with those of other molecular profiling platforms, in order to obtain a more complete molecular picture of the cell. This review offers perspective on the use of RPPA as a component of integrative molecular analysis, using recent case examples from The Cancer Genome Altas consortium, showing how RPPA may provide additional insight into cancer besides what other data platforms may provide. There also exists a clear need for effective visualization approaches to RPPA-based proteomic results; this was highlighted by the recent challenge, put forth by the HPN-DREAM consortium, to develop visualization methods for a highly complex RPPA dataset involving many cancer cell lines, stimuli, and inhibitors applied over time course. In this review, we put forth a number of general guidelines for effective visualization of complex molecular datasets, namely, showing the data, ordering data elements deliberately, enabling generalization, focusing on relevant specifics, and putting things into context. We give examples of how these principles can be utilized in visualizing the intrinsic subtypes of breast cancer and in meaningfully displaying the entire HPN-DREAM RPPA dataset within a single page. PMID:26185419

The optics inside an automated single molecule array analyzer

NASA Astrophysics Data System (ADS)

McGuigan, William; Fournier, David R.; Watson, Gary W.; Walling, Les; Gigante, Bill; Duffy, David C.; Rissin, David M.; Kan, Cheuk W.; Meyer, Raymond E.; Piech, Tomasz; Fishburn, Matthew W.

2014-02-01

Quanterix and Stratec Biomedical have developed an instrument that enables the automated measurement of multiple proteins at concentration ~1000 times lower than existing immunoassays. The instrument is based on Quanterix's proprietary Single Molecule Array technology (Simoa™ ) that facilitates the detection and quantification of biomarkers previously difficult to measure, thus opening up new applications in life science research and in-vitro diagnostics. Simoa is based on trapping individual beads in arrays of femtoliter-sized wells that, when imaged with sufficient resolution, allows for counting of single molecules associated with each bead. When used to capture and detect proteins, this approach is known as digital ELISA (Enzyme-linked immunosorbent assay). The platform developed is a merger of many science and engineering disciplines. This paper concentrates on the optical technologies that have enabled the development of a fully-automated single molecule analyzer. At the core of the system is a custom, wide field-of-view, fluorescence microscope that images arrays of microwells containing single molecules bound to magnetic beads. A consumable disc containing 24 microstructure arrays was developed previously in collaboration with Sony DADC. The system cadence requirements, array dimensions, and requirement to detect single molecules presented significant optical challenges. Specifically, the wide field-of-view needed to image the entire array resulted in the need for a custom objective lens. Additionally, cost considerations for the system required a custom solution that leveraged the image processing capabilities. This paper will discuss the design considerations and resultant optical architecture that has enabled the development of an automated digital ELISA platform.

Metallic Nanohole Arrays on Fluoropolymer Substrates as Small Label-Free Real-Time Bioprobes

PubMed Central

Yang, Jiun-Chan; Ji, Jin; Hogle, James M.; Larson, Dale N.

2009-01-01

We describe a nanoplasmonic probing platform that exploits small-dimension (≤ 20 μm2) ordered arrays of subwavelength holes for multiplexed, high spatial resolution, and real-time analysis on biorecognition events. Nanohole arrays are perforated on a super smooth gold surface (roughness RMS < 2.7 Å) attached on a fluoropolymer (FEP) substrate fabricated by a replica technique. The smooth surface of gold provides a superb environment for fabricating nanometer features and uniform immobilization of biomolecules. The refractive index matching between FEP and biological solutions contributes to ∼ 20% improvement on the sensing performance. Spectral studies on a series of small-dimension nanohole arrays from 1 μm2 to 20 μm2 indicate that the plasmonic sensing sensitivity improves as the gold-solution contact area increases. Our results also demonstrate that nanohole arrays with dimension as small as 1 μm2 can be used to effectively detect biomolecular binding events and analyze the binding kinetics. The future scientific opportunities opened by this nanohole platform include highly multiplexed analysis of ligand interactions with membrane proteins on high quality supported lipid bilayers. PMID:18710296

Comprehensive comparison of three commercial human whole-exome capture platforms.

PubMed

Asan; Xu, Yu; Jiang, Hui; Tyler-Smith, Chris; Xue, Yali; Jiang, Tao; Wang, Jiawei; Wu, Mingzhi; Liu, Xiao; Tian, Geng; Wang, Jun; Wang, Jian; Yang, Huangming; Zhang, Xiuqing

2011-09-28

Exome sequencing, which allows the global analysis of protein coding sequences in the human genome, has become an effective and affordable approach to detecting causative genetic mutations in diseases. Currently, there are several commercial human exome capture platforms; however, the relative performances of these have not been characterized sufficiently to know which is best for a particular study. We comprehensively compared three platforms: NimbleGen's Sequence Capture Array and SeqCap EZ, and Agilent's SureSelect. We assessed their performance in a variety of ways, including number of genes covered and capture efficacy. Differences that may impact on the choice of platform were that Agilent SureSelect covered approximately 1,100 more genes, while NimbleGen provided better flanking sequence capture. Although all three platforms achieved similar capture specificity of targeted regions, the NimbleGen platforms showed better uniformity of coverage and greater genotype sensitivity at 30- to 100-fold sequencing depth. All three platforms showed similar power in exome SNP calling, including medically relevant SNPs. Compared with genotyping and whole-genome sequencing data, the three platforms achieved a similar accuracy of genotype assignment and SNP detection. Importantly, all three platforms showed similar levels of reproducibility, GC bias and reference allele bias. We demonstrate key differences between the three platforms, particularly advantages of solutions over array capture and the importance of a large gene target set.

A Step Closer to Membrane Protein Multiplexed Nanoarrays Using Biotin-Doped Polypyrrole

PubMed Central

2015-01-01

Whether for fundamental biological research or for diagnostic and drug discovery applications, protein micro- and nanoarrays are attractive technologies because of their low sample consumption, high-throughput, and multiplexing capabilities. However, the arraying platforms developed so far are still not able to handle membrane proteins, and specific methods to selectively immobilize these hydrophobic and fragile molecules are needed to understand their function and structural complexity. Here we integrate two technologies, electropolymerization and amphipols, to demonstrate the electrically addressable functionalization of micro- and nanosurfaces with membrane proteins. Gold surfaces are selectively modified by electrogeneration of a polymeric film in the presence of biotin, where avidin conjugates can then be selectively immobilized. The method is successfully applied to the preparation of protein-multiplexed arrays by sequential electropolymerization and biomolecular functionalization steps. The surface density of the proteins bound to the electrodes can be easily tuned by adjusting the amount of biotin deposited during electropolymerization. Amphipols are specially designed amphipathic polymers that provide a straightforward method to stabilize and add functionalities to membrane proteins. Exploiting the strong affinity of biotin for streptavidin, we anchor distinct membrane proteins onto different electrodes via a biotin-tagged amphipol. Antibody-recognition events demonstrate that the proteins are stably immobilized and that the electrodeposition of polypyrrole films bearing biotin units is compatible with the protein-binding activity. Since polypyrrole films show good conductivity properties, the platform described here is particularly well suited to prepare electronically transduced bionanosensors. PMID:24476392

A Liquid Array Platform For the Multiplexed Analysis of Synthetic Molecule-Protein Interactions

PubMed Central

Doran, Todd M.; Kodadek, Thomas

2014-01-01

Synthetic molecule microarrays, consisting of many different compounds spotted onto a planar surface such as modified glass or cellulose, have proven to be useful tools for the multiplexed analysis of small molecule- and peptide-protein interactions. However, these arrays are technically difficult to manufacture and use with high reproducibility and require specialized equipment. Here we report a more convenient alternative comprised of color-encoded beads that display a small molecule protein ligand on the surface. Quantitative, multiplexed assay of protein binding to up to 24 different ligands can be achieved using a common flow cytometer for the readout. This technology should be useful for evaluating hits from library screening efforts, the determination of structure activity relationships and for certain types of serological analyses. PMID:24245981

RPPAML/RIMS: A metadata format and an information management system for reverse phase protein arrays

PubMed Central

Stanislaus, Romesh; Carey, Mark; Deus, Helena F; Coombes, Kevin; Hennessy, Bryan T; Mills, Gordon B; Almeida, Jonas S

2008-01-01

Background Reverse Phase Protein Arrays (RPPA) are convenient assay platforms to investigate the presence of biomarkers in tissue lysates. As with other high-throughput technologies, substantial amounts of analytical data are generated. Over 1000 samples may be printed on a single nitrocellulose slide. Up to 100 different proteins may be assessed using immunoperoxidase or immunoflorescence techniques in order to determine relative amounts of protein expression in the samples of interest. Results In this report an RPPA Information Management System (RIMS) is described and made available with open source software. In order to implement the proposed system, we propose a metadata format known as reverse phase protein array markup language (RPPAML). RPPAML would enable researchers to describe, document and disseminate RPPA data. The complexity of the data structure needed to describe the results and the graphic tools necessary to visualize them require a software deployment distributed between a client and a server application. This was achieved without sacrificing interoperability between individual deployments through the use of an open source semantic database, S3DB. This data service backbone is available to multiple client side applications that can also access other server side deployments. The RIMS platform was designed to interoperate with other data analysis and data visualization tools such as Cytoscape. Conclusion The proposed RPPAML data format hopes to standardize RPPA data. Standardization of data would result in diverse client applications being able to operate on the same set of data. Additionally, having data in a standard format would enable data dissemination and data analysis. PMID:19102773

A gold nanohole array based surface-enhanced Raman scattering biosensor for detection of silver(I) and mercury(II) in human saliva†

PubMed Central

Zheng, Peng; Li, Ming; Jurevic, Richard; Cushing, Scott K.; Liu, Yuxin

2015-01-01

A surface-enhanced Raman scattering (SERS) biosensor has been developed by incorporating a gold nanohole array with a SERS probe (a gold nanostar@Raman-reporter@silica sandwich structure) into a single detection platform via DNA hybridization, which circumvents the nanoparticle aggregation and the inefficient Raman scattering issues. Strong plasmonic coupling between the Au nanostar and the Au nanohole array results in a large enhancement of the electromagnetic field, leading to amplification of the SERS signal. The SERS sensor has been used to detect Ag(i) and Hg(ii) ions in human saliva because both the metal ions could be released from dental amalgam fillings. The developed SERS sensor can be adapted as a general detection platform for non-invasive measurements of a wide range of analytes such as metal ions, small molecules, DNA and proteins in body fluids. PMID:26008641

A Pneumococcal Protein Array as a Platform to Discover Serodiagnostic Antigens Against Infection*

PubMed Central

Olaya-Abril, Alfonso; Jiménez-Munguía, Irene; Gómez-Gascón, Lidia; Obando, Ignacio; Rodríguez-Ortega, Manuel J.

2015-01-01

Pneumonia is one of the most common and severe diseases associated with Streptococcus pneumoniae infections in children and adults. Etiological diagnosis of pneumococcal pneumonia in children is generally challenging because of limitations of diagnostic tests and interference with nasopharyngeal colonizing strains. Serological assays have recently gained interest to overcome some problems found with current diagnostic tests in pediatric pneumococcal pneumonia. To provide insight into this field, we have developed a protein array to screen the antibody response to many antigens simultaneously. Proteins were selected by experimental identification from a collection of 24 highly prevalent pediatric clinical isolates in Spain, using a proteomics approach consisting of “shaving” the cell surface with proteases and further LC/MS/MS analysis. Ninety-five proteins were recombinantly produced and printed on an array. We probed it with a collection of sera from children with pneumococcal pneumonia. From the set of the most seroprevalent antigens, we obtained a clear discriminant response for a group of three proteins (PblB, PulA, and PrtA) in children under 4 years old. We validated the results by ELISA and an immunostrip assay showed the translation to easy-to-use, affordable tests. Thus, the protein array here developed presents a tool for broad use in serodiagnostics. PMID:26183717

Interdigitated array of Pt electrodes for electrical stimulation and engineering of aligned muscle tissue.

PubMed

Ahadian, Samad; Ramón-Azcón, Javier; Ostrovidov, Serge; Camci-Unal, Gulden; Hosseini, Vahid; Kaji, Hirokazu; Ino, Kosuke; Shiku, Hitoshi; Khademhosseini, Ali; Matsue, Tomokazu

2012-09-21

Engineered skeletal muscle tissues could be useful for applications in tissue engineering, drug screening, and bio-robotics. It is well-known that skeletal muscle cells are able to differentiate under electrical stimulation (ES), with an increase in myosin production, along with the formation of myofibers and contractile proteins. In this study, we describe the use of an interdigitated array of electrodes as a novel platform to electrically stimulate engineered muscle tissues. The resulting muscle myofibers were analyzed and quantified in terms of their myotube characteristics and gene expression. The engineered muscle tissues stimulated through the interdigitated array of electrodes demonstrated superior performance and maturation compared to the corresponding tissues stimulated through a conventional setup (i.e., through Pt wires in close proximity to the muscle tissue). In particular, the ES of muscle tissue (voltage 6 V, frequency 1 Hz and duration 10 ms for 1 day) through the interdigitated array of electrodes resulted in a higher degree of C2C12 myotube alignment (∼80%) as compared to ES using Pt wires (∼65%). In addition, higher amounts of C2C12 myotube coverage area, myotube length, muscle transcription factors and protein biomarkers were found for myotubes stimulated through the interdigitated array of electrodes compared to those stimulated using the Pt wires. Due to the wide array of potential applications of ES for two- and three-dimensional (2D and 3D) engineered tissues, the suggested platform could be employed for a variety of cell and tissue structures to more efficiently investigate their response to electrical fields.

A fluorescent immunoassay for the determination of procalcitonin and C-reactive protein

NASA Astrophysics Data System (ADS)

Baldini, F.; Bolzoni, L.; Giannetti, A.; Porro, G.; Senesi, F.; Trono, C.

2009-05-01

The discrimination of viral and bacterial sepsis is an important issue in intensive care patients. For this purpose, the simultaneous measurements of different analytes such as C-reactive protein (CRP), procalcitonin (PCT), myeloperoxidase, interleukines and neopterin, are necessary. A novel optical platform was designed and realised for the implementation of fluorescence-based immunoassays. The core of the optical platform is a plastic biochip, formed by a series of microchannels each of them devoted to the determination of a single analyte. Sandwich assays for CRP and PCT spiked in serum were performed in order to demonstrate the reliability of a multi-array device.

Fiber-optic microsphere-based antibody array for the analysis of inflammatory cytokines in saliva.

PubMed

Blicharz, Timothy M; Siqueira, Walter L; Helmerhorst, Eva J; Oppenheim, Frank G; Wexler, Philip J; Little, Frédéric F; Walt, David R

2009-03-15

Antibody microarrays have emerged as useful tools for high-throughput protein analysis and candidate biomarker screening. We describe here the development of a multiplexed microsphere-based antibody array capable of simultaneously measuring 10 inflammatory protein mediators. Cytokine-capture microspheres were fabricated by covalently coupling monoclonal antibodies specific for cytokines of interest to fluorescently encoded 3.1 microm polymer microspheres. An optical fiber bundle containing approximately 50,000 individual 3.1 microm diameter fibers was chemically etched to create microwells in which cytokine-capture microspheres could be deposited. Microspheres were randomly distributed in the wells to produce an antibody array for performing a multiplexed sandwich immunoassay. The array responded specifically to recombinant cytokine solutions in a concentration-dependent fashion. The array was also used to examine endogenous mediator patterns in saliva supernatants from patients with pulmonary inflammatory diseases such as asthma and chronic obstructive pulmonary disease (COPD). This array technology may prove useful as a laboratory-based platform for inflammatory disease research and diagnostics, and its small footprint could also enable integration into a microfluidic cassette for use in point-of-care testing.

Glycan array data management at Consortium for Functional Glycomics.

PubMed

Venkataraman, Maha; Sasisekharan, Ram; Raman, Rahul

2015-01-01

Glycomics or the study of structure-function relationships of complex glycans has reshaped post-genomics biology. Glycans mediate fundamental biological functions via their specific interactions with a variety of proteins. Recognizing the importance of glycomics, large-scale research initiatives such as the Consortium for Functional Glycomics (CFG) were established to address these challenges. Over the past decade, the Consortium for Functional Glycomics (CFG) has generated novel reagents and technologies for glycomics analyses, which in turn have led to generation of diverse datasets. These datasets have contributed to understanding glycan diversity and structure-function relationships at molecular (glycan-protein interactions), cellular (gene expression and glycan analysis), and whole organism (mouse phenotyping) levels. Among these analyses and datasets, screening of glycan-protein interactions on glycan array platforms has gained much prominence and has contributed to cross-disciplinary realization of the importance of glycomics in areas such as immunology, infectious diseases, cancer biomarkers, etc. This manuscript outlines methodologies for capturing data from glycan array experiments and online tools to access and visualize glycan array data implemented at the CFG.

Exploiting fluorescence for multiplex immunoassays on protein microarrays

NASA Astrophysics Data System (ADS)

Herbáth, Melinda; Papp, Krisztián; Balogh, Andrea; Matkó, János; Prechl, József

2014-09-01

Protein microarray technology is becoming the method of choice for identifying protein interaction partners, detecting specific proteins, carbohydrates and lipids, or for characterizing protein interactions and serum antibodies in a massively parallel manner. Availability of the well-established instrumentation of DNA arrays and development of new fluorescent detection instruments promoted the spread of this technique. Fluorescent detection has the advantage of high sensitivity, specificity, simplicity and wide dynamic range required by most measurements. Fluorescence through specifically designed probes and an increasing variety of detection modes offers an excellent tool for such microarray platforms. Measuring for example the level of antibodies, their isotypes and/or antigen specificity simultaneously can offer more complex and comprehensive information about the investigated biological phenomenon, especially if we take into consideration that hundreds of samples can be measured in a single assay. Not only body fluids, but also cell lysates, extracted cellular components, and intact living cells can be analyzed on protein arrays for monitoring functional responses to printed samples on the surface. As a rapidly evolving area, protein microarray technology offers a great bulk of information and new depth of knowledge. These are the features that endow protein arrays with wide applicability and robust sample analyzing capability. On the whole, protein arrays are emerging new tools not just in proteomics, but glycomics, lipidomics, and are also important for immunological research. In this review we attempt to summarize the technical aspects of planar fluorescent microarray technology along with the description of its main immunological applications.

Analysis of Multiplexed Nanosensor Arrays Based on Near-Infrared Fluorescent Single-Walled Carbon Nanotubes.

PubMed

Dong, Juyao; Salem, Daniel P; Sun, Jessica H; Strano, Michael S

2018-04-24

The high-throughput, label-free detection of biomolecules remains an important challenge in analytical chemistry with the potential of nanosensors to significantly increase the ability to multiplex such assays. In this work, we develop an optical sensor array, printable from a single-walled carbon nanotube/chitosan ink and functionalized to enable a divalent ion-based proximity quenching mechanism for transducing binding between a capture protein or an antibody with the target analyte. Arrays of 5 × 6, 200 μm near-infrared (nIR) spots at a density of ≈300 spots/cm 2 are conjugated with immunoglobulin-binding proteins (proteins A, G, and L) for the detection of human IgG, mouse IgM, rat IgG2a, and human IgD. Binding kinetics are measured in a parallel, multiplexed fashion from each sensor spot using a custom laser scanning imaging configuration with an nIR photomultiplier tube detector. These arrays are used to examine cross-reactivity, competitive and nonspecific binding of analyte mixtures. We find that protein G and protein L functionalized sensors report selective responses to mouse IgM on the latter, as anticipated. Optically addressable platforms such as the one examined in this work have potential to significantly advance the real-time, multiplexed biomolecular detection of complex mixtures.

Innovations in biomedical nanoengineering: nanowell array biosensor.

PubMed

Seo, YoungTae; Jeong, Sunil; Lee, JuKyung; Choi, Hak Soo; Kim, Jonghan; Lee, HeaYeon

2018-01-01

Nanostructured biosensors have pioneered biomedical engineering by providing highly sensitive analyses of biomolecules. The nanowell array (NWA)-based biosensing platform is particularly innovative, where the small size of NWs within the array permits extremely profound sensing of a small quantity of biomolecules. Undoubtedly, the NWA geometry of a gently-sloped vertical wall is critical for selective docking of specific proteins without capillary resistances, and nanoprocessing has contributed to the fabrication of NWA electrodes on gold substrate such as molding process, e-beam lithography, and krypton-fluoride (KrF) stepper semiconductor method. The Lee group at the Mara Nanotech has established this NW-based biosensing technology during the past two decades by engineering highly sensitive electrochemical sensors and providing a broad range of detection methods from large molecules (e.g., cells or proteins) to small molecules (e.g., DNA and RNA). Nanosized gold dots in the NWA enhance the detection of electrochemical biosensing to the range of zeptomoles in precision against the complementary target DNA molecules. In this review, we discuss recent innovations in biomedical nanoengineering with a specific focus on novel NWA-based biosensors. We also describe our continuous efforts in achieving a label-free detection without non-specific binding while maintaining the activity and stability of immobilized biomolecules. This research can lay the foundation of a new platform for biomedical nanoengineering systems.

Innovations in biomedical nanoengineering: nanowell array biosensor

NASA Astrophysics Data System (ADS)

Seo, YoungTae; Jeong, Sunil; Lee, JuKyung; Choi, Hak Soo; Kim, Jonghan; Lee, HeaYeon

2018-04-01

Nanostructured biosensors have pioneered biomedical engineering by providing highly sensitive analyses of biomolecules. The nanowell array (NWA)-based biosensing platform is particularly innovative, where the small size of NWs within the array permits extremely profound sensing of a small quantity of biomolecules. Undoubtedly, the NWA geometry of a gently-sloped vertical wall is critical for selective docking of specific proteins without capillary resistances, and nanoprocessing has contributed to the fabrication of NWA electrodes on gold substrate such as molding process, e-beam lithography, and krypton-fluoride (KrF) stepper semiconductor method. The Lee group at the Mara Nanotech has established this NW-based biosensing technology during the past two decades by engineering highly sensitive electrochemical sensors and providing a broad range of detection methods from large molecules (e.g., cells or proteins) to small molecules (e.g., DNA and RNA). Nanosized gold dots in the NWA enhance the detection of electrochemical biosensing to the range of zeptomoles in precision against the complementary target DNA molecules. In this review, we discuss recent innovations in biomedical nanoengineering with a specific focus on novel NWA-based biosensors. We also describe our continuous efforts in achieving a label-free detection without non-specific binding while maintaining the activity and stability of immobilized biomolecules. This research can lay the foundation of a new platform for biomedical nanoengineering systems.

Listeriomics: an Interactive Web Platform for Systems Biology of Listeria

PubMed Central

Koutero, Mikael; Tchitchek, Nicolas; Cerutti, Franck; Lechat, Pierre; Maillet, Nicolas; Hoede, Claire; Chiapello, Hélène; Gaspin, Christine

2017-01-01

ABSTRACT As for many model organisms, the amount of Listeria omics data produced has recently increased exponentially. There are now >80 published complete Listeria genomes, around 350 different transcriptomic data sets, and 25 proteomic data sets available. The analysis of these data sets through a systems biology approach and the generation of tools for biologists to browse these various data are a challenge for bioinformaticians. We have developed a web-based platform, named Listeriomics, that integrates different tools for omics data analyses, i.e., (i) an interactive genome viewer to display gene expression arrays, tiling arrays, and sequencing data sets along with proteomics and genomics data sets; (ii) an expression and protein atlas that connects every gene, small RNA, antisense RNA, or protein with the most relevant omics data; (iii) a specific tool for exploring protein conservation through the Listeria phylogenomic tree; and (iv) a coexpression network tool for the discovery of potential new regulations. Our platform integrates all the complete Listeria species genomes, transcriptomes, and proteomes published to date. This website allows navigation among all these data sets with enriched metadata in a user-friendly format and can be used as a central database for systems biology analysis. IMPORTANCE In the last decades, Listeria has become a key model organism for the study of host-pathogen interactions, noncoding RNA regulation, and bacterial adaptation to stress. To study these mechanisms, several genomics, transcriptomics, and proteomics data sets have been produced. We have developed Listeriomics, an interactive web platform to browse and correlate these heterogeneous sources of information. Our website will allow listeriologists and microbiologists to decipher key regulation mechanism by using a systems biology approach. PMID:28317029

Electrocatalysis in DNA Sensors

PubMed Central

Furst, Ariel; Hill, Michael G.; Barton, Jacqueline K.

2014-01-01

Electrocatalysis is often thought of solely in the inorganic realm, most often applied to energy conversion in fuel cells. However, the ever-growing field of bioelectrocatalysis has made great strides in advancing technology for both biofuel cells as well as biological detection platforms. Within the context of bioelectrocatalytic detection systems, DNA-based platforms are especially prevalent. One subset of these platforms, the one we have developed, takes advantage of the inherent charge transport properties of DNA. Electrocatalysis coupled with DNA-mediated charge transport has enabled specific and sensitive detection of lesions, mismatches and DNA-binding proteins. Even greater signal amplification from these platforms is now being achieved through the incorporation of a secondary electrode to the platform both for patterning DNA arrays and for detection. Here, we describe the evolution of this new DNA sensor technology. PMID:25435647

Electrocatalysis in DNA Sensors.

PubMed

Furst, Ariel; Hill, Michael G; Barton, Jacqueline K

2014-12-14

Electrocatalysis is often thought of solely in the inorganic realm, most often applied to energy conversion in fuel cells. However, the ever-growing field of bioelectrocatalysis has made great strides in advancing technology for both biofuel cells as well as biological detection platforms. Within the context of bioelectrocatalytic detection systems, DNA-based platforms are especially prevalent. One subset of these platforms, the one we have developed, takes advantage of the inherent charge transport properties of DNA. Electrocatalysis coupled with DNA-mediated charge transport has enabled specific and sensitive detection of lesions, mismatches and DNA-binding proteins. Even greater signal amplification from these platforms is now being achieved through the incorporation of a secondary electrode to the platform both for patterning DNA arrays and for detection. Here, we describe the evolution of this new DNA sensor technology.

Circulating and synovial antibody profiling of juvenile arthritis patients by nucleic acid programmable protein arrays

PubMed Central

2012-01-01

Introduction Juvenile idiopathic arthritis (JIA) is a heterogeneous disease characterized by chronic joint inflammation of unknown cause in children. JIA is an autoimmune disease and small numbers of autoantibodies have been reported in JIA patients. The identification of antibody markers could improve the existing clinical management of patients. Methods A pilot study was performed on the application of a high-throughput platform, the nucleic acid programmable protein array (NAPPA), to assess the levels of antibodies present in the systemic circulation and synovial joint of a small cohort of juvenile arthritis patients. Plasma and synovial fluid from 10 JIA patients was screened for antibodies against 768 proteins on NAPPAs. Results Quantitative reproducibility of NAPPAs was demonstrated with > 0.95 intra-array and inter-array correlations. A strong correlation was also observed for the levels of antibodies between plasma and synovial fluid across the study cohort (r = 0.96). Differences in the levels of 18 antibodies were revealed between sample types across all patients. Patients were segregated into two clinical subtypes with distinct antibody signatures by unsupervised hierarchical cluster analysis. Conclusion The NAPPAs provide a high-throughput quantitatively reproducible platform to screen for disease-specific autoantibodies at the proteome level on a microscope slide. The strong correlation between the circulating antibody levels and those of the inflamed joint represents a novel finding and provides confidence to use plasma for discovery of autoantibodies in JIA, thus circumventing the challenges associated with joint aspiration. We expect that autoantibody profiling of JIA patients on NAPPAs could yield antibody markers that can act as criteria to stratify patients, predict outcomes and understand disease etiology at the molecular level. PMID:22510425

Molecular Occupancy of Nanodot Arrays.

PubMed

Cai, Haogang; Wolfenson, Haguy; Depoil, David; Dustin, Michael L; Sheetz, Michael P; Wind, Shalom J

2016-04-26

Single-molecule nanodot arrays, in which a biomolecule of choice (protein, nucleic acid, etc.) is bound to a metallic nanoparticle on a solid substrate, are becoming an increasingly important tool in the study of biomolecular and cellular interactions. We have developed an on-chip measurement protocol to monitor and control the molecular occupancy of nanodots. Arrays of widely spaced nanodots and nanodot clusters were fabricated on glass surfaces by nanolithography and functionalized with fluorescently labeled proteins. The molecular occupancy was determined by monitoring individual fluorophore bleaching events, while accounting for fluorescence quenching effects. We found that the occupancy can be interpreted as a packing problem, and depends on nanodot size and binding ligand concentration, where the latter is easily adjusted to compensate the flexibility of dimension control in nanofabrication. The results are scalable with nanodot cluster size, extending to large area close packed arrays. As an example, the nanoarray platform was used to probe the geometric requirement of T-cell activation at the single-molecule level.

Explore, Visualize, and Analyze Functional Cancer Proteomic Data Using the Cancer Proteome Atlas. | Office of Cancer Genomics

Cancer.gov

Reverse-phase protein arrays (RPPA) represent a powerful functional proteomic approach to elucidate cancer-related molecular mechanisms and to develop novel cancer therapies. To facilitate community-based investigation of the large-scale protein expression data generated by this platform, we have developed a user-friendly, open-access bioinformatic resource, The Cancer Proteome Atlas (TCPA, http://tcpaportal.org), which contains two separate web applications.

Proteomics Analysis of Cancer Exosomes Using a Novel Modified Aptamer-based Array (SOMAscanTM) Platform*

PubMed Central

Webber, Jason; Stone, Timothy C.; Katilius, Evaldas; Smith, Breanna C.; Gordon, Bridget; Mason, Malcolm D.; Tabi, Zsuzsanna; Brewis, Ian A.; Clayton, Aled

2014-01-01

We have used a novel affinity-based proteomics technology to examine the protein signature of small secreted extracellular vesicles called exosomes. The technology uses a new class of protein binding reagents called SOMAmers® (slow off-rate modified aptamers) and allows the simultaneous precise measurement of over 1000 proteins. Exosomes were highly purified from the Du145 prostate cancer cell line, by pooling selected fractions from a continuous sucrose gradient (within the density range of 1.1 to 1.2 g/ml), and examined under standard conditions or with additional detergent treatment by the SOMAscanTM array (version 3.0). Lysates of Du145 cells were also prepared, and the profiles were compared. Housekeeping proteins such as cyclophilin-A, LDH, and Hsp70 were present in exosomes, and we identified almost 100 proteins that were enriched in exosomes relative to cells. These included proteins of known association with cancer exosomes such as MFG-E8, integrins, and MET, and also those less widely reported as exosomally associated, such as ROR1 and ITIH4. Several proteins with no previously known exosomal association were confirmed as exosomally expressed in experiments using individual SOMAmer® reagents or antibodies in micro-plate assays. Western blotting confirmed the SOMAscanTM-identified enrichment of exosomal NOTCH-3, L1CAM, RAC1, and ADAM9. In conclusion, we describe here over 300 proteins of hitherto unknown association with prostate cancer exosomes and suggest that the SOMAmer®-based assay technology is an effective proteomics platform for exosome-associated biomarker discovery in diverse clinical settings. PMID:24505114

Co-Immobilization of Proteins and DNA Origami Nanoplates to Produce High-Contrast Biomolecular Nanoarrays.

PubMed

Hager, Roland; Burns, Jonathan R; Grydlik, Martyna J; Halilovic, Alma; Haselgrübler, Thomas; Schäffler, Friedrich; Howorka, Stefan

2016-06-01

The biofunctionalization of nanopatterned surfaces with DNA origami nanostructures is an important topic in nanobiotechnology. An unexplored challenge is, however, to co-immobilize proteins with DNA origami at pre-determined substrate sites in high contrast relative to the nontarget areas. The immobilization should, in addition, preferably be achieved on a transparent substrate to allow ultrasensitive optical detection. If successful, specific co-binding would be a step towards stoichiometrically defined arrays with few to individual protein molecules per site. Here, we successfully immobilize with high specificity positively charged avidin proteins and negatively charged DNA origami nanoplates on 100 nm-wide carbon nanoislands while suppressing undesired adsorption to surrounding nontarget areas. The arrays on glass slides achieve unprecedented selectivity factors of up to 4000 and allow ultrasensitive fluorescence read-out. The co-immobilization onto the nanoislands leads to layered biomolecular architectures, which are functional because bound DNA origami influences the number of capturing sites on the nanopatches for other proteins. The novel hybrid DNA origami-protein nanoarrays allow the fabrication of versatile research platforms for applications in biosensing, biophysics, and cell biology, and, in addition, represent an important step towards single-molecule protein arrays. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Layer-by-layer cell membrane assembly

NASA Astrophysics Data System (ADS)

Matosevic, Sandro; Paegel, Brian M.

2013-11-01

Eukaryotic subcellular membrane systems, such as the nuclear envelope or endoplasmic reticulum, present a rich array of architecturally and compositionally complex supramolecular targets that are as yet inaccessible. Here we describe layer-by-layer phospholipid membrane assembly on microfluidic droplets, a route to structures with defined compositional asymmetry and lamellarity. Starting with phospholipid-stabilized water-in-oil droplets trapped in a static droplet array, lipid monolayer deposition proceeds as oil/water-phase boundaries pass over the droplets. Unilamellar vesicles assembled layer-by-layer support functional insertion both of purified and of in situ expressed membrane proteins. Synthesis and chemical probing of asymmetric unilamellar and double-bilayer vesicles demonstrate the programmability of both membrane lamellarity and lipid-leaflet composition during assembly. The immobilized vesicle arrays are a pragmatic experimental platform for biophysical studies of membranes and their associated proteins, particularly complexes that assemble and function in multilamellar contexts in vivo.

arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays

PubMed Central

Menten, Björn; Pattyn, Filip; De Preter, Katleen; Robbrecht, Piet; Michels, Evi; Buysse, Karen; Mortier, Geert; De Paepe, Anne; van Vooren, Steven; Vermeesch, Joris; Moreau, Yves; De Moor, Bart; Vermeulen, Stefan; Speleman, Frank; Vandesompele, Jo

2005-01-01

Background The availability of the human genome sequence as well as the large number of physically accessible oligonucleotides, cDNA, and BAC clones across the entire genome has triggered and accelerated the use of several platforms for analysis of DNA copy number changes, amongst others microarray comparative genomic hybridization (arrayCGH). One of the challenges inherent to this new technology is the management and analysis of large numbers of data points generated in each individual experiment. Results We have developed arrayCGHbase, a comprehensive analysis platform for arrayCGH experiments consisting of a MIAME (Minimal Information About a Microarray Experiment) supportive database using MySQL underlying a data mining web tool, to store, analyze, interpret, compare, and visualize arrayCGH results in a uniform and user-friendly format. Following its flexible design, arrayCGHbase is compatible with all existing and forthcoming arrayCGH platforms. Data can be exported in a multitude of formats, including BED files to map copy number information on the genome using the Ensembl or UCSC genome browser. Conclusion ArrayCGHbase is a web based and platform independent arrayCGH data analysis tool, that allows users to access the analysis suite through the internet or a local intranet after installation on a private server. ArrayCGHbase is available at . PMID:15910681

High-density, microsphere-based fiber optic DNA microarrays.

PubMed

Epstein, Jason R; Leung, Amy P K; Lee, Kyong Hoon; Walt, David R

2003-05-01

A high-density fiber optic DNA microarray has been developed consisting of oligonucleotide-functionalized, 3.1-microm-diameter microspheres randomly distributed on the etched face of an imaging fiber bundle. The fiber bundles are comprised of 6000-50000 fused optical fibers and each fiber terminates with an etched well. The microwell array is capable of housing complementary-sized microspheres, each containing thousands of copies of a unique oligonucleotide probe sequence. The array fabrication process results in random microsphere placement. Determining the position of microspheres in the random array requires an optical encoding scheme. This array platform provides many advantages over other array formats. The microsphere-stock suspension concentration added to the etched fiber can be controlled to provide inherent sensor redundancy. Examining identical microspheres has a beneficial effect on the signal-to-noise ratio. As other sequences of interest are discovered, new microsphere sensing elements can be added to existing microsphere pools and new arrays can be fabricated incorporating the new sequences without altering the existing detection capabilities. These microarrays contain the smallest feature sizes (3 microm) of any DNA array, allowing interrogation of extremely small sample volumes. Reducing the feature size results in higher local target molecule concentrations, creating rapid and highly sensitive assays. The microsphere array platform is also flexible in its applications; research has included DNA-protein interaction profiles, microbial strain differentiation, and non-labeled target interrogation with molecular beacons. Fiber optic microsphere-based DNA microarrays have a simple fabrication protocol enabling their expansion into other applications, such as single cell-based assays.

Smart polymer brush nanostructures guide the self-assembly of pore-spanning lipid bilayers with integrated membrane proteins

NASA Astrophysics Data System (ADS)

Wilhelmina de Groot, G.; Demarche, Sophie; Santonicola, M. Gabriella; Tiefenauer, Louis; Vancso, G. Julius

2014-01-01

Nanopores in arrays on silicon chips are functionalized with pH-responsive poly(methacrylic acid) (PMAA) brushes and used as supports for pore-spanning lipid bilayers with integrated membrane proteins. Robust platforms are created by the covalent grafting of polymer brushes using surface-initiated atom transfer radical polymerization (ATRP), resulting in sensor chips that can be successfully reused over several assays. His-tagged proteins are selectively and reversibly bound to the nitrilotriacetic acid (NTA) functionalization of the PMAA brush, and consequently lipid bilayer membranes are formed. The enhanced membrane resistance as determined by electrochemical impedance spectroscopy and free diffusion of dyed lipids observed as fluorescence recovery after photobleaching confirmed the presence of lipid bilayers. Immobilization of the His-tagged membrane proteins on the NTA-modified PMAA brush near the pore edges is characterized by fluorescence microscopy. This system allows us to adjust the protein density in free-standing bilayers, which are stabilized by the polymer brush underneath. The potential application of the integrated platform for ion channel protein assays is demonstrated.

Optimized acoustic biochip integrated with microfluidics for biomarkers detection in molecular diagnostics.

PubMed

Papadakis, G; Friedt, J M; Eck, M; Rabus, D; Jobst, G; Gizeli, E

2017-09-01

The development of integrated platforms incorporating an acoustic device as the detection element requires addressing simultaneously several challenges of technological and scientific nature. The present work was focused on the design of a microfluidic module, which, combined with a dual or array type Love wave acoustic chip could be applied to biomedical applications and molecular diagnostics. Based on a systematic study we optimized the mechanics of the flow cell attachment and the sealing material so that fluidic interfacing/encapsulation would impose minimal losses to the acoustic wave. We have also investigated combinations of operating frequencies with waveguide materials and thicknesses for maximum sensitivity during the detection of protein and DNA biomarkers. Within our investigations neutravidin was used as a model protein biomarker and unpurified PCR amplified Salmonella DNA as the model genetic target. Our results clearly indicate the need for experimental verification of the optimum engineering and analytical parameters, in order to develop commercially viable systems for integrated analysis. The good reproducibility of the signal together with the ability of the array biochip to detect multiple samples hold promise for the future use of the integrated system in a Lab-on-a-Chip platform for application to molecular diagnostics.

Screening of Osteogenic-Enhancing Short Peptides from BMPs for Biomimetic Material Applications

PubMed Central

Kanie, Kei; Kurimoto, Rio; Tian, Jing; Ebisawa, Katsumi; Narita, Yuji; Honda, Hiroyuki; Kato, Ryuji

2016-01-01

Bone regeneration is an important issue in many situations, such as bone fracture and surgery. Umbilical cord mesenchymal stem cells (UC-MSCs) are promising cell sources for bone regeneration. Bone morphogenetic proteins and their bioactive peptides are biomolecules known to enhance the osteogenic differentiation of MSCs. However, fibrosis can arise during the development of implantable biomaterials. Therefore, it is important to control cell organization by enhancing osteogenic proliferation and differentiation and inhibiting fibroblast proliferation. Thus, we focused on the screening of such osteogenic-enhancing peptides. In the present study, we developed new peptide array screening platforms to evaluate cell proliferation and alkaline phosphatase activity in osteoblasts, UC-MSCs and fibroblasts. The conditions for the screening platform were first defined using UC-MSCs and an osteogenic differentiation peptide known as W9. Next, in silico screening to define the candidate peptides was carried out to evaluate the homology of 19 bone morphogenetic proteins. Twenty-five candidate 9-mer peptides were selected for screening. Finally, the screening of osteogenic-enhancing (osteogenic cell-selective proliferation and osteogenic differentiation) short peptide was carried out using the peptide array method, and three osteogenic-enhancing peptides were identified, confirming the validity of this screening. PMID:28773850

Duplexed sandwich immunoassays on a fiber-optic microarray.

PubMed

Rissin, David M; Walt, David R

2006-03-30

In this paper, we describe a duplexed imaging optical fiber array-based immunoassay for immunoglobulin A (IgA) and lactoferrin. To fabricate the individually addressable array, microspheres were functionalized with highly specific monoclonal antibodies. The microspheres were loaded in microwells etched into the distal face of an imaging optical fiber bundle. Two microsphere-based sandwich immunoassays were developed to simultaneously detect IgA and lactoferrin, two innate immune system proteins found in human saliva. Individual microspheres could be interrogated for the simultaneous measurement of both proteins. The working concentration range for IgA detection was between 700 pM and 100 nM, while the working concentration range for lactoferrin was between 385 pM and 10 nM. The cross-reactivity between detection antibodies and their non-specific targets was relatively low in comparison to the signal generated by the specific binding with their targets. These results suggest that the degree of multiplexing on this fiber-optic array platform can be increased beyond a duplex.

Increasing the sensitivity of reverse phase protein arrays by antibody-mediated signal amplification

PubMed Central

2010-01-01

Background Reverse phase protein arrays (RPPA) emerged as a useful experimental platform to analyze biological samples in a high-throughput format. Different signal detection methods have been described to generate a quantitative readout on RPPA including the use of fluorescently labeled antibodies. Increasing the sensitivity of RPPA approaches is important since many signaling proteins or posttranslational modifications are present at a low level. Results A new antibody-mediated signal amplification (AMSA) strategy relying on sequential incubation steps with fluorescently-labeled secondary antibodies reactive against each other is introduced here. The signal quantification is performed in the near-infrared range. The RPPA-based analysis of 14 endogenous proteins in seven different cell lines demonstrated a strong correlation (r = 0.89) between AMSA and standard NIR detection. Probing serial dilutions of human cancer cell lines with different primary antibodies demonstrated that the new amplification approach improved the limit of detection especially for low abundant target proteins. Conclusions Antibody-mediated signal amplification is a convenient and cost-effective approach for the robust and specific quantification of low abundant proteins on RPPAs. Contrasting other amplification approaches it allows target protein detection over a large linear range. PMID:20569466

Simultaneous electrical recording of cardiac electrophysiology and contraction on chip

DOE PAGES

Qian, Fang; Huang, Chao; Lin, Yi-Dong; ...

2017-04-18

Prevailing commercialized cardiac platforms for in vitro drug development utilize planar microelectrode arrays to map action potentials, or impedance sensing to record contraction in real time, but cannot record both functions on the same chip with high spatial resolution. We report a novel cardiac platform that can record cardiac tissue adhesion, electrophysiology, and contractility on the same chip. The platform integrates two independent yet interpenetrating sensor arrays: a microelectrode array for field potential readouts and an interdigitated electrode array for impedance readouts. Together, these arrays provide real-time, non-invasive data acquisition of both cardiac electrophysiology and contractility under physiological conditions andmore » under drug stimuli. Furthermore, we cultured human induced pluripotent stem cell-derived cardiomyocytes as a model system, and used to validate the platform with an excitation–contraction decoupling chemical. Preliminary data using the platform to investigate the effect of the drug norepinephrine are combined with computational efforts. Finally, this platform provides a quantitative and predictive assay system that can potentially be used for comprehensive assessment of cardiac toxicity earlier in the drug discovery process.« less

Simultaneous electrical recording of cardiac electrophysiology and contraction on chip

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qian, Fang; Huang, Chao; Lin, Yi-Dong

Prevailing commercialized cardiac platforms for in vitro drug development utilize planar microelectrode arrays to map action potentials, or impedance sensing to record contraction in real time, but cannot record both functions on the same chip with high spatial resolution. We report a novel cardiac platform that can record cardiac tissue adhesion, electrophysiology, and contractility on the same chip. The platform integrates two independent yet interpenetrating sensor arrays: a microelectrode array for field potential readouts and an interdigitated electrode array for impedance readouts. Together, these arrays provide real-time, non-invasive data acquisition of both cardiac electrophysiology and contractility under physiological conditions andmore » under drug stimuli. Furthermore, we cultured human induced pluripotent stem cell-derived cardiomyocytes as a model system, and used to validate the platform with an excitation–contraction decoupling chemical. Preliminary data using the platform to investigate the effect of the drug norepinephrine are combined with computational efforts. Finally, this platform provides a quantitative and predictive assay system that can potentially be used for comprehensive assessment of cardiac toxicity earlier in the drug discovery process.« less

Microfluidic platform for optimization of crystallization conditions

NASA Astrophysics Data System (ADS)

Zhang, Shuheng; Gerard, Charline J. J.; Ikni, Aziza; Ferry, Gilles; Vuillard, Laurent M.; Boutin, Jean A.; Ferte, Nathalie; Grossier, Romain; Candoni, Nadine; Veesler, Stéphane

2017-08-01

We describe a universal, high-throughput droplet-based microfluidic platform for crystallization. It is suitable for a multitude of applications, due to its flexibility, ease of use, compatibility with all solvents and low cost. The platform offers four modular functions: droplet formation, on-line characterization, incubation and observation. We use it to generate droplet arrays with a concentration gradient in continuous long tubing, without using surfactant. We control droplet properties (size, frequency and spacing) in long tubing by using hydrodynamic empirical relations. We measure droplet chemical composition using both an off-line and a real-time on-line method. Applying this platform to a complicated chemical environment, membrane proteins, we successfully handle crystallization, suggesting that the platform is likely to perform well in other circumstances. We validate the platform for fine-gradient screening and optimization of crystallization conditions. Additional on-line detection methods may well be integrated into this platform in the future, for instance, an on-line diffraction technique. We believe this method could find applications in fields such as fluid interaction engineering, live cell study and enzyme kinetics.

Multiplexed evaluation of capture agent binding kinetics using arrays of silicon photonic microring resonators.

PubMed

Byeon, Ji-Yeon; Bailey, Ryan C

2011-09-07

High affinity capture agents recognizing biomolecular targets are essential in the performance of many proteomic detection methods. Herein, we report the application of a label-free silicon photonic biomolecular analysis platform for simultaneously determining kinetic association and dissociation constants for two representative protein capture agents: a thrombin-binding DNA aptamer and an anti-thrombin monoclonal antibody. The scalability and inherent multiplexing capability of the technology make it an attractive platform for simultaneously evaluating the binding characteristics of multiple capture agents recognizing the same target antigen, and thus a tool complementary to emerging high-throughput capture agent generation strategies.

Near-infrared photoluminescence biosensing platform with gold nanorods-over-gallium arsenide nanohorn array.

PubMed

Zhang, Yiming; Jiang, Tao; Tang, Longhua

2017-11-15

The near-infrared (NIR) optical detection of biomolecules with high sensitivity and reliability have been expected, however, it is still a challenge. In this work, we present a gold nanorods (AuNRs)-over-gallium arsenide nanohorn-like array (GaAs NHA) system that can be used for the ultrasensitive and specific NIR photoluminescence (PL) detection of DNA and proteins. The fabrication of GaAs NHA involved the technique of colloidal lithography and inductively coupled plasma dry etching, yielding large-area and well-defined nanostructural array, and exhibiting an improved PL emission compared to the planar GaAs substrate. Importantly, we found that the DNA-bridged AuNRs attachment on NHA could further improve the PL intensity from GaAs, and thereby provide the basis for the NIR optical sensing of biological analytes. We demonstrated that DNA and thrombin could be sensitively and specifically detected, with the detection limit of 1 pM for target DNA and 10 pM for thrombin. Such ultrasensitive NIR optical platform can extend to the detection of other biomarkers and is promising for clinical diagnostics. Copyright © 2017 Elsevier B.V. All rights reserved.

Dynamic, electronically switchable surfaces for membrane protein microarrays.

PubMed

Tang, C S; Dusseiller, M; Makohliso, S; Heuschkel, M; Sharma, S; Keller, B; Vörös, J

2006-02-01

Microarray technology is a powerful tool that provides a high throughput of bioanalytical information within a single experiment. These miniaturized and parallelized binding assays are highly sensitive and have found widespread popularity especially during the genomic era. However, as drug diagnostics studies are often targeted at membrane proteins, the current arraying technologies are ill-equipped to handle the fragile nature of the protein molecules. In addition, to understand the complex structure and functions of proteins, different strategies to immobilize the probe molecules selectively onto a platform for protein microarray are required. We propose a novel approach to create a (membrane) protein microarray by using an indium tin oxide (ITO) microelectrode array with an electronic multiplexing capability. A polycationic, protein- and vesicle-resistant copolymer, poly(l-lysine)-grafted-poly(ethylene glycol) (PLL-g-PEG), is exposed to and adsorbed uniformly onto the microelectrode array, as a passivating adlayer. An electronic stimulation is then applied onto the individual ITO microelectrodes resulting in the localized release of the polymer thus revealing a bare ITO surface. Different polymer and biological moieties are specifically immobilized onto the activated ITO microelectrodes while the other regions remain protein-resistant as they are unaffected by the induced electrical potential. The desorption process of the PLL-g-PEG is observed to be highly selective, rapid, and reversible without compromising on the integrity and performance of the conductive ITO microelectrodes. As such, we have successfully created a stable and heterogeneous microarray of biomolecules by using selective electronic addressing on ITO microelectrodes. Both pharmaceutical diagnostics and biomedical technology are expected to benefit directly from this unique method.

Plasmonic Nanoholes in a Multi-Channel Microarray Format for Parallel Kinetic Assays and Differential Sensing

PubMed Central

Im, Hyungsoon; Lesuffleur, Antoine; Lindquist, Nathan C.; Oh, Sang-Hyun

2009-01-01

We present nanohole arrays in a gold film integrated with a 6-channel microfluidic chip for parallel measurements of molecular binding kinetics. Surface plasmon resonance effects in the nanohole arrays enable real-time label-free measurements of molecular binding events in each channel, while adjacent negative reference channels can record measurement artifacts such as bulk solution index changes, temperature variations, or changing light absorption in the liquid. Using this platform, streptavidin-biotin specific binding kinetics are measured at various concentrations with negative controls. A high-density microarray of 252 biosensing pixels is also demonstrated with a packing density of 106 sensing elements/cm2, which can potentially be coupled with a massively parallel array of microfluidic channels for protein microarray applications. PMID:19284776

Integrated microfluidic platforms for investigating neuronal networks

NASA Astrophysics Data System (ADS)

Kim, Hyung Joon

This dissertation describes the development and application of integrated microfluidics-based assay platforms to study neuronal activities in the nervous system in-vitro. The assay platforms were fabricated using soft lithography and micro/nano fabrication including microfluidics, surface patterning, and nanomaterial synthesis. The use of integrated microfluidics-based assay platform allows culturing and manipulating many types of neuronal tissues in precisely controlled microenvironment. Furthermore, they provide organized multi-cellular in-vitro model, long-term monitoring with live cell imaging, and compatibility with molecular biology techniques and electrophysiology experiment. In this dissertation, the integrated microfluidics-based assay platforms are developed for investigation of neuronal activities such as local protein synthesis, impairment of axonal transport by chemical/physical variants, growth cone path finding under chemical/physical cues, and synaptic transmission in neuronal circuit. Chapter 1 describes the motivation, objectives, and scope for developing in-vitro platform to study various neuronal activities. Chapter 2 introduces microfluidic culture platform for biochemical assay with large-scale neuronal tissues that are utilized as model system in neuroscience research. Chapter 3 focuses on the investigation of impaired axonal transport by beta-Amyloid and oxidative stress. The platform allows to control neuronal processes and to quantify mitochondrial movement in various regions of axons away from applied drugs. Chapter 4 demonstrates the development of microfluidics-based growth cone turning assay to elucidate the mechanism underlying axon guidance under soluble factors and shear flow. Using this platform, the behaviors of growth cone of mammalian neurons are verified under the gradient of inhibitory molecules and also shear flow in well-controlled manner. In Chapter 5, I combine in-vitro multicellular model with microfabricated MEA (multielectrode array) or nanowire electrode array to study electrophysiology in neuronal network. Also, "diode-like" microgrooves to control the number of neuronal processes is embedded in this platform. Chapter 6 concludes with a possible future direction of this work. Interfacing micro/nanotechnology with primary neuron culture would open many doors in fundamental neuroscience research and also biomedical innovation.

Modular nucleic acid assembled p/MHC microarrays for multiplexed sorting of antigen-specific T cells.

PubMed

Kwong, Gabriel A; Radu, Caius G; Hwang, Kiwook; Shu, Chengyi J; Ma, Chao; Koya, Richard C; Comin-Anduix, Begonya; Hadrup, Sine Reker; Bailey, Ryan C; Witte, Owen N; Schumacher, Ton N; Ribas, Antoni; Heath, James R

2009-07-22

The human immune system consists of a large number of T cells capable of recognizing and responding to antigens derived from various sources. The development of peptide-major histocompatibility (p/MHC) tetrameric complexes has enabled the direct detection of these antigen-specific T cells. With the goal of increasing throughput and multiplexing of T cell detection, protein microarrays spotted with defined p/MHC complexes have been reported, but studies have been limited due to the inherent instability and reproducibility of arrays produced via conventional spotted methods. Herein, we report on a platform for the detection of antigen-specific T cells on glass substrates that offers significant advantages over existing surface-bound schemes. In this approach, called "Nucleic Acid Cell Sorting (NACS)", single-stranded DNA oligomers conjugated site-specifically to p/MHC tetramers are employed to immobilize p/MHC tetramers via hybridization to a complementary-printed substrate. Fully assembled p/MHC arrays are used to detect and enumerate T cells captured from cellular suspensions, including primary human T cells collected from cancer patients. NACS arrays outperform conventional spotted arrays assessed in key criteria such as repeatability and homogeneity. The versatility of employing DNA sequences for cell sorting is exploited to enable the programmed, selective release of target populations of immobilized T cells with restriction endonucleases for downstream analysis. Because of the performance, facile and modular assembly of p/MHC tetramer arrays, NACS holds promise as a versatile platform for multiplexed T cell detection.

Phospholipid arrays on porous polymer coatings generated by micro-contact spotting

PubMed Central

de Freitas, Monica; Tröster, Lea-Marie; Jochum, Tobias; Levkin, Pavel A; Hirtz, Michael; Fuchs, Harald

2017-01-01

Nanoporous poly(2-hydroxyethyl methacrylate-co-ethylene dimethacrylate) (HEMA-EDMA) is used as a 3D mesh for spotting lipid arrays. Its porous structure is an ideal matrix for lipid ink to infiltrate, resulting in higher fluorescent signal intensity as compared to similar arrays on strictly 2D substrates like glass. The embedded lipid arrays show high stability against washing steps, while still being accessible for protein and antibody binding. To characterize binding to polymer-embedded lipids we have applied Streptavidin as well as biologically important biotinylated androgen receptor binding onto 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-(cap biotinyl) (Biotinyl Cap PE) and anti-DNP IgE recognition of 2,4-dinitrophenyl[1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-[6-[(2,4-dinitrophenyl)amino]hexanoyl] (DNP)] antigen. This approach adds lipid arrays to the range of HEMA polymer applications and makes this solid substrate a very attractive platform for a variety of bio-applications. PMID:28487815

Novel Abscisic Acid Antagonists Identified with Chemical Array Screening.

PubMed

Ito, Takuya; Kondoh, Yasumitsu; Yoshida, Kazuko; Umezawa, Taishi; Shimizu, Takeshi; Shinozaki, Kazuo; Osada, Hiroyuki

2015-11-01

Abscisic acid (ABA) signaling is involved in multiple processes in plants, such as water stress control and seed dormancy. Major regulators of ABA signaling are the PYR/PYL/RCAR family receptor proteins, group A protein phosphatases 2C (PP2Cs), and subclass III of SNF1-related protein kinase 2 (SnRK2). Novel ABA agonists and antagonists to modulate the functions of these proteins would not only contribute to clarification of the signaling mechanisms but might also be used to improve crop yields. To obtain small molecules that interact with Arabidopsis ABA receptor PYR1, we screened 24 275 compounds from a chemical library at the RIKEN Natural Products Depository by using a chemical array platform. Subsequent SnRK2 and PP2C assays narrowed down the candidates to two molecules. One antagonized ABA in a competitive manner and inhibited the formation of the PYR1-ABA-PP2C ternary complex. These compounds might have potential as bioprobes to analyze ABA signaling. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Comparison of three multiplex gastrointestinal platforms for the detection of gastroenteritis viruses

PubMed Central

Chhabra, Preeti; Gregoricus, Nicole; Weinberg, Geoffrey A.; Halasa, Natasha; Chappell, James; Hassan, Ferdaus; Selvarangan, Rangaraj; Mijatovic-Rustempasic, Slavica; Ward, M. Leanne; Bowen, Michael; Payne, Daniel C.; Vinjé, Jan

2018-01-01

Background Viruses are major etiological agents of childhood gastroenteritis. In recent years, several molecular platforms for the detection of viral enteric pathogens have become available. Objective/study design We evaluated the performance of three multiplex platforms including Biofire’s Gastrointestinal Panel (FilmArray), Luminex xTAG® Gastrointestinal Pathogen Panel (GPP), and the TaqMan Array Card (TAC) for the detection of five gastroenteritis viruses using a coded panel of 300 archived stool samples. Results The FilmArray detected a virus in 199 (96.1%) and the TAC in 172 (83.1%) of the 207 samples (187 samples positive for a single virus and 20 samples positive for more than one virus) whereas the GPP detected a virus in 100 (78.7%) of the 127 (97 positive for one virus and three positive for more than one virus) samples. Overall the clinical accuracy was highest for the FilmArray (98%) followed by TAC (97.2%) and GPP (96.9%). The sensitivity of the FilmArray, GPP and TAC platforms was highest for rotavirus (100%, 95.8%, and 89.6%, respectively) and lowest for adenovirus type 40/41 (97.4%, 57.9% and 68.4%). The specificity of the three platforms ranged from 95.6% (rotavirus) to 99.6% (norovirus/sapovirus) for the FilmArray, 99.6% (norovirus) to 100% (rotavirus/adenovirus) for GPP, and 98.9% (astrovirus) to 100% (rotavirus/sapovirus) for TAC. Conclusion The FilmArray demonstrated the best analytical performance followed by TAC. In recent years, the availability of multi-enteric molecular testing platforms has increased significantly and our data highlight the strengths and weaknesses of these platforms. PMID:28889082

An automated microfluidic platform for C. elegans embryo arraying, phenotyping, and long-term live imaging

NASA Astrophysics Data System (ADS)

Cornaglia, Matteo; Mouchiroud, Laurent; Marette, Alexis; Narasimhan, Shreya; Lehnert, Thomas; Jovaisaite, Virginija; Auwerx, Johan; Gijs, Martin A. M.

2015-05-01

Studies of the real-time dynamics of embryonic development require a gentle embryo handling method, the possibility of long-term live imaging during the complete embryogenesis, as well as of parallelization providing a population’s statistics, while keeping single embryo resolution. We describe an automated approach that fully accomplishes these requirements for embryos of Caenorhabditis elegans, one of the most employed model organisms in biomedical research. We developed a microfluidic platform which makes use of pure passive hydrodynamics to run on-chip worm cultures, from which we obtain synchronized embryo populations, and to immobilize these embryos in incubator microarrays for long-term high-resolution optical imaging. We successfully employ our platform to investigate morphogenesis and mitochondrial biogenesis during the full embryonic development and elucidate the role of the mitochondrial unfolded protein response (UPRmt) within C. elegans embryogenesis. Our method can be generally used for protein expression and developmental studies at the embryonic level, but can also provide clues to understand the aging process and age-related diseases in particular.

Integrated Platform for Expedited Synthesis–Purification–Testing of Small Molecule Libraries

PubMed Central

2017-01-01

The productivity of medicinal chemistry programs can be significantly increased through the introduction of automation, leading to shortened discovery cycle times. Herein, we describe a platform that consolidates synthesis, purification, quantitation, dissolution, and testing of small molecule libraries. The system was validated through the synthesis and testing of two libraries of binders of polycomb protein EED, and excellent correlation of obtained data with results generated through conventional approaches was observed. The fully automated and integrated platform enables batch-supported compound synthesis based on a broad array of chemical transformations with testing in a variety of biochemical assay formats. A library turnaround time of between 24 and 36 h was achieved, and notably, each library synthesis produces sufficient amounts of compounds for further evaluation in secondary assays thereby contributing significantly to the shortening of medicinal chemistry discovery cycles. PMID:28435537

Fabrication of biomolecules self-assembled on Au nanodot array for bioelectronic device.

PubMed

Lee, Taek; Kumar, Ajay Yagati; Yoo, Si-Youl; Jung, Mi; Min, Junhong; Choi, Jeong-Woo

2013-09-01

In the present study, an nano-platform composed of Au nanodot arrays on which biomolecules could be self-assembled was developed and investigated for a stable bioelectronic device platform. Au nanodot pattern was fabricated using a nanoporous alumina template. Two different biomolecules, a cytochrome c and a single strand DNA (ssDNA), were immobilized on the Au nanodot arrays. Cytochorme c and single stranded DNA could be immobilized on the Au nanodot using the chemical linker 11-MUA and thiol-modification by covalent bonding, respectively. The atomic structure of the fabricated nano-platform device was characterized by scanning electron microscopy (SEM) and atomic force microscopy (AFM). The electrical conductivity of biomolecules immobilized on the Au nanodot arrays was confirmed by scanning tunneling spectroscopy (STS). To investigate the activity of biomolecule-immobilized Au-nano dot array, the cyclic voltammetry was carried out. This proposed nano-platform device, which is composed of biomolecules, can be used for the construction of a novel bioelectronic device.

Systems Biology of Recombinant Protein Production in Bacillus megaterium

NASA Astrophysics Data System (ADS)

Biedendieck, Rebekka; Bunk, Boyke; Fürch, Tobias; Franco-Lara, Ezequiel; Jahn, Martina; Jahn, Dieter

Over the last two decades the Gram-positive bacterium Bacillus megaterium was systematically developed to a useful alternative protein production host. Multiple vector systems for high yield intra- and extracellular protein production were constructed. Strong inducible promoters were combined with DNA sequences for optimised ribosome binding sites, various leader peptides for protein export and N- as well as C-terminal affinity tags for affinity chromatographic purification of the desired protein. High cell density cultivation and recombinant protein production were successfully tested. For further system biology based control and optimisation of the production process the genomes of two B. megaterium strains were completely elucidated, DNA arrays designed, proteome, fluxome and metabolome analyses performed and all data integrated using the bioinformatics platform MEGABAC. Now, solid theoretical and experimental bases for primary modeling attempts of the production process are available.

The pitfalls of platform comparison: DNA copy number array technologies assessed

PubMed Central

2009-01-01

Background The accurate and high resolution mapping of DNA copy number aberrations has become an important tool by which to gain insight into the mechanisms of tumourigenesis. There are various commercially available platforms for such studies, but there remains no general consensus as to the optimal platform. There have been several previous platform comparison studies, but they have either described older technologies, used less-complex samples, or have not addressed the issue of the inherent biases in such comparisons. Here we describe a systematic comparison of data from four leading microarray technologies (the Affymetrix Genome-wide SNP 5.0 array, Agilent High-Density CGH Human 244A array, Illumina HumanCNV370-Duo DNA Analysis BeadChip, and the Nimblegen 385 K oligonucleotide array). We compare samples derived from primary breast tumours and their corresponding matched normals, well-established cancer cell lines, and HapMap individuals. By careful consideration and avoidance of potential sources of bias, we aim to provide a fair assessment of platform performance. Results By performing a theoretical assessment of the reproducibility, noise, and sensitivity of each platform, notable differences were revealed. Nimblegen exhibited between-replicate array variances an order of magnitude greater than the other three platforms, with Agilent slightly outperforming the others, and a comparison of self-self hybridizations revealed similar patterns. An assessment of the single probe power revealed that Agilent exhibits the highest sensitivity. Additionally, we performed an in-depth visual assessment of the ability of each platform to detect aberrations of varying sizes. As expected, all platforms were able to identify large aberrations in a robust manner. However, some focal amplifications and deletions were only detected in a subset of the platforms. Conclusion Although there are substantial differences in the design, density, and number of replicate probes, the comparison indicates a generally high level of concordance between platforms, despite differences in the reproducibility, noise, and sensitivity. In general, Agilent tended to be the best aCGH platform and Affymetrix, the superior SNP-CGH platform, but for specific decisions the results described herein provide a guide for platform selection and study design, and the dataset a resource for more tailored comparisons. PMID:19995423

MAPPI-DAT: data management and analysis for protein-protein interaction data from the high-throughput MAPPIT cell microarray platform.

PubMed

Gupta, Surya; De Puysseleyr, Veronic; Van der Heyden, José; Maddelein, Davy; Lemmens, Irma; Lievens, Sam; Degroeve, Sven; Tavernier, Jan; Martens, Lennart

2017-05-01

Protein-protein interaction (PPI) studies have dramatically expanded our knowledge about cellular behaviour and development in different conditions. A multitude of high-throughput PPI techniques have been developed to achieve proteome-scale coverage for PPI studies, including the microarray based Mammalian Protein-Protein Interaction Trap (MAPPIT) system. Because such high-throughput techniques typically report thousands of interactions, managing and analysing the large amounts of acquired data is a challenge. We have therefore built the MAPPIT cell microArray Protein Protein Interaction-Data management & Analysis Tool (MAPPI-DAT) as an automated data management and analysis tool for MAPPIT cell microarray experiments. MAPPI-DAT stores the experimental data and metadata in a systematic and structured way, automates data analysis and interpretation, and enables the meta-analysis of MAPPIT cell microarray data across all stored experiments. MAPPI-DAT is developed in Python, using R for data analysis and MySQL as data management system. MAPPI-DAT is cross-platform and can be ran on Microsoft Windows, Linux and OS X/macOS. The source code and a Microsoft Windows executable are freely available under the permissive Apache2 open source license at https://github.com/compomics/MAPPI-DAT. jan.tavernier@vib-ugent.be or lennart.martens@vib-ugent.be. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Assay development and case history of a 32K-biased library high-content MK2-EGFP translocation screen to identify p38 mitogen-activated protein kinase inhibitors on the ArrayScan 3.1 imaging platform.

PubMed

Trask, Oscar J; Baker, Audrey; Williams, Rhonda Gates; Nickischer, Debra; Kandasamy, Ramani; Laethem, Carmen; Johnston, Patricia A; Johnston, Paul A

2006-01-01

This chapter describes the conversion and assay development of a 96-well MK2-EGFP translocation assay into a higher density 384-well format high-content assay to be screened on the ArrayScan 3.1 imaging platform. The assay takes advantage of the well-substantiated hypothesis that mitogen-activated protein kinase-activating protein kinase-2 (MK2) is a substrate of p38 MAPK kinase and that p38-induced phosphorylation of MK-2 induces a nucleus-to-cytoplasm translocation. This chapter also presents a case history of the performance of the MK2-EGFP translocation assay, run as a "high-content" screen of a 32K kinase-biased library to identify p38 inhibitors. The assay performed very well and a number of putative p38 inhibitor hits were identified. Through the use of multiparameter data provided by the nuclear translocation algorithm and by checking images, a number of compounds were identified that were potential artifacts due to interference with the imaging format. These included fluorescent compounds, or compounds that dramatically reduced cell numbers due to cytotoxicity or by disrupting cell adherence. A total of 145 compounds produced IC(50) values <50.0 muM in the MK2-EGFP translocation assay, and a cross target query of the Lilly-RTP HTS database confirmed their inhibitory activity against in vitro kinase targets, including p38a. Compounds were confirmed structurally by LCMS analysis and profiled in cell-based imaging assays for MAPK signaling pathway selectivity. Three of the hit scaffolds identified in the MK2-EGFP translocation HCS run on the ArrayScan were selected for a p38a inhibitor hit-to-lead structure activity relationship (SAR) chemistry effort.

Microfluidic cell trap array for controlled positioning of single cells on adhesive micropatterns.

PubMed

Lin, Laiyi; Chu, Yeh-Shiu; Thiery, Jean Paul; Lim, Chwee Teck; Rodriguez, Isabel

2013-02-21

Adhesive micropattern arrays permit the continuous monitoring and systematic study of the behavior of spatially confined cells of well-defined shape and size in ordered configurations. This technique has contributed to defining mechanisms that control cell polarity and cell functions, including proliferation, apoptosis, differentiation and migration in two-dimensional cell culture systems. These micropattern studies often involve isolating a single cell on one adhesive protein micropattern using random seeding methods. Random seeding has been successful for isolated and, to a lesser degree, paired patterns, where two patterns are placed in close proximity. Using this method, we found that the probability of obtaining one cell per pattern decreases significantly as the number of micropatterns in a cluster increases, from 16% for paired micropatterns to 0.3% for clusters of 6 micropatterns. This work presents a simple yet effective platform based on a microfludic sieve-like trap array to exert precise control over the positioning of single cells on micropatterns. We observed a 4-fold improvement over random seeding in the efficiency of placing a pair of single cells on paired micropattern and a 40-fold improvement for 6-pattern clusters. The controlled nature of this platform can also allow the juxtaposition of two different cell populations through a simple modification in the trap arrangement. With excellent control of the identity, number and position of neighbouring cells, this cell-positioning platform provides a unique opportunity for the extension of two-dimensional micropattern studies beyond paired micropatterns to organizations containing many cells or different cell types.

Suspension arrays based on nanoparticle-encoded microspheres for high-throughput multiplexed detection

PubMed Central

Leng, Yuankui

2017-01-01

Spectrometrically or optically encoded microsphere based suspension array technology (SAT) is applicable to the high-throughput, simultaneous detection of multiple analytes within a small, single sample volume. Thanks to the rapid development of nanotechnology, tremendous progress has been made in the multiplexed detecting capability, sensitivity, and photostability of suspension arrays. In this review, we first focus on the current stock of nanoparticle-based barcodes as well as the manufacturing technologies required for their production. We then move on to discuss all existing barcode-based bioanalysis patterns, including the various labels used in suspension arrays, label-free platforms, signal amplification methods, and fluorescence resonance energy transfer (FRET)-based platforms. We then introduce automatic platforms for suspension arrays that use superparamagnetic nanoparticle-based microspheres. Finally, we summarize the current challenges and their proposed solutions, which are centered on improving encoding capacities, alternative probe possibilities, nonspecificity suppression, directional immobilization, and “point of care” platforms. Throughout this review, we aim to provide a comprehensive guide for the design of suspension arrays, with the goal of improving their performance in areas such as multiplexing capacity, throughput, sensitivity, and cost effectiveness. We hope that our summary on the state-of-the-art development of these arrays, our commentary on future challenges, and some proposed avenues for further advances will help drive the development of suspension array technology and its related fields. PMID:26021602

Fabrication of heterogeneous nanomaterial array by programmable heating and chemical supply within microfluidic platform towards multiplexed gas sensing application

PubMed Central

Yang, Daejong; Kang, Kyungnam; Kim, Donghwan; Li, Zhiyong; Park, Inkyu

2015-01-01

A facile top-down/bottom-up hybrid nanofabrication process based on programmable temperature control and parallel chemical supply within microfluidic platform has been developed for the all liquid-phase synthesis of heterogeneous nanomaterial arrays. The synthesized materials and locations can be controlled by local heating with integrated microheaters and guided liquid chemical flow within microfluidic platform. As proofs-of-concept, we have demonstrated the synthesis of two types of nanomaterial arrays: (i) parallel array of TiO2 nanotubes, CuO nanospikes and ZnO nanowires, and (ii) parallel array of ZnO nanowire/CuO nanospike hybrid nanostructures, CuO nanospikes and ZnO nanowires. The laminar flow with negligible ionic diffusion between different precursor solutions as well as localized heating was verified by numerical calculation and experimental result of nanomaterial array synthesis. The devices made of heterogeneous nanomaterial array were utilized as a multiplexed sensor for toxic gases such as NO2 and CO. This method would be very useful for the facile fabrication of functional nanodevices based on highly integrated arrays of heterogeneous nanomaterials. PMID:25634814

Using oriented peptide array libraries to evaluate methylarginine-specific antibodies and arginine methyltransferase substrate motifs

PubMed Central

Gayatri, Sitaram; Cowles, Martis W.; Vemulapalli, Vidyasiri; Cheng, Donghang; Sun, Zu-Wen; Bedford, Mark T.

2016-01-01

Signal transduction in response to stimuli relies on the generation of cascades of posttranslational modifications that promote protein-protein interactions and facilitate the assembly of distinct signaling complexes. Arginine methylation is one such modification, which is catalyzed by a family of nine protein arginine methyltransferases, or PRMTs. Elucidating the substrate specificity of each PRMT will promote a better understanding of which signaling networks these enzymes contribute to. Although many PRMT substrates have been identified, and their methylation sites mapped, the optimal target motif for each of the nine PRMTs has not been systematically addressed. Here we describe the use of Oriented Peptide Array Libraries (OPALs) to methodically dissect the preferred methylation motifs for three of these enzymes – PRMT1, CARM1 and PRMT9. In parallel, we show that an OPAL platform with a fixed methylarginine residue can be used to validate the methyl-specific and sequence-specific properties of antibodies that have been generated against different PRMT substrates, and can also be used to confirm the pan nature of some methylarginine-specific antibodies. PMID:27338245

Tracking serum antibody response to viral antigens with arrayed imaging reflectometry

NASA Astrophysics Data System (ADS)

Mace, Charles R.; Rose, Robert C.; Miller, Benjamin L.

2009-02-01

Arrayed Imaging Reflectometry, or "AIR", is a new label-free technique for detecting proteins that relies on bindinginduced changes in the response of an antireflective coating on the surface of a silicon ship. Because the technique provides high sensitivity, excellent dynamic range, and readily integrates with standard silicon wafer processing technology, it is an exceptionally attractive platform on which to build systems for detecting proteins in complex solutions. In our early research, we used AIR chips bearing secreted receptor proteins from enteropathogenic E. coli to develop sensors for this pathogen. Recently, we have been exploring an alternative strategy: Rather than detecting the pathogen directly, can one immobilize antigens from a pathogen, and employ AIR to detect antibody responses to those antigens? Such a strategy would provide enhanced sensitivity for pathogen detection (as the immune system essentially amplifies the "signal" caused by the presence of an organism to which it responds), and would also potentially prove useful in the process of vaccine development. We describe herein preliminary results in the application of such a strategy to the detection of antibodies to human papillomavirus (HPV).

A self-powered, one-step chip for rapid, quantitative and multiplexed detection of proteins from pinpricks of whole blood.

PubMed

Wang, Jun; Ahmad, Habib; Ma, Chao; Shi, Qihui; Vermesh, Ophir; Vermesh, Udi; Heath, James

2010-11-21

We describe an automated, self-powered chip based on lateral flow immunoassay for rapid, quantitative, and multiplex protein detection from pinpricks of whole blood. The device incorporates on-chip purification of blood plasma by employing inertial forces to focus blood cells away from the assay surface, where plasma proteins are captured and detected on antibody "barcode" arrays. Power is supplied from the capillary action of a piece of adsorbent paper, and sequentially drives, over a 40 minute period, the four steps required to capture serum proteins and then develop a multiplex immunoassay. An 11 protein panel is assayed from whole blood, with high sensitivity and high reproducibility. This inexpensive, self-contained, and easy to operate chip provides a useful platform for point-of-care diagnoses, particularly in resource-limited settings.

