A Multiplex Microsphere-Based Immunoassay Increases the Sensitivity of SIV-Specific Antibody Detection in Serum Samples and Mucosal Specimens Collected from Rhesus Macaques Infected with SIVmac239.

PubMed

Powell, Rebecca L R; Ouellette, Ian; Lindsay, Ross W; Parks, Christopher L; King, C Richter; McDermott, Adrian B; Morrow, Gavin

2013-06-01

Results from recent HIV-1 vaccine studies have indicated that high serum antibody (Ab) titers may not be necessary for Ab-mediated protection, and that Abs localized to mucosal sites might be critical for preventing infection. Enzyme-linked immunosorbent assay (ELISA) has been used for decades as the gold standard for Ab measurement, though recently, highly sensitive microsphere-based assays have become available, with potential utility for improved detection of Abs. In this study, we assessed the Bio-Plex(®) Suspension Array System for the detection of simian immunodeficiency virus (SIV)-specific Abs in rhesus macaques (RMs) chronically infected with SIV, whose serum or mucosal SIV-specific Ab titers were negative by ELISA. We developed a SIVmac239-specific 4-plex bead array for the simultaneous detection of Abs binding to Env, Gag, Pol, and Nef. The 4-plex assay was used to quantify SIV-specific serum IgG and rectal swab IgA titers from control (SIV-naive) and SIVmac239-infected RMs. The Bio-Plex assay specifically detected anti-SIV Abs in specimens from SIV-infected animals for all four analytes when compared to SIV-naive control samples (p≤0.04). Furthermore, in 70% of Env and 79% of Gag ELISA-negative serum samples, specific Ab was detected using the Bio-Plex assay. Similarly, 71% of Env and 48% of Gag ELISA-negative rectal swab samples were identified as positive using the Bio-Plex assay. Importantly, assay specificity (i.e., probability of true positives) was comparable to ELISA (94%-100%). The results reported here indicate that microsphere-based methods provide a substantial improvement over ELISA for the detection of Ab responses, aid in detecting specific Abs when analyzing samples containing low levels of Abs, such as during the early stages of a vaccine trial, and may be valuable in attempts to link protective efficacy of vaccines with induced Ab responses.

Human Engineering Operations and Habitability Assessment: A Process for Advanced Life Support Ground Facility Testbeds

NASA Technical Reports Server (NTRS)

Connolly, Janis H.; Arch, M.; Elfezouaty, Eileen Schultz; Novak, Jennifer Blume; Bond, Robert L. (Technical Monitor)

1999-01-01

Design and Human Engineering (HE) processes strive to ensure that the human-machine interface is designed for optimal performance throughout the system life cycle. Each component can be tested and assessed independently to assure optimal performance, but it is not until full integration that the system and the inherent interactions between the system components can be assessed as a whole. HE processes (which are defining/app lying requirements for human interaction with missions/systems) are included in space flight activities, but also need to be included in ground activities and specifically, ground facility testbeds such as Bio-Plex. A unique aspect of the Bio-Plex Facility is the integral issue of Habitability which includes qualities of the environment that allow humans to work and live. HE is a process by which Habitability and system performance can be assessed.

Quantification and Characterization of Volatiles Evolved During Extrusion of Rice and Soy Flours

NASA Technical Reports Server (NTRS)

Zasypkin, D.; Lertsiriyothin, W.; Lee, T. C.; Bourland, C. T.; Bond, Robert L. (Technical Monitor)

1999-01-01

NASA Johnson Space Center is designing and building a habitat (Bioregenerative Planetary Life Support Systems Test Complex, BIO-Plex) intended for evaluating advanced life support systems developed for long duration missions to the Moon or Mars where all consumables will be recycled and reused. A food system based on raw products obtained from higher plants (such as soybeans, rice and wheat) may be a central feature of a biological ly-based Advanced Life Support System (ALSS). In order to convert raw crops to edible ingredients or food items, multipurpose processing equipment such as an extruder is ideal. Volatile compounds evolved during the manufacturing of these food products may accumulate reaching toxic levels. Additionally, off-odors often dissipated in open-air environments without consequence, may cause significant discomfort in the BIO-Plex. Rice and defatted soy flours were adjusted to 16% moisture and triplicate samples were extruded using a table top single-screw extruder. The extrudate was collected in specially designed Tedlar bags from which air samples could be extracted. The samples were analyzed by GC-MS with special emphasis on compounds with Spacecraft Maximum Allowable Concentrations (SMAC). Results showed a combination of alcohols, aldehydes, ketones and carbonyl compounds in the different flours. Each compound and its SMAC value as well as its impact on the air revitalization system was discussed.

Comparison of two automated instruments for Epstein-Barr virus serology in a large adult hospital and implementation of an Epstein-Barr virus nuclear antigen-based testing algorithm.

PubMed

Al Sidairi, Hilal; Binkhamis, Khalifa; Jackson, Colleen; Roberts, Catherine; Heinstein, Charles; MacDonald, Jimmy; Needle, Robert; Hatchette, Todd F; LeBlanc, Jason J

2017-11-01

Serology remains the mainstay for diagnosis of Epstein-Barr virus (EBV) infection. This study compared two automated platforms (BioPlex 2200 and Architect i2000SR) to test three EBV serological markers: viral capsid antigen (VCA) immunoglobulins of class M (IgM), VCA immunoglobulins of class G (IgG) and EBV nuclear antigen-1 (EBNA-1) IgG. Using sera from 65 patients at various stages of EBV disease, BioPlex demonstrated near-perfect agreement for all EBV markers compared to a consensus reference. The agreement for Architect was near-perfect for VCA IgG and EBNA-1 IgG, and substantial for VCA IgM despite five equivocal results. Since the majority of testing in our hospital was from adults with EBNA-1 IgG positive results, post-implementation analysis of an EBNA-based algorithm showed advantages over parallel testing of the three serologic markers. This small verification demonstrated that both automated systems for EBV serology had good performance for all EBV markers, and an EBNA-based testing algorithm is ideal for an adult hospital.

Modeling of Solid Waste Processing Options in BIO-Plex

NASA Technical Reports Server (NTRS)

Rodriguez, Luis F.; Finn, Cory; Kang, Sukwon; Hogan, John; Luna, Bernadette (Technical Monitor)

2000-01-01

BIO-Plex is a ground-based test bed currently under development by NASA for testing technologies and practices that may be utilized in future long-term life support missions. All aspects of such an Advanced Life Support (ALS) System must be considered to confidently construct a reliable system, which will not only allow the crew to survive in harsh environments, but allow the crew time to perform meaningful research. Effective handling of solid wastes is a critical aspect of the system, especially when recovery of resources contained in the waste is required. This is particularly important for ALS Systems configurations that include a Biomass Production Chamber. In these cases, significant amounts of inedible biomass waste may be produced, which can ultimately serve as a repository of necessary resources for sustaining life, notably carbon, water, and plant nutrients. Numerous biological and physicochemical solid waste processing options have been considered. Biological options include composting, aerobic digestion, and anaerobic digestion. Physicochemical options include pyrolysis, SCWO (supercritical water oxidation), various incineration configurations, microwave incineration, magnetically assisted gasification, and low temperature plasma reaction. Modeling of these options is a necessary step to assist in the design process. A previously developed top-level model of BIO-Plex implemented in MATLAB Simulink (r) for the use of systems analysis and design has been adopted for this analysis. Presently, this model only considered incineration for solid waste processing. Present work, reported here, includes the expansion of this model to include a wider array of solid waste processing options selected from the above options, bearing in mind potential, near term solid waste treatment systems. Furthermore, a trade study has also been performed among these solid waste processing technologies in an effort to determine the ideal technology for long-term life support missions.

Rapid Identification of Shiga Toxin-Producing Escherichia coli O Serogroups from Fresh Produce and Raw Milk Enrichment Cultures by Luminex Bead-Based Suspension Array.

PubMed

Kase, Julie A; Maounounen-Laasri, Anna; Lin, Andrew

2016-09-01

The U.S. Food and Drug Administration's Bacteriological Analytical Manual (BAM) Chapter 4a describes a Luminex microbead-based suspension array used to screen colonies for 11 clinically relevant Shiga toxin-producing Escherichia coli (STEC) serogroups: O26, O45, O91, O103, O104, O111, O113, O121, O128, O145, and O157. We evaluated the usefulness of this method to identify STEC-positive enrichment samples before agar plating. Twelve E. coli strains were added to three types of fresh produce (bagged baby spinach, alfalfa sprouts, and cilantro) at levels near the detection limit of the test. A subset of these strains (six O serogroups) was similarly evaluated in raw milk. For comparison, portions of each of the 168 enrichment cultures were analyzed for serogroup by a real-time PCR assay and a Bio-Plex 200 assay with the bead-based suspensions. No false-positive results were obtained. Of the 112 samples with a reported cycle threshold (C T ) value, 101 undiluted, diluted, or extracted enrichment cultures also produced ratios above 5.0 in the Bio-Plex assay. When PCR C T values approached or were greater than 35, Bio-Plex detection became less reliable. Using undiluted or extracted enrichment cultures resulted in a significantly larger number of positive results. With the same enrichment material prepared for real-time PCR analysis as described in the BAM Chapter 4a, the STEC microbead-based suspension array can accurately screen food enrichment cultures.

Analysis of edible oil processing options for the BIO-Plex advanced life support system

NASA Technical Reports Server (NTRS)

Greenwalt, C. J.; Hunter, J.

2000-01-01

Edible oil is a critical component of the proposed plant-based Advanced Life Support (ALS) diet. Soybean, peanut, and single-cell oil are the oil source options to date. In terrestrial manufacture, oil is ordinarily extracted with hexane, an organic solvent. However, exposed solvents are not permitted in the spacecraft environment or in enclosed human tests by National Aeronautics and Space Administration due to their potential danger and handling difficulty. As a result, alternative oil-processing methods will need to be utilized. Preparation and recovery options include traditional dehulling, crushing, conditioning, and flaking, extrusion, pressing, water extraction, and supercritical extraction. These processing options were evaluated on criteria appropriate to the Advanced Life Support System and BIO-Plex application including: product quality, product stability, waste production, risk, energy needs, labor requirements, utilization of nonrenewable resources, usefulness of by-products, and versatility and mass of equipment to determine the most appropriate ALS edible oil-processing operation.

Effects of organic selenium and zinc on the aging process of laying hens

USDA-ARS?s Scientific Manuscript database

The objective of the study was to determine whether supplementing the diets of post-molted hens with organic selenium (Se) (Sel-Plex®) and/or organic Zinc (Zn) (Bio-Plex®) could improve laying hen performance. Prior to molting, 120-78 wk old laying hens were separated into four treatment groups of ...

FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining.

PubMed

Bachman, John A; Gyori, Benjamin M; Sorger, Peter K

2018-06-28

For automated reading of scientific publications to extract useful information about molecular mechanisms it is critical that genes, proteins and other entities be correctly associated with uniform identifiers, a process known as named entity linking or "grounding." Correct grounding is essential for resolving relationships among mined information, curated interaction databases, and biological datasets. The accuracy of this process is largely dependent on the availability of machine-readable resources associating synonyms and abbreviations commonly found in biomedical literature with uniform identifiers. In a task involving automated reading of ∼215,000 articles using the REACH event extraction software we found that grounding was disproportionately inaccurate for multi-protein families (e.g., "AKT") and complexes with multiple subunits (e.g."NF- κB"). To address this problem we constructed FamPlex, a manually curated resource defining protein families and complexes as they are commonly encountered in biomedical text. In FamPlex the gene-level constituents of families and complexes are defined in a flexible format allowing for multi-level, hierarchical membership. To create FamPlex, text strings corresponding to entities were identified empirically from literature and linked manually to uniform identifiers; these identifiers were also mapped to equivalent entries in multiple related databases. FamPlex also includes curated prefix and suffix patterns that improve named entity recognition and event extraction. Evaluation of REACH extractions on a test corpus of ∼54,000 articles showed that FamPlex significantly increased grounding accuracy for families and complexes (from 15 to 71%). The hierarchical organization of entities in FamPlex also made it possible to integrate otherwise unconnected mechanistic information across families, subfamilies, and individual proteins. Applications of FamPlex to the TRIPS/DRUM reading system and the Biocreative VI Bioentity Normalization Task dataset demonstrated the utility of FamPlex in other settings. FamPlex is an effective resource for improving named entity recognition, grounding, and relationship resolution in automated reading of biomedical text. The content in FamPlex is available in both tabular and Open Biomedical Ontology formats at https://github.com/sorgerlab/famplex under the Creative Commons CC0 license and has been integrated into the TRIPS/DRUM and REACH reading systems.

Development, Characterisation and Application of Monoclonal Antibodies for the Detection and Quantification of Infectious Salmon Anaemia Virus in Plasma Samples Using Luminex Bead Array Technology.

PubMed

Hoare, R; Thompson, K D; Herath, T; Collet, B; Bron, J E; Adams, A

2016-01-01

Infectious salmon anaemia virus (ISAV) is an orthomyxovirus that has had a significant economic impact on Atlantic salmon farming in Europe, North America and Chile. Monoclonal antibodies (mAbs) were developed against Segment 3 (encoding the viral nucleoprotein, NP) of the virus. Six of the mAbs were shown to be specific to ISAV and recognised all isolates from Scotland, Norway and Canada. They reacted with ISAV in enzyme-linked immunosorbent assay (ELISA), indirect fluorescent antibody technique (IFAT) and western blotting. They were also used to develop a novel detection method based on Luminex (Bio-Plex) bead-based flow cytometric technology for the detection of ISAV in the plasma of Atlantic salmon (Salmo salar L.) smolts experimentally infected with ISAV. Fish were challenged by intraperitoneal (i.p.) injection of virus at 50% Tissue Culture Infective Dose (TCID50) = 2.8 x106 per animal. Virus present in plasma of infected fish, collected at 0, 4, 8, 12, 16, 21 and 28 days post infection using a non-lethal sampling method (n = 12 at each time point), was quantified using the optimised Bio-Plex assay. The results obtained with this assay were compared with absolute quantification of the virus by RT-qPCR using SYBR Green I and TaqMan chemistries. The Bio-Plex assay developed using the NP mAbs appears to be a rapid, sensitive method for detecting and quantifying ISAV in small volumes of fish plasma and has the potential to be multiplexed for the detection of other fish pathogens (e.g. during co-infections). To our knowledge this is the first report of the use of Luminex (Bio-Plex) technology for the detection of a fish pathogen.

Developmental validation of the IrisPlex system: determination of blue and brown iris colour for forensic intelligence.

PubMed

Walsh, Susan; Lindenbergh, Alexander; Zuniga, Sofia B; Sijen, Titia; de Knijff, Peter; Kayser, Manfred; Ballantyne, Kaye N

2011-11-01

The IrisPlex system consists of a highly sensitive multiplex genotyping assay together with a statistical prediction model, providing users with the ability to predict blue and brown human eye colour from DNA samples with over 90% precision. This 'DNA intelligence' system is expected to aid police investigations by providing phenotypic information on unknown individuals when conventional DNA profiling is not informative. Falling within the new area of forensic DNA phenotyping, this paper describes the developmental validation of the IrisPlex assay following the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines for the application of DNA-based eye colour prediction to forensic casework. The IrisPlex assay produces complete SNP genotypes with only 31pg of DNA, approximately six human diploid cell equivalents, and is therefore more sensitive than commercial STR kits currently used in forensics. Species testing revealed human and primate specificity for a complete SNP profile. The assay is capable of producing accurate results from simulated casework samples such as blood, semen, saliva, hair, and trace DNA samples, including extremely low quantity samples. Due to its design, it can also produce full profiles with highly degraded samples often found in forensic casework. Concordance testing between three independent laboratories displayed reproducible results of consistent levels on varying types of simulated casework samples. With such high levels of sensitivity, specificity, consistency and reliability, this genotyping assay, as a core part of the IrisPlex system, operates in accordance with SWGDAM guidelines. Furthermore, as we demonstrated previously, the IrisPlex eye colour prediction system provides reliable results without the need for knowledge on the bio-geographic ancestry of the sample donor. Hence, the IrisPlex system, with its model-based prediction probability estimation of blue and brown human eye colour, represents a useful tool for immediate application in accredited forensic laboratories, to be used for forensic intelligence in tracing unknown individuals from crime scene samples. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Protein Multiplexed Immunoassay Analysis with R.