Array Simulations Platform (ASP) predicts NASA Data Link Module (NDLM) performance

NASA Technical Reports Server (NTRS)

Snook, Allen David

1993-01-01

Through a variety of imbedded theoretical and actual antenna patterns, the array simulation platform (ASP) enhanced analysis of the array antenna pattern effects for the KTx (Ku-Band Transmit) service of the NDLM (NASA Data Link Module). The ASP utilizes internally stored models of the NDLM antennas and can develop the overall pattern of antenna arrays through common array calculation techniques. ASP expertly assisted in the diagnosing of element phase shifter errors during KTx testing and was able to accurately predict the overall array pattern from combinations of the four internally held element patterns. This paper provides an overview of the use of the ASP software in the solving of array mis-phasing problems.

Molecular ping-pong Game of Life on a two-dimensional DNA origami array.

PubMed

Jonoska, N; Seeman, N C

2015-07-28

We propose a design for programmed molecular interactions that continuously change molecular arrangements in a predesigned manner. We introduce a model where environmental control through laser illumination allows platform attachment/detachment oscillations between two floating molecular species. The platform is a two-dimensional DNA origami array of tiles decorated with strands that provide both, the floating molecular tiles to attach and to pass communicating signals to neighbouring array tiles. In particular, we show how algorithmic molecular interactions can control cyclic molecular arrangements by exhibiting a system that can simulate the dynamics similar to two-dimensional cellular automata on a DNA origami array platform. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

A microfluidic separation platform using an array of slanted ramps

NASA Astrophysics Data System (ADS)

Risbud, Sumedh; Bernate, Jorge; Drazer, German

2013-03-01

The separation of the different components of a sample is a crucial step in many micro- and nano-fluidic applications, including the detection of infections, the capture of circulating tumor cells, the isolation of proteins, RNA and DNA, to mention but a few. Vector chromatography, in which different species migrate in different directions in a planar microfluidic device thus achieving spatial as well as temporal resolution, offers the promise of high selectivity along with high throughput. In this work, we present a microfluidic vector chromatography platform consisting of slanted ramps in a microfluidic channel for the separation of suspended particles. We construct these ramps using inclined UV lithography, such that the inclined portion of the ramps is upstream. We show that particles of different size displace laterally to a different extent when driven by a flow field over a slanted ramp. The flow close to the ramp reorients along the ramp, causing the size-dependent deflection of the particles. The cumulative effect of an array of these ramps would cause particles of different size to migrate in different directions, thus allowing their passive and continuous separation.

Analysis of Cysteine Redox Post-Translational Modifications in Cell Biology and Drug Pharmacology.

PubMed

Wani, Revati; Murray, Brion W

2017-01-01

Reversible cysteine oxidation is an emerging class of protein post-translational modification (PTM) that regulates catalytic activity, modulates conformation, impacts protein-protein interactions, and affects subcellular trafficking of numerous proteins. Redox PTMs encompass a broad array of cysteine oxidation reactions with different half-lives, topographies, and reactivities such as S-glutathionylation and sulfoxidation. Recent studies from our group underscore the lesser known effect of redox protein modifications on drug binding. To date, biological studies to understand mechanistic and functional aspects of redox regulation are technically challenging. A prominent issue is the lack of tools for labeling proteins oxidized to select chemotype/oxidant species in cells. Predictive computational tools and curated databases of oxidized proteins are facilitating structural and functional insights into regulation of the network of oxidized proteins or redox proteome. In this chapter, we discuss analytical platforms for studying protein oxidation, suggest computational tools currently available in the field to determine redox sensitive proteins, and begin to illuminate roles of cysteine redox PTMs in drug pharmacology.

Transitioning Streaming to Trapping in DC Insulator-based Dielectrophoresis for Biomolecules

PubMed Central

Camacho-Alanis, Fernanda; Gan, Lin; Ros, Alexandra

2012-01-01

Exploiting dielectrophoresis (DEP) to concentrate and separate biomolecules has recently shown large potential as a microscale bioanalytical tool. Such efforts however require tailored devices and knowledge of all interplaying transport mechanisms competing with dielectrophoresis (DEP). Specifically, a strong DEP contribution to the overall transport mechanism is necessary to exploit DEP of biomolecules for analytical applications such as separation and fractionation. Here, we present improved microfluidic devices combining optical lithography and focused ion beam milling (FIBM) for the manipulation of DNA and proteins using insulator-based dielectrophoresis (iDEP) and direct current (DC) electric fields. Experiments were performed on an elastomer platform forming the iDEP microfluidic device with integrated nanoposts and nanopost arrays. Microscale and nanoscale iDEP was studied for λ-DNA (48.5 kbp) and the protein bovine serum albumin (BSA). Numerical simulations were adapted to the various tested geometries revealing excellent qualitative agreement with experimental observations for streaming and trapping DEP. Both the experimental and simulation results indicate that DC iDEP trapping for λ-DNA occurs with tailored nanoposts fabricated via FIBM. Moreover, streaming iDEP concentration of BSA is improved with integrated nanopost arrays by a factor of 45 compared to microfabricated arrays. PMID:23441049

A Flexible Annular-Array Imaging Platform for Micro-Ultrasound

PubMed Central

Qiu, Weibao; Yu, Yanyan; Chabok, Hamid Reza; Liu, Cheng; Tsang, Fu Keung; Zhou, Qifa; Shung, K. Kirk; Zheng, Hairong; Sun, Lei

2013-01-01

Micro-ultrasound is an invaluable imaging tool for many clinical and preclinical applications requiring high resolution (approximately several tens of micrometers). Imaging systems for micro-ultrasound, including single-element imaging systems and linear-array imaging systems, have been developed extensively in recent years. Single-element systems are cheaper, but linear-array systems give much better image quality at a higher expense. Annular-array-based systems provide a third alternative, striking a balance between image quality and expense. This paper presents the development of a novel programmable and real-time annular-array imaging platform for micro-ultrasound. It supports multi-channel dynamic beamforming techniques for large-depth-of-field imaging. The major image processing algorithms were achieved by a novel field-programmable gate array technology for high speed and flexibility. Real-time imaging was achieved by fast processing algorithms and high-speed data transfer interface. The platform utilizes a printed circuit board scheme incorporating state-of-the-art electronics for compactness and cost effectiveness. Extensive tests including hardware, algorithms, wire phantom, and tissue mimicking phantom measurements were conducted to demonstrate good performance of the platform. The calculated contrast-to-noise ratio (CNR) of the tissue phantom measurements were higher than 1.2 in the range of 3.8 to 8.7 mm imaging depth. The platform supported more than 25 images per second for real-time image acquisition. The depth-of-field had about 2.5-fold improvement compared to single-element transducer imaging. PMID:23287923

Improved Protein Arrays for Quantitative Systems Analysis of the Dynamics of Signaling Pathway Interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Chin-Rang

Astronauts and workers in nuclear plants who repeatedly exposed to low doses of ionizing radiation (IR, <10 cGy) are likely to incur specific changes in signal transduction and gene expression in various tissues of their body. Remarkable advances in high throughput genomics and proteomics technologies enable researchers to broaden their focus from examining single gene/protein kinetics to better understanding global gene/protein expression profiling and biological pathway analyses, namely Systems Biology. An ultimate goal of systems biology is to develop dynamic mathematical models of interacting biological systems capable of simulating living systems in a computer. This Glue Grant is to complementmore » Dr. Boothman’s existing DOE grant (No. DE-FG02-06ER64186) entitled “The IGF1/IGF-1R-MAPK-Secretory Clusterin (sCLU) Pathway: Mediator of a Low Dose IR-Inducible Bystander Effect” to develop sensitive and quantitative proteomic technology that suitable for low dose radiobiology researches. An improved version of quantitative protein array platform utilizing linear Quantum dot signaling for systematically measuring protein levels and phosphorylation states for systems biology modeling is presented. The signals are amplified by a confocal laser Quantum dot scanner resulting in ~1000-fold more sensitivity than traditional Western blots and show the good linearity that is impossible for the signals of HRP-amplification. Therefore this improved protein array technology is suitable to detect weak responses of low dose radiation. Software is developed to facilitate the quantitative readout of signaling network activities. Kinetics of EGFRvIII mutant signaling was analyzed to quantify cross-talks between EGFR and other signaling pathways.« less

High-density fiber optic biosensor arrays

NASA Astrophysics Data System (ADS)

Epstein, Jason R.; Walt, David R.

2002-02-01

Novel approaches are required to coordinate the immense amounts of information derived from diverse genomes. This concept has influenced the expanded role of high-throughput DNA detection and analysis in the biological sciences. A high-density fiber optic DNA biosensor was developed consisting of oligonucleotide-functionalized, 3.1 mm diameter microspheres deposited into the etched wells on the distal face of a 500 micrometers imaging fiber bundle. Imaging fiber bundles containing thousands of optical fibers, each associated with a unique oligonucleotide probe sequence, were the foundation for an optically connected, individually addressable DNA detection platform. Different oligonucleotide-functionalized microspheres were combined in a stock solution, and randomly dispersed into the etched wells. Microsphere positions were registered from optical dyes incorporated onto the microspheres. The distribution process provided an inherent redundancy that increases the signal-to-noise ratio as the square root of the number of sensors examined. The representative amount of each probe-type in the array was dependent on their initial stock solution concentration, and as other sequences of interest arise, new microsphere elements can be added to arrays without altering the existing detection capabilities. The oligonucleotide probe sequences hybridize to fluorescently-labeled, complementary DNA target solutions. Fiber optic DNA microarray research has included DNA-protein interaction profiles, microbial strain differentiation, non-labeled target interrogation with molecular beacons, and single cell-based assays. This biosensor array is proficient in DNA detection linked to specific disease states, single nucleotide polymorphism (SNP's) discrimination, and gene expression analysis. This array platform permits multiple detection formats, provides smaller feature sizes, and enables sensor design flexibility. High-density fiber optic microarray biosensors provide a fast, reversible format with the detection limit of a few hundred molecules.

Small- Geo Solar Array: New Generation Of Solar Arrays For Commercial Telecom Satellites For Power Ranges Between 2,5 KW And 7,5 KW

NASA Astrophysics Data System (ADS)

Paarmann, Carola; Muller, Jens; Mende, Thomas; Borner, Carsten; Mascher, Rolf

2011-10-01

In the frame of the ESA supported Artes 11 program a new generation of GEO telecommunication satellites is under development. This platform will cover the power range from 2 to 5 kW. ASTRIUM GmbH is contracted to develop and design the Solar Array for this platform. Furthermore the manufacturing and the qualification of a PFM wing for the first flight model is foreseen. The satellite platform, called Small-GEO, is developed under the responsibility of OHB System. This first Small-GEO satellite is designated to be delivered to HISPASAT for operation. The concept of ASTRIUM GmbH is to use all the experiences from the very successful EUROSTAR 2000+, EUROSTAR-3000 and the ALPHABUS platform and to adapt the technologies to the Small- GEO Solar Array. With the benefit of the huge in-orbit heritage of these programs, the remaining risks for the Small-GEO Solar Array can be minimized. The development of the Small-GEO Solar Array extends the ASTRIUM GmbH product portfolio by covering now the complete power range between 2 kW and 31 kW. This paper provides an overview of the different configurations, their main design features and parameters.

Fabrication and analysis of microfiber array platform for optogenetics with cellular resolution

PubMed Central

Chen, Jian-Hong; Chou, Ming-Yi; Pan, Chien-Yuan; Wang, Lon A.

2016-01-01

Optogenetics has emerged as a revolutionary technology especially for neuroscience and has advanced continuously over the past decade. Conventional approaches for patterned in vivo optical illumination have a limitation on the implanted device size and achievable spatio-temporal resolution. In this work, we developed a fabrication process for a microfiber array platform. Arrayed poly(methyl methacrylate) (PMMA) microfibers were drawn from a polymer solution and packaged with polydimethylsiloxane (PDMS). The exposed end face of a packaged microfiber was tuned to have a size corresponding to a single cell. To demonstrate its capability for single cell optogenetics, HEK293T cells expressing channelrhodopsin-2 (ChR2) were cultured on the platform and excited with UV laser. We could then observe an elevation in the intracellular Ca2+ concentrations due to the influx of Ca2+ through the activated ChR2 into the cytosol. The statistical and simulation results indicate that the proposed microfiber array platform can be used for single cell optogenetic applications. PMID:27895984

Comparative immune responses of corals to stressors associated with offshore reef-based tourist platforms

PubMed Central

Lamb, Joleah B; van Oppen, Madeleine J H; Willis, Bette L; Bourne, David G

2015-01-01

Abstract Unravelling the contributions of local anthropogenic and seasonal environmental factors in suppressing the coral immune system is important for prioritizing management actions at reefs exposed to high levels of human activities. Here, we monitor health of the model coral Acropora millepora adjacent to a high-use and an unused reef-based tourist platform, plus a nearby control site without a platform, over 7 months spanning a typical austral summer. Comparisons of temporal patterns in a range of biochemical and genetic immune parameters (Toll-like receptor signalling pathway, lectin–complement system, prophenoloxidase-activating system and green fluorescent protein-like proteins) among healthy, injured and diseased corals revealed that corals exhibit a diverse array of immune responses to environmental and anthropogenic stressors. In healthy corals at the control site, expression of genes involved in the Toll-like receptor signalling pathway (MAPK p38, MEKK1, cFos and ATF4/5) and complement system (C3 and Bf) was modulated by seasonal environmental factors in summer months. Corals at reef platform sites experienced additional stressors over the summer, as evidenced by increased expression of various immune genes, including MAPK p38 and MEKK1. Despite increased expression of immune genes, signs of white syndromes were detected in 31% of study corals near tourist platforms in the warmest summer month. Evidence that colonies developing disease showed reduced expression of genes involved in the complement pathway prior to disease onset suggests that their immune systems may have been compromised. Responses to disease and physical damage primarily involved the melanization cascade and GFP-like proteins, and appeared to be sufficient for recovery when summer heat stress subsided. Overall, seasonal and anthropogenic factors may have interacted synergistically to overwhelm the immune systems of corals near reef platforms, leading to increased disease prevalence in summer at these sites. PMID:27293717

Miniature acoustic wave lysis system and uses thereof

DOEpatents

Branch, Darren W.; Vreeland, Erika Cooley; Smith, Gennifer Tanabe

2016-12-06

The present invention relates to an acoustic lysis system including a disposable cartridge that can be reversibly coupled to a platform having a small, high-frequency piezoelectric transducer array. In particular, the system releases viable DNA, RNA, and proteins from human or bacterial cells, without chemicals or additional processing, to enable high-speed sample preparation for clinical point-of-care medical diagnostics and use with nano/microfluidic cartridges. Also described herein are methods of making and using the system of the invention.

Single helically folded aromatic oligoamides that mimic the charge surface of double-stranded B-DNA

NASA Astrophysics Data System (ADS)

Ziach, Krzysztof; Chollet, Céline; Parissi, Vincent; Prabhakaran, Panchami; Marchivie, Mathieu; Corvaglia, Valentina; Bose, Partha Pratim; Laxmi-Reddy, Katta; Godde, Frédéric; Schmitter, Jean-Marie; Chaignepain, Stéphane; Pourquier, Philippe; Huc, Ivan

2018-05-01

Numerous essential biomolecular processes require the recognition of DNA surface features by proteins. Molecules mimicking these features could potentially act as decoys and interfere with pharmacologically or therapeutically relevant protein-DNA interactions. Although naturally occurring DNA-mimicking proteins have been described, synthetic tunable molecules that mimic the charge surface of double-stranded DNA are not known. Here, we report the design, synthesis and structural characterization of aromatic oligoamides that fold into single helical conformations and display a double helical array of negatively charged residues in positions that match the phosphate moieties in B-DNA. These molecules were able to inhibit several enzymes possessing non-sequence-selective DNA-binding properties, including topoisomerase 1 and HIV-1 integrase, presumably through specific foldamer-protein interactions, whereas sequence-selective enzymes were not inhibited. Such modular and synthetically accessible DNA mimics provide a versatile platform to design novel inhibitors of protein-DNA interactions.

A self-powered, one-step chip for rapid, quantitative and multiplexed detection of proteins from pinpricks of whole blood†

PubMed Central

Wang, Jun; Ahmad, Habib; Ma, Chao; Shi, Qihui; Vermesh, Ophir; Vermesh, Udi; Heath, James

2012-01-01

We describe an automated, self-powered chip based on lateral flow immunoassay for rapid, quantitative, and multiplex protein detection from pinpricks of whole blood. The device incorporates on-chip purification of blood plasma by employing inertial forces to focus blood cells away from the assay surface, where plasma proteins are captured and detected on antibody “barcode” arrays. Power is supplied from the capillary action of a piece of adsorbent paper, and sequentially drives, over a 40 minute period, the four steps required to capture serum proteins and then develop a multiplex immunoassay. An 11 protein panel is assayed from whole blood, with high sensitivity and high reproducibility. This inexpensive, self-contained, and easy to operate chip provides a useful platform for point-of-care diagnoses, particularly in resource-limited settings. PMID:20924527

Cell and tissue microarray technologies for protein and nucleic acid expression profiling.

PubMed

Cardano, Marina; Diaferia, Giuseppe R; Falavigna, Maurizio; Spinelli, Chiara C; Sessa, Fausto; DeBlasio, Pasquale; Biunno, Ida

2013-02-01

Tissue microarray (TMA) and cell microarray (CMA) are two powerful techniques that allow for the immunophenotypical characterization of hundreds of samples simultaneously. In particular, the CMA approach is particularly useful for immunophenotyping new stem cell lines (e.g., cardiac, neural, mesenchymal) using conventional markers, as well as for testing the specificity and the efficacy of newly developed antibodies. We propose the use of a tissue arrayer not only to perform protein expression profiling by immunohistochemistry but also to carry out molecular genetics studies. In fact, starting with several tissues or cell lines, it is possible to obtain the complete signature of each sample, describing the protein, mRNA and microRNA expression, and DNA mutations, or eventually to analyze the epigenetic processes that control protein regulation. Here we show the results obtained using the Galileo CK4500 TMA platform.

Mechanically latchable tiltable platform for forming micromirrors and micromirror arrays

DOEpatents

Garcia, Ernest J [Albuquerque, NM; Polosky, Marc A [Tijeras, NM; Sleefe, Gerard E [Cedar Crest, NM

2006-12-12

A microelectromechanical (MEM) apparatus is disclosed which includes a platform that can be electrostatically tilted from being parallel to a substrate on which the platform to being tilted at an angle of 1 20 degrees with respect to the substrate. Once the platform has been tilted to a maximum angle of tilt, the platform can be locked in position using an electrostatically-operable latching mechanism which engages a tab protruding below the platform. The platform has a light-reflective upper surface which can be optionally coated to provide an enhanced reflectivity and form a micromirror. An array of such micromirrors can be formed on a common substrate for applications including optical switching (e.g. for fiber optic communications), optical information processing, image projection displays or non-volatile optical memories.

Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis

PubMed Central

Holloway, Andrew J; Oshlack, Alicia; Diyagama, Dileepa S; Bowtell, David DL; Smyth, Gordon K

2006-01-01

Background Concerns are often raised about the accuracy of microarray technologies and the degree of cross-platform agreement, but there are yet no methods which can unambiguously evaluate precision and sensitivity for these technologies on a whole-array basis. Results A methodology is described for evaluating the precision and sensitivity of whole-genome gene expression technologies such as microarrays. The method consists of an easy-to-construct titration series of RNA samples and an associated statistical analysis using non-linear regression. The method evaluates the precision and responsiveness of each microarray platform on a whole-array basis, i.e., using all the probes, without the need to match probes across platforms. An experiment is conducted to assess and compare four widely used microarray platforms. All four platforms are shown to have satisfactory precision but the commercial platforms are superior for resolving differential expression for genes at lower expression levels. The effective precision of the two-color platforms is improved by allowing for probe-specific dye-effects in the statistical model. The methodology is used to compare three data extraction algorithms for the Affymetrix platforms, demonstrating poor performance for the commonly used proprietary algorithm relative to the other algorithms. For probes which can be matched across platforms, the cross-platform variability is decomposed into within-platform and between-platform components, showing that platform disagreement is almost entirely systematic rather than due to measurement variability. Conclusion The results demonstrate good precision and sensitivity for all the platforms, but highlight the need for improved probe annotation. They quantify the extent to which cross-platform measures can be expected to be less accurate than within-platform comparisons for predicting disease progression or outcome. PMID:17118209

Probing the Interaction of Dielectric Nanoparticles with Supported Lipid Membrane Coatings on Nanoplasmonic Arrays

PubMed Central

Ferhan, Abdul Rahim; Ma, Gamaliel Junren; Jackman, Joshua A.; Sut, Tun Naw; Park, Jae Hyeon; Cho, Nam-Joon

2017-01-01

The integration of supported lipid membranes with surface-based nanoplasmonic arrays provides a powerful sensing approach to investigate biointerfacial phenomena at membrane interfaces. While a growing number of lipid vesicles, protein, and nucleic acid systems have been explored with nanoplasmonic sensors, there has been only very limited investigation of the interactions between solution-phase nanomaterials and supported lipid membranes. Herein, we established a surface-based localized surface plasmon resonance (LSPR) sensing platform for probing the interaction of dielectric nanoparticles with supported lipid bilayer (SLB)-coated, plasmonic nanodisk arrays. A key emphasis was placed on controlling membrane functionality by tuning the membrane surface charge vis-à-vis lipid composition. The optical sensing properties of the bare and SLB-coated sensor surfaces were quantitatively compared, and provided an experimental approach to evaluate nanoparticle–membrane interactions across different SLB platforms. While the interaction of negatively-charged silica nanoparticles (SiNPs) with a zwitterionic SLB resulted in monotonic adsorption, a stronger interaction with a positively-charged SLB resulted in adsorption and lipid transfer from the SLB to the SiNP surface, in turn influencing the LSPR measurement responses based on the changing spatial proximity of transferred lipids relative to the sensor surface. Precoating SiNPs with bovine serum albumin (BSA) suppressed lipid transfer, resulting in monotonic adsorption onto both zwitterionic and positively-charged SLBs. Collectively, our findings contribute a quantitative understanding of how supported lipid membrane coatings influence the sensing performance of nanoplasmonic arrays, and demonstrate how the high surface sensitivity of nanoplasmonic sensors is well-suited for detecting the complex interactions between nanoparticles and lipid membranes. PMID:28644423

Micro-array versus nano-array platforms: a comparative study for ODN detection based on SPR enhanced ellipsometry

NASA Astrophysics Data System (ADS)

Celen, Burcu; Demirel, Gökhan; Piskin, Erhan

2011-04-01

The rapid and sensitive detection of DNA has recently attracted worldwide attention for a variety of disease diagnoses and detection of harmful bacteria in food and drink. In this paper, we carried out a comparative study based on surface plasmon resonance enhanced ellipsometry (SPREE) for the detection of oligodeoxynucleotides (ODNs) using micro- and nano-array platforms. The micro-arrayed surfaces were fabricated by a photolithography approach using different types of mask having varying size and shape. Well-ordered arrays of high aspect ratio polymeric nanotubes were also obtained using high molecular weight polystyrene (PS) and anodic aluminum oxide (AAO) membranes having 200 nm pore diameters. The SPREE sensors were then prepared by direct coupling of thiolated probe-ODNs, which contain suitable spacer arms, on gold-coated micro- and nano-arrayed surfaces. We experimentally demonstrated that, for the first time, gold-coated free standing polymeric nano-arrayed platforms can easily be produced and lead to a significant sensor sensitivity gain compared to that of the conventional SPREE surfaces of about four times. We believe that such an enhancement in sensor response could be useful for next generation sensor systems.

Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans.

PubMed

Haraksingh, Rajini R; Abyzov, Alexej; Urban, Alexander Eckehart

2017-04-24

High-resolution microarray technology is routinely used in basic research and clinical practice to efficiently detect copy number variants (CNVs) across the entire human genome. A new generation of arrays combining high probe densities with optimized designs will comprise essential tools for genome analysis in the coming years. We systematically compared the genome-wide CNV detection power of all 17 available array designs from the Affymetrix, Agilent, and Illumina platforms by hybridizing the well-characterized genome of 1000 Genomes Project subject NA12878 to all arrays, and performing data analysis using both manufacturer-recommended and platform-independent software. We benchmarked the resulting CNV call sets from each array using a gold standard set of CNVs for this genome derived from 1000 Genomes Project whole genome sequencing data. The arrays tested comprise both SNP and aCGH platforms with varying designs and contain between ~0.5 to ~4.6 million probes. Across the arrays CNV detection varied widely in number of CNV calls (4-489), CNV size range (~40 bp to ~8 Mbp), and percentage of non-validated CNVs (0-86%). We discovered strikingly strong effects of specific array design principles on performance. For example, some SNP array designs with the largest numbers of probes and extensive exonic coverage produced a considerable number of CNV calls that could not be validated, compared to designs with probe numbers that are sometimes an order of magnitude smaller. This effect was only partially ameliorated using different analysis software and optimizing data analysis parameters. High-resolution microarrays will continue to be used as reliable, cost- and time-efficient tools for CNV analysis. However, different applications tolerate different limitations in CNV detection. Our study quantified how these arrays differ in total number and size range of detected CNVs as well as sensitivity, and determined how each array balances these attributes. This analysis will inform appropriate array selection for future CNV studies, and allow better assessment of the CNV-analytical power of both published and ongoing array-based genomics studies. Furthermore, our findings emphasize the importance of concurrent use of multiple analysis algorithms and independent experimental validation in array-based CNV detection studies.

Methods for validating the presence of and characterizing proteins deposited onto an array

DOEpatents

Schabacker, Daniel S.

2010-09-21

A method of determining if proteins have been transferred from liquid-phase protein fractions to an array comprising staining the array with a total protein stain and imaging the array, optionally comparing the staining with a standard curve generated by staining known amounts of a known protein on the same or a similar array; a method of characterizing proteins transferred from liquid-phase protein fractions to an array including staining the array with a post-translational modification-specific (PTM-specific) stain and imaging the array and, optionally, after staining the array with a PTM-specific stain and imaging the array, washing the array, re-staining the array with a total protein stain, imaging the array, and comparing the imaging with the PTM-specific stain with the imaging with the total protein stain; stained arrays; and images of stained arrays.

Synthesis of porous NiO/CeO2 hybrid nanoflake arrays as a platform for electrochemical biosensing

NASA Astrophysics Data System (ADS)

Cui, Jiewu; Luo, Jinbao; Peng, Bangguo; Zhang, Xinyi; Zhang, Yong; Wang, Yan; Qin, Yongqiang; Zheng, Hongmei; Shu, Xia; Wu, Yucheng

2015-12-01

Porous NiO/CeO2 hybrid nanoflake arrays fabricated by a facile hydrothermal method were employed as substrates for electrochemical biosensors. The resulting NiO/CeO2 hybrid nanoflake arrays with a large specific surface area and good biocompatibility presented an excellent platform for electrochemical biosensing.Porous NiO/CeO2 hybrid nanoflake arrays fabricated by a facile hydrothermal method were employed as substrates for electrochemical biosensors. The resulting NiO/CeO2 hybrid nanoflake arrays with a large specific surface area and good biocompatibility presented an excellent platform for electrochemical biosensing. Electronic supplementary information (ESI) available: Optical photographs of the as-prepared samples, SEM, TEM, EDS, XRD and BET data of the samples are presented, I-t curves of glucose biosensors based on NiO and NiO/CeO2 NFAs, EIS results of different electrodes. See DOI: 10.1039/c5nr05924k

Gold nanoparticle-embedded silk protein-ZnO nanorod hybrids for flexible bio-photonic devices

NASA Astrophysics Data System (ADS)

Gogurla, Narendar; Kundu, Subhas C.; Ray, Samit K.

2017-04-01

Silk protein has been used as a biopolymer substrate for flexible photonic devices. Here, we demonstrate ZnO nanorod array hybrid photodetectors on Au nanoparticle-embedded silk protein for flexible optoelectronics. Hybrid samples exhibit optical absorption at the band edge of ZnO as well as plasmonic energy due to Au nanoparticles, making them attractive for selective UV and visible wavelength detection. The device prepared on Au-silk protein shows a much lower dark current and a higher photo to dark-current ratio of ∼105 as compared to the control sample without Au nanoparticles. The hybrid device also exhibits a higher specific detectivity due to higher responsivity arising from the photo-generated hole trapping by Au nanoparticles. Sharp pulses in the transient photocurrent have been observed in devices prepared on glass and Au-silk protein substrates due to the light induced pyroelectric effect of ZnO, enabling the demonstration of self-powered photodetectors at zero bias. Flexible hybrid detectors have been demonstrated on Au-silk/polyethylene terephthalate substrates, exhibiting characteristics similar to those fabricated on rigid glass substrates. A study of the performance of photodetectors with different bending angles indicates very good mechanical stability of silk protein based flexible devices. This novel concept of ZnO nanorod array photodetectors on a natural silk protein platform provides an opportunity to realize integrated flexible and self-powered bio-photonic devices for medical applications in near future.

Photopatterned free-standing polyacrylamide gels for microfluidic protein electrophoresis.

PubMed

Duncombe, Todd A; Herr, Amy E

2013-06-07

Designed for compatibility with slab-gel polyacrylamide gel electrophoresis (PAGE) reagents and instruments, we detail development of free-standing polyacrylamide gel (fsPAG) microstructures supporting electrophoretic performance rivalling that of microfluidic platforms. For the protein electrophoresis study described here, fsPAGE lanes are comprised of a sample reservoir and contiguous separation gel. No enclosed microfluidic channels are employed. The fsPAG devices (120 μm tall) are directly photopatterned atop of and covalently attached to planar polymer or glass surfaces. Leveraging the fast <1 h design-prototype-test cycle - significantly faster than mold based fabrication techniques - we optimize the fsPAG architecture to minimize injection dispersion for rapid (<1 min) and short (1 mm) protein separations. The facile fabrication and prototyping of the fsPAGE provides researchers a powerful tool for developing custom analytical assays. We highlight the utility of assay customization by fabricating a polyacrylamide gel with a spatial pore-size distribution and demonstrate the resulting enhancement in separation performance over a uniform gel. Further, we up-scale from a unit separation to an array of 96 concurrent fsPAGE assays in 10 min run time driven by one electrode pair. The fsPAG array layout matches that of a 96-well plate to facilitate integration of the planar free standing gel array with multi-channel pipettes while remaining compatible with conventional slab-gel PAGE reagents, such as staining for label-free protein detection. Notably, the entire fsPAGE workflow from fabrication, to operation, and readout uses readily available materials and instruments - making this technique highly accessible.

Construction and in vivo assembly of a catalytically proficient and hyperthermostable de novo enzyme.

PubMed

Watkins, Daniel W; Jenkins, Jonathan M X; Grayson, Katie J; Wood, Nicola; Steventon, Jack W; Le Vay, Kristian K; Goodwin, Matthew I; Mullen, Anna S; Bailey, Henry J; Crump, Matthew P; MacMillan, Fraser; Mulholland, Adrian J; Cameron, Gus; Sessions, Richard B; Mann, Stephen; Anderson, J L Ross

2017-08-25

Although catalytic mechanisms in natural enzymes are well understood, achieving the diverse palette of reaction chemistries in re-engineered native proteins has proved challenging. Wholesale modification of natural enzymes is potentially compromised by their intrinsic complexity, which often obscures the underlying principles governing biocatalytic efficiency. The maquette approach can circumvent this complexity by combining a robust de novo designed chassis with a design process that avoids atomistic mimicry of natural proteins. Here, we apply this method to the construction of a highly efficient, promiscuous, and thermostable artificial enzyme that catalyzes a diverse array of substrate oxidations coupled to the reduction of H 2 O 2 . The maquette exhibits kinetics that match and even surpass those of certain natural peroxidases, retains its activity at elevated temperature and in the presence of organic solvents, and provides a simple platform for interrogating catalytic intermediates common to natural heme-containing enzymes.Catalytic mechanisms of enzymes are well understood, but achieving diverse reaction chemistries in re-engineered proteins can be difficult. Here the authors show a highly efficient and thermostable artificial enzyme that catalyzes a diverse array of substrate oxidations coupled to the reduction of H 2 O 2 .

Integrated Microfluidic Lectin Barcode Platform for High-Performance Focused Glycomic Profiling

NASA Astrophysics Data System (ADS)

Shang, Yuqin; Zeng, Yun; Zeng, Yong

2016-02-01

Protein glycosylation is one of the key processes that play essential roles in biological functions and dysfunctions. However, progress in glycomics has considerably lagged behind genomics and proteomics, due in part to the enormous challenges in analysis of glycans. Here we present a new integrated and automated microfluidic lectin barcode platform to substantially improve the performance of lectin array for focused glycomic profiling. The chip design and flow control were optimized to promote the lectin-glycan binding kinetics and speed of lectin microarray. Moreover, we established an on-chip lectin assay which employs a very simple blocking method to effectively suppress the undesired background due to lectin binding of antibodies. Using this technology, we demonstrated focused differential profiling of tissue-specific glycosylation changes of a biomarker, CA125 protein purified from ovarian cancer cell line and different tissues from ovarian cancer patients in a fast, reproducible, and high-throughput fashion. Highly sensitive CA125 detection was also demonstrated with a detection limit much lower than the clinical cutoff value for cancer diagnosis. This microfluidic platform holds the potential to integrate with sample preparation functions to construct a fully integrated “sample-to-answer” microsystem for focused differential glycomic analysis. Thus, our technology should present a powerful tool in support of rapid advance in glycobiology and glyco-biomarker development.

Integrated Microfluidic Lectin Barcode Platform for High-Performance Focused Glycomic Profiling

PubMed Central

Shang, Yuqin; Zeng, Yun; Zeng, Yong

2016-01-01

Protein glycosylation is one of the key processes that play essential roles in biological functions and dysfunctions. However, progress in glycomics has considerably lagged behind genomics and proteomics, due in part to the enormous challenges in analysis of glycans. Here we present a new integrated and automated microfluidic lectin barcode platform to substantially improve the performance of lectin array for focused glycomic profiling. The chip design and flow control were optimized to promote the lectin-glycan binding kinetics and speed of lectin microarray. Moreover, we established an on-chip lectin assay which employs a very simple blocking method to effectively suppress the undesired background due to lectin binding of antibodies. Using this technology, we demonstrated focused differential profiling of tissue-specific glycosylation changes of a biomarker, CA125 protein purified from ovarian cancer cell line and different tissues from ovarian cancer patients in a fast, reproducible, and high-throughput fashion. Highly sensitive CA125 detection was also demonstrated with a detection limit much lower than the clinical cutoff value for cancer diagnosis. This microfluidic platform holds the potential to integrate with sample preparation functions to construct a fully integrated “sample-to-answer” microsystem for focused differential glycomic analysis. Thus, our technology should present a powerful tool in support of rapid advance in glycobiology and glyco-biomarker development. PMID:26831207

Retention in porous layer pillar array planar separation platforms

DOE PAGES

Lincoln, Danielle R.; Lavrik, Nickolay V.; Kravchenko, Ivan I.; ...

2016-08-11

Here, this work presents the retention capabilities and surface area enhancement of highly ordered, high-aspect-ratio, open-platform, two-dimensional (2D) pillar arrays when coated with a thin layer of porous silicon oxide (PSO). Photolithographically prepared pillar arrays were coated with 50–250 nm of PSO via plasma-enhanced chemical vapor deposition and then functionalized with either octadecyltrichlorosilane or n-butyldimethylchlorosilane. Theoretical calculations indicate that a 50 nm layer of PSO increases the surface area of a pillar nearly 120-fold. Retention capabilities were tested by observing capillary-action-driven development under various conditions, as well as by running one-dimensional separations on varying thicknesses of PSO. Increasing the thicknessmore » of PSO on an array clearly resulted in greater retention of the analyte(s) in question in both experiments. In culmination, a two-dimensional separation of fluorescently derivatized amines was performed to further demonstrate the capabilities of these fabricated platforms.« less

A Distributed Amplifier System for Bilayer Lipid Membrane (BLM) Arrays With Noise and Individual Offset Cancellation.

PubMed

Crescentini, Marco; Thei, Frederico; Bennati, Marco; Saha, Shimul; de Planque, Maurits R R; Morgan, Hywel; Tartagni, Marco

2015-06-01

Lipid bilayer membrane (BLM) arrays are required for high throughput analysis, for example drug screening or advanced DNA sequencing. Complex microfluidic devices are being developed but these are restricted in terms of array size and structure or have integrated electronic sensing with limited noise performance. We present a compact and scalable multichannel electrophysiology platform based on a hybrid approach that combines integrated state-of-the-art microelectronics with low-cost disposable fluidics providing a platform for high-quality parallel single ion channel recording. Specifically, we have developed a new integrated circuit amplifier based on a novel noise cancellation scheme that eliminates flicker noise derived from devices under test and amplifiers. The system is demonstrated through the simultaneous recording of ion channel activity from eight bilayer membranes. The platform is scalable and could be extended to much larger array sizes, limited only by electronic data decimation and communication capabilities.

Retention in porous layer pillar array planar separation platforms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lincoln, Danielle R.; Lavrik, Nickolay V.; Kravchenko, Ivan I.

Here, this work presents the retention capabilities and surface area enhancement of highly ordered, high-aspect-ratio, open-platform, two-dimensional (2D) pillar arrays when coated with a thin layer of porous silicon oxide (PSO). Photolithographically prepared pillar arrays were coated with 50–250 nm of PSO via plasma-enhanced chemical vapor deposition and then functionalized with either octadecyltrichlorosilane or n-butyldimethylchlorosilane. Theoretical calculations indicate that a 50 nm layer of PSO increases the surface area of a pillar nearly 120-fold. Retention capabilities were tested by observing capillary-action-driven development under various conditions, as well as by running one-dimensional separations on varying thicknesses of PSO. Increasing the thicknessmore » of PSO on an array clearly resulted in greater retention of the analyte(s) in question in both experiments. In culmination, a two-dimensional separation of fluorescently derivatized amines was performed to further demonstrate the capabilities of these fabricated platforms.« less

Cell and Tissue Microarray Technologies for Protein and Nucleic Acid Expression Profiling

PubMed Central

Cardano, Marina; Diaferia, Giuseppe R.; Falavigna, Maurizio; Spinelli, Chiara C.; Sessa, Fausto; DeBlasio, Pasquale

2013-01-01

Tissue microarray (TMA) and cell microarray (CMA) are two powerful techniques that allow for the immunophenotypical characterization of hundreds of samples simultaneously. In particular, the CMA approach is particularly useful for immunophenotyping new stem cell lines (e.g., cardiac, neural, mesenchymal) using conventional markers, as well as for testing the specificity and the efficacy of newly developed antibodies. We propose the use of a tissue arrayer not only to perform protein expression profiling by immunohistochemistry but also to carry out molecular genetics studies. In fact, starting with several tissues or cell lines, it is possible to obtain the complete signature of each sample, describing the protein, mRNA and microRNA expression, and DNA mutations, or eventually to analyze the epigenetic processes that control protein regulation. Here we show the results obtained using the Galileo CK4500 TMA platform. PMID:23172795

Nanoband array electrode as a platform for high sensitivity enzyme-based glucose biosensing.

PubMed

Falk, Magnus; Sultana, Reshma; Swann, Marcus J; Mount, Andrew R; Freeman, Neville J

2016-12-01

We describe a novel glucose biosensor based on a nanoband array electrode design, manufactured using standard semiconductor processing techniques, and bio-modified with glucose oxidase immobilized at the nanoband electrode surface. The nanoband array architecture allows for efficient diffusion of glucose and oxygen to the electrode, resulting in a thousand-fold improvement in sensitivity and wide linear range compared to a conventional electrode. The electrode constitutes a robust and manufacturable sensing platform. Copyright © 2016 Elsevier B.V. All rights reserved.

Design aspects of a solar array drive for spot, with a high platform stability objective

NASA Technical Reports Server (NTRS)

Cabillic, J.; Fournier, J. P.; Anstett, P.; Souliac, M.; Thomin, G.

1981-01-01

A solar array drive mechanism (MEGS) for the SPOT platform, which is a prototype of a multimission platform, is described. High-resolution cameras and other optical instruments are carried by the platform, requiring excellent platform stability in order to obtain high-quality pictures. Therefore, a severe requirement for the MEGS is the low level of disturbing torques it may generate considering the 0.6 times 10 to the minus 3 power deg/sec stability required. The mechanical design aspects aiming at reducing the mean friction torque, and therefore its fluctuations, are described as well as the method of compensation of the motor imperfections. It was concluded, however, that this is not sufficient to reach the stability requirement.

Sonochemically Fabricated Microelectrode Arrays for Use as Sensing Platforms

PubMed Central

Collyer, Stuart D.; Davis, Frank; Higson, Séamus P.J.

2010-01-01

The development, manufacture, modification and subsequent utilisation of sonochemically-formed microelectrode arrays is described for a range of applications. Initial fabrication of the sensing platform utilises ultrasonic ablation of electrochemically insulating polymers deposited upon conductive carbon substrates, forming an array of up to 70,000 microelectrode pores cm−2. Electrochemical and optical analyses using these arrays, their enhanced signal response and stir-independence area are all discussed. The growth of conducting polymeric “mushroom” protrusion arrays with entrapped biological entities, thereby forming biosensors is detailed. The simplicity and inexpensiveness of this approach, lending itself ideally to mass fabrication coupled with unrivalled sensitivity and stir independence makes commercial viability of this process a reality. Application of microelectrode arrays as functional components within sensors include devices for detection of chlorine, glucose, ethanol and pesticides. Immunosensors based on microelectrode arrays are described within this monograph for antigens associated with prostate cancer and transient ischemic attacks (strokes). PMID:22399926

The concentration principle applied to spaceborne solar arrays. Application to the coorbiting platform mission: Studies synthesis

NASA Astrophysics Data System (ADS)

Laget, R.

1986-01-01

Studies that led to selection of the distributed concentration biplane concept for the solar cell generator to be flown on the coorbiting platform mission, and the major characteristics of such a spaceborne solar array are summarized. It is concluded that there is not a considerable interest in concentration either for array area reduction or cost reduction, although improvements of 15% for both domains are feasible. Only predevelopment activities to verify concentrator performances and system studies to assess respective importance of cost and area saving may increase the level of interest of concentrator solar arrays for this kind of mission.

Genome-Wide Mapping of Copy Number Variation in Humans: Comparative Analysis of High Resolution Array Platforms

PubMed Central

Haraksingh, Rajini R.; Abyzov, Alexej; Gerstein, Mark; Urban, Alexander E.; Snyder, Michael

2011-01-01

Accurate and efficient genome-wide detection of copy number variants (CNVs) is essential for understanding human genomic variation, genome-wide CNV association type studies, cytogenetics research and diagnostics, and independent validation of CNVs identified from sequencing based technologies. Numerous, array-based platforms for CNV detection exist utilizing array Comparative Genome Hybridization (aCGH), Single Nucleotide Polymorphism (SNP) genotyping or both. We have quantitatively assessed the abilities of twelve leading genome-wide CNV detection platforms to accurately detect Gold Standard sets of CNVs in the genome of HapMap CEU sample NA12878, and found significant differences in performance. The technologies analyzed were the NimbleGen 4.2 M, 2.1 M and 3×720 K Whole Genome and CNV focused arrays, the Agilent 1×1 M CGH and High Resolution and 2×400 K CNV and SNP+CGH arrays, the Illumina Human Omni1Quad array and the Affymetrix SNP 6.0 array. The Gold Standards used were a 1000 Genomes Project sequencing-based set of 3997 validated CNVs and an ultra high-resolution aCGH-based set of 756 validated CNVs. We found that sensitivity, total number, size range and breakpoint resolution of CNV calls were highest for CNV focused arrays. Our results are important for cost effective CNV detection and validation for both basic and clinical applications. PMID:22140474

Defining Aggressive Prostate Cancer Using a 12-Gene Model1

PubMed Central

Riva, Alberto; Kim, Robert; Varambally, Sooryanarayana; He, Le; Kutok, Jeff; Aster, Jonathan C; Tang, Jeffery; Kuefer, Rainer; Hofer, Matthias D; Febbo, Phillip G; Chinnaiyan, Arul M; Rubin, Mark A

2006-01-01

Abstract The critical clinical question in prostate cancer research is: How do we develop means of distinguishing aggressive disease from indolent disease? Using a combination of proteomic and expression array data, we identified a set of 36 genes with concordant dysregulation of protein products that could be evaluated in situ by quantitative immunohistochemistry. Another five prostate cancer biomarkers were included using linear discriminant analysis, we determined that the optimal model used to predict prostate cancer progression consisted of 12 proteins. Using a separate patient population, transcriptional levels of the 12 genes encoding for these proteins predicted prostate-specific antigen failure in 79 men following surgery for clinically localized prostate cancer (P = .0015). This study demonstrates that cross-platform models can lead to predictive models with the possible advantage of being more robust through this selection process. PMID:16533427

Dynamic and label-free high-throughput detection of biomolecular interactions based on phase-shift interferometry

NASA Astrophysics Data System (ADS)

Li, Qiang; Huang, Guoliang; Gan, Wupeng; Chen, Shengyi

2009-08-01

Biomolecular interactions can be detected by many established technologies such as fluorescence imaging, surface plasmon resonance (SPR)[1-4], interferometry and radioactive labeling of the analyte. In this study, we have designed and constructed a label-free, real-time sensing platform and its operating imaging instrument that detects interactions using optical phase differences from the accumulation of biological material on solid substrates. This system allows us to monitor biomolecular interactions in real time and quantify concentration changes during micro-mixing processes by measuring the changes of the optical path length (OPD). This simple interferometric technology monitors the optical phase difference resulting from accumulated biomolecular mass. A label-free protein chip that forms a 4×4 probe array was designed and fabricated using a commercial microarray robot spotter on solid substrates. Two positive control probe lines of BSA (Bovine Serum Albumin) and two experimental human IgG and goat IgG was used. The binding of multiple protein targets was performed and continuously detected by using this label-free and real-time sensing platform.

Identification of Genetically Modified Maraba Virus as an Oncolytic Rhabdovirus

PubMed Central

Brun, Jan; McManus, Dan; Lefebvre, Charles; Hu, Kang; Falls, Theresa; Atkins, Harold; Bell, John C; McCart, J. Andrea; Mahoney, Douglas; Stojdl, David F

2010-01-01

To expand our current array of safe and potent oncolytic viruses, we screened a variety of wild-type (WT) rhabdoviruses against a panel of tumor cell lines. Our screen identified a number of viruses with varying degrees of killing activity. Maraba virus was the most potent of these strains. We built a recombinant system for the Maraba virus platform, engineered a series of attenuating mutations to expand its therapeutic index, and tested their potency in vitro and in vivo. A double mutant (MG1) strain containing both G protein (Q242R) and M protein (L123W) mutations attenuated Maraba virus in normal diploid cell lines, yet appeared to be hypervirulent in cancer cells. This selective attenuation was mediated through interferon (IFN)-dependent and -independent mechanisms. Finally, the Maraba MG1 strain had a 100-fold greater maximum tolerable dose (MTD) than WT Maraba in vivo and resulted in durable cures when systemically administered in syngeneic and xenograft models. In summary, we report a potent new oncolytic rhabdovirus platform with unique tumor-selective attenuating mutations. PMID:20551913

Identification of genetically modified Maraba virus as an oncolytic rhabdovirus.

PubMed

Brun, Jan; McManus, Dan; Lefebvre, Charles; Hu, Kang; Falls, Theresa; Atkins, Harold; Bell, John C; McCart, J Andrea; Mahoney, Douglas; Stojdl, David F

2010-08-01

To expand our current array of safe and potent oncolytic viruses, we screened a variety of wild-type (WT) rhabdoviruses against a panel of tumor cell lines. Our screen identified a number of viruses with varying degrees of killing activity. Maraba virus was the most potent of these strains. We built a recombinant system for the Maraba virus platform, engineered a series of attenuating mutations to expand its therapeutic index, and tested their potency in vitro and in vivo. A double mutant (MG1) strain containing both G protein (Q242R) and M protein (L123W) mutations attenuated Maraba virus in normal diploid cell lines, yet appeared to be hypervirulent in cancer cells. This selective attenuation was mediated through interferon (IFN)-dependent and -independent mechanisms. Finally, the Maraba MG1 strain had a 100-fold greater maximum tolerable dose (MTD) than WT Maraba in vivo and resulted in durable cures when systemically administered in syngeneic and xenograft models. In summary, we report a potent new oncolytic rhabdovirus platform with unique tumor-selective attenuating mutations.

Disc Antenna Enhanced Infrared Spectroscopy: From Self-Assembled Monolayers to Membrane Proteins.

PubMed

Pfitzner, Emanuel; Seki, Hirofumi; Schlesinger, Ramona; Ataka, Kenichi; Heberle, Joachim

2018-05-25

Plasmonic surfaces have emerged as a powerful platform for biomolecular sensing applications and can be designed to optimize the plasmonic resonance for probing molecular vibrations at utmost sensitivity. Here, we present a facile procedure to generate metallic microdisc antenna arrays that are employed in surface-enhanced infrared absorption (SEIRA) spectroscopy of biomolecules. Transmission electron microscopy (TEM) grids are used as shadow mask deployed during physical vapor deposition of gold. The resulting disc-shaped antennas exhibit enhancement factors of the vibrational bands of 4 × 10 4 giving rise to a detection limit <1 femtomol (10 -15 mol) of molecules. Surface-bound monolayers of 4-mercaptobenzoic acid show polyelectrolyte behavior when titrated with cations in the aqueous medium. Conformational rigidity of the self-assembled monolayer is validated by density functional theory calculations. The membrane protein sensory rhodopsin II is tethered to the disc antenna arrays and is fully functional as inferred from the light-induced SEIRA difference spectra. As an advance to previous studies, the accessible frequency range is improved and extended into the fingerprint region.

Chicken ovalbumin upstream promoter-transcription factor II regulates nuclear receptor, myogenic, and metabolic gene expression in skeletal muscle cells.

PubMed

Crowther, Lisa M; Wang, Shu-Ching Mary; Eriksson, Natalie A; Myers, Stephen A; Murray, Lauren A; Muscat, George E O

2011-02-24

We demonstrate that chicken ovalbumin upstream promoter-transcription factor II (COUP-TFII) mRNA is more abundantly expressed (than COUP-TFI mRNA) in skeletal muscle C2C12 cells and in (type I and II) skeletal muscle tissue from C57BL/10 mice. Consequently, we have utilized the ABI TaqMan Low Density Array (TLDA) platform to analyze gene expression changes specifically attributable to ectopic COUP-TFII (relative to vector only) expression in muscle cells. Utilizing a TLDA-based platform and 5 internal controls, we analyze the entire NR superfamily, 96 critical metabolic genes, and 48 important myogenic regulatory genes on the TLDA platform utilizing 5 internal controls. The low density arrays were analyzed by rigorous statistical analysis (with Genorm normalization, Bioconductor R, and the Empirical Bayes statistic) using the (integromics) statminer software. In addition, we validated the differentially expressed patho-physiologically relevant gene (identified on the TLDA platform) glucose transporter type 4 (Glut4). We demonstrated that COUP-TFII expression increased the steady state levels of Glut4 mRNA and protein, while ectopic expression of truncated COUP-TFII lacking helix 12 (COUP-TFΔH12) reduced Glut4 mRNA expression in C2C12 cells. Moreover, COUP-TFII expression trans-activated the Glut4 promoter (-997/+3), and ChIP analysis identified selective recruitment of COUP-TFII to a region encompassing a highly conserved SP1 binding site (in mouse, rat, and human) at nt positions -131/-118. Mutation of the SpI site ablated COUP-TFII mediated trans-activation of the Glut4 promoter. In conclusion, this study demonstrates that in skeletal muscle cells, COUP-TFII regulates several nuclear hormone receptors, and critical metabolic and muscle specific genes.

A force sensor using nanowire arrays to understand biofilm formation (Conference Presentation)

NASA Astrophysics Data System (ADS)

Sahoo, Prasana K.; Cavalli, Alessandro; Pelegati, Vitor B.; Murillo, Duber M.; Souza, Alessandra A.; Cesar, Carlos L.; Bakkers, Erik P. A. M.; Cotta, Monica A.

2016-03-01

Understanding the cellular signaling and function at the nano-bio interface can pave the way towards developing next-generation smart diagnostic tools. From this perspective, limited reports detail so far the cellular and subcellular forces exerted by bacterial cells during the interaction with abiotic materials. Nanowire arrays with high aspect ratio have been used to detect such small forces. In this regard, live force measurements were performed ex-vivo during the interaction of Xylella fastidiosa bacterial cells with InP nanowire arrays. The influence of nanowire array topography and surface chemistry on the response and motion of bacterial cells was studied in detail. The nanowire arrays were also functionalized with different cell adhesive promoters, such as amines and XadA1, an afimbrial protein of X.fastidiosa. By employing the well-defined InP nanowire arrays platform, and single cell confocal imaging system, we were able to trace the bacterial growth pattern, and show that their initial attachment locations are strongly influenced by the surface chemistry and nanoscale surface topography. In addition, we measure the cellular forces down to few nanonewton range using these nanowire arrays. In case of nanowire functionalized with XadA1, the force exerted by vertically and horizontally attached single bacteria on the nanowire is in average 14% and 26% higher than for the pristine array, respectively. These results provide an excellent basis for live-cell force measurements as well as unravel the range of forces involved during the early stages of bacterial adhesion and biofilm formation.

Cell motility regulation on a stepped micro pillar array device (SMPAD) with a discrete stiffness gradient.

PubMed

Lee, Sujin; Hong, Juhee; Lee, Junghoon

2016-02-28

Our tissues consist of individual cells that respond to the elasticity of their environment, which varies between and within tissues. To better understand mechanically driven cell migration, it is necessary to manipulate the stiffness gradient across a substrate. Here, we have demonstrated a new variant of the microfabricated polymeric pillar array platform that can decouple the stiffness gradient from the ECM protein area. This goal is achieved via a "stepped" micro pillar array device (SMPAD) in which the contact area with the cell was kept constant while the diameter of the pillar bodies was altered to attain the proper mechanical stiffness. Using double-step SU-8 mold fabrication, the diameter of the top of every pillar was kept uniform, whereas that of the bottom was changed, to achieve the desired substrate rigidity. Fibronectin was immobilized on the pillar tops, providing a focal adhesion site for cells. C2C12, HeLa and NIH3T3 cells were cultured on the SMPAD, and the motion of the cells was observed by time-lapse microscopy. Using this simple platform, which produces a purely physical stimulus, we observed that various types of cell behavior are affected by the mechanical stimulus of the environment. We also demonstrated directed cell migration guided by a discrete rigidity gradient by varying stiffness. Interestingly, cell velocity was highest at the highest stiffness. Our approach enables the regulation of the mechanical properties of the polymeric pillar array device and eliminates the effects of the size of the contact area. This technique is a unique tool for studying cellular motion and behavior relative to various stiffness gradients in the environment.

Biomimetic devices functionalized by membrane channel proteins

NASA Astrophysics Data System (ADS)

Schmidt, Jacob

2004-03-01

We are developing a new family of active materials which derive their functional properties from membrane proteins. These materials have two primary components: the proteins and the membranes themselves. I will discuss our recent work directed toward development of a generic platform for a "plug-and-play" philosophy of membrane protein engineering. By creating a stable biomimetic polymer membrane a single molecular monolayer thick, we will enable the exploitation of the function of any membrane protein, from pores and pumps to sensors and energy transducers. Our initial work has centered on the creation, study, and characterization of the biomimetic membranes. We are attempting to make large areas of membrane monolayers using Langmuir-Blodgett film formation as well as through arrays of microfabricated black lipid membrane-type septa. A number of techniques allow the insertion of protein into the membranes. As a benchmark, we have been employing a model system of voltage-gated pore proteins, which have electrically controllable porosities. I will report on the progress of this work, the characterization of the membranes, protein insertion processes, and the yield and functionality of the composite.

WebArray: an online platform for microarray data analysis

PubMed Central

Xia, Xiaoqin; McClelland, Michael; Wang, Yipeng

2005-01-01

Background Many cutting-edge microarray analysis tools and algorithms, including commonly used limma and affy packages in Bioconductor, need sophisticated knowledge of mathematics, statistics and computer skills for implementation. Commercially available software can provide a user-friendly interface at considerable cost. To facilitate the use of these tools for microarray data analysis on an open platform we developed an online microarray data analysis platform, WebArray, for bench biologists to utilize these tools to explore data from single/dual color microarray experiments. Results The currently implemented functions were based on limma and affy package from Bioconductor, the spacings LOESS histogram (SPLOSH) method, PCA-assisted normalization method and genome mapping method. WebArray incorporates these packages and provides a user-friendly interface for accessing a wide range of key functions of limma and others, such as spot quality weight, background correction, graphical plotting, normalization, linear modeling, empirical bayes statistical analysis, false discovery rate (FDR) estimation, chromosomal mapping for genome comparison. Conclusion WebArray offers a convenient platform for bench biologists to access several cutting-edge microarray data analysis tools. The website is freely available at . It runs on a Linux server with Apache and MySQL. PMID:16371165

In situ synthesis of protein arrays.

PubMed

He, Mingyue; Stoevesandt, Oda; Taussig, Michael J

2008-02-01

In situ or on-chip protein array methods use cell free expression systems to produce proteins directly onto an immobilising surface from co-distributed or pre-arrayed DNA or RNA, enabling protein arrays to be created on demand. These methods address three issues in protein array technology: (i) efficient protein expression and availability, (ii) functional protein immobilisation and purification in a single step and (iii) protein on-chip stability over time. By simultaneously expressing and immobilising many proteins in parallel on the chip surface, the laborious and often costly processes of DNA cloning, expression and separate protein purification are avoided. Recently employed methods reviewed are PISA (protein in situ array) and NAPPA (nucleic acid programmable protein array) from DNA and puromycin-mediated immobilisation from mRNA.

Vane array with one or more non-integral platforms

DOEpatents

Lohaus, Andrew S.; Campbell, Christian Xavier; Miller, Jr, Samuel R.; Marra, John J.

2016-07-12

A vane array adapted to be coupled to a vane carrier within a gas turbine engine is provided comprising: a plurality of elongated airfoils comprising at least a first airfoil and a second airfoil located adjacent to one another; a U-ring; first connector structure for coupling a radially inner end section of each of the first and second airfoils to the U-ring; second connector structure for coupling a radially outer end section of each of the first and second airfoils to the vane carrier; a platform extending between the first and second airfoils; and platform connector structure for coupling the platform to one of the U-ring and the vane carrier.

Affinity proteomics within rare diseases: a BIO-NMD study for blood biomarkers of muscular dystrophies

PubMed Central

Ayoglu, Burcu; Chaouch, Amina; Lochmüller, Hanns; Politano, Luisa; Bertini, Enrico; Spitali, Pietro; Hiller, Monika; Niks, Eric H; Gualandi, Francesca; Pontén, Fredrik; Bushby, Kate; Aartsma-Rus, Annemieke; Schwartz, Elena; Le Priol, Yannick; Straub, Volker; Uhlén, Mathias; Cirak, Sebahattin; ‘t Hoen, Peter A C; Muntoni, Francesco; Ferlini, Alessandra; Schwenk, Jochen M; Nilsson, Peter; Al-Khalili Szigyarto, Cristina

2014-01-01

Despite the recent progress in the broad-scaled analysis of proteins in body fluids, there is still a lack in protein profiling approaches for biomarkers of rare diseases. Scarcity of samples is the main obstacle hindering attempts to apply discovery driven protein profiling in rare diseases. We addressed this challenge by combining samples collected within the BIO-NMD consortium from four geographically dispersed clinical sites to identify protein markers associated with muscular dystrophy using an antibody bead array platform with 384 antibodies. Based on concordance in statistical significance and confirmatory results obtained from analysis of both serum and plasma, we identified eleven proteins associated with muscular dystrophy, among which four proteins were elevated in blood from muscular dystrophy patients: carbonic anhydrase III (CA3) and myosin light chain 3 (MYL3), both specifically expressed in slow-twitch muscle fibers and mitochondrial malate dehydrogenase 2 (MDH2) and electron transfer flavoprotein A (ETFA). Using age-matched sub-cohorts, 9 protein profiles correlating with disease progression and severity were identified, which hold promise for the development of new clinical tools for management of dystrophinopathies. PMID:24920607

Multiphoton photochemical crosslinking-based fabrication of protein micropatterns with controllable mechanical properties for single cell traction force measurements

NASA Astrophysics Data System (ADS)

Tong, Ming Hui; Huang, Nan; Zhang, Wei; Zhou, Zhuo Long; Ngan, Alfonso Hing Wan; Du, Yanan; Chan, Barbara Pui

2016-01-01

Engineering 3D microstructures with predetermined properties is critical for stem cell niche studies. We have developed a multiphoton femtosecond laser-based 3D printing platform, which generates complex protein microstructures in minutes. Here, we used the platform to test a series of fabrication and reagent parameters in precisely controlling the mechanical properties of protein micropillars. Atomic force microscopy was utilized to measure the reduced elastic modulus of the micropillars, and transmission electron microscopy was used to visualize the porosity of the structures. The reduced elastic modulus of the micropillars associated positively and linearly with the scanning power. On the other hand, the porosity and pore size of the micropillars associated inversely and linearly with the scanning power and reagent concentrations. While keeping the elastic modulus constant, the stiffness of the micropillars was controlled by varying their height. Subsequently, the single cell traction forces of rabbit chondrocytes, human dermal fibroblasts, human mesenchymal stem cells, and bovine nucleus pulposus cells (bNPCs) were successfully measured by culturing the cells on micropillar arrays of different stiffness. Our results showed that the traction forces of all groups showed positive relationship with stiffness, and that the chondrocytes and bNPCs generated the highest and lowest traction forces, respectively.

A microfabricated platform with hydrogel arrays for 3D mechanical stimulation of cells.

PubMed

Liu, Haijiao; Usprech, Jenna; Sun, Yu; Simmons, Craig A

2016-04-01

Cellular microenvironments present cells with multiple stimuli, including not only soluble biochemical and insoluble matrix cues but also mechanical factors. Biomaterial array platforms have been used to combinatorially and efficiently probe and define two-dimensional (2D) and 3D microenvironmental cues to guide cell functions for tissue engineering applications. However, there are few examples of array platforms that include dynamic mechanical forces, particularly to enable stretching of 3D cell-seeded biomaterials, which is relevant to engineering connective and cardiovascular tissues. Here we present a deformable membrane platform that enables 3D dynamic mechanical stretch of arrayed biomaterial constructs. Cell-seeded polyethylene glycol norbornene (PEG-NB) hydrogels were bound to miniaturized deformable membranes via a thiol-ene reaction with off-stoichiometry thiol-ene based polydimethylsiloxane (OSTE-PDMS) as the membrane material. Bonding to OSTE-PDMS enabled the 3D hydrogel microconstructs to be cyclically deformed and stretched by the membrane. As a first demonstration, human mesenchymal stromal cells (MSCs) embedded in PEG-NB were stretched for several days. They were found to be viable, spread in the 3D hydrogels, and exhibited a contractile myofibroblast phenotype when exposed to dynamic 3D mechanical deformation. This platform, which is readily scalable to larger arrays, enables systematic interrogation of the relationships between combinations of 3D mechanobiological cues and cellular responses, and thus has the potential to identify strategies to predictably control the construction of functional engineered tissues. Current high-throughput biomaterial screening approaches fail to consider the effects of dynamic mechanical stimulation, despite its importance in a wide variety of regenerative medicine applications. To meet this need, we developed a deformable membrane platform that enables 3D dynamic stretch of arrayed biomaterial constructs. Our approach combines microtechnologies fabricated with off-stoichiometry thiol-ene based polydimethylsiloxane membranes that can covalently bond cell-seeded polyethylene glycol norbornene 3D hydrogels, a model biomaterial with tunable adhesive, elastic and degradation characteristics. As a first demonstration, we show that human mesenchymal stromal cells embedded in hydrogels and subjected to dynamic mechanical stimulation undergo myofibroblast differentiation. This system is readily scaled up to larger arrays, and will enable systematic and efficient screening of combinations of 3D mechanobiological and biomaterial cues on cell fate and function. Copyright © 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

A novel lab-on-chip platform with integrated solid phase PCR and Supercritical Angle Fluorescence (SAF) microlens array for highly sensitive and multiplexed pathogen detection.

PubMed

Hung, Tran Quang; Chin, Wai Hoe; Sun, Yi; Wolff, Anders; Bang, Dang Duong

2017-04-15

Solid-phase PCR (SP-PCR) has become increasingly popular for molecular diagnosis and there have been a few attempts to incorporate SP-PCR into lab-on-a-chip (LOC) devices. However, their applicability for on-line diagnosis is hindered by the lack of sensitive and portable on-chip optical detection technology. In this paper, we addressed this challenge by combining the SP-PCR with super critical angle fluorescence (SAF) microlens array embedded in a microchip. We fabricated miniaturized SAF microlens array as part of a microfluidic chamber in thermoplastic material and performed multiplexed SP-PCR directly on top of the SAF microlens array. Attribute to the high fluorescence collection efficiency of the SAF microlens array, the SP-PCR assay on the LOC platform demonstrated a high sensitivity of 1.6 copies/µL, comparable to off-chip detection using conventional laser scanner. The combination of SP-PCR and SAF microlens array allows for on-chip highly sensitive and multiplexed pathogen detection with low-cost and compact optical components. The LOC platform would be widely used as a high-throughput biosensor to analyze food, clinical and environmental samples. Copyright © 2016 Elsevier B.V. All rights reserved.

High-density functional-RNA arrays as a versatile platform for studying RNA-based interactions.

PubMed

Phillips, Jack O; Butt, Louise E; Henderson, Charlotte A; Devonshire, Martin; Healy, Jess; Conway, Stuart J; Locker, Nicolas; Pickford, Andrew R; Vincent, Helen A; Callaghan, Anastasia J

2018-05-28

We are just beginning to unravel the myriad of interactions in which non-coding RNAs participate. The intricate RNA interactome is the foundation of many biological processes, including bacterial virulence and human disease, and represents unexploited resources for the development of potential therapeutic interventions. However, identifying specific associations of a given RNA from the multitude of possible binding partners within the cell requires robust high-throughput systems for their rapid screening. Here, we present the first demonstration of functional-RNA arrays as a novel platform technology designed for the study of such interactions using immobilized, active RNAs. We have generated high-density RNA arrays by an innovative method involving surface-capture of in vitro transcribed RNAs. This approach has significant advantages over existing technologies, particularly in its versatility in regards to binding partner character. Indeed, proof-of-principle application of RNA arrays to both RNA-small molecule and RNA-RNA pairings is demonstrated, highlighting their potential as a platform technology for mapping RNA-based networks and for pharmaceutical screening. Furthermore, the simplicity of the method supports greater user-accessibility over currently available technologies. We anticipate that functional-RNA arrays will find broad utility in the expanding field of RNA characterization.

Identification of Antibody Targets for Tuberculosis Serology using High-Density Nucleic Acid Programmable Protein Arrays*

PubMed Central

Song, Lusheng; Wallstrom, Garrick; Yu, Xiaobo; Hopper, Marika; Van Duine, Jennifer; Steel, Jason; Park, Jin; Wiktor, Peter; Kahn, Peter; Brunner, Al; Wilson, Douglas; Jenny-Avital, Elizabeth R.; Qiu, Ji; Labaer, Joshua; Magee, D. Mitchell; Achkar, Jacqueline M.

2017-01-01

Better and more diverse biomarkers for the development of simple point-of-care tests for active tuberculosis (TB), a clinically heterogeneous disease, are urgently needed. We generated a proteomic Mycobacterium tuberculosis (Mtb) High-Density Nucleic Acid Programmable Protein Array (HD-NAPPA) that used a novel multiplexed strategy for expedited high-throughput screening for antibody responses to the Mtb proteome. We screened sera from HIV uninfected and coinfected TB patients and controls (n = 120) from the US and South Africa (SA) using the multiplex HD-NAPPA for discovery, followed by deconvolution and validation through single protein HD-NAPPA with biologically independent samples (n = 124). We verified the top proteins with enzyme-linked immunosorbent assays (ELISA) using the original screening and validation samples (n = 244) and heretofore untested samples (n = 41). We identified 8 proteins with TB biomarker value; four (Rv0054, Rv0831c, Rv2031c and Rv0222) of these were previously identified in serology studies, and four (Rv0948c, Rv2853, Rv3405c, Rv3544c) were not known to elicit antibody responses. Using ELISA data, we created classifiers that could discriminate patients' TB status according to geography (US or SA) and HIV (HIV- or HIV+) status. With ROC curve analysis under cross validation, the classifiers performed with an AUC for US/HIV- at 0.807; US/HIV+ at 0.782; SA/HIV- at 0.868; and SA/HIV+ at 0.723. With this study we demonstrate a new platform for biomarker/antibody screening and delineate its utility to identify previously unknown immunoreactive proteins. PMID:28223349

Evolving serodiagnostics by rationally designed peptide arrays: the Burkholderia paradigm in Cystic Fibrosis

NASA Astrophysics Data System (ADS)

Peri, Claudio; Gori, Alessandro; Gagni, Paola; Sola, Laura; Girelli, Daniela; Sottotetti, Samantha; Cariani, Lisa; Chiari, Marcella; Cretich, Marina; Colombo, Giorgio

2016-09-01

Efficient diagnosis of emerging and novel bacterial infections is fundamental to guide decisions on therapeutic treatments. Here, we engineered a novel rational strategy to design peptide microarray platforms, which combines structural and genomic analyses to predict the binding interfaces between diverse protein antigens and antibodies against Burkholderia cepacia complex infections present in the sera of Cystic Fibrosis (CF) patients. The predicted binding interfaces on the antigens are synthesized in the form of isolated peptides and chemically optimized for controlled orientation on the surface. Our platform displays multiple Burkholderia-related epitopes and is shown to diagnose infected individuals even in presence of superinfections caused by other prevalent CF pathogens, with limited cost and time requirements. Moreover, our data point out that the specific patterns determined by combined probe responses might provide a characterization of Burkholderia infections even at the subtype level (genomovars). The method is general and immediately applicable to other bacteria.

Optimised 'on demand' protein arraying from DNA by cell free expression with the 'DNA to Protein Array' (DAPA) technology.

PubMed

Schmidt, Ronny; Cook, Elizabeth A; Kastelic, Damjana; Taussig, Michael J; Stoevesandt, Oda

2013-08-02

We have previously described a protein arraying process based on cell free expression from DNA template arrays (DNA Array to Protein Array, DAPA). Here, we have investigated the influence of different array support coatings (Ni-NTA, Epoxy, 3D-Epoxy and Polyethylene glycol methacrylate (PEGMA)). Their optimal combination yields an increased amount of detected protein and an optimised spot morphology on the resulting protein array compared to the previously published protocol. The specificity of protein capture was improved using a tag-specific capture antibody on a protein repellent surface coating. The conditions for protein expression were optimised to yield the maximum amount of protein or the best detection results using specific monoclonal antibodies or a scaffold binder against the expressed targets. The optimised DAPA system was able to increase by threefold the expression of a representative model protein while conserving recognition by a specific antibody. The amount of expressed protein in DAPA was comparable to those of classically spotted protein arrays. Reaction conditions can be tailored to suit the application of interest. DAPA represents a cost effective, easy and convenient way of producing protein arrays on demand. The reported work is expected to facilitate the application of DAPA for personalized medicine and screening purposes. Copyright © 2013 Elsevier B.V. All rights reserved.

Arraying proteins by cell-free synthesis.

PubMed

He, Mingyue; Wang, Ming-Wei

2007-10-01

Recent advances in life science have led to great motivation for the development of protein arrays to study functions of genome-encoded proteins. While traditional cell-based methods have been commonly used for generating protein arrays, they are usually a time-consuming process with a number of technical challenges. Cell-free protein synthesis offers an attractive system for making protein arrays, not only does it rapidly converts the genetic information into functional proteins without the need for DNA cloning, but also presents a flexible environment amenable to production of folded proteins or proteins with defined modifications. Recent advancements have made it possible to rapidly generate protein arrays from PCR DNA templates through parallel on-chip protein synthesis. This article reviews current cell-free protein array technologies and their proteomic applications.

Distinct human antibody response to the biological warfare agent Burkholderia mallei.

PubMed

Varga, John J; Vigil, Adam; DeShazer, David; Waag, David M; Felgner, Philip; Goldberg, Joanna B

2012-10-01

The genetic similarity between Burkholderia mallei (glanders) and Burkholderia pseudomallei (melioidosis) had led to the general assumption that pathogenesis of each bacterium would be similar. In 2000, the first human case of glanders in North America since 1945 was reported in a microbiology laboratory worker. Leveraging the availability of pre-exposure sera for this individual and employing the same well-characterized protein array platform that has been previously used to study a large cohort of melioidosis patients in southeast Asia, we describe the antibody response in a human with glanders. Analysis of 156 peptides present on the array revealed antibodies against 17 peptides with a > 2-fold increase in this infection. Unexpectedly, when the glanders data were compared with a previous data set from B. pseudomallei infections, there were only two highly increased antibodies shared between these two infections. These findings have implications in the diagnosis and treatment of B. mallei and B. pseudomallei infections.

Recent developments in OLED-based chemical and biological sensors

NASA Astrophysics Data System (ADS)

Shinar, Joseph; Zhou, Zhaoqun; Cai, Yuankun; Shinar, Ruth

2007-09-01

Recent developments in the structurally integrated OLED-based platform of luminescent chemical and biological sensors are reviewed. In this platform, an array of OLED pixels, which is structurally integrated with the sensing elements, is used as the photoluminescence (PL) excitation source. The structural integration is achieved by fabricating the OLED array and the sensing element on opposite sides of a common glass substrate or on two glass substrates that are attached back-to-back. As it does not require optical fibers, lens, or mirrors, it results in a uniquely simple, low-cost, and potentially rugged geometry. The recent developments on this platform include the following: (1) Enhancing the performance of gas-phase and dissolved oxygen sensors. This is achieved by (a) incorporating high-dielectric TiO II nanoparticles in the oxygen-sensitive Pt and Pd octaethylporphyrin (PtOEP and PdOEP, respectively)- doped polystyrene (PS) sensor films, and (b) embedding the oxygen-sensitive dyes in a matrix of polymer blends such as PS:polydimethylsiloxane (PDMS). (2) Developing sensor arrays for simultaneous detection of multiple serum analytes, including oxygen, glucose, lactate, and alcohol. The sensing element for each analyte consists of a PtOEP-doped PS oxygen sensor, and a solution containing the oxidase enzyme specific to the analyte. Each sensing element is coupled to two individually addressable OLED pixels and a Si photodiode photodetector (PD). (3) Enhancing the integration of the platform, whereby a PD array is also structurally integrated with the OLED array and sensing elements. This enhanced integration is achieved by fabricating an array of amorphous or nanocrystalline Si-based PDs, followed by fabrication of the OLED pixels in the gaps between these Si PDs.

Realizing the promise of reverse phase protein arrays for clinical, translational, and basic research: a workshop report: the RPPA (Reverse Phase Protein Array) society.