PubMed

Breen, Edmond J

2017-01-01

Plasma samples from 177 control and type 2 diabetes patients collected at three Australian hospitals are screened for 14 analytes using six custom-made multiplex kits across 60 96-well plates. In total 354 samples were collected from the patients, representing one baseline and one end point sample from each patient. R methods and source code for analyzing the analyte fluorescence response obtained from these samples by Luminex Bio-Plex ® xMap multiplexed immunoassay technology are disclosed. Techniques and R procedures for reading Bio-Plex ® result files for statistical analysis and data visualization are also presented. The need for technical replicates and the number of technical replicates are addressed as well as plate layout design strategies. Multinomial regression is used to determine plate to sample covariate balance. Methods for matching clinical covariate information to Bio-Plex ® results and vice versa are given. As well as methods for measuring and inspecting the quality of the fluorescence responses are presented. Both fixed and mixed-effect approaches for immunoassay statistical differential analysis are presented and discussed. A random effect approach to outlier analysis and detection is also shown. The bioinformatics R methodology present here provides a foundation for rigorous and reproducible analysis of the fluorescence response obtained from multiplexed immunoassays.

Environmental Systems Test Stand

NASA Astrophysics Data System (ADS)

Barta, D.; Young, J.; Ewert, M.; Lee, S.; Wells, P.; Fortson, R.; Castillo, J.

A test stand has been developed for the evaluation of prototype lighting, environmental control and crop cultivation technologies for plant production within an advanced life support system. Design of the test stand was based on preliminary designs of the center growth bay of the Biomass Production Chamber, one of several modules of the Bioregenerative Planetary Life Support Systems Test Complex (BIO- Plex). It consists of two controlled-environment shelves, each with 4.7 m2 of area for crop growth (150 cm width, 315 cm length). There are two chilled water loops, one for operation at conventional temperatures (5-10C) for air temperature and humidity control and one for operation at higher temperatures (15-50C) for waste heat acquisition and heating. Modular light boxes, utilizing either air-cooled or water- jacketed HPS lamps, have been developed. This modular design will allow for easy replacement of new lighting technologies within the light banks. An advanced data acquisition and control system has been developed utilizing localized, networked- based data acquisition modules and programmed with object-based control software.

A robust internal control for high-precision DNA methylation analyses by droplet digital PCR.

PubMed

Pharo, Heidi D; Andresen, Kim; Berg, Kaja C G; Lothe, Ragnhild A; Jeanmougin, Marine; Lind, Guro E

2018-01-01

Droplet digital PCR (ddPCR) allows absolute quantification of nucleic acids and has potential for improved non-invasive detection of DNA methylation. For increased precision of the methylation analysis, we aimed to develop a robust internal control for use in methylation-specific ddPCR. Two control design approaches were tested: (a) targeting a genomic region shared across members of a gene family and (b) combining multiple assays targeting different pericentromeric loci on different chromosomes. Through analyses of 34 colorectal cancer cell lines, the performance of the control assay candidates was optimized and evaluated, both individually and in various combinations, using the QX200™ droplet digital PCR platform (Bio-Rad). The best-performing control was tested in combination with assays targeting methylated CDO1 , SEPT9 , and VIM . A 4Plex panel consisting of EPHA3 , KBTBD4 , PLEKHF1 , and SYT10 was identified as the best-performing control. The use of the 4Plex for normalization reduced the variability in methylation values, corrected for differences in template amount, and diminished the effect of chromosomal aberrations. Positive Droplet Calling (PoDCall), an R-based algorithm for standardized threshold determination, was developed, ensuring consistency of the ddPCR results. Implementation of a robust internal control, i.e., the 4Plex, and an algorithm for automated threshold determination, PoDCall, in methylation-specific ddPCR increase the precision of DNA methylation analysis.

The HIrisPlex-S system for eye, hair and skin colour prediction from DNA: Introduction and forensic developmental validation.

PubMed

Chaitanya, Lakshmi; Breslin, Krystal; Zuñiga, Sofia; Wirken, Laura; Pośpiech, Ewelina; Kukla-Bartoszek, Magdalena; Sijen, Titia; Knijff, Peter de; Liu, Fan; Branicki, Wojciech; Kayser, Manfred; Walsh, Susan

2018-07-01

Forensic DNA Phenotyping (FDP), i.e. the prediction of human externally visible traits from DNA, has become a fast growing subfield within forensic genetics due to the intelligence information it can provide from DNA traces. FDP outcomes can help focus police investigations in search of unknown perpetrators, who are generally unidentifiable with standard DNA profiling. Therefore, we previously developed and forensically validated the IrisPlex DNA test system for eye colour prediction and the HIrisPlex system for combined eye and hair colour prediction from DNA traces. Here we introduce and forensically validate the HIrisPlex-S DNA test system (S for skin) for the simultaneous prediction of eye, hair, and skin colour from trace DNA. This FDP system consists of two SNaPshot-based multiplex assays targeting a total of 41 SNPs via a novel multiplex assay for 17 skin colour predictive SNPs and the previous HIrisPlex assay for 24 eye and hair colour predictive SNPs, 19 of which also contribute to skin colour prediction. The HIrisPlex-S system further comprises three statistical prediction models, the previously developed IrisPlex model for eye colour prediction based on 6 SNPs, the previous HIrisPlex model for hair colour prediction based on 22 SNPs, and the recently introduced HIrisPlex-S model for skin colour prediction based on 36 SNPs. In the forensic developmental validation testing, the novel 17-plex assay performed in full agreement with the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines, as previously shown for the 24-plex assay. Sensitivity testing of the 17-plex assay revealed complete SNP profiles from as little as 63 pg of input DNA, equalling the previously demonstrated sensitivity threshold of the 24-plex HIrisPlex assay. Testing of simulated forensic casework samples such as blood, semen, saliva stains, of inhibited DNA samples, of low quantity touch (trace) DNA samples, and of artificially degraded DNA samples as well as concordance testing, demonstrated the robustness, efficiency, and forensic suitability of the new 17-plex assay, as previously shown for the 24-plex assay. Finally, we provide an update to the publically available HIrisPlex website https://hirisplex.erasmusmc.nl/, now allowing the estimation of individual probabilities for 3 eye, 4 hair, and 5 skin colour categories from HIrisPlex-S input genotypes. The HIrisPlex-S DNA test represents the first forensically validated tool for skin colour prediction, and reflects the first forensically validated tool for simultaneous eye, hair and skin colour prediction from DNA. Copyright © 2018 Elsevier B.V. All rights reserved.

Magnetic bead based immuno-detection of Listeria monocytogenes and Listeria ivanovii from infant formula and leafy green vegetables using the Bio-Plex suspension array system.

PubMed

Day, J B; Basavanna, U

2015-04-01

Listeriosis, a disease contracted via the consumption of foods contaminated with pathogenic Listeria species, can produce severe symptoms and high mortality in susceptible people and animals. The development of molecular methods and immuno-based techniques for detection of pathogenic Listeria in foods has been challenging due to the presence of assay inhibiting food components. In this study, we utilize a macrophage cell culture system for the isolation and enrichment of Listeria monocytogenes and Listeria ivanovii from infant formula and leafy green vegetables for subsequent identification using the Luminex xMAP technique. Macrophage monolayers were exposed to infant formula, lettuce and celery contaminated with L. monocytogenes or L. ivanovii. Magnetic microspheres conjugated to Listeria specific antibody were used to capture Listeria from infected macrophages and then analyzed using the Bio-Plex 200 analyzer. As few as 10 CFU/mL or g of L. monocytogenes was detected in all foods tested. The detection limit for L. ivanovii was 10 CFU/mL in infant formula and 100 CFU/g in leafy greens. Microsphere bound Listeria obtained from infected macrophage lysates could also be isolated on selective media for subsequent confirmatory identification. This method presumptively identifies L. monocytogenes and L. ivanovii from infant formula, lettuce and celery in less than 28 h with confirmatory identifications completed in less than 48 h. Published by Elsevier Ltd.

Excited State Energetics and Dynamics of Large Molecules, Complexes and Clusters

DTIC Science & Technology

1988-07-01

tetracene. Ar (n=l-5) complexes, providing central information on microscopic solvent shifts. These studies were extended to M-metal atom com - plexes...corresponding to the bare molecule. At higher 2. Experimental stagnation pressures of Ar (p = 80-150 Toff) the contributions of van der Waals DPB. Ar, com - Our...gas aromatic-molecule complexes were docu- So - S1 transition of the trans-stilbene (TS)-Ar com - mented experimentally to lie in the rango - 30- plex

Comparison of Multiplex Suspension Array Large-Panel Kits for Profiling Cytokines and Chemokines in Rheumatoid Arthritis Patients

PubMed Central

Khan, Imran H.; Krishnan, V.V.; Ziman, Melanie; Janatpour, Kim; Wun, Ted; Luciw, Paul A.; Tuscano, Joseph

2015-01-01

Background Multiplex analysis allows measurements of a large number of analytes simultaneously in each sample. Based on the Luminex multiplex technology (xMAP), kits for measuring multiple cytokines and chemokines (immunomodulators) are commercially available and are useful in investigations on inflammatory diseases. This study evaluated four multiplex kits (Bio-Plex, LINCOplex, Fluorokine, and Beadlyte) that contained 27, 29, 20 and 22 analytes each, respectively, for the analysis of immunomodulators in plasma of rheumatoid arthritis (RA) patients who underwent treatment with antibody against CD20 (rituximab), a B-cell reductive therapy. Methods Multiplex kits were tested on serial plasma samples obtained from six RA patients at baseline and multiple time points (3, 6, and 9 months) post-treatment with rituximab. The RA patients included in this study had previously failed therapy with disease modifying anti-arthritis drugs (DMARD) and treatment with anti-TNFα antibody (infliximab). Results Computer modeling and hierarchical cluster analysis of the multiplex data allowed a comparison of the performance of multiplex assay kits and revealed profiles of immunomodulators in the RA patients. Conclusions In plasma of RA patients who appeared to have benefited from rituximab treatment the profile of significantly elevated immunomodulators by at least two of the three kits (BioPlex, LINCOplex, Beadlyte), is as follows: IL-12p70, Eotaxin, IL-4, TNFα, Il-9, IL-1β, IFNγ, IL-10, IL-6, and IL-13. Immunomodulator profiling by multiplex analysis may provide useful plasma biomarkers for monitoring response to B-cell reductive therapy in RA patients. PMID:18823005

Medical Management of Cutaneous Sulfur Mustard Injuries

DTIC Science & Technology

2009-01-01

negative pressure, (2) Amino-Plex® Spray (biO2 Cosmeceuticals International, Inc., Beverly Hills, CA), a nutritive cosmeceutical product that is...Inc., Beverly Hills, CA) is a nutritive cosmeceutical product that is designed to increase oxygen in cells, stimulate ATP synthesis, improve glucose... nutritive cosmeceutical product that is esigned to increase oxygen in cells, stimulate ATP synthesis, mprove glucose transportation, stimulate

High-throughput informative single nucleotide polymorphism-based typing of Neisseria gonorrhoeae using the Sequenom MassARRAY iPLEX platform.

PubMed

Trembizki, Ella; Smith, Helen; Lahra, Monica M; Chen, Marcus; Donovan, Basil; Fairley, Christopher K; Guy, Rebecca; Kaldor, John; Regan, David; Ward, James; Nissen, Michael D; Sloots, Theo P; Whiley, David M

2014-06-01

Neisseria gonorrhoeae antimicrobial resistance (AMR) is a global problem heightened by emerging resistance to ceftriaxone. Appropriate molecular typing methods are important for understanding the emergence and spread of N. gonorrhoeae AMR. We report on the development, validation and testing of a Sequenom MassARRAY iPLEX method for multilocus sequence typing (MLST)-style genotyping of N. gonorrhoeae isolates. An iPLEX MassARRAY method (iPLEX14SNP) was developed targeting 14 informative gonococcal single nucleotide polymorphisms (SNPs) previously shown to predict MLST types. The method was initially validated using 24 N. gonorrhoeae control isolates and was then applied to 397 test isolates collected throughout Queensland, Australia in the first half of 2012. The iPLEX14SNP method provided 100% accuracy for the control isolates, correctly identifying all 14 SNPs for all 24 isolates (336/336). For the 397 test isolates, the iPLEX14SNP assigned results for 5461 of the possible 5558 SNPs (SNP call rate 98.25%), with complete 14 SNP profiles obtained for 364 isolates. Based on the complete SNP profile data, there were 49 different sequence types identified in Queensland, with 11 of the 49 SNP profiles accounting for the majority (n = 280; 77%) of isolates. AMR was dominated by several geographically clustered sequence types. Using the iPLEX14SNP method, up to 384 isolates could be tested within 1 working day for less than Aus$10 per isolate. The iPLEX14SNP offers an accurate and high-throughput method for the MLST-style genotyping of N. gonorrhoeae and may prove particularly useful for large-scale studies investigating the emergence and spread of gonococcal AMR. © The Author 2014. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Developmental validation of the HIrisPlex system: DNA-based eye and hair colour prediction for forensic and anthropological usage.

PubMed

Walsh, Susan; Chaitanya, Lakshmi; Clarisse, Lindy; Wirken, Laura; Draus-Barini, Jolanta; Kovatsi, Leda; Maeda, Hitoshi; Ishikawa, Takaki; Sijen, Titia; de Knijff, Peter; Branicki, Wojciech; Liu, Fan; Kayser, Manfred

2014-03-01

Forensic DNA Phenotyping or 'DNA intelligence' tools are expected to aid police investigations and find unknown individuals by providing information on externally visible characteristics of unknown suspects, perpetrators and missing persons from biological samples. This is especially useful in cases where conventional DNA profiling or other means remain non-informative. Recently, we introduced the HIrisPlex system, capable of predicting both eye and hair colour from DNA. In the present developmental validation study, we demonstrate that the HIrisPlex assay performs in full agreement with the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines providing an essential prerequisite for future HIrisPlex applications to forensic casework. The HIrisPlex assay produces complete profiles down to only 63 pg of DNA. Species testing revealed human specificity for a complete HIrisPlex profile, while only non-human primates showed the closest full profile at 20 out of the 24 DNA markers, in all animals tested. Rigorous testing of simulated forensic casework samples such as blood, semen, saliva stains, hairs with roots as well as extremely low quantity touch (trace) DNA samples, produced complete profiles in 88% of cases. Concordance testing performed between five independent forensic laboratories displayed consistent reproducible results on varying types of DNA samples. Due to its design, the assay caters for degraded samples, underlined here by results from artificially degraded DNA and from simulated casework samples of degraded DNA. This aspect was also demonstrated previously on DNA samples from human remains up to several hundreds of years old. With this paper, we also introduce enhanced eye and hair colour prediction models based on enlarged underlying databases of HIrisPlex genotypes and eye/hair colour phenotypes (eye colour: N = 9188 and hair colour: N = 1601). Furthermore, we present an online web-based system for individual eye and hair colour prediction from full and partial HIrisPlex DNA profiles. By demonstrating that the HIrisPlex assay is fully compatible with the SWGDAM guidelines, we provide the first forensically validated DNA test system for parallel eye and hair colour prediction now available to forensic laboratories for immediate casework application, including missing person cases. Given the robustness and sensitivity described here and in previous work, the HIrisPlex system is also suitable for analysing old and ancient DNA in anthropological and evolutionary studies. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Efficient screening of environmental isolates for Saccharomyces cerevisiae strains that are suitable for brewing.

PubMed

Fujihara, Hidehiko; Hino, Mika; Takashita, Hideharu; Kajiwara, Yasuhiro; Okamoto, Keiko; Furukawa, Kensuke

2014-01-01

We developed an efficient screening method for Saccharomyces cerevisiae strains from environmental isolates. MultiPlex PCR was performed targeting four brewing S. cerevisiae genes (SSU1, AWA1, BIO6, and FLO1). At least three genes among the four were amplified from all S. cerevisiae strains. The use of this method allowed us to successfully obtain S. cerevisiae strains.

Natural and cross-inducible anti-SIV antibodies in Mauritian cynomolgus macaques

PubMed Central

Li, Hongzhao; Nykoluk, Mikaela; Li, Lin; Liu, Lewis R.; Omange, Robert W.; Soule, Geoff; Schroeder, Lukas T.; Toledo, Nikki; Kashem, Mohammad Abul; Correia-Pinto, Jorge F.; Liang, Binhua; Schultz-Darken, Nancy; Alonso, Maria J.; Whitney, James B.; Plummer, Francis A.