PubMed

Akbani, Rehan; Becker, Karl-Friedrich; Carragher, Neil; Goldstein, Ted; de Koning, Leanne; Korf, Ulrike; Liotta, Lance; Mills, Gordon B; Nishizuka, Satoshi S; Pawlak, Michael; Petricoin, Emanuel F; Pollard, Harvey B; Serrels, Bryan; Zhu, Jingchun

2014-07-01

Reverse phase protein array (RPPA) technology introduced a miniaturized "antigen-down" or "dot-blot" immunoassay suitable for quantifying the relative, semi-quantitative or quantitative (if a well-accepted reference standard exists) abundance of total protein levels and post-translational modifications across a variety of biological samples including cultured cells, tissues, and body fluids. The recent evolution of RPPA combined with more sophisticated sample handling, optical detection, quality control, and better quality affinity reagents provides exquisite sensitivity and high sample throughput at a reasonable cost per sample. This facilitates large-scale multiplex analysis of multiple post-translational markers across samples from in vitro, preclinical, or clinical samples. The technical power of RPPA is stimulating the application and widespread adoption of RPPA methods within academic, clinical, and industrial research laboratories. Advances in RPPA technology now offer scientists the opportunity to quantify protein analytes with high precision, sensitivity, throughput, and robustness. As a result, adopters of RPPA technology have recognized critical success factors for useful and maximum exploitation of RPPA technologies, including the following: preservation and optimization of pre-analytical sample quality, application of validated high-affinity and specific antibody (or other protein affinity) detection reagents, dedicated informatics solutions to ensure accurate and robust quantification of protein analytes, and quality-assured procedures and data analysis workflows compatible with application within regulated clinical environments. In 2011, 2012, and 2013, the first three Global RPPA workshops were held in the United States, Europe, and Japan, respectively. These workshops provided an opportunity for RPPA laboratories, vendors, and users to share and discuss results, the latest technology platforms, best practices, and future challenges and opportunities. The outcomes of the workshops included a number of key opportunities to advance the RPPA field and provide added benefit to existing and future participants in the RPPA research community. The purpose of this report is to share and disseminate, as a community, current knowledge and future directions of the RPPA technology. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Electrical Power Subsystem Integration and Test for the NPS Solar Cell Array Tester CubeSat

DTIC Science & Technology

2010-12-01

Earth’s Gravitational Constant MCU Microcontroller Unit MPPT Maximum Power Point Tracker NiCr Nickel Chromium NPS Naval Postgraduate School P...new testing platform was designed, built, and used to conduct integrated testing on CubeSat Kit (CSK) compatible devices. The power budgets and...acceptance test results obtained from the testing platform were used with a solar array power generation simulation, and a battery state of charge

The CAOS camera platform: ushering in a paradigm change in extreme dynamic range imager design

NASA Astrophysics Data System (ADS)

Riza, Nabeel A.

2017-02-01

Multi-pixel imaging devices such as CCD, CMOS and Focal Plane Array (FPA) photo-sensors dominate the imaging world. These Photo-Detector Array (PDA) devices certainly have their merits including increasingly high pixel counts and shrinking pixel sizes, nevertheless, they are also being hampered by limitations in instantaneous dynamic range, inter-pixel crosstalk, quantum full well capacity, signal-to-noise ratio, sensitivity, spectral flexibility, and in some cases, imager response time. Recently invented is the Coded Access Optical Sensor (CAOS) Camera platform that works in unison with current Photo-Detector Array (PDA) technology to counter fundamental limitations of PDA-based imagers while providing high enough imaging spatial resolution and pixel counts. Using for example the Texas Instruments (TI) Digital Micromirror Device (DMD) to engineer the CAOS camera platform, ushered in is a paradigm change in advanced imager design, particularly for extreme dynamic range applications.

Supersensitive fingerprinting of explosives by chemically modified nanosensors arrays.

PubMed

Lichtenstein, Amir; Havivi, Ehud; Shacham, Ronen; Hahamy, Ehud; Leibovich, Ronit; Pevzner, Alexander; Krivitsky, Vadim; Davivi, Guy; Presman, Igor; Elnathan, Roey; Engel, Yoni; Flaxer, Eli; Patolsky, Fernando

2014-06-24

The capability to detect traces of explosives sensitively, selectively and rapidly could be of great benefit for applications relating to civilian national security and military needs. Here, we show that, when chemically modified in a multiplexed mode, nanoelectrical devices arrays enable the supersensitive discriminative detection of explosive species. The fingerprinting of explosives is achieved by pattern recognizing the inherent kinetics, and thermodynamics, of interaction between the chemically modified nanosensors array and the molecular analytes under test. This platform allows for the rapid detection of explosives, from air collected samples, down to the parts-per-quadrillion concentration range, and represents the first nanotechnology-inspired demonstration on the selective supersensitive detection of explosives, including the nitro- and peroxide-derivatives, on a single electronic platform. Furthermore, the ultrahigh sensitivity displayed by our platform may allow the remote detection of various explosives, a task unachieved by existing detection technologies.

Supersensitive fingerprinting of explosives by chemically modified nanosensors arrays

NASA Astrophysics Data System (ADS)

Lichtenstein, Amir; Havivi, Ehud; Shacham, Ronen; Hahamy, Ehud; Leibovich, Ronit; Pevzner, Alexander; Krivitsky, Vadim; Davivi, Guy; Presman, Igor; Elnathan, Roey; Engel, Yoni; Flaxer, Eli; Patolsky, Fernando

2014-06-01

The capability to detect traces of explosives sensitively, selectively and rapidly could be of great benefit for applications relating to civilian national security and military needs. Here, we show that, when chemically modified in a multiplexed mode, nanoelectrical devices arrays enable the supersensitive discriminative detection of explosive species. The fingerprinting of explosives is achieved by pattern recognizing the inherent kinetics, and thermodynamics, of interaction between the chemically modified nanosensors array and the molecular analytes under test. This platform allows for the rapid detection of explosives, from air collected samples, down to the parts-per-quadrillion concentration range, and represents the first nanotechnology-inspired demonstration on the selective supersensitive detection of explosives, including the nitro- and peroxide-derivatives, on a single electronic platform. Furthermore, the ultrahigh sensitivity displayed by our platform may allow the remote detection of various explosives, a task unachieved by existing detection technologies.

A Universal Genome Array and Transcriptome Atlas for Brachypodium Distachyon

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mockler, Todd

Brachypodium distachyon is the premier experimental model grass platform and is related to candidate feedstock crops for bioethanol production. Based on the DOE-JGI Brachypodium Bd21 genome sequence and annotation we designed a whole genome DNA microarray platform. The quality of this array platform is unprecedented due to the exceptional quality of the Brachypodium genome assembly and annotation and the stringent probe selection criteria employed in the design. We worked with members of the international community and the bioinformatics/design team at Affymetrix at all stages in the development of the array. We used the Brachypodium arrays to interrogate the transcriptomes ofmore » plants grown in a variety of environmental conditions including diurnal and circadian light/temperature conditions and under a variety of environmental conditions. We examined the transciptional responses of Brachypodium seedlings subjected to various abiotic stresses including heat, cold, salt, and high intensity light. We generated a gene expression atlas representing various organs and developmental stages. The results of these efforts including all microarray datasets are published and available at online public databases.« less

A novel multifunctional electrochemical platform for simultaneous detection, elimination, and inactivation of pathogenic bacteria based on the Vancomycin-functionalised AgNPs/3D-ZnO nanorod arrays.

PubMed

Yang, Zhiqing; Wang, Yi; Zhang, Dun

2017-12-15

A novel fast, sensitive, and specific multifunctional electrochemical platform has been proposed for simultaneous detection, elimination, and inactivation of pathogenic bacteria for the first time. The platform is constituted with three-dimensional ZnO nanorod arrays (3D-ZnO) decorated with sliver nanoparticles (AgNPs) and functionalized with vancomycin (Van). Based on the specific recognition of Van for Gram-positive bacteria, the fabricated electrochemical platform has presented high detection sensitivity to Staphylococcus aureus with a low detection limit of 330cfu/mL and adaptable bacterial-elimination efficiency (50%) at low concentrations (1000-2000cfu/mL). Moreover, the platform has shown high antibacterial activity (99.99%) arising from the synergistic germicidal effect of the composited antibacterial AgNPs and Van units. The current work could provide new strategies to construct advanced platforms for simultaneous detection, elimination, and inactivation of various pathogenic bacteria. Copyright © 2017 Elsevier B.V. All rights reserved.

FRAP and Photoconversion in Multiple Arbitrary Regions of Interest Using a Programmable Array Microscope (PAM)

PubMed Central

Hagen, Guy M.; Caarls, Wouter; Lidke, Keith A.; de Vries, Anthony H. B.; Fritsch, Cornelia; Barisas, B. George; Arndt-Jovin, Donna J.; Jovin, Thomas M.

2011-01-01

Photomanipulation (photobleaching, photoactivation, or photoconversion) is an essential tool in fluorescence microscopy. Fluorescence recovery after photobleaching (FRAP) is commonly used for the determination of lateral diffusion constants of membrane proteins, and can be conveniently implemented in confocal laser scanning microscopy (CLSM). Such determinations provide important information on molecular dynamics in live cells. However, the CLSM platform is inherently limited for FRAP because of its inflexible raster (spot) scanning format. We have implemented FRAP and photoactivation protocols using structured illumination and detection in a programmable array microscope (PAM). The patterns are arbitrary in number and shape, dynamic and adjustable to and by the sample characteristics. We have used multi-spot PAM-FRAP to measure the lateral diffusion of the erbB3 (HER3) receptor tyrosine kinase labeled by fusion with mCitrine on untreated cells and after treatment with reagents that perturb the cytoskeleton or plasma membrane or activate co-expressed erbB1 (HER1, the EGF receptor EGFR). We also show the versatility of the PAM for photoactivation in arbitrary regions of interest, in cells expressing erbB3 fused with the photoconvertible fluorescent protein dronpa. PMID:19208387

Reconfigurable Microfluidic Magnetic Valve Arrays: Towards a Radiotherapy-Compatible Spheroid Culture Platform for the Combinatorial Screening of Cancer Therapies

PubMed Central

Labelle, Frédérique; Wong, Philip

2017-01-01

We introduce here a microfluidic cell culture platform or spheroid culture chamber array (SCCA) that can synthesize, culture, and enable fluorescence imaging of 3D cell aggregates (typically spheroids) directly on-chip while specifying the flow of reagents in each chamber via the use of an array of passive magnetic valves. The SCCA valves demonstrated sufficient resistance to burst (above 100 mBar), including after receiving radiotherapy (RT) doses of up to 8 Gy combined with standard 37 °C incubation for up to 7 days, enabling the simultaneous synthesis of multiple spheroids from different cell lines on the same array. Our results suggest that SCCA would be an asset in drug discovery processes, seeking to identify combinatorial treatments. PMID:28976942

Capture and X-ray diffraction studies of protein microcrystals in a microfluidic trap array

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lyubimov, Artem Y.; Stanford University, Stanford, CA 94305; Stanford University, Stanford, CA 94305

A microfluidic platform has been developed for the capture and X-ray analysis of protein microcrystals, affording a means to improve the efficiency of XFEL and synchrotron experiments. X-ray free-electron lasers (XFELs) promise to enable the collection of interpretable diffraction data from samples that are refractory to data collection at synchrotron sources. At present, however, more efficient sample-delivery methods that minimize the consumption of microcrystalline material are needed to allow the application of XFEL sources to a wide range of challenging structural targets of biological importance. Here, a microfluidic chip is presented in which microcrystals can be captured at fixed, addressablemore » points in a trap array from a small volume (<10 µl) of a pre-existing slurry grown off-chip. The device can be mounted on a standard goniostat for conducting diffraction experiments at room temperature without the need for flash-cooling. Proof-of-principle tests with a model system (hen egg-white lysozyme) demonstrated the high efficiency of the microfluidic approach for crystal harvesting, permitting the collection of sufficient data from only 265 single-crystal still images to permit determination and refinement of the structure of the protein. This work shows that microfluidic capture devices can be readily used to facilitate data collection from protein microcrystals grown in traditional laboratory formats, enabling analysis when cryopreservation is problematic or when only small numbers of crystals are available. Such microfluidic capture devices may also be useful for data collection at synchrotron sources.« less

Electrostatically Driven Large Aperture Micro-Mirror Actuator Assemblies for High Fill-Factor, Agile Optical Phase Arrays

DTIC Science & Technology

2015-06-18

platform assembly 2, with micro-mirror platform deflection, measured on actuation side ( PFa ) and side opposite actuation (PFo...beam micro-mirror platform assembly 1; micro-mirror platform deflection, measured on actuation side ( PFa ) and side opposite actuation (PFo...side ( PFa ) and side opposite actuation (PFo) ........................................................ 106 xiv Figure 73: Graph of measured 10-beam

Intra-Platform Repeatability and Inter-Platform Comparability of MicroRNA Microarray Technology

PubMed Central

Sato, Fumiaki; Tsuchiya, Soken; Terasawa, Kazuya; Tsujimoto, Gozoh

2009-01-01

Over the last decade, DNA microarray technology has provided a great contribution to the life sciences. The MicroArray Quality Control (MAQC) project demonstrated the way to analyze the expression microarray. Recently, microarray technology has been utilized to analyze a comprehensive microRNA expression profiling. Currently, several platforms of microRNA microarray chips are commercially available. Thus, we compared repeatability and comparability of five different microRNA microarray platforms (Agilent, Ambion, Exiqon, Invitrogen and Toray) using 309 microRNAs probes, and the Taqman microRNA system using 142 microRNA probes. This study demonstrated that microRNA microarray has high intra-platform repeatability and comparability to quantitative RT-PCR of microRNA. Among the five platforms, Agilent and Toray array showed relatively better performances than the others. However, the current lineup of commercially available microRNA microarray systems fails to show good inter-platform concordance, probably because of lack of an adequate normalization method and severe divergence in stringency of detection call criteria between different platforms. This study provided the basic information about the performance and the problems specific to the current microRNA microarray systems. PMID:19436744

Standardized UXO Technology Demonstration Site Blind Grid Scoring Record No. 806 (U.S. Geological Survey, TMGS Magnetometer/Towed Array)

DTIC Science & Technology

2007-05-01

BOX 25046, FEDERAL CENTER, M.S. 964 DENVER, CO 80225-0046 TECHNOLOGY TYPE/PLATFORM: TMGS MAGNETOMETER/TOWED ARRAY PREPARED BY: U.S. ARMY...GEOLOGICAL SURVEY, TMGS MAGNETOMETER/TOWED ARRAY) 8-CO-160-UXO-021 Karwatka, Michael... TMGS Magnetometer/Towed Array, MEC Unclassified Unclassified Unclassified SAR (Page ii Blank) i ACKNOWLEDGMENTS

Comparison of the Predictive Accuracy of DNA Array-Based Multigene Classifiers across cDNA Arrays and Affymetrix GeneChips

PubMed Central

Stec, James; Wang, Jing; Coombes, Kevin; Ayers, Mark; Hoersch, Sebastian; Gold, David L.; Ross, Jeffrey S; Hess, Kenneth R.; Tirrell, Stephen; Linette, Gerald; Hortobagyi, Gabriel N.; Symmans, W. Fraser; Pusztai, Lajos

2005-01-01

We examined how well differentially expressed genes and multigene outcome classifiers retain their class-discriminating values when tested on data generated by different transcriptional profiling platforms. RNA from 33 stage I-III breast cancers was hybridized to both Affymetrix GeneChip and Millennium Pharmaceuticals cDNA arrays. Only 30% of all corresponding gene expression measurements on the two platforms had Pearson correlation coefficient r ≥ 0.7 when UniGene was used to match probes. There was substantial variation in correlation between different Affymetrix probe sets matched to the same cDNA probe. When cDNA and Affymetrix probes were matched by basic local alignment tool (BLAST) sequence identity, the correlation increased substantially. We identified 182 genes in the Affymetrix and 45 in the cDNA data (including 17 common genes) that accurately separated 91% of cases in supervised hierarchical clustering in each data set. Cross-platform testing of these informative genes resulted in lower clustering accuracy of 45 and 79%, respectively. Several sets of accurate five-gene classifiers were developed on each platform using linear discriminant analysis. The best 100 classifiers showed average misclassification error rate of 2% on the original data that rose to 19.5% when tested on data from the other platform. Random five-gene classifiers showed misclassification error rate of 33%. We conclude that multigene predictors optimized for one platform lose accuracy when applied to data from another platform due to missing genes and sequence differences in probes that result in differing measurements for the same gene. PMID:16049308

A high-throughput microparticle microarray platform for dendritic cell-targeting vaccines.

PubMed

Acharya, Abhinav P; Clare-Salzler, Michael J; Keselowsky, Benjamin G

2009-09-01

Immunogenomic approaches combined with advances in adjuvant immunology are guiding progress toward rational design of vaccines. Furthermore, drug delivery platforms (e.g., synthetic particles) are demonstrating promise for increasing vaccine efficacy. Currently there are scores of known antigenic epitopes and adjuvants, and numerous synthetic delivery systems accessible for formulation of vaccines for various applications. However, the lack of an efficient means to test immune cell responses to the abundant combinations available represents a significant blockade on the development of new vaccines. In order to overcome this barrier, we report fabrication of a new class of microarray consisting of antigen/adjuvant-loadable poly(D,L lactide-co-glycolide) microparticles (PLGA MPs), identified as a promising carrier for immunotherapeutics, which are co-localized with dendritic cells (DCs), key regulators of the immune system and prime targets for vaccines. The intention is to utilize this high-throughput platform to optimize particle-based vaccines designed to target DCs in vivo for immune system-related disorders, such as autoimmune diseases, cancer and infection. Fabrication of DC/MP arrays leverages the use of standard contact printing miniarraying equipment in conjunction with surface modification to achieve co-localization of particles/cells on isolated islands while providing background non-adhesive surfaces to prevent off-island cell migration. We optimized MP overspotting pin diameter, accounting for alignment error, to allow construction of large, high-fidelity arrays. Reproducible, quantitative delivery of as few as 16+/-2 MPs per spot was demonstrated and two-component MP dosing arrays were constructed, achieving MP delivery which was independent of formulation, with minimal cross-contamination. Furthermore, quantification of spotted, surface-adsorbed MP degradation was demonstrated, potentially useful for optimizing MP release properties. Finally, we demonstrate DC co-localization with PLGA MPs on isolated islands and that DCs do not migrate between islands for up to 24 h. Using this platform, we intend to analyze modulation of DC function by providing multi-parameter combinatorial cues in the form of proteins, peptides and other immuno-modulatory molecules encapsulated in or tethered on MPs. Critically, the miniaturization attained enables high-throughput investigation of rare cell populations by reducing the requirement for cells and reagents by many-fold, facilitating advances in personalized vaccines which target DCs in vivo.

Simple and fast method for fabrication of endoscopic implantable sensor arrays.

PubMed

Tahirbegi, I Bogachan; Alvira, Margarita; Mir, Mònica; Samitier, Josep

2014-06-26

Here we have developed a simple method for the fabrication of disposable implantable all-solid-state ion-selective electrodes (ISE) in an array format without using complex fabrication equipment or clean room facilities. The electrodes were designed in a needle shape instead of planar electrodes for a full contact with the tissue. The needle-shape platform comprises 12 metallic pins which were functionalized with conductive inks and ISE membranes. The modified microelectrodes were characterized with cyclic voltammetry, scanning electron microscope (SEM), and optical interferometry. The surface area and roughness factor of each microelectrode were determined and reproducible values were obtained for all the microelectrodes on the array. In this work, the microelectrodes were modified with membranes for the detection of pH and nitrate ions to prove the reliability of the fabricated sensor array platform adapted to an endoscope.

CMG-Augmented Control of a Hovering VTOL Platform

NASA Technical Reports Server (NTRS)

Lim, K. B.; Moerder, D. D.

2007-01-01

This paper describes how Control Moment Gyroscopes (CMGs) can be used for stability augmentation to a thrust vectoring system for a generic Vertical Take-Off and Landing platform. The response characteristics of the platform which uses only thrust vectoring and a second configuration which includes a single-gimbal CMG array are simulated and compared for hovering flight while subject to severe air turbulence. Simulation results demonstrate the effectiveness of a CMG array in its ability to significantly reduce the agility requirement on the thrust vectoring system. Albeit simplifying physical assumptions on a generic CMG configuration, the numerical results also suggest that reasonably sized CMGs will likely be sufficient for a small hovering vehicle.

Mesenchymal stem cells cultured on magnetic nanowire substrates

NASA Astrophysics Data System (ADS)

Perez, Jose E.; Ravasi, Timothy; Kosel, Jürgen

2017-02-01

Stem cells have been shown to respond to extracellular mechanical stimuli by regulating their fate through the activation of specific signaling pathways. In this work, an array of iron nanowires (NWs) aligned perpendicularly to the surface was fabricated by pulsed electrodepositon in porous alumina templates followed by a partial removal of the alumina to reveal 2-3 μm of the NWs. This resulted in alumina substrates with densely arranged NWs of 33 nm in diameter separated by 100 nm. The substrates were characterized by scanning electron microscopy (SEM) energy dispersive x-ray analysis and vibrating sample magnetometer. The NW array was then used as a platform for the culture of human mesenchymal stem cells (hMSCs). The cells were stained for the cell nucleus and actin filaments, as well as immuno-stained for the focal adhesion protein vinculin, and then observed by fluorescence microscopy in order to characterize their spreading behavior. Calcein AM/ethidium homodimer-1 staining allowed the determination of cell viability. The interface between the cells and the NWs was studied using SEM. Results showed that hMSCs underwent a re-organization of actin filaments that translated into a change from an elongated to a spherical cell shape. Actin filaments and vinculin accumulated in bundles, suggesting the attachment and formation of focal adhesion points of the cells on the NWs. Though the overall number of cells attached on the NWs was lower compared to the control, the attached cells maintained a high viability (>90%) for up to 6 d. Analysis of the interface between the NWs and the cells confirmed the re-organization of F-actin and revealed the adhesion points of the cells on the NWs. Additionally, a net of filopodia surrounded each cell, suggesting the probing of the array to find additional adhesion points. The cells maintained their round shape for up to 6 d of culture. Overall, the NW array is a promising nanostructured platform for studying and influencing hMSCs differentiation.

Biomimetic surface patterning for long-term transmembrane access

PubMed Central

VanDersarl, Jules J.; Renaud, Philippe

2016-01-01

Here we present a planar patch clamp chip based on biomimetic cell membrane fusion. This architecture uses nanometer length-scale surface patterning to replicate the structure and function of membrane proteins, creating a gigaohm seal between the cell and a planar electrode array. The seal is generated passively during cell spreading, without the application of a vacuum to the cell surface. This interface can enable cell-attached and whole-cell recordings that are stable to 72 hours, and generates no visible damage to the cell. The electrodes can be very small (<5 μm) and closely packed, offering a high density platform for cellular measurement. PMID:27577519

Biomimetic surface patterning for long-term transmembrane access.

PubMed

VanDersarl, Jules J; Renaud, Philippe

2016-08-31

Here we present a planar patch clamp chip based on biomimetic cell membrane fusion. This architecture uses nanometer length-scale surface patterning to replicate the structure and function of membrane proteins, creating a gigaohm seal between the cell and a planar electrode array. The seal is generated passively during cell spreading, without the application of a vacuum to the cell surface. This interface can enable cell-attached and whole-cell recordings that are stable to 72 hours, and generates no visible damage to the cell. The electrodes can be very small (<5 μm) and closely packed, offering a high density platform for cellular measurement.

U.S. Marine Corps Level-Dependent Hearing Protector Assessment: Objective Measures of Hearing Protection Devices

DTIC Science & Technology

2014-01-01

12 4.2.1 Loudspeaker Array ...Instrumentation 4.2.1 Loudspeaker Array Target stimuli were presented from a spherical loudspeaker array consisting of 57 Meyer Sound MM-4XP miniature... loudspeaker array on a raised platform that placed their ears at the same elevation as the 0° loudspeaker ring. The chair was free to rotate 360° and

A large array of high-performance artificial stars using airship-supported small mirrors

NASA Astrophysics Data System (ADS)

Content, Robert; Foxwell, Mark; Murray, Graham J.

2004-10-01

We propose a practical system that can provide a large number of high performance artificial stars, of the order of a few hundred, using an array of small mirrors on an airship supported platform illuminated from the ground by a laser. Our concept offers several advantages over other guide star schemes: Airborne mirror arrays can furnish tip-tilt information; they also permit a considerable reduction in the total ground-laser power required; high intensity guide stars with very small angular image size are possible; and finally they offer very low scattered parasite laser light. More basic & simpler launch-laser & AO technologies can therefore be employed, with potentially huge cost savings, with potentially significant improvement in the quality of the AO correction. The general platform scheme and suitable lift technologies are also discussed. A novel concept for achieving precise positioning is presented whereby the platform & the lifting vehicle are linked by a tether, the platform having a degree of independent control. Our proposal would employ as the lift vehicle an autonomous high altitude airship of the type currently under widespread development in the commercial sector, for use as hubs for telecommunication networks, mobile telephone relay stations, etc.

Titanium dioxide nanowire sensor array integration on CMOS platform using deterministic assembly.

PubMed

Gall, Oren Z; Zhong, Xiahua; Schulman, Daniel S; Kang, Myungkoo; Razavieh, Ali; Mayer, Theresa S

2017-06-30

Nanosensor arrays have recently received significant attention due to their utility in a wide range of applications, including gas sensing, fuel cells, internet of things, and portable health monitoring systems. Less attention has been given to the production of sensor platforms in the μW range for ultra-low power applications. Here, we discuss how to scale the nanosensor energy demand by developing a process for integration of nanowire sensing arrays on a monolithic CMOS chip. This work demonstrates an off-chip nanowire fabrication method; subsequently nanowires link to a fused SiO 2 substrate using electric-field assisted directed assembly. The nanowire resistances shown in this work have the highest resistance uniformity reported to date of 18%, which enables a practical roadmap towards the coupling of nanosensors to CMOS circuits and signal processing systems. The article also presents the utility of optimizing annealing conditions of the off-chip metal-oxides prior to CMOS integration to avoid limitations of thermal budget and process incompatibility. In the context of the platform demonstrated here, directed assembly is a powerful tool that can realize highly uniform, cross-reactive arrays of different types of metal-oxide nanosensors suited for gas discrimination and signal processing systems.

Titanium dioxide nanowire sensor array integration on CMOS platform using deterministic assembly

NASA Astrophysics Data System (ADS)

Gall, Oren Z.; Zhong, Xiahua; Schulman, Daniel S.; Kang, Myungkoo; Razavieh, Ali; Mayer, Theresa S.

2017-06-01

Nanosensor arrays have recently received significant attention due to their utility in a wide range of applications, including gas sensing, fuel cells, internet of things, and portable health monitoring systems. Less attention has been given to the production of sensor platforms in the μW range for ultra-low power applications. Here, we discuss how to scale the nanosensor energy demand by developing a process for integration of nanowire sensing arrays on a monolithic CMOS chip. This work demonstrates an off-chip nanowire fabrication method; subsequently nanowires link to a fused SiO2 substrate using electric-field assisted directed assembly. The nanowire resistances shown in this work have the highest resistance uniformity reported to date of 18%, which enables a practical roadmap towards the coupling of nanosensors to CMOS circuits and signal processing systems. The article also presents the utility of optimizing annealing conditions of the off-chip metal-oxides prior to CMOS integration to avoid limitations of thermal budget and process incompatibility. In the context of the platform demonstrated here, directed assembly is a powerful tool that can realize highly uniform, cross-reactive arrays of different types of metal-oxide nanosensors suited for gas discrimination and signal processing systems.

Carbon Nanotube Arrays for Intracellular Delivery and Biological Applications

NASA Astrophysics Data System (ADS)

Golshadi, Masoud

Introducing nucleic acids into mammalian cells is a crucial step to elucidate biochemical pathways, modify gene expression in immortalized cells, primary cells, and stem cells, and intoduces new approaches for clinical diagnostics and therapeutics. Current gene transfer technologies, including lipofection, electroporation, and viral delivery, have enabled break-through advances in basic and translational science to enable derivation and programming of embryonic stem cells, advanced gene editing using CRISPR (Clustered regularly interspaced short palindromic repeats), and development of targeted anti-tumor therapy using chimeric antigen receptors in T-cells (CAR-T). Despite these successes, current transfection technologies are time consuming and limited by the inefficient introduction of test molecules into large populations of target cells, and the cytotoxicity of the techniques. Moreover, many cell types cannot be consistently transfected by lipofection or electroporation (stem cells, T-cells) and viral delivery has limitations to the size of experimental DNA that can be packaged. In this dissertation, a novel coverslip-like platform consisting of an array of aligned hollow carbon nanotubes (CNTs) embedded in a sacrificial template is developed that enhances gene transfer capabilities, including high efficiency, low toxicity, in an expanded range of target cells, with the potential to transfer mixed combinations of protein and nucleic acids. The CNT array devices are fabricated by a scalable template-based manufacturing method using commercially available membranes, eliminating the need for nano-assembly. High efficient transfection has been demonstrated by delivering various cargos (nanoparticles, dye and plasmid DNA) into populations of cells, achieving 85% efficiency of plasmid DNA delivery into immortalized cells. Moreover, the CNT-mediated transfection of stem cells shows 3 times higher efficiency compared to current lipofection methods. Evaluating the cell-CNT interaction elucidates the importance of the geometrical properties of CNT arrays (CNT exposed length and surface morphology) on transfection efficiency. The results indicate that densely-packed and shortly-exposed CNT arrays with planar surface will enhance gene delivery using this new platform. This technology offers a significant increase in efficiency and cell viability, along with the ease of use compared to current standard methods, which demonstrates its potential to accelerate the development of new cell models to study intractable diseases, decoding the signaling pathways, and drug discovery.

Identification of discriminant proteins through antibody profiling, methods and apparatus for identifying an individual

DOEpatents

Apel, William A.; Thompson, Vicki S; Lacey, Jeffrey A.; Gentillon, Cynthia A.

2016-08-09

A method for determining a plurality of proteins for discriminating and positively identifying an individual based from a biological sample. The method may include profiling a biological sample from a plurality of individuals against a protein array including a plurality of proteins. The protein array may include proteins attached to a support in a preselected pattern such that locations of the proteins are known. The biological sample may be contacted with the protein array such that a portion of antibodies in the biological sample reacts with and binds to the proteins forming immune complexes. A statistical analysis method, such as discriminant analysis, may be performed to determine discriminating proteins for distinguishing individuals. Proteins of interest may be used to form a protein array. Such a protein array may be used, for example, to compare a forensic sample from an unknown source with a sample from a known source.

Identification of discriminant proteins through antibody profiling, methods and apparatus for identifying an individual

DOEpatents

Thompson, Vicki S; Lacey, Jeffrey A; Gentillon, Cynthia A; Apel, William A

2015-03-03

A method for determining a plurality of proteins for discriminating and positively identifying an individual based from a biological sample. The method may include profiling a biological sample from a plurality of individuals against a protein array including a plurality of proteins. The protein array may include proteins attached to a support in a preselected pattern such that locations of the proteins are known. The biological sample may be contacted with the protein array such that a portion of antibodies in the biological sample reacts with and binds to the proteins forming immune complexes. A statistical analysis method, such as discriminant analysis, may be performed to determine discriminating proteins for distinguishing individuals. Proteins of interest may be used to form a protein array. Such a protein array may be used, for example, to compare a forensic sample from an unknown source with a sample from a known source.

Optical Manipulation of Single Magnetic Beads in a Microwell Array on a Digital Microfluidic Chip.

PubMed

Decrop, Deborah; Brans, Toon; Gijsenbergh, Pieter; Lu, Jiadi; Spasic, Dragana; Kokalj, Tadej; Beunis, Filip; Goos, Peter; Puers, Robert; Lammertyn, Jeroen

2016-09-06

The detection of single molecules in magnetic microbead microwell array formats revolutionized the development of digital bioassays. However, retrieval of individual magnetic beads from these arrays has not been realized until now despite having great potential for studying captured targets at the individual level. In this paper, optical tweezers were implemented on a digital microfluidic platform for accurate manipulation of single magnetic beads seeded in a microwell array. Successful optical trapping of magnetic beads was found to be dependent on Brownian motion of the beads, suggesting a 99% chance of trapping a vibrating bead. A tailor-made experimental design was used to screen the effect of bead type, ionic buffer strength, surfactant type, and concentration on the Brownian activity of beads in microwells. With the optimal conditions, the manipulation of magnetic beads was demonstrated by their trapping, retrieving, transporting, and repositioning to a desired microwell on the array. The presented platform combines the strengths of digital microfluidics, digital bioassays, and optical tweezers, resulting in a powerful dynamic microwell array system for single molecule and single cell studies.

A platform to screen for C-type lectin receptor-binding carbohydrates and their potential for cell-specific targeting and immune modulation.

PubMed

Maglinao, Maha; Eriksson, Magdalena; Schlegel, Mark K; Zimmermann, Stephanie; Johannssen, Timo; Götze, Sebastian; Seeberger, Peter H; Lepenies, Bernd

2014-02-10

Myeloid C-type lectin receptors (CLRs) in innate immunity represent a superfamily of pattern recognition receptors that recognize carbohydrate structures on pathogens and self-antigens. The primary interaction of an antigen-presenting cell and a pathogen shapes the following immune response. Therefore, the identification of CLR ligands that can either enhance or modulate the immune response is of interest. We have developed a screening platform based on glycan arrays to identify immune modulatory carbohydrate ligands of CLRs. A comprehensive library of CLRs was expressed by fusing the extracellular part of each respective CLR, the part containing the carbohydrate-recognition domain (CRD), to the Fc fragment of human IgG1 molecules. CLR-Fc fusion proteins display the CRD in a dimeric form, are properly glycosylated, and can be detected by a secondary antibody with a conjugated fluorophore. Thus, they are valuable tools for high-throughput screening. We were able to identify novel carbohydrate binders of CLRs using the glycan array technology. These CLR-binding carbohydrates were then covalently attached to the model antigen ovalbumin. The ovalbumin neoglycoconjugates were used in a dendritic cell/T cell co-culture assay to stimulate transgenic T cells in vitro. In addition, mice were immunized with these conjugates to analyze the immune modulatory properties of the CLR ligands in vivo. The CLR ligands induced an increased Th1 cytokine production in vitro and modulated the humoral response in vivo. The platform described here allows for the identification of CLR ligands, as well as the evaluation of each ligand's cell-specific targeting and immune modulatory properties. Copyright © 2013 Elsevier B.V. All rights reserved.

Streptococcus pneumoniae Supragenome Hybridization Arrays for Profiling of Genetic Content and Gene Expression.

PubMed

Kadam, Anagha; Janto, Benjamin; Eutsey, Rory; Earl, Joshua P; Powell, Evan; Dahlgren, Margaret E; Hu, Fen Z; Ehrlich, Garth D; Hiller, N Luisa

2015-02-02

There is extensive genomic diversity among Streptococcus pneumoniae isolates. Approximately half of the comprehensive set of genes in the species (the supragenome or pangenome) is present in all the isolates (core set), and the remaining is unevenly distributed among strains (distributed set). The Streptococcus pneumoniae Supragenome Hybridization (SpSGH) array provides coverage for an extensive set of genes and polymorphisms encountered within this species, capturing this genomic diversity. Further, the capture is quantitative. In this manner, the SpSGH array allows for both genomic and transcriptomic analyses of diverse S. pneumoniae isolates on a single platform. In this unit, we present the SpSGH array, and describe in detail its design and implementation for both genomic and transcriptomic analyses. The methodology can be applied to construction and modification of SpSGH array platforms, as well to other bacterial species as long as multiple whole-genome sequences are available that collectively capture the vast majority of the species supragenome. Copyright © 2015 John Wiley & Sons, Inc.

Global assessment of genomic variation in cattle by genome resequencing and high-throughput genotyping

PubMed Central

2011-01-01

Background Integration of genomic variation with phenotypic information is an effective approach for uncovering genotype-phenotype associations. This requires an accurate identification of the different types of variation in individual genomes. Results We report the integration of the whole genome sequence of a single Holstein Friesian bull with data from single nucleotide polymorphism (SNP) and comparative genomic hybridization (CGH) array technologies to determine a comprehensive spectrum of genomic variation. The performance of resequencing SNP detection was assessed by combining SNPs that were identified to be either in identity by descent (IBD) or in copy number variation (CNV) with results from SNP array genotyping. Coding insertions and deletions (indels) were found to be enriched for size in multiples of 3 and were located near the N- and C-termini of proteins. For larger indels, a combination of split-read and read-pair approaches proved to be complementary in finding different signatures. CNVs were identified on the basis of the depth of sequenced reads, and by using SNP and CGH arrays. Conclusions Our results provide high resolution mapping of diverse classes of genomic variation in an individual bovine genome and demonstrate that structural variation surpasses sequence variation as the main component of genomic variability. Better accuracy of SNP detection was achieved with little loss of sensitivity when algorithms that implemented mapping quality were used. IBD regions were found to be instrumental for calculating resequencing SNP accuracy, while SNP detection within CNVs tended to be less reliable. CNV discovery was affected dramatically by platform resolution and coverage biases. The combined data for this study showed that at a moderate level of sequencing coverage, an ensemble of platforms and tools can be applied together to maximize the accurate detection of sequence and structural variants. PMID:22082336

An experimental platform for pulsed-power driven magnetic reconnection

NASA Astrophysics Data System (ADS)

Hare, J. D.; Suttle, L. G.; Lebedev, S. V.; Loureiro, N. F.; Ciardi, A.; Chittenden, J. P.; Clayson, T.; Eardley, S. J.; Garcia, C.; Halliday, J. W. D.; Robinson, T.; Smith, R. A.; Stuart, N.; Suzuki-Vidal, F.; Tubman, E. R.

2018-05-01

We describe a versatile pulsed-power driven platform for magnetic reconnection experiments, based on the exploding wire arrays driven in parallel [Suttle et al., Phys. Rev. Lett. 116, 225001 (2016)]. This platform produces inherently magnetised plasma flows for the duration of the generator current pulse (250 ns), resulting in a long-lasting reconnection layer. The layer exists for long enough to allow the evolution of complex processes such as plasmoid formation and movement to be diagnosed by a suite of high spatial and temporal resolution laser-based diagnostics. We can access a wide range of magnetic reconnection regimes by changing the wire material or moving the electrodes inside the wire arrays. We present results with aluminium and carbon wires, in which the parameters of the inflows and the layer that forms are significantly different. By moving the electrodes inside the wire arrays, we change how strongly the inflows are driven. This enables us to study both symmetric reconnection in a range of different regimes and asymmetric reconnection.

Enhanced Quality Factor Label-free Biosensing with Micro-Cantilevers Integrated into Microfluidic Systems.

PubMed

Kartanas, Tadas; Ostanin, Victor; Challa, Pavan Kumar; Daly, Ronan; Charmet, Jerome; Knowles, Tuomas P J

2017-11-21

Microelectromechanical systems (MEMS) have enabled the development of a new generation of sensor platforms. Acoustic sensor operation in liquid, the native environment of biomolecules, causes, however, significant degradation of sensing performance due to viscous drag and relies on the availability of capture molecules to bind analytes of interest to the sensor surface. Here, we describe a strategy to interface MEMS sensors with microfluidic platforms through an aerosol spray. Our sensing platform comprises a microfluidic spray nozzle and a microcantilever array operated in dynamic mode within a closed loop oscillator. A solution containing the analyte is sprayed uniformly through picoliter droplets onto the microcantilever surface; the micrometer-scale drops evaporate rapidly and leave the solutes behind, adding to the mass of the cantilever. This sensing scheme results in a 50-fold increase in the quality factor compared to operation in liquid, yet allows the analytes to be introduced into the sensing system from a solution phase. It achieves a 370 femtogram limit of detection, and we demonstrate quantitative label-free analysis of inorganic salts and model proteins. These results demonstrate that the standard resolution limits of cantilever sensing in dynamic mode can be overcome with the integration of spray microfluidics with MEMS.

Automated reagent-dispensing system for microfluidic cell biology assays.

PubMed

Ly, Jimmy; Masterman-Smith, Michael; Ramakrishnan, Ravichandran; Sun, Jing; Kokubun, Brent; van Dam, R Michael

2013-12-01

Microscale systems that enable measurements of oncological phenomena at the single-cell level have a great capacity to improve therapeutic strategies and diagnostics. Such measurements can reveal unprecedented insights into cellular heterogeneity and its implications into the progression and treatment of complicated cellular disease processes such as those found in cancer. We describe a novel fluid-delivery platform to interface with low-cost microfluidic chips containing arrays of microchambers. Using multiple pairs of needles to aspirate and dispense reagents, the platform enables automated coating of chambers, loading of cells, and treatment with growth media or other agents (e.g., drugs, fixatives, membrane permeabilizers, washes, stains, etc.). The chips can be quantitatively assayed using standard fluorescence-based immunocytochemistry, microscopy, and image analysis tools, to determine, for example, drug response based on differences in protein expression and/or activation of cellular targets on an individual-cell level. In general, automation of fluid and cell handling increases repeatability, eliminates human error, and enables increased throughput, especially for sophisticated, multistep assays such as multiparameter quantitative immunocytochemistry. We report the design of the automated platform and compare several aspects of its performance to manually-loaded microfluidic chips.

Protein-Based Nanomedicine Platforms for Drug Delivery

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ma Ham, Aihui; Tang, Zhiwen; Wu, Hong

2009-08-03

Drug delivery systems have been developed for many years, however some limitations still hurdle the pace of going to clinical phase, for example, poor biodistribution, drug molecule cytotoxicity, tissue damage, quick clearance from the circulation system, solubility and stability of drug molecules. To overcome the limitations of drug delivery, biomaterials have to be developed and applied to drug delivery to protect the drug molecules and to enhance the drug’s efficacy. Protein-based nanomedicine platforms for drug delivery are platforms comprised of naturally self-assembled protein subunits of the same protein or a combination of proteins making up a complete system. They aremore » ideal for drug delivery platforms due to their biocompatibility and biodegradability coupled with low toxicity. A variety of proteins have been used and characterized for drug delivery systems including the ferritin/apoferritin protein cage, plant derived viral capsids, the small Heat shock protein (sHsp) cage, albumin, soy and whey protein, collagen, and gelatin. There are many different types and shapes that have been prepared to deliver drug molecules using protein-based platforms including the various protein cages, microspheres, nanoparticles, hydrogels, films, minirods and minipellets. There are over 30 therapeutic compounds that have been investigated with protein-based drug delivery platforms for the potential treatment of various cancers, infectious diseases, chronic diseases, autoimmune diseases. In protein-based drug delivery platforms, protein cage is the most newly developed biomaterials for drug delivery and therapeutic applications. Their uniform sizes, multifunctions, and biodegradability push them to the frontier for drug delivery. In this review, the recent strategic development of drug delivery has been discussed with a special emphasis upon the polymer based, especially protein-based nanomedicine platforms for drug delivery. The advantages and disadvantages are also discussed for each type of protein based drug delivery system.« less

Earth Science Geostationary Platform Technology

NASA Technical Reports Server (NTRS)

Wright, Robert L. (Editor); Campbell, Thomas G. (Editor)

1989-01-01

The objective of the workshop was to address problems in science and in four technology areas (large space antenna technology, microwave sensor technology, electromagnetics-phased array adaptive systems technology, and optical metrology technology) related to Earth Science Geostationary Platform missions.

A silk-based scaffold platform with tunable architecture for engineering critically-sized tissue constructs.

PubMed

Wray, Lindsay S; Rnjak-Kovacina, Jelena; Mandal, Biman B; Schmidt, Daniel F; Gil, Eun Seok; Kaplan, David L

2012-12-01

In the field of tissue engineering and regenerative medicine there is significant unmet need for critically-sized, fully degradable biomaterial scaffold systems with tunable properties for optimizing tissue formation in vitro and tissue regeneration in vivo. To address this need, we have developed a silk-based scaffold platform that has tunable material properties, including localized and bioactive functionalization, degradation rate, and mechanical properties and that provides arrays of linear hollow channels for delivery of oxygen and nutrients throughout the scaffold bulk. The scaffolds can be assembled with dimensions that range from millimeters to centimeters, addressing the need for a critically-sized platform for tissue formation. We demonstrate that the hollow channel arrays support localized and confluent endothelialization. This new platform offers a unique and versatile tool for engineering 'tailored' scaffolds for a range of tissue engineering and regenerative medicine needs. Copyright © 2012 Elsevier Ltd. All rights reserved.

Base resolution methylome profiling: considerations in platform selection, data preprocessing and analysis

PubMed Central

Sun, Zhifu; Cunningham, Julie; Slager, Susan; Kocher, Jean-Pierre

2015-01-01

Bisulfite treatment-based methylation microarray (mainly Illumina 450K Infinium array) and next-generation sequencing (reduced representation bisulfite sequencing, Agilent SureSelect Human Methyl-Seq, NimbleGen SeqCap Epi CpGiant or whole-genome bisulfite sequencing) are commonly used for base resolution DNA methylome research. Although multiple tools and methods have been developed and used for the data preprocessing and analysis, confusions remains for these platforms including how and whether the 450k array should be normalized; which platform should be used to better fit researchers’ needs; and which statistical models would be more appropriate for differential methylation analysis. This review presents the commonly used platforms and compares the pros and cons of each in methylome profiling. We then discuss approaches to study design, data normalization, bias correction and model selection for differentially methylated individual CpGs and regions. PMID:26366945

The chemiluminescence based Ziplex automated workstation focus array reproduces ovarian cancer Affymetrix GeneChip expression profiles.

PubMed

Quinn, Michael C J; Wilson, Daniel J; Young, Fiona; Dempsey, Adam A; Arcand, Suzanna L; Birch, Ashley H; Wojnarowicz, Paulina M; Provencher, Diane; Mes-Masson, Anne-Marie; Englert, David; Tonin, Patricia N

2009-07-06

As gene expression signatures may serve as biomarkers, there is a need to develop technologies based on mRNA expression patterns that are adaptable for translational research. Xceed Molecular has recently developed a Ziplex technology, that can assay for gene expression of a discrete number of genes as a focused array. The present study has evaluated the reproducibility of the Ziplex system as applied to ovarian cancer research of genes shown to exhibit distinct expression profiles initially assessed by Affymetrix GeneChip analyses. The new chemiluminescence-based Ziplex gene expression array technology was evaluated for the expression of 93 genes selected based on their Affymetrix GeneChip profiles as applied to ovarian cancer research. Probe design was based on the Affymetrix target sequence that favors the 3' UTR of transcripts in order to maximize reproducibility across platforms. Gene expression analysis was performed using the Ziplex Automated Workstation. Statistical analyses were performed to evaluate reproducibility of both the magnitude of expression and differences between normal and tumor samples by correlation analyses, fold change differences and statistical significance testing. Expressions of 82 of 93 (88.2%) genes were highly correlated (p < 0.01) in a comparison of the two platforms. Overall, 75 of 93 (80.6%) genes exhibited consistent results in normal versus tumor tissue comparisons for both platforms (p < 0.001). The fold change differences were concordant for 87 of 93 (94%) genes, where there was agreement between the platforms regarding statistical significance for 71 (76%) of 87 genes. There was a strong agreement between the two platforms as shown by comparisons of log2 fold differences of gene expression between tumor versus normal samples (R = 0.93) and by Bland-Altman analysis, where greater than 90% of expression values fell within the 95% limits of agreement. Overall concordance of gene expression patterns based on correlations, statistical significance between tumor and normal ovary data, and fold changes was consistent between the Ziplex and Affymetrix platforms. The reproducibility and ease-of-use of the technology suggests that the Ziplex array is a suitable platform for translational research.

Calibration of a fluxgate magnetometer array and its application in magnetic object localization

NASA Astrophysics Data System (ADS)

Pang, Hongfeng; Luo, Shitu; Zhang, Qi; Li, Ji; Chen, Dixiang; Pan, Mengchun; Luo, Feilu

2013-07-01

The magnetometer array is effective for magnetic object detection and localization. Calibration is important to improve the accuracy of the magnetometer array. A magnetic sensor array built with four three-axis DM-050 fluxgate magnetometers is designed, which is connected by a cross aluminum frame. In order to improve the accuracy of the magnetometer array, a calibration process is presented. The calibration process includes magnetometer calibration, coordinate transformation and misalignment calibration. The calibration system consists of a magnetic sensor array, a GSM-19T proton magnetometer, a two-dimensional nonmagnetic rotation platform, a 12 V-dc portable power device and two portable computers. After magnetometer calibration, the RMS error has been decreased from an original value of 125.559 nT to a final value of 1.711 nT (a factor of 74). After alignment, the RMS error of misalignment has been decreased from 1322.3 to 6.0 nT (a factor of 220). Then, the calibrated array deployed on the nonmagnetic rotation platform is used for ferromagnetic object localization. Experimental results show that the estimated errors of X, Y and Z axes are -0.049 m, 0.008 m and 0.025 m, respectively. Thus, the magnetometer array is effective for magnetic object detection and localization in three dimensions.

Advanced propulsion for LEO and GEO platforms

NASA Technical Reports Server (NTRS)

Sovey, James S.; Pidgeon, David J.

1990-01-01

Mission requirements and mass savings applicable to specific low earth orbit and geostationary earth orbit platforms using three highly developed propulsion systems are described. Advanced hypergolic bipropellant thrusters and hydrazine arcjets can provide about 11 percent additional instrument payload to 14,000 kg LEO platforms. By using electric propulsion on a 8,000 kg class GEO platform, mass savings in excess of 15 percent of the beginning-of-life platform mass are obtained. Effects of large, advanced technology solar arrays and antennas on platform propulsion requirements are also discussed.

Capture and 3D culture of colonic crypts and colonoids in a microarray platform.

PubMed

Wang, Yuli; Ahmad, Asad A; Shah, Pavak K; Sims, Christopher E; Magness, Scott T; Allbritton, Nancy L

2013-12-07

Crypts are the basic structural and functional units of colonic epithelium and can be isolated from the colon and cultured in vitro into multi-cell spheroids termed "colonoids". Both crypts and colonoids are ideal building blocks for construction of an in vitro tissue model of the colon. Here we proposed and tested a microengineered platform for capture and in vitro 3D culture of colonic crypts and colonoids. An integrated platform was fabricated from polydimethylsiloxane which contained two fluidic layers separated by an array of cylindrical microwells (150 μm diameter, 150 μm depth) with perforated bottoms (30 μm opening, 10 μm depth) termed "microstrainers". As fluid moved through the array, crypts or colonoids were retained in the microstrainers with a >90% array-filling efficiency. Matrigel as an extracellular matrix was then applied to the microstrainers to generate isolated Matrigel pockets encapsulating the crypts or colonoids. After supplying the essential growth factors, epidermal growth factor, Wnt-3A, R-spondin 2 and noggin, 63 ± 13% of the crypts and 77 ± 8% of the colonoids cultured in the microstrainers over a 48-72 h period formed viable 3D colonoids. Thus colonoid growth on the array was similar to that under standard culture conditions (78 ± 5%). Additionally the colonoids displayed the same morphology and similar numbers of stem and progenitor cells as those under standard culture conditions. Immunofluorescence staining confirmed that the differentiated cell-types of the colon, goblet cells, enteroendocrine cells and absorptive enterocytes, formed on the array. To demonstrating the utility of the array in tracking the colonoid fate, quantitative fluorescence analysis was performed on the arrayed colonoids exposed to reagents such as Wnt-3A and the γ-secretase inhibitor LY-411575. The successful formation of viable, multi-cell type colonic tissue on the microengineered platform represents a first step in the building of a "colon-on-a-chip" with the goal of producing the physiologic structure and organ-level function of the colon for controlled experiments.

Simple and Fast Method for Fabrication of Endoscopic Implantable Sensor Arrays

PubMed Central

Tahirbegi, I. Bogachan; Alvira, Margarita; Mir, Mònica; Samitier, Josep

2014-01-01

Here we have developed a simple method for the fabrication of disposable implantable all-solid-state ion-selective electrodes (ISE) in an array format without using complex fabrication equipment or clean room facilities. The electrodes were designed in a needle shape instead of planar electrodes for a full contact with the tissue. The needle-shape platform comprises 12 metallic pins which were functionalized with conductive inks and ISE membranes. The modified microelectrodes were characterized with cyclic voltammetry, scanning electron microscope (SEM), and optical interferometry. The surface area and roughness factor of each microelectrode were determined and reproducible values were obtained for all the microelectrodes on the array. In this work, the microelectrodes were modified with membranes for the detection of pH and nitrate ions to prove the reliability of the fabricated sensor array platform adapted to an endoscope. PMID:24971473

Development of transparent microwell arrays for optical monitoring and dissection of microbial communities

DOE PAGES

Halsted, Michelle; Wilmoth, Jared L.; Briggs, Paige A.; ...

2016-09-29

Microbial communities are incredibly complex systems that dramatically and ubiquitously influence our lives. They help to shape our climate and environment, impact agriculture, drive business, and have a tremendous bearing on healthcare and physical security. Spatial confinement, as well as local variations in physical and chemical properties, affects development and interactions within microbial communities that occupy critical niches in the environment. Recent work has demonstrated the use of silicon based microwell arrays, combined with parylene lift-off techniques, to perform both deterministic and stochastic assembly of microbial communities en masse, enabling the high-throughput screening of microbial communities for their response tomore » growth in confined environments under different conditions. The implementation of a transparent microwell array platform can expand and improve the imaging modalities that can be used to characterize these assembled communities. In this paper, the fabrication and characterization of a next generation transparent microwell array is described. The transparent arrays, comprised of SU-8 patterned on a glass coverslip, retain the ability to use parylene lift-off by integrating a low temperature atomic layer deposition of silicon dioxide into the fabrication process. This silicon dioxide layer prevents adhesion of the parylene material to the patterned SU-8, facilitating dry lift-off, and maintaining the ability to easily assemble microbial communities within the microwells. These transparent microwell arrays can screen numerous community compositions using continuous, high resolution, imaging. Finally, the utility of the design was successfully demonstrated through the stochastic seeding and imaging of green fluorescent protein expressing Escherichia coli using both fluorescence and brightfield microscopies.« less

Development of Ultra-Low Power Metal Oxide Sensors and Arrays for Embedded Applications

NASA Astrophysics Data System (ADS)

Lutz, Brent; Wind, Rikard; Kostelecky, Clayton; Routkevitch, Dmitri; Deininger, Debra

2011-09-01

Metal oxide semiconductor sensors are widely used as individual sensors and in arrays, and a variety of designs for low power microhotplates have been demonstrated.1 Synkera Technologies has developed an embeddable chemical microsensor platform, based on a unique ceramic MEMS technology, for practical implementation in cell phones and other mobile electronic devices. Key features of this microsensor platform are (1) small size, (2) ultra-low power consumption, (3) high chemical sensitivity, (4) accurate response to a wide-range of threats, and (5) low cost. The sensor platform is enabled by a combination of advances in ceramic micromachining, and precision deposition of sensing films inside the high aspect ratio pores of anodic aluminum oxide (AAO).

DOE Office of Scientific and Technical Information (OSTI.GOV)

Halsted, Michelle; Wilmoth, Jared L.; Briggs, Paige A.

Microbial communities are incredibly complex systems that dramatically and ubiquitously influence our lives. They help to shape our climate and environment, impact agriculture, drive business, and have a tremendous bearing on healthcare and physical security. Spatial confinement, as well as local variations in physical and chemical properties, affects development and interactions within microbial communities that occupy critical niches in the environment. Recent work has demonstrated the use of silicon based microwell arrays, combined with parylene lift-off techniques, to perform both deterministic and stochastic assembly of microbial communities en masse, enabling the high-throughput screening of microbial communities for their response tomore » growth in confined environments under different conditions. The implementation of a transparent microwell array platform can expand and improve the imaging modalities that can be used to characterize these assembled communities. In this paper, the fabrication and characterization of a next generation transparent microwell array is described. The transparent arrays, comprised of SU-8 patterned on a glass coverslip, retain the ability to use parylene lift-off by integrating a low temperature atomic layer deposition of silicon dioxide into the fabrication process. This silicon dioxide layer prevents adhesion of the parylene material to the patterned SU-8, facilitating dry lift-off, and maintaining the ability to easily assemble microbial communities within the microwells. These transparent microwell arrays can screen numerous community compositions using continuous, high resolution, imaging. Finally, the utility of the design was successfully demonstrated through the stochastic seeding and imaging of green fluorescent protein expressing Escherichia coli using both fluorescence and brightfield microscopies.« less

Platform for immobilization and observation of subcellular processes

DOEpatents

McKnight, Timothy E.; Kalluri, Udaya C.; Melechko, Anatoli V.

2014-08-26

A method of immobilizing matter for imaging that includes providing an array of nanofibers and directing matter to the array of the nanofibers. The matter is immobilized when contacting at least three nanofibers of the array of nanofibers simultaneously. Adjacent nanofibers in the array of nanofibers may be separated by a pitch as great as 100 microns. The immobilized matter on the array of nanofibers may then be imaged. In some examples, the matter may be cell matter, such as protoplasts.

Development of a Digital Microarray with Interferometric Reflectance Imaging

NASA Astrophysics Data System (ADS)

Sevenler, Derin

This dissertation describes a new type of molecular assay for nucleic acids and proteins. We call this technique a digital microarray since it is conceptually similar to conventional fluorescence microarrays, yet it performs enumerative ('digital') counting of the number captured molecules. Digital microarrays are approximately 10,000-fold more sensitive than fluorescence microarrays, yet maintain all of the strengths of the platform including low cost and high multiplexing (i.e., many different tests on the same sample simultaneously). Digital microarrays use gold nanorods to label the captured target molecules. Each gold nanorod on the array is individually detected based on its light scattering, with an interferometric microscopy technique called SP-IRIS. Our optimized high-throughput version of SP-IRIS is able to scan a typical array of 500 spots in less than 10 minutes. Digital DNA microarrays may have utility in applications where sequencing is prohibitively expensive or slow. As an example, we describe a digital microarray assay for gene expression markers of bacterial drug resistance.

Distinct human antibody response to the biological warfare agent Burkholderia mallei

PubMed Central

Varga, John J.; Vigil, Adam; DeShazer, David; Waag, David M.; Felgner, Philip; Goldberg, Joanna B.

2012-01-01

The genetic similarity between Burkholderia mallei (glanders) and Burkholderia pseudomallei (melioidosis) had led to the general assumption that pathogenesis of each bacterium would be similar. In 2000, the first human case of glanders in North America since 1945 was reported in a microbiology laboratory worker. Leveraging the availability of pre-exposure sera for this individual and employing the same well-characterized protein array platform that has been previously used to study a large cohort of melioidosis patients in southeast Asia, we describe the antibody response in a human with glanders. Analysis of 156 peptides present on the array revealed antibodies against 17 peptides with a > 2-fold increase in this infection. Unexpectedly, when the glanders data were compared with a previous data set from B. pseudomallei infections, there were only two highly increased antibodies shared between these two infections. These findings have implications in the diagnosis and treatment of B. mallei and B. pseudomallei infections. PMID:23076276

Microarray Technology for the Diagnosis of Fetal Chromosomal Aberrations: Which Platform Should We Use?

PubMed Central

Karampetsou, Evangelia; Morrogh, Deborah; Chitty, Lyn

2014-01-01

The advantage of microarray (array) over conventional karyotype for the diagnosis of fetal pathogenic chromosomal anomalies has prompted the use of microarrays in prenatal diagnostics. In this review we compare the performance of different array platforms (BAC, oligonucleotide CGH, SNP) and designs (targeted, whole genome, whole genome, and targeted, custom) and discuss their advantages and disadvantages in relation to prenatal testing. We also discuss the factors to consider when implementing a microarray testing service for the diagnosis of fetal chromosomal aberrations. PMID:26237396

Microintaglio Printing for Soft Lithography-Based in Situ Microarrays

PubMed Central

Biyani, Manish; Ichiki, Takanori

2015-01-01

Advances in lithographic approaches to fabricating bio-microarrays have been extensively explored over the last two decades. However, the need for pattern flexibility, a high density, a high resolution, affordability and on-demand fabrication is promoting the development of unconventional routes for microarray fabrication. This review highlights the development and uses of a new molecular lithography approach, called “microintaglio printing technology”, for large-scale bio-microarray fabrication using a microreactor array (µRA)-based chip consisting of uniformly-arranged, femtoliter-size µRA molds. In this method, a single-molecule-amplified DNA microarray pattern is self-assembled onto a µRA mold and subsequently converted into a messenger RNA or protein microarray pattern by simultaneously producing and transferring (immobilizing) a messenger RNA or a protein from a µRA mold to a glass surface. Microintaglio printing allows the self-assembly and patterning of in situ-synthesized biomolecules into high-density (kilo-giga-density), ordered arrays on a chip surface with µm-order precision. This holistic aim, which is difficult to achieve using conventional printing and microarray approaches, is expected to revolutionize and reshape proteomics. This review is not written comprehensively, but rather substantively, highlighting the versatility of microintaglio printing for developing a prerequisite platform for microarray technology for the postgenomic era. PMID:27600226

The strategy, organization, and progress of the HUPO Human Proteome Project.

PubMed

Omenn, Gilbert S

2014-04-04

The Human Proteome Project is a major, comprehensive initiative of the Human Proteome Organization. This global collaborative effort aims to identify and characterize at least one protein product and many PTM, SAP, and splice variant isoforms from the 20,300 human protein-coding genes. The deliverables are an extensive parts list and an array of technology platforms, reagents, spectral libraries, and linked knowledge bases that advance the field and facilitate the use of proteomics by a much wider community of life scientists. Such enablement will help address the Grand Challenge of using proteomics to bridge major gaps between evidence of genomic variation and diverse phenotypes. The HUPO Human Proteome Project (HPP) has made an outstanding launch, including a special issue of the Journal of Proteome Research on the Chromosome-centric HPP with a total of 48 articles. This article is part of a Special Issue: Can Proteomics Fill the Gap Between Genomics and Phenotypes? © 2013.

Digitized molecular diagnostics: reading disk-based bioassays with standard computer drives.

PubMed

Li, Yunchao; Ou, Lily M L; Yu, Hua-Zhong

2008-11-01

We report herein a digital signal readout protocol for screening disk-based bioassays with standard optical drives of ordinary desktop/notebook computers. Three different types of biochemical recognition reactions (biotin-streptavidin binding, DNA hybridization, and protein-protein interaction) were performed directly on a compact disk in a line array format with the help of microfluidic channel plates. Being well-correlated with the optical darkness of the binding sites (after signal enhancement by gold nanoparticle-promoted autometallography), the reading error levels of prerecorded audio files can serve as a quantitative measure of biochemical interaction. This novel readout protocol is about 1 order of magnitude more sensitive than fluorescence labeling/scanning and has the capability of examining multiplex microassays on the same disk. Because no modification to either hardware or software is needed, it promises a platform technology for rapid, low-cost, and high-throughput point-of-care biomedical diagnostics.

Disposable inkjet-printed electrochemical platform for detection of clinically relevant HER-2 breast cancer biomarker.

PubMed

Carvajal, Susanita; Fera, Samantha N; Jones, Abby L; Baldo, Thaisa A; Mosa, Islam M; Rusling, James F; Krause, Colleen E

2018-05-01

Rapidly fabricated, disposable sensor platforms hold tremendous promise for point-of-care detection. Here, we present an inexpensive (< $0.25) fully inkjet printed electrochemical sensor with integrated counter, reference, and working electrodes that is easily scalable for commercial fabrication. The electrochemical sensor platform featured an inkjet printed gold working 8-electrode array (WEA) and counter electrode (CE), along with an inkjet -printed silver electrode that was chlorinated with bleach to produce a Ag/AgCl quasi-reference electrode (RE). As proof of concept, the electrochemical sensor was successfully applied for detection of clinically relevant breast cancer biomarker Human Epidermal Growth Factor Receptor 2 (HER-2). Capture antibodies were bound to a chemically modified surface on the WEA and placed into a microfluidic device. A full sandwich immunoassay was constructed following a simultaneous injection of target protein, biotinylated antibody, and polymerized horseradish peroxide labels into the microfluidic device housing the WEA. With an ultra fast assay time, of only 15mins a clinically relevant limit of detection of 12pgmL -1 was achieved. Excellent reproducibility and sensitivity were observed through recovery assays preformed in human serum with recoveries ranging from 76% to 103%. These easily fabricated and scalable electrochemical sensor platforms can be readily adapted for multiplex detection following this rapid assay protocol for cancer diagnostics. Copyright © 2018 Elsevier B.V. All rights reserved.

Development of an Influenza virus protein array using Sortagging technology

PubMed Central

Sinisi, Antonia; Popp, Maximilian Wei-Lin; Antos, John M.; Pansegrau, Werner; Savino, Silvana; Nissum, Mikkel; Rappuoli, Rino; Ploegh, Hidde L.; Buti, Ludovico

2013-01-01

Protein array technology is an emerging tool that enables high throughput screening of protein-protein or protein-lipid interactions and identification of immunodominant antigens during the course of a bacterial or viral infection. In this work we developed an Influenza virus protein array using the sortase-mediated transpeptidation reaction known as “Sortagging”. LPETG-tagged Influenza virus proteins from bacterial and eukaryotic cellular extracts were immobilized at their carboxyl-termini onto a pre-activated amine-glass slide coated with a Gly3 linker. Immobilized proteins were revealed by specific antibodies and the newly generated Sortag-protein chip can be used as a device for antigen and/or antibody screening. The specificity of the Sortase A (SrtA) reaction avoids purification steps in array building and allows immobilization of proteins in an oriented fashion. Previously, this versatile technology has been successfully employed for protein labeling and protein conjugation. Here, the tool is implemented to covalently link proteins of a viral genome onto a solid support. The system could readily be scaled up to proteins of larger genomes in order to develop protein arrays for high throughput screening. PMID:22594688

Retargeting of adenovirus vectors through genetic fusion of a single-chain or single-domain antibody to capsid protein IX.

PubMed

Poulin, Kathy L; Lanthier, Robert M; Smith, Adam C; Christou, Carin; Risco Quiroz, Milagros; Powell, Karen L; O'Meara, Ryan W; Kothary, Rashmi; Lorimer, Ian A; Parks, Robin J

2010-10-01

Adenovirus (Ad) vectors are the most commonly used system for gene therapy applications, due in part to their ability to infect a wide array of cell types and tissues. However, many therapies would benefit from the ability to target the Ad vector only to specific cells, such as tumor cells for cancer gene therapy. In this study, we investigated the utility of capsid protein IX (pIX) as a platform for the presentation of single-chain variable-fragment antibodies (scFv) and single-domain antibodies (sdAb) for virus retargeting. We show that scFv can be displayed on the capsid through genetic fusion to native pIX but that these molecules fail to retarget the virus, due to improper folding of the scFv. Redirecting expression of the fusion protein to the endoplasmic reticulum (ER) results in correct folding of the scFv and allows it to recognize its epitope; however, ER-targeted pIX-scFv was incorporated into the Ad capsid at a very low level which was not sufficient to retarget virus infection. In contrast, a pIX-sdAb construct was efficiently incorporated into the Ad capsid and enhanced virus infection of cells expressing the targeted receptor. Taken together, our data indicate that pIX is an effective platform for presentation of large targeting polypeptides on the surface of the virus capsid, but the nature of the ligand can significantly affect its association with virions.

An Exosome-Based Vaccine Platform Imparts Cytotoxic T Lymphocyte Immunity Against Viral Antigens.

PubMed

Anticoli, Simona; Manfredi, Francesco; Chiozzini, Chiara; Arenaccio, Claudia; Olivetta, Eleonora; Ferrantelli, Flavia; Capocefalo, Antonio; Falcone, Emiliana; Ruggieri, Anna; Federico, Maurizio

2018-04-01

Exosomes are 50-150 nm sized nanovesicles released by all eukaryotic cells. The authors very recently described a method to engineer exosomes in vivo with the E7 protein of Human Papilloma Virus (HPV). This technique consists in the intramuscular injection of a DNA vector expressing HPV-E7 fused at the C-terminus of an exosome-anchoring protein, that is, Nef mut , the authors previously characterized for its high levels of incorporation in exosomes. In this configuration, the ≈11 kDa E7 protein elicited a both strong and effective antigen-specific cytotoxic T lymphocyte (CTL) immunity. Attempting to establish whether this method could have general applicability, the authors expanded the immunogenicity studies toward an array of viral products of various origin and size including Ebola Virus VP24, VP40 and NP, Influenza Virus NP, Crimean-Congo Hemorrhagic Fever NP, West Nile Virus NS3, and Hepatitis C Virus NS3. All antigens appeared stable upon fusion with Nef mut , and are uploaded in exosomes at levels comparable to Nef mut . When injected in mice, DNA vectors expressing the diverse fusion products elicited a well detectable antigen-specific CD8 + T cell response associating with a cytotoxic activity potent enough to kill peptide-loaded and/or antigen-expressing syngeneic cells. These data definitely proven both effectiveness and flexibility of this innovative CTL vaccine platform. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Real-time imaging of microparticles and living cells with CMOS nanocapacitor arrays

NASA Astrophysics Data System (ADS)

Laborde, C.; Pittino, F.; Verhoeven, H. A.; Lemay, S. G.; Selmi, L.; Jongsma, M. A.; Widdershoven, F. P.

2015-09-01

Platforms that offer massively parallel, label-free biosensing can, in principle, be created by combining all-electrical detection with low-cost integrated circuits. Examples include field-effect transistor arrays, which are used for mapping neuronal signals and sequencing DNA. Despite these successes, however, bioelectronics has so far failed to deliver a broadly applicable biosensing platform. This is due, in part, to the fact that d.c. or low-frequency signals cannot be used to probe beyond the electrical double layer formed by screening salt ions, which means that under physiological conditions the sensing of a target analyte located even a short distance from the sensor (∼1 nm) is severely hampered. Here, we show that high-frequency impedance spectroscopy can be used to detect and image microparticles and living cells under physiological salt conditions. Our assay employs a large-scale, high-density array of nanoelectrodes integrated with CMOS electronics on a single chip and the sensor response depends on the electrical properties of the analyte, allowing impedance-based fingerprinting. With our platform, we image the dynamic attachment and micromotion of BEAS, THP1 and MCF7 cancer cell lines in real time at submicrometre resolution in growth medium, demonstrating the potential of the platform for label/tracer-free high-throughput screening of anti-tumour drug candidates.

Evaluation of second-generation sequencing of 19 dilated cardiomyopathy genes for clinical applications.

PubMed

Gowrisankar, Sivakumar; Lerner-Ellis, Jordan P; Cox, Stephanie; White, Emily T; Manion, Megan; LeVan, Kevin; Liu, Jonathan; Farwell, Lisa M; Iartchouk, Oleg; Rehm, Heidi L; Funke, Birgit H

2010-11-01

Medical sequencing for diseases with locus and allelic heterogeneities has been limited by the high cost and low throughput of traditional sequencing technologies. "Second-generation" sequencing (SGS) technologies allow the parallel processing of a large number of genes and, therefore, offer great promise for medical sequencing; however, their use in clinical laboratories is still in its infancy. Our laboratory offers clinical resequencing for dilated cardiomyopathy (DCM) using an array-based platform that interrogates 19 of more than 30 genes known to cause DCM. We explored both the feasibility and cost effectiveness of using PCR amplification followed by SGS technology for sequencing these 19 genes in a set of five samples enriched for known sequence alterations (109 unique substitutions and 27 insertions and deletions). While the analytical sensitivity for substitutions was comparable to that of the DCM array (98%), SGS technology performed better than the DCM array for insertions and deletions (90.6% versus 58%). Overall, SGS performed substantially better than did the current array-based testing platform; however, the operational cost and projected turnaround time do not meet our current standards. Therefore, efficient capture methods and/or sample pooling strategies that shorten the turnaround time and decrease reagent and labor costs are needed before implementing this platform into routine clinical applications.

High-Density Dielectrophoretic Microwell Array for Detection, Capture, and Single-Cell Analysis of Rare Tumor Cells in Peripheral Blood.

PubMed

Morimoto, Atsushi; Mogami, Toshifumi; Watanabe, Masaru; Iijima, Kazuki; Akiyama, Yasuyuki; Katayama, Koji; Futami, Toru; Yamamoto, Nobuyuki; Sawada, Takeshi; Koizumi, Fumiaki; Koh, Yasuhiro

2015-01-01

Development of a reliable platform and workflow to detect and capture a small number of mutation-bearing circulating tumor cells (CTCs) from a blood sample is necessary for the development of noninvasive cancer diagnosis. In this preclinical study, we aimed to develop a capture system for molecular characterization of single CTCs based on high-density dielectrophoretic microwell array technology. Spike-in experiments using lung cancer cell lines were conducted. The microwell array was used to capture spiked cancer cells, and captured single cells were subjected to whole genome amplification followed by sequencing. A high detection rate (70.2%-90.0%) and excellent linear performance (R2 = 0.8189-0.9999) were noted between the observed and expected numbers of tumor cells. The detection rate was markedly higher than that obtained using the CellSearch system in a blinded manner, suggesting the superior sensitivity of our system in detecting EpCAM- tumor cells. Isolation of single captured tumor cells, followed by detection of EGFR mutations, was achieved using Sanger sequencing. Using a microwell array, we established an efficient and convenient platform for the capture and characterization of single CTCs. The results of a proof-of-principle preclinical study indicated that this platform has potential for the molecular characterization of captured CTCs from patients.

Recent developments using TowerJazz SiGe BiCMOS platform for mmWave and THz applications

NASA Astrophysics Data System (ADS)

Kar-Roy, Arjun; Howard, David; Preisler, Edward J.; Racanelli, Marco

2013-05-01

In this paper, we report on the highest speed 240GHz/340GHz FT/FMAX NPN which is now available for product designs in the SBC18H4 process variant of TowerJazz's mature 0.18μm SBC18 silicon germanium (SiGe) BiCMOS technology platform. NFMIN of ~2dB at 50GHz has been obtained with these NPNs. We also describe the integration of earlier generation NPNs with FT/FMAX of 240GHz/280GHz into SBC13H3, a 0.13μm SiGe BiCMOS technology platform. Next, we detail the integration of the deep silicon via (DSV), through silicon via (TSV), high-resistivity substrate, sub-field stitching and hybrid-stitching capability into the 0.18μm SBC18 technology platform to enable higher performance and highly integrated product designs. The integration of SBC18H3 into a thick-film SOI substrate, with essentially unchanged FT and FMAX, is also described. We also report on recent circuit demonstrations using the SBC18H3 platform: (1) a 4-element phased-array 70-100GHz broadband transmit and receive chip with flat saturated power greater than 5dBm and conversion gain of 33dB; (2) a fully integrated W-band 9-element phase-controllable array with responsivity of 800MV/W and receiver NETD is 0.45K with 20ms integration time; (3) a 16-element 4x4 phased-array transmitter with scanning in both the E- and H-planes with maximum EIRP of 23-25 dBm at 100-110GHz; (4) a power efficient 200GHz VCO with -7.25dBm output power and tuning range of 3.5%; and (5) a 320GHz 16-element imaging receiver array with responsivity of 18KV/W at 315GHz, a 3dB bandwidth of 25GHz and a low NEP of 34pW/Hz1/2. Wafer-scale large-die implementation of the phased-arrays and mmWave imagers using stitching in TowerJazz SBC18 process are also discussed.

Single-Cell Detection and Collection of Persister Bacteria in a Directly Accessible Femtoliter Droplet Array.

PubMed

Iino, Ryota; Sakakihara, Shouichi; Matsumoto, Yoshimi; Nishino, Kunihiko

2016-01-01

A directly accessible femtoliter droplet array as a platform for single-cell detection and collection of persister bacteria is described. Device microfabrication, femtoliter droplet array formation and concomitant enclosure of single cells, long-term culture and observation of single cells in droplets, and collection of identified persisters from single droplets are described in detail.

Large-Scale Femtoliter Droplet Array for Single Cell Efflux Assay of Bacteria.

PubMed

Iino, Ryota; Sakakihara, Shouichi; Matsumoto, Yoshimi; Nishino, Kunihiko

2018-01-01

Large-scale femtoliter droplet array as a platform for single cell efflux assay of bacteria is described. Device microfabrication, femtoliter droplet array formation and concomitant enclosure of single bacterial cells, fluorescence-based detection of efflux activity at the single cell level, and collection of single cells from droplet and subsequent gene analysis are described in detail.

Photo-Induced Click Chemistry for DNA Surface Structuring by Direct Laser Writing.