2017-01-01

Cynomolgus macaques are an increasingly important nonhuman primate model for HIV vaccine research. SIV-free animals without pre-existing anti-SIV immune responses are generally needed to evaluate the effect of vaccine-induced immune responses against the vaccine epitopes. Here, in order to select such animals for vaccine studies, we screened 108 naïve female Mauritian cynomolgus macaques for natural (baseline) antibodies to SIV antigens using a Bio-Plex multiplex system. The antigens included twelve 20mer peptides overlapping the twelve SIV protease cleavage sites (-10/+10), respectively (PCS peptides), and three non-PCS Gag or Env peptides. Natural antibodies to SIV antigens were detected in subsets of monkeys. The antibody reactivity to SIV was further confirmed by Western blot using purified recombinant SIV Gag and Env proteins. As expected, the immunization of monkeys with PCS antigens elicited anti-PCS antibodies. However, unexpectedly, antibodies to non-PCS peptides were also induced, as shown by both Bio-Plex and Western blot analyses, while the non-PCS peptides do not share sequence homology with PCS peptides. The presence of natural and vaccine cross-inducible SIV antibodies in Mauritian cynomolgus macaques should be considered in animal selection, experimental design and result interpretation, for their best use in HIV vaccine research. PMID:28982126

Improved eye- and skin-color prediction based on 8 SNPs.

PubMed

Hart, Katie L; Kimura, Shey L; Mushailov, Vladimir; Budimlija, Zoran M; Prinz, Mechthild; Wurmbach, Elisa

2013-06-01

To improve the 7-plex system to predict eye and skin color by increasing precision and detailed phenotypic descriptions. Analysis of an eighth single nucleotide polymorphism (SNP), rs12896399 (SLC24A4), showed a statistically significant association with human eye color (P=0.007) but a rather poor strength of agreement (κ=0.063). This SNP was added to the 7-plex system (rs12913832 at HERC2, rs1545397 at OCA2, rs16891982 at SLC45A2, rs1426654 at SLC24A5, rs885479 at MC1R, rs6119471 at ASIP, and rs12203592 at IRF4). Further, the instruction guidelines on the interpretation of genotypes were changed to create a new 8-plex system. This was based on the analysis of an 803-sample training set of various populations. The newly developed 8-plex system can predict the eye colors brown, green, and blue, and skin colors light, not dark, and not light. It is superior to the 7-plex system with its additional ability to predict blue eye and light skin color. The 8-plex system was tested on an additional 212 samples, the test set. Analysis showed that the number of positive descriptions for eye colors as being brown, green, or blue increased significantly (P=6.98e-15, z-score: -7.786). The error rate for eye-color prediction was low, at approximately 5%, while the skin color prediction showed no error in the test set (1% in training set). We can conclude that the new 8-plex system for the prediction of eye and skin color substantially enhances its former version.

Improvement and automation of a real-time PCR assay for vaginal fluids.

PubMed

De Vittori, E; Giampaoli, S; Barni, F; Baldi, M; Berti, A; Ripani, L; Romano Spica, V

2016-05-01

The identification of vaginal fluids is crucial in forensic science. Several molecular protocols based on PCR amplification of mfDNA (microflora DNA) specific for vaginal bacteria are now available. Unfortunately mfDNA extraction and PCR reactions require manual optimization of several steps. The aim of present study was the verification of a partial automatization of vaginal fluids identification through two instruments widely diffused in forensic laboratories: EZ1 Advanced robot and Rotor Gene Q 5Plex HRM. Moreover, taking advantage of 5-plex thermocycler technology, the ForFluid kit performances were improved by expanding the mfDNA characterization panel with a new bacterial target for vaginal fluids and with an internal positive control (IPC) to monitor PCR inhibition. Results underlined the feasibility of a semi-automated extraction of mfDNA using a BioRobot and demonstrated the analytical improvements of the kit. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Human Centered Autonomous and Assistant Systems Testbed for Exploration Operations

NASA Technical Reports Server (NTRS)

Malin, Jane T.; Mount, Frances; Carreon, Patricia; Torney, Susan E.

2001-01-01

The Engineering and Mission Operations Directorates at NASA Johnson Space Center are combining laboratories and expertise to establish the Human Centered Autonomous and Assistant Systems Testbed for Exploration Operations. This is a testbed for human centered design, development and evaluation of intelligent autonomous and assistant systems that will be needed for human exploration and development of space. This project will improve human-centered analysis, design and evaluation methods for developing intelligent software. This software will support human-machine cognitive and collaborative activities in future interplanetary work environments where distributed computer and human agents cooperate. We are developing and evaluating prototype intelligent systems for distributed multi-agent mixed-initiative operations. The primary target domain is control of life support systems in a planetary base. Technical approaches will be evaluated for use during extended manned tests in the target domain, the Bioregenerative Advanced Life Support Systems Test Complex (BIO-Plex). A spinoff target domain is the International Space Station (ISS) Mission Control Center (MCC). Prodl}cts of this project include human-centered intelligent software technology, innovative human interface designs, and human-centered software development processes, methods and products. The testbed uses adjustable autonomy software and life support systems simulation models from the Adjustable Autonomy Testbed, to represent operations on the remote planet. Ground operations prototypes and concepts will be evaluated in the Exploration Planning and Operations Center (ExPOC) and Jupiter Facility.

Clinical accuracy of a PLEX-ID flu device for simultaneous detection and identification of influenza viruses A and B.

PubMed

Tang, Yi-Wei; Lowery, Kristin S; Valsamakis, Alexandra; Schaefer, Virginia C; Chappell, James D; White-Abell, Jill; Quinn, Criziel D; Li, Haijing; Washington, Cicely A; Cromwell, Jenna; Giamanco, Chantel M; Forman, Michael; Holden, Jeffery; Rothman, Richard E; Parker, Michelle L; Ortenberg, Elaine V; Zhang, Lei; Lin, Yea-Lin; Gaydos, Charlotte A

2013-01-01

Respiratory tract infections caused by influenza A and B viruses often present nonspecifically, and a rapid, high-throughput laboratory technique that can identify influenza viruses is clinically and epidemiologically desirable. The PLEX-ID Flu assay (Abbott Molecular Inc., Des Plaines, IL) incorporates multilocus PCR and electrospray ionization-mass spectrometry to detect and differentiate influenza A 2009 H1N1 (H1N1-p), seasonal H1N1 (H1N1-s), influenza A H3N2, and influenza B viruses in nasopharyngeal swab (NPS) specimens. The clinical performance characteristics of the PLEX-ID Flu assay in symptomatic patients were determined in this multicenter trial. A total of 2,617 prospectively and retrospectively collected NPS specimens from patients with influenza-like illness between February 2008 and 28 May 2010 were eligible for inclusion in the study. Each specimen was tested in parallel by the PLEX-ID Flu assay and by the Prodesse ProFLU+ assay (Prodesse Inc., Madison, WI), to detect influenza A and B viruses. Specimens testing positive for influenza A virus by ProFLU+ were subtyped as H1N1-p, H1N1-s, or H3N2 by using the ProFAST+ assay (Gen-Probe Prodesse Inc.). The reproducibility of the PLEX-ID Flu assay ranged from 98.3 to 100.0%, as determined by testing a nine-specimen panel at three clinical sites on each of 5 days. Positive percent agreements (PPAs) and negative percent agreements (NPAs) of the PLEX-ID Flu assay were 94.5% and 99.0% for influenza A virus and 96.0% and 99.9% for influenza B virus, respectively. For the influenza A virus subtyping characterization, the PLEX-ID Flu assay had PPAs and NPAs of 98.3% and 97.5% for H1N1-p, 88.6% and 100.0% for H1N1-s, and 98.0% and 99.9% for H3N2, respectively. The overall agreements between the PLEX-ID and Prodesse ProFLU+/ProFAST+ assays were 97.1 to 100.0%. Bidirectional Sanger sequencing analysis revealed that 87.5% of 96 discrepant results between the PLEX-ID Flu and ProFLU+/ProFAST+ assays were found upon influenza A virus detection and H1N1-p subtyping. The PLEX-ID Flu assay demonstrated a high level of accuracy for the simultaneous detection and identification of influenza A and B viruses in patient specimens, providing a new laboratory tool for the rapid diagnosis and management of influenza A and B virus infections.

Development and characterization of novel 8-plex DiLeu isobaric labels for quantitative proteomics and peptidomics

PubMed Central

Frost, Dustin C.; Greer, Tyler; Xiang, Feng; Liang, Zhidan; Li, Lingjun

2015-01-01

Rationale Relative quantification of proteins via their enzymatically digested peptide products determines disease biomarker candidate lists in discovery studies. Isobaric label-based strategies using TMT and iTRAQ allow for up to 10 samples to be multiplexed in one experiment, but their expense limits their use. The demand for cost-effective tagging reagents capable of multiplexing many samples led us to develop an 8-plex version of our isobaric labeling reagent, DiLeu. Methods The original 4-plex DiLeu reagent was extended to an 8-plex set by coupling isotopic variants of dimethylated leucine to an alanine balance group designed to offset the increasing mass of the label’s reporter group. Tryptic peptides from a single protein digest, a protein mixture digest, and Saccharomyces cerevisiae lysate digest were labeled with 8-plex DiLeu and analyzed via nanoLC-MS2 on a Q-Exactive Orbitrap mass spectrometer. Characteristics of 8-plex DiLeu-labeled peptides, including quantitative accuracy and fragmentation, were examined. Results An 8-plex set of DiLeu reagents with 1 Da-spaced reporters was synthesized at a yield of 36%. The average cost to label eight 100 μg peptide samples was calculated to be approximately $15. Normalized collision energy tests on the Q-Exactive revealed that a higher-energy collisional dissociation value of 27 generated the optimum number of high-quality spectral matches. Relative quantification of DiLeu-labeled peptides yielded normalized median ratios accurate to within 12% of their expected values. Conclusions Cost-effective 8-plex DiLeu reagents can be synthesized and applied to relative peptide and protein quantification. These labels increase the multiplexing capacity of our previous 4-plex implementation without requiring high-resolution instrumentation to resolve reporter ion signals. PMID:25981542

A semi-automated multiplex high-throughput assay for measuring IgG antibodies against Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) domains in small volumes of plasma.

PubMed

Cham, Gerald K K; Kurtis, Jonathan; Lusingu, John; Theander, Thor G; Jensen, Anja T R; Turner, Louise

2008-06-12

The level of antibodies against PfEMP1 is routinely quantified by the conventional microtitre enzyme-linked immunosorbent assay (ELISA). However, ELISA only measures one analyte at a time and requires a relatively large plasma volume if the complete antibody profile of the sample is to be obtained. Furthermore, assay-to-assay variation and the problem of storage of antigen can influence ELISA results. The bead-based assay described here uses the BioPlex100 (BioRad, Hercules, CA, USA) system which can quantify multiple antibodies simultaneously in a small plasma volume. A total of twenty nine PfEMP1 domains were PCR amplified from 3D7 genomic DNA, expressed in the Baculovirus system and purified by metal-affinity chromatography. The antibody reactivity level to the recombinant PfEMP1 proteins in human hyper-immune plasma was measured by ELISA. In parallel, these recombinant PfEMP1 proteins were covalently coupled onto beads each having its own unique detection signal and the human hyper-immune plasma reactivity was detected for each individual protein using a BioPlex100 system. Protein-coupled beads were analysed at two time points seven months apart, before and after lyophilization and the results compared to determine the effect of storage and lyophilization respectively on the beads. Multiplexed protein-coupled beads from twenty eight unique bead populations were evaluated on the BioPlex100 system against pooled human hyper-immune plasma before and after lyophilization. The bead-based assay was sensitive, accurate and reproducible. Four recombinant PfEMP1 proteins C17, D5, D9 and D12, selected on the basis that they showed a spread of median fluorescent intensity (MFI) values from low to high when analysed by the bead-based assay were analysed by ELISA and the results from both analyses were highly correlated. The Spearman's rank correlation coefficients (Rho) were > or = 0.86, (P < 0.0001) for all comparisons. Bead-based assays gave similar results regardless of whether they were performed on individual beads or on multiplexed beads; lyophilization had no impact on the assay performance. Spearman's rank correlation coefficients (Rho) were > or = 0.97, (P < 0.0001) for all comparisons. Importantly, the reactivity of protein-coupled non-lyophilized beads decreased with long term storage at 4 degrees C in the dark. Using this lyophilized multiplex assay, antibody reactivity levels to twenty eight different recombinant PfEMP1 proteins were simultaneously measured using a single microliter of plasma. Thus, the assay reported here provides a useful tool for rapid and efficient quantification of antibody reactivity against PfEMP1 variants in human plasma.

Development of Conceptual Design Support Tool Founded on Formalization of Conceptual Design Process for Regenerative Life Support Systems

NASA Astrophysics Data System (ADS)

Miyajima, Hiroyuki; Yuhara, Naohiro

Regenerative Life Support Systems (RLSS), which maintain human lives by recycling substances essential for living, are comprised of humans, plants, and material circulation systems. The plants supply food to the humans or reproduce water and gases by photosynthesis, while the material circulation systems recycle physicochemically and circulate substances disposed by humans and plants. RLSS attracts attention since manned space activities have been shifted from previous short trips to long-term stay activities as such base as a space station, a lunar base, and a Mars base. The present typical space base is the International Space Station (ISS), a manned experimental base for prolonged stays, where RLSS recycles only water and air. In order to accommodate prolonged and extended manned activity in future space bases, developing RLSS that implements food production and regeneration of resources at once using plants is expected. The configuration of RLSS should be designed to suit its own duty, for which design requirements for RLSS with an unprecedented configuration may arise. Accordingly, it is necessary to establish a conceptual design method for generalized RLSS. It is difficult, however, to systematize the design process by analyzing previous design because there are only a few ground-experimental facilities, namely CEEF (Closed Ecology Experiment Facilities) of Japan, BIO-Plex (Bioregenerative Planetary Life Support Systems Test Complex) of the U.S., and BIOS3 of Russia. Thus a conceptual design method which doesn’t rely on previous design examples is required for generalized RLSS from the above reasons. This study formalizes a conceptual design process, and develops a conceptual design support tool for RLSS based on this design process.

Analysis of Reproducibility of Proteome Coverage and Quantitation Using Isobaric Mass Tags (iTRAQ and TMT).

PubMed

Casey, Tammy M; Khan, Javed M; Bringans, Scott D; Koudelka, Tomas; Takle, Pari S; Downs, Rachael A; Livk, Andreja; Syme, Robert A; Tan, Kar-Chun; Lipscombe, Richard J

2017-02-03

This study aimed to compare the depth and reproducibility of total proteome and differentially expressed protein coverage in technical duplicates and triplicates using iTRAQ 4-plex, iTRAQ 8-plex, and TMT 6-plex reagents. The analysis was undertaken because comprehensive comparisons of isobaric mass tag reproducibility have not been widely reported in the literature. The highest number of proteins was identified with 4-plex, followed by 8-plex and then 6-plex reagents. Quantitative analyses revealed that more differentially expressed proteins were identified with 4-plex reagents than 8-plex reagents and 6-plex reagents. Replicate reproducibility was determined to be ≥69% for technical duplicates and ≥57% for technical triplicates. The results indicate that running an 8-plex or 6-plex experiment instead of a 4-plex experiment resulted in 26 or 39% fewer protein identifications, respectively. When 4-plex spectra were searched with three software tools-ProteinPilot, Mascot, and Proteome Discoverer-the highest number of protein identifications were obtained with Mascot. The analysis of negative controls demonstrated the importance of running experiments as replicates. Overall, this study demonstrates the advantages of using iTRAQ 4-plex reagents over iTRAQ 8-plex and TMT 6-plex reagents, provides estimates of technical duplicate and triplicate reproducibility, and emphasizes the value of running replicate samples.

Use of Bioregenerative Technologies for Advanced Life Support: Some Considerations for BIO-Plex and Related Testbeds

NASA Technical Reports Server (NTRS)

Wheeler, Raymond M.; Strayer, Richard F.

1997-01-01

A review of bioregenerative life support concepts is provided as a guide for developing ground-based testbeds for NASA's Advanced Life Support Program. Key among these concepts are the use of controlled environment plant culture for the production of food, oxygen, and clean water, and the use of bacterial bioreactors for degrading wastes and recycling nutrients. Candidate crops and specific bioreactor approaches are discussed based on experiences from the. Kennedy Space Center Advanced Life Support Breadboard Project, and a review of related literature is provided.

Comparison of 3 kidney injury multiplex panels in rats.

PubMed

John-Baptiste, Annette; Vitsky, Allison; Sace, Frederick; Zong, Qing; Ko, Mira; Yafawi, Rolla; Liu, Ling

2012-01-01

Kidney injury biomarkers have been utilized by pharmaceutical companies as a means to assess the potential of candidate drugs to induce nephrotoxicity. Multiple platforms and assay methods exist, but the comparison of these methods has not been described. Millipore's Kidney Toxicity panel, EMD/Novagen's Widescreen Kidney Toxicity panel, and Meso Scales Kidney Injury panel were selected based on published information. Kidney injury molecule 1, cystatin C, clusterin, and osteopontin were the 4 biomarkers common among all kits tested and the focus of this study. Rats were treated with a low and high dose of para-aminophenol, a known nephrotoxicant, and urine samples were collected and analyzed on the Bio-Plex 200 or MSD's Sector Imager 6000, according to manufacturers specifications. Comparatively, of the 3 kits, Millipore was the most consistent in detecting elevations of 3 out of the 4 biomarkers at both dose levels and indicated time points.