PubMed

Kerbs, Antonina; Mueller, Patrick; Kaupp, Michael; Ahmed, Ishtiaq; Quick, Alexander S; Abt, Doris; Wegener, Martin; Niemeyer, Christof M; Barner-Kowollik, Christopher; Fruk, Ljiljana

2017-04-11

Oligonucleotides containing photo-caged dienes were prepared and shown to react quantitatively in a light-induced Diels-Alder cycloaddition with functional maleimides in aqueous solution within minutes. Due to its high yield and fast rate, the reaction was exploited for DNA surface patterning with sub-micrometer resolution employing direct laser writing (DLW). Functional DNA arrays were written by direct laser writing (DLW) in variable patterns, which were further encoded with fluorophores and proteins through DNA directed immobilization. This mild and efficient light-driven platform technology holds promise for the fabrication of complex bioarrays with sub-micron resolution. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Paper Capillary Enables Effective Sampling for Microfluidic Paper Analytical Devices.

PubMed

Shangguan, Jin-Wen; Liu, Yu; Wang, Sha; Hou, Yun-Xuan; Xu, Bi-Yi; Xu, Jing-Juan; Chen, Hong-Yuan

2018-06-06

Paper capillary is introduced to enable effective sampling on microfluidic paper analytical devices. By coupling mac-roscale capillary force of paper capillary and microscale capillary forces of native paper, fluid transport can be flexibly tailored with proper design. Subsequently, a hybrid-fluid-mode paper capillary device was proposed, which enables fast and reliable sampling in an arrayed form, with less surface adsorption and bias for different components. The resulting device thus well supports high throughput, quantitative, and repeatable assays all by hands operation. With all these merits, multiplex analysis of ions, proteins, and microbe have all been realized on this platform, which has paved the way to level-up analysis on μPADs.

Real-time PCR array as a universal platform for the detection of genetically modified crops and its application in identifying unapproved genetically modified crops in Japan.

PubMed

Mano, Junichi; Shigemitsu, Natsuki; Futo, Satoshi; Akiyama, Hiroshi; Teshima, Reiko; Hino, Akihiro; Furui, Satoshi; Kitta, Kazumi

2009-01-14

We developed a novel type of real-time polymerase chain reaction (PCR) array with TaqMan chemistry as a platform for the comprehensive and semiquantitative detection of genetically modified (GM) crops. Thirty primer-probe sets for the specific detection of GM lines, recombinant DNA (r-DNA) segments, endogenous reference genes, and donor organisms were synthesized, and a 96-well PCR plate was prepared with a different primer-probe in each well as the real-time PCR array. The specificity and sensitivity of the array were evaluated. A comparative analysis with the data and publicly available information on GM crops approved in Japan allowed us to assume the possibility of unapproved GM crop contamination. Furthermore, we designed a Microsoft Excel spreadsheet application, Unapproved GMO Checker version 2.01, which helps process all the data of real-time PCR arrays for the easy assumption of unapproved GM crop contamination. The spreadsheet is available free of charge at http://cse.naro.affrc.go.jp/jmano/index.html .

Construction of a versatile SNP array for pyramiding useful genes of rice.

PubMed

Kurokawa, Yusuke; Noda, Tomonori; Yamagata, Yoshiyuki; Angeles-Shim, Rosalyn; Sunohara, Hidehiko; Uehara, Kanako; Furuta, Tomoyuki; Nagai, Keisuke; Jena, Kshirod Kumar; Yasui, Hideshi; Yoshimura, Atsushi; Ashikari, Motoyuki; Doi, Kazuyuki

2016-01-01

DNA marker-assisted selection (MAS) has become an indispensable component of breeding. Single nucleotide polymorphisms (SNP) are the most frequent polymorphism in the rice genome. However, SNP markers are not readily employed in MAS because of limitations in genotyping platforms. Here the authors report a Golden Gate SNP array that targets specific genes controlling yield-related traits and biotic stress resistance in rice. As a first step, the SNP genotypes were surveyed in 31 parental varieties using the Affymetrix Rice 44K SNP microarray. The haplotype information for 16 target genes was then converted to the Golden Gate platform with 143-plex markers. Haplotypes for the 14 useful allele are unique and can discriminate among all other varieties. The genotyping consistency between the Affymetrix microarray and the Golden Gate array was 92.8%, and the accuracy of the Golden Gate array was confirmed in 3 F2 segregating populations. The concept of the haplotype-based selection by using the constructed SNP array was proofed. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Footwear scanning systems and methods

DOEpatents

Fernandes, Justin L.; McMakin, Douglas L.; Sheen, David M.; Tedeschi, Jonathan R.

2017-07-25

Methods and apparatus for scanning articles, such as footwear, to provide information regarding the contents of the articles are described. According to one aspect, a footwear scanning system includes a platform configured to contact footwear to be scanned, an antenna array configured to transmit electromagnetic waves through the platform into the footwear and to receive electromagnetic waves from the footwear and the platform, a transceiver coupled with antennas of the antenna array and configured to apply electrical signals to at least one of the antennas to generate the transmitted electromagnetic waves and to receive electrical signals from at least another of the antennas corresponding to the electromagnetic waves received by the others of the antennas, and processing circuitry configured to process the received electrical signals from the transceiver to provide information regarding contents within the footwear.

Non-Hermitian engineering of single mode two dimensional laser arrays

PubMed Central

Teimourpour, Mohammad H.; Ge, Li; Christodoulides, Demetrios N.; El-Ganainy, Ramy

2016-01-01

A new scheme for building two dimensional laser arrays that operate in the single supermode regime is proposed. This is done by introducing an optical coupling between the laser array and lossy pseudo-isospectral chains of photonic resonators. The spectrum of this discrete reservoir is tailored to suppress all the supermodes of the main array except the fundamental one. This spectral engineering is facilitated by employing the Householder transformation in conjunction with discrete supersymmetry. The proposed scheme is general and can in principle be used in different platforms such as VCSEL arrays and photonic crystal laser arrays. PMID:27698355

Toward active-matrix lab-on-a-chip: programmable electrofluidic control enabled by arrayed oxide thin film transistors.

PubMed

Noh, Joo Hyon; Noh, Jiyong; Kreit, Eric; Heikenfeld, Jason; Rack, Philip D

2012-01-21

Agile micro- and nano-fluidic control is critical to numerous life science and chemical science synthesis as well as kinetic and thermodynamic studies. To this end, we have demonstrated the use of thin film transistor arrays as an active matrix addressing method to control an electrofluidic array. Because the active matrix method minimizes the number of control lines necessary (m + n lines for the m×n element array), the active matrix addressing method integrated with an electrofluidic platform can be a significant breakthrough for complex electrofluidic arrays (increased size or resolution) with enhanced function, agility and programmability. An amorphous indium gallium zinc oxide (a-IGZO) semiconductor active layer is used because of its high mobility of 1-15 cm(2) V(-1) s(-1), low-temperature processing and transparency for potential spectroscopy and imaging. Several electrofluidic functionalities are demonstrated using a simple 2 × 5 electrode array connected to a 2 × 5 IGZO thin film transistor array with the semiconductor channel width of 50 μm and mobility of 6.3 cm(2) V(-1) s(-1). Additionally, using the TFT device characteristics, active matrix addressing schemes are discussed as the geometry of the electrode array can be tailored to act as a storage capacitor element. Finally, requisite material and device parameters are discussed in context with a VGA scale active matrix addressed electrofluidic platform.

Combined array CGH plus SNP genome analyses in a single assay for optimized clinical testing

PubMed Central

Wiszniewska, Joanna; Bi, Weimin; Shaw, Chad; Stankiewicz, Pawel; Kang, Sung-Hae L; Pursley, Amber N; Lalani, Seema; Hixson, Patricia; Gambin, Tomasz; Tsai, Chun-hui; Bock, Hans-Georg; Descartes, Maria; Probst, Frank J; Scaglia, Fernando; Beaudet, Arthur L; Lupski, James R; Eng, Christine; Wai Cheung, Sau; Bacino, Carlos; Patel, Ankita

2014-01-01

In clinical diagnostics, both array comparative genomic hybridization (array CGH) and single nucleotide polymorphism (SNP) genotyping have proven to be powerful genomic technologies utilized for the evaluation of developmental delay, multiple congenital anomalies, and neuropsychiatric disorders. Differences in the ability to resolve genomic changes between these arrays may constitute an implementation challenge for clinicians: which platform (SNP vs array CGH) might best detect the underlying genetic cause for the disease in the patient? While only SNP arrays enable the detection of copy number neutral regions of absence of heterozygosity (AOH), they have limited ability to detect single-exon copy number variants (CNVs) due to the distribution of SNPs across the genome. To provide comprehensive clinical testing for both CNVs and copy-neutral AOH, we enhanced our custom-designed high-resolution oligonucleotide array that has exon-targeted coverage of 1860 genes with 60 000 SNP probes, referred to as Chromosomal Microarray Analysis – Comprehensive (CMA-COMP). Of the 3240 cases evaluated by this array, clinically significant CNVs were detected in 445 cases including 21 cases with exonic events. In addition, 162 cases (5.0%) showed at least one AOH region >10 Mb. We demonstrate that even though this array has a lower density of SNP probes than other commercially available SNP arrays, it reliably detected AOH events >10 Mb as well as exonic CNVs beyond the detection limitations of SNP genotyping. Thus, combining SNP probes and exon-targeted array CGH into one platform provides clinically useful genetic screening in an efficient manner. PMID:23695279

ArrayInitiative - a tool that simplifies creating custom Affymetrix CDFs

PubMed Central

2011-01-01

Background Probes on a microarray represent a frozen view of a genome and are quickly outdated when new sequencing studies extend our knowledge, resulting in significant measurement error when analyzing any microarray experiment. There are several bioinformatics approaches to improve probe assignments, but without in-house programming expertise, standardizing these custom array specifications as a usable file (e.g. as Affymetrix CDFs) is difficult, owing mostly to the complexity of the specification file format. However, without correctly standardized files there is a significant barrier for testing competing analysis approaches since this file is one of the required inputs for many commonly used algorithms. The need to test combinations of probe assignments and analysis algorithms led us to develop ArrayInitiative, a tool for creating and managing custom array specifications. Results ArrayInitiative is a standalone, cross-platform, rich client desktop application for creating correctly formatted, custom versions of manufacturer-provided (default) array specifications, requiring only minimal knowledge of the array specification rules and file formats. Users can import default array specifications, import probe sequences for a default array specification, design and import a custom array specification, export any array specification to multiple output formats, export the probe sequences for any array specification and browse high-level information about the microarray, such as version and number of probes. The initial release of ArrayInitiative supports the Affymetrix 3' IVT expression arrays we currently analyze, but as an open source application, we hope that others will contribute modules for other platforms. Conclusions ArrayInitiative allows researchers to create new array specifications, in a standard format, based upon their own requirements. This makes it easier to test competing design and analysis strategies that depend on probe definitions. Since the custom array specifications are easily exported to the manufacturer's standard format, researchers can analyze these customized microarray experiments using established software tools, such as those available in Bioconductor. PMID:21548938

Comparative Evaluation of Recombinant Protein Production in Different Biofactories: The Green Perspective

PubMed Central

Capaldi, Stefano

2014-01-01

In recent years, the production of recombinant pharmaceutical proteins in heterologous systems has increased significantly. Most applications involve complex proteins and glycoproteins that are difficult to produce, thus promoting the development and improvement of a wide range of production platforms. No individual system is optimal for the production of all recombinant proteins, so the diversity of platforms based on plants offers a significant advantage. Here, we discuss the production of four recombinant pharmaceutical proteins using different platforms, highlighting from these examples the unique advantages of plant-based systems over traditional fermenter-based expression platforms. PMID:24745008

Potentials and capabilities of the Extracellular Vesicle (EV) Array.

PubMed

Jørgensen, Malene Møller; Bæk, Rikke; Varming, Kim

2015-01-01

Extracellular vesicles (EVs) and exosomes are difficult to enrich or purify from biofluids, hence quantification and phenotyping of these are tedious and inaccurate. The multiplexed, highly sensitive and high-throughput platform of the EV Array presented by Jørgensen et al., (J Extracell Vesicles, 2013; 2: 10) has been refined regarding the capabilities of the method for characterization and molecular profiling of EV surface markers. Here, we present an extended microarray platform to detect and phenotype plasma-derived EVs (optimized for exosomes) for up to 60 antigens without any enrichment or purification prior to analysis.

Design and analysis of photonic crystal coupled cavity arrays for quantum simulation

NASA Astrophysics Data System (ADS)

Majumdar, Arka; Rundquist, Armand; Bajcsy, Michal; Dasika, Vaishno D.; Bank, Seth R.; Vučković, Jelena

2012-11-01

We performed an experimental study of coupled optical cavity arrays in a photonic crystal platform. We find that the coupling between the cavities is significantly larger than the fabrication-induced disorder in the cavity frequencies. Satisfying this condition is necessary for using such cavity arrays to generate strongly correlated photons, which has potential application in the quantum simulation of many-body systems.

Application of carbohydrate microarray technology for the detection of Burkholderia pseudomallei, Bacillus anthracis and Francisella tularensis antibodies.

PubMed

Parthasarathy, N; Saksena, R; Kováč, P; Deshazer, D; Peacock, S J; Wuthiekanun, V; Heine, H S; Friedlander, A M; Cote, C K; Welkos, S L; Adamovicz, J J; Bavari, S; Waag, D M

2008-11-03

We developed a microarray platform by immobilizing bacterial 'signature' carbohydrates onto epoxide modified glass slides. The carbohydrate microarray platform was probed with sera from non-melioidosis and melioidosis (Burkholderia pseudomallei) individuals. The platform was also probed with sera from rabbits vaccinated with Bacillus anthracis spores and Francisella tularensis bacteria. By employing this microarray platform, we were able to detect and differentiate B. pseudomallei, B. anthracis and F. tularensis antibodies in infected patients, and infected or vaccinated animals. These antibodies were absent in the sera of naïve test subjects. The advantages of the carbohydrate microarray technology over the traditional indirect hemagglutination and microagglutination tests for the serodiagnosis of melioidosis and tularemia are discussed. Furthermore, this array is a multiplex carbohydrate microarray for the detection of all three biothreat bacterial infections including melioidosis, anthrax and tularemia with one, multivalent device. The implication is that this technology could be expanded to include a wide array of infectious and biothreat agents.

Microelectrode Arrays: A Physiologically-based Neurotoxicity Testing Platform for the 21st Century

EPA Science Inventory

Microelectrode Arrays (MEAs) have been in use over the past decade and a half to study multiple aspects ofelectrically excitable cells. Inparticular, MEAs have been applied to explore the pharmacological and toxicological effects ofnumerous compounds on spontaneous activity ofneu...

Design and fabrication of an angle-scanning based platform for the construction of surface plasmon resonance biosensor

NASA Astrophysics Data System (ADS)

Hu, Jiandong; Cao, Baiqiong; Wang, Shun; Li, Jianwei; Wei, Wensong; Zhao, Yuanyuan; Hu, Xinran; Zhu, Juanhua; Jiang, Min; Sun, Xiaohui; Chen, Ruipeng; Ma, Liuzheng

2016-03-01

A sensing system for an angle-scanning optical surface-plasmon-resonance (SPR) based biosensor has been designed with a laser line generator in which a P polarizer is embedded to utilize as an excitation source for producing the surface plasmon wave. In this system, the emitting beam from the laser line generator is controlled to realize the angle-scanning using a variable speed direct current (DC) motor. The light beam reflected from the prism deposited with a 50 nm Au film is then captured using the area CCD array which was controlled by a personal computer (PC) via a universal serial bus (USB) interface. The photoelectric signals from the high speed digital camera (an area CCD array) were converted by a 16 bit A/D converter before it transferred to the PC. One of the advantages of this SPR biosensing platform is greatly demonstrated by the label-free and real-time bio-molecular analysis without moving the area CCD array by following the laser line generator. It also could provide a low-cost surface plasmon resonance platform to improve the detection range in the measurement of bioanalytes. The SPR curve displayed on the PC screen promptly is formed by the effective data from the image on the area CCD array and the sensing responses of the platform to bulk refractive indices were calibrated using various concentrations of ethanol solution. These ethanol concentrations indicated with volumetric fraction of 5%, 10%, 15%, 20%, and 25%, respectively, were experimented to validate the performance of the angle-scanning optic SPR biosensing platform. As a result, the SPR sensor was capable to detect a change in the refractive index of the ethanol solution with the relative high linearity at the correlation coefficient of 0.9842. This greatly enhanced detection range is obtained from the position relationship between the laser line generator and the right-angle prism to allow direct quantification of the samples over a wide range of concentrations.

Intracellular Protein Delivery System Using a Target-Specific Repebody and Translocation Domain of Bacterial Exotoxin.

PubMed

Kim, Hee-Yeon; Kang, Jung Ae; Ryou, Jeong-Hyun; Lee, Gyeong Hee; Choi, Dae Seong; Lee, Dong Eun; Kim, Hak-Sung

2017-11-17

With the high efficacy of protein-based therapeutics and plenty of intracellular drug targets, cytosolic protein delivery in a cell-specific manner has attracted considerable attention in the field of precision medicine. Herein, we present an intracellular protein delivery system based on a target-specific repebody and the translocation domain of Pseudomonas aeruginosa exotoxin A. The delivery platform was constructed by genetically fusing an EGFR-specific repebody as a targeting moiety to the translocation domain, while a protein cargo was fused to the C-terminal end of the delivery platform. The delivery platform was revealed to efficiently translocate a protein cargo to the cytosol in a target-specific manner. We demonstrate the utility and potential of the delivery platform by showing a remarkable tumor regression with negligible toxicity in a xenograft mice model when gelonin was used as the cytotoxic protein cargo. The present platform can find wide applications to the cell-selective cytosolic delivery of diverse proteins in many areas.

Membrane Protein Incorporation into Nano-Bioelectronics: An insight into Rhodopsin Controlled SiNW-FET Devices

NASA Astrophysics Data System (ADS)

Tunuguntla, Ramya

Biological systems use different energy sources to interact with their environments by creating ion gradients, membrane electric potentials, or a proton motive force to accomplish strikingly complex tasks on the nanometer length scale, such as energy harvesting, and whole organism replication. Most of this activity involves a vast arsenal of active and passive ion channels, membrane receptors and ion pumps that mediate complex and precise transport across biological membranes. Despite the remarkable rate of progress exhibited by modern microelectronic devices, they still cannot compete with the efficiency and precision of biological systems on the component level. At the same time, the sophistication of these molecular machines provides an excellent opportunity to use them in hybrid bioelectronic devices where such a combination could deliver enhanced electronic functionality and enable seamless bi-directional interfaces between man-made and biological assemblies. Artificial membrane systems allow researchers to study the structure and function of membrane proteins in a matrix that approximates their natural environment and to integrate these proteins in ex-vivo devices such as electronic biosensors, thin-film protein arrays, or bio-fuel cells. Since most membrane proteins have vectorial functions, both functional studies and applications require effective control over protein orientation within a lipid bilayer. In our work, we have explored the role of the bilayer surface charge in determining transmembrane protein orientation and functionality during formation of proteoliposomes. We reconstituted a model vectorial ion pump, proteorhodopsin, in liposomes of opposite charges and varying charge densities and determined the resultant protein orientation. Antibody-binding assay and proteolysis of proteoliposomes showed physical evidence of preferential orientation, and functional assays verified vectorial nature of ion transport in this system. Our results indicate that the manipulation of lipid composition can indeed control orientation of an asymmetrically charged membrane protein, proteorhodopsin, in liposomes. One-dimensional inorganic nanostructures, which have critical dimensions comparable to the sizes of biological molecules, form an excellent materials platform for building such integrated structures. Researchers already use silicon nanowire-based field effect transistors functionalized with molecular recognition sites in a diverse array of biosensors. In our group, we have been developing a platform for integration of membrane protein functionality and electronic devices using a 1-D phospholipid bilayer device architecture. In these devices, the membrane proteins reside within the lipid bilayer that covers a nanowire channel of a field-effect transistor. This lipid bilayer performs several functions: it shields the nanowire from the solution species; it serves as a native-like environment for membrane proteins and preserves their functionality, integrity, and even vectorality. In this work, we show that a 1-D bilayer device incorporating a rhodopsin proton pump allows us to couple light-driven proton transport to a bioelectronic circuit. We also report that we were able to adapt another distinctive feature of biological signal processing---their widespread use of modifiers, co-factors, and mediator molecules---to regulate and fine-tune the operational characteristics of the bioelectronic device. In our example, we use co-assembly of protein channels and ionophores in the 1-D bilayer to modify the device output levels and response time.

Building biochips: a protein production pipeline

NASA Astrophysics Data System (ADS)

de Carvalho-Kavanagh, Marianne G. S.; Albala, Joanna S.

2004-06-01

Protein arrays are emerging as a practical format in which to study proteins in high-throughput using many of the same techniques as that of the DNA microarray. The key advantage to array-based methods for protein study is the potential for parallel analysis of thousands of samples in an automated, high-throughput fashion. Building protein arrays capable of this analysis capacity requires a robust expression and purification system capable of generating hundreds to thousands of purified recombinant proteins. We have developed a method to utilize LLNL-I.M.A.G.E. cDNAs to generate recombinant protein libraries using a baculovirus-insect cell expression system. We have used this strategy to produce proteins for analysis of protein/DNA and protein/protein interactions using protein microarrays in order to understand the complex interactions of proteins involved in homologous recombination and DNA repair. Using protein array techniques, a novel interaction between the DNA repair protein, Rad51B, and histones has been identified.

Comparison of Comparative Genomic Hybridization Technologies across Microarray Platforms

EPA Science Inventory

In the 2007 Association of Biomolecular Resource Facilities (ABRF) Microarray Research Group (MARG) project, we analyzed HL-60 DNA with five platforms: Agilent, Affymetrix 500K, Affymetrix U133 Plus 2.0, Illumina, and RPCI 19K BAC arrays. Copy number variation (CNV) was analyzed ...

Self-Referenced Smartphone-Based Nanoplasmonic Imaging Platform for Colorimetric Biochemical Sensing.

PubMed

Wang, Xinhao; Chang, Te-Wei; Lin, Guohong; Gartia, Manas Ranjan; Liu, Gang Logan

2017-01-03

Colorimetric sensors usually suffer due to errors from variation in light source intensity, the type of light source, the Bayer filter algorithm, and the sensitivity of the camera to incoming light. Here, we demonstrate a self-referenced portable smartphone-based plasmonic sensing platform integrated with an internal reference sample along with an image processing method to perform colorimetric sensing. Two sensing principles based on unique nanoplasmonics enabled phenomena from a nanostructured plasmonic sensor, named as nanoLCA (nano Lycurgus cup array), were demonstrated here for colorimetric biochemical sensing: liquid refractive index sensing and optical absorbance enhancement sensing. Refractive indices of colorless liquids were measured by simple smartphone imaging and color analysis. Optical absorbance enhancement in the colorimetric biochemical assay was achieved by matching the plasmon resonance wavelength with the chromophore's absorbance peak wavelength. Such a sensing mechanism improved the limit of detection (LoD) by 100 times in a microplate reader format. Compared with a traditional colorimetric assay such as urine testing strips, a smartphone plasmon enhanced colorimetric sensing system provided 30 times improvement in the LoD. The platform was applied for simulated urine testing to precisely identify the samples with higher protein concentration, which showed potential point-of-care and early detection of kidney disease with the smartphone plasmonic resonance sensing system.

Telecom-Wavelength Bottom-up Nanobeam Lasers on Silicon-on-Insulator.

PubMed

Kim, Hyunseok; Lee, Wook-Jae; Farrell, Alan C; Balgarkashi, Akshay; Huffaker, Diana L

2017-09-13

Semiconductor nanowire lasers are considered promising ultracompact and energy-efficient light sources in the field of nanophotonics. Although the integration of nanowire lasers onto silicon photonic platforms is an innovative path toward chip-scale optical communications and photonic integrated circuits, operating nanowire lasers at telecom-wavelengths remains challenging. Here, we report on InGaAs nanowire array lasers on a silicon-on-insulator platform operating up to 1440 nm at room temperature. Bottom-up photonic crystal nanobeam cavities are formed by growing nanowires as ordered arrays using selective-area epitaxy, and single-mode lasing by optical pumping is demonstrated. We also show that arrays of nanobeam lasers with individually tunable wavelengths can be integrated on a single chip by the simple adjustment of the lithographically defined growth pattern. These results exemplify a practical approach toward nanowire lasers for silicon photonics.

Integration of reconfigurable potentiometric electrochemical sensors into a digital microfluidic platform.

PubMed

Farzbod, Ali; Moon, Hyejin

2018-05-30

This paper presents the demonstration of on-chip fabrication of a potassium-selective sensor array enabled by electrowetting on dielectric digital microfluidics for the first time. This demonstration proves the concept that electrochemical sensors can be seamlessly integrated with sample preparation units in a digital microfluidic platform. More significantly, the successful on-chip fabrication of a sensor array indicates that sensors become reconfigurable and have longer lifetime in a digital microfluidic platform. The on-chip fabrication of ion-selective electrodes includes electroplating Ag followed by forming AgCl layer by chemical oxidation and depositing a thin layer of desired polymer-based ion selective membrane on one of the sensor electrodes. In this study, potassium ionophores work as potassium ion channels and make the membrane selective to potassium ions. This selectiveness results in the voltage difference across the membrane layer, which is correlated with potassium ion concentration. The calibration curve of the fabricated potassium-selective electrode demonstrates the slope of 58 mV/dec for potassium concentration in KCl sample solutions and shows good agreement with the ideal Nernstian response. The proposed sensor platform is an outstanding candidate for a portable home-use for continuous monitoring of ions thanks to its advantages such as easy automation of sample preparation and detection processes, elongated sensor lifetime, minimal membrane and sample consumption, and user-definable/reconfigurable sensor array. Copyright © 2018 Elsevier B.V. All rights reserved.

A microfluidic cigarette smoke collecting platform for simultaneous sample extraction and multiplex analysis.

PubMed

Hu, Shan-Wen; Xu, Bi-Yi; Qiao, Shu; Zhao, Ge; Xu, Jing-Juan; Chen, Hong-Yuan; Xie, Fu-Wei

2016-04-01

In this work, we report a novel microfluidic gas collecting platform aiming at simultaneous sample extraction and multiplex mass spectrometry (MS) analysis. An alveolar-mimicking elastic polydimethylsiloxane (PDMS) structures was designed to move dynamically driven by external pressure. The movement was well tuned both by its amplitude and rhythm following the natural process of human respiration. By integrating the alveolar units into arrays and assembling them to gas channels, a cyclic contraction/expansion system for gas inhale and exhale was successfully constructed. Upon equipping this system with a droplet array on the alveolar array surface, we were able to get information of inhaled smoke in a new strategy. Here, with cigarette smoke as an example, analysis of accumulation for target molecules during passive smoking is taken. Relationships between the breathing times, distances away from smokers and inhaled content of nicotine are clarified. Further, by applying different types of extraction solvent droplets on different locations of the droplet array, simultaneous extraction of nicotine, formaldehyde and caproic acid in sidestream smoke (SS) are realized. Since the extract droplets are spatially separated, they can be directly analyzed by MS which is fast and can rid us of all complex sample separation and purification steps. Combining all these merits, this small, cheap and portable platform might find wide application in inhaled air pollutant analysis both in and outdoors. Copyright © 2015 Elsevier B.V. All rights reserved.

A Decade of Ocean Acoustic Measurements from R/P FLIP

NASA Astrophysics Data System (ADS)

D'Spain, G. L.

2002-12-01

Studies of the properties of low frequency acoustic fields in the ocean continue to benefit from the use of manned, stable offshore platforms such as R/P FLIP. A major benefit is providing the at-sea stability required for deployment of extremely large aperture line arrays, line arrays composed of both acoustic motion and acoustic pressure sensors, and arrays that provide measurements in all 3 spatial dimensions. In addition, FLIP provides a high-profile (25 m) observation post with 360 deg coverage for simultaneous visual observations of marine mammals. A few examples of the scientific results that have been achieved over this past decade with ocean acoustic data collected on FLIP are presented. These results include the normal mode decomposition of earthquake T phases to study their generation and water/land coupling characteristics using a 3000 m vertical aperture hydrophone array, simultaneous vertical and horizontal directional information on the underwater sound field from line arrays of hydrophones and geophones, the strange nightime chorusing behavior of fish measured by 3D array aperture, the mirage effect caused by bathymetry changes in inversions for source location in shallow water, and the diving behavior of blue whales determined from 1D recordings of their vocalizations. Presently, FLIP serves as the central data recording platform in ocean acoustic studies using AUV's.

Multienzyme-nanoparticles amplification for sensitive virus genotyping in microfluidic microbeads array using Au nanoparticle probes and quantum dots as labels.

PubMed

Zhang, He; Liu, Lian; Li, Cheuk-Wing; Fu, Huayang; Chen, Yao; Yang, Mengsu

2011-11-15

A novel microfluidic device with microbeads array was developed and sensitive genotyping of human papillomavirus was demonstrated using a multiple-enzyme labeled oligonucleotide-Au nanoparticle bioconjugate as the detection tool. This method utilizes microbeads as sensing platform that was functionalized with the capture probes and modified electron rich proteins, and uses the horseradish peroxidase (HRP)-functionalized gold nanoparticles as label with a secondary DNA probe. The functionalized microbeads were independently introduced into the arrayed chambers using the loading chip slab. A single channel was used to generate weir structures to confine the microbeads and make the beads array accessible by microfluidics. Through "sandwich" hybridization, the enzyme-functionalized Au nanoparticles labels were brought close to the surface of microbeads. The oxidation of biotin-tyramine by hydrogen peroxide resulted in the deposition of multiple biotin moieties onto the surface of beads. This deposition is markedly increased in the presence of immobilized electron rich proteins. Streptavidin-labeled quantum dots were then allowed to bind to the deposited biotin moieties and displayed the signal. Enhanced detection sensitivity was achieved where the large surface area of Au nanoparticle carriers increased the amount HRP bound per sandwiched hybridization. The on-chip genotyping method could discriminate as low as 1fmol/L (10zmol/chip, SNR>3) synthesized HPV oligonucleotides DNA. The chip-based signal enhancement of the amplified assay resulted in 1000 times higher sensitivity than that of off-chip test. In addition, this on-chip format could discriminate and genotype 10copies/μL HPV genomic DNA using the PCR products. These results demonstrated that this on-chip approach can achieve highly sensitive detection and genotyping of target DNA and can be further developed for detection of disease-related biomolecules at the lowest level at their earliest incidence. Copyright © 2011 Elsevier B.V. All rights reserved.

Designing of a small wearable conformal phased array antenna for wireless communications

NASA Astrophysics Data System (ADS)

Roy, Sayan

In this thesis, a unique design of a self-adapting conformal phased-array antenna system for wireless communications is presented. The antenna system is comprised of one microstrip antenna array and a sensor circuit. A 1x4 printed microstrip patch antenna array was designed on a flexible substrate with a resonant frequency of 2.47 GHz. However, the performance of the antenna starts to degrade as the curvature of the surface of the substrate changes. To recover the performance of the system, a flexible sensor circuitry was designed. This sensor circuitry uses analog phase shifters, a flexible resistor and operational-amplifier circuitry to compensate the phase of each array element of the antenna. The proposed analytical method for phase compensation has been first verified by designing an RF test platform consisting of a microstrip antenna array, commercially available analog phase shifters, analog voltage attenuators, 4-port power dividers and amplifiers. The platform can be operated through a LabVIEW GUI interface using a 12-bit digital-to-analog converter. This test board was used to design and calibrate the sensor circuitry by observing the behavior of the antenna array system on surfaces with different curvatures. In particular, this phased array antenna system was designed to be used on the surface of a spacesuit or any other flexible prototype. This work was supported in part by the Defense Miroelectronics Activity (DMEA), NASA ND EPSCoR and DARPA/MTO.

Using peptide array to identify binding motifs and interaction networks for modular domains.

PubMed

Li, Shawn S-C; Wu, Chenggang

2009-01-01

Specific protein-protein interactions underlie all essential biological processes and form the basis of cellular signal transduction. The recognition of a short, linear peptide sequence in one protein by a modular domain in another represents a common theme of macromolecular recognition in cells, and the importance of this mode of protein-protein interaction is highlighted by the large number of peptide-binding domains encoded by the human genome. This phenomenon also provides a unique opportunity to identify protein-protein binding events using peptide arrays and complementary biochemical assays. Accordingly, high-density peptide array has emerged as a useful tool by which to map domain-mediated protein-protein interaction networks at the proteome level. Using the Src-homology 2 (SH2) and 3 (SH3) domains as examples, we describe the application of oriented peptide array libraries in uncovering specific motifs recognized by an SH2 domain and the use of high-density peptide arrays in identifying interaction networks mediated by the SH3 domain. Methods reviewed here could also be applied to other modular domains, including catalytic domains, that recognize linear peptide sequences.

Miniaturized ceramic platform for metal oxide gas sensors array

NASA Astrophysics Data System (ADS)

Samotaev, N. N.

2016-10-01

In work is developing an ultra-fast, low cost and technology flexible process for production array of ceramic MEMS microhotplates for using in semiconductor gas sensors orientated to small series applications, where is sufficient to produce 10-100 samples with a different layout of heaters and membrane per day.

Biofunctionalization on alkylated silicon substrate surfaces via "click" chemistry.

PubMed

Qin, Guoting; Santos, Catherine; Zhang, Wen; Li, Yan; Kumar, Amit; Erasquin, Uriel J; Liu, Kai; Muradov, Pavel; Trautner, Barbara Wells; Cai, Chengzhi

2010-11-24

Biofunctionalization of silicon substrates is important to the development of silicon-based biosensors and devices. Compared to conventional organosiloxane films on silicon oxide intermediate layers, organic monolayers directly bound to the nonoxidized silicon substrates via Si-C bonds enhance the sensitivity of detection and the stability against hydrolytic cleavage. Such monolayers presenting a high density of terminal alkynyl groups for bioconjugation via copper-catalyzed azide-alkyne 1,3-dipolar cycloaddition (CuAAC, a "click" reaction) were reported. However, yields of the CuAAC reactions on these monolayer platforms were low. Also, the nonspecific adsorption of proteins on the resultant surfaces remained a major obstacle for many potential biological applications. Herein, we report a new type of "clickable" monolayers grown by selective, photoactivated surface hydrosilylation of α,ω-alkenynes, where the alkynyl terminal is protected with a trimethylgermanyl (TMG) group, on hydrogen-terminated silicon substrates. The TMG groups on the film are readily removed in aqueous solutions in the presence of Cu(I). Significantly, the degermanylation and the subsequent CuAAC reaction with various azides could be combined into a single step in good yields. Thus, oligo(ethylene glycol) (OEG) with an azido tag was attached to the TMG-alkyne surfaces, leading to OEG-terminated surfaces that reduced the nonspecific adsorption of protein (fibrinogen) by >98%. The CuAAC reaction could be performed in microarray format to generate arrays of mannose and biotin with varied densities on the protein-resistant OEG background. We also demonstrated that the monolayer platform could be functionalized with mannose for highly specific capturing of living targets (Escherichia coli expressing fimbriae) onto the silicon substrates.

DNA-Mediated Patterning of Single Quantum Dot Nanoarrays: A Reusable Platform for Single-Molecule Control

NASA Astrophysics Data System (ADS)

Huang, Da; Freeley, Mark; Palma, Matteo

2017-03-01

We present a facile strategy of general applicability for the assembly of individual nanoscale moieties in array configurations with single-molecule control. Combining the programming ability of DNA as a scaffolding material with a one-step lithographic process, we demonstrate the patterning of single quantum dots (QDs) at predefined locations on silicon and transparent glass surfaces: as proof of concept, clusters of either one, two, or three QDs were assembled in highly uniform arrays with a 60 nm interdot spacing within each cluster. Notably, the platform developed is reusable after a simple cleaning process and can be designed to exhibit different geometrical arrangements.

PCR/LDR/universal array platforms for the diagnosis of infectious disease.

PubMed

Pingle, Maneesh; Rundell, Mark; Das, Sanchita; Golightly, Linnie M; Barany, Francis

2010-01-01

Infectious diseases account for between 14 and 17 million deaths worldwide each year. Accurate and rapid diagnosis of bacterial, fungal, viral, and parasitic infections is therefore essential to reduce the morbidity and mortality associated with these diseases. Classical microbiological and serological methods have long served as the gold standard for diagnosis but are increasingly being replaced by molecular diagnostic methods that demonstrate increased sensitivity and specificity and provide an identification of the etiologic agent in a shorter period of time. PCR/LDR coupled with universal array detection provides a highly sensitive and specific platform for the detection and identification of bacterial and viral infections.

PCR/LDR/Universal Array Platforms for the Diagnosis of Infectious Disease

PubMed Central

Pingle, Maneesh; Rundell, Mark; Das, Sanchita; Golightly, Linnie M.; Barany, Francis

2015-01-01

Infectious diseases account for between 14 and 17 million deaths worldwide each year. Accurate and rapid diagnosis of bacterial, fungal, viral, and parasitic infections is therefore essential to reduce the morbidity and mortality associated with these diseases. Classical microbiological and serological methods have long served as the gold standard for diagnosis but are increasingly being replaced by molecular diagnostic methods that demonstrate increased sensitivity and specificity and provide an identification of the etiologic agent in a shorter period of time. PCR/LDR coupled with universal array detection provides a highly sensitive and specific platform for the detection and identification of bacterial and viral infections. PMID:20217576

High power solar array switching regulation

NASA Technical Reports Server (NTRS)

Decker, D. K.; Cassinelli, J.; Valgora, M.

1981-01-01

It is pointed out that spacecraft utilization projections for the 1980s and beyond show a trend toward extended lifetimes and larger electric power systems. The need for improved power management and energy transfer arising in connection with this trend has resulted in the conduction of a Solar Array Switching Power Management study. A description is presented of initial development work performed in the study, taking into account the characteristics for three mission classes. Attention is given to the manned LEO platform (250-kW average load), the unmanned GEO platform (50-kW average load), and an ion propulsion orbit transfer vehicle (50- to 250 kW load).

Flow-through nanohole array based sensor implemented on analogue smartphone components

NASA Astrophysics Data System (ADS)

Gomez-Cruz, Juan; Nair, Srijit; Ascanio, Gabriel; Escobedo, Carlos

2017-08-01

Mobile communications have massively populated the consumer electronics market over the past few years and it is now ubiquitous, providing a timeless opportunity for the development of smartphone-based technologies as point-of-care (POC) diagnosis tools1 . The expectation for a fully integrated smartphone-based sensor that enables applications such as environmental monitoring, explosive detection and biomedical analysis has increased among the scientific community in the past few years2,3. The commercialization forecast for smartphone-based sensing technologies is very promising, but reliable, miniature and cost-effective sensing platforms that can adapt to portable electronics in still under development. In this work, we present an integrated sensing platform based on flow-through metallic nanohole arrays. The nanohole arrays are 260 nm in diameter and 520 nm in pitch, fabricated using Focused Ion Beam (FIB) lithography. A white LED resembling a smartphone flash LED serves as light source to excite surface plasmons and the signal is recorded via a Complementary Metal-Oxide-Semiconductor (CMOS) module. The sensing abilities of the integrated sensing platform is demonstrated for the detection of (i) changes in bulk refractive index (RI), (ii) real-time monitoring of surface modification by receptor-analyte system of streptavidin-biotin.

In Situ Localized Growth of Ordered Metal Oxide Hollow Sphere Array on Microheater Platform for Sensitive, Ultra-Fast Gas Sensing.

PubMed

Rao, Ameya; Long, Hu; Harley-Trochimczyk, Anna; Pham, Thang; Zettl, Alex; Carraro, Carlo; Maboudian, Roya

2017-01-25

A simple and versatile strategy is presented for the localized on-chip synthesis of an ordered metal oxide hollow sphere array directly on a low power microheater platform to form a closely integrated miniaturized gas sensor. Selective microheater surface modification through fluorinated monolayer self-assembly and its subsequent microheater-induced thermal decomposition enables the position-controlled deposition of an ordered two-dimensional colloidal sphere array, which serves as a sacrificial template for metal oxide growth via homogeneous chemical precipitation; this strategy ensures control in both the morphology and placement of the sensing material on only the active heated area of the microheater platform, providing a major advantage over other methods of presynthesized nanomaterial integration via suspension coating or printing. A fabricated tin oxide hollow sphere-based sensor shows high sensitivity (6.5 ppb detection limit) and selectivity toward formaldehyde, and extremely fast response (1.8 s) and recovery (5.4 s) times. This flexible and scalable method can be used to fabricate high performance miniaturized gas sensors with a variety of hollow nanostructured metal oxides for a range of applications, including combining multiple metal oxides for superior sensitivity and tunable selectivity.

Structurally Integrated Photoluminescent Chemical and Biological Sensors: An Organic Light-Emitting Diode-Based Platform

NASA Astrophysics Data System (ADS)

Shinar, J.; Shinar, R.

The chapter describes the development, advantages, challenges, and potential of an emerging, compact photoluminescence-based sensing platform for chemical and biological analytes, including multiple analytes. In this platform, the excitation source is an array of organic light-emitting device (OLED) pixels that is structurally integrated with the sensing component. Steps towards advanced integration with additionally a thin-film-based photodetector are also described. The performance of the OLED-based sensing platform is examined for gas-phase and dissolved oxygen, glucose, lactate, ethanol, hydrazine, and anthrax lethal factor.

Microfluidic platform for efficient Nanodisc assembly, membrane protein incorporation, and purification.

PubMed

Wade, James H; Jones, Joshua D; Lenov, Ivan L; Riordan, Colleen M; Sligar, Stephen G; Bailey, Ryan C

2017-08-22

The characterization of integral membrane proteins presents numerous analytical challenges on account of their poor activity under non-native conditions, limited solubility in aqueous solutions, and low expression in most cell culture systems. Nanodiscs are synthetic model membrane constructs that offer many advantages for studying membrane protein function by offering a native-like phospholipid bilayer environment. The successful incorporation of membrane proteins within Nanodiscs requires experimental optimization of conditions. Standard protocols for Nanodisc formation can require large amounts of time and input material, limiting the facile screening of formation conditions. Capitalizing on the miniaturization and efficient mass transport inherent to microfluidics, we have developed a microfluidic platform for efficient Nanodisc assembly and purification, and demonstrated the ability to incorporate functional membrane proteins into the resulting Nanodiscs. In addition to working with reduced sample volumes, this platform simplifies membrane protein incorporation from a multi-stage protocol requiring several hours or days into a single platform that outputs purified Nanodiscs in less than one hour. To demonstrate the utility of this platform, we incorporated Cytochrome P450 into Nanodiscs of variable size and lipid composition, and present spectroscopic evidence for the functional active site of the membrane protein. This platform is a promising new tool for membrane protein biology and biochemistry that enables tremendous versatility for optimizing the incorporation of membrane proteins using microfluidic gradients to screen across diverse formation conditions.

Arrayed water-in-oil droplet bilayers for membrane transport analysis.

PubMed

Watanabe, R; Soga, N; Hara, M; Noji, H

2016-08-02

The water-in-oil droplet bilayer is a simple and useful lipid bilayer system for membrane transport analysis. The droplet interface bilayer is readily formed by the contact of two water-in-oil droplets enwrapped by a phospholipid monolayer. However, the size of individual droplets with femtoliter volumes in a high-throughput manner is difficult to control, resulting in low sensitivity and throughput of membrane transport analysis. To overcome this drawback, in this study, we developed a novel micro-device in which a large number of droplet interface bilayers (>500) are formed at a time by using femtoliter-sized droplet arrays immobilized on a hydrophobic/hydrophilic substrate. The droplet volume was controllable from 3.5 to 350 fL by changing the hydrophobic/hydrophilic pattern on the device, allowing high-throughput analysis of membrane transport mechanisms including membrane permeability to solutes (e.g., ions or small molecules) with or without the aid of transport proteins. Thus, this novel platform broadens the versatility of water-in-oil droplet bilayers and will pave the way for novel analytical and pharmacological applications such as drug screening.

Magnetic wire trap arrays for biomarker-based molecular detection

NASA Astrophysics Data System (ADS)

Vieira, Gregory; Mahajan, Kalpesh; Ruan, Gang; Winter, Jessica; Sooryakumar, R.

2012-02-01

Submicrometer-scale magnetic devices built on chip-based platforms have recently been shown to present opportunities for new particle trapping and manipulation technologies. Meanwhile, advances in nanoparticle fabrication allow for the building of custom-made particles with precise control of their size, composition, and other properties such as magnetism, fluorescence, and surface biomarker characteristics. In particular, carefully tailored surface biomarkers facilitate precise binding to targeted molecules, self-actuated construction of hybrid structures, and fluorescence-based detection schemes. Based on these progresses, we present an on-chip detection mechanism for molecules with known surface markers. Hybrid nanostructures consisting of micelle nanoparticles, fluorescent quantum dots, and superparamagnetic iron oxide nanoparticles are used to detect proteins or DNA molecules. The target is detected by the magnetic and fluorescent functionalities of the composite nanostructure, whereas in the absence of the target these signals are not present. Underlying this approach is the simultaneous manipulation via ferromagnetic zigzag nanowire arrays and imaging via quantum dot excitation. This chip-based detection technique could provide a powerful, low cost tool for ultrasensitive molecule detection with ramifications in healthcare diagnostics and small-scale chemical synthesis.

Nanohole Arrays of Mixed Designs and Microwriting for Simultaneous and Multiple Protein Binding Studies

PubMed Central

Ji, Jin; Yang, Jiun-Chan; Larson, Dale N.

2009-01-01

We demonstrate using nanohole arrays of mixed designs and a microwriting process based on dip-pen nanolithography to monitor multiple, different protein binding events simultaneously in real time based on the intensity of Extraordinary Optical Transmission of nanohole arrays. The microwriting process and small footprint of the individual nanohole arrays enabled us to observe different binding events located only 16μm apart, achieving high spatial resolution. We also present a novel concept that incorporates nanohole arrays of different designs to improve confidence and accuracy of binding studies. For proof of concept, two types of nanohole arrays, designed to exhibit opposite responses to protein bindings, were fabricated on one transducer. Initial studies indicate that the mixed designs could help to screen out artifacts such as protein intrinsic signals, providing improved accuracy of binding interpretation. PMID:19297143

Organic electrochemical transistor array for recording transepithelial ion transport of human airway epithelial cells.

PubMed

Yao, Chunlei; Xie, Changyan; Lin, Peng; Yan, Feng; Huang, Pingbo; Hsing, I-Ming

2013-12-03

An organic electrochemical transistor array is integrated with human airway epithelial cells. This integration provides a novel method to couple transepithelial ion transport with electrical current. Activation and inhibition of transepithelial ion transport are readily detected with excellent time resolution. The organic electrochemical transistor array serves as a promising platform for physiological studies and drug testing. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Monolithic integration of an InP-based 4 × 25 GHz photodiode array to an O-band arrayed waveguide grating demultiplexer

NASA Astrophysics Data System (ADS)

Ye, Han; Han, Qin; Lv, Qianqian; Pan, Pan; An, Junming; Yang, Xiaohong

2017-12-01

We demonstrate the monolithic integration of a uni-traveling carrier photodiode array with a 4 channel, O-band arrayed waveguide grating demultiplexer on the InP platform by the selective area growth technique. An extended coupling layer at the butt-joint is adopted to ensure both good fabrication compatibility and high photodiode quantum efficiency of 77%. The fabricated integrated chip exhibits a uniform bandwidth over 25 GHz for each channel and a crosstalk below -22 dB.

Image science team

NASA Technical Reports Server (NTRS)

Ando, K.

1982-01-01

A substantial technology base of solid state pushbroom sensors exists and is in the process of further evolution at both GSFC and JPL. Technologies being developed relate to short wave infrared (SWIR) detector arrays; HgCdTe hybrid detector arrays; InSb linear and area arrays; passive coolers; spectral beam splitters; the deposition of spectral filters on detector arrays; and the functional design of the shuttle/space platform imaging spectrometer (SIS) system. Spatial and spectral characteristics of field, aircraft and space multispectral sensors are summaried. The status, field of view, and resolution of foreign land observing systems are included.

Controlled Breast Cancer Microarrays for the Deconvolution of Cellular Multilayering and Density Effects upon Drug Responses

PubMed Central

Håkanson, Maria; Kobel, Stefan; Lutolf, Matthias P.; Textor, Marcus; Cukierman, Edna; Charnley, Mirren

2012-01-01

Background Increasing evidence shows that the cancer microenvironment affects both tumorigenesis and the response of cancer to drug treatment. Therefore in vitro models that selectively reflect characteristics of the in vivo environment are greatly needed. Current methods allow us to screen the effect of extrinsic parameters such as matrix composition and to model the complex and three-dimensional (3D) cancer environment. However, 3D models that reflect characteristics of the in vivo environment are typically too complex and do not allow the separation of discrete extrinsic parameters. Methodology/Principal Findings In this study we used a poly(ethylene glycol) (PEG) hydrogel-based microwell array to model breast cancer cell behavior in multilayer cell clusters that allows a rigorous control of the environment. The innovative array fabrication enables different matrix proteins to be integrated into the bottom surface of microwells. Thereby, extrinsic parameters including dimensionality, type of matrix coating and the extent of cell-cell adhesion could be independently studied. Our results suggest that cell to matrix interactions and increased cell-cell adhesion, at high cell density, induce independent effects on the response to Taxol in multilayer breast cancer cell clusters. In addition, comparing the levels of apoptosis and proliferation revealed that drug resistance mediated by cell-cell adhesion can be related to altered cell cycle regulation. Conversely, the matrix-dependent response to Taxol did not correlate with proliferation changes suggesting that cell death inhibition may be responsible for this effect. Conclusions/Significance The application of the PEG hydrogel platform provided novel insight into the independent role of extrinsic parameters controlling drug response. The presented platform may not only become a useful tool for basic research related to the role of the cancer microenvironment but could also serve as a complementary platform for in vitro drug development. PMID:22792141

Telescope Array Control System Based on Wireless Touch Screen Platform

NASA Astrophysics Data System (ADS)

Fu, Xia-nan; Huang, Lei; Wei, Jian-yan

2017-10-01

Ground-based Wide Angle Cameras (GMAC) are the ground-based observational facility for the SVOM (Space Variable Object Monitor) astronomical satellite of Sino-French cooperation, and Mini-GWAC is the pathfinder and supplement of GWAC. In the context of the Mini-GWAC telescope array, this paper introduces the design and implementation of a kind of telescope array control system based on the wireless touch screen platform. We describe the development and implementation of the system in detail in terms of control system principle, system hardware structure, software design, experiment, and test etc. The system uses a touch-control PC which is based on the Windows CE system as the upper computer, while the wireless transceiver module and PLC (Programmable Logic Controller) are taken as the system kernel. It has the advantages of low cost, reliable data transmission, and simple operation. And the control system has been applied to the Mini-GWAC successfully.

Coaxial tube array space transmission line characterization

NASA Technical Reports Server (NTRS)

Switzer, Colleen A.; Bents, David J.

1987-01-01

The coaxial tube array tether/transmission line used to connect an SP-100 nuclear power system to the space station was characterized over the range of reactor-to-platform separation distances of 1 to 10 km. Characterization was done with respect to array performance, physical dimensions and masses. Using a fixed design procedure, a family of designs was generated for the same power level (300 kWe), power loss (1.5 percent), and meteoroid survival probability (99.5 percent over 10 yr). To differentiate between vacuum insulated and gas insulated lines, two different maximum values of the E field were considered: 20 kV/cm (appropriate to vacuum insulation) and 50 kV/cm (compressed SF6). Core conductor, tube, bumper, standoff, spacer and bumper support dimensions, and masses were also calculated. The results of the characterization show mainly how transmission line size and mass scale with reactor-to-platform separation distance.

Coaxial tube array space transmission line characterization

NASA Astrophysics Data System (ADS)

Switzer, Colleen A.; Bents, David J.

The coaxial tube array tether/transmission line used to connect an SP-100 nuclear power system to the space station was characterized over the range of reactor-to-platform separation distances of 1 to 10 km. Characterization was done with respect to array performance, physical dimensions and masses. Using a fixed design procedure, a family of designs was generated for the same power level (300 kWe), power loss (1.5 percent), and meteoroid survival probability (99.5 percent over 10 yr). To differentiate between vacuum insulated and gas insulated lines, two different maximum values of the E field were considered: 20 kV/cm (appropriate to vacuum insulation) and 50 kV/cm (compressed SF6). Core conductor, tube, bumper, standoff, spacer and bumper support dimensions, and masses were also calculated. The results of the characterization show mainly how transmission line size and mass scale with reactor-to-platform separation distance.

A novel ultrasonic phased array inspection system to NDT for offshore platform structures

NASA Astrophysics Data System (ADS)

Wang, Hua; Shan, Baohua; Wang, Xin; Ou, Jinping

2007-01-01

A novel ultrasonic phased array detection system is developed for nondestructive testing (NDT). The purpose of the system is to make acquisition of data in real-time from 64-element ultrasonic phased array transducer, and to enable real- time processing of the acquired data. The system is composed of five main parts: master unit, main board, eight transmit/receive units, a 64-element transducer and an external PC. The system can be used with 64 element transducers, excite 32 elements, receive and sample echo signals form 32 elements simultaneously at 62.5MHz with 8 bit precision. The external PC is used as the user interface showing the real time images and controls overall operation of the system through USB serial link. The use of Universal Serial Bus (USB) improves the transform speed and reduces hardware interface complexity. The program of the system is written in Visual C++.NET and is platform independent.

Graphene Microcapsule Arrays for Combinatorial Electron Microscopy and Spectroscopy in Liquids

DOE PAGES

Yulaev, Alexander; Guo, Hongxuan; Strelcov, Evgheni; ...

2017-04-27

Atomic-scale thickness, molecular impermeability, low atomic number, and mechanical strength make graphene an ideal electron-transparent membrane for material characterization in liquids and gases with scanning electron microscopy and spectroscopy. Here in this paper, we present a novel sample platform made of an array of thousands of identical isolated graphene-capped microchannels with high aspect ratio. A combination of a global wide field of view with high resolution local imaging of the array allows for high throughput in situ studies as well as for combinatorial screening of solutions, liquid interfaces, and immersed samples. We demonstrate the capabilities of this platform by studyingmore » a pure water sample in comparison with alkali halide solutions, a model electrochemical plating process, and beam-induced crystal growth in liquid electrolyte. Spectroscopic characterization of liquid interfaces and immersed objects with Auger and X-ray fluorescence analysis through the graphene membrane are also demonstrated.« less

Mass spectrometry-based monitoring of millisecond protein–ligand binding dynamics using an automated microfluidic platform

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cong, Yongzheng; Katipamula, Shanta; Trader, Cameron D.

2016-01-01

Characterizing protein-ligand binding dynamics is crucial for understanding protein function and developing new therapeutic agents. We have developed a novel microfluidic platform that features rapid mixing of protein and ligand solutions, variable incubation times, and on-chip electrospray ionization to perform label-free, solution-based monitoring of protein-ligand binding dynamics. This platform offers many advantages including automated processing, rapid mixing, and low sample consumption.

Mapping protein-protein interactions using yeast two-hybrid assays.

PubMed

Mehla, Jitender; Caufield, J Harry; Uetz, Peter

2015-05-01

Yeast two-hybrid (Y2H) screens are an efficient system for mapping protein-protein interactions and whole interactomes. The screens can be performed using random libraries or collections of defined open reading frames (ORFs) called ORFeomes. This protocol describes both library and array-based Y2H screening, with an emphasis on array-based assays. Array-based Y2H is commonly used to test a number of "prey" proteins for interactions with a single "bait" (target) protein or pool of proteins. The advantage of this approach is the direct identification of interacting protein pairs without further downstream experiments: The identity of the preys is known and does not require further confirmation. In contrast, constructing and screening a random prey library requires identification of individual prey clones and systematic retesting. Retesting is typically performed in an array format. © 2015 Cold Spring Harbor Laboratory Press.

Selective deposition and self-assembly of triblock copolymers into matrix arrays for membrane protein production.

PubMed

Andreasson-Ochsner, Mirjam; Fu, Zhikang; May, Sylvia; Xiu, Low Ying; Nallani, Madhavan; Sinner, Eva-Kathrin

2012-01-31

To improve the stability of cell membrane mimics, there has been growing interest in the use of block copolymers. Here, we present an easy approach to create an array of planar polymeric matrices capable of hosting membrane proteins. The array of polymeric matrices was formed by the selective deposition of triblock copolymers onto an array of hydrophilic islands situated within a hydrophobic background. The thickness of these matrices corresponds to the length of a single polymer chain. These polymeric matrices were used to host cell-free expressed membrane proteins, and offers a prototype from which a membrane protein array can be created for diagnostics or drug discovery purposes. © 2011 American Chemical Society

Method to determine thermal profiles of nanoscale circuitry

DOEpatents

Zettl, Alexander K; Begtrup, Gavi E

2013-04-30

A platform that can measure the thermal profiles of devices with nanoscale resolution has been developed. The system measures the local temperature by using an array of nanoscale thermometers. This process can be observed in real time using a high resolution imagining technique such as electron microscopy. The platform can operate at extremely high temperatures.

Evanescent wave coupling in terahertz waveguide arrays.

PubMed

Reichel, K S; Sakoda, N; Mendis, R; Mittleman, D M

2013-07-15

We study energy transfer among an array of identical finite-width parallel-plate waveguides in close proximity, via evanescent wave coupling of broadband terahertz waves. We observe stronger coupling with larger plate separations and longer propagation paths. This work establishes a platform to investigate new opportunities for THz components and devices based on evanescent wave coupling.

Diversity Arrays Technology (DArT) platform for genotyping and mapping in carrot (Daucus carota L.)

USDA-ARS?s Scientific Manuscript database

Carrot is one of the most important root vegetable crops grown worldwide on more than one million hectares. Its progenitor, wild Daucus carota, is a weed commonly occurring across continents in the temperate climatic zone. Diversity Array Technology (DArT) is a microarray-based molecular marker syst...

Use of ultrasonic array method for positioning multiple partial discharge sources in transformer oil.

PubMed

Xie, Qing; Tao, Junhan; Wang, Yongqiang; Geng, Jianghai; Cheng, Shuyi; Lü, Fangcheng

2014-08-01

Fast and accurate positioning of partial discharge (PD) sources in transformer oil is very important for the safe, stable operation of power systems because it allows timely elimination of insulation faults. There is usually more than one PD source once an insulation fault occurs in the transformer oil. This study, which has both theoretical and practical significance, proposes a method of identifying multiple PD sources in the transformer oil. The method combines the two-sided correlation transformation algorithm in the broadband signal focusing and the modified Gerschgorin disk estimator. The method of classification of multiple signals is used to determine the directions of arrival of signals from multiple PD sources. The ultrasonic array positioning method is based on the multi-platform direction finding and the global optimization searching. Both the 4 × 4 square planar ultrasonic sensor array and the ultrasonic array detection platform are built to test the method of identifying and positioning multiple PD sources. The obtained results verify the validity and the engineering practicability of this method.

Integrated chemiresistor array for small sensor platforms

DOE Office of Scientific and Technical Information (OSTI.GOV)

HUGHES,ROBERT C.; CASALNUOVO,STEPHEN A.; WESSENDORF,KURT O.

2000-04-13

Chemiresistors are fabricated from materials that change their electrical resistance when exposed to certain chemical species. Composites of soluble polymers with metallic particles have shown remarkable sensitivity to many volatile organic chemicals, depending on the ability of the analyte molecules to swell the polymer matrix. These sensors can be made extremely small (< 100 square microns), operate at ambient temperatures, and require almost no power to read-out. However, the chemiresistor itself is only a part of a more complex sensor system that delivers chemical information to a user who can act on the information. The authors present the design, fabricationmore » and performance of a chemiresistor array chip with four different chemiresistor materials, heaters and a temperature sensor. They also show the design and fabrication of an integrated chemiresistor array, where the electronics to read-out the chemiresistors is on the same chip with the electrodes for the chemiresistors. The circuit was designed to perform several functions to make the sensor data more useful. This low-power, integrated chemiresistor array is small enough to be deployed on a Sandia-developed microrobot platform.« less

MDAnalysis: a toolkit for the analysis of molecular dynamics simulations.

PubMed

Michaud-Agrawal, Naveen; Denning, Elizabeth J; Woolf, Thomas B; Beckstein, Oliver

2011-07-30

MDAnalysis is an object-oriented library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. It is written in the Python language with some performance-critical code in C. It uses the powerful NumPy package to expose trajectory data as fast and efficient NumPy arrays. It has been tested on systems of millions of particles. Many common file formats of simulation packages including CHARMM, Gromacs, Amber, and NAMD and the Protein Data Bank format can be read and written. Atoms can be selected with a syntax similar to CHARMM's powerful selection commands. MDAnalysis enables both novice and experienced programmers to rapidly write their own analytical tools and access data stored in trajectories in an easily accessible manner that facilitates interactive explorative analysis. MDAnalysis has been tested on and works for most Unix-based platforms such as Linux and Mac OS X. It is freely available under the GNU General Public License from http://mdanalysis.googlecode.com. Copyright © 2011 Wiley Periodicals, Inc.

MDA5 assembles into a polar helical filament on dsRNA

PubMed Central

Berke, Ian C.; Yu, Xiong; Modis, Yorgo; Egelman, Edward H.

2012-01-01

Melanoma differentiation-associated protein 5 (MDA5) detects viral dsRNA in the cytoplasm. On binding of RNA, MDA5 forms polymers, which trigger assembly of the signaling adaptor mitochondrial antiviral-signaling protein (MAVS) into its active fibril form. The molecular mechanism of MDA5 signaling is not well understood, however. Here we show that MDA5 forms helical filaments on dsRNA and report the 3D structure of the filaments using electron microscopy (EM) and image reconstruction. MDA5 assembles into a polar, single-start helix around the RNA. Fitting of an MDA5 homology model into the structure suggests a key role for the MDA5 C-terminal domain in cooperative filament assembly. Our study supports a signal transduction mechanism in which the helical array of MDA5 within filaments nucleates the assembly of MAVS fibrils. We conclude that MDA5 is a polymerization-dependent signaling platform that uses the amyloid-like self-propagating properties of MAVS to amplify signaling. PMID:23090998

Development of an Ultraflex-Based Thin Film Solar Array for Space Applications

NASA Technical Reports Server (NTRS)

White, Steve; Douglas, Mark; Spence, Brian; Jones, P. Alan; Piszczor, Michael F.

2003-01-01

As flexible thin film photovoltaic (FTFPV) cell technology is developed for space applications, integration into a viable solar array structure that optimizes the attributes of this cell technology is critical. An advanced version of ABLE'sS UltraFlex solar array platform represents a near-term, low-risk approach to demonstrating outstanding array performance with the implementation of FTFPV technology. Recent studies indicate that an advanced UltraFlex solar array populated with 15% efficient thin film cells can achieve over 200 W/kg EOL. An overview on the status of hardware development and the future potential of this technology is presented.

Cost-effective flow-through nanohole array-based biosensing platform for the label-free detection of uropathogenic E. coli in real time.

PubMed

Gomez-Cruz, Juan; Nair, Srijit; Manjarrez-Hernandez, Angel; Gavilanes-Parra, Sandra; Ascanio, Gabriel; Escobedo, Carlos

2018-05-30

Rapid, inexpensive and sensitive detection of uropathogenic Escherichia coli (UPEC), a common cause of ascending urinary tract infections (UTIs) including cystitis and pyelonephritis, is critical given the increasing number of cases and its recurrence worldwide. In this paper, we present a label-free nanoplasmonic sensing platform, built with off-the-shelf optical and electronic components, which can detect intact UPEC at concentrations lower than the physiological limit for UTI diagnosis, in real time. The sensing platform consists of a red LED light source, lens assembly, CMOS detector, Raspberry Pi interface in conjugation with a metallic flow-through nanohole array-based sensor. Detection is achieved exploiting nanoplasmonic phenomena from the nanohole arrays through surface plasmon resonance imaging (SPRi) technique. The platform has a bulk sensitivity of 212 pixel intensity unit (PIU)/refractive index unit (RIU), and a resolution in the order of 10 -6 RIU. We demonstrate capture and detection of UPEC with a detection limit of ~100 CFU/ml - a concentration well below the threshold limit for UTI diagnosis in clinical samples. We also demonstrate detection of UPEC in spiked human urine samples for two different concentrations of bacteria. This work is particularly relevant for point-of-care applications, especially for regions around the world where accessibility to medical facilities is heavily dependent upon economy, and availability. Copyright © 2018 Elsevier B.V. All rights reserved.

Hydrodynamic trapping for rapid assembly and in situ electrical characterization of droplet interface bilayer arrays

DOE PAGES

Nguyen, Mary -Anne; Srijanto, Bernadeta; Collier, C. Patrick; ...

2016-08-02

The droplet interface bilayer (DIB) is a modular technique for assembling planar lipid membranes between water droplets in oil. The DIB method thus provides a unique capability for developing digital, droplet-based membrane platforms for rapid membrane characterization, drug screening and ion channel recordings. This paper demonstrates a new, low-volume microfluidic system that automates droplet generation, sorting, and sequential trapping in designated locations to enable the rapid assembly of arrays of DIBs. The channel layout of the device is guided by an equivalent circuit model, which predicts that a serial arrangement of hydrodynamic DIB traps enables sequential droplet placement and minimizesmore » the hydrodynamic pressure developed across filled traps to prevent squeeze-through of trapped droplets. Furthermore, the incorporation of thin-film electrodes fabricated via evaporation metal deposition onto the glass substrate beneath the channels allows for the first time in situ, simultaneous electrical interrogation of multiple DIBs within a sealed device. Combining electrical measurements with imaging enables measurements of membrane capacitance and resistance and bilayer area, and our data show that DIBs formed in different trap locations within the device exhibit similar sizes and transport properties. Simultaneous, single channel recordings of ion channel gating in multiple membranes are obtained when alamethicin peptides are incorporated into the captured droplets, qualifying the thin-film electrodes as a means for measuring stimuli-responsive functions of membrane-bound biomolecules. Furthermore, this novel microfluidic-electrophysiology platform provides a reproducible, high throughput method for performing electrical measurements to study transmembrane proteins and biomembranes in low-volume, droplet-based membranes.« less

Hydrodynamic trapping for rapid assembly and in situ electrical characterization of droplet interface bilayer arrays

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nguyen, Mary -Anne; Srijanto, Bernadeta; Collier, C. Patrick

The droplet interface bilayer (DIB) is a modular technique for assembling planar lipid membranes between water droplets in oil. The DIB method thus provides a unique capability for developing digital, droplet-based membrane platforms for rapid membrane characterization, drug screening and ion channel recordings. This paper demonstrates a new, low-volume microfluidic system that automates droplet generation, sorting, and sequential trapping in designated locations to enable the rapid assembly of arrays of DIBs. The channel layout of the device is guided by an equivalent circuit model, which predicts that a serial arrangement of hydrodynamic DIB traps enables sequential droplet placement and minimizesmore » the hydrodynamic pressure developed across filled traps to prevent squeeze-through of trapped droplets. Furthermore, the incorporation of thin-film electrodes fabricated via evaporation metal deposition onto the glass substrate beneath the channels allows for the first time in situ, simultaneous electrical interrogation of multiple DIBs within a sealed device. Combining electrical measurements with imaging enables measurements of membrane capacitance and resistance and bilayer area, and our data show that DIBs formed in different trap locations within the device exhibit similar sizes and transport properties. Simultaneous, single channel recordings of ion channel gating in multiple membranes are obtained when alamethicin peptides are incorporated into the captured droplets, qualifying the thin-film electrodes as a means for measuring stimuli-responsive functions of membrane-bound biomolecules. Furthermore, this novel microfluidic-electrophysiology platform provides a reproducible, high throughput method for performing electrical measurements to study transmembrane proteins and biomembranes in low-volume, droplet-based membranes.« less

Space-Time Adaptive Processing for Airborne Radar

DTIC Science & Technology

1994-12-13

horizontal plane Uniform linear antenna array (possibly columns of a planar array) Identical element patterns 13 14 15 9 7 7,33 7 7 Target Model ...Parameters for Example Scenario 31 3 Assumptions Made for Radar System and Signal Model 52 4 Platform and Interference Scenario for Baseline Scenario. 61 5...pulses, is addressed first. Fully adaptive STAP requires the solution to a system of linear equations of size MN, where N is the number of array

A Molecular Simulation Study of Antibody-Antigen Interactions on Surfaces for the Rational Design of Next-Generation Antibody Microarrays

NASA Astrophysics Data System (ADS)

Bush, Derek B.

Antibody microarrays constitute a next-generation sensing platform that has the potential to revolutionize the way that molecular detection is conducted in many scientific fields. Unfortunately, current technologies have not found mainstream use because of reliability problems that undermine trust in their results. Although several factors are involved, it is believed that undesirable protein interactions with the array surface are a fundamental source of problems where little detail about the molecular-level biophysics are known. A better understanding of antibody stability and antibody-antigen binding on the array surface is needed to improve microarray technology. Despite the availability of many laboratory methods for studying protein stability and binding, these methods either do not work when the protein is attached to a surface or they do not provide the atomistic structural information that is needed to better understand protein behavior on the surface. As a result, molecular simulation has emerged as the primary method for studying proteins on surfaces because it can provide metrics and views of atomistic structures and molecular motion. Using an advanced, coarse-grain, protein-surface model this study investigated how antibodies react to and function on different types of surfaces. Three topics were addressed: (1) the stability of individual antibodies on surfaces, (2) antibody binding to small antigens while on a surface, and (3) antibody binding to large antigens while on a surface. The results indicate that immobilizing antibodies or antibody fragments in an upright orientation on a hydrophilic surface can provide the molecules with thermal stability similar to their native aqueous stability, enhance antigen binding strength, and minimize the entropic cost of binding. Furthermore, the results indicate that it is more difficult for large antigens to approach the surface than small antigens, that multiple binding sites can aid antigen binding, and that antigen flexiblity simultaneously helps and hinders the binding process as it approaches the surface. The results provide hope that next-generation microarrays and other devices decorated with proteins can be improved through rational design.

Spatially controlled coating of continuous liquid Interface production microneedles for transdermal protein delivery.

PubMed

Caudill, Cassie L; Perry, Jillian L; Tian, Shaomin; Luft, J Christopher; DeSimone, Joseph M

2018-06-09

Microneedle patches, arrays of micron-scale projections that penetrate skin in a minimally invasive manner, are a promising tool for transdermally delivering therapeutic proteins. However, current microneedle fabrication techniques are limited in their ability to fabricate microneedles rapidly and with a high degree of control over microneedle design parameters. We have previously demonstrated the ability to fabricate microneedle patches with a range of compositions and geometries using the novel additive manufacturing technique Continuous Liquid Interface Production (CLIP). Here, we establish a method for dip coating CLIP microneedles with protein cargo in a spatially controlled manner. Microneedle coating mask devices were fabricated with CLIP and utilized to coat polyethylene glycol-based CLIP microneedles with model proteins bovine serum albumin, ovalbumin, and lysozyme. The design of the coating mask device was used to control spatial deposition and loading of coated protein cargo on the microneedles. CLIP microneedles rapidly released coated protein cargo both in solution and upon insertion into porcine skin. The model enzyme lysozyme was shown to retain its activity throughout the CLIP microneedle coating process, and permeation of bovine serum albumin across full thickness porcine skin was observed after application with coated CLIP microneedles. Protein-coated CLIP microneedles were applied to live mice and showed sustained retention of protein cargo in the skin over 72 h. These results demonstrate the utility of a versatile coating platform for preparation of precisely coated microneedles for transdermal therapeutic delivery. Copyright © 2018. Published by Elsevier B.V.

Nullspace MUSIC and Improved Radio Frequency Emitter Geolocation from a Mobile Antenna Array

NASA Astrophysics Data System (ADS)

Kintz, Andrew L.

This work advances state-of-the-art Radio Frequency (RF) emitter geolocation from an airborne or spaceborne antenna array. With an antenna array, geolocation is based on Direction of Arrival (DOA) estimation algorithms such as MUSIC. The MUSIC algorithm applies to arbitrary arrays of polarization sensitive antennas and yields high resolution. However, MUSIC fails to obtain its theoretical resolution for simultaneous, closely spaced, co-frequency signals. We propose the novel Nullspace MUSIC algorithm, which outperforms MUSIC and its existing modifications while maintaining MUSIC(apostrophe)s fundamental orthogonality test. Nullspace MUSIC applies a divide-and-conquer approach and estimates a single DOA at a time. Additionally, an antenna array on an aircraft cannot be perfectly calibrated. RF waves are blocked, reflected, and scattered in a time-varying fashion by the platform around the antenna array. Consequently, full-wave electromagnetics simulations or demanding measurements of the entire platform cannot eliminate the mismatch between the true, in-situ antenna patterns and the antenna patterns that are available for DOA estimation (the antenna array manifold). Platform-induced manifold mismatch severely degrades MUSIC(apostrophe)s resolution and accuracy. We show that Nullspace MUSIC improves DOA accuracy for well separated signals that are incident on an airborne antenna array. Conventionally, geolocation from a mobile platform draws Lines of Bearing (LOB) from the antenna array along the DOAs to find the locations where the DOAs intersect with the ground. However, averaging the LOBs in the global coordinate system yields large errors due to geometric dilution of precision. Since averaging positions fails, a single emitter is typically located by finding the position on the ground that yields the Minimum Apparent Angular Error (MAAE) for the DOA estimates over a flight. We extend the MAAE approach to cluster LOBs from multiple emitters. MAAE clustering geolocates multiple simultaneous and co-frequency emitters in spite of highly erratic DOA estimates. We also mitigate manifold mismatch by applying the Direct Mapping Method (DMM). DMM averages DOA spectra on the earth(apostrophe)s surface and estimates the emitter locations directly from the composite spectrum. In the example results presented, our goal is to geolocate four diversely polarized emitters with a seven-element antenna array. This is too challenging for MAAE and DMM. We fuse Nullspace MUSIC and DMM into the novel Nullspace DMM algorithm and demonstrate that Nullspace DMM locates all emitters. Finally, we apply the proposed geolocation algorithms to real-world experimental data. A six-element antenna array and Data Collection System (DCS) were installed on a small aircraft. The DCS recorded signals from four live transmitters during a three-hour flight over Columbus, Ohio. The four emitters were geolocated from various segments of the flight. As expected, individual DOA estimates were erratic and widespread due to the airplane(apostrophe)s perturbations of the measured array manifold. MAAE and DMM locate at most three of the four emitters. On the other hand, Nullspace DMM yields unambiguous estimates for every emitter in every flight segment. The successful experimental trials show that Nullspace DMM could significantly enhance airborne emitter geolocation in missions such as RF spectrum enforcement, locating unknown transmitters for defense, and search and rescue operations.

The IMS Software Integration Platform

DTIC Science & Technology

1993-04-12

products to incorporate all data shared by the IMS applications. Some entities (time-series, images, a algorithm -specific parameters) must be managed...dbwhoanii, dbcancel Transaction Management: dbcommit, dbrollback Key Counter Assignment: dbgetcounter String Handling: cstr ~to~pad, pad-to- cstr Error...increment *value; String Maniputation: int cstr topad (array, string, arraylength) char *array, *string; int arrayjlength; int pad tocstr (string

Diversity, genetic mapping, and signatures of domestication in the carrot (Daucus carota L.) genome, as revealed by Diversity Arrays Technology (DArT) markers

USDA-ARS?s Scientific Manuscript database

Carrot is one of the most economically important vegetables worldwide, however, genetic and genomic resources supporting carrot breeding remain limited. We developed a Diversity Arrays Technology (DArT) platform for wild and cultivated carrot and used it to investigate genetic diversity and to devel...

Superconducting Quantum Interference Device Array Based High Frequency Direction Finding on an Airborne Platform

DTIC Science & Technology

is performed using the MUSIC algorithm on the signals received on the non-uniform phased array, and the ESPRIT algorithm is used on the signals...received on the non-colocated vector sensor. The simulation results show that the MUSIC algorithm using 2D Bi-SQUIDs is able to differentiate two signals

Integrated protein analysis platform based on column switch recycling size exclusion chromatography, microenzymatic reactor and microRPLC-ESI-MS/MS.