Molecular identification of common Salmonella serovars using multiplex DNA sensor-based suspension array.

PubMed

Aydin, Muhsin; Carter-Conger, Jacqueline; Gao, Ning; Gilmore, David F; Ricke, Steven C; Ahn, Soohyoun

2018-04-01

Salmonella is one of major foodborne pathogens and the leading cause of foodborne illness-related hospitalizations and deaths. It is critical to develop a sensitive and rapid detection assay that can identify Salmonella to ensure food safety. In this study, a DNA sensor-based suspension array system of high multiplexing ability was developed to identify eight Salmonella serovars commonly associated with foodborne outbreaks to the serotype level. Each DNA sensor was prepared by activating pre-encoded microspheres with oligonucleotide probes that are targeting virulence genes and serovar-specific regions. The mixture of 12 different types of DNA sensors were loaded into a 96-well microplate and used as a 12-plex DNA sensor array platform. DNA isolated from Salmonella was amplified by multiplex polymerase chain reaction (mPCR), and the presence of Salmonella was determined by reading fluorescent signals from hybridization between probes on DNA sensors and fluorescently labeled target DNA using the Bio-Plex® system. The developed multiplex array was able to detect synthetic DNA at the concentration as low as 100 fM and various Salmonella serovars as low as 100 CFU/mL within 1 h post-PCR. Sensitivity of this assay was further improved to 1 CFU/mL with 6-h enrichment. The array system also correctly and specifically identified serotype of tested Salmonella strains without any cross-reactivity with other common foodborne pathogens. Our results indicate the developed DNA sensor suspension array can be a rapid and reliable high-throughput method for simultaneous detection and molecular identification of common Salmonella serotypes.

Multiplex quantification of four DNA targets in one reaction with Bio-Rad droplet digital PCR system for GMO detection

NASA Astrophysics Data System (ADS)

Dobnik, David; Štebih, Dejan; Blejec, Andrej; Morisset, Dany; Žel, Jana

2016-10-01

The advantages of the digital PCR technology are already well documented until now. One way to achieve better cost efficiency of the technique is to use it in a multiplexing strategy. Droplet digital PCR platforms, which include two fluorescence filters, support at least duplex reactions and with some developments and optimization higher multiplexing is possible. The present study not only shows a development of multiplex assays in droplet digital PCR, but also presents a first thorough evaluation of several parameters in such multiplex digital PCR. Two 4-plex assays were developed for quantification of 8 different DNA targets (7 genetically modified maize events and maize endogene). Per assay, two of the targets were labelled with one fluorophore and two with another. As current analysis software does not support analysis of more than duplex, a new R- and Shiny-based web application analysis tool (http://bit.ly/ddPCRmulti) was developed that automates the analysis of 4-plex results. In conclusion, the two developed multiplex assays are suitable for quantification of GMO maize events and the same approach can be used in any other field with a need for accurate and reliable quantification of multiple DNA targets.

Multiplex quantification of four DNA targets in one reaction with Bio-Rad droplet digital PCR system for GMO detection.

PubMed

Dobnik, David; Štebih, Dejan; Blejec, Andrej; Morisset, Dany; Žel, Jana

2016-10-14

The advantages of the digital PCR technology are already well documented until now. One way to achieve better cost efficiency of the technique is to use it in a multiplexing strategy. Droplet digital PCR platforms, which include two fluorescence filters, support at least duplex reactions and with some developments and optimization higher multiplexing is possible. The present study not only shows a development of multiplex assays in droplet digital PCR, but also presents a first thorough evaluation of several parameters in such multiplex digital PCR. Two 4-plex assays were developed for quantification of 8 different DNA targets (7 genetically modified maize events and maize endogene). Per assay, two of the targets were labelled with one fluorophore and two with another. As current analysis software does not support analysis of more than duplex, a new R- and Shiny-based web application analysis tool (http://bit.ly/ddPCRmulti) was developed that automates the analysis of 4-plex results. In conclusion, the two developed multiplex assays are suitable for quantification of GMO maize events and the same approach can be used in any other field with a need for accurate and reliable quantification of multiple DNA targets.

Bona fide colour: DNA prediction of human eye and hair colour from ancient and contemporary skeletal remains

PubMed Central

2013-01-01

Background DNA analysis of ancient skeletal remains is invaluable in evolutionary biology for exploring the history of species, including humans. Contemporary human bones and teeth, however, are relevant in forensic DNA analyses that deal with the identification of perpetrators, missing persons, disaster victims or family relationships. They may also provide useful information towards unravelling controversies that surround famous historical individuals. Retrieving information about a deceased person’s externally visible characteristics can be informative in both types of DNA analyses. Recently, we demonstrated that human eye and hair colour can be reliably predicted from DNA using the HIrisPlex system. Here we test the feasibility of the novel HIrisPlex system at establishing eye and hair colour of deceased individuals from skeletal remains of various post-mortem time ranges and storage conditions. Methods Twenty-one teeth between 1 and approximately 800 years of age and 5 contemporary bones were subjected to DNA extraction using standard organic protocol followed by analysis using the HIrisPlex system. Results Twenty-three out of 26 bone DNA extracts yielded the full 24 SNP HIrisPlex profile, therefore successfully allowing model-based eye and hair colour prediction. HIrisPlex analysis of a tooth from the Polish general Władysław Sikorski (1881 to 1943) revealed blue eye colour and blond hair colour, which was positively verified from reliable documentation. The partial profiles collected in the remaining three cases (two contemporary samples and a 14th century sample) were sufficient for eye colour prediction. Conclusions Overall, we demonstrate that the HIrisPlex system is suitable, sufficiently sensitive and robust to successfully predict eye and hair colour from ancient and contemporary skeletal remains. Our findings, therefore, highlight the HIrisPlex system as a promising tool in future routine forensic casework involving skeletal remains, including ancient DNA studies, for the prediction of eye and hair colour of deceased individuals. PMID:23317428

Bona fide colour: DNA prediction of human eye and hair colour from ancient and contemporary skeletal remains.

PubMed

Draus-Barini, Jolanta; Walsh, Susan; Pośpiech, Ewelina; Kupiec, Tomasz; Głąb, Henryk; Branicki, Wojciech; Kayser, Manfred

2013-01-14

DNA analysis of ancient skeletal remains is invaluable in evolutionary biology for exploring the history of species, including humans. Contemporary human bones and teeth, however, are relevant in forensic DNA analyses that deal with the identification of perpetrators, missing persons, disaster victims or family relationships. They may also provide useful information towards unravelling controversies that surround famous historical individuals. Retrieving information about a deceased person's externally visible characteristics can be informative in both types of DNA analyses. Recently, we demonstrated that human eye and hair colour can be reliably predicted from DNA using the HIrisPlex system. Here we test the feasibility of the novel HIrisPlex system at establishing eye and hair colour of deceased individuals from skeletal remains of various post-mortem time ranges and storage conditions. Twenty-one teeth between 1 and approximately 800 years of age and 5 contemporary bones were subjected to DNA extraction using standard organic protocol followed by analysis using the HIrisPlex system. Twenty-three out of 26 bone DNA extracts yielded the full 24 SNP HIrisPlex profile, therefore successfully allowing model-based eye and hair colour prediction. HIrisPlex analysis of a tooth from the Polish general Władysław Sikorski (1881 to 1943) revealed blue eye colour and blond hair colour, which was positively verified from reliable documentation. The partial profiles collected in the remaining three cases (two contemporary samples and a 14th century sample) were sufficient for eye colour prediction. Overall, we demonstrate that the HIrisPlex system is suitable, sufficiently sensitive and robust to successfully predict eye and hair colour from ancient and contemporary skeletal remains. Our findings, therefore, highlight the HIrisPlex system as a promising tool in future routine forensic casework involving skeletal remains, including ancient DNA studies, for the prediction of eye and hair colour of deceased individuals.

Effects of microbial DNA on human DNA profiles generated using the PowerPlex® 16 HS system.

PubMed

Dembinski, Gina M; Picard, Christine J

2017-11-01

Most crime scenes are not sterile and therefore may be contaminated with environmental DNA, especially if a decomposing body is found. Collecting biological evidence from this individual will yield DNA samples mixed with microbial DNA. This also becomes important if postmortem swabs are collected from sexually assaulted victims. Although genotyping kits undergo validation tests, including bacterial screens, they do not account for the diverse microbial load during decomposition. We investigated the effect of spiking human DNA samples with known concentrations of DNA from 17 microbe species associated with decomposition on DNA profiles produced using the Promega PowerPlex ® HS system. Two species, Bacillus subtilis and Mycobacterium smegmatis, produced an extraneous allele at the TPOX locus. When repeated with the PowerPlex ® Fusion kit, the extra allele no longer amplified with these two species. This experiment demonstrates that caution should be exhibited if microbial load is high and the PowerPlex ® 16HS system is used. Copyright © 2017 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

Food System Trade Study for a Near-Term Mars Mission

NASA Technical Reports Server (NTRS)

Levri, Julie; Luna, Bernadette (Technical Monitor)

2000-01-01

This paper evaluates several food system options for a near-term Mars mission, based on plans for the 120-day BIO-Plex test. Food systems considered in the study are based on the International Space Station (ISS) Assembly Phase and Assembly Complete food systems. The four systems considered are: 1) ISS assembly phase food system (US portion) with individual packaging without salad production; 2) ISS assembly phase food system (US portion) with individual packaging, with salad production; 3) ISS assembly phase food system (US portion) with bulk packaging, with salad production; 4) ISS assembly complete food system (US portion) with bulk packaging with salad and refrigeration/freezing. The food system options are assessed using equivalent system mass (ESM), which evaluates each option based upon the mass, volume, power, cooling and crewtime requirements that are associated with each food system option. However, since ESM is unable to elucidate the differences in psychological benefits between the food systems, a qualitative evaluation of each option is also presented.

Bringing colour back after 70 years: Predicting eye and hair colour from skeletal remains of World War II victims using the HIrisPlex system.

PubMed

Chaitanya, Lakshmi; Pajnič, Irena Zupanič; Walsh, Susan; Balažic, Jože; Zupanc, Tomaž; Kayser, Manfred

2017-01-01

Retrieving information about externally visible characteristics from DNA can provide investigative leads to find unknown perpetrators, and can also help in disaster victim and other missing person identification cases. Aiming for the application to both types of forensic casework, we previously developed and forensically validated the HIrisPlex test system enabling parallel DNA prediction of eye and hair colour. Although a recent proof-of-principle study demonstrated the general suitability of the HIrisPlex system for successfully analysing DNA from bones and teeth of various storage times and conditions, practical case applications to human remains are scarce. In this study, we applied the HIrisPlex system to 49 DNA samples obtained from bones or teeth of World War II victims excavated at six sites, mostly mass graves, in Slovenia. PCR-based DNA quantification ranged from 4pg/μl to 313pg/μl and on an average was 41pg/μl across all samples. All 49 samples generated complete HIrisPlex profiles with the exception of one MC1R DNA marker (N29insA) missing in 83.7% of the samples. In 44 of the 49 samples (89.8%) complete 15-loci autosomal STR (plus amelogenin) profiles were obtained. Of 5 pairs of skeletal remains for which STR profiling suggested an origin in the same individuals, respectively, 4 showed the same HIrisPlex profiles and predicted eye and hair colours, respectively, while discrepancies in one pair (sample 26 and 43) are likely to be explained by DNA quantity and quality issues observed in sample 43. Sample 43 had the lowest DNA concentration of only 4pg/μl, producing least reliable STR results and could be misleading in concluding that samples 43 and 26 originate from the same individual. The HIrisPlex-predicted eye and hair colours from two skeletal samples, suggested to derive from two brothers via STR profiling together with a living sister, were confirmed by the living sister's report. Overall, we demonstrate that after more than 70 years, HIrisPlex-based eye and hair colour prediction from skeletal remains is feasible with high success rate. Our results further encourage the use of the HIrisPlex system in missing person/disaster victim identification to aid the identification process in cases where ante-mortem samples or putative relatives are not directly available, and DNA predicted eye and hair colour information provides leads for locating them, allowing STRbased individual identification. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Detection of respiratory viruses on air filters from aircraft.

PubMed

Korves, T M; Johnson, D; Jones, B W; Watson, J; Wolk, D M; Hwang, G M

2011-09-01

To evaluate the feasibility of identifying viruses from aircraft cabin air, we evaluated whether respiratory viruses trapped by commercial aircraft air filters can be extracted and detected using a multiplex PCR, bead-based assay. The ResPlex II assay was first tested for its ability to detect inactivated viruses applied to new filter material; all 18 applications of virus at a high concentration were detected. The ResPlex II assay was then used to test for 18 respiratory viruses on 48 used air filter samples from commercial aircraft. Three samples tested positive for viruses, and three viruses were detected: rhinovirus, influenza A and influenza B. For 33 of 48 samples, internal PCR controls performed suboptimally, suggesting sample matrix effect. In some cases, influenza and rhinovirus RNA can be detected on aircraft air filters, even more than 10 days after the filters were removed from aircraft. With protocol modifications to overcome PCR inhibition, air filter sampling and the ResPlex II assay could be used to characterize viruses in aircraft cabin air. Information about viruses in aircraft could support public health measures to reduce disease transmission within aircraft and between cities. © The MITRE corporation. Letters in Applied Microbiology © 2011 The Society for Applied Microbiology.

Two brothers' alleged paternity for a child: who is the father?

PubMed

Dogan, Muhammed; Kara, Umut; Emre, Ramazan; Fung, Wing Kam; Canturk, Kemal Murat

2015-06-01

In paternity cases where individuals are close relatives, it may be necessary to evaluate mother's DNA profile (trio test) and to increase the number of polymorphic STR loci that are analyzed. In our case, two alleged fathers who are brothers and the child (duo case) were analyzed based on 20 STR loci; however, no exclusions could be achieved. Then trio test (with mother) was performed using the Identifiler Plus kit (Applied Biosystems) and no exclusions could be achieved again. Analysis performed with the ESS Plex Plus kit (Qiagen), the paternity of one of the two alleged fathers was rejected only on 2 STR loci. We made the calculations of power of exclusion values to interpret our results more properly. The probability of exclusion (PE) is calculated as 0.9776546 in 15 loci of Identifiler Plus kit without mother. The PE is calculated as 0.9942803, if 5 additional loci from ESS Plex Plus kit are typed. The PE becomes 0.9961048 for the Identifiler Plus kit in trio analysis. If both Identifiler Plus and ESS Plex Plus kits are used for testing, the PE is calculated as 0.999431654, which indicates that the combined kits are highly discriminating.

Developmental validation of the PowerPlex(®) ESI 16 and PowerPlex(®) ESI 17 Systems: STR multiplexes for the new European standard.

PubMed

Tucker, Valerie C; Hopwood, Andrew J; Sprecher, Cynthia J; McLaren, Robert S; Rabbach, Dawn R; Ensenberger, Martin G; Thompson, Jonelle M; Storts, Douglas R

2011-11-01

In response to the ENFSI and EDNAP groups' call for new STR multiplexes for Europe, Promega(®) developed a suite of four new DNA profiling kits. This paper describes the developmental validation study performed on the PowerPlex(®) ESI 16 (European Standard Investigator 16) and the PowerPlex(®) ESI 17 Systems. The PowerPlex(®) ESI 16 System combines the 11 loci compatible with the UK National DNA Database(®), contained within the AmpFlSTR(®) SGM Plus(®) PCR Amplification Kit, with five additional loci: D2S441, D10S1248, D22S1045, D1S1656 and D12S391. The multiplex was designed to reduce the amplicon size of the loci found in the AmpFlSTR(®) SGM Plus(®) kit. This design facilitates increased robustness and amplification success for the loci used in the national DNA databases created in many countries, when analyzing degraded DNA samples. The PowerPlex(®) ESI 17 System amplifies the same loci as the PowerPlex(®) ESI 16 System, but with the addition of a primer pair for the SE33 locus. Tests were designed to address the developmental validation guidelines issued by the Scientific Working Group on DNA Analysis Methods (SWGDAM), and those of the DNA Advisory Board (DAB). Samples processed include DNA mixtures, PCR reactions spiked with inhibitors, a sensitivity series, and 306 United Kingdom donor samples to determine concordance with data generated with the AmpFlSTR(®) SGM Plus(®) kit. Allele frequencies from 242 white Caucasian samples collected in the United Kingdom are also presented. The PowerPlex(®) ESI 16 and ESI 17 Systems are robust and sensitive tools, suitable for the analysis of forensic DNA samples. Full profiles were routinely observed with 62.5pg of a fully heterozygous single source DNA template. This high level of sensitivity was found to impact on mixture analyses, where 54-86% of unique minor contributor alleles were routinely observed in a 1:19 mixture ratio. Improved sensitivity combined with the robustness afforded by smaller amplicons has substantially improved the quantity of data obtained from degraded samples, and the improved chemistry confers exceptional tolerance to high levels of laboratory prepared inhibitors. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Revision of the SNPforID 34-plex forensic ancestry test: Assay enhancements, standard reference sample genotypes and extended population studies.

PubMed

Fondevila, M; Phillips, C; Santos, C; Freire Aradas, A; Vallone, P M; Butler, J M; Lareu, M V; Carracedo, A

2013-01-01

A revision of an established 34 SNP forensic ancestry test has been made by swapping the under-performing rs727811 component SNP with the highly informative rs3827760 that shows a near-fixed East Asian specific allele. We collated SNP variability data for the revised SNP set in 66 reference populations from 1000 Genomes and HGDP-CEPH panels and used this as reference data to analyse four U.S. populations showing a range of admixture patterns. The U.S. Hispanics sample in particular displayed heterogeneous values of co-ancestry between European, Native American and African contributors, likely to reflect in part, the way this disparate group is defined using cultural as well as population genetic parameters. The genotyping of over 700 U.S. population samples also provided the opportunity to thoroughly gauge peak mobility variation and peak height ratios observed from routine use of the single base extension chemistry of the 34-plex test. Finally, the genotyping of the widely used DNA profiling Standard Reference Material samples plus other control DNAs completes the audit of the 34-plex assay to allow forensic practitioners to apply this test more readily in their own laboratories. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Multiplex quantification of four DNA targets in one reaction with Bio-Rad droplet digital PCR system for GMO detection

PubMed Central

Dobnik, David; Štebih, Dejan; Blejec, Andrej; Morisset, Dany; Žel, Jana

2016-01-01

The advantages of the digital PCR technology are already well documented until now. One way to achieve better cost efficiency of the technique is to use it in a multiplexing strategy. Droplet digital PCR platforms, which include two fluorescence filters, support at least duplex reactions and with some developments and optimization higher multiplexing is possible. The present study not only shows a development of multiplex assays in droplet digital PCR, but also presents a first thorough evaluation of several parameters in such multiplex digital PCR. Two 4-plex assays were developed for quantification of 8 different DNA targets (7 genetically modified maize events and maize endogene). Per assay, two of the targets were labelled with one fluorophore and two with another. As current analysis software does not support analysis of more than duplex, a new R- and Shiny-based web application analysis tool (http://bit.ly/ddPCRmulti) was developed that automates the analysis of 4-plex results. In conclusion, the two developed multiplex assays are suitable for quantification of GMO maize events and the same approach can be used in any other field with a need for accurate and reliable quantification of multiple DNA targets. PMID:27739510

OzPythonPlex: An optimised forensic STR multiplex assay set for the Australasian carpet python (Morelia spilota).

PubMed

Ciavaglia, Sherryn; Linacre, Adrian

2018-05-01

Reptile species, and in particular snakes, are protected by national and international agreements yet are commonly handled illegally. To aid in the enforcement of such legislation, we report on the development of three 11-plex assays from the genome of the carpet python to type 24 loci of tetra-nucleotide and penta-nucleotide repeat motifs (pure, compound and complex included). The loci range in size between 70 and 550 bp. Seventeen of the loci are newly characterised with the inclusion of seven previously developed loci to facilitate cross-comparison with previous carpet python genotyping studies. Assays were optimised in accordance with human forensic profiling kits using one nanogram template DNA. Three loci are included in all three of the multiplex reactions as quality assurance markers, to ensure sample identity and genotyping accuracy is maintained across the three profiling assays. Allelic ladders have been developed for the three assays to ensure consistent and precise allele designation. A DNA reference database of allele frequencies is presented based on 249 samples collected from throughout the species native range. A small number of validation tests are conducted to demonstrate the utility of these multiplex assays. We suggest further appropriate validation tests that should be conducted prior to the application of the multiplex assays in criminal investigations involving carpet pythons. Copyright © 2018 Elsevier B.V. All rights reserved.

Lecithin-based novel cationic nanocarriers (LeciPlex) I: fabrication, characterization and evaluation.

PubMed

Date, Abhijit A; Srivastava, Deepika; Nagarsenker, Mangal S; Mulherkar, Rita; Panicker, Lata; Aswal, Vinod; Hassan, Puthusserickal A; Steiniger, Frank; Thamm, Jana; Fahr, Alfred

2011-10-01

In the present investigation, the feasibility of fabricating novel self-assembled cationic nanocarriers (LeciPlex) containing cetyltrimethylammonium bromide (CTAB) or didodecyldimethylammonium bromide (DDAB) and soybean lecithin using pharmaceutically acceptable biocompatible solvents such as 2-Pyrrolidone (Soluphor P) and diethyleneglycol monoethyl ether (Transcutol) was established. The interaction between DDAB/CTAB and soybean lecithin in the nanocarriers was confirmed by differential scanning calorimetry and in vitro antimicrobial studies. The positive charge on the nanocarriers was confirmed by zeta potential analysis. Transmission electron microscopy analysis could not reveal sufficient information regarding the internal structure of the nanocarriers, whereas cryotransmission electron microscopy studies indicated that these novel nanocarriers have unilamellar structure. Small-angle neutron scattering studies confirmed interaction of cationic surfactant (DDAB) and lecithin in the nanocarriers and confirmed the presence of unilamellar nanostructures. Various hydrophobic drugs could be encapsulated in the CTAB/DDAB-based lecithin nanocarriers (CTAB-LeciPlex or DDAB-LeciPlex) irrespective of their difference in log p-values. In vitro antimicrobial studies on triclosan-loaded LeciPlex confirmed entrapment of triclosan in the nanocarriers. The ability of CTAB-LeciPlex and DDAB-LeciPlex to condense plasmid DNA was established using agarose gel electrophoresis. DDAB-LeciPlex could successfully transfect pDNA in HEK-293 cells indicating potential in gene delivery.

Echinacea complex--chemical view and anti-asthmatic profile.

PubMed

Šutovská, Martina; Capek, Peter; Kazimierová, Ivana; Pappová, Lenka; Jošková, Marta; Matulová, Mária; Fraňová, Soňa; Pawlaczyk, Izabela; Gancarz, Roman

2015-12-04

Echinacea purpurea (L.) Moench is one of the mostly used herbs in the traditional medicine for the treatment of respiratory diseases. Modern interest in Echinacea is directed to its immunomodulatory activity. Recent studies have shown that secretion of asthma-related cytokines in the bronchial epithelial cells can be reversed by Echinacea preparations. To examine the pharmacodynamics profile of Echinacea active principles, a complex has been isolated from its flowers by alkaline extraction and has been tested using an animal model of allergic asthma. The structural features of Echinacea purpurea complex was determined using chemical and spectroscopic methods. Allergic inflammation of the airways was induced by repetitive exposure of guinea pigs to ovalbumin. Echinacea complex was then administered 14 days in 50mg/kg b.w. daily dose perorally. Bronchodilatory effect was verified as decrease in the specific airway resistance (sRaw) in vivo and by reduced contraction amplitude (mN) of tracheal and pulmonary smooth muscle to cumulative concentrations of acetylcholine and histamine in vitro. The impact on mucociliary clearance evaluated measurement of ciliary beat frequency (CBF) in vitro using LabVIEW™ Software. Anti-inflammatory effect of Echinacea complex was verified by changes in exhaled NO levels and by Bio-Plex® assay of Th2 cytokine concentrations (IL-4, IL-5, IL-13 and TNF-alpha) in serum and bronchoalveolar lavage fluid (BALF). Chemical and spectroscopic studies confirmed the presence of carbohydrates, phenolic compounds and proteins, as well as the dominance of rhamnogalacturonan and arabinogalactan moieties in Echinacea complex. The significant decrease in sRaw values and suppressed histamine and acetylcholine-induced contractile amplitude of isolated airways smooth muscle that were similar to effects of control drug salbutamol confirmed Echinacea complex bronchodilatory activity. The anti-inflammatory effect was comparable with that of control agent budesonide and was verified as significantly reduced exhaled NO levels and concentration of Th2 cytokines in serum and BALF. The values of CBF were changed only insignificantly on long-term administration of Echinacea complex suggested its minimal negative impact on mucociliary clearance. Pharmacodynamic studies have confirmed significant bronchodilatory and anti-inflammatory effects of Echinacea complex that was similar to effects of classic synthetic drugs. Thus, results provide a scientific basis for the application of this herb in traditional medicine as a supplementary treatment of allergic disorders of the airways, such as asthma. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Positive association between leptin serum levels and disease activity on endoscopy in inflammatory bowel disease: A case-control study

PubMed Central

Trejo-Vazquez, Fabiola; Garza-Veloz, Idalia; Villela-Ramirez, Gabriela Alejandra; Ortiz-Castro, Yolanda; Mauricio-Saucedo, Panfilo; Cardenas-Vargas, Edith; Diaz-Baez, Mariana; Cid-Baez, Miguel A.; Castañeda-Miranda, Rodrigo; Ortiz-Rodriguez, Jose Manuel; Solis-Sanchez, Luis Octavio; Martinez-Fierro, Margarita L.

2018-01-01

Inflammatory bowel disease (IBD) includes ulcerative colitis (UC), Crohn's disease (CD) and indeterminate colitis. As these subtypes of IBD display important differences in the behavior of the natural course of the disease, the identification of non-invasive markers for IBD is important. The aim of the present study was to evaluate the serum levels of 10 adipokines and their association with endoscopic activity in IBD. The 10-protein profile (C-peptide, ghrelin, gastric inhibitory polypeptide, glucagon-like peptide-1, glucagon, insulin, leptin, plasminogen activator inhibitor-1, resistin and visfatin) was evaluated using serum from 53 participants (23 UC and 11 CD patients, as well as 19 controls) from Zacatecas (Mexico) by using the Bio-Plex Pro Human Diabetes 10-Plex Panel (Bio-Rad Laboratories, Inc.). Compared with those in the controls, leptin levels were significantly lower in patients with IBD (P=4.9×10−4). In addition, serum leptin displayed differences between groups with and without disease activity on endoscopy (P<0.001). Among the study population, serum leptin levels of <5,494 pg/ml significantly increased the odds of IBD by 12.8-fold [odds ratio (OR)=12.8, 95% confidence interval (CI)=3.04–53.9, P=0.001]. In addition, patients with serum leptin levels of <2,498 pg/ml displayed 5.8-fold greater odds of disease activity on endoscopy among the study population (OR=5.8, 95% CI=1.52–22.4, P=0.013). No differences in the serum levels of the remaining proteins were identified between the groups. Among the study population, serum leptin was associated with an increased risk of IBD and with disease activity on endoscopy. Additional studies will be necessary to validate the use of leptin as a non-invasive biomarker of IBD severity. PMID:29545852

Habitability as a Tier One Criterion in Exploration Mission and Vehicle Design. Part 1; Habitability

NASA Technical Reports Server (NTRS)

Adams, Constance M.; McCurdy, Matthew Riegel

1999-01-01

Habitability and human factors are necessary criteria to include in the iterative process of Tier I mission design. Bringing these criteria in at the first, conceptual stage of design for exploration and other human-rated missions can greatly reduce mission development costs, raise the level of efficiency and viability, and improve the chances of success. In offering a rationale for this argument, the authors give an example of how the habitability expert can contribute to early mission and vehicle architecture by defining the formal implications of a habitable vehicle, assessing the viability of units already proposed for exploration missions on the basis of these criteria, and finally, by offering an optimal set of solutions for an example mission. In this, the first of three papers, we summarize the basic factors associated with habitability, delineate their formal implications for crew accommodations in a long-duration environment, and show examples of how these principles have been applied in two projects at NASA's Johnson Space Center: the BIO-Plex test facility, and TransHab.

Investigator® HDplex (Qiagen) reference population database for forensic use in Argentina.

PubMed

Martínez, Gustavo; Borosky, Alicia; Corach, Daniel; Llull, Cintia; Locarno, Laura; Lojo, Mercedes; Marino, Miguel; Miozzo, María Cecilia; Modesti, Nidia; Pacharoni, Carla; Pilili, Juan Pablo; Ramella, María Isabel; Sala, Andrea; Schaller, Cecilia; Vullo, Carlos; Toscanini, Ulises

2017-01-01

Currently, autosomal Short Tandem Repeat (STR) markers represent the method of election in forensic human identification. Commercial kits of most common use nowadays -e.g. PowerPlex ® Fusion, Promega Corp.; AmpFlSTR GlobalFiler, Thermofisher scientific; Investigator 24Plex QS,Qiagen-, allow the co-amplification of 23 highly polymorphic STR loci providing a high discrimination power in human identity testing. However, in complex kinship analysis and familial database searches involving distant relationships, additional DNA typing is often required in order to achieve well-founded conclusions. The recently developed kit Investigator ® HDplex (Qiagen) co-amplify twelve autosomal STRs markers (D7S1517, D3S1744, D12S391, D2S1360, D6S474, D4S2366, D8S1132, D5S2500, D18S51, D21S2055, D10S2325, SE33), nine of which are not present in the above mentioned kits, providing a set of efficient supplementary markers for human identification purposes. In this study we genotyped a sample of 980 individuals from urban areas of ten Argentinean provinces using the Investigator ® HDplex kit, aiming to provide forensic estimates for use in forensic casework and parentage testing in Argentina. We report reference allelic frequency databases for each of the provinces studied as well as for the combined samples. No deviation of Hardy-Weinberg equilibrium was observed. A reasonable discrimination capacity and power of exclusion was estimated which allowed predicting an acceptable forensic behavior of this kit, either to be used as the main STR panel for simple cases or as an auxiliary tool in complex cases. Additionally, population comparison tests showed that the studied samples are relatively homogeneous across the country for these STR set. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

IVIG Versus PLEX in the Treatment of Worsening Myasthenia Gravis: What is the Evidence?: A Critically Appraised Topic.

PubMed

Dhawan, Priya S; Goodman, Brent P; Harper, Charles M; Bosch, Peter E; Hoffman-Snyder, Charlene R; Wellik, Kay E; Wingerchuk, Dean M; Demaerschalk, Bart M

2015-05-01

Immune therapies such as intravenous immunoglobulin (IVIG) and plasma exchange (PLEX) are first line in the treatment of worsening myasthenia gravis. Although PLEX is favored in myasthenic crisis, IVIG is increasingly used in exacerbations due to cost and ease of administration. To review and critically assess current evidence on the effects of IVIG and PLEX on functional outcomes in patients with worsening myasthenia gravis. A structured critical appraisal was conducted on the objective topic. This included a creation of a structured question based on a clinical scenario, comprehensive literature search, selection of evidence for review, and critical appraisal of selected evidence. Evidence was summarized and commentary provided. Participants included consultant and resident neurologists, a medical librarian, clinical epidemiologists, and content experts in the field of neuromuscular neurology. A single-blinded, randomized-controlled trial that compared IVIG and PLEX in 84 patients with worsening myasthenia gravis was selected for review. Primary outcome measure was functional status at 14 days after treatment, as assessed by the Quantitative Myasthenia Gravis Score. Change in Quantitative Myasthenia Gravis Score at day 14 for all subjects was 4.0, without statistically significant differences between IVIG and PLEX groups. IVIG and PLEX are equally effective in worsening myasthenia gravis. Treatment decisions may depend on several variables, including presence of respiratory distress, medical comorbidities, access to medication, and cost. PLEX will likely remain the treatment of choice in true myasthenic crisis.

[Consistency study of PowerPlex 21 kit and Goldeneye 20A kit and forensic application].

PubMed

Ren, He; Liu, Ying; Zhang, Qing-Xia; Jiao, Zhang-Ping

2014-06-01

To ensure the consistency of genotype results for PowerPlex 21 kit and Goldeneye 20A kit. The STR loci were amplified in DNA samples from 205 unrelated individuals in Beijing Han population. And consistency of 19 overlap STR loci typing were observed. The genetic polymorphism of D1S1656 locus was obtained. All 19 overlap loci typing showed consistent. The proportion of peak height of heterozygous loci in two kits showed no statistical difference (P > 0.05). The observed heterozygosis of D1S1656 was 0.878. The discrimination power was 0.949. The excluding probability of paternity of triplet was 0.751. The excluding probability of paternity of diploid was 0.506. The polymorphism information content was 0.810. PowerPlex 21 kit and Goldeneye 20A kit present a good consistency. The primer design is reasonable. The polymorphism of D1S1656 is good. The two kits can be used for human genetic analysis, paternity test, and individual identification in forensic practice.