PubMed

Yuan, Huiming; Zhou, Yuan; Zhang, Lihua; Liang, Zhen; Zhang, Yukui

2009-10-30

An integrated platform with the combination of proteins and peptides separation was established via the unit of on-line proteins digestion, by which proteins were in sequence separated by column switch recycling size exclusion chromatography (csrSEC), on-line digested by an immobilized trypsin microreactor, trapped and desalted by two parallel C8 precolumns, separated by microRPLC with the linear gradient of organic modifier concentration, and identified by ESI-MS/MS. A 6-protein mixture, with Mr ranging from 10 kDa to 80 kDa, was used to evaluate the performance of the integrated platform, and all proteins were identified with sequence coverage over 5.67%. Our experimental results demonstrate that such an integrated platform is of advantages such as good time compatibility, high peak capacity, and facile automation, which might be a promising approach for proteome study.

Growth of Vertically Aligned ZnO Nanowire Arrays Using Bilayered Metal Catalysts

DTIC Science & Technology

2012-01-01

12] J. P. Liu, C. X. Guo, C. M. Li et al., “Carbon-decorated ZnO nanowire array: a novel platform for direct electrochemistry of enzymes and...cited. Vertically aligned, high-density ZnO nanowires (NWs) were grown for the first time on c-plane sapphire using binary alloys of Ni/Au or Cu/Au as...deleterious to the ZnO NW array growth. Significant improvement of the Au adhesion on the substrate was noted, opening the potential for direct

Analog 65/130 nm CMOS 5 GHz Sub-Arrays with ROACH-2 FPGA Beamformers for Hybrid Aperture-Array Receivers

DTIC Science & Technology

2017-03-20

sub-array, which is based on all-pass filters (APFs) is realized using 130 nm CMOS technology. Approximate- discrete Fourier transform (a-DFT...fixed beams are directed at known directions [9]. The proposed approximate- discrete Fourier transform (a-DFT) based multi-beamformer [9] yields L...to digital conversion daughter board. occurs in the discrete time domain (in ROACH-2 FPGA platform) following signal digitization (see Figs. 1(d) and

Harnessing Gene Conversion in Chicken B Cells to Create a Human Antibody Sequence Repertoire

PubMed Central

Schusser, Benjamin; Yi, Henry; Collarini, Ellen J.; Izquierdo, Shelley Mettler; Harriman, William D.; Etches, Robert J.; Leighton, Philip A.

2013-01-01

Transgenic chickens expressing human sequence antibodies would be a powerful tool to access human targets and epitopes that have been intractable in mammalian hosts because of tolerance to conserved proteins. To foster the development of the chicken platform, it is beneficial to validate transgene constructs using a rapid, cell culture-based method prior to generating fully transgenic birds. We describe a method for the expression of human immunoglobulin variable regions in the chicken DT40 B cell line and the further diversification of these genes by gene conversion. Chicken VL and VH loci were knocked out in DT40 cells and replaced with human VK and VH genes. To achieve gene conversion of human genes in chicken B cells, synthetic human pseudogene arrays were inserted upstream of the functional human VK and VH regions. Proper expression of chimeric IgM comprised of human variable regions and chicken constant regions is shown. Most importantly, sequencing of DT40 genetic variants confirmed that the human pseudogene arrays contributed to the generation of diversity through gene conversion at both the Igl and Igh loci. These data show that engineered pseudogene arrays produce a diverse pool of human antibody sequences in chicken B cells, and suggest that these constructs will express a functional repertoire of chimeric antibodies in transgenic chickens. PMID:24278246

HaloTag Technology: A Versatile Platform for Biomedical Applications

PubMed Central

2015-01-01

Exploration of protein function and interaction is critical for discovering links among genomics, proteomics, and disease state; yet, the immense complexity of proteomics found in biological systems currently limits our investigational capacity. Although affinity and autofluorescent tags are widely employed for protein analysis, these methods have been met with limited success because they lack specificity and require multiple fusion tags and genetic constructs. As an alternative approach, the innovative HaloTag protein fusion platform allows protein function and interaction to be comprehensively analyzed using a single genetic construct with multiple capabilities. This is accomplished using a simplified process, in which a variable HaloTag ligand binds rapidly to the HaloTag protein (usually linked to the protein of interest) with high affinity and specificity. In this review, we examine all current applications of the HaloTag technology platform for biomedical applications, such as the study of protein isolation and purification, protein function, protein–protein and protein–DNA interactions, biological assays, in vitro cellular imaging, and in vivo molecular imaging. In addition, novel uses of the HaloTag platform are briefly discussed along with potential future applications. PMID:25974629

Micro-algae come of age as a platform for recombinant protein production

PubMed Central

Specht, Elizabeth; Miyake-Stoner, Shigeki

2010-01-01

A complete set of genetic tools is still being developed for the micro-alga Chlamydomonas reinhardtii. Yet even with this incomplete set, this photosynthetic single-celled plant has demonstrated significant promise as a platform for recombinant protein expression. In recent years, techniques have been developed that allow for robust expression of genes from both the nuclear and plastid genome. With these advances, many research groups have examined the pliability of this and other micro-algae as biological machines capable of producing recombinant peptides and proteins. This review describes recent successes in recombinant protein production in Chlamydomonas, including production of complex mammalian therapeutic proteins and monoclonal antibodies at levels sufficient for production at economic parity with existing production platforms. These advances have also shed light on the details of algal protein production at the molecular level, and provide insight into the next steps for optimizing micro-algae as a useful platform for the production of therapeutic and industrially relevant recombinant proteins. PMID:20556634

Validation of Biomarker Proteins Using Reverse Capture Protein Microarrays.

PubMed

Jozwik, Catherine; Eidelman, Ofer; Starr, Joshua; Pollard, Harvey B; Srivastava, Meera

2017-01-01

Genomics has revolutionized large-scale and high-throughput sequencing and has led to the discovery of thousands of new proteins. Protein chip technology is emerging as a miniaturized and highly parallel platform that is suited to rapid, simultaneous screening of large numbers of proteins and the analysis of various protein-binding activities, enzyme substrate relationships, and posttranslational modifications. Specifically, reverse capture protein microarrays provide the most appropriate platform for identifying low-abundance, disease-specific biomarker proteins in a sea of high-abundance proteins from biological fluids such as blood, serum, plasma, saliva, urine, and cerebrospinal fluid as well as tissues and cells obtained by biopsy. Samples from hundreds of patients can be spotted in serial dilutions on many replicate glass slides. Each slide can then be probed with one specific antibody to the biomarker of interest. That antibody's titer can then be determined quantitatively for each patient, allowing for the statistical assessment and validation of the diagnostic or prognostic utility of that particular antigen. As the technology matures and the availability of validated, platform-compatible antibodies increases, the platform will move further into the desirable realm of discovery science for detecting and quantitating low-abundance signaling proteins. In this chapter, we describe methods for the successful application of the reverse capture protein microarray platform for which we have made substantial contributions to the development and application of this method, particularly in the use of body fluids other than serum/plasma.

Stiffened lipid platforms at molecular force foci.

PubMed

Anishkin, Andriy; Kung, Ching

2013-03-26

How mechanical forces are sensed remains largely mysterious. The forces that gate prokaryotic and several eukaryotic channels were found to come from the lipid membrane. Our survey of animal cells found that membrane force foci all have cholesterol-gathering proteins and are reinforced with cholesterol. This result is evident in overt force sensors at the tips of stereocilia for vertebrate hearing and the touch receptor of Caenorhabditis elegans and mammalian neurons. For less specialized cells, cadherins sustain the force between neighboring cells and integrins between cells and matrix. These tension bearers also pass through and bind to a cholesterol-enriched platform before anchoring to cytoskeleton through other proteins. Cholesterol, in alliance with sphingomyelin and specialized proteins, enforces a more ordered structure in the bilayer. Such a stiffened platform can suppress mechanical noise, redirect, rescale, and confine force. We speculate that such platforms may be dynamic. The applied force may allow disordered-phase lipids to enter the platform-staging channel opening in the thinner mobile neighborhood. The platform may also contain specialized protein/lipid subdomains enclosing mechanosensitive channels to open with localized tension. Such a dynamic stage can mechanically operate structurally disparate channels or enzymes without having to tie them directly to cadherin, integrin, or other protein tethers.

Towards Clinical Molecular Diagnosis of Inherited Cardiac Conditions: A Comparison of Bench-Top Genome DNA Sequencers

PubMed Central

Wilkinson, Samuel L.; John, Shibu; Walsh, Roddy; Novotny, Tomas; Valaskova, Iveta; Gupta, Manu; Game, Laurence; Barton, Paul J R.; Cook, Stuart A.; Ware, James S.

2013-01-01

Background Molecular genetic testing is recommended for diagnosis of inherited cardiac disease, to guide prognosis and treatment, but access is often limited by cost and availability. Recently introduced high-throughput bench-top DNA sequencing platforms have the potential to overcome these limitations. Methodology/Principal Findings We evaluated two next-generation sequencing (NGS) platforms for molecular diagnostics. The protein-coding regions of six genes associated with inherited arrhythmia syndromes were amplified from 15 human samples using parallelised multiplex PCR (Access Array, Fluidigm), and sequenced on the MiSeq (Illumina) and Ion Torrent PGM (Life Technologies). Overall, 97.9% of the target was sequenced adequately for variant calling on the MiSeq, and 96.8% on the Ion Torrent PGM. Regions missed tended to be of high GC-content, and most were problematic for both platforms. Variant calling was assessed using 107 variants detected using Sanger sequencing: within adequately sequenced regions, variant calling on both platforms was highly accurate (Sensitivity: MiSeq 100%, PGM 99.1%. Positive predictive value: MiSeq 95.9%, PGM 95.5%). At the time of the study the Ion Torrent PGM had a lower capital cost and individual runs were cheaper and faster. The MiSeq had a higher capacity (requiring fewer runs), with reduced hands-on time and simpler laboratory workflows. Both provide significant cost and time savings over conventional methods, even allowing for adjunct Sanger sequencing to validate findings and sequence exons missed by NGS. Conclusions/Significance MiSeq and Ion Torrent PGM both provide accurate variant detection as part of a PCR-based molecular diagnostic workflow, and provide alternative platforms for molecular diagnosis of inherited cardiac conditions. Though there were performance differences at this throughput, platforms differed primarily in terms of cost, scalability, protocol stability and ease of use. Compared with current molecular genetic diagnostic tests for inherited cardiac arrhythmias, these NGS approaches are faster, less expensive, and yet more comprehensive. PMID:23861798

Open Source High Content Analysis Utilizing Automated Fluorescence Lifetime Imaging Microscopy.

PubMed

Görlitz, Frederik; Kelly, Douglas J; Warren, Sean C; Alibhai, Dominic; West, Lucien; Kumar, Sunil; Alexandrov, Yuriy; Munro, Ian; Garcia, Edwin; McGinty, James; Talbot, Clifford; Serwa, Remigiusz A; Thinon, Emmanuelle; da Paola, Vincenzo; Murray, Edward J; Stuhmeier, Frank; Neil, Mark A A; Tate, Edward W; Dunsby, Christopher; French, Paul M W

2017-01-18

We present an open source high content analysis instrument utilizing automated fluorescence lifetime imaging (FLIM) for assaying protein interactions using Förster resonance energy transfer (FRET) based readouts of fixed or live cells in multiwell plates. This provides a means to screen for cell signaling processes read out using intramolecular FRET biosensors or intermolecular FRET of protein interactions such as oligomerization or heterodimerization, which can be used to identify binding partners. We describe here the functionality of this automated multiwell plate FLIM instrumentation and present exemplar data from our studies of HIV Gag protein oligomerization and a time course of a FRET biosensor in live cells. A detailed description of the practical implementation is then provided with reference to a list of hardware components and a description of the open source data acquisition software written in µManager. The application of FLIMfit, an open source MATLAB-based client for the OMERO platform, to analyze arrays of multiwell plate FLIM data is also presented. The protocols for imaging fixed and live cells are outlined and a demonstration of an automated multiwell plate FLIM experiment using cells expressing fluorescent protein-based FRET constructs is presented. This is complemented by a walk-through of the data analysis for this specific FLIM FRET data set.

Integration of cardiac proteome biology and medicine by a specialized knowledgebase.

PubMed

Zong, Nobel C; Li, Haomin; Li, Hua; Lam, Maggie P Y; Jimenez, Rafael C; Kim, Christina S; Deng, Ning; Kim, Allen K; Choi, Jeong Ho; Zelaya, Ivette; Liem, David; Meyer, David; Odeberg, Jacob; Fang, Caiyun; Lu, Hao-Jie; Xu, Tao; Weiss, James; Duan, Huilong; Uhlen, Mathias; Yates, John R; Apweiler, Rolf; Ge, Junbo; Hermjakob, Henning; Ping, Peipei

2013-10-12

Omics sciences enable a systems-level perspective in characterizing cardiovascular biology. Integration of diverse proteomics data via a computational strategy will catalyze the assembly of contextualized knowledge, foster discoveries through multidisciplinary investigations, and minimize unnecessary redundancy in research efforts. The goal of this project is to develop a consolidated cardiac proteome knowledgebase with novel bioinformatics pipeline and Web portals, thereby serving as a new resource to advance cardiovascular biology and medicine. We created Cardiac Organellar Protein Atlas Knowledgebase (COPaKB; www.HeartProteome.org), a centralized platform of high-quality cardiac proteomic data, bioinformatics tools, and relevant cardiovascular phenotypes. Currently, COPaKB features 8 organellar modules, comprising 4203 LC-MS/MS experiments from human, mouse, drosophila, and Caenorhabditis elegans, as well as expression images of 10,924 proteins in human myocardium. In addition, the Java-coded bioinformatics tools provided by COPaKB enable cardiovascular investigators in all disciplines to retrieve and analyze pertinent organellar protein properties of interest. COPaKB provides an innovative and interactive resource that connects research interests with the new biological discoveries in protein sciences. With an array of intuitive tools in this unified Web server, nonproteomics investigators can conveniently collaborate with proteomics specialists to dissect the molecular signatures of cardiovascular phenotypes.

Open Source High Content Analysis Utilizing Automated Fluorescence Lifetime Imaging Microscopy

PubMed Central

Warren, Sean C.; Alibhai, Dominic; West, Lucien; Kumar, Sunil; Alexandrov, Yuriy; Munro, Ian; Garcia, Edwin; McGinty, James; Talbot, Clifford; Serwa, Remigiusz A.; Thinon, Emmanuelle; da Paola, Vincenzo; Murray, Edward J.; Stuhmeier, Frank; Neil, Mark A. A.; Tate, Edward W.; Dunsby, Christopher; French, Paul M. W.

2017-01-01

We present an open source high content analysis instrument utilizing automated fluorescence lifetime imaging (FLIM) for assaying protein interactions using Förster resonance energy transfer (FRET) based readouts of fixed or live cells in multiwell plates. This provides a means to screen for cell signaling processes read out using intramolecular FRET biosensors or intermolecular FRET of protein interactions such as oligomerization or heterodimerization, which can be used to identify binding partners. We describe here the functionality of this automated multiwell plate FLIM instrumentation and present exemplar data from our studies of HIV Gag protein oligomerization and a time course of a FRET biosensor in live cells. A detailed description of the practical implementation is then provided with reference to a list of hardware components and a description of the open source data acquisition software written in µManager. The application of FLIMfit, an open source MATLAB-based client for the OMERO platform, to analyze arrays of multiwell plate FLIM data is also presented. The protocols for imaging fixed and live cells are outlined and a demonstration of an automated multiwell plate FLIM experiment using cells expressing fluorescent protein-based FRET constructs is presented. This is complemented by a walk-through of the data analysis for this specific FLIM FRET data set. PMID:28190060

Single step generation of protein arrays from DNA by cell-free expression and in situ immobilisation (PISA method).

PubMed

He, M; Taussig, M J

2001-08-01

We describe a format for production of protein arrays termed 'protein in situ array' (PISA). A PISA is rapidly generated in one step directly from PCR-generated DNA fragments by cell-free protein expression and in situ immobilisation at a surface. The template for expression is DNA encoding individual proteins or domains, which is produced by PCR using primers designed from information in DNA databases. Coupled transcription and translation is carried out on a surface to which the tagged protein adheres as soon as it is synthesised. Because proteins generated by cell-free synthesis are usually soluble and functional, this method can overcome problems of insolubility or degradation associated with bacterial expression of recombinant proteins. Moreover, the use of PCR-generated DNA enables rapid production of proteins or domains based on genome information alone and will be particularly useful where cloned material is not available. Here we show that human single-chain antibody fragments (three domain, V(H)/K form) and an enzyme (luciferase) can be functionally arrayed by the PISA method.

Peptide Array X-Linking (PAX): A New Peptide-Protein Identification Approach

PubMed Central

Okada, Hirokazu; Uezu, Akiyoshi; Soderblom, Erik J.; Moseley, M. Arthur; Gertler, Frank B.; Soderling, Scott H.

2012-01-01

Many protein interaction domains bind short peptides based on canonical sequence consensus motifs. Here we report the development of a peptide array-based proteomics tool to identify proteins directly interacting with ligand peptides from cell lysates. Array-formatted bait peptides containing an amino acid-derived cross-linker are photo-induced to crosslink with interacting proteins from lysates of interest. Indirect associations are removed by high stringency washes under denaturing conditions. Covalently trapped proteins are subsequently identified by LC-MS/MS and screened by cluster analysis and domain scanning. We apply this methodology to peptides with different proline-containing consensus sequences and show successful identifications from brain lysates of known and novel proteins containing polyproline motif-binding domains such as EH, EVH1, SH3, WW domains. These results suggest the capacity of arrayed peptide ligands to capture and subsequently identify proteins by mass spectrometry is relatively broad and robust. Additionally, the approach is rapid and applicable to cell or tissue fractions from any source, making the approach a flexible tool for initial protein-protein interaction discovery. PMID:22606326

A method for the isolation and characterization of functional murine monoclonal antibodies by single B cell cloning.

PubMed

Carbonetti, Sara; Oliver, Brian G; Vigdorovich, Vladimir; Dambrauskas, Nicholas; Sack, Brandon; Bergl, Emilee; Kappe, Stefan H I; Sather, D Noah

2017-09-01

Monoclonal antibody technologies have enabled dramatic advances in immunology, the study of infectious disease, and modern medicine over the past 40years. However, many monoclonal antibody discovery procedures are labor- and time-intensive, low efficiency, and expensive. Here we describe an optimized mAb discovery platform for the rapid and efficient isolation, cloning and characterization of monoclonal antibodies in murine systems. In this platform, antigen-binding splenic B cells from immunized mice are isolated by FACS and cocultured with CD40L positive cells to induce proliferation and mAb production. After 12days of coculture, cell culture supernatants are screened for antigen, and IgG positivity and RNA is isolated for reverse-transcription. Positive-well cDNA is then amplified by PCR and the resulting amplicons can be cloned into ligation-independent expression vectors, which are then used directly to transfect HEK293 cells for recombinant antibody production. After 4days of growth, conditioned medium can be screened using biolayer interferometry for antigen binding and affinity measurements. Using this method, we were able to isolate six unique, functional monoclonal antibodies against an antigen of the human malaria parasite Plasmodium falciparum. Importantly, this method incorporates several important advances that circumvent the need for single-cell PCR, restriction cloning, and large scale protein production, and can be applied to a wide array of protein antigens. Copyright © 2017 Elsevier B.V. All rights reserved.

Biomass-bioenergy crops in the United States: a changing paradigm

Treesearch

Jane M-F Johnson; Mark D. Coleman; Russ Gesch; Adbullah Jaradat; Rob Mitchell; Don Reicosky; W.W. Wilhelm

2007-01-01

The world energy paradigm is changing from one based on petroleum to one based on a mixture of energy platforms. This change is precipitated by a finite petroleum supply, an expanding global demand, and political instability in areas with major petroleum reserves. The mixed energy platform will include an array of renewable energy sources. The agricultural and forestry...

Rad-Hard Structured ASIC Body of Knowledge

NASA Technical Reports Server (NTRS)

Heidecker, Jason

2013-01-01

Structured Application-Specific Integrated Circuit (ASIC) technology is a platform between traditional ASICs and Field-Programmable Gate Arrays (FPGA). The motivation behind structured ASICs is to combine the low nonrecurring engineering costs (NRE) costs of FPGAs with the high performance of ASICs. This report provides an overview of the structured ASIC platforms that are radiation-hardened and intended for space application

Supercontinuum white light lasers for flow cytometry

PubMed Central

Telford, William G.; Subach, Fedor V.; Verkhusha, Vladislav V.

2009-01-01

Excitation of fluorescent probes for flow cytometry has traditionally been limited to a few discrete laser lines, an inherent limitation in our ability to excite the vast array of fluorescent probes available for cellular analysis. In this report, we have used a supercontinuum (SC) white light laser as an excitation source for flow cytometry. By selectively filtering the wavelength of interest, almost any laser wavelength in the visible spectrum can be separated and used for flow cytometric analysis. The white light lasers used in this study were integrated into a commercial flow cytometry platform, and a series of high-transmission bandpass filters used to select wavelength ranges from the blue (~480 nm) to the long red (>700 nm). Cells labeled with a variety of fluorescent probes or expressing fluorescent proteins were then analyzed, in comparison with traditional lasers emitting at wavelengths similar to the filtered SC source. Based on a standard sensitivity metric, the white light laser bandwidths produced similar excitation levels to traditional lasers for a wide variety of fluorescent probes and expressible proteins. Sensitivity assessment using fluorescent bead arrays confirmed that the SC laser and traditional sources resulted in similar levels of detection sensitivity. Supercontinuum white light laser sources therefore have the potential to remove a significant barrier in flow cytometric analysis, namely the limitation of excitation wavelengths. Almost any visible wavelength range can be made available for excitation, allowing access to virtually any fluorescent probe, and permitting “fine-tuning” of excitation wavelength to particular probes. PMID:19072836

Detection of Foodborne Pathogenic Bacteria using Bacteriophage Tail Spike Proteins

NASA Astrophysics Data System (ADS)

Poshtiban, Somayyeh

Foodborne infections are worldwide health problem with tremendous social and financial impacts. Efforts are focused on developing accurate and reliable technologies for detection of food contaminations in early stages preferably on-site. This thesis focuses on interfacing engineering and biology by combining phage receptor binding proteins (RBPs) with engineered platforms including microresonator-based biosensors, magnetic particles and polymerase chain reaction (PCR) to develop bacterial detection sensors. We used phage RBPs as target specific bioreceptors to develop an enhanced microresonator array for bacterial detection. These resonator beams are optimized to feature a high natural frequency while offer large surface area for capture of bacteria. Theoretical analysis indicates a high mass sensitivity with a threshold for the detection of a single bacterial cell. We used phage RBPs as target specific bioreceptors, and successfully demonstrated the application of these phage RBB-immobilized arrays for specific detection of C. jejuni cells. We also developed a RBP-derivatized magnetic pre-enrichment method as an upstream sample preparation method to improve sensitivity and specificity of PCR for detection of bacterial cells in various food samples. The combination of RBP-based magnetic separation and real-time PCR allowed the detection of small number of bacteria in artificially contaminated food samples without any need for time consuming pre-enrichment step through culturing. We also looked into integration of the RBP-based magnetic separation with PCR onto a single microfluidic lab-on-a-chip to reduce the overall turnaround time.

Immunoproteomic Profiling of Antiviral Antibodies in New-Onset Type 1 Diabetes Using Protein Arrays

PubMed Central

Bian, Xiaofang; Wallstrom, Garrick; Davis, Amy; Wang, Jie; Park, Jin; Throop, Andrea; Steel, Jason; Yu, Xiaobo; Wasserfall, Clive; Schatz, Desmond; Atkinson, Mark

2016-01-01

The rapid rise in the incidence of type 1 diabetes (T1D) suggests the involvement of environmental factors including viral infections. We evaluated the association between viral infections and T1D by profiling antiviral antibodies using a high-throughput immunoproteomics approach in patients with new-onset T1D. We constructed a viral protein array comprising the complete proteomes of seven viruses associated with T1D and open reading frames from other common viruses. Antibody responses to 646 viral antigens were assessed in 42 patients with T1D and 42 age- and sex-matched healthy control subjects (mean age 12.7 years, 50% males). Prevalence of antiviral antibodies agreed with known infection rates for the corresponding virus based on epidemiological studies. Antibody responses to Epstein-Barr virus (EBV) were significantly higher in case than control subjects (odds ratio 6.6; 95% CI 2.0–25.7), whereas the other viruses showed no differences. The EBV and T1D association was significant in both sex and age subgroups (≤12 and >12 years), and there was a trend toward early EBV infections among the case subjects. These results suggest a potential role for EBV in T1D development. We believe our innovative immunoproteomics platform is useful for understanding the role of viral infections in T1D and other disorders where associations between viral infection and disease are unclear. PMID:26450993

Scalable, Lightweight, Integrated and Quick-to-Assemble (SLIQ) Hyperdrives for Functional Circuit Dissection.

PubMed

Liang, Li; Oline, Stefan N; Kirk, Justin C; Schmitt, Lukas Ian; Komorowski, Robert W; Remondes, Miguel; Halassa, Michael M

2017-01-01

Independently adjustable multielectrode arrays are routinely used to interrogate neuronal circuit function, enabling chronic in vivo monitoring of neuronal ensembles in freely behaving animals at a single-cell, single spike resolution. Despite the importance of this approach, its widespread use is limited by highly specialized design and fabrication methods. To address this, we have developed a Scalable, Lightweight, Integrated and Quick-to-assemble multielectrode array platform. This platform additionally integrates optical fibers with independently adjustable electrodes to allow simultaneous single unit recordings and circuit-specific optogenetic targeting and/or manipulation. In current designs, the fully assembled platforms are scalable from 2 to 32 microdrives, and yet range 1-3 g, light enough for small animals. Here, we describe the design process starting from intent in computer-aided design, parameter testing through finite element analysis and experimental means, and implementation of various applications across mice and rats. Combined, our methods may expand the utility of multielectrode recordings and their continued integration with other tools enabling functional dissection of intact neural circuits.

Three-dimensional spheroid culture targeting versatile tissue bioassays using a PDMS-based hanging drop array.

PubMed

Kuo, Ching-Te; Wang, Jong-Yueh; Lin, Yu-Fen; Wo, Andrew M; Chen, Benjamin P C; Lee, Hsinyu

2017-06-29

Biomaterial-based tissue culture platforms have emerged as useful tools to mimic in vivo physiological microenvironments in experimental cell biology and clinical studies. We describe herein a three-dimensional (3D) tissue culture platform using a polydimethylsiloxane (PDMS)-based hanging drop array (PDMS-HDA) methodology. Multicellular spheroids can be achieved within 24 h and further boosted by incorporating collagen fibrils in PDMS-HDA. In addition, the spheroids generated from different human tumor cells exhibited distinct sensitivities toward drug chemotherapeutic agents and radiation as compared with two-dimensional (2D) cultures that often lack in vivo-like biological insights. We also demonstrated that multicellular spheroids may enable key hallmarks of tissue-based bioassays, including drug screening, tumor dissemination, cell co-culture, and tumor invasion. Taken together, these results offer new opportunities not only to achieve the active control of 3D multicellular spheroids on demand, but also to establish a rapid and cost-effective platform to study anti-cancer therapeutics and tumor microenvironments.

Micropillar arrays as a high-throughput screening platform for therapeutics in multiple sclerosis.

PubMed

Mei, Feng; Fancy, Stephen P J; Shen, Yun-An A; Niu, Jianqin; Zhao, Chao; Presley, Bryan; Miao, Edna; Lee, Seonok; Mayoral, Sonia R; Redmond, Stephanie A; Etxeberria, Ainhoa; Xiao, Lan; Franklin, Robin J M; Green, Ari; Hauser, Stephen L; Chan, Jonah R

2014-08-01

Functional screening for compounds that promote remyelination represents a major hurdle in the development of rational therapeutics for multiple sclerosis. Screening for remyelination is problematic, as myelination requires the presence of axons. Standard methods do not resolve cell-autonomous effects and are not suited for high-throughput formats. Here we describe a binary indicant for myelination using micropillar arrays (BIMA). Engineered with conical dimensions, micropillars permit resolution of the extent and length of membrane wrapping from a single two-dimensional image. Confocal imaging acquired from the base to the tip of the pillars allows for detection of concentric wrapping observed as 'rings' of myelin. The platform is formatted in 96-well plates, amenable to semiautomated random acquisition and automated detection and quantification. Upon screening 1,000 bioactive molecules, we identified a cluster of antimuscarinic compounds that enhance oligodendrocyte differentiation and remyelination. Our findings demonstrate a new high-throughput screening platform for potential regenerative therapeutics in multiple sclerosis.

Miniaturizable Ion-Selective Arrays Based on Highly Stable Polymer Membranes for Biomedical Applications

PubMed Central

Mir, Mònica; Lugo, Roberto; Tahirbegi, Islam Bogachan; Samitier, Josep

2014-01-01

Poly(vinylchloride) (PVC) is the most common polymer matrix used in the fabrication of ion-selective electrodes (ISEs). However, the surfaces of PVC-based sensors have been reported to show membrane instability. In an attempt to overcome this limitation, here we developed two alternative methods for the preparation of highly stable and robust ion-selective sensors. These platforms are based on the selective electropolymerization of poly(3,4-ethylenedioxythiophene) (PEDOT), where the sulfur atoms contained in the polymer covalently interact with the gold electrode, also permitting controlled selective attachment on a miniaturized electrode in an array format. This platform sensor was improved with the crosslinking of the membrane compounds with poly(ethyleneglycol) diglycidyl ether (PEG), thus also increasing the biocompatibility of the sensor. The resulting ISE membranes showed faster signal stabilization of the sensor response compared with that of the PVC matrix and also better reproducibility and stability, thus making these platforms highly suitable candidates for the manufacture of robust implantable sensors. PMID:24999717

CNV-WebStore: online CNV analysis, storage and interpretation.

PubMed

Vandeweyer, Geert; Reyniers, Edwin; Wuyts, Wim; Rooms, Liesbeth; Kooy, R Frank

2011-01-05

Microarray technology allows the analysis of genomic aberrations at an ever increasing resolution, making functional interpretation of these vast amounts of data the main bottleneck in routine implementation of high resolution array platforms, and emphasising the need for a centralised and easy to use CNV data management and interpretation system. We present CNV-WebStore, an online platform to streamline the processing and downstream interpretation of microarray data in a clinical context, tailored towards but not limited to the Illumina BeadArray platform. Provided analysis tools include CNV analsyis, parent of origin and uniparental disomy detection. Interpretation tools include data visualisation, gene prioritisation, automated PubMed searching, linking data to several genome browsers and annotation of CNVs based on several public databases. Finally a module is provided for uniform reporting of results. CNV-WebStore is able to present copy number data in an intuitive way to both lab technicians and clinicians, making it a useful tool in daily clinical practice.

Non-invasive, transdermal, path-selective and specific glucose monitoring via a graphene-based platform

NASA Astrophysics Data System (ADS)

Lipani, Luca; Dupont, Bertrand G. R.; Doungmene, Floriant; Marken, Frank; Tyrrell, Rex M.; Guy, Richard H.; Ilie, Adelina

2018-06-01

Currently, there is no available needle-free approach for diabetics to monitor glucose levels in the interstitial fluid. Here, we report a path-selective, non-invasive, transdermal glucose monitoring system based on a miniaturized pixel array platform (realized either by graphene-based thin-film technology, or screen-printing). The system samples glucose from the interstitial fluid via electroosmotic extraction through individual, privileged, follicular pathways in the skin, accessible via the pixels of the array. A proof of principle using mammalian skin ex vivo is demonstrated for specific and `quantized' glucose extraction/detection via follicular pathways, and across the hypo- to hyper-glycaemic range in humans. Furthermore, the quantification of follicular and non-follicular glucose extraction fluxes is clearly shown. In vivo continuous monitoring of interstitial fluid-borne glucose with the pixel array was able to track blood sugar in healthy human subjects. This approach paves the way to clinically relevant glucose detection in diabetics without the need for invasive, finger-stick blood sampling.

Toward Intelligent Synthetic Neural Circuits: Directing and Accelerating Neuron Cell Growth by Self-Rolled-Up Silicon Nitride Microtube Array

PubMed Central

2015-01-01

In neural interface platforms, cultures are often carried out on a flat, open, rigid, and opaque substrate, posing challenges to reflecting the native microenvironment of the brain and precise engagement with neurons. Here we present a neuron cell culturing platform that consists of arrays of ordered microtubes (2.7–4.4 μm in diameter), formed by strain-induced self-rolled-up nanomembrane (s-RUM) technology using ultrathin (<40 nm) silicon nitride (SiNx) film on transparent substrates. These microtubes demonstrated robust physical confinement and unprecedented guidance effect toward outgrowth of primary cortical neurons, with a coaxially confined configuration resembling that of myelin sheaths. The dynamic neural growth inside the microtube, evaluated with continuous live-cell imaging, showed a marked increase (20×) of the growth rate inside the microtube compared to regions outside the microtubes. We attribute the dramatic accelerating effect and precise guiding of the microtube array to three-dimensional (3D) adhesion and electrostatic interaction with the SiNx microtubes, respectively. This work has clear implications toward building intelligent synthetic neural circuits by arranging the size, site, and patterns of the microtube array, for potential treatment of neurological disorders. PMID:25329686

The High-Throughput Protein Sample Production Platform of the Northeast Structural Genomics Consortium

PubMed Central

Xiao, Rong; Anderson, Stephen; Aramini, James; Belote, Rachel; Buchwald, William A.; Ciccosanti, Colleen; Conover, Ken; Everett, John K.; Hamilton, Keith; Huang, Yuanpeng Janet; Janjua, Haleema; Jiang, Mei; Kornhaber, Gregory J.; Lee, Dong Yup; Locke, Jessica Y.; Ma, Li-Chung; Maglaqui, Melissa; Mao, Lei; Mitra, Saheli; Patel, Dayaban; Rossi, Paolo; Sahdev, Seema; Sharma, Seema; Shastry, Ritu; Swapna, G.V.T.; Tong, Saichu N.; Wang, Dongyan; Wang, Huang; Zhao, Li; Montelione, Gaetano T.; Acton, Thomas B.

2014-01-01

We describe the core Protein Production Platform of the Northeast Structural Genomics Consortium (NESG) and outline the strategies used for producing high-quality protein samples. The platform is centered on the cloning, expression and purification of 6X-His-tagged proteins using T7-based Escherichia coli systems. The 6X-His tag allows for similar purification procedures for most targets and implementation of high-throughput (HTP) parallel methods. In most cases, the 6X-His-tagged proteins are sufficiently purified (> 97% homogeneity) using a HTP two-step purification protocol for most structural studies. Using this platform, the open reading frames of over 16,000 different targeted proteins (or domains) have been cloned as > 26,000 constructs. Over the past nine years, more than 16,000 of these expressed protein, and more than 4,400 proteins (or domains) have been purified to homogeneity in tens of milligram quantities (see Summary Statistics, http://nesg.org/statistics.html). Using these samples, the NESG has deposited more than 900 new protein structures to the Protein Data Bank (PDB). The methods described here are effective in producing eukaryotic and prokaryotic protein samples in E. coli. This paper summarizes some of the updates made to the protein production pipeline in the last five years, corresponding to phase 2 of the NIGMS Protein Structure Initiative (PSI-2) project. The NESG Protein Production Platform is suitable for implementation in a large individual laboratory or by a small group of collaborating investigators. These advanced automated and/or parallel cloning, expression, purification, and biophysical screening technologies are of broad value to the structural biology, functional proteomics, and structural genomics communities. PMID:20688167

Floating gate memory with charge storage dots array formed by Dps protein modified with site-specific binding peptides

NASA Astrophysics Data System (ADS)

Kamitake, Hiroki; Uenuma, Mutsunori; Okamoto, Naofumi; Horita, Masahiro; Ishikawa, Yasuaki; Yamashita, Ichro; Uraoka, Yukiharu

2015-05-01

We report a nanodot (ND) floating gate memory (NFGM) with a high-density ND array formed by a biological nano process. We utilized two kinds of cage-shaped proteins displaying SiO2 binding peptide (minTBP-1) on their outer surfaces: ferritin and Dps, which accommodate cobalt oxide NDs in their cavities. The diameters of the cobalt NDs were regulated by the cavity sizes of the proteins. Because minTBP-1 is strongly adsorbed on the SiO2 surface, high-density cobalt oxide ND arrays were obtained by a simple spin coating process. The densities of cobalt oxide ND arrays based on ferritin and Dps were 6.8 × 1011 dots cm-2 and 1.2 × 1012 dots cm-2, respectively. After selective protein elimination and embedding in a metal-oxide-semiconductor (MOS) capacitor, the charge capacities of both ND arrays were evaluated by measuring their C-V characteristics. The MOS capacitor embedded with the Dps ND array showed a wider memory window than the device embedded with the ferritin ND array. Finally, we fabricated an NFGM with a high-density ND array based on Dps, and confirmed its competent writing/erasing characteristics and long retention time.

The development and application of a quantitative peptide microarray platform to SH2 domain specificity space

NASA Astrophysics Data System (ADS)

Engelmann, Brett Warren

The Src homology 2 (SH2) domains evolved alongside protein tyrosine kinases (PTKs) and phosphatases (PTPs) in metazoans to recognize the phosphotyrosine (pY) post-translational modification. The human genome encodes 121 SH2 domains within 111 SH2 domain containing proteins that represent the primary mechanism for cellular signal transduction immediately downstream of PTKs. Despite pY recognition contributing to roughly half of the binding energy, SH2 domains possess substantial binding specificity, or affinity discrimination between phosphopeptide ligands. This specificity is largely imparted by amino acids (AAs) adjacent to the pY, typically from positions +1 to +4 C-terminal to the pY. Much experimental effort has been undertaken to construct preferred binding motifs for many SH2 domains. However, due to limitations in previous experimental methodologies these motifs do not account for the interplay between AAs. It was therefore not known how AAs within the context of individual peptides function to impart SH2 domain specificity. In this work we identified the critical role context plays in defining SH2 domain specificity for physiological ligands. We also constructed a high quality interactome using 50 SH2 domains and 192 physiological ligands. We next developed a quantitative high-throughput (Q-HTP) peptide microarray platform to assess the affinities four SH2 domains have for 124 physiological ligands. We demonstrated the superior characteristics of our platform relative to preceding approaches and validated our results using established biophysical techniques, literature corroboration, and predictive algorithms. The quantitative information provided by the arrays was leveraged to investigate SH2 domain binding distributions and identify points of binding overlap. Our microarray derived affinity estimates were integrated to produce quantitative interaction motifs capable of predicting interactions. Furthermore, our microarrays proved capable of resolving subtle contextual differences within motifs that modulate interaction affinities. We conclude that contextually informed specificity profiling of protein interaction domains using the methodologies developed in this study can inform efforts to understand the interconnectivity of signaling networks in normal and aberrant states. Three supplementary tables containing detailed lists of peptides, interactions, and sources of corroborative information are provided.

Single-molecule detection of protein efflux from microorganisms using fluorescent single-walled carbon nanotube sensor arrays

NASA Astrophysics Data System (ADS)

Landry, Markita Patricia; Ando, Hiroki; Chen, Allen Y.; Cao, Jicong; Kottadiel, Vishal Isaac; Chio, Linda; Yang, Darwin; Dong, Juyao; Lu, Timothy K.; Strano, Michael S.

2017-05-01

A distinct advantage of nanosensor arrays is their ability to achieve ultralow detection limits in solution by proximity placement to an analyte. Here, we demonstrate label-free detection of individual proteins from Escherichia coli (bacteria) and Pichia pastoris (yeast) immobilized in a microfluidic chamber, measuring protein efflux from single organisms in real time. The array is fabricated using non-covalent conjugation of an aptamer-anchor polynucleotide sequence to near-infrared emissive single-walled carbon nanotubes, using a variable chemical spacer shown to optimize sensor response. Unlabelled RAP1 GTPase and HIV integrase proteins were selectively detected from various cell lines, via large near-infrared fluorescent turn-on responses. We show that the process of E. coli induction, protein synthesis and protein export is highly stochastic, yielding variability in protein secretion, with E. coli cells undergoing division under starved conditions producing 66% fewer secreted protein products than their non-dividing counterparts. We further demonstrate the detection of a unique protein product resulting from T7 bacteriophage infection of E. coli, illustrating that nanosensor arrays can enable real-time, single-cell analysis of a broad range of protein products from various cell types.

Mapping transcription factor interactome networks using HaloTag protein arrays.

PubMed

Yazaki, Junshi; Galli, Mary; Kim, Alice Y; Nito, Kazumasa; Aleman, Fernando; Chang, Katherine N; Carvunis, Anne-Ruxandra; Quan, Rosa; Nguyen, Hien; Song, Liang; Alvarez, José M; Huang, Shao-Shan Carol; Chen, Huaming; Ramachandran, Niroshan; Altmann, Stefan; Gutiérrez, Rodrigo A; Hill, David E; Schroeder, Julian I; Chory, Joanne; LaBaer, Joshua; Vidal, Marc; Braun, Pascal; Ecker, Joseph R

2016-07-19

Protein microarrays enable investigation of diverse biochemical properties for thousands of proteins in a single experiment, an unparalleled capacity. Using a high-density system called HaloTag nucleic acid programmable protein array (HaloTag-NAPPA), we created high-density protein arrays comprising 12,000 Arabidopsis ORFs. We used these arrays to query protein-protein interactions for a set of 38 transcription factors and transcriptional regulators (TFs) that function in diverse plant hormone regulatory pathways. The resulting transcription factor interactome network, TF-NAPPA, contains thousands of novel interactions. Validation in a benchmarked in vitro pull-down assay revealed that a random subset of TF-NAPPA validated at the same rate of 64% as a positive reference set of literature-curated interactions. Moreover, using a bimolecular fluorescence complementation (BiFC) assay, we confirmed in planta several interactions of biological interest and determined the interaction localizations for seven pairs. The application of HaloTag-NAPPA technology to plant hormone signaling pathways allowed the identification of many novel transcription factor-protein interactions and led to the development of a proteome-wide plant hormone TF interactome network.

BeadArray Expression Analysis Using Bioconductor

PubMed Central

Ritchie, Matthew E.; Dunning, Mark J.; Smith, Mike L.; Shi, Wei; Lynch, Andy G.

2011-01-01

Illumina whole-genome expression BeadArrays are a popular choice in gene profiling studies. Aside from the vendor-provided software tools for analyzing BeadArray expression data (GenomeStudio/BeadStudio), there exists a comprehensive set of open-source analysis tools in the Bioconductor project, many of which have been tailored to exploit the unique properties of this platform. In this article, we explore a number of these software packages and demonstrate how to perform a complete analysis of BeadArray data in various formats. The key steps of importing data, performing quality assessments, preprocessing, and annotation in the common setting of assessing differential expression in designed experiments will be covered. PMID:22144879

Hyperspectral imaging to monitor simultaneously multiple protein subtypes and live track their spatial dynamics: a new platform to screen drugs for CNS diseases

NASA Astrophysics Data System (ADS)

Labrecque, S.; Sylvestre, J.-P.; Marcet, S.; Mangiarini, F.; Verhaegen, M.; De Koninck, P.; Blais-Ouellette, S.

2015-03-01

In the past decade, the efficacy of existing therapies and the discovery of innovative treatments for Central Nervous System (CNS) diseases have been limited by the lack of appropriate methods to investigate complex molecular processes at the synaptic level. In order to better understand the fundamental mechanisms that regulate diseases of the CNS, a fast fluorescence hyperspectral imaging platform was designed to track simultaneously various neurotransmitter receptors trafficking in and out of synapses. With this hyperspectral imaging platform, it was possible to image simultaneously five different synaptic proteins, including subtypes of glutamate receptors (mGluR, NMDAR, AMPAR), postsynaptic density proteins, and signaling proteins. This new imaging platform allows fast simultaneous acquisitions of at least five fluorescent markers in living neurons with a high spatial resolution. This technique provides an effective method to observe several synaptic proteins at the same time, thus study how drugs for CNS impact the spatial dynamics of these proteins.

Mass Spectrometry-Based Screening Platform Reveals Orco Interactome in Drosophila melanogaster.

PubMed

Yu, Kate E; Kim, Do-Hyoung; Kim, Yong-In; Jones, Walton D; Lee, J Eugene

2018-02-28

Animals use their odorant receptors to receive chemical information from the environment. Insect odorant receptors differ from the G protein-coupled odorant receptors in vertebrates and nematodes, and very little is known about their protein-protein interactions. Here, we introduce a mass spectrometric platform designed for the large-scale analysis of insect odorant receptor protein-protein interactions. Using this platform, we obtained the first Orco interactome from Drosophila melanogaster . From a total of 1,186 identified proteins, we narrowed the interaction candidates to 226, of which only two-thirds have been named. These candidates include the known olfactory proteins Or92a and Obp51a. Around 90% of the proteins having published names likely function inside the cell, and nearly half of these intracellular proteins are associated with the endomembrane system. In a basic loss-of-function electrophysiological screen, we found that the disruption of eight (i.e., Rab5, CG32795, Mpcp, Tom70, Vir-1, CG30427, Eaat1, and CG2781) of 28 randomly selected candidates affects olfactory responses in vivo . Thus, because this Orco interactome includes physiologically meaningful candidates, we anticipate that our platform will help guide further research on the molecular mechanisms of the insect odorant receptor family.

A Nanocoaxial-Based Electrochemical Sensor for the Detection of Cholera Toxin

NASA Astrophysics Data System (ADS)

Archibald, Michelle; Rizal, Binod; Connolly, Timothy; Burns, Michael J.; Naughton, Michael J.; Chiles, Thomas C.; Biology; Physics Collaboration

We report a nanocoax-based electrochemical sensor for the detection of bacterial toxins using an electrochemical enzyme-linked immunosorbent assay (ELISA) and differential pulse voltammetry (DPV). The device architecture is composed of vertically-oriented, nanoscale coaxial electrodes, with coax cores and shields serving as integrated working and counter electrodes, respectively. Proof-of-concept was demonstrated for the detection of cholera toxin (CT), with a linear dynamic range of detection was 10 ng/ml - 1 µg/ml, and a limit of detection (LOD) of 2 ng/ml. This level of sensitivity is comparable to the standard optical ELISA used widely in clinical applications. The nanocoax array thus matches the detection profile of the standard ELISA while providing a simple electrochemical readout and a miniaturized platform with multiplexing capabilities, toward point-of-care (POC) implementation. In addition, next generation nanocoax devices with extended cores are currently under development, which would provide a POC platform amenable for biofunctionalization of ELISA receptor proteins directly onto the device. This work was supported by the National Institutes of Health (National Cancer Institute Award No. CA137681 and National Institute of Allergy and Infectious Diseases Award No. AI100216).

High-Yield Resveratrol Production in Engineered Escherichia coli ▿ †

PubMed Central

Lim, Chin Giaw; Fowler, Zachary L.; Hueller, Thomas; Schaffer, Steffen; Koffas, Mattheos A. G.

2011-01-01

Plant polyphenols have been the subject of several recent scientific investigations since many of the molecules in this class have been found to be highly active in the human body, with a plethora of health-promoting activities against a variety of diseases, including heart disease, diabetes, and cancer, and with even the potential to slow aging. Further development of these potent natural therapeutics hinges on the formation of robust industrial production platforms designed using specifically selected as well as engineered protein sources along with the construction of optimal expression platforms. In this work, we first report the investigation of various stilbene synthases from an array of plant species considering structure-activity relationships, their expression efficiency in microorganisms, and their ability to synthesize resveratrol. Second, we looked into the construct environment of recombinantly expressed stilbene synthases, including different promoters, construct designs, and host strains, to create an Escherichia coli strain capable of producing superior resveratrol titers sufficient for commercial usage. Further improvement of metabolic capabilities of the recombinant strain aimed at improving the intracellular malonyl-coenzyme A pool, a resveratrol precursor, resulted in a final improved titer of 2.3 g/liter resveratrol. PMID:21441338

Epigenetics of prostate cancer.

PubMed

McKee, Tawnya C; Tricoli, James V

2015-01-01

The introduction of novel technologies that can be applied to the investigation of the molecular underpinnings of human cancer has allowed for new insights into the mechanisms associated with tumor development and progression. They have also advanced the diagnosis, prognosis and treatment of cancer. These technologies include microarray and other analysis methods for the generation of large-scale gene expression data on both mRNA and miRNA, next-generation DNA sequencing technologies utilizing a number of platforms to perform whole genome, whole exome, or targeted DNA sequencing to determine somatic mutational differences and gene rearrangements, and a variety of proteomic analysis platforms including liquid chromatography/mass spectrometry (LC/MS) analysis to survey alterations in protein profiles in tumors. One other important advancement has been our current ability to survey the methylome of human tumors in a comprehensive fashion through the use of sequence-based and array-based methylation analysis (Bock et al., Nat Biotechnol 28:1106-1114, 2010; Harris et al., Nat Biotechnol 28:1097-1105, 2010). The focus of this chapter is to present and discuss the evidence for key genes involved in prostate tumor development, progression, or resistance to therapy that are regulated by methylation-induced silencing.

Integrating prior knowledge in multiple testing under dependence with applications to detecting differential DNA methylation.

PubMed

Kuan, Pei Fen; Chiang, Derek Y

2012-09-01

DNA methylation has emerged as an important hallmark of epigenetics. Numerous platforms including tiling arrays and next generation sequencing, and experimental protocols are available for profiling DNA methylation. Similar to other tiling array data, DNA methylation data shares the characteristics of inherent correlation structure among nearby probes. However, unlike gene expression or protein DNA binding data, the varying CpG density which gives rise to CpG island, shore and shelf definition provides exogenous information in detecting differential methylation. This article aims to introduce a robust testing and probe ranking procedure based on a nonhomogeneous hidden Markov model that incorporates the above-mentioned features for detecting differential methylation. We revisit the seminal work of Sun and Cai (2009, Journal of the Royal Statistical Society: Series B (Statistical Methodology)71, 393-424) and propose modeling the nonnull using a nonparametric symmetric distribution in two-sided hypothesis testing. We show that this model improves probe ranking and is robust to model misspecification based on extensive simulation studies. We further illustrate that our proposed framework achieves good operating characteristics as compared to commonly used methods in real DNA methylation data that aims to detect differential methylation sites. © 2012, The International Biometric Society.

Nanostructured optical fibre arrays for high-density biochemical sensing and remote imaging.

PubMed

Deiss, F; Sojic, N; White, D J; Stoddart, P R

2010-01-01

Optical fibre bundles usually comprise a few thousand to tens of thousands of individually clad glass optical fibres. The ordered arrangement of the fibres enables coherent transmission of an image through the bundle and therefore enables analysis and viewing in remote locations. In fused bundles, this architecture has also been used to fabricate arrays of various micro to nano-scale surface structures (micro/nanowells, nanotips, triangles, etc.) over relatively large areas. These surface structures have been used to obtain new optical and analytical capabilities. Indeed, the imaging bundle can be thought of as a "starting material" that can be sculpted by a combination of fibre drawing and selective wet-chemical etching processes. A large variety of bioanalytical applications have thus been developed, ranging from nano-optics to DNA nanoarrays. For instance, nanostructured optical surfaces with intrinsic light-guiding properties have been exploited as surface-enhanced Raman scattering (SERS) platforms and as near-field probe arrays. They have also been productively associated with electrochemistry to fabricate arrays of transparent nanoelectrodes with electrochemiluminescent imaging properties. The confined geometry of the wells has been loaded with biosensing materials and used as femtolitre-sized vessels to detect single molecules. This review describes the fabrication of high-density nanostructured optical fibre arrays and summarizes the large range of optical and bioanalytical applications that have been developed, reflecting the versatility of this ordered light-guiding platform.

Multiplexing detection of IgG against Plasmodium falciparum pregnancy-specific antigens

PubMed Central

Fonseca, Ana Maria; Quinto, Llorenç; Jiménez, Alfons; González, Raquel; Bardají, Azucena; Maculuve, Sonia; Dobaño, Carlota; Rupérez, Maria; Vala, Anifa; Aponte, John J.; Sevene, Esperanza; Macete, Eusebio; Menéndez, Clara

2017-01-01

Background Pregnant women exposed to Plasmodium falciparum generate antibodies against VAR2CSA, the parasite protein that mediates adhesion of infected erythrocytes to the placenta. There is a need of high-throughput tools to determine the fine specificity of these antibodies that can be used to identify immune correlates of protection and exposure. Here we aimed at developing a multiplex-immunoassay to detect antibodies against VAR2CSA antigens. Methods and findings We constructed two multiplex-bead arrays, one composed of 3 VAR2CSA recombinant-domains (DBL3X, DBL5Ɛ and DBL6Ɛ) and another composed of 46 new peptides covering VAR2CSA conserved and semi-conserved regions. IgG reactivity was similar in multiplexed and singleplexed determinations (Pearson correlation, protein array: R2 = 0.99 and peptide array: R2 = 0.87). IgG recognition of 25 out of 46 peptides and all recombinant-domains was higher in pregnant Mozambican women (n = 106) than in Mozambican men (n = 102) and Spanish individuals (n = 101; p<0.05). Agreement of IgG levels detected in cryopreserved plasma and in elutions from dried blood spots was good after exclusion of inappropriate filter papers. Under heterogeneous levels of exposure to malaria, similar seropositivity cutoffs were obtained using finite mixture models applied to antibodies measured on pregnant Mozambican women and average of antibodies measured on pregnant Spanish women never exposed to malaria. The application of the multiplex-bead array developed here, allowed the assessment of higher IgG levels and seroprevalences against VAR2CSA-derived antigens in women pregnant during 2003–2005 than during 2010–2012, in accordance with the levels of malaria transmission reported for these years in Mozambique. Conclusions The multiplex bead-based immunoassay to detect antibodies against selected 25 VAR2CSA new-peptides and recombinant-domains was successfully implemented. Analysis of field samples showed that responses were specific among pregnant women and dependent on the level of exposure to malaria. This platform provides a high-throughput approach to investigating correlates of protection and identifying serological markers of exposure for malaria in pregnancy. PMID:28715465

Stiffened lipid platforms at molecular force foci

PubMed Central

Anishkin, Andriy; Kung, Ching

2013-01-01

How mechanical forces are sensed remains largely mysterious. The forces that gate prokaryotic and several eukaryotic channels were found to come from the lipid membrane. Our survey of animal cells found that membrane force foci all have cholesterol-gathering proteins and are reinforced with cholesterol. This result is evident in overt force sensors at the tips of stereocilia for vertebrate hearing and the touch receptor of Caenorhabditis elegans and mammalian neurons. For less specialized cells, cadherins sustain the force between neighboring cells and integrins between cells and matrix. These tension bearers also pass through and bind to a cholesterol-enriched platform before anchoring to cytoskeleton through other proteins. Cholesterol, in alliance with sphingomyelin and specialized proteins, enforces a more ordered structure in the bilayer. Such a stiffened platform can suppress mechanical noise, redirect, rescale, and confine force. We speculate that such platforms may be dynamic. The applied force may allow disordered-phase lipids to enter the platform-staging channel opening in the thinner mobile neighborhood. The platform may also contain specialized protein/lipid subdomains enclosing mechanosensitive channels to open with localized tension. Such a dynamic stage can mechanically operate structurally disparate channels or enzymes without having to tie them directly to cadherin, integrin, or other protein tethers. PMID:23476066

Cell-free protein synthesis from genomically recoded bacteria enables multisite incorporation of noncanonical amino acids.

PubMed

Martin, Rey W; Des Soye, Benjamin J; Kwon, Yong-Chan; Kay, Jennifer; Davis, Roderick G; Thomas, Paul M; Majewska, Natalia I; Chen, Cindy X; Marcum, Ryan D; Weiss, Mary Grace; Stoddart, Ashleigh E; Amiram, Miriam; Ranji Charna, Arnaz K; Patel, Jaymin R; Isaacs, Farren J; Kelleher, Neil L; Hong, Seok Hoon; Jewett, Michael C

2018-03-23

Cell-free protein synthesis has emerged as a powerful approach for expanding the range of genetically encoded chemistry into proteins. Unfortunately, efforts to site-specifically incorporate multiple non-canonical amino acids into proteins using crude extract-based cell-free systems have been limited by release factor 1 competition. Here we address this limitation by establishing a bacterial cell-free protein synthesis platform based on genomically recoded Escherichia coli lacking release factor 1. This platform was developed by exploiting multiplex genome engineering to enhance extract performance by functionally inactivating negative effectors. Our most productive cell extracts enabled synthesis of 1,780 ± 30 mg/L superfolder green fluorescent protein. Using an optimized platform, we demonstrated the ability to introduce 40 identical p-acetyl-L-phenylalanine residues site specifically into an elastin-like polypeptide with high accuracy of incorporation ( ≥ 98%) and yield (96 ± 3 mg/L). We expect this cell-free platform to facilitate fundamental understanding and enable manufacturing paradigms for proteins with new and diverse chemistries.

System for beaming power from earth to a high altitude platform

DOEpatents

Friedman, Herbert W.; Porter, Terry J.

2002-01-01

Power is transmitted to a high altitude platform by an array of diode pumped solid state lasers each operated at a single range of laser wavelengths outside of infrared and without using adaptive optics. Each laser produces a beam with a desired arrival spot size. An aircraft avoidance system uses a radar system for automatic control of the shutters of the lasers.

Noninvasive noble metal nanoparticle arrays for surface-enhanced Raman spectroscopy of proteins

NASA Astrophysics Data System (ADS)

Inya-Agha, Obianuju; Forster, Robert J.; Keyes, Tia E.

2007-02-01

Noble metal nanoparticles arrays are well established substrates for surface enhanced Raman spectroscopy (SERS). Their ability to enhance optical fields is based on the interaction of their surface valence electrons with incident electromagnetic radiation. In the array configuration, noble metal nanoparticles have been used to produce SER spectral enhancements of up to 10 8 orders of magnitude, making them useful for the trace analysis of physiologically relevant analytes such as proteins and peptides. Electrostatic interactions between proteins and metal surfaces result in the preferential adsorption of positively charged protein domains onto metal surfaces. This preferential interaction has the effect of disrupting the native conformation of the protein fold, with a concomitant loss of protein function. A major historic advantage of Raman microspectroscopy has been is its non-invasive nature; protein denaturation on the metal surfaces required for SER spectroscopy renders it a much more invasive technique. Further, part of the analytical power of Raman spectroscopy lies in its use as a secondary conformation probe. The protein structural loss which occurs on the metal surface results in secondary conformation readings which are not true to the actual native state of the analyte. This work presents a method for chemical fabrication of noble metal SERS arrays with surface immobilized layers which can protect protein native conformation without excessively mitigating the electromagnetic enhancements of spectra. Peptide analytes are used as model systems for proteins. Raman spectra of alpha lactalbumin on surfaces and when immobilized on these novel arrays are compared. We discuss the ability of the surface layer to protect protein structure whilst improving signal intensity.

Quantifying EGFR alterations in the lung cancer genome with nanofluidic digital PCR arrays.

PubMed

Wang, Jun; Ramakrishnan, Ramesh; Tang, Zhe; Fan, Weiwen; Kluge, Amy; Dowlati, Afshin; Jones, Robert C; Ma, Patrick C

2010-04-01

The EGFR [epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)] gene is known to harbor genomic alterations in advanced lung cancer involving gene amplification and kinase mutations that predict the clinical response to EGFR-targeted inhibitors. Methods for detecting such molecular changes in lung cancer tumors are desirable. We used a nanofluidic digital PCR array platform and 16 cell lines and 20 samples of genomic DNA from resected tumors (stages I-III) to quantify the relative numbers of copies of the EGFR gene and to detect mutated EGFR alleles in lung cancer. We assessed the relative number of EGFR gene copies by calculating the ratio of the number of EGFR molecules (measured with a 6-carboxyfluorescein-labeled Scorpion assay) to the number of molecules of the single-copy gene RPP30 (ribonuclease P/MRP 30kDa subunit) (measured with a 6-carboxy-X-rhodamine-labeled TaqMan assay) in each panel. To assay for the EGFR L858R (exon 21) mutation and exon 19 in-frame deletions, we used the ARMS and Scorpion technologies in a DxS/Qiagen EGFR29 Mutation Test Kit for the digital PCR array. The digital array detected and quantified rare gefitinib/erlotinib-sensitizing EGFR mutations (0.02%-9.26% abundance) that were present in formalin-fixed, paraffin-embedded samples of early-stage resectable lung tumors without an associated increase in gene copy number. Our results also demonstrated the presence of intratumor molecular heterogeneity for the clinically relevant EGFR mutated alleles in these early-stage lung tumors. The digital PCR array platform allows characterization and quantification of oncogenes, such as EGFR, at the single-molecule level. Use of this nanofluidics platform may provide deeper insight into the specific roles of clinically relevant kinase mutations during different stages of lung tumor progression and may be useful in predicting the clinical response to EGFR-targeted inhibitors.

Radiation-Hardened Wafer Scale Integration

DTIC Science & Technology

1989-10-25

unlimited. LEXINGTON MASSACHUSETTS EXECUTIVE SUMMARY A focal plane processor (FPP) for a large array of LWIR photodetectors on a space platform must...It seems certain that large. scanning LWIR arrays will once again be of interest in the future, though their specifications will differ from those... nonuniformity and defects in the ZMR material, but films of good quality produced by this technique are now available commercially from Kopin Corporation. Such

Glyco-Immune Diagnostic Signatures and Therapeutic Targets of Mesothelioma

DTIC Science & Technology

2015-09-01

Mesothelioma; Glycan Array; Immunoprofiles; Robotic Arrayer 16. SECURITY CLASSIFICATION OF: U 17. LIMITATION OF ABSTRACT: UU 18. NUMBER OF PAGES 19 19a...PROJECT SUMMARY: General Comments: This project involved novel technology in which biochemically synthesized glycans were robotically printed on glass...include 386 glycans and the platform was known as the PGA-400. (Figure 1) A standard robotic technology for printing a large range of

Assessment of a novel multi-array normalization method based on spike-in control probes suitable for microRNA datasets with global decreases in expression.

PubMed

Sewer, Alain; Gubian, Sylvain; Kogel, Ulrike; Veljkovic, Emilija; Han, Wanjiang; Hengstermann, Arnd; Peitsch, Manuel C; Hoeng, Julia

2014-05-17

High-quality expression data are required to investigate the biological effects of microRNAs (miRNAs). The goal of this study was, first, to assess the quality of miRNA expression data based on microarray technologies and, second, to consolidate it by applying a novel normalization method. Indeed, because of significant differences in platform designs, miRNA raw data cannot be normalized blindly with standard methods developed for gene expression. This fundamental observation motivated the development of a novel multi-array normalization method based on controllable assumptions, which uses the spike-in control probes to adjust the measured intensities across arrays. Raw expression data were obtained with the Exiqon dual-channel miRCURY LNA™ platform in the "common reference design" and processed as "pseudo-single-channel". They were used to apply several quality metrics based on the coefficient of variation and to test the novel spike-in controls based normalization method. Most of the considerations presented here could be applied to raw data obtained with other platforms. To assess the normalization method, it was compared with 13 other available approaches from both data quality and biological outcome perspectives. The results showed that the novel multi-array normalization method reduced the data variability in the most consistent way. Further, the reliability of the obtained differential expression values was confirmed based on a quantitative reverse transcription-polymerase chain reaction experiment performed for a subset of miRNAs. The results reported here support the applicability of the novel normalization method, in particular to datasets that display global decreases in miRNA expression similarly to the cigarette smoke-exposed mouse lung dataset considered in this study. Quality metrics to assess between-array variability were used to confirm that the novel spike-in controls based normalization method provided high-quality miRNA expression data suitable for reliable downstream analysis. The multi-array miRNA raw data normalization method was implemented in an R software package called ExiMiR and deposited in the Bioconductor repository.

Assessment of a novel multi-array normalization method based on spike-in control probes suitable for microRNA datasets with global decreases in expression

PubMed Central

2014-01-01

Background High-quality expression data are required to investigate the biological effects of microRNAs (miRNAs). The goal of this study was, first, to assess the quality of miRNA expression data based on microarray technologies and, second, to consolidate it by applying a novel normalization method. Indeed, because of significant differences in platform designs, miRNA raw data cannot be normalized blindly with standard methods developed for gene expression. This fundamental observation motivated the development of a novel multi-array normalization method based on controllable assumptions, which uses the spike-in control probes to adjust the measured intensities across arrays. Results Raw expression data were obtained with the Exiqon dual-channel miRCURY LNA™ platform in the “common reference design” and processed as “pseudo-single-channel”. They were used to apply several quality metrics based on the coefficient of variation and to test the novel spike-in controls based normalization method. Most of the considerations presented here could be applied to raw data obtained with other platforms. To assess the normalization method, it was compared with 13 other available approaches from both data quality and biological outcome perspectives. The results showed that the novel multi-array normalization method reduced the data variability in the most consistent way. Further, the reliability of the obtained differential expression values was confirmed based on a quantitative reverse transcription–polymerase chain reaction experiment performed for a subset of miRNAs. The results reported here support the applicability of the novel normalization method, in particular to datasets that display global decreases in miRNA expression similarly to the cigarette smoke-exposed mouse lung dataset considered in this study. Conclusions Quality metrics to assess between-array variability were used to confirm that the novel spike-in controls based normalization method provided high-quality miRNA expression data suitable for reliable downstream analysis. The multi-array miRNA raw data normalization method was implemented in an R software package called ExiMiR and deposited in the Bioconductor repository. PMID:24886675

Proteomic analysis of Medulloblastoma reveals functional biology with translational potential.

PubMed

Rivero-Hinojosa, Samuel; Lau, Ling San; Stampar, Mojca; Staal, Jerome; Zhang, Huizhen; Gordish-Dressman, Heather; Northcott, Paul A; Pfister, Stefan M; Taylor, Michael D; Brown, Kristy J; Rood, Brian R

2018-06-07

Genomic characterization has begun to redefine diagnostic classifications of cancers. However, it remains a challenge to infer disease phenotypes from genomic alterations alone. To help realize the promise of genomics, we have performed a quantitative proteomics investigation using Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) and 41 tissue samples spanning the 4 genomically based subgroups of medulloblastoma and control cerebellum. We have identified and quantitated thousands of proteins across these groups and find that we are able to recapitulate the genomic subgroups based upon subgroup restricted and differentially abundant proteins while also identifying subgroup specific protein isoforms. Integrating our proteomic measurements with genomic data, we calculate a poor correlation between mRNA and protein abundance. Using EPIC 850 k methylation array data on the same tissues, we also investigate the influence of copy number alterations and DNA methylation on the proteome in an attempt to characterize the impact of these genetic features on the proteome. Reciprocally, we are able to use the proteome to identify which genomic alterations result in altered protein abundance and thus are most likely to impact biology. Finally, we are able to assemble protein-based pathways yielding potential avenues for clinical intervention. From these, we validate the EIF4F cap-dependent translation pathway as a novel druggable pathway in medulloblastoma. Thus, quantitative proteomics complements genomic platforms to yield a more complete understanding of functional tumor biology and identify novel therapeutic targets for medulloblastoma.

Year 2 Report: Protein Function Prediction Platform

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, C E

2012-04-27

Upon completion of our second year of development in a 3-year development cycle, we have completed a prototype protein structure-function annotation and function prediction system: Protein Function Prediction (PFP) platform (v.0.5). We have met our milestones for Years 1 and 2 and are positioned to continue development in completion of our original statement of work, or a reasonable modification thereof, in service to DTRA Programs involved in diagnostics and medical countermeasures research and development. The PFP platform is a multi-scale computational modeling system for protein structure-function annotation and function prediction. As of this writing, PFP is the only existing fullymore » automated, high-throughput, multi-scale modeling, whole-proteome annotation platform, and represents a significant advance in the field of genome annotation (Fig. 1). PFP modules perform protein functional annotations at the sequence, systems biology, protein structure, and atomistic levels of biological complexity (Fig. 2). Because these approaches provide orthogonal means of characterizing proteins and suggesting protein function, PFP processing maximizes the protein functional information that can currently be gained by computational means. Comprehensive annotation of pathogen genomes is essential for bio-defense applications in pathogen characterization, threat assessment, and medical countermeasure design and development in that it can short-cut the time and effort required to select and characterize protein biomarkers.« less

Fabrication of Pop-up Detector Arrays on Si Wafers

NASA Technical Reports Server (NTRS)

Li, Mary J.; Allen, Christine A.; Gordon, Scott A.; Kuhn, Jonathan L.; Mott, David B.; Stahle, Caroline K.; Wang, Liqin L.

1999-01-01

High sensitivity is a basic requirement for a new generation of thermal detectors. To meet the requirement, close-packed, two-dimensional silicon detector arrays have been developed in NASA Goddard Space Flight Center. The goal of the task is to fabricate detector arrays configured with thermal detectors such as infrared bolometers and x-ray calorimeters to use in space fliGht missions. This paper focuses on the fabrication and the mechanical testing of detector arrays in a 0.2 mm pixel size, the smallest pop-up detectors being developed so far. These array structures, nicknamed "PUDS" for "Pop-Up Detectors", are fabricated on I pm thick, single-crystal, silicon membranes. Their designs have been refined so we can utilize the flexibility of thin silicon films by actually folding the silicon membranes to 90 degrees in order to obtain close-packed two-dimensional arrays. The PUD elements consist of a detector platform and two legs for mechanical support while also serving as electrical and thermal paths. Torsion bars and cantilevers connecting the detector platform to the legs provide additional flexures for strain relief. Using micro-electromechanical structure (MEMS) fabrication techniques, including photolithography, anisotropic chemical etching, reactive-ion etching, and laser dicing, we have fabricated PLTD detector arrays of fourteen designs with a variation of four parameters including cantilever length, torsion bar length and width, and leg length. Folding tests were conducted to test mechanical stress distribution for the array structures. We obtained folding yields and selected optimum design parameters to reach minimal stress levels. Computer simulation was also employed to verify mechanical behaviors of PUDs in the folding process. In addition, scanning electron microscopy was utilized to examine the flatness of detectors and the alignment of detector pixels in arrays. The fabrication of thermistors and heaters on the pop-up detectors is under way, preparing us for the next step of the experiment, the thermal test.

Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar).

PubMed

Houston, Ross D; Taggart, John B; Cézard, Timothé; Bekaert, Michaël; Lowe, Natalie R; Downing, Alison; Talbot, Richard; Bishop, Stephen C; Archibald, Alan L; Bron, James E; Penman, David J; Davassi, Alessandro; Brew, Fiona; Tinch, Alan E; Gharbi, Karim; Hamilton, Alastair

2014-02-06

Dense single nucleotide polymorphism (SNP) genotyping arrays provide extensive information on polymorphic variation across the genome of species of interest. Such information can be used in studies of the genetic architecture of quantitative traits and to improve the accuracy of selection in breeding programs. In Atlantic salmon (Salmo salar), these goals are currently hampered by the lack of a high-density SNP genotyping platform. Therefore, the aim of the study was to develop and test a dense Atlantic salmon SNP array. SNP discovery was performed using extensive deep sequencing of Reduced Representation (RR-Seq), Restriction site-Associated DNA (RAD-Seq) and mRNA (RNA-Seq) libraries derived from farmed and wild Atlantic salmon samples (n = 283) resulting in the discovery of > 400 K putative SNPs. An Affymetrix Axiom® myDesign Custom Array was created and tested on samples of animals of wild and farmed origin (n = 96) revealing a total of 132,033 polymorphic SNPs with high call rate, good cluster separation on the array and stable Mendelian inheritance in our sample. At least 38% of these SNPs are from transcribed genomic regions and therefore more likely to include functional variants. Linkage analysis utilising the lack of male recombination in salmonids allowed the mapping of 40,214 SNPs distributed across all 29 pairs of chromosomes, highlighting the extensive genome-wide coverage of the SNPs. An identity-by-state clustering analysis revealed that the array can clearly distinguish between fish of different origins, within and between farmed and wild populations. Finally, Y-chromosome-specific probes included on the array provide an accurate molecular genetic test for sex. This manuscript describes the first high-density SNP genotyping array for Atlantic salmon. This array will be publicly available and is likely to be used as a platform for high-resolution genetics research into traits of evolutionary and economic importance in salmonids and in aquaculture breeding programs via genomic selection.

Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar)

PubMed Central

2014-01-01

Background Dense single nucleotide polymorphism (SNP) genotyping arrays provide extensive information on polymorphic variation across the genome of species of interest. Such information can be used in studies of the genetic architecture of quantitative traits and to improve the accuracy of selection in breeding programs. In Atlantic salmon (Salmo salar), these goals are currently hampered by the lack of a high-density SNP genotyping platform. Therefore, the aim of the study was to develop and test a dense Atlantic salmon SNP array. Results SNP discovery was performed using extensive deep sequencing of Reduced Representation (RR-Seq), Restriction site-Associated DNA (RAD-Seq) and mRNA (RNA-Seq) libraries derived from farmed and wild Atlantic salmon samples (n = 283) resulting in the discovery of > 400 K putative SNPs. An Affymetrix Axiom® myDesign Custom Array was created and tested on samples of animals of wild and farmed origin (n = 96) revealing a total of 132,033 polymorphic SNPs with high call rate, good cluster separation on the array and stable Mendelian inheritance in our sample. At least 38% of these SNPs are from transcribed genomic regions and therefore more likely to include functional variants. Linkage analysis utilising the lack of male recombination in salmonids allowed the mapping of 40,214 SNPs distributed across all 29 pairs of chromosomes, highlighting the extensive genome-wide coverage of the SNPs. An identity-by-state clustering analysis revealed that the array can clearly distinguish between fish of different origins, within and between farmed and wild populations. Finally, Y-chromosome-specific probes included on the array provide an accurate molecular genetic test for sex. Conclusions This manuscript describes the first high-density SNP genotyping array for Atlantic salmon. This array will be publicly available and is likely to be used as a platform for high-resolution genetics research into traits of evolutionary and economic importance in salmonids and in aquaculture breeding programs via genomic selection. PMID:24524230

Development and evaluation of the first high-throughput SNP array for common carp (Cyprinus carpio)

PubMed Central

2014-01-01

Background A large number of single nucleotide polymorphisms (SNPs) have been identified in common carp (Cyprinus carpio) but, as yet, no high-throughput genotyping platform is available for this species. C. carpio is an important aquaculture species that accounts for nearly 14% of freshwater aquaculture production worldwide. We have developed an array for C. carpio with 250,000 SNPs and evaluated its performance using samples from various strains of C. carpio. Results The SNPs used on the array were selected from two resources: the transcribed sequences from RNA-seq data of four strains of C. carpio, and the genome re-sequencing data of five strains of C. carpio. The 250,000 SNPs on the resulting array are distributed evenly across the reference C.carpio genome with an average spacing of 6.6 kb. To evaluate the SNP array, 1,072 C. carpio samples were collected and tested. Of the 250,000 SNPs on the array, 185,150 (74.06%) were found to be polymorphic sites. Genotyping accuracy was checked using genotyping data from a group of full-siblings and their parents, and over 99.8% of the qualified SNPs were found to be reliable. Analysis of the linkage disequilibrium on all samples and on three domestic C.carpio strains revealed that the latter had the longer haplotype blocks. We also evaluated our SNP array on 80 samples from eight species related to C. carpio, with from 53,526 to 71,984 polymorphic SNPs. An identity by state analysis divided all the samples into three clusters; most of the C. carpio strains formed the largest cluster. Conclusions The Carp SNP array described here is the first high-throughput genotyping platform for C. carpio. Our evaluation of this array indicates that it will be valuable for farmed carp and for genetic and population biology studies in C. carpio and related species. PMID:24762296

Development and evaluation of the first high-throughput SNP array for common carp (Cyprinus carpio).

PubMed

Xu, Jian; Zhao, Zixia; Zhang, Xiaofeng; Zheng, Xianhu; Li, Jiongtang; Jiang, Yanliang; Kuang, Youyi; Zhang, Yan; Feng, Jianxin; Li, Chuangju; Yu, Juhua; Li, Qiang; Zhu, Yuanyuan; Liu, Yuanyuan; Xu, Peng; Sun, Xiaowen

2014-04-24

A large number of single nucleotide polymorphisms (SNPs) have been identified in common carp (Cyprinus carpio) but, as yet, no high-throughput genotyping platform is available for this species. C. carpio is an important aquaculture species that accounts for nearly 14% of freshwater aquaculture production worldwide. We have developed an array for C. carpio with 250,000 SNPs and evaluated its performance using samples from various strains of C. carpio. The SNPs used on the array were selected from two resources: the transcribed sequences from RNA-seq data of four strains of C. carpio, and the genome re-sequencing data of five strains of C. carpio. The 250,000 SNPs on the resulting array are distributed evenly across the reference C.carpio genome with an average spacing of 6.6 kb. To evaluate the SNP array, 1,072 C. carpio samples were collected and tested. Of the 250,000 SNPs on the array, 185,150 (74.06%) were found to be polymorphic sites. Genotyping accuracy was checked using genotyping data from a group of full-siblings and their parents, and over 99.8% of the qualified SNPs were found to be reliable. Analysis of the linkage disequilibrium on all samples and on three domestic C.carpio strains revealed that the latter had the longer haplotype blocks. We also evaluated our SNP array on 80 samples from eight species related to C. carpio, with from 53,526 to 71,984 polymorphic SNPs. An identity by state analysis divided all the samples into three clusters; most of the C. carpio strains formed the largest cluster. The Carp SNP array described here is the first high-throughput genotyping platform for C. carpio. Our evaluation of this array indicates that it will be valuable for farmed carp and for genetic and population biology studies in C. carpio and related species.

Intercepted signals for ionospheric science

NASA Astrophysics Data System (ADS)

Lind, F. D.; Erickson, P. J.; Coster, A. J.; Foster, J. C.; Marchese, J. R.; Berkowitz, Z.; Sahr, J. D.

2013-05-01

The ISIS array (Intercepted Signals for Ionospheric Science) is a distributed, coherent software radio array designed for the study of geospace phenomena by observing the scatter of ambient radio frequency (RF) signals. ISIS data acquisition and analysis is performed using the MIDAS-M platform (Millstone Data Acquisition System - Mobile). Observations of RF signals can be performed between HF and L-band using the Array nodes and appropriate antennas. The deployment of the Array focuses on observations of the plasmasphere boundary layer. We discuss the concept of the coherent software radio array, describe the ISIS hardware, and give examples of data from the system for selected applications. In particular, we include the first observations of E region irregularities using the Array. We also present single-site passive radar observations of both meteor trails and E region irregularities using adaptive filtering techniques.

Evaluation of high throughput gene expression platforms using a genomic biomarker signature for prediction of skin sensitization.

PubMed

Forreryd, Andy; Johansson, Henrik; Albrekt, Ann-Sofie; Lindstedt, Malin

2014-05-16

Allergic contact dermatitis (ACD) develops upon exposure to certain chemical compounds termed skin sensitizers. To reduce the occurrence of skin sensitizers, chemicals are regularly screened for their capacity to induce sensitization. The recently developed Genomic Allergen Rapid Detection (GARD) assay is an in vitro alternative to animal testing for identification of skin sensitizers, classifying chemicals by evaluating transcriptional levels of a genomic biomarker signature. During assay development and biomarker identification, genome-wide expression analysis was applied using microarrays covering approximately 30,000 transcripts. However, the microarray platform suffers from drawbacks in terms of low sample throughput, high cost per sample and time consuming protocols and is a limiting factor for adaption of GARD into a routine assay for screening of potential sensitizers. With the purpose to simplify assay procedures, improve technical parameters and increase sample throughput, we assessed the performance of three high throughput gene expression platforms--nCounter®, BioMark HD™ and OpenArray®--and correlated their performance metrics against our previously generated microarray data. We measured the levels of 30 transcripts from the GARD biomarker signature across 48 samples. Detection sensitivity, reproducibility, correlations and overall structure of gene expression measurements were compared across platforms. Gene expression data from all of the evaluated platforms could be used to classify most of the sensitizers from non-sensitizers in the GARD assay. Results also showed high data quality and acceptable reproducibility for all platforms but only medium to poor correlations of expression measurements across platforms. In addition, evaluated platforms were superior to the microarray platform in terms of cost efficiency, simplicity of protocols and sample throughput. We evaluated the performance of three non-array based platforms using a limited set of transcripts from the GARD biomarker signature. We demonstrated that it was possible to achieve acceptable discriminatory power in terms of separation between sensitizers and non-sensitizers in the GARD assay while reducing assay costs, simplify assay procedures and increase sample throughput by using an alternative platform, providing a first step towards the goal to prepare GARD for formal validation and adaption of the assay for industrial screening of potential sensitizers.

Antibody Protein Array Analysis of the Tear Film Cytokines

PubMed Central

Li, Shimin; Sack, Robert; Vijmasi, Trinka; Sathe, Sonal; Beaton, Ann; Quigley, David; Gallup, Marianne; McNamara, Nancy A.

2013-01-01

Purpose Many bioactive proteins including cytokines are reported to increase in dry eye disease although the specific profile and concentration of inflammatory mediators varies considerably from study to study. In part this variability results from inherent difficulties in quantifying low abundance proteins in a limited sample volume using relatively low sensitivity dot ELISA methods. Additional complexity comes with the use of pooled samples collected using a variety of techniques and intrinsic variation in the diurnal pattern of individual tear proteins. The current study describes a recent advance in the area of proteomics that has allowed the identification of dozens of low abundance proteins in human tear samples. Methods Commercially available stationary phase antibody protein arrays were adapted to improve suitability for use in small volume biological fluid analysis with particular emphasis on tear film proteomics. Arrays were adapted to allow simultaneous screening for a panel of inflammatory cytokines in low volume tear samples collected from individual eyes. Results A preliminary study comparing tear array results in a small population of Sjögren’s syndrome patients was conducted. The multiplex microplate array assays of cytokines in tear fluid present an unanticipated challenge due to the unique nature of tear fluid. The presence of factors that exhibit an affinity for plastic, capture antibodies and IgG and create a complex series of matrix effects profoundly impacting the reliability of dot ELISA, including with elevated levels of background reactivity and reduction in capacity to bind targeted protein. Conclusions Preliminary results using tears collected from patients with Sjögren’s syndrome reveal methodological advantages of protein array technology and support the concept that autoimmune-mediated dry eye disease has an inflammatory component. They also emphasize the inherent difficulties one can face when interpreting the results of micro-well arrays that result from blooming effects, matrix effects, image saturation and cross-talk between capture and probe antibodies that can greatly reduce signal-to-noise and limit the ability to obtain meaningful results. PMID:18677223

Microstamped Petri Dishes for Scanning Electrochemical Microscopy Analysis of Arrays of Microtissues

PubMed Central

Sridhar, Adithya; de Boer, Hans L.; van den Berg, Albert; Le Gac, Séverine

2014-01-01

While scanning electrochemical microscopy (SECM) is a powerful technique for non-invasive analysis of cells, SECM-based assays remain scarce and have been mainly limited so far to single cells, which is mostly due to the absence of suitable platform for experimentation on 3D cellular aggregates or microtissues. Here, we report stamping of a Petri dish with a microwell array for large-scale production of microtissues followed by their in situ analysis using SECM. The platform is realized by hot embossing arrays of microwells (200 μm depth; 400 μm diameter) in commercially available Petri dishes, using a PDMS stamp. Microtissues form spontaneously in the microwells, which is demonstrated here using various cell lines (e.g., HeLa, C2C12, HepG2 and MCF-7). Next, the respiratory activity of live HeLa microtissues is assessed by monitoring the oxygen reduction current in constant height mode and at various distances above the platform surface. Typically, at a 40 μm distance from the microtissue, a 30% decrease in the oxygen reduction current is measured, while above 250 μm, no influence of the presence of the microtissues is detected. After exposure to a model drug (50% ethanol), no such changes in oxygen concentration are found at any height in solution, which reflects that microtissues are not viable anymore. This is furthermore confirmed using conventional live/dead fluorescent stains. This live/dead assay demonstrates the capability of the proposed approach combining SECM and microtissue arrays formed in a stamped Petri dish for conducting cellular assays in a non-invasive way on 3D cellular models. PMID:24690887

Rapid Bacterial Detection via an All-Electronic CMOS Biosensor

PubMed Central

Nikkhoo, Nasim; Cumby, Nichole; Gulak, P. Glenn; Maxwell, Karen L.

2016-01-01

The timely and accurate diagnosis of infectious diseases is one of the greatest challenges currently facing modern medicine. The development of innovative techniques for the rapid and accurate identification of bacterial pathogens in point-of-care facilities using low-cost, portable instruments is essential. We have developed a novel all-electronic biosensor that is able to identify bacteria in less than ten minutes. This technology exploits bacteriocins, protein toxins naturally produced by bacteria, as the selective biological detection element. The bacteriocins are integrated with an array of potassium-selective sensors in Complementary Metal Oxide Semiconductor technology to provide an inexpensive bacterial biosensor. An electronic platform connects the CMOS sensor to a computer for processing and real-time visualization. We have used this technology to successfully identify both Gram-positive and Gram-negative bacteria commonly found in human infections. PMID:27618185

Low-Power Optical Trapping of Nanoparticles and Proteins with Resonant Coaxial Nanoaperture Using 10 nm Gap.

PubMed

Yoo, Daehan; Gurunatha, Kargal L; Choi, Han-Kyu; Mohr, Daniel A; Ertsgaard, Christopher T; Gordon, Reuven; Oh, Sang-Hyun

2018-06-13

We present optical trapping with a 10 nm gap resonant coaxial nanoaperture in a gold film. Large arrays of 600 resonant plasmonic coaxial nanoaperture traps are produced on a single chip via atomic layer lithography with each aperture tuned to match a 785 nm laser source. We show that these single coaxial apertures can act as efficient nanotweezers with a sharp potential well, capable of trapping 30 nm polystyrene nanoparticles and streptavidin molecules with a laser power as low as 4.7 mW. Furthermore, the resonant coaxial nanoaperture enables real-time label-free detection of the trapping events via simple transmission measurements. Our fabrication technique is scalable and reproducible, since the critical nanogap dimension is defined by atomic layer deposition. Thus our platform shows significant potential to push the limit of optical trapping technologies.

The growing impact of lyophilized cell-free protein expression systems

PubMed Central

Hunt, J. Porter; Yang, Seung Ook; Wilding, Kristen M.; Bundy, Bradley C.

2017-01-01

ABSTRACT Recently reported shelf-stable, on-demand protein synthesis platforms are enabling new possibilities in biotherapeutics, biosensing, biocatalysis, and high throughput protein expression. Lyophilized cell-free protein expression systems not only overcome cold-storage limitations, but also enable stockpiling for on-demand synthesis and completely sterilize the protein synthesis platform. Recently reported high-yield synthesis of cytotoxic protein Onconase from lyophilized E. coli extract preparations demonstrates the utility of lyophilized cell-free protein expression and its potential for creating on-demand biotherapeutics, vaccines, biosensors, biocatalysts, and high throughput protein synthesis. PMID:27791452

Tensile-stressed microelectromechanical apparatus and tiltable micromirrors formed therefrom

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fleming, James G.

A microelectromechanical (MEM) apparatus is disclosed which includes a pair of tensile-stressed actuators suspending a platform above a substrate to tilt the platform relative to the substrate. A tensile stress built into the actuators initially tilts the platform when a sacrificial material used in fabrication of the MEM apparatus is removed. Further tilting of the platform can occur with a change in the ambient temperature about the MEM apparatus, or by applying a voltage to one or both of the tensile-stressed actuators. The MEM apparatus can be used to form a tiltable micromirror or an array of such devices, andmore » also has applications for thermal management within satellites.« less

Disposable sensor based on enzyme-free Ni nanowire array electrode to detect glutamate.

PubMed

Jamal, Mamun; Hasan, Maksudul; Mathewson, Alan; Razeeb, Kafil M

2013-02-15

Enzyme free electrochemical sensor platform based on a vertically aligned nickel nanowire array (NiNAE) and Pt coated nickel nanowire array (Pt/NiNAE) have been developed to detect glutamate. Morphological characterisation of Ni electrodes was carried out using scanning and transmission electron microscopy combined with energy dispersive X-ray (SEM-EDX), X-ray diffraction (XRD) and transmission electron microscopy (TEM). Cyclic voltammetry (CV) and amperometry were used to evaluate the catalytic activity of the NiNAE and the Pt/NiNAE for glutamate. It has been found that both NiNAE and Pt/NiNAE electrodes showed remarkably enhanced electrocatalytic activity towards glutamate compared to planar Ni electrodes, and showed higher catalytic activity when compared to other metallic nanostructure electrodes such as gold nanowire array electrodes (AuNAE) and Pt coated gold nanowire array electrode (Pt/AuNAE). The sensitivity of NiNAE and Pt/NiNAE has been found to be 65 and 96 μA mM(-1) cm(-2), respectively, which is approximately 6 to 9 times higher than the state of the art glutamate sensor. Under optimal detection conditions, the as prepared sensors exhibited linear behaviour for glutamate detection in the concentration up to 8mM for both NiNAE and Pt/NiNAE with a limit of detection of 68 and 83 μM, respectively. Experimental results show that the vertically aligned ordered nickel nanowire array electrode (NiNAE) has significant promise for fabricating cost effective, enzyme-less, sensitive, stable and selective sensor platform. Copyright © 2012 Elsevier B.V. All rights reserved.

Ordered nanoparticle arrays formed on engineered chaperonin protein templates

NASA Technical Reports Server (NTRS)

McMillan, R. Andrew; Paavola, Chad D.; Howard, Jeanie; Chan, Suzanne L.; Zaluzec, Nestor J.; Trent, Jonathan D.

2002-01-01

Traditional methods for fabricating nanoscale arrays are usually based on lithographic techniques. Alternative new approaches rely on the use of nanoscale templates made of synthetic or biological materials. Some proteins, for example, have been used to form ordered two-dimensional arrays. Here, we fabricated nanoscale ordered arrays of metal and semiconductor quantum dots by binding preformed nanoparticles onto crystalline protein templates made from genetically engineered hollow double-ring structures called chaperonins. Using structural information as a guide, a thermostable recombinant chaperonin subunit was modified to assemble into chaperonins with either 3 nm or 9 nm apical pores surrounded by chemically reactive thiols. These engineered chaperonins were crystallized into two-dimensional templates up to 20 microm in diameter. The periodic solvent-exposed thiols within these crystalline templates were used to size-selectively bind and organize either gold (1.4, 5 or 10nm) or CdSe-ZnS semiconductor (4.5 nm) quantum dots into arrays. The order within the arrays was defined by the lattice of the underlying protein crystal. By combining the self-assembling properties of chaperonins with mutations guided by structural modelling, we demonstrate that quantum dots can be manipulated using modified chaperonins and organized into arrays for use in next-generation electronic and photonic devices.

TIPMaP: a web server to establish transcript isoform profiles from reliable microarray probes.

PubMed

Chitturi, Neelima; Balagannavar, Govindkumar; Chandrashekar, Darshan S; Abinaya, Sadashivam; Srini, Vasan S; Acharya, Kshitish K

2013-12-27

Standard 3' Affymetrix gene expression arrays have contributed a significantly higher volume of existing gene expression data than other microarray platforms. These arrays were designed to identify differentially expressed genes, but not their alternatively spliced transcript forms. No resource can currently identify expression pattern of specific mRNA forms using these microarray data, even though it is possible to do this. We report a web server for expression profiling of alternatively spliced transcripts using microarray data sets from 31 standard 3' Affymetrix arrays for human, mouse and rat species. The tool has been experimentally validated for mRNAs transcribed or not-detected in a human disease condition (non-obstructive azoospermia, a male infertility condition). About 4000 gene expression datasets were downloaded from a public repository. 'Good probes' with complete coverage and identity to latest reference transcript sequences were first identified. Using them, 'Transcript specific probe-clusters' were derived for each platform and used to identify expression status of possible transcripts. The web server can lead the user to datasets corresponding to specific tissues, conditions via identifiers of the microarray studies or hybridizations, keywords, official gene symbols or reference transcript identifiers. It can identify, in the tissues and conditions of interest, about 40% of known transcripts as 'transcribed', 'not-detected' or 'differentially regulated'. Corresponding additional information for probes, genes, transcripts and proteins can be viewed too. We identified the expression of transcripts in a specific clinical condition and validated a few of these transcripts by experiments (using reverse transcription followed by polymerase chain reaction). The experimental observations indicated higher agreements with the web server results, than contradictions. The tool is accessible at http://resource.ibab.ac.in/TIPMaP. The newly developed online tool forms a reliable means for identification of alternatively spliced transcript-isoforms that may be differentially expressed in various tissues, cell types or physiological conditions. Thus, by making better use of existing data, TIPMaP avoids the dependence on precious tissue-samples, in experiments with a goal to establish expression profiles of alternative splice forms--at least in some cases.

Synthesis of Conformal Phased Antenna Arrays With A Novel Multiobjective Invasive Weed Optimization Algorithm

NASA Astrophysics Data System (ADS)

Li, Wen Tao; Hei, Yong Qiang; Shi, Xiao Wei

2018-04-01

By virtue of the excellent aerodynamic performances, conformal phased arrays have been attracting considerable attention. However, for the synthesis of patterns with low/ultra-low sidelobes of the conventional conformal arrays, the obtained dynamic range ratios of amplitude excitations could be quite high, which results in stringent requirements on various error tolerances for practical implementation. Time-modulated array (TMA) has the advantages of low sidelobe and reduced dynamic range ratio requirement of amplitude excitations. This paper takes full advantages of conformal antenna arrays and time-modulated arrays. The active-element-pattern, including element mutual coupling and platform effects, is employed in the whole design process. To optimize the pulse durations and the switch-on instants of the time-modulated elements, multiobjective invasive weed optimization (MOIWO) algorithm based on the nondominated sorting of the solutions is proposed. A S-band 8-element cylindrical conformal array is designed and a S-band 16-element cylindrical-parabolic conformal array is constructed and tested at two different steering angles.

Cambridge Healthtech Institute's Third Annual Conference on Lab-on-a-Chip and Microarrays. 22-24 January 2001, Zurich, Switzerland.

PubMed

Jain, K K

2001-02-01

Cambridge Healthtech Institute's Third Annual Conference on Lab-on-a-Chip and Microarray technology covered the latest advances in this technology and applications in life sciences. Highlights of the meetings are reported briefly with emphasis on applications in genomics, drug discovery and molecular diagnostics. There was an emphasis on microfluidics because of the wide applications in laboratory and drug discovery. The lab-on-a-chip provides the facilities of a complete laboratory in a hand-held miniature device. Several microarray systems have been used for hybridisation and detection techniques. Oligonucleotide scanning arrays provide a versatile tool for the analysis of nucleic acid interactions and provide a platform for improving the array-based methods for investigation of antisense therapeutics. A method for analysing combinatorial DNA arrays using oligonucleotide-modified gold nanoparticle probes and a conventional scanner has considerable potential in molecular diagnostics. Various applications of microarray technology for high-throughput screening in drug discovery and single nucleotide polymorphisms (SNP) analysis were discussed. Protein chips have important applications in proteomics. With the considerable amount of data generated by the different technologies using microarrays, it is obvious that the reading of the information and its interpretation and management through the use of bioinformatics is essential. Various techniques for data analysis were presented. Biochip and microarray technology has an essential role to play in the evolving trends in healthcare, which integrate diagnosis with prevention/treatment and emphasise personalised medicines.

Highly Sensitive and Reproducible SERS Sensor for Biological pH Detection Based on a Uniform Gold Nanorod Array Platform.

PubMed

Bi, Liyan; Wang, Yunqing; Yang, Ying; Li, Yuling; Mo, Shanshan; Zheng, Qingyin; Chen, Lingxin

2018-05-09

Conventional research on surface-enhanced Raman scattering (SERS)-based pH sensors often depends on nanoparticle aggregation, whereas the variability in nanoparticle aggregation gives rise to poor repeatability in the SERS signal. Herein, we fabricated a gold nanorod array platform via an efficient evaporative self-assembly method. The platform exhibits great SERS sensitivity with an enhancement factor of 5.6 × 10 7 and maintains excellent recyclability and reproducibility with relative standard deviation (RSD) values of less than 8%. On the basis of the platform, we developed a highly sensitive bovine serum albumin (BSA)-coated 4-mercaptopyridine (4-MPy)-linked (BMP) SERS-based pH sensor to report pH ranging from pH 3.0 to pH 8.0. The intensity ratio variation of 1004 and 1096 cm -1 in 4-MPy showed excellent pH sensitivity, which decreased as the surrounding pH increased. Furthermore, this BMP SERS-based pH sensor was employed to measure the pH value in C57BL/6 mouse blood. We have demonstrated that the pH sensor has great advantages such as good stability, reliability, and accuracy, which could be extended for the design of point-of-care devices.

A bioanalytical platform for simultaneous detection and quantification of biological toxins.

PubMed

Weingart, Oliver G; Gao, Hui; Crevoisier, François; Heitger, Friedrich; Avondet, Marc-André; Sigrist, Hans

2012-01-01

Prevalent incidents support the notion that toxins, produced by bacteria, fungi, plants or animals are increasingly responsible for food poisoning or intoxication. Owing to their high toxicity some toxins are also regarded as potential biological warfare agents. Accordingly, control, detection and neutralization of toxic substances are a considerable economic burden to food safety, health care and military biodefense. The present contribution describes a new versatile instrument and related procedures for array-based simultaneous detection of bacterial and plant toxins using a bioanalytical platform which combines the specificity of covalently immobilized capture probes with a dedicated instrumentation and immuno-based microarray analytics. The bioanalytical platform consists of a microstructured polymer slide serving both as support of printed arrays and as incubation chamber. The platform further includes an easy-to-operate instrument for simultaneous slide processing at selectable assay temperature. Cy5 coupled streptavidin is used as unifying fluorescent tracer. Fluorescence image analysis and signal quantitation allow determination of the toxin's identity and concentration. The system's performance has been investigated by immunological detection of Botulinum Neurotoxin type A (BoNT/A), Staphylococcal enterotoxin B (SEB), and the plant toxin ricin. Toxins were detectable at levels as low as 0.5-1 ng · mL(-1) in buffer or in raw milk.

A Bioanalytical Platform for Simultaneous Detection and Quantification of Biological Toxins

PubMed Central

Weingart, Oliver G.; Gao, Hui; Crevoisier, François; Heitger, Friedrich; Avondet, Marc-André; Sigrist, Hans

2012-01-01

Prevalent incidents support the notion that toxins, produced by bacteria, fungi, plants or animals are increasingly responsible for food poisoning or intoxication. Owing to their high toxicity some toxins are also regarded as potential biological warfare agents. Accordingly, control, detection and neutralization of toxic substances are a considerable economic burden to food safety, health care and military biodefense. The present contribution describes a new versatile instrument and related procedures for array-based simultaneous detection of bacterial and plant toxins using a bioanalytical platform which combines the specificity of covalently immobilized capture probes with a dedicated instrumentation and immuno-based microarray analytics. The bioanalytical platform consists of a microstructured polymer slide serving both as support of printed arrays and as incubation chamber. The platform further includes an easy-to-operate instrument for simultaneous slide processing at selectable assay temperature. Cy5 coupled streptavidin is used as unifying fluorescent tracer. Fluorescence image analysis and signal quantitation allow determination of the toxin’s identity and concentration. The system’s performance has been investigated by immunological detection of Botulinum Neurotoxin type A (BoNT/A), Staphylococcal enterotoxin B (SEB), and the plant toxin ricin. Toxins were detectable at levels as low as 0.5–1 ng·mL−1 in buffer or in raw milk. PMID:22438766

Design, implementation, and application of a microresonator platform for measuring energy dissipation by internal friction in nanowires.

PubMed

Das, Kaushik; Sosale, Guruprasad; Vengallatore, Srikar

2012-12-21

Accurate measurements of internal friction in nanowires are required for the rational design of high-Q resonators used in nanoelectromechanical systems and for fundamental studies of nanomechanical behavior. However, measuring internal friction is challenging because of the difficulties associated with identifying the contributions of material dissipation to structural damping. Here, we present an approach for overcoming these difficulties by using a composite microresonator platform that is calibrated against the ultimate limits of thermoelastic damping. The platform consists of an array of nanowires patterned at the root of a low-loss single-crystal silicon microcantilever. The structure is processed using a lift-off technique, implemented using electron-beam lithography, to achieve excellent control over the size, alignment, dispersion and location of the nanowire array. As the first application of this platform, we measured internal friction at room temperature in aluminum nanowires that ranged from 50 to 100 nm in thickness and 100 to 400 nm in width. Internal friction is ~0.03 at frequencies of 6.5-21 kHz. Transmission electron microscopy of the nanocrystalline grain structure, and comparison with previously measured values of internal friction in continuous thin films of aluminum, suggest that grain-boundary sliding is a major source of internal friction in these nanowires.

Multiplexed protein detection using antibody-conjugated microbead arrays in a microfabricated electrophoretic device

PubMed Central

Barbee, Kristopher D.; Hsiao, Alexander P.; Roller, Eric E.; Huang, Xiaohua

2011-01-01

We report the development of a microfabricated electrophoretic device for assembling high-density arrays of antibody-conjugated microbeads for chip-based protein detection. The device consists of a flow cell formed between a gold-coated silicon chip with an array of microwells etched in a silicon dioxide film and a glass coverslip with a series of thin gold counter electrode lines. We have demonstrated that 0.4 and 1 μm beads conjugated with antibodies can be rapidly assembled into the microwells by applying a pulsed electric field across the chamber. By assembling step-wise a mixture of fluorescently labeled antibody-conjugated microbeads, we incorporated both spatial and fluorescence encoding strategies to demonstrate significant multiplexing capabilities. We have shown that these antibody-conjugated microbead arrays can be used to perform on-chip sandwich immunoassays to detect test antigens at concentrations as low as 40 pM (6 ng/mL). A finite element model was also developed to examine the electric field distribution within the device for different counter electrode configurations over a range of line pitches and chamber heights. This device will be useful for assembling high-density, encoded antibody arrays for multiplexed detection of proteins and other types of protein-conjugated microbeads for applications such as the analysis of protein-protein interactions. PMID:20820631

Establishment and Comparison of Two Different Diagnostic Platforms for Detection of DENV1 NS1 Protein

PubMed Central

Tang, Yin-Liang; Chiu, Chien-Yu; Lin, Chun-Yu; Huang, Chung-Hao; Chen, Yen-Hsu; Destura, Raul V.; Chao, Day-Yu; Wu, Han-Chung

2015-01-01

Dengue virus (DENV) infection is currently at pandemic levels, with populations in tropical and subtropical regions at greatest risk of infection. Early diagnosis and management remain the cornerstone for good clinical outcomes, thus efficient and accurate diagnostic technology in the early stage of the disease is urgently needed. Serotype-specific monoclonal antibodies (mAbs) against the DENV1 nonstructural protein 1 (NS1), DA12-4, DA13-2, and DA15-3, which were recently generated using the hybridoma technique, are suitable for use in diagnostic platforms. Immunofluorescence assay (IFA), enzyme-linked immunosorbent assay (ELISA) and Western blot analysis further confirmed the serotype specificity of these three monoclonal antibodies. The ELISA-based diagnostic platform was established using the combination of two highly sensitive mAbs (DA15-3 and DB20-6). The same combination was also used for the flow cytometry-based diagnostic platform. We report here the detection limits of flow cytometry-based and ELISA-based diagnostic platforms using these mAbs to be 0.1 and 1 ng/mL, respectively. The collected clinical patient serum samples were also assayed by these two serotyping diagnostic platforms. The sensitivity and specificity for detecting NS1 protein of DENV1 are 90% and 96%, respectively. The accuracy of our platform for testing clinical samples is more advanced than that of the two commercial NS1 diagnostic platforms. In conclusion, our platforms are suitable for the early detection of NS1 protein in DENV1 infected patients. PMID:26610481

High-throughput screening based on label-free detection of small molecule microarrays

NASA Astrophysics Data System (ADS)

Zhu, Chenggang; Fei, Yiyan; Zhu, Xiangdong

2017-02-01

Based on small-molecule microarrays (SMMs) and oblique-incidence reflectivity difference (OI-RD) scanner, we have developed a novel high-throughput drug preliminary screening platform based on label-free monitoring of direct interactions between target proteins and immobilized small molecules. The screening platform is especially attractive for screening compounds against targets of unknown function and/or structure that are not compatible with functional assay development. In this screening platform, OI-RD scanner serves as a label-free detection instrument which is able to monitor about 15,000 biomolecular interactions in a single experiment without the need to label any biomolecule. Besides, SMMs serves as a novel format for high-throughput screening by immobilization of tens of thousands of different compounds on a single phenyl-isocyanate functionalized glass slide. Based on the high-throughput screening platform, we sequentially screened five target proteins (purified target proteins or cell lysate containing target protein) in high-throughput and label-free mode. We found hits for respective target protein and the inhibition effects for some hits were confirmed by following functional assays. Compared to traditional high-throughput screening assay, the novel high-throughput screening platform has many advantages, including minimal sample consumption, minimal distortion of interactions through label-free detection, multi-target screening analysis, which has a great potential to be a complementary screening platform in the field of drug discovery.

Photoacoustic and Ultrasonic Image-Guided Needle Biopsy of the Prostate

DTIC Science & Technology

2015-02-01

demonstrated in Figures 2 & 3 were performed with a linear array coupled with a Verasonics Vantage 128 US system ( Verasonics Inc., Redmond, WA...the Verasonics ultrasound platform, is suited for eventual clinical trials. The Verasonics acquisition is coordinated with a LabVIEW data...Recently we acquired and integrated an ATL C9-5 end-fire transrectal array (Philips Medical Systems, Bothell, WA) with our Verasonics system. Figure 3

A novel biosensor array with a wheel-like pattern for glucose, lactate and choline based on electrochemiluminescence imaging.

PubMed

Zhou, Zhenyu; Xu, Linru; Wu, Suozhu; Su, Bin

2014-10-07

Electrochemiluminescence (ECL) imaging provides a superior approach to achieve array detection because of its ability for ultrasensitive multiplex analysis. In this paper, we reported a novel ECL imaging biosensor array modified with an enzyme/carbon nanotubes/chitosan composite film for the determination of glucose, choline and lactate. The biosensor array was constructed by integrating a patterned indium tin oxide (ITO) glass plate with six perforated poly(dimethylsiloxane) (PDMS) covers. ECL is generated by the electrochemical reaction between luminol and hydrogen peroxide that is produced by the enzyme catalysed oxidation of different substrates with molecular oxygen, and ECL images were captured by a charge-coupled device (CCD) camera. The separated electrochemical micro-cells enabled simultaneous assay of six samples at different concentrations. From the established calibration curves, the detection limits were 14 μM for glucose, 40 μM for lactate and 97 μM for choline, respectively. Moreover, multicomponent assays and cross reactivity were also studied, both of which were satisfied for the analysis. This biosensing platform based on ECL imaging shows many distinct advantages, including miniaturization, low cost, and multi-functionalization. We believe that this novel ECL imaging biosensor platform will have potential applications in clinical diagnostics, medicine and food inspection.

A paper-based microbial fuel cell array for rapid and high-throughput screening of electricity-producing bacteria.

PubMed

Choi, Gihoon; Hassett, Daniel J; Choi, Seokheun

2015-06-21

There is a large global effort to improve microbial fuel cell (MFC) techniques and advance their translational potential toward practical, real-world applications. Significant boosts in MFC performance can be achieved with the development of new techniques in synthetic biology that can regulate microbial metabolic pathways or control their gene expression. For these new directions, a high-throughput and rapid screening tool for microbial biopower production is needed. In this work, a 48-well, paper-based sensing platform was developed for the high-throughput and rapid characterization of the electricity-producing capability of microbes. 48 spatially distinct wells of a sensor array were prepared by patterning 48 hydrophilic reservoirs on paper with hydrophobic wax boundaries. This paper-based platform exploited the ability of paper to quickly wick fluid and promoted bacterial attachment to the anode pads, resulting in instant current generation upon loading of the bacterial inoculum. We validated the utility of our MFC array by studying how strategic genetic modifications impacted the electrochemical activity of various Pseudomonas aeruginosa mutant strains. Within just 20 minutes, we successfully determined the electricity generation capacity of eight isogenic mutants of P. aeruginosa. These efforts demonstrate that our MFC array displays highly comparable performance characteristics and identifies genes in P. aeruginosa that can trigger a higher power density.

A systems approach to designing next generation vaccines: combining α-galactose modified antigens with nanoparticle platforms

NASA Astrophysics Data System (ADS)

Phanse, Yashdeep; Carrillo-Conde, Brenda R.; Ramer-Tait, Amanda E.; Broderick, Scott; Kong, Chang Sun; Rajan, Krishna; Flick, Ramon; Mandell, Robert B.; Narasimhan, Balaji; Wannemuehler, Michael J.

2014-01-01

Innovative vaccine platforms are needed to develop effective countermeasures against emerging and re-emerging diseases. These platforms should direct antigen internalization by antigen presenting cells and promote immunogenic responses. This work describes an innovative systems approach combining two novel platforms, αGalactose (αGal)-modification of antigens and amphiphilic polyanhydride nanoparticles as vaccine delivery vehicles, to rationally design vaccine formulations. Regimens comprising soluble αGal-modified antigen and nanoparticle-encapsulated unmodified antigen induced a high titer, high avidity antibody response with broader epitope recognition of antigenic peptides than other regimen. Proliferation of antigen-specific CD4+ T cells was also enhanced compared to a traditional adjuvant. Combining the technology platforms and augmenting immune response studies with peptide arrays and informatics analysis provides a new paradigm for rational, systems-based design of next generation vaccine platforms against emerging and re-emerging pathogens.

Functional comparison of microarray data across multiple platforms using the method of percentage of overlapping functions.

PubMed

Li, Zhiguang; Kwekel, Joshua C; Chen, Tao

2012-01-01

Functional comparison across microarray platforms is used to assess the comparability or similarity of the biological relevance associated with the gene expression data generated by multiple microarray platforms. Comparisons at the functional level are very important considering that the ultimate purpose of microarray technology is to determine the biological meaning behind the gene expression changes under a specific condition, not just to generate a list of genes. Herein, we present a method named percentage of overlapping functions (POF) and illustrate how it is used to perform the functional comparison of microarray data generated across multiple platforms. This method facilitates the determination of functional differences or similarities in microarray data generated from multiple array platforms across all the functions that are presented on these platforms. This method can also be used to compare the functional differences or similarities between experiments, projects, or laboratories.

Multi-mode sensor processing on a dynamically reconfigurable massively parallel processor array

NASA Astrophysics Data System (ADS)

Chen, Paul; Butts, Mike; Budlong, Brad; Wasson, Paul

2008-04-01

This paper introduces a novel computing architecture that can be reconfigured in real time to adapt on demand to multi-mode sensor platforms' dynamic computational and functional requirements. This 1 teraOPS reconfigurable Massively Parallel Processor Array (MPPA) has 336 32-bit processors. The programmable 32-bit communication fabric provides streamlined inter-processor connections with deterministically high performance. Software programmability, scalability, ease of use, and fast reconfiguration time (ranging from microseconds to milliseconds) are the most significant advantages over FPGAs and DSPs. This paper introduces the MPPA architecture, its programming model, and methods of reconfigurability. An MPPA platform for reconfigurable computing is based on a structural object programming model. Objects are software programs running concurrently on hundreds of 32-bit RISC processors and memories. They exchange data and control through a network of self-synchronizing channels. A common application design pattern on this platform, called a work farm, is a parallel set of worker objects, with one input and one output stream. Statically configured work farms with homogeneous and heterogeneous sets of workers have been used in video compression and decompression, network processing, and graphics applications.

Co-fabrication of chitosan and epoxy photoresist to form microwell arrays with permeable hydrogel bottoms

PubMed Central

Ornoff, Douglas M.; Wang, Yuli; Proctor, Angela; Shah, Akash S.; Allbritton, Nancy L.

2015-01-01

Microfabrication technology offers the potential to create biological platforms with customizable patterns and surface chemistries, allowing precise control over the biochemical microenvironment to which a cell or group of cells is exposed. However, most microfabricated platforms grow cells on impermeable surfaces. This report describes the co-fabrication of a micropatterned epoxy photoresist film with a chitosan film to create a freestanding array of permeable, hydrogel-bottomed microwells. These films possess optical properties ideal for microscopy applications, and the chitosan layers are semi-permeable with a molecular exclusion of 9.9 ± 2.1 kDa. By seeding cells into the microwells, overlaying inert mineral oil, and supplying media via the bottom surface, this hybrid film permits cells to be physically isolated from one another but maintained in culture for at least 4 days. Arrays co-fabricated using these materials reduce both large-molecular-weight biochemical crosstalk between cells and mixing of different clonal populations, and will enable high-throughput studies of cellular heterogeneity with increased ability to customize dynamic interrogations compared to materials in currently available technologies. PMID:26447557

A Highly Sensitive Porous Silicon (P-Si)-Based Human Kallikrein 2 (hK2) Immunoassay Platform toward Accurate Diagnosis of Prostate Cancer

PubMed Central

Lee, Sang Wook; Hosokawa, Kazuo; Kim, Soyoun; Jeong, Ok Chan; Lilja, Hans; Laurell, Thomas; Maeda, Mizuo

2015-01-01

Levels of total human kallikrein 2 (hK2), a protein involved the pathology of prostate cancer (PCa), could be used as a biomarker to aid in the diagnosis of this disease. In this study, we report on a porous silicon antibody immunoassay platform for the detection of serum levels of total hK2. The surface of porous silicon has a 3-dimensional macro- and nanoporous structure, which offers a large binding capacity for capturing probe molecules. The tailored pore size of the porous silicon also allows efficient immobilization of antibodies by surface adsorption, and does not require chemical immobilization. Monoclonal hK2 capture antibody (6B7) was dispensed onto P-Si chip using a piezoelectric dispenser. In total 13 × 13 arrays (169 spots) were spotted on the chip with its single spot volume of 300 pL. For an optimization of capture antibody condition, we firstly performed an immunoassay of the P-Si microarray under a titration series of hK2 in pure buffer (PBS) at three different antibody densities (75, 100 and 145 µg/mL). The best performance of the microarray platform was seen at 100 µg/mL of the capture antibody concentration (LOD was 100 fg/mL). The platform then was subsequently evaluated for a titration series of serum-spiked hK2 samples. The developed platform utilizes only 15 µL of serum per test and the total assay time is about 3 h, including immobilization of the capture antibody. The detection limit of the hK2 assay was 100 fg/mL in PBS buffer and 1 pg/mL in serum with a dynamic range of 106 (10−4 to 102 ng/mL). PMID:26007739

A Highly Sensitive Porous Silicon (P-Si)-Based Human Kallikrein 2 (hK2) Immunoassay Platform toward Accurate Diagnosis of Prostate Cancer.

PubMed

Lee, Sang Wook; Hosokawa, Kazuo; Kim, Soyoun; Jeong, Ok Chan; Lilja, Hans; Laurell, Thomas; Maeda, Mizuo

2015-05-22

Levels of total human kallikrein 2 (hK2), a protein involved the pathology of prostate cancer (PCa), could be used as a biomarker to aid in the diagnosis of this disease. In this study, we report on a porous silicon antibody immunoassay platform for the detection of serum levels of total hK2. The surface of porous silicon has a 3-dimensional macro- and nanoporous structure, which offers a large binding capacity for capturing probe molecules. The tailored pore size of the porous silicon also allows efficient immobilization of antibodies by surface adsorption, and does not require chemical immobilization. Monoclonal hK2 capture antibody (6B7) was dispensed onto P-Si chip using a piezoelectric dispenser. In total 13 × 13 arrays (169 spots) were spotted on the chip with its single spot volume of 300 pL. For an optimization of capture antibody condition, we firstly performed an immunoassay of the P-Si microarray under a titration series of hK2 in pure buffer (PBS) at three different antibody densities (75, 100 and 145 µg/mL). The best performance of the microarray platform was seen at 100 µg/mL of the capture antibody concentration (LOD was 100 fg/mL). The platform then was subsequently evaluated for a titration series of serum-spiked hK2 samples. The developed platform utilizes only 15 µL of serum per test and the total assay time is about 3 h, including immobilization of the capture antibody. The detection limit of the hK2 assay was 100 fg/mL in PBS buffer and 1 pg/mL in serum with a dynamic range of 106 (10(-4) to 10(2) ng/mL).

Monolithic integration of a silica AWG and Ge photodiodes on Si photonic platform for one-chip WDM receiver.

PubMed

Nishi, Hidetaka; Tsuchizawa, Tai; Kou, Rai; Shinojima, Hiroyuki; Yamada, Takashi; Kimura, Hideaki; Ishikawa, Yasuhiko; Wada, Kazumi; Yamada, Koji

2012-04-09

On the silicon (Si) photonic platform, we monolithically integrated a silica-based arrayed-waveguide grating (AWG) and germanium (Ge) photodiodes (PDs) using low-temperature fabrication technology. We confirmed demultiplexing by the AWG, optical-electrical signal conversion by Ge PDs, and high-speed signal detection at all channels. In addition, we mounted a multichannel transimpedance amplifier/limiting amplifier (TIA/LA) circuit on the fabricated AWG-PD device using flip-chip bonding technology. The results show the promising potential of our Si photonic platform as a photonics-electronics convergence.

A Hardware Platform for Tuning of MEMS Devices Using Closed-Loop Frequency Response

NASA Technical Reports Server (NTRS)

Ferguson, Michael I.; MacDonald, Eric; Foor, David

2005-01-01

We report on the development of a hardware platform for integrated tuning and closed-loop operation of MEMS gyroscopes. The platform was developed and tested for the second generation JPL/Boeing Post-Resonator MEMS gyroscope. The control of this device is implemented through a digital design on a Field Programmable Gate Array (FPGA). A software interface allows the user to configure, calibrate, and tune the bias voltages on the micro-gyro. The interface easily transitions to an embedded solution that allows for the miniaturization of the system to a single chip.

Suspended microfluidics.

PubMed

Casavant, Benjamin P; Berthier, Erwin; Theberge, Ashleigh B; Berthier, Jean; Montanez-Sauri, Sara I; Bischel, Lauren L; Brakke, Kenneth; Hedman, Curtis J; Bushman, Wade; Keller, Nancy P; Beebe, David J

2013-06-18

Although the field of microfluidics has made significant progress in bringing new tools to address biological questions, the accessibility and adoption of microfluidics within the life sciences are still limited. Open microfluidic systems have the potential to lower the barriers to adoption, but the absence of robust design rules has hindered their use. Here, we present an open microfluidic platform, suspended microfluidics, that uses surface tension to fill and maintain a fluid in microscale structures devoid of a ceiling and floor. We developed a simple and ubiquitous model predicting fluid flow in suspended microfluidic systems and show that it encompasses many known capillary phenomena. Suspended microfluidics was used to create arrays of collagen membranes, mico Dots (μDots), in a horizontal plane separating two fluidic chambers, demonstrating a transwell platform able to discern collective or individual cellular invasion. Further, we demonstrated that μDots can also be used as a simple multiplexed 3D cellular growth platform. Using the μDot array, we probed the combined effects of soluble factors and matrix components, finding that laminin mitigates the growth suppression properties of the matrix metalloproteinase inhibitor GM6001. Based on the same fluidic principles, we created a suspended microfluidic metabolite extraction platform using a multilayer biphasic system that leverages the accessibility of open microchannels to retrieve steroids and other metabolites readily from cell culture. Suspended microfluidics brings the high degree of fluidic control and unique functionality of closed microfluidics into the highly accessible and robust platform of open microfluidics.

Suspended microfluidics

PubMed Central

Casavant, Benjamin P.; Berthier, Erwin; Theberge, Ashleigh B.; Berthier, Jean; Montanez-Sauri, Sara I.; Bischel, Lauren L.; Brakke, Kenneth; Hedman, Curtis J.; Bushman, Wade; Keller, Nancy P.; Beebe, David J.

2013-01-01

Although the field of microfluidics has made significant progress in bringing new tools to address biological questions, the accessibility and adoption of microfluidics within the life sciences are still limited. Open microfluidic systems have the potential to lower the barriers to adoption, but the absence of robust design rules has hindered their use. Here, we present an open microfluidic platform, suspended microfluidics, that uses surface tension to fill and maintain a fluid in microscale structures devoid of a ceiling and floor. We developed a simple and ubiquitous model predicting fluid flow in suspended microfluidic systems and show that it encompasses many known capillary phenomena. Suspended microfluidics was used to create arrays of collagen membranes, mico Dots (μDots), in a horizontal plane separating two fluidic chambers, demonstrating a transwell platform able to discern collective or individual cellular invasion. Further, we demonstrated that μDots can also be used as a simple multiplexed 3D cellular growth platform. Using the μDot array, we probed the combined effects of soluble factors and matrix components, finding that laminin mitigates the growth suppression properties of the matrix metalloproteinase inhibitor GM6001. Based on the same fluidic principles, we created a suspended microfluidic metabolite extraction platform using a multilayer biphasic system that leverages the accessibility of open microchannels to retrieve steroids and other metabolites readily from cell culture. Suspended microfluidics brings the high degree of fluidic control and unique functionality of closed microfluidics into the highly accessible and robust platform of open microfluidics. PMID:23729815

Microfabricated Nickel Based Sensors for Hostile and High Pressure Environments

NASA Astrophysics Data System (ADS)

Holt, Christopher Michael Bjustrom

This thesis outlines the development of two platforms for integrating microfabricated sensors with high pressure feedthroughs for application in hostile high temperature high pressure environments. An application in oil well production logging is explored and two sensors were implemented with these platforms for application in an oil well. The first platform developed involved microfabrication directly onto a cut and polished high pressure feedthrough. This technique enables a system that is more robust than the wire bonded silicon die technique used for MEMS integration in pressure sensors. Removing wire bonds from the traditional MEMS package allows for direct interface of a microfabricated sensor with a hostile high pressure fluid environment which is not currently possible. During the development of this platform key performance metrics included pressure testing to 70MPa and temperature cycling from 20°C to 200°C. This platform enables electronics integration with a variety of microfabricated electrical and thermal based sensors which can be immersed within the oil well environment. The second platform enabled free space fabrication of nickel microfabricated devices onto an array of pins using a thick tin sacrificial layer. This technique allowed microfabrication of metal MEMS that are released by distances of 1cm from their substrate. This method is quite flexible and allows for fabrication to be done on any pin array substrate regardless of surface quality. Being able to place released MEMS sensors directly onto traditional style circuit boards, ceramic circuit boards, electrical connectors, ribbon cables, pin headers, or high pressure feedthroughs greatly improves the variety of possible applications and reduces fabrication costs. These two platforms were then used to fabricate thermal conductivity sensors that showed excellent performance for distinguishing between oil, water, and gas phases. Testing was conducted at various flow rates and performance of the released platform was shown to be better than the performance seen in the anchored sensors while both platforms were significantly better than a simply fabricated wrapped wire sensor. The anchored platform was also used to demonstrate a traditional capacitance based fluid dielectric sensor which was found to work similarly to conventional commercial capacitance probes while being significantly smaller in size.

Development of an inducible platform for intercellular protein delivery.

PubMed

Siller, Richard; Dufour, Eric; Lycke, Max; Wilmut, Ian; Jung, Yong-Wook; Park, In Hyun; Sullivan, Gareth J

2017-04-30

A challenge to protein based therapies is the ability to produce biologically active proteins and their ensured delivery. Various approaches have been utilised including fusion of protein transduction domains with a protein or biomolecule of interest. A compounding issue is lack of specificity, efficiency and indeed whether the protein fusions are actually translocated into the cell and not merely an artefact of the fixation process. Here we present a novel platform, allowing the inducible export and uptake of a protein of interest. The system utilises a combination of the Tetracyline repressor system, combined with a fusion protein containing the N-terminal signal peptide from human chorionic gonadotropin beta-subunit, and a C-terminal poly-arginine domain for efficient uptake by target cells. This novel platform was validated using enhanced green fluorescent protein as the gene of interest. Doxycycline efficiently induced expression of the fusion protein. The human chorionic gonadotropin beta-subunit facilitated the export of the fusion protein into the cell culture media. Finally, the fusion protein was able to efficiently enter into neighbouring cells (target cells), mediated by the poly-arginine cell penetrating peptide. Importantly we have addressed the issue of whether the observed uptake is an artefact of the fixation process or indeed genuine translocation. In addition this platform provides a number of potential applications in diverse areas such as stem cell biology, immune therapy and cancer targeting therapies. Copyright © 2017 Elsevier B.V. All rights reserved.

A multimode electromechanical parametric resonator array

PubMed Central

Mahboob, I.; Mounaix, M.; Nishiguchi, K.; Fujiwara, A.; Yamaguchi, H.

2014-01-01

Electromechanical resonators have emerged as a versatile platform in which detectors with unprecedented sensitivities and quantum mechanics in a macroscopic context can be developed. These schemes invariably utilise a single resonator but increasingly the concept of an array of electromechanical resonators is promising a wealth of new possibilities. In spite of this, experimental realisations of such arrays have remained scarce due to the formidable challenges involved in their fabrication. In a variation to this approach, we identify 75 harmonic vibration modes in a single electromechanical resonator of which 7 can also be parametrically excited. The parametrically resonating modes exhibit vibrations with only 2 oscillation phases which are used to build a binary information array. We exploit this array to execute a mechanical byte memory, a shift-register and a controlled-NOT gate thus vividly illustrating the availability and functionality of an electromechanical resonator array by simply utilising higher order vibration modes. PMID:24658349

Nine-channel wavelength tunable single mode laser array based on slots.

PubMed

Guo, Wei-Hua; Lu, Qiaoyin; Nawrocka, Marta; Abdullaev, Azat; O'Callaghan, James; Donegan, John F

2013-04-22

A 9-channel wavelength tunable single-mode laser array based on slots is presented. The fabricated laser array demonstrated a threshold current in a range of 19~21 mA with the SOA unbiased at 20°C under continuous wave condition. Stable single mode performances have been observed with side-mode suppression-ratio (SMSR) > 50 dB. The output power higher than 37 mW was obtained at the SOA injected current of 70 mA for all the 9 channels within the laser array. A wavelength quasi-continuous tuning range of about 27 nm has been achieved for the laser array with the temperature variations from 10°C to 45°C. This array platform is of a single growth and monolithically integrable. It can be easily fabricated by standard photolithography. In addition, it potentially removes the yield problem due to the uncertainty of the facet cleaving.

Integrated optical phased arrays for quasi-Bessel-beam generation.

PubMed

Notaros, Jelena; Poulton, Christopher V; Byrd, Matthew J; Raval, Manan; Watts, Michael R

2017-09-01

Integrated optical phased arrays for generating quasi-Bessel beams are proposed and experimentally demonstrated in a CMOS-compatible platform. Owing to their elongated central beams, Bessel beams have applications in a range of fields, including multiparticle trapping and laser lithography. In this Letter, continuous Bessel theory is manipulated to formulate the phase and amplitude conditions necessary for generating free-space-propagating Bessel-Gauss beams using on-chip optical phased arrays. Discussion of the effects of select phased array parameters on the generated beam's figures of merit is included. A one-dimensional splitter-tree-based phased array architecture is modified to enable arbitrary passive control of the array's element phase and amplitude distributions. This architecture is used to experimentally demonstrate on-chip quasi-Bessel-beam generation with a ∼14  mm Bessel length and ∼30  μm power full width at half maximum.

Micropatterned arrays of porous silicon: toward sensory biointerfaces.

PubMed

Flavel, Benjamin S; Sweetman, Martin J; Shearer, Cameron J; Shapter, Joseph G; Voelcker, Nicolas H

2011-07-01

We describe the fabrication of arrays of porous silicon spots by means of photolithography where a positive photoresist serves as a mask during the anodization process. In particular, photoluminescent arrays and porous silicon spots suitable for further chemical modification and the attachment of human cells were created. The produced arrays of porous silicon were chemically modified by means of a thermal hydrosilylation reaction that facilitated immobilization of the fluorescent dye lissamine, and alternatively, the cell adhesion peptide arginine-glycine-aspartic acid-serine. The latter modification enabled the selective attachment of human lens epithelial cells on the peptide functionalized regions of the patterns. This type of surface patterning, using etched porous silicon arrays functionalized with biological recognition elements, presents a new format of interfacing porous silicon with mammalian cells. Porous silicon arrays with photoluminescent properties produced by this patterning strategy also have potential applications as platforms for in situ monitoring of cell behavior.

Non-Faradaic electrochemical detection of protein interactions by integrated neuromorphic CMOS sensors.

PubMed

Jacquot, Blake C; Muñoz, Nini; Branch, Darren W; Kan, Edwin C

2008-05-15

Electronic detection of the binding event between biotinylated bovine serum albumen (BSA) and streptavidin is demonstrated with the chemoreceptive neuron MOS (CnuMOS) device. Differing from the ion-sensitive field-effect transistors (ISFET), CnuMOS, with the potential of the extended floating gate determined by both the sensing and control gates in a neuromorphic style, can provide protein detection without requiring analyte reference electrodes. In comparison with the microelectrode arrays, measurements are gathered through purely capacitive, non-Faradaic interactions across insulating interfaces. By using a (3-glycidoxypropyl)trimethoxysilane (3-GPS) self-assembled monolayer (SAM) as a simple covalent link for attaching proteins to a silicon dioxide sensing surface, a fully integrated, electrochemical detection platform is realized for protein interactions through monotone large-signal measurements or small-signal impedance spectroscopy. Calibration curves were created to coordinate the sensor response with ellipsometric measurements taken on witness samples. By monitoring the film thickness of streptavidin capture, a sensitivity of 25ng/cm2 or 2A of film thickness was demonstrated. With an improved noise floor the sensor can detect down to 2ng/(cm2mV) based on the calibration curve. AC measurements are shown to significantly reduce long-term sensor drift. Finally, a noise analysis of electrochemical data indicates 1/f(alpha) behavior with a noise floor beginning at approximately 1Hz.

Digital Microarrays: Single-Molecule Readout with Interferometric Detection of Plasmonic Nanorod Labels.

PubMed

Sevenler, Derin; Daaboul, George G; Ekiz Kanik, Fulya; Ünlü, Neşe Lortlar; Ünlü, M Selim

2018-05-21

DNA and protein microarrays are a high-throughput technology that allow the simultaneous quantification of tens of thousands of different biomolecular species. The mediocre sensitivity and limited dynamic range of traditional fluorescence microarrays compared to other detection techniques have been the technology's Achilles' heel and prevented their adoption for many biomedical and clinical diagnostic applications. Previous work to enhance the sensitivity of microarray readout to the single-molecule ("digital") regime have either required signal amplifying chemistry or sacrificed throughput, nixing the platform's primary advantages. Here, we report the development of a digital microarray which extends both the sensitivity and dynamic range of microarrays by about 3 orders of magnitude. This technique uses functionalized gold nanorods as single-molecule labels and an interferometric scanner which can rapidly enumerate individual nanorods by imaging them with a 10× objective lens. This approach does not require any chemical signal enhancement such as silver deposition and scans arrays with a throughput similar to commercial fluorescence scanners. By combining single-nanoparticle enumeration and ensemble measurements of spots when the particles are very dense, this system achieves a dynamic range of about 6 orders of magnitude directly from a single scan. As a proof-of-concept digital protein microarray assay, we demonstrated detection of hepatitis B virus surface antigen in buffer with a limit of detection of 3.2 pg/mL. More broadly, the technique's simplicity and high-throughput nature make digital microarrays a flexible platform technology with a wide range of potential applications in biomedical research and clinical diagnostics.

Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy.

PubMed

Jung, Ki-Hong; Dardick, Christopher; Bartley, Laura E; Cao, Peijian; Phetsom, Jirapa; Canlas, Patrick; Seo, Young-Su; Shultz, Michael; Ouyang, Shu; Yuan, Qiaoping; Frank, Bryan C; Ly, Eugene; Zheng, Li; Jia, Yi; Hsia, An-Ping; An, Kyungsook; Chou, Hui-Hsien; Rocke, David; Lee, Geun Cheol; Schnable, Patrick S; An, Gynheung; Buell, C Robin; Ronald, Pamela C

2008-10-06

Studies of gene function are often hampered by gene-redundancy, especially in organisms with large genomes such as rice (Oryza sativa). We present an approach for using transcriptomics data to focus functional studies and address redundancy. To this end, we have constructed and validated an inexpensive and publicly available rice oligonucleotide near-whole genome array, called the rice NSF45K array. We generated expression profiles for light- vs. dark-grown rice leaf tissue and validated the biological significance of the data by analyzing sources of variation and confirming expression trends with reverse transcription polymerase chain reaction. We examined trends in the data by evaluating enrichment of gene ontology terms at multiple false discovery rate thresholds. To compare data generated with the NSF45K array with published results, we developed publicly available, web-based tools (www.ricearray.org). The Oligo and EST Anatomy Viewer enables visualization of EST-based expression profiling data for all genes on the array. The Rice Multi-platform Microarray Search Tool facilitates comparison of gene expression profiles across multiple rice microarray platforms. Finally, we incorporated gene expression and biochemical pathway data to reduce the number of candidate gene products putatively participating in the eight steps of the photorespiration pathway from 52 to 10, based on expression levels of putatively functionally redundant genes. We confirmed the efficacy of this method to cope with redundancy by correctly predicting participation in photorespiration of a gene with five paralogs. Applying these methods will accelerate rice functional genomics.

Digital detection of multiple minority mutants and expression levels of multiple colorectal cancer-related genes using digital-PCR coupled with bead-array.

PubMed

Huang, Huan; Li, Shuo; Sun, Lizhou; Zhou, Guohua

2015-01-01

To simultaneously analyze mutations and expression levels of multiple genes on one detection platform, we proposed a method termed "multiplex ligation-dependent probe amplification-digital amplification coupled with hydrogel bead-array" (MLPA-DABA) and applied it to diagnose colorectal cancer (CRC). CRC cells and tissues were sampled to extract nucleic acid, perform MLPA with sequence-tagged probes, perform digital emulsion polymerase chain reaction (PCR), and produce a hydrogel bead-array to immobilize beads and form a single bead layer on the array. After hybridization with fluorescent probes, the number of colored beads, which reflects the abundance of expressed genes and the mutation rate, was counted for diagnosis. Only red or green beads occurred on the chips in the mixed samples, indicating the success of single-molecule PCR. When a one-source sample was analyzed using mixed MLPA probes, beads of only one color occurred, suggesting the high specificity of the method in analyzing CRC mutation and gene expression. In gene expression analysis of a CRC tissue from one CRC patient, the mutant percentage was 3.1%, and the expression levels of CRC-related genes were much higher than those of normal tissue. The highly sensitive MLPA-DABA succeeds in the relative quantification of mutations and gene expressions of exfoliated cells in stool samples of CRC patients on the same chip platform. MLPA-DABA coupled with hydrogel bead-array is a promising method in the non-invasive diagnosis of CRC.

Transparent Nanopore Cavity Arrays Enable Highly Parallelized Optical Studies of Single Membrane Proteins on Chip.

PubMed

Diederichs, Tim; Nguyen, Quoc Hung; Urban, Michael; Tampé, Robert; Tornow, Marc

2018-06-13

Membrane proteins involved in transport processes are key targets for pharmaceutical research and industry. Despite continuous improvements and new developments in the field of electrical readouts for the analysis of transport kinetics, a well-suited methodology for high-throughput characterization of single transporters with nonionic substrates and slow turnover rates is still lacking. Here, we report on a novel architecture of silicon chips with embedded nanopore microcavities, based on a silicon-on-insulator technology for high-throughput optical readouts. Arrays containing more than 14 000 inverted-pyramidal cavities of 50 femtoliter volumes and 80 nm circular pore openings were constructed via high-resolution electron-beam lithography in combination with reactive ion etching and anisotropic wet etching. These cavities feature both, an optically transparent bottom and top cap. Atomic force microscopy analysis reveals an overall extremely smooth chip surface, particularly in the vicinity of the nanopores, which exhibits well-defined edges. Our unprecedented transparent chip design provides parallel and independent fluorescent readout of both cavities and buffer reservoir for unbiased single-transporter recordings. Spreading of large unilamellar vesicles with efficiencies up to 96% created nanopore-supported lipid bilayers, which are stable for more than 1 day. A high lipid mobility in the supported membrane was determined by fluorescent recovery after photobleaching. Flux kinetics of α-hemolysin were characterized at single-pore resolution with a rate constant of 0.96 ± 0.06 × 10 -3 s -1 . Here, we deliver an ideal chip platform for pharmaceutical research, which features high parallelism and throughput, synergistically combined with single-transporter resolution.

Multiplex array proteomics detects increased MMP-8 in CSF after spinal cord injury.

PubMed

Light, Matthew; Minor, Kenneth H; DeWitt, Peter; Jasper, Kyle H; Davies, Stephen J A

2012-06-11

A variety of methods have been used to study inflammatory changes in the acutely injured spinal cord. Recently novel multiplex assays have been used in an attempt to overcome limitations in numbers of available targets studied in a single experiment. Other technical challenges in developing pre-clinical rodent models to investigate biomarkers in cerebrospinal fluid (CSF) include relatively small volumes of sample and low concentrations of target proteins. The primary objective of this study was to characterize the inflammatory profile present in CSF at a subacute time point in a clinically relevant rodent model of traumatic spinal cord injury (SCI). Our other aim was to test a microarray proteomics platform specifically for this application. A 34 cytokine sandwich ELISA microarray was used to study inflammatory changes in CSF samples taken 12 days post-cervical SCI in adult rats. The difference between the median foreground signal and the median background signal was measured. Bonferroni and Benjamini-Hochburg multiple testing corrections were applied to limit the False Discovery Rate (FDR), and a linear mixed model was used to account for repeated measures in the array. We report a novel subacute SCI biomarker, elevated levels of matrix metalloproteinase-8 protein in CSF, and discuss application of statistical models designed for multiplex testing. Major advantages of this assay over conventional methods include high-throughput format, good sensitivity, and reduced sample consumption. This method can be useful for creating comprehensive inflammatory profiles, and biomarkers can be used in the clinic to assess injury severity and to objectively grade response to therapy.

3D Nanochannel Array Platform for High-throughput Cell Manipulation and Nano-electroporation

NASA Astrophysics Data System (ADS)

Chang, Lingqian

Electroporation is one of the most common non-viral methods for gene delivery. Recent progress in gene therapy has offered special opportunities to electroporation for in vitro and in vivo applications. However, conventional bulk electroporation (BEP) inevitably causes serious cell damage and stochastic transfection between cells. Microfluidic electroporation (MEP) has been claimed to provide benign single cell transfection for the last decade. Nevertheless, the intracellular transport in both MEP and BEP systems is highly diffusion-dominant, which prevents precise dose control and high uniformity. In this Ph.D. research, we developed a 3D nanochannel-electroporation (3D NEP) platform for mass cell transfection. A silicon-based nanochannel array (3D NEP) chip was designed and fabricated for cell manipulation and electroporation. The chip, designed as Z-directional microchannel - nanochannel array, was fabricated by clean room techniques including projection photolithography and deep reactive-ion etching (DRIE). The fabricated 3D NEP chip is capable of handling 40,000 cells per 1 cm2, up to 1 million per wafer (100 mm diameter). High-throughput cell manipulation technologies were investigated for precise alignment of individual cells to the nanochannel array, a key step for NEP to achieve dose control. We developed three techniques for cell trapping in this work. (1) Magnetic tweezers (MTs) were integrated on the chip to remotely control cells under a programmed magnetic field. (2) A positive dielectrophoresis (pDEP) power system was built as an alternative to trap cells onto the nanochannel array using DEP force. (3) A novel yet simple 'dipping-trap' method was used to rapidly trap cells onto a nanochannel array, aligned by a micro-cap array pattern on the 3D NEP chip, which eventually offered 70 - 90 % trapping efficiency and 90 % specificity. 3D NEP platforms were assembled for cell transfection based on the Si-based nanochannel array chip and cell manipulation techniques. Cells were patterned on the nanochannel array and collectively were electroporated in parallel, injected with cargo in Z-direction. Controlling the dose was demonstrated with the external pulse durations at high-throughput. The 'electrophoretic'- expedited delivery of large molecular weight plasmids were demonstrated with large numbers of primary cells simultaneously, which cannot be achieved in BEP and MEP. Two clinically valuable case studies were performed with our 3D NEP for living cell sensing / interrogation. (1) In the case of in vitro transfection of primary cardiomyocytes, we studied the dose-effects of miR-29 on mitochondrial changes and the suppression of the Mcl-1 gene in adult mouse cardiomyocytes by precisely controlling the miR-29 dose injected. (2) Glioma stem cells (GSCs), a type of cell hypothesized to be highly aggressive and to lead to the relapses of gliobastoma in human brain, was studied at single cell resolution on 3D NEP platform. The developed 3D NEP system moves towards clinically oriented and user-friendly tools for life science applications. The batch-treated cells with controlled dosage delivery provide a useful tool for single cell analysis. The pioneering experiments in this work have demonstrated the 3D NEP for the applications of cell reprogramming, adoptive immunotherapy, in vitro cardiomyocytes transfection and glioma stem cells study.

A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers.

PubMed

Şenbabaoğlu, Yasin; Sümer, Selçuk Onur; Sánchez-Vega, Francisco; Bemis, Debra; Ciriello, Giovanni; Schultz, Nikolaus; Sander, Chris

2016-02-01

Protein expression and post-translational modification levels are tightly regulated in neoplastic cells to maintain cellular processes known as 'cancer hallmarks'. The first Pan-Cancer initiative of The Cancer Genome Atlas (TCGA) Research Network has aggregated protein expression profiles for 3,467 patient samples from 11 tumor types using the antibody based reverse phase protein array (RPPA) technology. The resultant proteomic data can be utilized to computationally infer protein-protein interaction (PPI) networks and to study the commonalities and differences across tumor types. In this study, we compare the performance of 13 established network inference methods in their capacity to retrieve the curated Pathway Commons interactions from RPPA data. We observe that no single method has the best performance in all tumor types, but a group of six methods, including diverse techniques such as correlation, mutual information, and regression, consistently rank highly among the tested methods. We utilize the high performing methods to obtain a consensus network; and identify four robust and densely connected modules that reveal biological processes as well as suggest antibody-related technical biases. Mapping the consensus network interactions to Reactome gene lists confirms the pan-cancer importance of signal transduction pathways, innate and adaptive immune signaling, cell cycle, metabolism, and DNA repair; and also suggests several biological processes that may be specific to a subset of tumor types. Our results illustrate the utility of the RPPA platform as a tool to study proteomic networks in cancer.

HIFU Monitoring and Control with Dual-Mode Ultrasound Arrays

NASA Astrophysics Data System (ADS)

Casper, Andrew Jacob

The biological effects of high-intensity focused ultrasound (HIFU) have been known and studied for decades. HIFU has been shown capable of treating a wide variety of diseases and disorders. However, despite its demonstrated potential, HIFU has been slow to gain clinical acceptance. This is due, in part, to the difficulty associated with robustly monitoring and controlling the delivery of the HIFU energy. The non-invasive nature of the surgery makes the assessment of treatment progression difficult, leading to long treatment times and a significant risk of under treatment. This thesis research develops new techniques and systems for robustly monitoring HIFU therapies for the safe and efficacious delivery of the intended treatment. Systems and algorithms were developed for the two most common modes of HIFU delivery systems: single-element and phased array applicators. Delivering HIFU with a single element transducer is a widely used technique in HIFU therapies. The simplicity of a single element offers many benefits in terms of cost and overall system complexity. Typical monitoring schemes rely on an external device (e.g. diagnostic ultrasound or MRI) to assess the progression of therapy. The research presented in this thesis explores using the same element to both deliver and monitor the HIFU therapy. The use of a dual-mode ultrasound transducer (DMUT) required the development of an FPGA based single-channel arbitrary waveform generator and high-speed data acquisition unit. Data collected from initial uncontrolled ablations led to the development of monitoring and control algorithms which were implemented directly on the FPGA. Close integration between the data acquisition and arbitrary waveform units allowed for fast, low latency control over the ablation process. Results are presented that demonstrate control of HIFU therapies over a broad range of intensities and in multiple in vitro tissues. The second area of investigation expands the DMUT research to an ultrasound phased-array. The phased-array allows for electronic steering of the HIFU focus and imaging of the acoustic medium. Investigating the dual-mode ultrasound array (DMUA) required the design and construction of a novel ultrasound-guided focused ultrasound (USgFUS) platform. The platform consisted of custom hardware designed for the unique requirements of operating a phased-array in both therapeutic and imaging modes. The platform also required the development of FPGA based signal processing and GPU based beamforming algorithms for online monitoring of the therapy process. The results presented in this thesis represent the first demonstration of a real-time USgFUS platform based around a DMUA. Experimental imaging and therapy results from series of animal experiments, including a 12 animal GLP study, are presented. In addition, in vitro control results, which build upon the DMUT work, are presented.

Design, Fabrication, and In Vitro Testing of an Anti-biofouling Glaucoma Micro-shunt.

PubMed

Harake, Ryan S; Ding, Yuzhe; Brown, J David; Pan, Tingrui

2015-10-01

Glaucoma, one of the leading causes of irreversible blindness, is a progressive neurodegenerative disease. Chronic elevated intraocular pressure (IOP), a prime risk factor for glaucoma, can be treated by aqueous shunts, implantable devices, which reduce IOP in glaucoma patients by providing alternative aqueous outflow pathways. Although initially effective at delaying glaucoma progression, contemporary aqueous shunts often lead to numerous complications and only 50% of implanted devices remain functional after 5 years. In this work, we introduce a novel micro-device which provides an innovative platform for IOP reduction in glaucoma patients. The device design features an array of parallel micro-channels to provide precision aqueous outflow resistance control. Additionally, the device's microfluidic channels are composed of a unique combination of polyethylene glycol materials in order to provide enhanced biocompatibility and resistance to problematic channel clogging from biofouling of aqueous proteins. The microfabrication process employed to produce the devices results in additional advantages such as enhanced device uniformity and increased manufacturing throughput. Surface characterization experimental results show the device's surfaces exhibit significantly less non-specific protein adsorption compared to traditional implant materials. Results of in vitro flow experiments verify the device's ability to provide aqueous resistance control, continuous long-term stability through 10-day protein flow testing, and safety from risk of infection due to bacterial ingression.

Electrochemically mediated polymerization for highly sensitive detection of protein kinase activity.

PubMed

Hu, Qiong; Wang, Qiangwei; Jiang, Cuihua; Zhang, Jian; Kong, Jinming; Zhang, Xueji

2018-07-01

Protein kinases play a pivotal role in cellular regulation and signal transduction, the detection of protein kinase activity and inhibition is therefore of great importance to clinical diagnosis and drug discovery. In this work, a novel electrochemical platform using the electrochemically mediated polymerization as an efficient and cost-effective signal amplification strategy is described for the highly sensitive detection of protein kinase activity. This platform involves 1) the phosphorylation of substrate peptide by protein kinase, 2) the attachment of alkyl halide to the phosphorylated sites via the carboxylate-Zr 4+ -phosphate chemistry, and 3) the in situ grafting of electroactive polymers from the phosphorylated sites through the electrochemically mediated atom transfer radical polymerization (eATRP) at a negative potential, in the presence of the surface-attached alkyl halide as the initiator and the electroactive tag-conjugated acrylate as the monomer, respectively. Due to the electrochemically mediated polymerization, a large number of electroactive tags can be linked to each phosphorylated site, thereby greatly improving the detection sensitivity. This platform has been successfully applied to detect the activity of cAMP-dependent protein kinase (PKA) with a detection limit down to 1.63 mU mL -1 . Results also demonstrate that it is highly selective and can be used for the screening of protein kinase inhibitors. The potential application of our platform for protein kinase activity detection in complex biological samples has been further verified using normal human serum and HepG2 cell lysate. Moreover, our platform is operationally simple, highly efficient and cost-effective, thus holding great potential in protein kinase detection and inhibitor screening. Copyright © 2018 Elsevier B.V. All rights reserved.

Single Platform Geolocation of Radio Frequency Emitters

DTIC Science & Technology

2015-03-26

Error SNR Signal to Noise Ratio SOI Signal of Interest STK Systems Tool Kit UCA Uniform Circular Array WGS World Geodetic System xv SINGLE PLATFORM...Section 2.6 describes a method to visualize the confidence of estimated parameters. 2.1 Coordinate Systems and Reference Frames The following...be used to visualize the confidence surface using the method developed in Section 2.6. The NLO method will be shown to be the minimization of the

A Microwell-Printing Fabrication Strategy for the On-Chip Templated Biosynthesis of Protein Microarrays for Surface Plasmon Resonance Imaging

PubMed Central

Manuel, Gerald; Lupták, Andrej; Corn, Robert M.

2017-01-01

A two-step templated, ribosomal biosynthesis/printing method for the fabrication of protein microarrays for surface plasmon resonance imaging (SPRI) measurements is demonstrated. In the first step, a sixteen component microarray of proteins is created in microwells by cell free on chip protein synthesis; each microwell contains both an in vitro transcription and translation (IVTT) solution and 350 femtomoles of a specific DNA template sequence that together are used to create approximately 40 picomoles of a specific hexahistidine-tagged protein. In the second step, the protein microwell array is used to contact print one or more protein microarrays onto nitrilotriacetic acid (NTA)-functionalized gold thin film SPRI chips for real-time SPRI surface bioaffinity adsorption measurements. Even though each microwell array element only contains approximately 40 picomoles of protein, the concentration is sufficiently high for the efficient bioaffinity adsorption and capture of the approximately 100 femtomoles of hexahistidine-tagged protein required to create each SPRI microarray element. As a first example, the protein biosynthesis process is verified with fluorescence imaging measurements of a microwell array containing His-tagged green fluorescent protein (GFP), yellow fluorescent protein (YFP) and mCherry (RFP), and then the fidelity of SPRI chips printed from this protein microwell array is ascertained by measuring the real-time adsorption of various antibodies specific to these three structurally related proteins. This greatly simplified two-step synthesis/printing fabrication methodology eliminates most of the handling, purification and processing steps normally required in the synthesis of multiple protein probes, and enables the rapid fabrication of SPRI protein microarrays from DNA templates for the study of protein-protein bioaffinity interactions. PMID:28706572

Ultra-thin layer chromatography with integrated silver colloid-based SERS detection.

PubMed

Wallace, Ryan A; Lavrik, Nickolay V; Sepaniak, Michael J

2017-01-01

Simplified lab-on-a-chip techniques are desirable for quick and efficient detection of analytes of interest in the field. The following work involves the use of deterministic pillar arrays on the micro-scale as a platform to separate compounds, and the use of Ag colloid within the arrays as a source of increased signal via surface enhanced Raman spectroscopy (SERS). One problem traditionally seen with SERS surfaces containing Ag colloid is oxidation; however, our platforms are superhydrophobic, reducing the amount of oxidation taking place on the surface of the Ag colloid. This work includes the successful separation and SERS detection of a fluorescent dye compounds (resorufin and sulforhodamine 640), fluorescent anti-tumor drugs (Adriamycin and Daunomycin), and purine and pyrimidine bases (adenine, cytosine, guanine, hypoxanthine, and thymine). © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Progress on CBET Platform at the Nike Laser

NASA Astrophysics Data System (ADS)

Weaver, J. L.; McKenty, P.; Oh, J.; Kehne, D.; Schmitt, A. J.; Obenschain, S.; Serlin, V.; Lehmberg, R.; Tsung, F.