Constructing STR multiplexes for individual identification of Hungarian red deer.

PubMed

Szabolcsi, Zoltan; Egyed, Balazs; Zenke, Petra; Padar, Zsolt; Borsy, Adrienn; Steger, Viktor; Pasztor, Erzsebet; Csanyi, Sandor; Buzas, Zsuzsanna; Orosz, Laszlo

2014-07-01

Red deer is the most valuable game of the fauna in Hungary, and there is a strong need for genetic identification of individuals. For this purpose, 10 tetranucleotide STR markers were developed and amplified in two 5-plex systems. The study presented here includes the flanking region sequence analysis and the allele nomenclature of the 10 loci as well as the PCR optimization of the DeerPlex I and II. LD pairwise tests and cross-species similarity analyses showed the 10 loci to be independently inherited. Considerable levels of genetic differences between two subpopulations were recorded, and F(ST) was 0.034 using AMOVA. The average probability of identity (PI(ave)) was at the value of 2.6736 × 10(-15). This low value for PI(ave) nearly eliminates false identification. An illegal hunting case solved by DeerPlex is described herein. The calculated likelihood ratio (LR) illustrates the potential of the 10 red deer microsatellite markers for forensic investigations. © 2014 American Academy of Forensic Sciences.

The Role of Habitability Studies in Space Facility and Vehicle Design

NASA Technical Reports Server (NTRS)

Adams, Constance M.

1999-01-01

This document is a viewgraph presentation which reviews the role of the space architect in designing a space vehicle with habitability as a chief concern. Habitability is composed of the qualities of the environment or system which support the crew in working and living. All the impacts from habitability are interdependent; i.e., impacts to well-being can impact performance, safety or efficiency. After reviewing the issues relating to habitability the presentation discusses the application of these issues in two case studies. The first studies the Bio-Plex Hab chamber which includes designs of the living and working areas. The second case study is the ISS-TransHab which is being studied as a prototype for Mars transit.

Eurasiaplex: a forensic SNP assay for differentiating European and South Asian ancestries.

PubMed

Phillips, C; Freire Aradas, A; Kriegel, A K; Fondevila, M; Bulbul, O; Santos, C; Serrulla Rech, F; Perez Carceles, M D; Carracedo, Á; Schneider, P M; Lareu, M V

2013-05-01

We have selected a set of single nucleotide polymorphisms (SNPs) with the specific aim of differentiating European and South Asian ancestries. The SNPs were combined into a 23-plex SNaPshot primer extension assay: Eurasiaplex, designed to complement an existing 34-plex forensic ancestry test with both marker sets occupying well-spaced genomic positions, enabling their combination as single profile submissions to the Bayesian Snipper forensic ancestry inference system. We analyzed the ability of Eurasiaplex plus 34plex SNPs to assign ancestry to a total 1648 profiles from 16 European, 7 Middle East, 13 Central-South Asian and 21 East Asian populations. Ancestry assignment likelihoods were estimated from Snipper using training sets of five-group data (three Eurasian groups, East Asian and African genotypes) and four-group data (Middle East genotypes removed). Five-group differentiations gave assignment success of 91% for NW European populations, 72% for Middle East populations and 39% for Central-South Asian populations, indicating Middle East individuals are not reliably differentiated from either Europeans or Central-South Asians. Four-group differentiations provided markedly improved assignment success rates of 97% for most continental Europeans tested (excluding Turkish and Adygei at the far eastern edge of Europe) and 95% for Central-South Asians, despite applying a probability threshold for the highest likelihood ratio above '100 times more likely'. As part of the assessment of the sensitivity of Eurasiaplex to analyze challenging forensic material we detail Eurasiaplex and 34-plex SNP typing to infer ancestry of a cranium recovered from the sea, achieving 82% SNP genotype completeness. Therefore, Eurasiaplex provides an informative and forensically robust approach to the differentiation of European and South Asian ancestries amongst Eurasian populations. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Electron Paramagnetic Resonance Spectroscopy of Vanadium (IV) Complexes and Related Species.

DTIC Science & Technology

1980-07-27

Extensive near infrared (4000-650cm " ) investigations on VOCl 2 complexes have been made by many workers [21,39,43-49]. However the far infrared ...to facilitate the assignment of cation and ligand bacds. 4.2.1.2 Near Infrared Spectroscopy There are three principal reasons for measuriiio the... near infrared spectra of the co!;,plexes: (a) To establish the purity of the complex (b) To establish the bondi ng mode of the 1 i ( nd (c) To establish

[Efficiency of 27-plex single nucleotide polymorphism multiplex system for ancestry inference in different populations].

PubMed

Feng, Xing-Ling; Sun, Qi-Fan; Liu, Hong; Wei, Yi-Liang; DU, Wei-An; Li, Cai-Xia; Chen, Ling; Liu, Chao

2016-04-20

To validate the efficiency of 27-plex single nucleotide polymorphism (SNP) multiplex system for ancestry inference. The 27-plex SNP system was validated for its sensitivity and species specificity. A total of 533 samples were collected from African, Southern Chinese Han, China's ethic minorities (Yi, Hui, Miao, Tibet, and Uygur), European, Central Asian, Western Asian, Southern Asian, Southeast Asian and South American populations for clustering analysis of the genotypes by citing 3 representative continental ancestral groups [East Asia (CHB), Europe (CEU), and Africa (YRI)] from HapMap database. The system sensitivity is 0.125 ng. Twenty and six genotypes were detected in chimpanzee and monkeys, respectively. Except in rs10496971, no more products were found in other animals. The system was capable of differentiating intercontinental populations but not of distinguishing between East Asian and Southeast Asian population or between Southern Chinese Han population and Chinese Ethnic populations (Hui, Miao, Yi and Tibet). This system achieved a 100% accuracy for intercontinental population source inference for 46 blind test samples. 27-plex SNPs multiplex system has a high sensitivity and species specificity and can correctly differentiate the ancestry origins of individuals from African, European and East Asian for criminal case investigation. But this system is not capable of distinguishing subpopulation groups and more specific ancestry-informative markers are needed to improve its recognition of Southeast Asian and Chinese ethnic populations.

High-Resolution Enabled 12-Plex DiLeu Isobaric Tags for Quantitative Proteomics

PubMed Central

2015-01-01

Multiplex isobaric tags (e.g., tandem mass tags (TMT) and isobaric tags for relative and absolute quantification (iTRAQ)) are a valuable tool for high-throughput mass spectrometry based quantitative proteomics. We have developed our own multiplex isobaric tags, DiLeu, that feature quantitative performance on par with commercial offerings but can be readily synthesized in-house as a cost-effective alternative. In this work, we achieve a 3-fold increase in the multiplexing capacity of the DiLeu reagent without increasing structural complexity by exploiting mass defects that arise from selective incorporation of 13C, 15N, and 2H stable isotopes in the reporter group. The inclusion of eight new reporter isotopologues that differ in mass from the existing four reporters by intervals of 6 mDa yields a 12-plex isobaric set that preserves the synthetic simplicity and quantitative performance of the original implementation. We show that the new reporter variants can be baseline-resolved in high-resolution higher-energy C-trap dissociation (HCD) spectra, and we demonstrate accurate 12-plex quantitation of a DiLeu-labeled Saccharomyces cerevisiae lysate digest via high-resolution nano liquid chromatography–tandem mass spectrometry (nanoLC–MS2) analysis on an Orbitrap Elite mass spectrometer. PMID:25405479

Hi-Plex for Simple, Accurate, and Cost-Effective Amplicon-based Targeted DNA Sequencing.

PubMed

Pope, Bernard J; Hammet, Fleur; Nguyen-Dumont, Tu; Park, Daniel J

2018-01-01

Hi-Plex is a suite of methods to enable simple, accurate, and cost-effective highly multiplex PCR-based targeted sequencing (Nguyen-Dumont et al., Biotechniques 58:33-36, 2015). At its core is the principle of using gene-specific primers (GSPs) to "seed" (or target) the reaction and universal primers to "drive" the majority of the reaction. In this manner, effects on amplification efficiencies across the target amplicons can, to a large extent, be restricted to early seeding cycles. Product sizes are defined within a relatively narrow range to enable high-specificity size selection, replication uniformity across target sites (including in the context of fragmented input DNA such as that derived from fixed tumor specimens (Nguyen-Dumont et al., Biotechniques 55:69-74, 2013; Nguyen-Dumont et al., Anal Biochem 470:48-51, 2015), and application of high-specificity genetic variant calling algorithms (Pope et al., Source Code Biol Med 9:3, 2014; Park et al., BMC Bioinformatics 17:165, 2016). Hi-Plex offers a streamlined workflow that is suitable for testing large numbers of specimens without the need for automation.

Developmental validation of the PowerPlex(®) Fusion System for analysis of casework and reference samples: A 24-locus multiplex for new database standards.

PubMed

Oostdik, Kathryn; Lenz, Kristy; Nye, Jeffrey; Schelling, Kristin; Yet, Donald; Bruski, Scott; Strong, Joshua; Buchanan, Clint; Sutton, Joel; Linner, Jessica; Frazier, Nicole; Young, Hays; Matthies, Learden; Sage, Amber; Hahn, Jeff; Wells, Regina; Williams, Natasha; Price, Monica; Koehler, Jody; Staples, Melisa; Swango, Katie L; Hill, Carolyn; Oyerly, Karen; Duke, Wendy; Katzilierakis, Lesley; Ensenberger, Martin G; Bourdeau, Jeanne M; Sprecher, Cynthia J; Krenke, Benjamin; Storts, Douglas R

2014-09-01

The original CODIS database based on 13 core STR loci has been overwhelmingly successful for matching suspects with evidence. Yet there remain situations that argue for inclusion of more loci and increased discrimination. The PowerPlex(®) Fusion System allows simultaneous amplification of the following loci: Amelogenin, D3S1358, D1S1656, D2S441, D10S1248, D13S317, Penta E, D16S539, D18S51, D2S1338, CSF1PO, Penta D, TH01, vWA, D21S11, D7S820, D5S818, TPOX, DYS391, D8S1179, D12S391, D19S433, FGA, and D22S1045. The comprehensive list of loci amplified by the system generates a profile compatible with databases based on either the expanded CODIS or European Standard Set (ESS) requirements. Developmental validation testing followed SWGDAM guidelines and demonstrated the quality and robustness of the PowerPlex(®) Fusion System across a number of variables. Consistent and high-quality results were compiled using data from 12 separate forensic and research laboratories. The results verify that the PowerPlex(®) Fusion System is a robust and reliable STR-typing multiplex suitable for human identification. Copyright © 2014 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

The minimal cost of life in space.

PubMed

Drysdale, A E; Rutkze, C J; Albright, L D; LaDue, R L

2004-01-01

The cost of keeping people alive in space is assessed from a theoretical viewpoint and using two actual designs for plant growth systems. While life support is theoretically not very demanding, our ability to implement life support is well below theoretical limits. A theoretical limit has been calculated from requirements and the state of the art for plant growth has been calculated using data from the BIO-Plex PDR and from the Cornell CEA prototype system. The very low efficiency of our current approaches results in a high mission impact, though we can still see how to get a significant reduction in cost of food when compared to supplying it from Earth. Seeing the distribution of costs should allow us to improve our current designs. c2004 COSPAR. Published by Elsevier Ltd. All rights reserved.

The minimal cost of life in space

NASA Technical Reports Server (NTRS)

Drysdale, A. E.; Rutkze, C. J.; Albright, L. D.; LaDue, R. L.

2004-01-01

The cost of keeping people alive in space is assessed from a theoretical viewpoint and using two actual designs for plant growth systems. While life support is theoretically not very demanding, our ability to implement life support is well below theoretical limits. A theoretical limit has been calculated from requirements and the state of the art for plant growth has been calculated using data from the BIO-Plex PDR and from the Cornell CEA prototype system. The very low efficiency of our current approaches results in a high mission impact, though we can still see how to get a significant reduction in cost of food when compared to supplying it from Earth. Seeing the distribution of costs should allow us to improve our current designs. c2004 COSPAR. Published by Elsevier Ltd. All rights reserved.

Needle echogenicity in ultrasound-guided lumbar spine injections: a cadaveric study.

PubMed

Gofeld, Michael; Krashin, Daniel L; Ahn, Sangmin

2013-01-01

Echogenicity of regional anesthesia needles has been tested on different preclinical models; however, previous studies were done in an ideal experimental setting utilizing high-frequency insonation and superficially located targets. Because steep-angle deep injections are typically required for spinal and other chronic pain procedures, and low-frequency transducers are used, further feasibility study is warranted. To determine effectiveness of steep-angle deep injections, typically required for spinal and other chronic pain procedures. Experimental laboratory study. Willed Body Program, University of Washington. In-plane lumbar spine procedures with 50° and 70° angles were performed on a human cadaver. The images and video clips of a non-echogenic (Quincke-type) and echogenic (SonoPlex, StimuQuick, and EchoStim) needle placements were presented to 3 blinded assessors who rated the needle visibility on a 4-point scale. The data was statistically analyzed to determine the differences in visibility between the needles with and without the digital image enhancement, and to compare the video clips to captured images. ANOVA analysis demonstrated that overall SonoPlex was significantly better (P = 0.02) than other needles. SonoPlex maintained its superiority in the subset of facet joint injections (P = 0.02), followed by Quincke-type, then the StimuQuik, and EchoStim needles. In deep procedures, EchoStim was comparable with SonoPlex (P = 0.03), and they both were better than the other 2 needles. The enhanced images received higher rates, with a 0.6 point mean improved rating (P = 0). This study is limited by choice of needles, number of experiments performed, and potential postmortem changes of echogenicity. The SonoPlex needle appeared to have better echogenicity in this study. While non-echogenic Quincke-type needle visibility was adequate in superficial placements, it was limited in deep injections. An imaging enhancement is effective in improving needle visibility and should be used whenever possible.

Bio-nano interactions detected by nanochannel electrophoresis.

PubMed

Luan, Binquan

2016-08-01

Engineered nanoparticles have been widely used in industry and are present in many consumer products. However, their bio-safeties especially in a long term are largely unknown. Here, a nanochannel-electrophoresis-based method is proposed for detecting the potential bio-nano interactions that may further lead to damages to human health and/or biological environment. Through proof-of-concept molecular dynamics simulations, it was demonstrated that the transport of a protein-nanoparticle complex is very different from that of a protein along. By monitoring the change of ionic currents induced by a transported analyte as well as the transport velocities of the analyte, the complex (with bio-nano interaction) can be clearly distinguished from the protein alone (with no interaction with tested nanoparticles). © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Clinical Sensitivity of Cystic Fibrosis Mutation Panels in a Diverse Population.

PubMed

Hughes, Erin E; Stevens, Colleen F; Saavedra-Matiz, Carlos A; Tavakoli, Norma P; Krein, Lea M; Parker, April; Zhang, Zhen; Maloney, Breanne; Vogel, Beth; DeCelie-Germana, Joan; Kier, Catherine; Anbar, Ran D; Berdella, Maria N; Comber, Paul G; Dozor, Allen J; Goetz, Danielle M; Guida, Louis; Kattan, Meyer; Ting, Andrew; Voter, Karen Z; van Roey, Patrick; Caggana, Michele; Kay, Denise M

2016-02-01

Infants are screened for cystic fibrosis (CF) in New York State (NYS) using an IRT-DNA algorithm. The purpose of this study was to validate and assess clinical validity of the US FDA-cleared Illumina MiSeqDx CF 139-Variant Assay (139-VA) in the diverse NYS CF population. The study included 439 infants with CF identified via newborn screening (NBS) from 2002 to 2012. All had been screened using the Abbott Molecular CF Genotyping Assay or the Hologic InPlex CF Molecular Test. All with CF and zero or one mutation were tested using the 139-VA. DNA extracted from dried blood spots was reliably and accurately genotyped using the 139-VA. Sixty-three additional mutations were identified. Clinical sensitivity of three panels ranged from 76.2% (23 mutations recommended for screening by ACMG/ACOG) to 79.7% (current NYS 39-mutation InPlex panel), up to 86.0% for the 139-VA. For all, sensitivity was highest in Whites and lowest in the Black population. Although the sample size was small, there was a nearly 20% increase in sensitivity for the Black CF population using the 139-VA (68.2%) over the ACMG/ACOG and InPlex panels (both 50.0%). Overall, the 139-VA is more sensitive than other commercially available panels, and could be considered for NBS, clinical, or research laboratories conducting CF screening. © 2015 WILEY PERIODICALS, INC.