2015-11-01

Cross-beam energy transport (CBET) studies are underway at the Nike krypton-fluoride (KrF) laser at NRL. This facility has unique characteristics that provide an excellent platform for CBET work - including short wavelength (248 nm), large bandwidth (1-3 THz), beam smoothing by induced spatial incoherence (ISI), and full aperture focal spot zooming. Nike's two beam arrays are widely separated (135° in azimuth) which facilitates CBET studies in a nearly opposing geometry, relevant to Polar Direct Drive implosions. Various target types are planned: planar slabs, cylindrical and spherical shells, and low-density targets. The solid targets will be used to examine gradient geometries and the latter will access larger volume, more uniform plasmas. The initial campaign is exploring changes observed by scattered light diagnostics for both beam arrays as the probe laser spectrum is modified. Work supported by DoE/NNSA.

Refolding of proteins from inclusion bodies: rational design and recipes.

PubMed

Basu, Anindya; Li, Xiang; Leong, Susanna Su Jan

2011-10-01

The need to develop protein biomanufacturing platforms that can deliver proteins quickly and cost-effectively is ever more pressing. The rapid rate at which genomes can now be sequenced demands efficient protein production platforms for gene function identification. There is a continued need for the biotech industry to deliver new and more effective protein-based drugs to address new diseases. Bacterial production platforms have the advantage of high expression yields, but insoluble expression of many proteins necessitates the development of diverse and optimised refolding-based processes. Strategies employed to eliminate insoluble expression are reviewed, where it is concluded that inclusion bodies are difficult to eliminate for various reasons. Rational design of refolding systems and recipes are therefore needed to expedite production of recombinant proteins. This review article discusses efforts towards rational design of refolding systems and recipes, which can be guided by the development of refolding screening platforms that yield both qualitative and quantitative information on the progression of a given refolding process. The new opportunities presented by light scattering technologies for developing rational protein refolding buffer systems which in turn can be used to develop new process designs armed with better monitoring and controlling functionalities are discussed. The coupling of dynamic and static light scattering methodologies for incorporation into future bioprocess designs to ensure delivery of high-quality refolded proteins at faster rates is also discussed.

Automated Camera Array Fine Calibration

NASA Technical Reports Server (NTRS)

Clouse, Daniel; Padgett, Curtis; Ansar, Adnan; Cheng, Yang

2008-01-01

Using aerial imagery, the JPL FineCalibration (JPL FineCal) software automatically tunes a set of existing CAHVOR camera models for an array of cameras. The software finds matching features in the overlap region between images from adjacent cameras, and uses these features to refine the camera models. It is not necessary to take special imagery of a known target and no surveying is required. JPL FineCal was developed for use with an aerial, persistent surveillance platform.

Optimization study on the magnetic field of superconducting Halbach Array magnet

NASA Astrophysics Data System (ADS)

Shen, Boyang; Geng, Jianzhao; Li, Chao; Zhang, Xiuchang; Fu, Lin; Zhang, Heng; Ma, Jun; Coombs, T. A.

2017-07-01

This paper presents the optimization on the strength and homogeneity of magnetic field from superconducting Halbach Array magnet. Conventional Halbach Array uses a special arrangement of permanent magnets which can generate homogeneous magnetic field. Superconducting Halbach Array utilizes High Temperature Superconductor (HTS) to construct an electromagnet to work below its critical temperature, which performs equivalently to the permanent magnet based Halbach Array. The simulations of superconducting Halbach Array were carried out using H-formulation based on B-dependent critical current density and bulk approximation, with the FEM platform COMSOL Multiphysics. The optimization focused on the coils' location, as well as the geometry and numbers of coils on the premise of maintaining the total amount of superconductor. Results show Halbach Array configuration based superconducting magnet is able to generate the magnetic field with intensity over 1 Tesla and improved homogeneity using proper optimization methods. Mathematical relation of these optimization parameters with the intensity and homogeneity of magnetic field was developed.

Ras plasma membrane signalling platforms

PubMed Central

2005-01-01

The plasma membrane is a complex, dynamic structure that provides platforms for the assembly of many signal transduction pathways. These platforms have the capacity to impose an additional level of regulation on cell signalling networks. In this review, we will consider specifically how Ras proteins interact with the plasma membrane. The focus will be on recent studies that provide novel spatial and dynamic insights into the micro-environments that different Ras proteins utilize for signal transduction. We will correlate these recent studies suggesting Ras proteins might operate within a heterogeneous plasma membrane with earlier biochemical work on Ras signal transduction. PMID:15954863

Multiple intermediates on the energy landscape of a 15-HEAT-repeat protein

PubMed Central

Tsytlonok, Maksym; Craig, Patricio O.; Sivertsson, Elin; Serquera, David; Perrett, Sarah; Best, Robert B.; Wolynes, Peter G.; Itzhaki, Laura S.

2014-01-01

Repeat proteins are a special class of modular, non-globular proteins composed of small structural motifs arrayed to form elongated architectures and stabilised solely by short-range contacts. We find a remarkable complexity in the unfolding of the large HEAT repeat protein PR65/A. In contrast to what has been seen for small repeat proteins in which unfolding propagates from one end, the HEAT array of PR65/A ruptures at multiple distant sites, leading to intermediate states with non-contiguous folded subdomains. Kinetic analysis allows us to define a network of intermediates and to delineate the pathways that connect them. There is a dominant sequence of unfolding, reflecting a non-uniform distribution of stability across the repeat array; however the unfolding of certain intermediates is competitive, leading to parallel pathways. Theoretical models accounting for the heterogeneous contact density in the folded structure are able to rationalize the variation in stability across the array. This variation in stability also suggests how folding may direct function in a large repeat protein: The stability distribution enables certain regions to present rigid motifs for molecular recognition while affording others flexibility to broaden the search area as in a fly-casting mechanism. Thus PR65/A uses the two ends of the repeat array to bind diverse partners and thereby coordinate the dephosphorylation of many different substrates and of multiple sites within hyperphosphorylated substrates. PMID:24120762

How Well Does Physician Selection of Microbiologic Tests Identify Clostridium difficile and other Pathogens in Paediatric Diarrhoea? Insights Using Multiplex PCR-Based Detection

PubMed Central

Stockmann, Chris; Rogatcheva, Margarita; Harrel, Brian; Vaughn, Mike; Crisp, Rob; Poritz, Mark; Thatcher, Stephanie; Korgenski, Ernest K; Barney, Trenda; Daly, Judy; Pavia, Andrew T

2014-01-01

The objective of this study was to compare the aetiologic yield of standard of care microbiologic testing ordered by physicians with that of a multiplex PCR platform. Stool specimens obtained from children and young adults with gastrointestinal illness were evaluated by standard laboratory methods and a developmental version of the FilmArray Gastrointestinal Diagnostic System (FilmArray GI Panel), a rapid multiplex PCR platform that detects 23 bacterial, viral, and protozoal agents. Results were classified according to the microbiologic tests requested by the treating physician. A median of 3 (range 1-10) microbiologic tests were performed by the clinical laboratory during 378 unique diarrhoeal episodes. A potential aetiologic agent was identified in 46% of stool specimens by standard laboratory methods and in 65% of specimens tested using the FilmArray GI Panel (P<0.001). For those patients who only had Clostridium difficile testing requested, an alternative pathogen was identified in 29% of cases with the FilmArray GI Panel. Notably, 11 (12%) cases of norovirus were identified among children who only had testing for C. difficile ordered. Among those who had C. difficile testing ordered in combination with other tests, an additional pathogen was identified in 57% of stool specimens with the FilmArray GI Panel. For patients who had no C. difficile testing performed, the FilmArray GI Panel identified a pathogen in 63% of cases, including C. difficile in 8%. Physician-specified laboratory testing may miss important diarrhoeal pathogens. Additionally, standard laboratory testing is likely to underestimate co-infections with multiple infectious diarrhoeagenic agents. PMID:25599941

New Tricks for “Old” Domains: How Novel Architectures and Promiscuous Hubs Contributed to the Organization and Evolution of the ECM

PubMed Central

Cromar, Graham; Wong, Ka-Chun; Loughran, Noeleen; On, Tuan; Song, Hongyan; Xiong, Xuejian; Zhang, Zhaolei; Parkinson, John

2014-01-01

The extracellular matrix (ECM) is a defining characteristic of metazoans and consists of a meshwork of self-assembling, fibrous proteins, and their functionally related neighbours. Previous studies, focusing on a limited number of gene families, suggest that vertebrate complexity predominantly arose through the duplication and subsequent modification of retained, preexisting ECM genes. These genes provided the structural underpinnings to support a variety of specialized tissues, as well as a platform for the organization of spatio-temporal signaling and cell migration. However, the relative contributions of ancient versus novel domains to ECM evolution have not been quantified across the full range of ECM proteins. Here, utilizing a high quality list comprising 324 ECM genes, we reveal general and clade-specific domain combinations, identifying domains of eukaryotic and metazoan origin recruited into new roles in approximately two-third of the ECM proteins in humans representing novel vertebrate proteins. We show that, rather than acquiring new domains, sampling of new domain combinations has been key to the innovation of paralogous ECM genes during vertebrate evolution. Applying a novel framework for identifying potentially important, noncontiguous, conserved arrangements of domains, we find that the distinct biological characteristics of the ECM have arisen through unique evolutionary processes. These include the preferential recruitment of novel domains to existing architectures and the utilization of high promiscuity domains in organizing the ECM network around a connected array of structural hubs. Our focus on ECM proteins reveals that distinct types of proteins and/or the biological systems in which they operate have influenced the types of evolutionary forces that drive protein innovation. This emphasizes the need for rigorously defined systems to address questions of evolution that focus on specific systems of interacting proteins. PMID:25323955

Methods and devices for protein assays

DOEpatents

Chhabra, Swapnil [San Jose, CA; Cintron, Jose M [Indianapolis, IN; Shediac, Renee [Oakland, CA

2009-11-03

Methods and devices for protein assays based on Edman degradation in microfluidic channels are disclosed herein. As disclosed, the cleaved amino acid residues may be immobilized in an array format and identified by detectable labels, such as antibodies, which specifically bind given amino acid residues. Alternatively, the antibodies are immobilized in an array format and the cleaved amino acids are labeled identified by being bound by the antibodies in the array.

Glycan microarray screening assay for glycosyltransferase specificities.

PubMed

Peng, Wenjie; Nycholat, Corwin M; Razi, Nahid

2013-01-01

Glycan microarrays represent a high-throughput approach to determining the specificity of glycan-binding proteins against a large set of glycans in a single format. This chapter describes the use of a glycan microarray platform for evaluating the activity and substrate specificity of glycosyltransferases (GTs). The methodology allows simultaneous screening of hundreds of immobilized glycan acceptor substrates by in situ incubation of a GT and its appropriate donor substrate on the microarray surface. Using biotin-conjugated donor substrate enables direct detection of the incorporated sugar residues on acceptor substrates on the array. In addition, the feasibility of the method has been validated using label-free donor substrate combined with lectin-based detection of product to assess enzyme activity. Here, we describe the application of both procedures to assess the specificity of a recombinant human α2-6 sialyltransferase. This technique is readily adaptable to studying other glycosyltransferases.

Combinatorial microfluidic droplet engineering for biomimetic material synthesis

PubMed Central

Bawazer, Lukmaan A.; McNally, Ciara S.; Empson, Christopher J.; Marchant, William J.; Comyn, Tim P.; Niu, Xize; Cho, Soongwon; McPherson, Michael J.; Binks, Bernard P.; deMello, Andrew; Meldrum, Fiona C.

2016-01-01

Although droplet-based systems are used in a wide range of technologies, opportunities for systematically customizing their interface chemistries remain relatively unexplored. This article describes a new microfluidic strategy for rapidly tailoring emulsion droplet compositions and properties. The approach uses a simple platform for screening arrays of droplet-based microfluidic devices and couples this with combinatorial selection of the droplet compositions. Through the application of genetic algorithms over multiple screening rounds, droplets with target properties can be rapidly generated. The potential of this method is demonstrated by creating droplets with enhanced stability, where this is achieved by selecting carrier fluid chemistries that promote titanium dioxide formation at the droplet interfaces. The interface is a mixture of amorphous and crystalline phases, and the resulting composite droplets are biocompatible, supporting in vitro protein expression in their interiors. This general strategy will find widespread application in advancing emulsion properties for use in chemistry, biology, materials, and medicine. PMID:27730209

Robust and versatile ionic liquid microarrays achieved by microcontact printing

NASA Astrophysics Data System (ADS)

Gunawan, Christian A.; Ge, Mengchen; Zhao, Chuan

2014-04-01

Lab-on-a-chip and miniaturized systems have gained significant popularity motivated by marked differences in material performance at the micro-to-nano-scale realm. However, to fully exploit micro-to-nano-scale chemistry, solvent volatility and lack of reproducibility need to be overcome. Here, we combine the non-volatile and versatile nature of ionic liquids with microcontact printing in an attempt to establish a facile protocol for high throughput fabrication of open microreactors and microfluidics. The micropatterned ionic liquid droplets have been demonstrated as electrochemical cells and reactors for microfabrication of metals and charge transfer complexes, substrates for immobilization of proteins and as membrane-free high-performance amperometric gas sensor arrays. The results suggest that miniaturized ionic liquid systems can be used to solve the problems of solvent volatility and slow mass transport in viscous ionic liquids in lab-on-a-chip devices, thus providing a versatile platform for a diverse number of applications.

Protein recognition by a pattern-generating fluorescent molecular probe.

PubMed

Pode, Zohar; Peri-Naor, Ronny; Georgeson, Joseph M; Ilani, Tal; Kiss, Vladimir; Unger, Tamar; Markus, Barak; Barr, Haim M; Motiei, Leila; Margulies, David

2017-12-01

Fluorescent molecular probes have become valuable tools in protein research; however, the current methods for using these probes are less suitable for analysing specific populations of proteins in their native environment. In this study, we address this gap by developing a unimolecular fluorescent probe that combines the properties of small-molecule-based probes and cross-reactive sensor arrays (the so-called chemical 'noses/tongues'). On the one hand, the probe can detect different proteins by generating unique identification (ID) patterns, akin to cross-reactive arrays. On the other hand, its unimolecular scaffold and selective binding enable this ID-generating probe to identify combinations of specific protein families within complex mixtures and to discriminate among isoforms in living cells, where macroscopic arrays cannot access. The ability to recycle the molecular device and use it to track several binding interactions simultaneously further demonstrates how this approach could expand the fluorescent toolbox currently used to detect and image proteins.

Protein recognition by a pattern-generating fluorescent molecular probe

NASA Astrophysics Data System (ADS)

Pode, Zohar; Peri-Naor, Ronny; Georgeson, Joseph M.; Ilani, Tal; Kiss, Vladimir; Unger, Tamar; Markus, Barak; Barr, Haim M.; Motiei, Leila; Margulies, David

2017-12-01

Fluorescent molecular probes have become valuable tools in protein research; however, the current methods for using these probes are less suitable for analysing specific populations of proteins in their native environment. In this study, we address this gap by developing a unimolecular fluorescent probe that combines the properties of small-molecule-based probes and cross-reactive sensor arrays (the so-called chemical 'noses/tongues'). On the one hand, the probe can detect different proteins by generating unique identification (ID) patterns, akin to cross-reactive arrays. On the other hand, its unimolecular scaffold and selective binding enable this ID-generating probe to identify combinations of specific protein families within complex mixtures and to discriminate among isoforms in living cells, where macroscopic arrays cannot access. The ability to recycle the molecular device and use it to track several binding interactions simultaneously further demonstrates how this approach could expand the fluorescent toolbox currently used to detect and image proteins.

Breast Reference Set Application: Karen Anderson-ASU (2014) — EDRN Public Portal

Cancer.gov

In order to increase the predictive value of tumor-specific antibodies for use as immunodiagnostics, our EDRN BDL has developed a novel protein microarray technology, termed Nucleic Acid Protein Programmable Array (NAPPA), which circumvents many of the limitations of traditional protein microarrays. NAPPA arrays are generated by printing full-length cDNAs encoding the target proteins at each feature of the array. The proteins are then transcribed and translated by a cell-free system and immobilized in situ using epitope tags fused to the proteins. Sera are added, and bound IgG is detected by standard secondary reagents. Using a sequential screening strategy to select AAb from 4,988 candidate tumor antigens, we have identified 28 potential AAb biomarkers for the early detection of breast cancer, and here we propose to evaluate these biomarkers using the EDRN Breast Cancer Reference Set.

Structure and assembly of a paramyxovirus matrix protein

PubMed Central

Battisti, Anthony J.; Meng, Geng; Winkler, Dennis C.; McGinnes, Lori W.; Plevka, Pavel; Steven, Alasdair C.; Morrison, Trudy G.; Rossmann, Michael G.

2012-01-01

Many pleomorphic, lipid-enveloped viruses encode matrix proteins that direct their assembly and budding, but the mechanism of this process is unclear. We have combined X-ray crystallography and cryoelectron tomography to show that the matrix protein of Newcastle disease virus, a paramyxovirus and relative of measles virus, forms dimers that assemble into pseudotetrameric arrays that generate the membrane curvature necessary for virus budding. We show that the glycoproteins are anchored in the gaps between the matrix proteins and that the helical nucleocapsids are associated in register with the matrix arrays. About 90% of virions lack matrix arrays, suggesting that, in agreement with previous biological observations, the matrix protein needs to dissociate from the viral membrane during maturation, as is required for fusion and release of the nucleocapsid into the host’s cytoplasm. Structure and sequence conservation imply that other paramyxovirus matrix proteins function similarly. PMID:22891297

Structure and assembly of a paramyxovirus matrix protein.

PubMed

Battisti, Anthony J; Meng, Geng; Winkler, Dennis C; McGinnes, Lori W; Plevka, Pavel; Steven, Alasdair C; Morrison, Trudy G; Rossmann, Michael G

2012-08-28

Many pleomorphic, lipid-enveloped viruses encode matrix proteins that direct their assembly and budding, but the mechanism of this process is unclear. We have combined X-ray crystallography and cryoelectron tomography to show that the matrix protein of Newcastle disease virus, a paramyxovirus and relative of measles virus, forms dimers that assemble into pseudotetrameric arrays that generate the membrane curvature necessary for virus budding. We show that the glycoproteins are anchored in the gaps between the matrix proteins and that the helical nucleocapsids are associated in register with the matrix arrays. About 90% of virions lack matrix arrays, suggesting that, in agreement with previous biological observations, the matrix protein needs to dissociate from the viral membrane during maturation, as is required for fusion and release of the nucleocapsid into the host's cytoplasm. Structure and sequence conservation imply that other paramyxovirus matrix proteins function similarly.

Quantification of Protein Biomarker Using SERS Nano-Stress Sensing with Peak Intensity Ratiometry

NASA Astrophysics Data System (ADS)

Goh, Douglas; Kong, Kien Voon; Jayakumar, Perumal; Gong, Tianxun; Dinish, U. S.; Olivo, Malini

We report a surface enhanced Raman spectroscopy (SERS) ratiometry method based on peak intensity coupled in a nano-stress sensing platform to detect and quantify biological molecules. Herein, we employed an antibody-conjugated p-aminothiophenol (ATP) functionalized on a bimetallic-film-over-nanosphere (BMFON) substrate as a sensitive SERS platform to detect human haptoglobin (Hp) protein, which is an acute phase protein and a biomarker for various cancers. Correlation between change in the ATP spectral characteristics and concentration of Hp protein was established by examining the peak intensity ratio at 1572cm-1 and 1592cm-1 that reflects the degree of stress experienced by the aromatic ring of ATP during Hp protein-antibody interaction. Development of this platform shows the potential in developing a low-cost and sensitive SERS sensor for the pre-screening of various biomarkers.

Portable point-of-care blood analysis system for global health (Conference Presentation)

NASA Astrophysics Data System (ADS)

Dou, James J.; Aitchison, James Stewart; Chen, Lu; Nayyar, Rakesh

2016-03-01

In this paper we present a portable blood analysis system based on a disposable cartridge and hand-held reader. The platform can perform all the sample preparation, detection and waste collection required to complete a clinical test. In order to demonstrate the utility of this approach a CD4 T cell enumeration was carried out. A handheld, point-of-care CD4 T cell system was developed based on this system. In particular we will describe a pneumatic, active pumping method to control the on-chip fluidic actuation. Reagents for the CD4 T cell counting assay were dried on a reagent plug to eliminate the need for cold chain storage when used in the field. A micromixer based on the active fluidic actuation was designed to complete sample staining with fluorescent dyes that was dried on the reagent plugs. A novel image detection and analysis algorithm was developed to detect and track the flight of target particles and cells during each analysis. The handheld, point-of-care CD4 testing system was benchmarked against clinical cytometer. The experimental results demonstrated experimental results were closely matched with the flow cytometry. The same platform can be further expanded into a bead-array detection system where other types of biomolecules such as proteins can be detected using the same detection system.

Lectin-Array Blotting.

PubMed

Pazos, Raquel; Echevarria, Juan; Hernandez, Alvaro; Reichardt, Niels-Christian

2017-09-01

Aberrant protein glycosylation is a hallmark of cancer, infectious diseases, and autoimmune or neurodegenerative disorders. Unlocking the potential of glycans as disease markers will require rapid and unbiased glycoproteomics methods for glycan biomarker discovery. The present method is a facile and rapid protocol for qualitative analysis of protein glycosylation in complex biological mixtures. While traditional lectin arrays only provide an average signal for the glycans in the mixture, which is usually dominated by the most abundant proteins, our method provides individual lectin binding profiles for all proteins separated in the gel electrophoresis step. Proteins do not have to be excised from the gel for subsequent analysis via the lectin array but are transferred by contact diffusion from the gel to a glass slide presenting multiple copies of printed lectin arrays. Fluorescently marked glycoproteins are trapped by the printed lectins via specific carbohydrate-lectin interactions and after a washing step their binding profile with up to 20 lectin probes is analyzed with a fluorescent scanner. The method produces the equivalent of 20 lectin blots in a single experiment, giving detailed insight into the binding epitopes present in the fractionated proteins. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Too much data, but little inter-changeability: a lesson learned from mining public data on tissue specificity of gene expression.

PubMed

Li, Shuyu; Li, Yiqun Helen; Wei, Tao; Su, Eric Wen; Duffin, Kevin; Liao, Birong

2006-10-25

The tissue expression pattern of a gene often provides an important clue to its potential role in a biological process. A vast amount of gene expression data have been and are being accumulated in public repository through different technology platforms. However, exploitations of these rich data sources remain limited in part due to issues of technology standardization. Our objective is to test the data comparability between SAGE and microarray technologies, through examining the expression pattern of genes under normal physiological states across variety of tissues. There are 42-54% of genes showing significant correlations in tissue expression patterns between SAGE and GeneChip, with 30-40% of genes whose expression patterns are positively correlated and 10-15% of genes whose expression patterns are negatively correlated at a statistically significant level (p = 0.05). Our analysis suggests that the discrepancy on the expression patterns derived from technology platforms is not likely from the heterogeneity of tissues used in these technologies, or other spurious correlations resulting from microarray probe design, abundance of genes, or gene function. The discrepancy can be partially explained by errors in the original assignment of SAGE tags to genes due to the evolution of sequence databases. In addition, sequence analysis has indicated that many SAGE tags and Affymetrix array probe sets are mapped to different splice variants or different sequence regions although they represent the same gene, which also contributes to the observed discrepancies between SAGE and array expression data. To our knowledge, this is the first report attempting to mine gene expression patterns across tissues using public data from different technology platforms. Unlike previous similar studies that only demonstrated the discrepancies between the two gene expression platforms, we carried out in-depth analysis to further investigate the cause for such discrepancies. Our study shows that the exploitation of rich public expression resource requires extensive knowledge about the technologies, and experiment. Informatic methodologies for better interoperability among platforms still remain a gap. One of the areas that can be improved practically is the accurate sequence mapping of SAGE tags and array probes to full-length genes.

A Mismatch EndoNuclease Array-Based Methodology (MENA) for Identifying Known SNPs or Novel Point Mutations.

PubMed

Comeron, Josep M; Reed, Jordan; Christie, Matthew; Jacobs, Julia S; Dierdorff, Jason; Eberl, Daniel F; Manak, J Robert

2016-04-05

Accurate and rapid identification or confirmation of single nucleotide polymorphisms (SNPs), point mutations and other human genomic variation facilitates understanding the genetic basis of disease. We have developed a new methodology (called MENA (Mismatch EndoNuclease Array)) pairing DNA mismatch endonuclease enzymology with tiling microarray hybridization in order to genotype both known point mutations (such as SNPs) as well as identify previously undiscovered point mutations and small indels. We show that our assay can rapidly genotype known SNPs in a human genomic DNA sample with 99% accuracy, in addition to identifying novel point mutations and small indels with a false discovery rate as low as 10%. Our technology provides a platform for a variety of applications, including: (1) genotyping known SNPs as well as confirming newly discovered SNPs from whole genome sequencing analyses; (2) identifying novel point mutations and indels in any genomic region from any organism for which genome sequence information is available; and (3) screening panels of genes associated with particular diseases and disorders in patient samples to identify causative mutations. As a proof of principle for using MENA to discover novel mutations, we report identification of a novel allele of the beethoven (btv) gene in Drosophila, which encodes a ciliary cytoplasmic dynein motor protein important for auditory mechanosensation.

Evaluating De-centralised and Distributional Options for the Distributed Electronic Warfare Situation Awareness and Response Test Bed

DTIC Science & Technology

2013-12-01

effectors (deployed on ground based or aerial platforms) to detect , identify, locate, track or suppress stationary or slow moving surface based RF...ground based or aerial platforms) to detect , identify, locate, track or suppress stationary or slow moving surface based RF emitting targets. In the...Electronic Support EO Electro-Optic FPGAs Field Programmable Gate Arrays IR Infra-red LADAR Laser Detection and Ranging OSX Mac OS X; the apple

Gold patterned biochips for on-chip immuno-MALDI-TOF MS: SPR imaging coupled multi-protein MS analysis.

PubMed

Kim, Young Eun; Yi, So Yeon; Lee, Chang-Soo; Jung, Yongwon; Chung, Bong Hyun

2012-01-21

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) analysis of immuno-captured target protein efficiently complements conventional immunoassays by offering rich molecular information such as protein isoforms or modifications. Direct immobilization of antibodies on MALDI solid support enables both target enrichment and MS analysis on the same plate, allowing simplified and potentially multiplexing protein MS analysis. Reliable on-chip immuno-MALDI-TOF MS for multiple biomarkers requires successful adaptation of antibody array biochips, which also must accommodate consistent reaction conditions on antibody arrays during immuno-capture and MS analysis. Here we developed a facile fabrication process of versatile antibody array biochips for reliable on-chip MALDI-TOF-MS analysis of multiple immuno-captured proteins. Hydrophilic gold arrays surrounded by super-hydrophobic surfaces were formed on a gold patterned biochip via spontaneous chemical or protein layer deposition. From antibody immobilization to MALDI matrix treatment, this hydrophilic/phobic pattern allowed highly consistent surface reactions on each gold spot. Various antibodies were immobilized on these gold spots both by covalent coupling or protein G binding. Four different protein markers were successfully analyzed on the present immuno-MALDI biochip from complex protein mixtures including serum samples. Tryptic digests of captured PSA protein were also effectively detected by on-chip MALDI-TOF-MS. Moreover, the present MALDI biochip can be directly applied to the SPR imaging system, by which antibody and subsequent antigen immobilization were successfully monitored.

Biomimetic vibrissal sensing for robots

PubMed Central

Pearson, Martin J.; Mitchinson, Ben; Sullivan, J. Charles; Pipe, Anthony G.; Prescott, Tony J.

2011-01-01

Active vibrissal touch can be used to replace or to supplement sensory systems such as computer vision and, therefore, improve the sensory capacity of mobile robots. This paper describes how arrays of whisker-like touch sensors have been incorporated onto mobile robot platforms taking inspiration from biology for their morphology and control. There were two motivations for this work: first, to build a physical platform on which to model, and therefore test, recent neuroethological hypotheses about vibrissal touch; second, to exploit the control strategies and morphology observed in the biological analogue to maximize the quality and quantity of tactile sensory information derived from the artificial whisker array. We describe the design of a new whiskered robot, Shrewbot, endowed with a biomimetic array of individually controlled whiskers and a neuroethologically inspired whisking pattern generation mechanism. We then present results showing how the morphology of the whisker array shapes the sensory surface surrounding the robot's head, and demonstrate the impact of active touch control on the sensory information that can be acquired by the robot. We show that adopting bio-inspired, low latency motor control of the rhythmic motion of the whiskers in response to contact-induced stimuli usefully constrains the sensory range, while also maximizing the number of whisker contacts. The robot experiments also demonstrate that the sensory consequences of active touch control can be usefully investigated in biomimetic robots. PMID:21969690

Point-Focus Concentration Compact Telescoping Array: Extreme Environments Solar Power Base Phase Final Report

NASA Technical Reports Server (NTRS)

McEachen, Michael E.; Murphy, Dave; Meinhold, Shen; Spink, Jim; Eskenazi, Mike; O'Neill, Mark

2017-01-01

Orbital ATK, in partnership with Mark ONeill LLC (MOLLC), has developed a novel solar array platform, PFC-CTA, which provides a significant advance in performance and cost reduction compared to all currently available space solar systems. PFC refers to the Point Focus Concentration of light provided by MOLLCs thin, flat Fresnel optics. These lenses focus light to a point of approximately 100 times the intensity of the ambient light, onto a solar cell of approximately 125th the size of the lens. CTA stands for Compact Telescoping Array, which is the solar array blanket structural platform originally devised by NASA and currently being advanced by Orbital ATK and partners under NASA and AFRL funding to a projected TRL 5+ by late-2018.The NASA Game Changing Development Extreme Environment Solar Power (EESP) Base Phase study has enabled Orbital ATK to refine component designs, perform component level and system performance analyses, and test prototype hardware of the key elements of PFC-CTA, and increased the TRL of PFC-specific technology elements to TRL 4. Key performance metrics currently projected are as follows: Scalability from 5 kW to 300 kW per wing (AM0); Specific Power 500 Wkg (AM0); Stowage Efficiency 100 kWm3; 5:1 margin on pointing tolerance vs. capability; 50 launched cost savings; Wide range of operability between Venus and Saturn by active andor passive thermal management.

Design of a Dissolving Microneedle Platform for Transdermal Delivery of a Fixed-Dose Combination of Cardiovascular Drugs.

PubMed

Quinn, Helen L; Bonham, Louise; Hughes, Carmel M; Donnelly, Ryan F

2015-10-01

Microneedles (MNs) are a minimally invasive drug delivery platform, designed to enhance transdermal drug delivery by breaching the stratum corneum. For the first time, this study describes the simultaneous delivery of a combination of three drugs using a dissolving polymeric MN system. In the present study, aspirin, lisinopril dihydrate, and atorvastatin calcium trihydrate were used as exemplar cardiovascular drugs and formulated into MN arrays using two biocompatible polymers, poly(vinylpyrrollidone) and poly(methylvinylether/maleic acid). Following fabrication, dissolution, mechanical testing, and determination of drug recovery from the MN arrays, in vitro drug delivery studies were undertaken, followed by HPLC analysis. All three drugs were successfully delivered in vitro across neonatal porcine skin, with similar permeation profiles achieved from both polymer formulations. An average of 126.3 ± 18.1 μg of atorvastatin calcium trihydrate was delivered, notably lower than the 687.9 ± 101.3 μg of lisinopril and 3924 ± 1011 μg of aspirin, because of the hydrophobic nature of the atorvastatin molecule and hence poor dissolution from the array. Polymer deposition into the skin may be an issue with repeat application of such a MN array, hence future work will consider more appropriate MN systems for continuous use, alongside tailoring delivery to less hydrophilic compounds. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association.

Model-based variance-stabilizing transformation for Illumina microarray data.

PubMed

Lin, Simon M; Du, Pan; Huber, Wolfgang; Kibbe, Warren A

2008-02-01

Variance stabilization is a step in the preprocessing of microarray data that can greatly benefit the performance of subsequent statistical modeling and inference. Due to the often limited number of technical replicates for Affymetrix and cDNA arrays, achieving variance stabilization can be difficult. Although the Illumina microarray platform provides a larger number of technical replicates on each array (usually over 30 randomly distributed beads per probe), these replicates have not been leveraged in the current log2 data transformation process. We devised a variance-stabilizing transformation (VST) method that takes advantage of the technical replicates available on an Illumina microarray. We have compared VST with log2 and Variance-stabilizing normalization (VSN) by using the Kruglyak bead-level data (2006) and Barnes titration data (2005). The results of the Kruglyak data suggest that VST stabilizes variances of bead-replicates within an array. The results of the Barnes data show that VST can improve the detection of differentially expressed genes and reduce false-positive identifications. We conclude that although both VST and VSN are built upon the same model of measurement noise, VST stabilizes the variance better and more efficiently for the Illumina platform by leveraging the availability of a larger number of within-array replicates. The algorithms and Supplementary Data are included in the lumi package of Bioconductor, available at: www.bioconductor.org.

Biomimetic vibrissal sensing for robots.

PubMed

Pearson, Martin J; Mitchinson, Ben; Sullivan, J Charles; Pipe, Anthony G; Prescott, Tony J

2011-11-12

Active vibrissal touch can be used to replace or to supplement sensory systems such as computer vision and, therefore, improve the sensory capacity of mobile robots. This paper describes how arrays of whisker-like touch sensors have been incorporated onto mobile robot platforms taking inspiration from biology for their morphology and control. There were two motivations for this work: first, to build a physical platform on which to model, and therefore test, recent neuroethological hypotheses about vibrissal touch; second, to exploit the control strategies and morphology observed in the biological analogue to maximize the quality and quantity of tactile sensory information derived from the artificial whisker array. We describe the design of a new whiskered robot, Shrewbot, endowed with a biomimetic array of individually controlled whiskers and a neuroethologically inspired whisking pattern generation mechanism. We then present results showing how the morphology of the whisker array shapes the sensory surface surrounding the robot's head, and demonstrate the impact of active touch control on the sensory information that can be acquired by the robot. We show that adopting bio-inspired, low latency motor control of the rhythmic motion of the whiskers in response to contact-induced stimuli usefully constrains the sensory range, while also maximizing the number of whisker contacts. The robot experiments also demonstrate that the sensory consequences of active touch control can be usefully investigated in biomimetic robots.

Laser-ablative engineering of phase singularities in plasmonic metamaterial arrays for biosensing applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aristov, Andrey I.; Kabashin, Andrei V., E-mail: kabashin@lp3.univ-mrs.fr; Zywietz, Urs

2014-02-17

By using methods of laser-induced transfer combined with nanoparticle lithography, we design and fabricate large-area gold nanoparticle-based metamaterial arrays exhibiting extreme Heaviside-like phase jumps in reflected light due to a strong diffractive coupling of localized plasmons. When employed in sensing schemes, these phase singularities provide the sensitivity of 5 × 10{sup 4} deg. of phase shift per refractive index unit change that is comparable with best values reported for plasmonic biosensors. The implementation of sensor platforms on the basis of such metamaterial arrays promises a drastic improvement of sensitivity and cost efficiency of plasmonic biosensing devices.

Quantum many-body dynamics of strongly interacting atom arrays

NASA Astrophysics Data System (ADS)

Bernien, Hannes; Keesling, Alexander; Levine, Harry; Schwartz, Sylvain; Omran, Ahmed; Anschuetz, Eric; Endres, Manuel; Vuletic, Vladan; Greiner, Markus; Lukin, Mikhail

2017-04-01

The coherent interaction between large numbers of particles gives rise to fascinating quantum many-body effects and lies at the center of quantum simulations and quantum information processing. The development of systems consisting of many, well-controlled particles with tunable interactions is an outstanding challenge. Here we present a new platform based on large, reconfigurable arrays of individually trapped atoms. Strong interactions between these atoms are enabled by exciting them to Rydberg states. This flexible approach allows access to vastly different regimes with interactions tunable over several orders of magnitude. We study the coherent many-body dynamics in varying array geometries and observe the formation of Rydberg crystals.

Mechanical behaviour of staggered array of mineralised collagen fibrils in protein matrix: Effects of fibril dimensions and failure energy in protein matrix.

PubMed

Lai, Zheng Bo; Yan, Cheng

2017-01-01

Many biological composite materials such as bone have demonstrated unique mechanical performance, i.e., a combination of superior stiffness and toughness. It has become increasingly clear that the constituents at the nano- and micro-length scales play a critical role in determining the mechanical performance of these biological composites. In this study, the underlying mechanisms governing the mechanical behaviour of the staggered array of mineralised collagen fibrils (MCF) embedded in extra-fibrillar protein matrix were numerically investigated. The evolution of damage zone in protein was estimated using cohesive zone models (CZM). The results indicate that the mechanisms and mechanical behaviour of MCF array are largely dependent on the MCF dimensions and the intrinsic failure energy in extra-fibrillar protein matrix. Copyright © 2016 Elsevier Ltd. All rights reserved.

A microfluidic cell culture array with various oxygen tensions.

PubMed

Peng, Chien-Chung; Liao, Wei-Hao; Chen, Ying-Hua; Wu, Chueh-Yu; Tung, Yi-Chung

2013-08-21

Oxygen tension plays an important role in regulating various cellular functions in both normal physiology and disease states. Therefore, drug testing using conventional in vitro cell models under normoxia often possesses limited prediction capability. A traditional method of setting an oxygen tension in a liquid medium is by saturating it with a gas mixture at the desired level of oxygen, which requires bulky gas cylinders, sophisticated control, and tedious interconnections. Moreover, only a single oxygen tension can be tested at the same time. In this paper, we develop a microfluidic cell culture array platform capable of performing cell culture and drug testing under various oxygen tensions simultaneously. The device is fabricated using an elastomeric material, polydimethylsiloxane (PDMS) and the well-developed multi-layer soft lithography (MSL) technique. The prototype device has 4 × 4 wells, arranged in the same dimensions as a conventional 96-well plate, for cell culture. The oxygen tensions are controlled by spatially confined oxygen scavenging chemical reactions underneath the wells using microfluidics. The platform takes advantage of microfluidic phenomena while exhibiting the combinatorial diversities achieved by microarrays. Importantly, the platform is compatible with existing cell incubators and high-throughput instruments (liquid handling systems and plate readers) for cost-effective setup and straightforward operation. Utilizing the developed platform, we successfully perform drug testing using an anti-cancer drug, triapazamine (TPZ), on adenocarcinomic human alveolar basal epithelial cell line (A549) under three oxygen tensions ranging from 1.4% to normoxia. The developed platform is promising to provide a more meaningful in vitro cell model for various biomedical applications while maintaining desired high throughput capabilities.

Development of FEB Test Platform for ATLAS New Small Wheel Upgrade

NASA Astrophysics Data System (ADS)

Lu, Houbing; Hu, Kun; Wang, Xu; Li, Feng; Han, Liang; Jin, Ge

2016-10-01

This concept of test platform is based on the test requirements of the front-end board (FEB) which is developed for the phase I upgrade of the small Thin Gap Chamber(sTGC) detector on New Small Wheel(NSW) of ATLAS. The front-end electronics system of sTGC consists of 1,536 FEBs with about 322,000 readout of strips, wires and pads in total. A test platform for FEB with up to 256 channels has been designed to keep the testing efficiency at a controllable level. We present the circuit model architecture of the platform, and its functions and implementation as well. The firmware based on Field Programmable Gate Array (FPGA) and the software based on PC have been developed, and basic test methods have been established. FEB readout measurements have been performed in analog injection from the test platform, which will provide a fast and efficient test method for the production of FEB.

A Biosensor-CMOS Platform and Integrated Readout Circuit in 0.18-μm CMOS Technology for Cancer Biomarker Detection.

PubMed

Alhoshany, Abdulaziz; Sivashankar, Shilpa; Mashraei, Yousof; Omran, Hesham; Salama, Khaled N

2017-08-23

This paper presents a biosensor-CMOS platform for measuring the capacitive coupling of biorecognition elements. The biosensor is designed, fabricated, and tested for the detection and quantification of a protein that reveals the presence of early-stage cancer. For the first time, the spermidine/spermine N1 acetyltransferase (SSAT) enzyme has been screened and quantified on the surface of a capacitive sensor. The sensor surface is treated to immobilize antibodies, and the baseline capacitance of the biosensor is reduced by connecting an array of capacitors in series for fixed exposure area to the analyte. A large sensing area with small baseline capacitance is implemented to achieve a high sensitivity to SSAT enzyme concentrations. The sensed capacitance value is digitized by using a 12-bit highly digital successive-approximation capacitance-to-digital converter that is implemented in a 0.18 μm CMOS technology. The readout circuit operates in the near-subthreshold regime and provides power and area efficient operation. The capacitance range is 16.137 pF with a 4.5 fF absolute resolution, which adequately covers the concentrations of 10 mg/L, 5 mg/L, 2.5 mg/L, and 1.25 mg/L of the SSAT enzyme. The concentrations were selected as a pilot study, and the platform was shown to demonstrate high sensitivity for SSAT enzymes on the surface of the capacitive sensor. The tested prototype demonstrated 42.5 μS of measurement time and a total power consumption of 2.1 μW.

A Biosensor-CMOS Platform and Integrated Readout Circuit in 0.18-μm CMOS Technology for Cancer Biomarker Detection

PubMed Central

Alhoshany, Abdulaziz; Sivashankar, Shilpa; Mashraei, Yousof; Omran, Hesham; Salama, Khaled N.

2017-01-01

This paper presents a biosensor-CMOS platform for measuring the capacitive coupling of biorecognition elements. The biosensor is designed, fabricated, and tested for the detection and quantification of a protein that reveals the presence of early-stage cancer. For the first time, the spermidine/spermine N1 acetyltransferase (SSAT) enzyme has been screened and quantified on the surface of a capacitive sensor. The sensor surface is treated to immobilize antibodies, and the baseline capacitance of the biosensor is reduced by connecting an array of capacitors in series for fixed exposure area to the analyte. A large sensing area with small baseline capacitance is implemented to achieve a high sensitivity to SSAT enzyme concentrations. The sensed capacitance value is digitized by using a 12-bit highly digital successive-approximation capacitance-to-digital converter that is implemented in a 0.18 μm CMOS technology. The readout circuit operates in the near-subthreshold regime and provides power and area efficient operation. The capacitance range is 16.137 pF with a 4.5 fF absolute resolution, which adequately covers the concentrations of 10 mg/L, 5 mg/L, 2.5 mg/L, and 1.25 mg/L of the SSAT enzyme. The concentrations were selected as a pilot study, and the platform was shown to demonstrate high sensitivity for SSAT enzymes on the surface of the capacitive sensor. The tested prototype demonstrated 42.5 μS of measurement time and a total power consumption of 2.1 μW. PMID:28832523

Ultra-high-aspect-orthogonal and tunable three dimensional polymeric nanochannel stack array for BioMEMS applications

NASA Astrophysics Data System (ADS)

Heo, Joonseong; Kwon, Hyukjin J.; Jeon, Hyungkook; Kim, Bumjoo; Kim, Sung Jae; Lim, Geunbae

2014-07-01

Nanofabrication technologies have been a strong advocator for new scientific fundamentals that have never been described by traditional theory, and have played a seed role in ground-breaking nano-engineering applications. In this study, we fabricated ultra-high-aspect (~106 with O(100) nm nanochannel opening and O(100) mm length) orthogonal nanochannel array using only polymeric materials. Vertically aligned nanochannel arrays in parallel can be stacked to form a dense nano-structure. Due to the flexibility and stretchability of the material, one can tune the size and shape of the nanochannel using elongation and even roll the stack array to form a radial-uniformly distributed nanochannel array. The roll can be cut at discretionary lengths for incorporation with a micro/nanofluidic device. As examples, we demonstrated ion concentration polarization with the device for Ohmic-limiting/overlimiting current-voltage characteristics and preconcentrated charged species. The density of the nanochannel array was lower than conventional nanoporous membranes, such as anodic aluminum oxide membranes (AAO). However, accurate controllability over the nanochannel array dimensions enabled multiplexed one microstructure-on-one nanostructure interfacing for valuable biological/biomedical microelectromechanical system (BioMEMS) platforms, such as nano-electroporation.Nanofabrication technologies have been a strong advocator for new scientific fundamentals that have never been described by traditional theory, and have played a seed role in ground-breaking nano-engineering applications. In this study, we fabricated ultra-high-aspect (~106 with O(100) nm nanochannel opening and O(100) mm length) orthogonal nanochannel array using only polymeric materials. Vertically aligned nanochannel arrays in parallel can be stacked to form a dense nano-structure. Due to the flexibility and stretchability of the material, one can tune the size and shape of the nanochannel using elongation and even roll the stack array to form a radial-uniformly distributed nanochannel array. The roll can be cut at discretionary lengths for incorporation with a micro/nanofluidic device. As examples, we demonstrated ion concentration polarization with the device for Ohmic-limiting/overlimiting current-voltage characteristics and preconcentrated charged species. The density of the nanochannel array was lower than conventional nanoporous membranes, such as anodic aluminum oxide membranes (AAO). However, accurate controllability over the nanochannel array dimensions enabled multiplexed one microstructure-on-one nanostructure interfacing for valuable biological/biomedical microelectromechanical system (BioMEMS) platforms, such as nano-electroporation. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr00350k

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yulaev, Alexander; Guo, Hongxuan; Strelcov, Evgheni

Atomic-scale thickness, molecular impermeability, low atomic number, and mechanical strength make graphene an ideal electron-transparent membrane for material characterization in liquids and gases with scanning electron microscopy and spectroscopy. Here in this paper, we present a novel sample platform made of an array of thousands of identical isolated graphene-capped microchannels with high aspect ratio. A combination of a global wide field of view with high resolution local imaging of the array allows for high throughput in situ studies as well as for combinatorial screening of solutions, liquid interfaces, and immersed samples. We demonstrate the capabilities of this platform by studyingmore » a pure water sample in comparison with alkali halide solutions, a model electrochemical plating process, and beam-induced crystal growth in liquid electrolyte. Spectroscopic characterization of liquid interfaces and immersed objects with Auger and X-ray fluorescence analysis through the graphene membrane are also demonstrated.« less

A CCD experimental platform for large telescope in Antarctica based on FPGA

NASA Astrophysics Data System (ADS)

Zhu, Yuhua; Qi, Yongjun

2014-07-01

The CCD , as a detector , is one of the important components of astronomical telescopes. For a large telescope in Antarctica, a set of CCD detector system with large size, high sensitivity and low noise is indispensable. Because of the extremely low temperatures and unattended, system maintenance and software and hardware upgrade become hard problems. This paper introduces a general CCD controller experiment platform, using Field programmable gate array FPGA, which is, in fact, a large-scale field reconfigurable array. Taking the advantage of convenience to modify the system, construction of driving circuit, digital signal processing module, network communication interface, control algorithm validation, and remote reconfigurable module may realize. With the concept of integrated hardware and software, the paper discusses the key technology of building scientific CCD system suitable for the special work environment in Antarctica, focusing on the method of remote reconfiguration for controller via network and then offering a feasible hardware and software solution.

Fiber-Optic Array Scanning Technology (FAST) for Detection and Molecular Characterization of Circulating Tumor Cells.

PubMed

Ao, Zheng; Liu, Xiaohe

2017-01-01

Circulating tumor cell (CTC) as an important component in "liquid biopsy" holds crucial clinical relevance in cancer prognosis, treatment efficiency evaluation, prediction and potentially early detection. Here, we present a Fiber-optic Array Scanning Technology (FAST) that enables antigen-agnostic, size-agnostic detection of CTC. By immunofluorescence staining detection of a combination of a panel of markers, FAST technology can be applied to detect rare CTC in non-small cell lung cancer (NSCLC) setting with high sensitivity and specificity. In combination with Automated Digital Microscopy (ADM) platform, companion markers on CTC such as Vimentin and Programmed death-ligand 1 (PD-L1) can also be analyzed to further characterize these CTCs. FAST data output is also compatible with downstream single cell picking platforms. Single cell can be isolated post ADM confirmation and used for "actionable" genetic mutations analysis.

C-MEMS for bio-sensing applications

NASA Astrophysics Data System (ADS)

Song, Yin; Agrawal, Richa; Wang, Chunlei

2015-05-01

Developing highly sensitive, selective, and reproducible miniaturized bio-sensing platforms require reliable biointerface which should be compatible with microfabrication techniques. In this study, we have fabricated pyrolyzed carbon arrays with high surface area as a bio-sensing electrode, and developed the surface functionalization methods to increase biomolecules immobilization efficiency and further understand electrochemical phenomena at biointerfaces. The carbon microelectrode arrays with high aspect ratio have been fabricated by carbon microelectromechanical systems (C-MEMS) and nanomaterials such as graphene have been integrated to further increase surface area. To achieve the efficient covalent immobilization of biomolecules, various oxidation and reduction functionalization methods have been investigated. The oxidation treatment in this study includes vacuum ultraviolet, electrochemical activation, UV/Ozone and oxygen RIE. The reduction treatment includes direct amination and diazonium grafting. The developed bio-sensing platform was then applied for several applications, such as: DNA sensor; H2O2 sensor; aptamer sensor and HIV sensor.

Arrays of microscopic organic LEDs for high-resolution optogenetics

PubMed Central

Steude, Anja; Witts, Emily C.; Miles, Gareth B.; Gather, Malte C.

2016-01-01

Optogenetics is a paradigm-changing new method to study and manipulate the behavior of cells with light. Following major advances of the used genetic constructs over the last decade, the light sources required for optogenetic control are now receiving increased attention. We report a novel optogenetic illumination platform based on high-density arrays of microscopic organic light-emitting diodes (OLEDs). Because of the small dimensions of each array element (6 × 9 μm2) and the use of ultrathin device encapsulation, these arrays enable illumination of cells with unprecedented spatiotemporal resolution. We show that adherent eukaryotic cells readily proliferate on these arrays, and we demonstrate specific light-induced control of the ionic current across the membrane of individual live cells expressing different optogenetic constructs. Our work paves the way for the use of OLEDs for cell-specific optogenetic control in cultured neuronal networks and for acute brain slices, or as implants in vivo. PMID:27386540

Stacked, Filtered Multi-Channel X-Ray Diode Array

DOE Office of Scientific and Technical Information (OSTI.GOV)

MacNeil, Lawrence P.; Dutra, Eric C.; Raphaelian, Mark

2015-08-01

This system meets the need for a low-cost, robust X-ray diode array to use for experiments in hostile environments on multiple platforms, and for experiments utilizing forces that may destroy the diode(s). Since these uses require a small size with a minimal single line-of-sight, a parallel array often cannot be used. So a stacked, filtered multi-channel X-ray diode array was developed that was called the MiniXRD. The design was modeled, built, and tested at National Security Technologies, LLC (NSTec) Livermore Operations (LO) to determine fundamental characteristics. Then, several different systems were fielded as ancillary “ridealong” diagnostics at several national facilitiesmore » to allow us to iteratively improve the design and usability. Presented here are design considerations and experimental results. This filtered diode array is currently at Technical Readiness Level (TRL) 6.« less

Prospects for quantum computing with an array of ultracold polar paramagnetic molecules.

PubMed

Karra, Mallikarjun; Sharma, Ketan; Friedrich, Bretislav; Kais, Sabre; Herschbach, Dudley

2016-03-07

Arrays of trapped ultracold molecules represent a promising platform for implementing a universal quantum computer. DeMille [Phys. Rev. Lett. 88, 067901 (2002)] has detailed a prototype design based on Stark states of polar (1)Σ molecules as qubits. Herein, we consider an array of polar (2)Σ molecules which are, in addition, inherently paramagnetic and whose Hund's case (b) free-rotor pair-eigenstates are Bell states. We show that by subjecting the array to combinations of concurrent homogeneous and inhomogeneous electric and magnetic fields, the entanglement of the array's Stark and Zeeman states can be tuned and the qubit sites addressed. Two schemes for implementing an optically controlled CNOT gate are proposed and their feasibility discussed in the face of the broadening of spectral lines due to dipole-dipole coupling and the inhomogeneity of the electric and magnetic fields.

1D array of dark spot traps formed by counter-propagating nested Gaussian laser beams for trapping and moving atomic qubits

NASA Astrophysics Data System (ADS)

Gillen-Christandl, Katharina; Frazer, Travis D.

2017-04-01

The standing wave of two identical counter-propagating Gaussian laser beams constitutes a 1D array of bright spots that can serve as traps for single neutral atoms for quantum information operations. Detuning the frequency of one of the beams causes the array to start moving, effectively forming a conveyor belt for the qubits. Using a pair of nested Gaussian laser beams with different beam waists, however, forms a standing wave with a 1D array of dark spot traps confined in all dimensions. We have computationally explored the trap properties and limitations of this configuration and, trading off trap depth and frequencies with the number of traps and trap photon scattering rates, we determined the laser powers and beam waists needed for useful 1D arrays of dark spot traps for trapping and transporting atomic qubits in neutral atom quantum computing platforms.

New customizable phased array UT instrument opens door for furthering research and better industrial implementation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dao, Gavin; Ginzel, Robert

2014-02-18

Phased array UT as an inspection technique in itself continues to gain wide acceptance. However, there is much room for improvement in terms of implementation of Phased Array (PA) technology for every unique NDT application across several industries (e.g. oil and petroleum, nuclear and power generation, steel manufacturing, etc.). Having full control of the phased array instrument and customizing a software solution is necessary for more seamless and efficient inspections, from setting the PA parameters, collecting data and reporting, to the final analysis. NDT researchers and academics also need a flexible and open platform to be able to control variousmore » aspects of the phased array process. A high performance instrument with advanced PA features, faster data rates, a smaller form factor, and capability to adapt to specific applications, will be discussed.« less

Balloon platform for extended-life astronomy research

NASA Technical Reports Server (NTRS)

Ostwald, L. T.

1974-01-01

A configuration has been developed for a long-life balloon platform to carry pointing telescopes weighing as much as 80 pounds (36 kg) to point at selected celestial targets. A platform of this configuration weighs about 375 pounds (170 kg) gross and can be suspended from a high altitude super pressure balloon for a lifetime of several months. The balloon platform contains a solar array and storage batteries for electrical power, up and down link communications equipment, and navigational and attitude control systems for orienting the scientific instrument. A biaxial controller maintains the telescope attitude in response to look-angle data stored in an on-board computer memory which is updated periodically by ground command. Gimbal angles are computed by using location data derived by an on-board navigational receiver.

High-performance hardware implementation of a parallel database search engine for real-time peptide mass fingerprinting

PubMed Central

Bogdán, István A.; Rivers, Jenny; Beynon, Robert J.; Coca, Daniel

2008-01-01

Motivation: Peptide mass fingerprinting (PMF) is a method for protein identification in which a protein is fragmented by a defined cleavage protocol (usually proteolysis with trypsin), and the masses of these products constitute a ‘fingerprint’ that can be searched against theoretical fingerprints of all known proteins. In the first stage of PMF, the raw mass spectrometric data are processed to generate a peptide mass list. In the second stage this protein fingerprint is used to search a database of known proteins for the best protein match. Although current software solutions can typically deliver a match in a relatively short time, a system that can find a match in real time could change the way in which PMF is deployed and presented. In a paper published earlier we presented a hardware design of a raw mass spectra processor that, when implemented in Field Programmable Gate Array (FPGA) hardware, achieves almost 170-fold speed gain relative to a conventional software implementation running on a dual processor server. In this article we present a complementary hardware realization of a parallel database search engine that, when running on a Xilinx Virtex 2 FPGA at 100 MHz, delivers 1800-fold speed-up compared with an equivalent C software routine, running on a 3.06 GHz Xeon workstation. The inherent scalability of the design means that processing speed can be multiplied by deploying the design on multiple FPGAs. The database search processor and the mass spectra processor, running on a reconfigurable computing platform, provide a complete real-time PMF protein identification solution. Contact: d.coca@sheffield.ac.uk PMID:18453553

Assessing the efficacy of vesicle fusion with planar membrane arrays using a mitochondrial porin as reporter

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pszon-Bartosz, Kamila; Hansen, Jesper S.; Technical University of Denmark, Department of Micro- and Nanotechnology, DK-2800 Kongens Lyngby

2011-03-04

Research highlights: {yields} We have established a vesicle fusion efficacy assay based on the major non-specific porin of Fusobacterium nucleatum (FomA). {yields} Maximal fusion obtained was almost 150,000 porin insertions during 20 min. {yields} Incorporation can be either first order or exponential kinetics which has implications for establishing protein delivery to biomimetic membranes. -- Abstract: Reconstitution of functionally active membrane protein into artificially made lipid bilayers is a challenge that must be overcome to create a membrane-based biomimetic sensor and separation device. In this study we address the efficacy of proteoliposome fusion with planar membrane arrays. We establish a proteinmore » incorporation efficacy assay using the major non-specific porin of Fusobacterium nucleatum (FomA) as reporter. We use electrical conductance measurements and fluorescence microscopy to characterize proteoliposome fusion with an array of planar membranes. We show that protein reconstitution in biomimetic membrane arrays may be quantified using the developed FomA assay. Specifically, we show that FomA vesicles are inherently fusigenic. Optimal FomA incorporation is obtained with a proteoliposome lipid-to-protein molar ratio (LPR) = 50 more than 10{sup 5} FomA proteins could be incorporated in a bilayer array with a total membrane area of 2 mm{sup 2} within 20 min. This novel assay for quantifying protein delivery into lipid bilayers may be a useful tool in developing biomimetic membrane applications.« less

A Label-Free Fluorescent Array Sensor Utilizing Liposome Encapsulating Calcein for Discriminating Target Proteins by Principal Component Analysis

PubMed Central

Imamura, Ryota; Murata, Naoki; Shimanouchi, Toshinori; Yamashita, Kaoru; Fukuzawa, Masayuki; Noda, Minoru

2017-01-01

A new fluorescent arrayed biosensor has been developed to discriminate species and concentrations of target proteins by using plural different phospholipid liposome species encapsulating fluorescent molecules, utilizing differences in permeation of the fluorescent molecules through the membrane to modulate liposome-target protein interactions. This approach proposes a basically new label-free fluorescent sensor, compared with the common technique of developed fluorescent array sensors with labeling. We have confirmed a high output intensity of fluorescence emission related to characteristics of the fluorescent molecules dependent on their concentrations when they leak from inside the liposomes through the perturbed lipid membrane. After taking an array image of the fluorescence emission from the sensor using a CMOS imager, the output intensities of the fluorescence were analyzed by a principal component analysis (PCA) statistical method. It is found from PCA plots that different protein species with several concentrations were successfully discriminated by using the different lipid membranes with high cumulative contribution ratio. We also confirmed that the accuracy of the discrimination by the array sensor with a single shot is higher than that of a single sensor with multiple shots. PMID:28714873

A Label-Free Fluorescent Array Sensor Utilizing Liposome Encapsulating Calcein for Discriminating Target Proteins by Principal Component Analysis.

PubMed

Imamura, Ryota; Murata, Naoki; Shimanouchi, Toshinori; Yamashita, Kaoru; Fukuzawa, Masayuki; Noda, Minoru

2017-07-15

A new fluorescent arrayed biosensor has been developed to discriminate species and concentrations of target proteins by using plural different phospholipid liposome species encapsulating fluorescent molecules, utilizing differences in permeation of the fluorescent molecules through the membrane to modulate liposome-target protein interactions. This approach proposes a basically new label-free fluorescent sensor, compared with the common technique of developed fluorescent array sensors with labeling. We have confirmed a high output intensity of fluorescence emission related to characteristics of the fluorescent molecules dependent on their concentrations when they leak from inside the liposomes through the perturbed lipid membrane. After taking an array image of the fluorescence emission from the sensor using a CMOS imager, the output intensities of the fluorescence were analyzed by a principal component analysis (PCA) statistical method. It is found from PCA plots that different protein species with several concentrations were successfully discriminated by using the different lipid membranes with high cumulative contribution ratio. We also confirmed that the accuracy of the discrimination by the array sensor with a single shot is higher than that of a single sensor with multiple shots.

High-Throughput Protein Expression Using a Combination of Ligation-Independent Cloning (LIC) and Infrared Fluorescent Protein (IFP) Detection

PubMed Central

Dortay, Hakan; Akula, Usha Madhuri; Westphal, Christin; Sittig, Marie; Mueller-Roeber, Bernd

2011-01-01

Protein expression in heterologous hosts for functional studies is a cumbersome effort. Here, we report a superior platform for parallel protein expression in vivo and in vitro. The platform combines highly efficient ligation-independent cloning (LIC) with instantaneous detection of expressed proteins through N- or C-terminal fusions to infrared fluorescent protein (IFP). For each open reading frame, only two PCR fragments are generated (with three PCR primers) and inserted by LIC into ten expression vectors suitable for protein expression in microbial hosts, including Escherichia coli, Kluyveromyces lactis, Pichia pastoris, the protozoon Leishmania tarentolae, and an in vitro transcription/translation system. Accumulation of IFP-fusion proteins is detected by infrared imaging of living cells or crude protein extracts directly after SDS-PAGE without additional processing. We successfully employed the LIC-IFP platform for in vivo and in vitro expression of ten plant and fungal proteins, including transcription factors and enzymes. Using the IFP reporter, we additionally established facile methods for the visualisation of protein-protein interactions and the detection of DNA-transcription factor interactions in microtiter and gel-free format. We conclude that IFP represents an excellent reporter for high-throughput protein expression and analysis, which can be easily extended to numerous other expression hosts using the setup reported here. PMID:21541323

[Construction and application of bioinformatic analysis platform for aquatic pathogen based on the MilkyWay-2 supercomputer].

PubMed

Fang, Xiang; Li, Ning-qiu; Fu, Xiao-zhe; Li, Kai-bin; Lin, Qiang; Liu, Li-hui; Shi, Cun-bin; Wu, Shu-qin

2015-07-01

As a key component of life science, bioinformatics has been widely applied in genomics, transcriptomics, and proteomics. However, the requirement of high-performance computers rather than common personal computers for constructing a bioinformatics platform significantly limited the application of bioinformatics in aquatic science. In this study, we constructed a bioinformatic analysis platform for aquatic pathogen based on the MilkyWay-2 supercomputer. The platform consisted of three functional modules, including genomic and transcriptomic sequencing data analysis, protein structure prediction, and molecular dynamics simulations. To validate the practicability of the platform, we performed bioinformatic analysis on aquatic pathogenic organisms. For example, genes of Flavobacterium johnsoniae M168 were identified and annotated via Blast searches, GO and InterPro annotations. Protein structural models for five small segments of grass carp reovirus HZ-08 were constructed by homology modeling. Molecular dynamics simulations were performed on out membrane protein A of Aeromonas hydrophila, and the changes of system temperature, total energy, root mean square deviation and conformation of the loops during equilibration were also observed. These results showed that the bioinformatic analysis platform for aquatic pathogen has been successfully built on the MilkyWay-2 supercomputer. This study will provide insights into the construction of bioinformatic analysis platform for other subjects.

Proteomic platform for the identification of proteins in olive (Olea europaea) pulp.

PubMed

Capriotti, Anna Laura; Cavaliere, Chiara; Foglia, Patrizia; Piovesana, Susy; Samperi, Roberto; Stampachiacchiere, Serena; Laganà, Aldo

2013-10-24

The nutritional and cancer-protective properties of the oil extracted mechanically from the ripe fruits of Olea europaea trees are attracting constantly more attention worldwide. The preparation of high-quality protein samples from plant tissues for proteomic analysis poses many challenging problems. In this study we employed a proteomic platform based on two different extraction methods, SDS and CHAPS based protocols, followed by two precipitation protocols, TCA/acetone and MeOH precipitation, in order to increase the final number of identified proteins. The use of advanced MS techniques in combination with the Swissprot and NCBI Viridiplantae databases and TAIR10 Arabidopsis database allowed us to identify 1265 proteins, of which 22 belong to O. europaea. The application of this proteomic platform for protein extraction and identification will be useful also for other proteomic studies on recalcitrant plant/fruit tissues. Copyright © 2013. Published by Elsevier B.V.

Parylene C-Based Flexible Electronics for pH Monitoring Applications

PubMed Central

Trantidou, Tatiana; Tariq, Mehvesh; Terracciano, Cesare M.; Toumazou, Christofer; Prodromakis, Themistoklis

2014-01-01

Emerging materials in the field of implantable sensors should meet the needs for biocompatibility; transparency; flexibility and integrability. In this work; we present an integrated approach for implementing flexible bio-sensors based on thin Parylene C films that serve both as flexible support substrates and as active H+ sensing membranes within the same platform. Using standard micro-fabrication techniques; a miniaturized 40-electrode array was implemented on a 5 μm-thick Parylene C film. A thin capping film (1 μm) of Parylene on top of the array was plasma oxidized and served as the pH sensing membrane. The sensor was evaluated with the use of extended gate discrete MOSFETs to separate the chemistry from the electronics and prolong the lifetime of the sensor. The chemical sensing array spatially maps the local pH levels; providing a reliable and rapid-response (<5 s) system with a sensitivity of 23 mV/pH. Moreover; it preserves excellent encapsulation integrity and low chemical drifts (0.26–0.38 mV/min). The proposed approach is able to deliver hybrid flexible sensing platforms that will facilitate concurrent electrical and chemical recordings; with application in real-time physiological recordings of organs and tissues. PMID:24988379

Multifluorophore DNA Origami Beacon as a Biosensing Platform.

PubMed

Selnihhin, Denis; Sparvath, Steffen Møller; Preus, Søren; Birkedal, Victoria; Andersen, Ebbe Sloth

2018-05-24

Biosensors play increasingly important roles in many fields, from clinical diagnosis to environmental monitoring, and there is a growing need for cheap and simple analytical devices. DNA nanotechnology provides methods for the creation of sophisticated biosensors, however many of the developed DNA-based sensors are limited by cumbersome and time-consuming readouts involving advanced experimental techniques. Here we describe design, construction, and characterization of an optical DNA origami nanobiosensor device exploiting arrays of precisely positioned organic fluorophores. Two arrays of donor and acceptor fluorophores make up a multifluorophore Förster resonance energy-transfer pair that results in a high-output signal for microscopic detection of single devices. Arrangement of fluorophores into arrays increases the signal-to-noise ratio, allowing detection of signal output from singular biosensors using a conventional fluorescence microscopy setup. Single device analysis enables detection of target DNA sequences in concentrations down to 100 pM in <45 min. We expect that the presented nanobiosensor can function as a general platform for incorporating sensor modules for a variety of targets and that the strong signal amplification properties may allow detection in portable microscope systems to be used for biosensor applications in the field.

Parylene C-based flexible electronics for pH monitoring applications.

PubMed

Trantidou, Tatiana; Tariq, Mehvesh; Terracciano, Cesare M; Toumazou, Christofer; Prodromakis, Themistoklis

2014-07-01

Emerging materials in the field of implantable sensors should meet the needs for biocompatibility; transparency; flexibility and integrability. In this work; we present an integrated approach for implementing flexible bio-sensors based on thin Parylene C films that serve both as flexible support substrates and as active H(+) sensing membranes within the same platform. Using standard micro-fabrication techniques; a miniaturized 40-electrode array was implemented on a 5 μm-thick Parylene C film. A thin capping film (1 μm) of Parylene on top of the array was plasma oxidized and served as the pH sensing membrane. The sensor was evaluated with the use of extended gate discrete MOSFETs to separate the chemistry from the electronics and prolong the lifetime of the sensor. The chemical sensing array spatially maps the local pH levels; providing a reliable and rapid-response (<5 s) system with a sensitivity of 23 mV/pH. Moreover; it preserves excellent encapsulation integrity and low chemical drifts (0.26-0.38 mV/min). The proposed approach is able to deliver hybrid flexible sensing platforms that will facilitate concurrent electrical and chemical recordings; with application in real-time physiological recordings of organs and tissues.

An SDR-Based Real-Time Testbed for GNSS Adaptive Array Anti-Jamming Algorithms Accelerated by GPU

PubMed Central

Xu, Hailong; Cui, Xiaowei; Lu, Mingquan

2016-01-01

Nowadays, software-defined radio (SDR) has become a common approach to evaluate new algorithms. However, in the field of Global Navigation Satellite System (GNSS) adaptive array anti-jamming, previous work has been limited due to the high computational power demanded by adaptive algorithms, and often lack flexibility and configurability. In this paper, the design and implementation of an SDR-based real-time testbed for GNSS adaptive array anti-jamming accelerated by a Graphics Processing Unit (GPU) are documented. This testbed highlights itself as a feature-rich and extendible platform with great flexibility and configurability, as well as high computational performance. Both Space-Time Adaptive Processing (STAP) and Space-Frequency Adaptive Processing (SFAP) are implemented with a wide range of parameters. Raw data from as many as eight antenna elements can be processed in real-time in either an adaptive nulling or beamforming mode. To fully take advantage of the parallelism resource provided by the GPU, a batched method in programming is proposed. Tests and experiments are conducted to evaluate both the computational and anti-jamming performance. This platform can be used for research and prototyping, as well as a real product in certain applications. PMID:26978363

Dataset from chemical gas sensor array in turbulent wind tunnel.

PubMed

Fonollosa, Jordi; Rodríguez-Luján, Irene; Trincavelli, Marco; Huerta, Ramón

2015-06-01

The dataset includes the acquired time series of a chemical detection platform exposed to different gas conditions in a turbulent wind tunnel. The chemo-sensory elements were sampling directly the environment. In contrast to traditional approaches that include measurement chambers, open sampling systems are sensitive to dispersion mechanisms of gaseous chemical analytes, namely diffusion, turbulence, and advection, making the identification and monitoring of chemical substances more challenging. The sensing platform included 72 metal-oxide gas sensors that were positioned at 6 different locations of the wind tunnel. At each location, 10 distinct chemical gases were released in the wind tunnel, the sensors were evaluated at 5 different operating temperatures, and 3 different wind speeds were generated in the wind tunnel to induce different levels of turbulence. Moreover, each configuration was repeated 20 times, yielding a dataset of 18,000 measurements. The dataset was collected over a period of 16 months. The data is related to "On the performance of gas sensor arrays in open sampling systems using Inhibitory Support Vector Machines", by Vergara et al.[1]. The dataset can be accessed publicly at the UCI repository upon citation of [1]: http://archive.ics.uci.edu/ml/datasets/Gas+sensor+arrays+in+open+sampling+settings.

Flexible nanopillar-based electrochemical sensors for genetic detection of foodborne pathogens

NASA Astrophysics Data System (ADS)

Park, Yoo Min; Lim, Sun Young; Jeong, Soon Woo; Song, Younseong; Bae, Nam Ho; Hong, Seok Bok; Choi, Bong Gill; Lee, Seok Jae; Lee, Kyoung G.

2018-06-01

Flexible and highly ordered nanopillar arrayed electrodes have brought great interest for many electrochemical applications, especially to the biosensors, because of its unique mechanical and topological properties. Herein, we report an advanced method to fabricate highly ordered nanopillar electrodes produced by soft-/photo-lithography and metal evaporation. The highly ordered nanopillar array exhibited the superior electrochemical and mechanical properties in regard with the wide space to response with electrolytes, enabling the sensitive analysis. As-prepared gold and silver electrodes on nanopillar arrays exhibit great and stable electrochemical performance to detect the amplified gene from foodborne pathogen of Escherichia coli O157:H7. Additionally, lightweight, flexible, and USB-connectable nanopillar-based electrochemical sensor platform improves the connectivity, portability, and sensitivity. Moreover, we successfully confirm the performance of genetic analysis using real food, specially designed intercalator, and amplified gene from foodborne pathogens with high reproducibility (6% standard deviation) and sensitivity (10 × 1.01 CFU) within 25 s based on the square wave voltammetry principle. This study confirmed excellent mechanical and chemical characteristics of nanopillar electrodes have a great and considerable electrochemical activity to apply as genetic biosensor platform in the fields of point-of-care testing (POCT).

An SDR-Based Real-Time Testbed for GNSS Adaptive Array Anti-Jamming Algorithms Accelerated by GPU.

PubMed

Xu, Hailong; Cui, Xiaowei; Lu, Mingquan

2016-03-11

Nowadays, software-defined radio (SDR) has become a common approach to evaluate new algorithms. However, in the field of Global Navigation Satellite System (GNSS) adaptive array anti-jamming, previous work has been limited due to the high computational power demanded by adaptive algorithms, and often lack flexibility and configurability. In this paper, the design and implementation of an SDR-based real-time testbed for GNSS adaptive array anti-jamming accelerated by a Graphics Processing Unit (GPU) are documented. This testbed highlights itself as a feature-rich and extendible platform with great flexibility and configurability, as well as high computational performance. Both Space-Time Adaptive Processing (STAP) and Space-Frequency Adaptive Processing (SFAP) are implemented with a wide range of parameters. Raw data from as many as eight antenna elements can be processed in real-time in either an adaptive nulling or beamforming mode. To fully take advantage of the parallelism resource provided by the GPU, a batched method in programming is proposed. Tests and experiments are conducted to evaluate both the computational and anti-jamming performance. This platform can be used for research and prototyping, as well as a real product in certain applications.

High-density CMOS Microelectrode Array System for Impedance Spectroscopy and Imaging of Biological Cells.

PubMed

Vijay, Viswam; Raziyeh, Bounik; Amir, Shadmani; Jelena, Dragas; Alicia, Boos Julia; Axel, Birchler; Jan, Müller; Yihui, Chen; Andreas, Hierlemann

2017-01-26

A monolithic measurement platform was implemented to enable label-free in-vitro electrical impedance spectroscopy measurements of cells on multi-functional CMOS microelectrode array. The array includes 59,760 platinum microelectrodes, densely packed within a 4.5 mm × 2.5 mm sensing region at a pitch of 13.5 μm. The 32 on-chip lock-in amplifiers can be used to measure the impedance of any arbitrarily chosen electrodes on the array by applying a sinusoidal voltage, generated by an on-chip waveform generator with a frequency range from 1 Hz to 1 MHz, and measuring the respective current. Proof-of-concept measurements of impedance sensing and imaging are shown in this paper. Correlations between cell detection through optical microscopy and electrochemical impedance scanning were established.

An optimized library for reference-based deconvolution of whole-blood biospecimens assayed using the Illumina HumanMethylationEPIC BeadArray.

PubMed

Salas, Lucas A; Koestler, Devin C; Butler, Rondi A; Hansen, Helen M; Wiencke, John K; Kelsey, Karl T; Christensen, Brock C

2018-05-29

Genome-wide methylation arrays are powerful tools for assessing cell composition of complex mixtures. We compare three approaches to select reference libraries for deconvoluting neutrophil, monocyte, B-lymphocyte, natural killer, and CD4+ and CD8+ T-cell fractions based on blood-derived DNA methylation signatures assayed using the Illumina HumanMethylationEPIC array. The IDOL algorithm identifies a library of 450 CpGs, resulting in an average R 2  = 99.2 across cell types when applied to EPIC methylation data collected on artificial mixtures constructed from the above cell types. Of the 450 CpGs, 69% are unique to EPIC. This library has the potential to reduce unintended technical differences across array platforms.

Scalable loading of a two-dimensional trapped-ion array

PubMed Central

Bruzewicz, Colin D.; McConnell, Robert; Chiaverini, John; Sage, Jeremy M.

2016-01-01

Two-dimensional arrays of trapped-ion qubits are attractive platforms for scalable quantum information processing. Sufficiently rapid reloading capable of sustaining a large array, however, remains a significant challenge. Here with the use of a continuous flux of pre-cooled neutral atoms from a remotely located source, we achieve fast loading of a single ion per site while maintaining long trap lifetimes and without disturbing the coherence of an ion quantum bit in an adjacent site. This demonstration satisfies all major criteria necessary for loading and reloading extensive two-dimensional arrays, as will be required for large-scale quantum information processing. Moreover, the already high loading rate can be increased by loading ions in parallel with only a concomitant increase in photo-ionization laser power and no need for additional atomic flux. PMID:27677357

Novel applications of array comparative genomic hybridization in molecular diagnostics.

PubMed

Cheung, Sau W; Bi, Weimin

2018-05-31

In 2004, the implementation of array comparative genomic hybridization (array comparative genome hybridization [CGH]) into clinical practice marked a new milestone for genetic diagnosis. Array CGH and single-nucleotide polymorphism (SNP) arrays enable genome-wide detection of copy number changes in a high resolution, and therefore microarray has been recognized as the first-tier test for patients with intellectual disability or multiple congenital anomalies, and has also been applied prenatally for detection of clinically relevant copy number variations in the fetus. Area covered: In this review, the authors summarize the evolution of array CGH technology from their diagnostic laboratory, highlighting exonic SNP arrays developed in the past decade which detect small intragenic copy number changes as well as large DNA segments for the region of heterozygosity. The applications of array CGH to human diseases with different modes of inheritance with the emphasis on autosomal recessive disorders are discussed. Expert commentary: An exonic array is a powerful and most efficient clinical tool in detecting genome wide small copy number variants in both dominant and recessive disorders. However, whole-genome sequencing may become the single integrated platform for detection of copy number changes, single-nucleotide changes as well as balanced chromosomal rearrangements in the near future.

SKA aperture array verification system: electromagnetic modeling and beam pattern measurements using a micro UAV

NASA Astrophysics Data System (ADS)

de Lera Acedo, E.; Bolli, P.; Paonessa, F.; Virone, G.; Colin-Beltran, E.; Razavi-Ghods, N.; Aicardi, I.; Lingua, A.; Maschio, P.; Monari, J.; Naldi, G.; Piras, M.; Pupillo, G.

2018-03-01

In this paper we present the electromagnetic modeling and beam pattern measurements of a 16-elements ultra wideband sparse random test array for the low frequency instrument of the Square Kilometer Array telescope. We discuss the importance of a small array test platform for the development of technologies and techniques towards the final telescope, highlighting the most relevant aspects of its design. We also describe the electromagnetic simulations and modeling work as well as the embedded-element and array pattern measurements using an Unmanned Aerial Vehicle system. The latter are helpful both for the validation of the models and the design as well as for the future instrumental calibration of the telescope thanks to the stable, accurate and strong radio frequency signal transmitted by the UAV. At this stage of the design, these measurements have shown a general agreement between experimental results and numerical data and have revealed the localized effect of un-calibrated cable lengths in the inner side-lobes of the array pattern.

Development and Evaluation of a 9K SNP Array for Peach by Internationally Coordinated SNP Detection and Validation in Breeding Germplasm

PubMed Central

Scalabrin, Simone; Gilmore, Barbara; Lawley, Cynthia T.; Gasic, Ksenija; Micheletti, Diego; Rosyara, Umesh R.; Cattonaro, Federica; Vendramin, Elisa; Main, Dorrie; Aramini, Valeria; Blas, Andrea L.; Mockler, Todd C.; Bryant, Douglas W.; Wilhelm, Larry; Troggio, Michela; Sosinski, Bryon; Aranzana, Maria José; Arús, Pere; Iezzoni, Amy; Morgante, Michele; Peace, Cameron

2012-01-01

Although a large number of single nucleotide polymorphism (SNP) markers covering the entire genome are needed to enable molecular breeding efforts such as genome wide association studies, fine mapping, genomic selection and marker-assisted selection in peach [Prunus persica (L.) Batsch] and related Prunus species, only a limited number of genetic markers, including simple sequence repeats (SSRs), have been available to date. To address this need, an international consortium (The International Peach SNP Consortium; IPSC) has pursued a coordinated effort to perform genome-scale SNP discovery in peach using next generation sequencing platforms to develop and characterize a high-throughput Illumina Infinium® SNP genotyping array platform. We performed whole genome re-sequencing of 56 peach breeding accessions using the Illumina and Roche/454 sequencing technologies. Polymorphism detection algorithms identified a total of 1,022,354 SNPs. Validation with the Illumina GoldenGate® assay was performed on a subset of the predicted SNPs, verifying ∼75% of genic (exonic and intronic) SNPs, whereas only about a third of intergenic SNPs were verified. Conservative filtering was applied to arrive at a set of 8,144 SNPs that were included on the IPSC peach SNP array v1, distributed over all eight peach chromosomes with an average spacing of 26.7 kb between SNPs. Use of this platform to screen a total of 709 accessions of peach in two separate evaluation panels identified a total of 6,869 (84.3%) polymorphic SNPs. The almost 7,000 SNPs verified as polymorphic through extensive empirical evaluation represent an excellent source of markers for future studies in genetic relatedness, genetic mapping, and dissecting the genetic architecture of complex agricultural traits. The IPSC peach SNP array v1 is commercially available and we expect that it will be used worldwide for genetic studies in peach and related stone fruit and nut species. PMID:22536421

Enhanced oxygen permeability in membrane-bottomed concave microwells for the formation of pancreatic islet spheroids.

PubMed

Lee, GeonHui; Jun, Yesl; Jang, HeeYeong; Yoon, Junghyo; Lee, JaeSeo; Hong, MinHyung; Chung, Seok; Kim, Dong-Hwee; Lee, SangHoon

2018-01-01

Oxygen availability is a critical factor in regulating cell viability that ultimately contributes to the normal morphogenesis and functionality of human tissues. Among various cell culture platforms, construction of 3D multicellular spheroids based on microwell arrays has been extensively applied to reconstitute in vitro human tissue models due to its precise control of tissue culture conditions as well as simple fabrication processes. However, an adequate supply of oxygen into the spheroidal cellular aggregation still remains one of the main challenges to producing healthy in vitro spheroidal tissue models. Here, we present a novel design for controlling the oxygen distribution in concave microwell arrays. We show that oxygen permeability into the microwell is tightly regulated by varying the poly-dimethylsiloxane (PDMS) bottom thickness of the concave microwells. Moreover, we validate the enhanced performance of the engineered microwell arrays by culturing non-proliferated primary rat pancreatic islet spheroids on varying bottom thickness from 10 μm to 1050 μm. Morphological and functional analyses performed on the pancreatic islet spheroids grown for 14 days prove the long-term stability, enhanced viability, and increased hormone secretion under the sufficient oxygen delivery conditions. We expect our results could provide knowledge on oxygen distribution in 3-dimensional spheroidal cell structures and critical design concept for tissue engineering applications. In this study, we present a noble design to control the oxygen distribution in concave microwell arrays for the formation of highly functional pancreatic islet spheroids by engineering the bottom of the microwells. Our new platform significantly enhanced oxygen permeability that turned out to improve cell viability and spheroidal functionality compared to the conventional thick-bottomed 3-D culture system. Therefore, we believe that this could be a promising medical biotechnology platform to further develop high-throughput tissue screening system as well as in vivo-mimicking customised 3-D tissue culture systems. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Peptides and Anti-peptide Antibodies for Small and Medium Scale Peptide and Anti-peptide Affinity Microarrays: Antigenic Peptide Selection, Immobilization, and Processing.

PubMed

Zhang, Fan; Briones, Andrea; Soloviev, Mikhail

2016-01-01

This chapter describes the principles of selection of antigenic peptides for the development of anti-peptide antibodies for use in microarray-based multiplex affinity assays and also with mass-spectrometry detection. The methods described here are mostly applicable to small to medium scale arrays. Although the same principles of peptide selection would be suitable for larger scale arrays (with 100+ features) the actual informatics software and printing methods may well be different. Because of the sheer number of proteins/peptides to be processed and analyzed dedicated software capable of processing all the proteins and an enterprise level array robotics may be necessary for larger scale efforts. This report aims to provide practical advice to those who develop or use arrays with up to ~100 different peptide or protein features.

Dynamic application of microprojection arrays to skin induces circulating protein extravasation for enhanced biomarker capture and detection.

PubMed

Coffey, Jacob W; Meliga, Stefano C; Corrie, Simon R; Kendall, Mark A F

2016-04-01

Surface modified microprojection arrays are a needle-free alternative to capture circulating biomarkers from the skin in vivo for diagnosis. The concentration and turnover of biomarkers in the interstitial fluid, however, may limit the amount of biomarker that can be accessed by microprojection arrays and ultimately their capture efficiency. Here we report that microprojection array insertion induces protein extravasation from blood vessels and increases the concentration of biomarkers in skin, which can synergistically improve biomarker capture. Regions of blood vessels in skin were identified in the upper dermis and subcutaneous tissue by multi-photon microscopy. Insertion of microprojection array designs with varying projection length (40-190 μm), density (5000-20,408 proj.cm(-2)) and array size (4-36 mm(2)) did not affect the degree of extravasation. Furthermore, the location of extravasated protein did not correlate with projection penetration to these highly vascularised regions, suggesting extravasation was not caused by direct puncture of blood vessels. Biomarker extravasation was also induced by dynamic application of flat control surfaces, and varied with the impact velocity, further supporting this conclusion. The extravasated protein distribution correlated well with regions of high mechanical stress generated during insertion, quantified by finite element models. Using this approach to induce extravasation prior to microprojection array-based biomarker capture, anti-influenza IgG was captured within a 2 min application time, demonstrating that extravasation can lead to rapid biomarker sampling and significantly improved microprojection array capture efficiency. These results have broad implications for the development of transdermal devices that deliver to and sample from the skin. Crown Copyright © 2016. Published by Elsevier Ltd. All rights reserved.

Using a silver-enhanced microarray sandwich structure to improve SERS sensitivity for protein detection.

PubMed

Gu, Xuefang; Yan, Yuerong; Jiang, Guoqing; Adkins, Jason; Shi, Jian; Jiang, Guomin; Tian, Shu

2014-03-01

A simple and sensitive method, based on surface-enhanced Raman scattering (SERS), for immunoassay and label-free protein detection is reported. A series of bowl-shaped silver cavity arrays were fabricated by electrodeposition using a self-assembled polystyrene spheres template. The reflection spectra of these cavity arrays were recorded as a function of film thickness, and then correlated with SERS enhancement using sodium thiophenolate as the probe molecule. The results reveal that SERS enhancement can be maximized when the frequency of both the incident laser and the Raman scattering approach the frequency of the localized surface plasmon resonance. The optimized array was then used as the bottom layer of a silver nanoparticle-protein-bowl-shaped silver cavity array sandwich. The second layer of silver was introduced by the interactions between the proteins in the middle layer of the sandwich architecture and silver nanoparticles. Human IgG bound to the surface of this microcavity array can retain its recognition function. With the Raman reporter molecules labeled on the antibody, a detection limit down to 0.1 ng mL(-1) for human IgG is easily achieved. Furthermore, the SERS spectra of label-free proteins (catalase, cytochrome C, avidin and lysozyme) from the assembled sandwich have excellent reproducibility and high quality. The results reveal that the proposed approach has potential for use in qualitative and quantitative detection of biomolecules.

Reconfigurable, Intelligently-Adaptive, Communication System, an SDR Platform

NASA Technical Reports Server (NTRS)

Roche, Rigoberto

2016-01-01

The Space Telecommunications Radio System (STRS) provides a common, consistent framework to abstract the application software from the radio platform hardware. STRS aims to reduce the cost and risk of using complex, configurable and reprogrammable radio systems across NASA missions. The Glenn Research Center (GRC) team made a software-defined radio (SDR) platform STRS compliant by adding an STRS operating environment and a field programmable gate array (FPGA) wrapper, capable of implementing each of the platforms interfaces, as well as a test waveform to exercise those interfaces. This effort serves to provide a framework toward waveform development on an STRS compliant platform to support future space communication systems for advanced exploration missions. Validated STRS compliant applications provided tested code with extensive documentation to potentially reduce risk, cost and efforts in development of space-deployable SDRs. This paper discusses the advantages of STRS, the integration of STRS onto a Reconfigurable, Intelligently-Adaptive, Communication System (RIACS) SDR platform, the sample waveform, and wrapper development efforts. The paper emphasizes the infusion of the STRS Architecture onto the RIACS platform for potential use in next generation SDRs for advance exploration missions.

Multiscale Modelling of Relationships between Protein Classes and Drug Behavior Across all Diseases Using the CANDO Platform

PubMed Central

Samudrala, Ram

2015-01-01

We have examined the effect of eight different protein classes (channels, GPCRs, kinases, ligases, nuclear receptors, proteases, phosphatases, transporters) on the benchmarking performance of the CANDO drug discovery and repurposing platform (http://protinfo.org/cando). The first version of the CANDO platform utilizes a matrix of predicted interactions between 48278 proteins and 3733 human ingestible compounds (including FDA approved drugs and supplements) that map to 2030 indications/diseases using a hierarchical chem and bio-informatic fragment based docking with dynamics protocol (> one billion predicted interactions considered). The platform uses similarity of compound-proteome interaction signatures as indicative of similar functional behavior and benchmarking accuracy is calculated across 1439 indications/diseases with more than one approved drug. The CANDO platform yields a significant correlation (0.99, p-value < 0.0001) between the number of proteins considered and benchmarking accuracy obtained indicating the importance of multitargeting for drug discovery. Average benchmarking accuracies range from 6.2 % to 7.6 % for the eight classes when the top 10 ranked compounds are considered, in contrast to a range of 5.5 % to 11.7 % obtained for the comparison/control sets consisting of 10, 100, 1000, and 10000 single best performing proteins. These results are generally two orders of magnitude better than the average accuracy of 0.2% obtained when randomly generated (fully scrambled) matrices are used. Different indications perform well when different classes are used but the best accuracies (up to 11.7% for the top 10 ranked compounds) are achieved when a combination of classes are used containing the broadest distribution of protein folds. Our results illustrate the utility of the CANDO approach and the consideration of different protein classes for devising indication specific protocols for drug repurposing as well as drug discovery. PMID:25694071

An integrated centrifugo-opto-microfluidic platform for arraying, analysis, identification and manipulation of individual cells.

PubMed

Burger, R; Kurzbuch, D; Gorkin, R; Kijanka, G; Glynn, M; McDonagh, C; Ducrée, J

2015-01-21

In this work we present a centrifugal microfluidic system enabling highly efficient collective trapping and alignment of particles such as microbeads and cells, their multi-colour fluorescent detection and subsequent manipulation by optical tweezers. We demonstrate array-based capture and imaging followed by "cherry-picking" of individual particles, first for fluorescently labelled polystyrene (PS) beads and then for cells. Different cell lines are discriminated based on intracellular as well as surface-based markers.

One of many microphones arrayed under the path of the F-5E SSBE aircraft to record sonic booms

NASA Image and Video Library

2004-01-13

One of many microphones arrayed under the path of the F-5E SSBE (Shaped Sonic Boom Experiment) aircraft to record sonic booms. The SSBE (Shaped Sonic Boom Experiment) was formerly known as the Shaped Sonic Boom Demonstration, or SSBD, and is part of DARPA's Quiet Supersonic Platform (QSP) program. On August 27, 2003, the F-5E SSBD aircraft demonstrated a method to reduce the intensity of sonic booms.

Realizing topological edge states in a silicon nitride microring-based photonic integrated circuit.

PubMed

Yin, Chenxuan; Chen, Yujie; Jiang, Xiaohui; Zhang, Yanfeng; Shao, Zengkai; Xu, Pengfei; Yu, Siyuan

2016-10-15

Topological edge states in a photonic integrated circuit based on the platform of silicon nitride are demonstrated with a two-dimensional coupled resonator optical waveguide array involving the synthetic magnetic field for photons at near-infrared wavelengths. Measurements indicate that the topological edge states can be observed at certain wavelengths, with light travelling around the boundary of the array. Combined with the induced disorders in fabrication near the edge, the system shows the defect immunity under the topological protection of edge states.

Exosome platform for diagnosis and monitoring of traumatic brain injury

PubMed Central

Taylor, Douglas D.; Gercel-Taylor, Cicek

2014-01-01

We have previously demonstrated the release of membranous structures by cells into their extracellular environment, which are termed exosomes, microvesicles or extracellular vesicles depending on specific characteristics, including size, composition and biogenesis pathway. With activation, injury, stress, transformation or infection, cells express proteins and RNAs associated with the cellular responses to these events. The exosomes released by these cells can exhibit an array of proteins, lipids and nucleic acids linked to these physiologic events. This review focuses on exosomes associated with traumatic brain injury, which may be both diagnostic and a causative factor in the progression of the injury. Based on current data, exosomes play essential roles as conveyers of intercellular communication and mediators of many of the pathological conditions associated with development, progression and therapeutic failures and cellular stress in a variety of pathologic conditions. These extracellular vesicles express components responsible for angiogenesis promotion, stromal remodelling, signal pathway activation through growth factor/receptor transfer, chemoresistance, immunologic activation and genetic exchange. These circulating exosomes not only represent a central mediator of the pro-inflammatory microenvironment linked with secondary brain injury, but their presence in the peripheral circulation may serve as a surrogate for biopsies, enabling real-time diagnosis and monitoring of neurodegenerative progression. PMID:25135964

NUP98-PHF23 is a chromatin modifying oncoprotein that causes a wide array of leukemias sensitive to inhibition of PHD domain histone reader function

PubMed Central

Gough, Sheryl M; Lee, Fan; Yang, Fan; Walker, Robert L; Zhu, Yeulin J; Pineda, Marbin; Onozawa, Masahiro; Chung, Yang Jo; Bilke, Sven; Wagner, Elise K; Denu, John M; Ning, Yi; Xu, Bowen; Wang, Gang Greg; Meltzer, Paul S; Aplan, Peter D

2014-01-01

In this report, we show that expression of a NUP98-PHF23 (NP23) fusion, associated with acute myeloid leukemia (AML) in humans, leads to myeloid, erythroid, T-cell, and B-cell leukemia in mice. The leukemic and pre-leukemic tissues display a stem cell-like expression signature including Hoxa, Hoxb, and Meis1 genes. The PHF23 PHD domain is known to bind H3K4me3 residues, and chromatin immunoprecipitation experiments demonstrated that the NP23 protein bound chromatin at a specific subset of H3K4me3 sites, including Hoxa, Hoxb, and Meis1. Treatment of NP23 cells with disulfiram, which inhibits the binding of PHD domains to H3K4me3 residues, rapidly and selectively killed NP23 myeloblasts; cell death was preceded by decreased expression of Hoxa, Hoxb, and Meis1. Furthermore, AML driven by a related fusion gene, NUP98-JARID1A (NJL), was also sensitive to disulfiram. Thus, the NP23 mouse provides a platform to evaluate compounds that disrupt binding of oncogenic PHD proteins to H3K4me3. PMID:24535671

Quantitative performance characterization of three-dimensional noncontact fluorescence molecular tomography

NASA Astrophysics Data System (ADS)

Favicchio, Rosy; Psycharakis, Stylianos; Schönig, Kai; Bartsch, Dusan; Mamalaki, Clio; Papamatheakis, Joseph; Ripoll, Jorge; Zacharakis, Giannis

2016-02-01

Fluorescent proteins and dyes are routine tools for biological research to describe the behavior of genes, proteins, and cells, as well as more complex physiological dynamics such as vessel permeability and pharmacokinetics. The use of these probes in whole body in vivo imaging would allow extending the range and scope of current biomedical applications and would be of great interest. In order to comply with a wide variety of application demands, in vivo imaging platform requirements span from wide spectral coverage to precise quantification capabilities. Fluorescence molecular tomography (FMT) detects and reconstructs in three dimensions the distribution of a fluorophore in vivo. Noncontact FMT allows fast scanning of an excitation source and noninvasive measurement of emitted fluorescent light using a virtual array detector operating in free space. Here, a rigorous process is defined that fully characterizes the performance of a custom-built horizontal noncontact FMT setup. Dynamic range, sensitivity, and quantitative accuracy across the visible spectrum were evaluated using fluorophores with emissions between 520 and 660 nm. These results demonstrate that high-performance quantitative three-dimensional visible light FMT allowed the detection of challenging mesenteric lymph nodes in vivo and the comparison of spectrally distinct fluorescent reporters in cell culture.

Molecular Design of Antifouling Polymer Brushes Using Sequence-Specific Peptoids.

PubMed

Lau, King Hang Aaron; Sileika, Tadas S; Park, Sung Hyun; Sousa, Ana Maria Leal; Burch, Patrick; Szleifer, Igal; Messersmith, Phillip B

2015-01-07

Material systems that can be used to flexibly and precisely define the chemical nature and molecular arrangement of a surface would be invaluable for the control of complex biointerfacial interactions. For example, progress in antifouling polymer biointerfaces that prevent non-specific protein adsorption and cell attachment, which can significantly improve the performance of an array of biomedical and industrial applications, is hampered by a lack of chemical models to identify the molecular features conferring their properties. Poly(N-substituted glycine) "peptoids" are peptidomimetic polymers that can be conveniently synthesized with specific monomer sequences and chain lengths, and are presented as a versatile platform for investigating the molecular design of antifouling polymer brushes. Zwitterionic antifouling polymer brushes have captured significant recent attention, and a targeted library of zwitterionic peptoid brushes with a different charge densities, hydration, separations between charged groups, chain lengths, and grafted chain densities, is quantitatively evaluated for their antifouling properties through a range of protein adsorption and cell attachment assays. Specific zwitterionic brush designs were found to give rise to distinct but subtle differences in properties. The results also point to the dominant roles of the grafted chain density and chain length in determining the performance of antifouling polymer brushes.

CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins.

PubMed

Couvin, David; Bernheim, Aude; Toffano-Nioche, Claire; Touchon, Marie; Michalik, Juraj; Néron, Bertrand; C Rocha, Eduardo P; Vergnaud, Gilles; Gautheret, Daniel; Pourcel, Christine

2018-05-22

CRISPR (clustered regularly interspaced short palindromic repeats) arrays and their associated (Cas) proteins confer bacteria and archaea adaptive immunity against exogenous mobile genetic elements, such as phages or plasmids. CRISPRCasFinder allows the identification of both CRISPR arrays and Cas proteins. The program includes: (i) an improved CRISPR array detection tool facilitating expert validation based on a rating system, (ii) prediction of CRISPR orientation and (iii) a Cas protein detection and typing tool updated to match the latest classification scheme of these systems. CRISPRCasFinder can either be used online or as a standalone tool compatible with Linux operating system. All third-party software packages employed by the program are freely available. CRISPRCasFinder is available at https://crisprcas.i2bc.paris-saclay.fr.

Production of therapeutic proteins in algae, analysis of expression of seven human proteins in the chloroplast of Chlamydomonas reinhardtii

PubMed Central

Rasala, Beth A; Muto, Machiko; Lee, Philip A; Jager, Michal; Cardoso, Rosa MF; Behnke, Craig A; Kirk, Peter; Hokanson, Craig A; Crea, Roberto; Mendez, Michael; Mayfield, Stephen P

2010-01-01

Summary Recombinant proteins are widely used today in many industries, including the biopharmaceutical industry, and can be expressed in bacteria, yeasts, mammalian and insect cell cultures, or in transgenic plants and animals. In addition, transgenic algae have also been shown to support recombinant protein expression, both from the nuclear and chloroplast genomes. However, to date, there are only a few reports on recombinant proteins expressed in the algal chloroplast. It is unclear if this is due to few attempts or to limitations of the system that preclude expression of many proteins. Thus, we sought to assess the versatility of transgenic algae as a recombinant protein production platform. To do this, we tested whether the algal chloroplast could support the expression of a diverse set of current or potential human therapeutic proteins. Of the seven proteins chosen, greater than 50% expressed at levels sufficient for commercial production. Three expressed at 2% to 3% of total soluble protein, while a forth protein accumulated to similar levels when translationally fused to a well-expressed serum amyloid protein. All of the algal chloroplast-expressed proteins are soluble and showed biological activity comparable to that of the same proteins expressed using traditional production platforms. Thus, the success rate, expression levels, and bioactivty achieved demonstrate the utility of C. reinhardtii as a robust platform for human therapeutic protein production. PMID:20230484

Micro-Analyzer: automatic preprocessing of Affymetrix microarray data.

PubMed

Guzzi, Pietro Hiram; Cannataro, Mario

2013-08-01

A current trend in genomics is the investigation of the cell mechanism using different technologies, in order to explain the relationship among genes, molecular processes and diseases. For instance, the combined use of gene-expression arrays and genomic arrays has been demonstrated as an effective instrument in clinical practice. Consequently, in a single experiment different kind of microarrays may be used, resulting in the production of different types of binary data (images and textual raw data). The analysis of microarray data requires an initial preprocessing phase, that makes raw data suitable for use on existing analysis platforms, such as the TIGR M4 (TM4) Suite. An additional challenge to be faced by emerging data analysis platforms is the ability to treat in a combined way those different microarray formats coupled with clinical data. In fact, resulting integrated data may include both numerical and symbolic data (e.g. gene expression and SNPs regarding molecular data), as well as temporal data (e.g. the response to a drug, time to progression and survival rate), regarding clinical data. Raw data preprocessing is a crucial step in analysis but is often performed in a manual and error prone way using different software tools. Thus novel, platform independent, and possibly open source tools enabling the semi-automatic preprocessing and annotation of different microarray data are needed. The paper presents Micro-Analyzer (Microarray Analyzer), a cross-platform tool for the automatic normalization, summarization and annotation of Affymetrix gene expression and SNP binary data. It represents the evolution of the μ-CS tool, extending the preprocessing to SNP arrays that were not allowed in μ-CS. The Micro-Analyzer is provided as a Java standalone tool and enables users to read, preprocess and analyse binary microarray data (gene expression and SNPs) by invoking TM4 platform. It avoids: (i) the manual invocation of external tools (e.g. the Affymetrix Power Tools), (ii) the manual loading of preprocessing libraries, and (iii) the management of intermediate files, such as results and metadata. Micro-Analyzer users can directly manage Affymetrix binary data without worrying about locating and invoking the proper preprocessing tools and chip-specific libraries. Moreover, users of the Micro-Analyzer tool can load the preprocessed data directly into the well-known TM4 platform, extending in such a way also the TM4 capabilities. Consequently, Micro Analyzer offers the following advantages: (i) it reduces possible errors in the preprocessing and further analysis phases, e.g. due to the incorrect choice of parameters or due to the use of old libraries, (ii) it enables the combined and centralized pre-processing of different arrays, (iii) it may enhance the quality of further analysis by storing the workflow, i.e. information about the preprocessing steps, and (iv) finally Micro-Analzyer is freely available as a standalone application at the project web site http://sourceforge.net/projects/microanalyzer/. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

SNPConvert: SNP Array Standardization and Integration in Livestock Species.

PubMed

Nicolazzi, Ezequiel Luis; Marras, Gabriele; Stella, Alessandra

2016-06-09

One of the main advantages of single nucleotide polymorphism (SNP) array technology is providing genotype calls for a specific number of SNP markers at a relatively low cost. Since its first application in animal genetics, the number of available SNP arrays for each species has been constantly increasing. However, conversely to that observed in whole genome sequence data analysis, SNP array data does not have a common set of file formats or coding conventions for allele calling. Therefore, the standardization and integration of SNP array data from multiple sources have become an obstacle, especially for users with basic or no programming skills. Here, we describe the difficulties related to handling SNP array data, focusing on file formats, SNP allele coding, and mapping. We also present SNPConvert suite, a multi-platform, open-source, and user-friendly set of tools to overcome these issues. This tool, which can be integrated with open-source and open-access tools already available, is a first step towards an integrated system to standardize and integrate any type of raw SNP array data. The tool is available at: https://github. com/nicolazzie/SNPConvert.git.

Extended Hubbard model for mesoscopic transport in donor arrays in silicon

NASA Astrophysics Data System (ADS)

Le, Nguyen H.; Fisher, Andrew J.; Ginossar, Eran

2017-12-01

Arrays of dopants in silicon are promising platforms for the quantum simulation of the Fermi-Hubbard model. We show that the simplest model with only on-site interaction is insufficient to describe the physics of an array of phosphorous donors in silicon due to the strong intersite interaction in the system. We also study the resonant tunneling transport in the array at low temperature as a mean of probing the features of the Hubbard physics, such as the Hubbard bands and the Mott gap. Two mechanisms of localization which suppresses transport in the array are investigated: The first arises from the electron-ion core attraction and is significant at low filling; the second is due to the sharp oscillation in the tunnel coupling caused by the intervalley interference of the donor electron's wave function. This disorder in the tunnel coupling leads to a steep exponential decay of conductance with channel length in one-dimensional arrays, but its effect is less prominent in two-dimensional ones. Hence, it is possible to observe resonant tunneling transport in a relatively large array in two dimensions.

Constitutional 3p26.3 terminal microdeletion in an adolescent with neuroblastoma.

PubMed

Pezzolo, Annalisa; Sementa, Angela Rita; Lerone, Margherita; Morini, Martina; Ognibene, Marzia; Defferrari, Raffaella; Mazzocco, Katia; Conte, Massimo; Gigliotti, Anna Rita; Garaventa, Alberto; Pistoia, Vito; Varesio, Luigi

2017-05-04

Neuroblastoma (NB) is a common and often lethal cancer of early childhood that accounts for 10% of pediatric cancer mortality. Incidence peaks in infancy and then rapidly declines, with less than 5% of cases diagnosed in children and adolescents ≥ 10 y. There is increasing evidence that NB has unique biology and an chronic disease course in older children and adolescents, but ultimately dismal survival. We describe a rare constitutional 3p26.3 terminal microdeletion which occurred in an adolescent with NB, with apparently normal phenotype without neurocognitive defects. We evaluated the association of expression of genes involved in the microdeletion with NB patient outcomes using R2 platform. We screened NB patient's tumor cells for CHL1 protein expression using immunofluorescence. Constitutional and tumor DNA were tested by array-comparative genomic hybridization and single nucleotide-polymorphism-array analyses. Peripheral blood mononuclear cells from the patient showed a 2.54 Mb sub-microscopic constitutional terminal 3p deletion that extended to band p26.3. The microdeletion 3p disrupted the CNTN4 gene and the neighboring CNTN6 and CHL1 genes were hemizygously deleted, each of these genes encode neuronal cell adhesion molecules. Low expression of CNTN6 and CNTN4 genes did not stratify NB patients, whereas low CHL1 expression characterized 417 NB patients having worse overall survival. CHL1 protein expression on tumor cells from the patient was weaker than positive control. This is the first report of a constitutional 3p26.3 deletion in a NB patient. Since larger deletions of 3p, indicative of the presence of one or more tumor suppressor genes in this region, occur frequently in neuroblastoma, our results pave the way to the identification of one putative NB suppressor genes mapping in 3p26.3.

Immunoproteomic Profiling of Antiviral Antibodies in New-Onset Type 1 Diabetes Using Protein Arrays.

PubMed

Bian, Xiaofang; Wallstrom, Garrick; Davis, Amy; Wang, Jie; Park, Jin; Throop, Andrea; Steel, Jason; Yu, Xiaobo; Wasserfall, Clive; Schatz, Desmond; Atkinson, Mark; Qiu, Ji; LaBaer, Joshua

2016-01-01

The rapid rise in the incidence of type 1 diabetes (T1D) suggests the involvement of environmental factors including viral infections. We evaluated the association between viral infections and T1D by profiling antiviral antibodies using a high-throughput immunoproteomics approach in patients with new-onset T1D. We constructed a viral protein array comprising the complete proteomes of seven viruses associated with T1D and open reading frames from other common viruses. Antibody responses to 646 viral antigens were assessed in 42 patients with T1D and 42 age- and sex-matched healthy control subjects (mean age 12.7 years, 50% males). Prevalence of antiviral antibodies agreed with known infection rates for the corresponding virus based on epidemiological studies. Antibody responses to Epstein-Barr virus (EBV) were significantly higher in case than control subjects (odds ratio 6.6; 95% CI 2.0-25.7), whereas the other viruses showed no differences. The EBV and T1D association was significant in both sex and age subgroups (≤12 and >12 years), and there was a trend toward early EBV infections among the case subjects. These results suggest a potential role for EBV in T1D development. We believe our innovative immunoproteomics platform is useful for understanding the role of viral infections in T1D and other disorders where associations between viral infection and disease are unclear. © 2016 by the American Diabetes Association. Readers may use this article as long as the work is properly cited, the use is educational and not for profit, and the work is not altered.

The production of KIR-Fc fusion proteins and their use in a multiplex HLA class I binding assay.

PubMed

Hilton, Hugo G; Moesta, Achim K; Guethlein, Lisbeth A; Blokhuis, Jeroen; Parham, Peter; Norman, Paul J

2015-10-01

Soluble recombinant proteins that comprise the extracellular part of a surface expressed receptor attached to the Fc region of an IgG antibody have facilitated the determination of ligand specificity for an array of immune system receptors. Among such receptors is the family of killer cell immunoglobulin-like receptors (KIR) that recognize HLA class I ligands. These receptors, expressed on natural killer (NK) cells and T cells, play important roles in both immune defense and placental development in early pregnancy. Here we describe a method for the production of two domain KIR-Fc fusion proteins using baculovirus infected insect cells. This method is more scalable than traditional mammalian cell expression systems and produces efficiently folded proteins that carry posttranslational modifications found in native KIR. We also describe a multiplex binding assay using the Luminex platform that determines the avidity and specificity of two domain KIR-Fc for a panel of microbeads, each coated with one of 97 HLA class I allotypes. This assay is simple to perform, and represents a major improvement over the assays used previously, which were limited in the number of KIR and HLA class I combinations that could be assayed at any one time. The results obtained from this assay can be used to predict the response of NK cell and T cells when their KIR recognize HLA class I. Copyright © 2015 Elsevier B.V. All rights reserved.

A microfluidic biochip platform for electrical quantification of proteins.

PubMed

Valera, Enrique; Berger, Jacob; Hassan, Umer; Ghonge, Tanmay; Liu, Julia; Rappleye, Michael; Winter, Jackson; Abboud, Daniel; Haidry, Zeeshan; Healey, Ryan; Hung, Na-Teng; Leung, Nathaniel; Mansury, Naif; Hasnain, Alexander; Lannon, Christine; Price, Zachary; White, Karen; Bashir, Rashid

2018-05-15

Sepsis, an adverse auto-immune response to an infection often causing life-threatening complications, results in the highest mortality and treatment cost of any illness in US hospitals. Several immune biomarker levels, including Interleukin 6 (IL-6), have shown a high correlation to the onset and progression of sepsis. Currently, no technology diagnoses and stratifies sepsis progression using biomarker levels. This paper reports a microfluidic biochip platform to detect proteins in undiluted human plasma samples. The device uses a differential enumeration platform that integrates Coulter counting principles, antigen specific capture chambers, and micro size bead based immunodetection to quantify cytokines. This microfluidic biochip was validated as a potential point of care technology by quantifying IL-6 from plasma samples (n = 29) with good correlation (R2 = 0.81) and agreement (Bland-Altman) compared to controls. In combination with previous applications, this point of care platform can potentially detect cell and protein biomarkers simultaneously for sepsis stratification.

Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa.

PubMed

Bassil, Nahla V; Davis, Thomas M; Zhang, Hailong; Ficklin, Stephen; Mittmann, Mike; Webster, Teresa; Mahoney, Lise; Wood, David; Alperin, Elisabeth S; Rosyara, Umesh R; Koehorst-Vanc Putten, Herma; Monfort, Amparo; Sargent, Daniel J; Amaya, Iraida; Denoyes, Beatrice; Bianco, Luca; van Dijk, Thijs; Pirani, Ali; Iezzoni, Amy; Main, Dorrie; Peace, Cameron; Yang, Yilong; Whitaker, Vance; Verma, Sujeet; Bellon, Laurent; Brew, Fiona; Herrera, Raul; van de Weg, Eric

2015-03-07

A high-throughput genotyping platform is needed to enable marker-assisted breeding in the allo-octoploid cultivated strawberry Fragaria × ananassa. Short-read sequences from one diploid and 19 octoploid accessions were aligned to the diploid Fragaria vesca 'Hawaii 4' reference genome to identify single nucleotide polymorphisms (SNPs) and indels for incorporation into a 90 K Affymetrix® Axiom® array. We report the development and preliminary evaluation of this array. About 36 million sequence variants were identified in a 19 member, octoploid germplasm panel. Strategies and filtering pipelines were developed to identify and incorporate markers of several types: di-allelic SNPs (66.6%), multi-allelic SNPs (1.8%), indels (10.1%), and ploidy-reducing "haploSNPs" (11.7%). The remaining SNPs included those discovered in the diploid progenitor F. iinumae (3.9%), and speculative "codon-based" SNPs (5.9%). In genotyping 306 octoploid accessions, SNPs were assigned to six classes with Affymetrix's "SNPolisher" R package. The highest quality classes, PolyHigh Resolution (PHR), No Minor Homozygote (NMH), and Off-Target Variant (OTV) comprised 25%, 38%, and 1% of array markers, respectively. These markers were suitable for genetic studies as demonstrated in the full-sib family 'Holiday' × 'Korona' with the generation of a genetic linkage map consisting of 6,594 PHR SNPs evenly distributed across 28 chromosomes with an average density of approximately one marker per 0.5 cM, thus exceeding our goal of one marker per cM. The Affymetrix IStraw90 Axiom array is the first high-throughput genotyping platform for cultivated strawberry and is commercially available to the worldwide scientific community. The array's high success rate is likely driven by the presence of naturally occurring variation in ploidy level within the nominally octoploid genome, and by effectiveness of the employed array design and ploidy-reducing strategies. This array enables genetic analyses including generation of high-density linkage maps, identification of quantitative trait loci for economically important traits, and genome-wide association studies, thus providing a basis for marker-assisted breeding in this high value crop.

Serological profiling of the EBV immune response in Chronic Fatigue Syndrome using a peptide microarray.

PubMed

Loebel, Madlen; Eckey, Maren; Sotzny, Franziska; Hahn, Elisabeth; Bauer, Sandra; Grabowski, Patricia; Zerweck, Johannes; Holenya, Pavlo; Hanitsch, Leif G; Wittke, Kirsten; Borchmann, Peter; Rüffer, Jens-Ulrich; Hiepe, Falk; Ruprecht, Klemens; Behrends, Uta; Meindl, Carola; Volk, Hans-Dieter; Reimer, Ulf; Scheibenbogen, Carmen

2017-01-01

Epstein-Barr-Virus (EBV) plays an important role as trigger or cofactor for various autoimmune diseases. In a subset of patients with Chronic Fatigue Syndrome (CFS) disease starts with infectious mononucleosis as late primary EBV-infection, whereby altered levels of EBV-specific antibodies can be observed in another subset of patients. We performed a comprehensive mapping of the IgG response against EBV comparing 50 healthy controls with 92 CFS patients using a microarray platform. Patients with multiple sclerosis (MS), systemic lupus erythematosus (SLE) and cancer-related fatigue served as controls. 3054 overlapping peptides were synthesised as 15-mers from 14 different EBV proteins. Array data was validated by ELISA for selected peptides. Prevalence of EBV serotypes was determined by qPCR from throat washing samples. EBV type 1 infections were found in patients and controls. EBV seroarray profiles between healthy controls and CFS were less divergent than that observed for MS or SLE. We found significantly enhanced IgG responses to several EBNA-6 peptides containing a repeat sequence in CFS patients compared to controls. EBNA-6 peptide IgG responses correlated well with EBNA-6 protein responses. The EBNA-6 repeat region showed sequence homologies to various human proteins. Patients with CFS had a quite similar EBV IgG antibody response pattern as healthy controls. Enhanced IgG reactivity against an EBNA-6 repeat sequence and against EBNA-6 protein is found in CFS patients. Homologous sequences of various human proteins with this EBNA-6 repeat sequence might be potential targets for antigenic mimicry.

Modular protein switches derived from antibody mimetic proteins.

PubMed

Nicholes, N; Date, A; Beaujean, P; Hauk, P; Kanwar, M; Ostermeier, M

2016-02-01

Protein switches have potential applications as biosensors and selective protein therapeutics. Protein switches built by fusion of proteins with the prerequisite input and output functions are currently developed using an ad hoc process. A modular switch platform in which existing switches could be readily adapted to respond to any ligand would be advantageous. We investigated the feasibility of a modular protein switch platform based on fusions of the enzyme TEM-1 β-lactamase (BLA) with two different antibody mimetic proteins: designed ankyrin repeat proteins (DARPins) and monobodies. We created libraries of random insertions of the gene encoding BLA into genes encoding a DARPin or a monobody designed to bind maltose-binding protein (MBP). From these libraries, we used a genetic selection system for β-lactamase activity to identify genes that conferred MBP-dependent ampicillin resistance to Escherichia coli. Some of these selected genes encoded switch proteins whose enzymatic activity increased up to 14-fold in the presence of MBP. We next introduced mutations into the antibody mimetic domain of these switches that were known to cause binding to different ligands. To different degrees, introduction of the mutations resulted in switches with the desired specificity, illustrating the potential modularity of these platforms. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Creation of a Human Secretome: A Novel Composite Library of Human Secreted Proteins: Validation Using Ovarian Cancer Gene Expression Data and a Virtual Secretome Array.

PubMed

Vathipadiekal, Vinod; Wang, Victoria; Wei, Wei; Waldron, Levi; Drapkin, Ronny; Gillette, Michael; Skates, Steven; Birrer, Michael

2015-11-01

To generate a comprehensive "Secretome" of proteins potentially found in the blood and derive a virtual Affymetrix array. To validate the utility of this database for the discovery of novel serum-based biomarkers using ovarian cancer transcriptomic data. The secretome was constructed by aggregating the data from databases of known secreted proteins, transmembrane or membrane proteins, signal peptides, G-protein coupled receptors, or proteins existing in the extracellular region, and the virtual array was generated by mapping them to Affymetrix probeset identifiers. Whole-genome microarray data from ovarian cancer, normal ovarian surface epithelium, and fallopian tube epithelium were used to identify transcripts upregulated in ovarian cancer. We established the secretome from eight public databases and a virtual array consisting of 16,521 Affymetrix U133 Plus 2.0 probesets. Using ovarian cancer transcriptomic data, we identified candidate blood-based biomarkers for ovarian cancer and performed bioinformatic validation by demonstrating rediscovery of known biomarkers including CA125 and HE4. Two novel top biomarkers (FGF18 and GPR172A) were validated in serum samples from an independent patient cohort. We present the secretome, comprising the most comprehensive resource available for protein products that are potentially found in the blood. The associated virtual array can be used to translate gene-expression data into cancer biomarker discovery. A list of blood-based biomarkers for ovarian cancer detection is reported and includes CA125 and HE4. FGF18 and GPR172A were identified and validated by ELISA as being differentially expressed in the serum of ovarian cancer patients compared with controls. ©2015 American Association for Cancer Research.

ChIP-chip.

PubMed

Kim, Tae Hoon; Dekker, Job

2018-05-01

ChIP-chip can be used to analyze protein-DNA interactions in a region-wide and genome-wide manner. DNA microarrays contain PCR products or oligonucleotide probes that are designed to represent genomic sequences. Identification of genomic sites that interact with a specific protein is based on competitive hybridization of the ChIP-enriched DNA and the input DNA to DNA microarrays. The ChIP-chip protocol can be divided into two main sections: Amplification of ChIP DNA and hybridization of ChIP DNA to arrays. A large amount of DNA is required to hybridize to DNA arrays, and hybridization to a set of multiple commercial arrays that represent the entire human genome requires two rounds of PCR amplifications. The relative hybridization intensity of ChIP DNA and that of the input DNA is used to determine whether the probe sequence is a potential site of protein-DNA interaction. Resolution of actual genomic sites bound by the protein is dependent on the size of the chromatin and on the genomic distance between the probes on the array. As with expression profiling using gene chips, ChIP-chip experiments require multiple replicates for reliable statistical measure of protein-DNA interactions. © 2018 Cold Spring Harbor Laboratory Press.

Photolithographic Synthesis of High-Density DNA and RNA Arrays on Flexible, Transparent, and Easily Subdivided Plastic Substrates.

PubMed

Holden, Matthew T; Carter, Matthew C D; Wu, Cheng-Hsien; Wolfer, Jamison; Codner, Eric; Sussman, Michael R; Lynn, David M; Smith, Lloyd M

2015-11-17

The photolithographic fabrication of high-density DNA and RNA arrays on flexible and transparent plastic substrates is reported. The substrates are thin sheets of poly(ethylene terephthalate) (PET) coated with cross-linked polymer multilayers that present hydroxyl groups suitable for conventional phosphoramidite-based nucleic acid synthesis. We demonstrate that by modifying array synthesis procedures to accommodate the physical and chemical properties of these materials, it is possible to synthesize plastic-backed oligonucleotide arrays with feature sizes as small as 14 μm × 14 μm and feature densities in excess of 125 000/cm(2), similar to specifications attainable using rigid substrates such as glass or glassy carbon. These plastic-backed arrays are tolerant to a wide range of hybridization temperatures, and improved synthetic procedures are described that enable the fabrication of arrays with sequences up to 50 nucleotides in length. These arrays hybridize with S/N ratios comparable to those fabricated on otherwise identical arrays prepared on glass or glassy carbon. This platform supports the enzymatic synthesis of RNA arrays and proof-of-concept experiments are presented showing that the arrays can be readily subdivided into smaller arrays (or "millichips") using common laboratory-scale laser cutting tools. These results expand the utility of oligonucleotide arrays fabricated on plastic substrates and open the door to new applications for these important bioanalytical tools.

An integrated cell-free metabolic platform for protein production and synthetic biology

PubMed Central

Jewett, Michael C; Calhoun, Kara A; Voloshin, Alexei; Wuu, Jessica J; Swartz, James R

2008-01-01

Cell-free systems offer a unique platform for expanding the capabilities of natural biological systems for useful purposes, i.e. synthetic biology. They reduce complexity, remove structural barriers, and do not require the maintenance of cell viability. Cell-free systems, however, have been limited by their inability to co-activate multiple biochemical networks in a single integrated platform. Here, we report the assessment of biochemical reactions in an Escherichia coli cell-free platform designed to activate natural metabolism, the Cytomim system. We reveal that central catabolism, oxidative phosphorylation, and protein synthesis can be co-activated in a single reaction system. Never before have these complex systems been shown to be simultaneously activated without living cells. The Cytomim system therefore promises to provide the metabolic foundation for diverse ab initio cell-free synthetic biology projects. In addition, we describe an improved Cytomim system with enhanced protein synthesis yields (up to 1200 mg/l in 2 h) and lower costs to facilitate production of protein therapeutics and biochemicals that are difficult to make in vivo because of their toxicity, complexity, or unusual cofactor requirements. PMID:18854819

Magneto-nanosensor platform for probing low-affinity protein–protein interactions and identification of a low-affinity PD-L1/PD-L2 interaction

PubMed Central

Lee, Jung-Rok; Bechstein, Daniel J. B.; Ooi, Chin Chun; Patel, Ashka; Gaster, Richard S.; Ng, Elaine; Gonzalez, Lino C.; Wang, Shan X.

2016-01-01

Substantial efforts have been made to understand the interactions between immune checkpoint receptors and their ligands targeted in immunotherapies against cancer. To carefully characterize the complete network of interactions involved and the binding affinities between their extracellular domains, an improved kinetic assay is needed to overcome limitations with surface plasmon resonance (SPR). Here, we present a magneto-nanosensor platform integrated with a microfluidic chip that allows measurement of dissociation constants in the micromolar-range. High-density conjugation of magnetic nanoparticles with prey proteins allows multivalent receptor interactions with sensor-immobilized bait proteins, more closely mimicking natural-receptor clustering on cells. The platform has advantages over traditional SPR in terms of insensitivity of signal responses to pH and salinity, less consumption of proteins and better sensitivities. Using this platform, we characterized the binding affinities of the PD-1—PD-L1/PD-L2 co-inhibitory receptor system, and discovered an unexpected interaction between the two known PD-1 ligands, PD-L1 and PD-L2. PMID:27447090

Dielectrophoresis-Enhanced Plasmonic Sensing with Gold Nanohole Arrays

PubMed Central

2015-01-01

We experimentally demonstrate dielectrophoretic concentration of biological analytes on the surface of a gold nanohole array, which concurrently acts as a nanoplasmonic sensor and gradient force generator. The combination of nanohole-enhanced dielectrophoresis, electroosmosis, and extraordinary optical transmission through the periodic gold nanohole array enables real-time label-free detection of analyte molecules in a 5 μL droplet using concentrations as low as 1 pM within a few minutes, which is more than 1000 times faster than purely diffusion-based binding. The nanohole-based optofluidic platform demonstrated here is straightforward to construct, applicable to both charged and neutral molecules, and performs a novel function that cannot be accomplished using conventional surface plasmon resonance sensors. PMID:24646075

Enabling systematic interrogation of protein-protein interactions in live cells with a versatile ultra-high-throughput biosensor platform | Office of Cancer Genomics

Cancer.gov

The vast datasets generated by next generation gene sequencing and expression profiling have transformed biological and translational research. However, technologies to produce large-scale functional genomics datasets, such as high-throughput detection of protein-protein interactions (PPIs), are still in early development. While a number of powerful technologies have been employed to detect PPIs, a singular PPI biosensor platform featured with both high sensitivity and robustness in a mammalian cell environment remains to be established.

Chemotaxis cluster 1 proteins form cytoplasmic arrays in Vibrio cholerae and are stabilized by a double signaling domain receptor DosM.

PubMed

Briegel, Ariane; Ortega, Davi R; Mann, Petra; Kjær, Andreas; Ringgaard, Simon; Jensen, Grant J

2016-09-13

Nearly all motile bacterial cells use a highly sensitive and adaptable sensory system to detect changes in nutrient concentrations in the environment and guide their movements toward attractants and away from repellents. The best-studied bacterial chemoreceptor arrays are membrane-bound. Many motile bacteria contain one or more additional, sometimes purely cytoplasmic, chemoreceptor systems. Vibrio cholerae contains three chemotaxis clusters (I, II, and III). Here, using electron cryotomography, we explore V. cholerae's cytoplasmic chemoreceptor array and establish that it is formed by proteins from cluster I. We further identify a chemoreceptor with an unusual domain architecture, DosM, which is essential for formation of the cytoplasmic arrays. DosM contains two signaling domains and spans the two-layered cytoplasmic arrays. Finally, we present evidence suggesting that this type of receptor is important for the structural stability of the cytoplasmic array.

NEPTUNE: an under-sea plate scale observatory

NASA Technical Reports Server (NTRS)

Beauchamp, P. M.; Heath, G. R.; Maffei, A.; Chave, A.; Howe, B.; Wilcock, W.; Delaney, J.; Kirkham, H.

2002-01-01

The NEPTUNE project will establish a linked array of undersea observatories on the Juan de Fuca tectonic plate. This observatory will provide a new kind of research platform for real-time, long-term, plate-scale studies in the ocean and Earth sciences.

Low-loss compact multilayer silicon nitride platform for 3D photonic integrated circuits.

PubMed

Shang, Kuanping; Pathak, Shibnath; Guan, Binbin; Liu, Guangyao; Yoo, S J B

2015-08-10

We design, fabricate, and demonstrate a silicon nitride (Si(3)N(4)) multilayer platform optimized for low-loss and compact multilayer photonic integrated circuits. The designed platform, with 200 nm thick waveguide core and 700 nm interlayer gap, is compatible for active thermal tuning and applicable to realizing compact photonic devices such as arrayed waveguide gratings (AWGs). We achieve ultra-low loss vertical couplers with 0.01 dB coupling loss, multilayer crossing loss of 0.167 dB at 90° crossing angle, 50 μm bending radius, 100 × 2 μm(2) footprint, lateral misalignment tolerance up to 400 nm, and less than -52 dB interlayer crosstalk at 1550 nm wavelength. Based on the designed platform, we demonstrate a 27 × 32 × 2 multilayer star coupler.

Tissue matrix arrays for high throughput screening and systems analysis of cell function

PubMed Central

Beachley, Vince Z.; Wolf, Matthew T.; Sadtler, Kaitlyn; Manda, Srikanth S.; Jacobs, Heather; Blatchley, Michael; Bader, Joel S.; Pandey, Akhilesh; Pardoll, Drew; Elisseeff, Jennifer H.

2015-01-01

Cell and protein arrays have demonstrated remarkable utility in the high-throughput evaluation of biological responses; however, they lack the complexity of native tissue and organs. Here, we describe tissue extracellular matrix (ECM) arrays for screening biological outputs and systems analysis. We spotted processed tissue ECM particles as two-dimensional arrays or incorporated them with cells to generate three-dimensional cell-matrix microtissue arrays. We then investigated the response of human stem, cancer, and immune cells to tissue ECM arrays originating from 11 different tissues, and validated the 2D and 3D arrays as representative of the in vivo microenvironment through quantitative analysis of tissue-specific cellular responses, including matrix production, adhesion and proliferation, and morphological changes following culture. The biological outputs correlated with tissue proteomics, and network analysis identified several proteins linked to cell function. Our methodology enables broad screening of ECMs to connect tissue-specific composition with biological activity, providing a new resource for biomaterials research and translation. PMID:26480475

CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics.

PubMed

Gai, Xiaowu; Perin, Juan C; Murphy, Kevin; O'Hara, Ryan; D'arcy, Monica; Wenocur, Adam; Xie, Hongbo M; Rappaport, Eric F; Shaikh, Tamim H; White, Peter S

2010-02-04

Recent studies have shown that copy number variations (CNVs) are frequent in higher eukaryotes and associated with a substantial portion of inherited and acquired risk for various human diseases. The increasing availability of high-resolution genome surveillance platforms provides opportunity for rapidly assessing research and clinical samples for CNV content, as well as for determining the potential pathogenicity of identified variants. However, few informatics tools for accurate and efficient CNV detection and assessment currently exist. We developed a suite of software tools and resources (CNV Workshop) for automated, genome-wide CNV detection from a variety of SNP array platforms. CNV Workshop includes three major components: detection, annotation, and presentation of structural variants from genome array data. CNV detection utilizes a robust and genotype-specific extension of the Circular Binary Segmentation algorithm, and the use of additional detection algorithms is supported. Predicted CNVs are captured in a MySQL database that supports cohort-based projects and incorporates a secure user authentication layer and user/admin roles. To assist with determination of pathogenicity, detected CNVs are also annotated automatically for gene content, known disease loci, and gene-based literature references. Results are easily queried, sorted, filtered, and visualized via a web-based presentation layer that includes a GBrowse-based graphical representation of CNV content and relevant public data, integration with the UCSC Genome Browser, and tabular displays of genomic attributes for each CNV. To our knowledge, CNV Workshop represents the first cohesive and convenient platform for detection, annotation, and assessment of the biological and clinical significance of structural variants. CNV Workshop has been successfully utilized for assessment of genomic variation in healthy individuals and disease cohorts and is an ideal platform for coordinating multiple associated projects. Available on the web at: http://sourceforge.net/projects/cnv.

Modular, Reconfigurable, High-Energy Systems Stepping Stones

NASA Technical Reports Server (NTRS)

Howell, Joe T.; Carrington, Connie K.; Mankins, John C.

2005-01-01

Modular, Reconfigurable, High-Energy Systems are Stepping Stones to provide capabilities for energy-rich infrastructure strategically located in space to support a variety of exploration scenarios. Abundant renewable energy at lunar or L1 locations could support propellant production and storage in refueling scenarios that enable affordable exploration. Renewable energy platforms in geosynchronous Earth orbits can collect and transmit power to satellites, or to Earth-surface locations. Energy-rich space technologies also enable the use of electric-powered propulsion systems that could efficiently deliver cargo and exploration facilities to remote locations. A first step to an energy-rich space infrastructure is a 100-kWe class solar-powered platform in Earth orbit. The platform would utilize advanced technologies in solar power collection and generation, power management and distribution, thermal management, and electric propulsion. It would also provide a power-rich free-flying platform to demonstrate in space a portfolio of technology flight experiments. This paper presents a preliminary design concept for a 100-kWe solar-powered satellite with the capability to flight-demonstrate a variety of payload experiments and to utilize electric propulsion. State-of-the-art solar concentrators, highly efficient multi-junction solar cells, integrated thermal management on the arrays, and innovative deployable structure design and packaging make the 100-kW satellite feasible for launch on one existing launch vehicle. Higher voltage arrays and power management and distribution (PMAD) systems reduce or eliminate the need for massive power converters, and could enable direct- drive of high-voltage solar electric thrusters.

Dynamic gene expression response to altered gravity in human T cells.

PubMed

Thiel, Cora S; Hauschild, Swantje; Huge, Andreas; Tauber, Svantje; Lauber, Beatrice A; Polzer, Jennifer; Paulsen, Katrin; Lier, Hartwin; Engelmann, Frank; Schmitz, Burkhard; Schütte, Andreas; Layer, Liliana E; Ullrich, Oliver

2017-07-12

We investigated the dynamics of immediate and initial gene expression response to different gravitational environments in human Jurkat T lymphocytic cells and compared expression profiles to identify potential gravity-regulated genes and adaptation processes. We used the Affymetrix GeneChip® Human Transcriptome Array 2.0 containing 44,699 protein coding genes and 22,829 non-protein coding genes and performed the experiments during a parabolic flight and a suborbital ballistic rocket mission to cross-validate gravity-regulated gene expression through independent research platforms and different sets of control experiments to exclude other factors than alteration of gravity. We found that gene expression in human T cells rapidly responded to altered gravity in the time frame of 20 s and 5 min. The initial response to microgravity involved mostly regulatory RNAs. We identified three gravity-regulated genes which could be cross-validated in both completely independent experiment missions: ATP6V1A/D, a vacuolar H + -ATPase (V-ATPase) responsible for acidification during bone resorption, IGHD3-3/IGHD3-10, diversity genes of the immunoglobulin heavy-chain locus participating in V(D)J recombination, and LINC00837, a long intergenic non-protein coding RNA. Due to the extensive and rapid alteration of gene expression associated with regulatory RNAs, we conclude that human cells are equipped with a robust and efficient adaptation potential when challenged with altered gravitational environments.

Molecular Profiles for Lung Cancer Pathogenesis and Detection in US Veterans

DTIC Science & Technology

2012-10-01

will be further strengthened via Multiple Reaction Monitoring ( MRM ) performed on the remaining samples by the Vanderbilt group. MRM using mass...proteomics detects all protein changes in the sample in an unfocused fashion, MRM is targeted and highly selective, allowing us to specifically look for...proteins of interest. To this end, we have generated a list of candidate proteins for MRM utilizing shotgun proteomic, mRNA array, and miRNA array

Camera array based light field microscopy

PubMed Central

Lin, Xing; Wu, Jiamin; Zheng, Guoan; Dai, Qionghai

2015-01-01

This paper proposes a novel approach for high-resolution light field microscopy imaging by using a camera array. In this approach, we apply a two-stage relay system for expanding the aperture plane of the microscope into the size of an imaging lens array, and utilize a sensor array for acquiring different sub-apertures images formed by corresponding imaging lenses. By combining the rectified and synchronized images from 5 × 5 viewpoints with our prototype system, we successfully recovered color light field videos for various fast-moving microscopic specimens with a spatial resolution of 0.79 megapixels at 30 frames per second, corresponding to an unprecedented data throughput of 562.5 MB/s for light field microscopy. We also demonstrated the use of the reported platform for different applications, including post-capture refocusing, phase reconstruction, 3D imaging, and optical metrology. PMID:26417490

Rapid Characterization of Bacterial Electrogenicity Using a Single-Sheet Paper-Based Electrofluidic Array

PubMed Central

Gao, Yang; Hassett, Daniel J.; Choi, Seokheun

2017-01-01

Electrogenicity, or bacterial electron transfer capacity, is an important application which offers environmentally sustainable advances in the fields of biofuels, wastewater treatment, bioremediation, desalination, and biosensing. Significant boosts in this technology can be achieved with the growth of synthetic biology that manipulates microbial electron transfer pathways, thereby potentially significantly improving their electrogenic potential. There is currently a need for a high-throughput, rapid, and highly sensitive test array to evaluate the electrogenic properties of newly discovered and/or genetically engineered bacterial species. In this work, we report a single-sheet, paper-based electrofluidic (incorporating both electronic and fluidic structure) screening platform for rapid, sensitive, and potentially high-throughput characterization of bacterial electrogenicity. This novel screening array uses (i) a commercially available wax printer for hydrophobic wax patterning on a single sheet of paper and (ii) water-dispersed electrically conducting polymer mixture, poly(3,4-ethylenedioxythiophene):polystyrene sulfonate, for full integration of electronic and fluidic components into the paper substrate. The engineered 3-D, microporous, hydrophilic, and conductive paper structure provides a large surface area for efficient electron transfer. This results in rapid and sensitive power assessment of electrogenic bacteria from a microliter sample volume. We validated the effectiveness of the sensor array using hypothesis-driven genetically modified Pseudomonas aeruginosa mutant strains. Within 20 min, we observed that the sensor platform successfully measured the electricity-generating capacities of five isogenic mutants of P. aeruginosa while distinguishing their differences from genetically unmodified bacteria. PMID:28798914

ArraySolver: an algorithm for colour-coded graphical display and Wilcoxon signed-rank statistics for comparing microarray gene expression data.

PubMed

Khan, Haseeb Ahmad

2004-01-01

The massive surge in the production of microarray data poses a great challenge for proper analysis and interpretation. In recent years numerous computational tools have been developed to extract meaningful interpretation of microarray gene expression data. However, a convenient tool for two-groups comparison of microarray data is still lacking and users have to rely on commercial statistical packages that might be costly and require special skills, in addition to extra time and effort for transferring data from one platform to other. Various statistical methods, including the t-test, analysis of variance, Pearson test and Mann-Whitney U test, have been reported for comparing microarray data, whereas the utilization of the Wilcoxon signed-rank test, which is an appropriate test for two-groups comparison of gene expression data, has largely been neglected in microarray studies. The aim of this investigation was to build an integrated tool, ArraySolver, for colour-coded graphical display and comparison of gene expression data using the Wilcoxon signed-rank test. The results of software validation showed similar outputs with ArraySolver and SPSS for large datasets. Whereas the former program appeared to be more accurate for 25 or fewer pairs (n < or = 25), suggesting its potential application in analysing molecular signatures that usually contain small numbers of genes. The main advantages of ArraySolver are easy data selection, convenient report format, accurate statistics and the familiar Excel platform.

ArraySolver: An Algorithm for Colour-Coded Graphical Display and Wilcoxon Signed-Rank Statistics for Comparing Microarray Gene Expression Data

PubMed Central

2004-01-01

The massive surge in the production of microarray data poses a great challenge for proper analysis and interpretation. In recent years numerous computational tools have been developed to extract meaningful interpretation of microarray gene expression data. However, a convenient tool for two-groups comparison of microarray data is still lacking and users have to rely on commercial statistical packages that might be costly and require special skills, in addition to extra time and effort for transferring data from one platform to other. Various statistical methods, including the t-test, analysis of variance, Pearson test and Mann–Whitney U test, have been reported for comparing microarray data, whereas the utilization of the Wilcoxon signed-rank test, which is an appropriate test for two-groups comparison of gene expression data, has largely been neglected in microarray studies. The aim of this investigation was to build an integrated tool, ArraySolver, for colour-coded graphical display and comparison of gene expression data using the Wilcoxon signed-rank test. The results of software validation showed similar outputs with ArraySolver and SPSS for large datasets. Whereas the former program appeared to be more accurate for 25 or fewer pairs (n ≤ 25), suggesting its potential application in analysing molecular signatures that usually contain small numbers of genes. The main advantages of ArraySolver are easy data selection, convenient report format, accurate statistics and the familiar Excel platform. PMID:18629036

Nanoscale Surface Plasmonics Sensor With Nanofluidic Control

NASA Technical Reports Server (NTRS)

Wei, Jianjun; Singhal, Sameer; Waldeck, David H.; Kofke, Matthew

2013-01-01

Conventional quantitative protein assays of bodily fluids typically involve multiple steps to obtain desired measurements. Such methods are not well suited for fast and accurate assay measurements in austere environments such as spaceflight and in the aftermath of disasters. Consequently, there is a need for a protein assay technology capable of routinely monitoring proteins in austere environments. For example, there is an immediate need for a urine protein assay to assess astronaut renal health during spaceflight. The disclosed nanoscale surface plasmonics sensor provides a core detection method that can be integrated to a lab-on-chip device that satisfies the unmet need for such a protein assay technology. Assays based upon combinations of nanoholes, nanorings, and nanoslits with transmission surface plasmon resonance (SPR) are used for assays requiring extreme sensitivity, and are capable of detecting specific analytes at concentrations as low as picomole to femtomole level in well-controlled environments. The device operates in a transmission mode configuration in which light is directed at one planar surface of the array, which functions as an optical aperture. The incident light induces surface plasmon light transmission from the opposite surface of the array. The presence of a target analyte is detected by changes in the spectrum of light transmitted by the array when a target analyte induces a change in the refractive index of the fluid within the nanochannels. This occurs, for example, when a target analyte binds to a receptor fixed to the walls of the nanochannels in the array. Independent fluid handling capability for individual nanoarrays on a nanofluidic chip containing a plurality of nanochannel arrays allows each array to be used to sense a different target analyte and/or for paired arrays to analyze control and test samples simultaneously in parallel. The present invention incorporates transmission mode nanoplasmonics and nanofluidics into a single, microfluidically controlled device. The device comprises one or more arrays of aligned nanochannels that are in fluid communication with inflowing and outflowing fluid handling manifolds that control the flow of fluid through the arrays. The array acts as an aperture in a plasmonic sensor. Fluid, in the form of a liquid or a gas and comprising a sample for analysis, is moved from an inlet manifold through the nanochannel array, and out through an exit manifold. The fluid may also contain a reagent used to modify the interior surfaces of the nanochannels, and/or a reagent required for the detection of an analyte.

Mount control system of the ASTRI SST-2M prototype for the Cherenkov Telescope Array

NASA Astrophysics Data System (ADS)

Antolini, Elisa; Tosti, Gino; Tanci, Claudio; Bagaglia, Marco; Canestrari, Rodolfo; Cascone, Enrico; Gambini, Giorgio; Nucciarelli, Giuliano; Pareschi, Giovanni; Scuderi, Salvo; Stringhetti, Luca; Busatta, Andrea; Giacomel, Stefano; Marchiori, Gianpietro; Manfrin, Cristiana; Marcuzzi, Enrico; Di Michele, Daniele; Grigolon, Carlo; Guarise, Paolo

2016-08-01

The ASTRI SST-2M telescope is an end-to-end prototype proposed for the Small Size class of Telescopes (SST) of the future Cherenkov Telescope Array (CTA). The prototype is installed in Italy at the INAF observing station located at Serra La Nave on Mount Etna (Sicily) and it was inaugurated in September 2014. This paper presents the software and hardware architecture and development of the system dedicated to the control of the mount, health, safety and monitoring systems of the ASTRI SST-2M telescope prototype. The mount control system installed on the ASTRI SST-2M telescope prototype makes use of standard and widely deployed industrial hardware and software. State of the art of the control and automation industries was selected in order to fulfill the mount related functional and safety requirements with assembly compactness, high reliability, and reduced maintenance. The software package was implemented with the Beckhoff TwinCAT version 3 environment for the software Programmable Logical Controller (PLC), while the control electronics have been chosen in order to maximize the homogeneity and the real time performance of the system. The integration with the high level controller (Telescope Control System) has been carried out by choosing the open platform communications Unified Architecture (UA) protocol, supporting rich data model while offering compatibility with the PLC platform. In this contribution we show how the ASTRI approach for the design and implementation of the mount control system has made the ASTRI SST-2M prototype a standalone intelligent machine, able to fulfill requirements and easy to be integrated in an array configuration such as the future ASTRI mini-array proposed to be installed at the southern site of the Cherenkov Telescope Array (CTA).

Tumor Touch Imprints as Source for Whole Genome Analysis of Neuroblastoma Tumors

PubMed Central

Brunner, Clemens; Brunner-Herglotz, Bettina; Ziegler, Andrea; Frech, Christian; Amann, Gabriele; Ladenstein, Ruth; Ambros, Inge M.; Ambros, Peter F.

2016-01-01

Introduction Tumor touch imprints (TTIs) are routinely used for the molecular diagnosis of neuroblastomas by interphase fluorescence in-situ hybridization (I-FISH). However, in order to facilitate a comprehensive, up-to-date molecular diagnosis of neuroblastomas and to identify new markers to refine risk and therapy stratification methods, whole genome approaches are needed. We examined the applicability of an ultra-high density SNP array platform that identifies copy number changes of varying sizes down to a few exons for the detection of genomic changes in tumor DNA extracted from TTIs. Material and Methods DNAs were extracted from TTIs of 46 neuroblastoma and 4 other pediatric tumors. The DNAs were analyzed on the Cytoscan HD SNP array platform to evaluate numerical and structural genomic aberrations. The quality of the data obtained from TTIs was compared to that from randomly chosen fresh or fresh frozen solid tumors (n = 212) and I-FISH validation was performed. Results SNP array profiles were obtained from 48 (out of 50) TTI DNAs of which 47 showed genomic aberrations. The high marker density allowed for single gene analysis, e.g. loss of nine exons in the ATRX gene and the visualization of chromothripsis. Data quality was comparable to fresh or fresh frozen tumor SNP profiles. SNP array results were confirmed by I-FISH. Conclusion TTIs are an excellent source for SNP array processing with the advantage of simple handling, distribution and storage of tumor tissue on glass slides. The minimal amount of tumor tissue needed to analyze whole genomes makes TTIs an economic surrogate source in the molecular diagnostic work up of tumor samples. PMID:27560999

Dual-mode acoustic wave biosensors microarrays

NASA Astrophysics Data System (ADS)

Auner, Gregory W.; Shreve, Gina; Ying, Hao; Newaz, Golam; Hughes, Chantelle; Xu, Jianzeng

2003-04-01

We have develop highly sensitive and selective acoustic wave biosensor arrays with signal analysis systems to provide a fingerprint for the real-time identification and quantification of a wide array of bacterial pathogens and environmental health hazards. We have developed an unique highly sensitive dual mode acoustic wave platform prototype that, when combined with phage based selective detection elements, form a durable bacteria sensor. Arrays of these new real-time biosensors are integrated to form a biosensor array on a chip. This research and development program optimizes advanced piezoelectric aluminum nitride wide bandgap semiconductors, novel micromachining processes, advanced device structures, selective phage displays development and immobilization techniques, and system integration and signal analysis technology to develop the biosensor arrays. The dual sensor platform can be programmed to sense in a gas, vapor or liquid environment by switching between acoustic wave resonate modes. Such a dual mode sensor has tremendous implications for applications involving monitoring of pathogenic microorganisms in the clinical setting due to their ability to detect airborne pathogens. This provides a number of applications including hospital settings such as intensive care or other in-patient wards for the reduction of nosocomial infections and maintenance of sterile environments in surgical suites. Monitoring for airborn pathogen transmission in public transportation areas such as airplanes may be useful for implementation of strategies for redution of airborn transmission routes. The ability to use the same sensor in the liquid sensing mode is important for tracing the source of airborn pathogens to local liquid sources. Sensing of pathogens in saliva will be useful for sensing oral pathogens and support of decision-making strategies regarding prevention of transmission and support of treatment strategies.

MixHMM: Inferring Copy Number Variation and Allelic Imbalance Using SNP Arrays and Tumor Samples Mixed with Stromal Cells

PubMed Central

Schulz, Vincent; Chen, Min; Tuck, David

2010-01-01

Background Genotyping platforms such as single nucleotide polymorphism (SNP) arrays are powerful tools to study genomic aberrations in cancer samples. Allele specific information from SNP arrays provides valuable information for interpreting copy number variation (CNV) and allelic imbalance including loss-of-heterozygosity (LOH) beyond that obtained from the total DNA signal available from array comparative genomic hybridization (aCGH) platforms. Several algorithms based on hidden Markov models (HMMs) have been designed to detect copy number changes and copy-neutral LOH making use of the allele information on SNP arrays. However heterogeneity in clinical samples, due to stromal contamination and somatic alterations, complicates analysis and interpretation of these data. Methods We have developed MixHMM, a novel hidden Markov model using hidden states based on chromosomal structural aberrations. MixHMM allows CNV detection for copy numbers up to 7 and allows more complete and accurate description of other forms of allelic imbalance, such as increased copy number LOH or imbalanced amplifications. MixHMM also incorporates a novel sample mixing model that allows detection of tumor CNV events in heterogeneous tumor samples, where cancer cells are mixed with a proportion of stromal cells. Conclusions We validate MixHMM and demonstrate its advantages with simulated samples, clinical tumor samples and a dilution series of mixed samples. We have shown that the CNVs of cancer cells in a tumor sample contaminated with up to 80% of stromal cells can be detected accurately using Illumina BeadChip and MixHMM. Availability The MixHMM is available as a Python package provided with some other useful tools at http://genecube.med.yale.edu:8080/MixHMM. PMID:20532221

ATP-dependent chromatin assembly is functionally distinct from chromatin remodeling

PubMed Central

Torigoe, Sharon E; Patel, Ashok; Khuong, Mai T; Bowman, Gregory D; Kadonaga, James T

2013-01-01

Chromatin assembly involves the combined action of ATP-dependent motor proteins and histone chaperones. Because motor proteins in chromatin assembly also function as chromatin remodeling factors, we investigated the relationship between ATP-driven chromatin assembly and chromatin remodeling in the generation of periodic nucleosome arrays. We found that chromatin remodeling-defective Chd1 motor proteins are able to catalyze ATP-dependent chromatin assembly. The resulting nucleosomes are not, however, spaced in periodic arrays. Wild-type Chd1, but not chromatin remodeling-defective Chd1, can catalyze the conversion of randomly-distributed nucleosomes into periodic arrays. These results reveal a functional distinction between ATP-dependent nucleosome assembly and chromatin remodeling, and suggest a model for chromatin assembly in which randomly-distributed nucleosomes are formed by the nucleosome assembly function of Chd1, and then regularly-spaced nucleosome arrays are generated by the chromatin remodeling activity of Chd1. These findings uncover an unforeseen level of specificity in the role of motor proteins in chromatin assembly. DOI: http://dx.doi.org/10.7554/eLife.00863.001 PMID:23986862

Status report of the end-to-end ASKAP software system: towards early science operations

NASA Astrophysics Data System (ADS)

Guzman, Juan Carlos; Chapman, Jessica; Marquarding, Malte; Whiting, Matthew

2016-08-01

The Australian SKA Pathfinder (ASKAP) is a novel centimetre radio synthesis telescope currently in the commissioning phase and located in the midwest region of Western Australia. It comprises of 36 x 12 m diameter reflector antennas each equipped with state-of-the-art and award winning Phased Array Feeds (PAF) technology. The PAFs provide a wide, 30 square degree field-of-view by forming up to 36 separate dual-polarisation beams at once. This results in a high data rate: 70 TB of correlated visibilities in an 8-hour observation, requiring custom-written, high-performance software running in dedicated High Performance Computing (HPC) facilities. The first six antennas equipped with first-generation PAF technology (Mark I), named the Boolardy Engineering Test Array (BETA) have been in use since 2014 as a platform to test PAF calibration and imaging techniques, and along the way it has been producing some great science results. Commissioning of the ASKAP Array Release 1, that is the first six antennas with second-generation PAFs (Mark II) is currently under way. An integral part of the instrument is the Central Processor platform hosted at the Pawsey Supercomputing Centre in Perth, which executes custom-written software pipelines, designed specifically to meet the ASKAP imaging requirements of wide field of view and high dynamic range. There are three key hardware components of the Central Processor: The ingest nodes (16 x node cluster), the fast temporary storage (1 PB Lustre file system) and the processing supercomputer (200 TFlop system). This High-Performance Computing (HPC) platform is managed and supported by the Pawsey support team. Due to the limited amount of data generated by BETA and the first ASKAP Array Release, the Central Processor platform has been running in a more "traditional" or user-interactive mode. But this is about to change: integration and verification of the online ingest pipeline starts in early 2016, which is required to support the full 300 MHz bandwidth for Array Release 1; followed by the deployment of the real-time data processing components. In addition to the Central Processor, the first production release of the CSIRO ASKAP Science Data Archive (CASDA) has also been deployed in one of the Pawsey Supercomputing Centre facilities and it is integrated to the end-to-end ASKAP data flow system. This paper describes the current status of the "end-to-end" data flow software system from preparing observations to data acquisition, processing and archiving; and the challenges of integrating an HPC facility as a key part of the instrument. It also shares some lessons learned since the start of integration activities and the challenges ahead in preparation for the start of the Early Science program.