A silent allele in the locus D5S818 contained within the PowerPlex®21 PCR Amplification Kit.

PubMed

Chen, Ling; Tai, Yunchun; Qiu, Pingming; Du, Weian; Liu, Chao

2015-11-01

Three paternity tests cases were found with a single locus mismatch at the locus D5S818 with PowerPlex®21 PCR Amplification Kit (Promega). Forward and reverse primers were redesigned to type the samples again and to evaluate if there were alleles dropped out. The results showed the existence of a silent allele 12 in all the three families, due to a point mutation that changed cytosine to adenine at 90 nucleotides upstream from the 5' end of the AGAT repeat sequences in all the six individuals. A single locus mismatch due to a silent allele may occur in any locus using any kit. Therefore, we recommend using multiple kits to confirm the results in paternity testing cases with mismatches, especially when there is a single locus mismatch with homozygote involved. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Establishment of a 10-Plex Quantitative Fluorescent-PCR Assay for Rapid Diagnosis of Sex Chromosome Aneuploidies

PubMed Central

Xie, Xingmei; Liang, Qiaoyi

2014-01-01

Sex chromosome aneuploidies occur commonly in the general population, with an incidence of 1 in 400 newborns. However, no tests specifically targeting sex chromosomes have been carried out in prenatal diagnosis or newborn screening, resulting in late recognition of these diseases. In this study, a rapid diagnostic method for sex chromosome aneuploidies was established using Quantitative Fluorescent-PCR (QF-PCR). Ten markers were included in one multiplex QF-PCR assay, including two sex determination genes (AMXY and SRY), five X-linked short tandem repeats (STRs; DXS1053, DXS981, DXS6809, DXS1187, and DXS8377), one X/Y-common STR (X22), and two autosomal STRs (D13S305 and D21S11). Retrospective tests of 70 cases with known cytogenetic results indicated that the 10-plex QF-PCR assay could well determine sex chromosome copy numbers by both allelic peak numbers and a sex chromosome dosage calculation with the autosomal STRs as internal controls. Prospective comparison with cytogenetic karyotyping on 534 cases confirmed that the 10-plex QF-PCR assay could be well employed for sex chromosome aneuploidy diagnosis in at least the Chinese Han population. This is the first QF-PCR test for the diagnosis of sex chromosome aneuploidies in the Chinese population. This test is superior to previous designs by including up to 8 sex-linked markers covering different parts of sex chromosomes as well as employing internal controls for copy number dosage calculation in a single PCR reaction. Due to simple technique and data analysis, as well as easy implementation within routine clinical services, this method is of great clinical application value and could be widely applied. PMID:25207978

Research Topics on Cluttered Environments Interrogation and Propagation

DTIC Science & Technology

2014-11-04

propagation in random and complex media and looked at specific applications associated with imaging and communication through a cluttered medium...imaging and communication schemes. We have used the results on the fourth moment to analyze wavefront correction schemes and obtained novel...and com- plex media and looked at specific applications associated with imaging and communication through a cluttered medium. The main new

Human Information Processing in the Dynamic Environment (HIPDE)

DTIC Science & Technology

2008-01-01

Albery, 1990) and image mental rotation/orientation (Nethus, et al., 1993). However, because SD typically occurs at low G levels, there is little...cuity C om plex D ecision M aking A ccuracy C om plex D ecision M aking R T C om plex D ecision M aking E fficiency Tracking S low M...cerebral tissue frequently continues to persist even at relatively low Gz levels (including accelerations as low as 3 Gz) during long, multiple peak

Simulating Surface Oil Transport During the Deepwater Horizon Oil Spill: Experiments with the BioCast System

DTIC Science & Technology

2014-01-25

Virtual Special Issue Gulf of Mexico Modelling – Lessons from the spill Simulating surface oil transport during the Deepwater Horizon oil spill ...ocean surface materials. The Deepwater Horizon oil spill in the Gulf of Mexico provided a test case for the Bio-Optical Forecasting (BioCast) system...addition of explicit sources and sinks of surface oil concentrations provides a framework for increasingly complex oil spill modeling efforts that extend

SSC San Diego Biennial Review 2003. Command and Control

DTIC Science & Technology

2003-01-01

systems. IMAT systems use scientific visualizations, three- dimensional graphics, and animations to illustrate com- plex physical interactions in mission...Again, interactive animations are used to explain underlying concepts. For exam- ple, for principles of beamforming using a phased array, a three...solve complex problems. Experts type natural language text, use mouse clicks to provide hints for explanation generation, and use mouse clicks to

JPLEX: Java Simplex Implementation with Branch-and-Bound Search for Automated Test Assembly

ERIC Educational Resources Information Center

Park, Ryoungsun; Kim, Jiseon; Dodd, Barbara G.; Chung, Hyewon

2011-01-01

JPLEX, short for Java simPLEX, is an automated test assembly (ATA) program. It is a mixed integer linear programming (MILP) solver written in Java. It reads in a configuration file, solves the minimization problem, and produces an output file for postprocessing. It implements the simplex algorithm to create a fully relaxed solution and…

Complex Impedance, DSC and Lithium-7 NMR Studies of Poly(propylene oxide) Complexed with LiN(SO2CF3)2 and with LiAsF6

DTIC Science & Technology

1994-01-01

re- plexes. This feature is commonly observed when the moved by room temperature evaporation under par- heating rate is different from previous cooling...It is apparent from fig. 1 that some shallow teflon dishes. Prior to use, the acetonitrile overshoot (an apparent endotherm ) is observed just was...or tial vacuum ( - 20 mm) and the final preparation heating rates that the material has experienced. Con- step consisted of heating the samples to

Periodontal ligament versus bone marrow mesenchymal stem cells in combination with Bio-Oss scaffolds for ectopic and in situ bone formation: A comparative study in the rat.

PubMed

Yu, Bo-Han; Zhou, Qian; Wang, Zuo-Lin

2014-08-01

The aim of this study was to compare the osteogenic effects of periodontal ligament stem cells (PDLSCs) versus bone marrow mesenchymal stem cells (BMMSCs) in combination with Bio-Oss scaffolds on subcutaneous and critical-size defects in the immunodeficient rat calvarium. PDLSCs and BMMSCs were obtained from the same canine donor. Twenty-four rats were randomly assigned to one of four experimental groups (n = 6 each): group A (no-graft negative control), group B (Bio-Oss positive control), group C (BMMSC/Bio-Oss test group), and group D (PDLSC/Bio-Oss test group). Eight weeks post-transplantation, ectopic and in situ bone regeneration was evaluated by micro-computed tomography (µ-CT), histology, histomorphometry, and immunohistochemistry. The stem cell/Bio-Oss constructs were significantly superior to the controls in terms of their ability to promote osteogenesis (p < 0.01), while the PDLSC/Bio-Oss construct tended to be superior to the BMMSC/Bio-Oss construct. Thus, engineered stem cell/Bio-Oss complexes can successfully reconstruct critical-size defects in rats, and PDLSCs and BMMSCs are both suitable as seed cells. © The Author(s) 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

Broad-Range Direct Detection and Identification of Fungi by Use of the PLEX-ID PCR-Electrospray Ionization Mass Spectrometry (ESI-MS) System

PubMed Central

Simner, Patricia J.; Uhl, James R.; Hall, Leslie; Weber, Michelle M.; Walchak, Robert C.; Buckwalter, Seanne

2013-01-01

The PLEX-ID system is a novel technology that couples PCR amplification and electrospray ionization-mass spectrometry to identify pathogens directly in clinical specimens. The analytical performance of the PLEX-ID Broad Fungal assay was compared with that of traditional culture identification by using 91 characterized fungal culture isolates (64 manufacturer-claimed and 27 nonclaimed organisms) and directly by using 395 respiratory specimens. Discordant results were resolved by D2 large-subunit ribosomal DNA fungal sequencing. Environmental studies were performed to monitor for potential contamination. The PLEX-ID Broad Fungal assay correctly identified 95.6% (87/91) and 81.3% (74/91) of the culture isolates to the genus and species levels, respectively. Of the manufacturer-claimed organisms, 100% (64/64) and 92.2% (59/64) were correctly identified to the genus and species levels, respectively. Direct analysis of respiratory specimens resulted in 67.6% (267/395) and 66.6% (263/395) agreement with culture results to the genus and species levels, respectively, with 16.2% (64/395) of the results discordant with culture and 16.2% (64/395) not detected by the system. The majority (>95%) of the isolates not detected directly by the PLEX-ID system ultimately grew in low quantities in culture (≤20 colonies). In 20.3% (35/172) of the respiratory specimens where no growth was observed in culture, the PLEX-ID system identified a fungus, suggesting a potential increase in sensitivity over culture in some instances. The PLEX-ID system provides a rapid method for the detection of a broad array of fungi directly in respiratory specimens and has the potential of impacting turnaround times and patient care by reducing the need to wait for the growth of an organism in culture. PMID:23515540

Post-injection hybridization of complementary DNA strands on capillary electrophoresis platforms: a novel solution for dsDNA artifacts.

PubMed

McLaren, Robert S; Ensenberger, Martin G; Budowle, Bruce; Rabbach, Dawn; Fulmer, Patricia M; Sprecher, Cindy J; Bessetti, Joseph; Sundquist, Terri M; Storts, Douglas R

2008-09-01

Several laboratories have reported the occurrence of a split or n-1 peak at the vWA locus in PowerPlex 16 and PowerPlex ES amplification products separated on 4- and 16-capillary electrophoresis instruments. The root cause of this artifact is post-PCR reannealing of the unlabeled, unincorporated vWA primer to the 3'-end of the tetramethylrhodamine (TMR)-labeled strand of the vWA amplicon. This reannealing occurs in the capillary post-electrokinetic injection. The split peak is eliminated by incorporation into the loading cocktail of a sacrificial hybridization sequence (SHS) oligonucleotide that is complementary to the vWA primer. The SHS preferentially anneals to the primer instead of the TMR-labeled strand of the vWA amplicon. In addition, the n-10/n-18 artifact that may be seen at the vWA locus was determined to be due to double-stranded amplicon formed post-electrokinetic injection into the capillary. This was also eliminated by adding in two Complementary Oligo Targets (COT1 and COT2) in addition to the SHS oligonucleotide into the loading cocktail. These three oligonucleotides are complementary to the 33 bases at the 5'-end of the unlabeled vWA amplicon strand and the 60 bases at its 3'-end and therefore compete for hybridization to the TMR-labeled amplicon strand. Incorporation of these three oligonucleotides in the Internal Lane Standard 600 (ILS600) eliminate both the split peak and n-10/n-18 artifact in PowerPlex 16 and PowerPlex ES amplification products without affecting sizing of alleles at the vWA locus or any locus in the PowerPlex 16, PowerPlex Y, PowerPlex ES, AmpFlSTR Profiler Plus ID, AmpFlSTR Cofiler, and AmpFlSTR SGM Plus kits.

Comparative effects between electronic and cigarette smoke in human keratinocytes and epithelial lung cells.

PubMed

Cervellati, F; Muresan, X M; Sticozzi, C; Gambari, R; Montagner, G; Forman, H J; Torricelli, C; Maioli, E; Valacchi, G

2014-08-01

Information about the harmful effects of vaping is sparse and inconsistent, therefore, since the use of electronic cigarettes (e-CIGs) has become increasingly popular as a tool to limit tobacco smoking, it is urgent to establish the toxicity of the commercial e-CIGs. Skin (HaCaT) and lung (A549) cells, the main targets of cigarette smoke (CS), were exposed to e-CIG vapor and CS using an in vitro system. The cytotoxic effect of the exposure was analyzed in both cell types by ultrastructural morphology, Trypan Blue exclusion test and LDH assay. In addition, pro-inflammatory cytokines were measured by the Bio-Plex assay. The cytotoxic components of e-CIG were restrained to the flavoring compound and, to a lesser extent, to nicotine although their effects were less harmful to that of CS. Humectants alone exhibited no cytotoxicity but induced the release of cytokines and pro-inflammatory mediators. Based on our results, we can state that exposure to e-CIG vapors results in far less toxic than exposure to CS. In fact, besides the deleterious effect of flavor and nicotine, even the humectants alone are able to evocate cytokines release. This study will hopefully promote the development of safer e-CIGs to help people quit smoking. Copyright © 2014 Elsevier Ltd. All rights reserved.

Supercolor coding methods for large-scale multiplexing of biochemical assays.

PubMed

Rajagopal, Aditya; Scherer, Axel; Homyk, Andrew; Kartalov, Emil

2013-08-20

We present a novel method for the encoding and decoding of multiplexed biochemical assays. The method enables a theoretically unlimited number of independent targets to be detected and uniquely identified in any combination in the same sample. For example, the method offers easy access to 12-plex and larger PCR assays, as contrasted to the current 4-plex assays. This advancement would allow for large panels of tests to be run simultaneously in the same sample, saving reagents, time, consumables, and manual labor, while also avoiding the traditional loss of sensitivity due to sample aliquoting. Thus, the presented method is a major technological breakthrough with far-reaching impact on biotechnology, biomedical science, and clinical diagnostics. Herein, we present the mathematical theory behind the method as well as its experimental proof of principle using Taqman PCR on sequences specific to infectious diseases.

Collection and Testing of Respiratory Samples

ClinicalTrials.gov

2017-04-03

QIAGEN ResPlex II Advanced Panel; Influenza A; Respiratory Syncytial Virus Infections; Infection Due to Human Parainfluenza Virus 1; Parainfluenza Type 2; Parainfluenza Type 3; Parainfluenza Type 4; Human Metapneumovirus A/B; Rhinovirus; Coxsackie Virus/Echovirus; Adenovirus Types B/C/E; Coronavirus Subtypes 229E; Coronavirus Subtype NL63; Coronavirus Subtype OC43; Coronavirus Subtype HKU1; Human Bocavirus; Artus Influenza A/B RT-PCR Test; Influenza B

Quantitative, multiplexed workflow for deep analysis of human blood plasma and biomarker discovery by mass spectrometry.

PubMed

Keshishian, Hasmik; Burgess, Michael W; Specht, Harrison; Wallace, Luke; Clauser, Karl R; Gillette, Michael A; Carr, Steven A

2017-08-01

Proteomic characterization of blood plasma is of central importance to clinical proteomics and particularly to biomarker discovery studies. The vast dynamic range and high complexity of the plasma proteome have, however, proven to be serious challenges and have often led to unacceptable tradeoffs between depth of coverage and sample throughput. We present an optimized sample-processing pipeline for analysis of the human plasma proteome that provides greatly increased depth of detection, improved quantitative precision and much higher sample analysis throughput as compared with prior methods. The process includes abundant protein depletion, isobaric labeling at the peptide level for multiplexed relative quantification and ultra-high-performance liquid chromatography coupled to accurate-mass, high-resolution tandem mass spectrometry analysis of peptides fractionated off-line by basic pH reversed-phase (bRP) chromatography. The overall reproducibility of the process, including immunoaffinity depletion, is high, with a process replicate coefficient of variation (CV) of <12%. Using isobaric tags for relative and absolute quantitation (iTRAQ) 4-plex, >4,500 proteins are detected and quantified per patient sample on average, with two or more peptides per protein and starting from as little as 200 μl of plasma. The approach can be multiplexed up to 10-plex using tandem mass tags (TMT) reagents, further increasing throughput, albeit with some decrease in the number of proteins quantified. In addition, we provide a rapid protocol for analysis of nonfractionated depleted plasma samples analyzed in 10-plex. This provides ∼600 quantified proteins for each of the ten samples in ∼5 h of instrument time.

EPA Recommends Modifications to Part of Industri-plex Superfund Cleanup in Woburn, Mass.

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) proposes recommended modifications to part of the cleanup of the Industri-plex Superfund Site in Woburn, Mass. Beginning today (May 3, 2018), there will be a 14-day public comment period on EPA’s proposal.

Bioregenerative life support: not a picnic

NASA Technical Reports Server (NTRS)

Knott, W. M.

1998-01-01

If humans are to live permanently in space, regenerative life support systems are an enabling technology and must replace the picnic approach of taking all supplies required for each mission. These systems are classified by technologies as either physical/chemical or bioregenerative. Both of these system-types can recycle water, remove carbon dioxide, produce oxygen, and recover essential elements from waste products. Bioregenerative can also produce food, thus, making it essential if humans are to exist in space independent of earth. A solely bioregenerative life support system includes plants as a biomass production module and microbial organisms in bioreactors as a resource recovery module. In the Advanced Life Support Program, bioregenerative life support systems are being investigated through a research and technology development project which includes large scale testing as part of the Breadboard Project and human tests conducted in the soon to be constructed BioPlex facility. Research and technology development efforts are directed toward optimizing biomass productivity in controlled chambers by developing light weight, energy efficient, and automated systems; recycling liquid and solid wastes; baselining the operation of bioreactors; determining system microbial stability; assessing chemical contamination; and building models required for long term system operations. The program will include space flight studies in the near future to determine if these life support technologies will function in microgravity. When a bioregenerative system is finally incorporated into a mission, the conversion from a picnic and resupply mentality to permanent recycling and independence from earth will be complete.

Development of a High Throughput Assay for Rapid and Accurate 10-Plex Detection of Citrus Pathogens

USDA-ARS?s Scientific Manuscript database

The need to reliably detect and identify multiple plant pathogens simultaneously, especially in woody perennial hosts, has led to development of new molecular diagnostic approaches. In this study, a Luminex-based system was developed that provided a robust and sensitive test for simultaneous detect...

Development of a novel hexa-plex PCR method for identification and serotyping of Salmonella species.

PubMed

Li, Ruichao; Wang, Yang; Shen, Jianzhong; Wu, Congming

2014-01-01

Salmonella is one of the most important foodborne pathogens, which causes a huge economic burden worldwide. To detect Salmonella rapidly is very meaningful in preventing salmonellosis and decreasing economic losses. Currently, isolation of Salmonella is confirmed by biochemical and serobased serotyping methods, which are time consuming, labor intensive, and complicated. To solve this problem, a hexa-plex polymerase chain reaction (PCR) method was developed using comparative genomics analysis and multiplex PCR technology to detect Salmonella and Salmonella Typhimurium, Salmonella Enteritidis, Salmonella Agona, Salmonella Choleraesuis, and Salmonella Pullorum simultaneously. The accuracy of this method was tested by a collection of 142 Salmonella. Furthermore, the strategy described in this article to mine serovar-specific fragments for Salmonella could be used to find specific fragments for other Salmonella serotypes and bacteria. The combination of this strategy and multiplex PCR is promising in the rapid identification of foodborne pathogens.

Population genetic data of the AmpFℓSTR® Identifiler® Plus and PowerPlex® 16 HS STR loci in four Canadian populations.

PubMed

Laurin, Nancy; Milot, Emmanuel

2014-03-01

Allele frequencies and forensically relevant population statistics were estimated for the short tandem repeat (STR) loci of the AmpFℓSTR® Identifiler® Plus and PowerPlex® 16 HS amplification kits, including D2S1338, D19S433, Penta D, and Penta E, for three First Nations Aboriginal populations and for Caucasians in Canada. The cumulative power of discrimination was ≥ 0.999999999999984 and the cumulative power of exclusion was ≥ 0.999929363 for both amplification systems in all populations. No significant departure from Hardy-Weinberg equilibrium was detected for D2S1338, D19S433, Penta D, and Penta E or the 13 Combined DNA Index System core STR loci after correction for multiple testing. Significant genetic diversity was observed between these four populations. Comparison with published frequency data for other populations is also presented.

Well Conditioned Formulations for Open Surface Scattering

DTIC Science & Technology

2008-08-01

region on the negative real half of the com- plex plane and tend to cluster about a few points. With few exceptions12, the eigenvalues have converged...a relatively small region on the negative real half of the complex plane and they tend to cluster about a few points. We were surprised, however, to...theory and the results from a numerical implementation. We also discuss a 2d extension of the Poincare -Bertrand identity could be used to develop an

Typeability of PowerPlex Y (Promega) profiles in selected tissue samples incubated in various environments.

PubMed

Niemcunowicz-Janica, Anna; Pepiński, Witold; Janica, Jacek Robert; Janica, Jerzy; Skawrońska, Małgorzata; Koc-Zórawska, Ewa

2007-01-01

In cases of decomposed bodies, Y chromosomal STR markers may be useful in identification of a male relative. The authors assessed typeability of PowerPlex Y (Promega) loci in post mortem tissue material stored in various environments. Kidney, spleen and pancreas specimens were collected during autopsies of five persons aged 20-30 years, whose time of death was determined within the limit of 14 hours. Tissue material was incubated at 21 degrees C and 4 degrees C in various environmental conditions. DNA was extracted by the organic method from tissue samples collected in 7-day intervals and subsequently typed using the PowerPlexY-STR kit and ABI 310. A fast decrease in the typeability rate was seen in specimens incubated in peat soil and in sand. Kidney tissue samples were typeable in all PowerPlexY-STR loci within 63 days of incubation at 4 degrees C. Faster DNA degradation was recorded in spleen and pancreas specimens. In samples with negative genotyping results, no DNA was found by fluorometric quantitation. Decomposed soft tissues are a potential material for DNA typing.

Developmental validation of the PowerPlex(®) Fusion 6C System.

PubMed

Ensenberger, Martin G; Lenz, Kristy A; Matthies, Learden K; Hadinoto, Gregory M; Schienman, John E; Przech, Angela J; Morganti, Michael W; Renstrom, Daniel T; Baker, Victoria M; Gawrys, Kori M; Hoogendoorn, Marlijn; Steffen, Carolyn R; Martín, Pablo; Alonso, Antonio; Olson, Hope R; Sprecher, Cynthia J; Storts, Douglas R

2016-03-01

The PowerPlex(®) Fusion 6C System is a 27-locus, six-dye, multiplex that includes all markers in the expanded CODIS core loci and increases overlap with STR database standards throughout the world. Additionally, it contains two, rapidly mutating, Y-STRs and is capable of both casework and database workflows, including direct amplification. A multi-laboratory developmental validation study was performed on the PowerPlex(®) Fusion 6C System. Here, we report the results of that study which followed SWGDAM guidelines and includes data for: species specificity, sensitivity, stability, precision, reproducibility and repeatability, case-type samples, concordance, stutter, DNA mixtures, and PCR-based procedures. Where appropriate we report data from both extracted DNA samples and direct amplification samples from various substrates and collection devices. Samples from all studies were separated on both Applied Biosystems 3500 series and 6-dye capable 3130 series Genetic Analyzers and data is reported for each. Together, the data validate the design and demonstrate the performance of the PowerPlex(®) Fusion 6C System. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Developmental validation of the PowerPlex(®) ESI 16/17 Fast and PowerPlex(®) ESX 16/17 Fast Systems.

PubMed

McLaren, Robert S; Bourdeau-Heller, Jeanne; Patel, Jaynish; Thompson, Jonelle M; Pagram, Jenny; Loake, Thomas; Beesley, David; Pirttimaa, Markus; Hill, Carolyn R; Duewer, David L; Kline, Margaret C; Butler, John M; Storts, Douglas R

2014-11-01

The PowerPlex(®) ESI 16 Fast, ESI 17 Fast, ESX 16 Fast, and ESX 17 Fast Systems represent faster cycling versions (50min or less) of the PowerPlex(®) ESI and ESX Systems released by Promega in 2009 to accommodate the ENFSI and EDNAP groups' call for new STR multiplexes for Europe. In addition to amplification of purified DNA samples, these new faster cycling systems allow for direct amplification from single-source blood and buccal samples deposited on FTA(®) and nonFTA paper as well as from SwabSolution™ extracts of buccal swabs without the need for purification and quantitation. There are no changes to the autosomal primer pair sequences in the PowerPlex(®) ESI Fast and ESX Fast Systems compared to the original multiplexes, and full concordance at all autosomal loci and amelogenin was observed with data generated previously with the original PowerPlex(®) ESI and ESX Systems. This paper describes the developmental validation study performed on these new fast systems following guidelines issued by the Scientific Working Group on DNA Analysis Methods (SWGDAM) and those of the DNA Advisory Board (DAB). Validation data demonstrate that these systems are sensitive for detecting low levels of DNA while also being capable of generating robust profiles from the high amount of input DNA present in direct-amplification samples. These systems are also tolerant to both high concentrations of PCR inhibitors as well as to slight variations in the final concentration of master mix and primer pair present in the amplification reaction that might be encountered due to pipetting error. The results of this validation study demonstrate that these systems may be used on multiple thermal cyclers and capillary electrophoresis platforms. Copyright © 2014 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Lanthanide Fluorobenzoates as Bio-Probes: a Quest for the Optimal Ligand Fluorination Degree.

PubMed

Kalyakina, Alena S; Utochnikova, Valentina V; Bushmarinov, Ivan S; Le-Deygen, Irina M; Volz, Daniel; Weis, Patrick; Schepers, Ute; Kuzmina, Natalia P; Bräse, Stefan

2017-10-20

The thorough study of fluorinated benzoates of lanthanides (Eu, Tb, Nd, Er, Yb, Gd, La, Lu) is reported. Their composition in single crystal and powder state revealed two predominant structural motifs. An in-depth luminescence study has been performed on the reported fluorobenzoates, showing, that terbium and europium complexes in solid state possess high luminescence intensity with the quantum yield of up to 69 %. High solubility in most organic solvents, as well as in water, combined with the high luminescence intensity in water solution and non-toxicity allowed the testing of europium complexes as bioprobes in cellulo. Among all tested fluorobenzoates, europium 2-fluorobenzoate dihydrate combined the best luminescent properties, thermodynamic stability, aqueous solubility, and non-toxicity, and was shown to be a viable bio-marker. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Selenium Supplementation in Fish: A Combined Chemical and Biomolecular Study to Understand Sel-Plex Assimilation and Impact on Selenoproteome Expression in Rainbow Trout (Oncorhynchus mykiss)

PubMed Central

Sweetman, John; Martin, Samuel A. M.; Feldmann, Jörg; Secombes, Christopher J.

2015-01-01

Background Selenium (Se) is an essential oligonutrient, as a component of several Se-containing proteins (selenoproteins), which exert important biological functions within an organism. In livestock, Se-enriched products have been proposed as dietary supplements to be included into functional feeds for animal preventive health care. To this end, it is important to understand the optimal range of concentrations for supplementation and how long it takes to be assimilated into the organism. Methods In this study, rainbow trout (Oncorhynchus mykiss) were fed a control diet containing 0.9 g Kg-1 Se or the same diet supplemented with a Se-Yeast product (Sel-Plex) to achieve Se concentrations ranging from 1.5–8.9 g Kg-1 for a period of ten weeks. Fish were sampled every two weeks for analysis. The kinetics of Se bioaccumulation and the effects on fish selenoprotein expression was determined in different tissues combining chemical and bimolecular techniques. Results The Sel-Plex enriched diets did not have any effect on survival and growth performance. The highest Se levels were found in liver and kidney followed by muscle and blood cells. Analysis of the Se concentration factor showed that liver is able to initially regulate the amount of Se accumulated. However, with higher dietary Se level (4.8 and 8.9 g Kg-1) and longer times of exposure (10 weeks), regulation is ineffective and the Se tissue concentration increases. The expression of the selected trout selenoprotein transcripts showed an inverse correlation with Sel-Plex augmentation in most cases. In liver, kidney and blood cells the highest up-regulation of the trout selenoprotein genes was seen mostly in the group fed the diet enriched with the lowest concentration of Sel-Plex (0.5 g Kg-1) for 10 weeks. Conclusion Sel-Plex may represent an excellent Se supplement to deliver a high level of Se without provoking harm to the fish and to guarantee the maximal absorption of the element. According to our results, a dietary supplementation of Sel-Plex between 0.5 and 4 g Kg-1 may allow maximal benefits, whereas 8 g Kg-1 may be excessive for the purpose of supplementation. PMID:25978314

BioBlend: automating pipeline analyses within Galaxy and CloudMan.

PubMed

Sloggett, Clare; Goonasekera, Nuwan; Afgan, Enis

2013-07-01

We present BioBlend, a unified API in a high-level language (python) that wraps the functionality of Galaxy and CloudMan APIs. BioBlend makes it easy for bioinformaticians to automate end-to-end large data analysis, from scratch, in a way that is highly accessible to collaborators, by allowing them to both provide the required infrastructure and automate complex analyses over large datasets within the familiar Galaxy environment. http://bioblend.readthedocs.org/. Automated installation of BioBlend is available via PyPI (e.g. pip install bioblend). Alternatively, the source code is available from the GitHub repository (https://github.com/afgane/bioblend) under the MIT open source license. The library has been tested and is working on Linux, Macintosh and Windows-based systems.

Industri-Plex, OU-1, Master Cover Certification Report: Industri-Plex Site: September 30, 2008: Appendix C, C.1-C.2

EPA Pesticide Factsheets

2012-04-22

... Sincerely, \\ -/) I iJ/;5.~~.k. -r--7~.~~- ... 2.i:

International Conference on Mathematical Methods in Electromagnetic Theory (MMET 2000), Volume 2 Held in Kharkov, Ukraine on September 12-15, 2000

DTIC Science & Technology

2000-09-01

frequencies of the WG-modes of the resonator are determined as the points on the complex frequency plane for which nontrivial solutions of (3) exist...allow to determine a surface impedance of end-walls using the experimentally measured frequencies and basic Q-factors of resonance oscillations of a...Y0 = Y,. The com- plex eigen frequencies K’ = Re< + i. Im< (v is the number of the resonance in the zones

A histologic, histomorphometric, and radiographic comparison between two complexes of CenoBoen/CenoMembrane and Bio-Oss/Bio-Gide in lateral ridge augmentation: A clinical trial.

PubMed

Amoian, Babak; Moudi, Ehsan; Majidi, Maryam Seyed; Ali Tabatabaei, S M

2016-09-01

Several grafting materials have been used for alveolar ridge augmentation. The literature lacks researches to compare CenoBone to other grafting materials. The aim of this study was to compare CenoBone/CenoMembrane complex to Bio-Oss/Bio-Gide complex in lateral alveolar bone augmentation in terms of radiographic, histologic, and histomorphometric parameters. In this randomized controlled trial, ten patients who needed lateral ridge augmentation were selected and augmentations were done using either of CenoBone/CenoMembrane or Bio-Oss/Bio-Gide complexes. In the re-entry surgery in 6 months following augmentation, core biopsies were taken and clinical, radiographic, histologic, and histomorphometric evaluations were performed. No statistically significant difference was seen between groups except for the number of blood vessels and percentage of residual graft materials. CenoBone seems to present a comparable lateral ridge augmentation to Bio-Oss in.

Toxicity of monazite particulates and its attenuation with a complex of bio-protectors.

PubMed

Katsnelson, B A; Yeremenko, Olga S; Privalova, Larissa I; Makeyev, O H; Degtyareva, Tamara D; Beresneva, Olga Yu; Valamina, Irene E; Minihaliyeva, Ilzira A; Sutunkova, Marina P; Kireyeva, Ekaterina P; Bukhantsev, V A; Dovzenko, E I; Minin, V V; Kulikov, E S; Kostykova, Svetlana V; Nazukin, A S

2009-01-01

Workers employed on mining, processing and storage of monazite are at risk of exposure to dust with expected adverse health effects. To study the adverse health effects of monazite particles in experiments on rats and to test the possibility of attenuating these effects. Outbred white rats were injected intratracheally with a suspension of ground monazite concentrate (MC) in order to investigate the cellular response of the lower airways 24 hours later and the organism's status 6 months after the injection. The bio-protective complex (BPC) tested in these experiments consisted of glutamate, an iodine preparation, methionine, a polyvitamin-polymineral composition, and/or "Eicosavitol" (fish oil preparation rich in PUFA, predominantly of the omega 3-group). Bio-protectors were administered together with the rat food and drink daily for one month before the MC injection in the short-term experiment, or over 6 months after such injection in the long-term experiment. MC induced manifestations of its cytotoxicity, fibrogenicity and systemic toxicity as well as genotoxicity. The tested BPC attenuated virtually all these effects. Although a similar protective potential of "Eicosavitol" against almost all of them was lower compared with that of BPC, combining BPC with "Eicosavitol" provided, as a rule, the greatest protective effect. It may be assumed that the many-sided adverse effects of MC on the organism is due, at least partially, to the presence in its composition of not only rare earth elements but also of natural radioisotopes of the thorium and uranium families. The combination of the bio-protectors tested was highly effective and may be recommended for administering in periodic preventive programmes to exposed workers.

Source and Biological Response of Biochar Organic Compounds Released into Water; Relationships with Bio-Oil Composition and Carbonization Degree.

PubMed

Ghidotti, Michele; Fabbri, Daniele; Mašek, Ondřej; Mackay, Colin Logan; Montalti, Marco; Hornung, Andreas

2017-06-06

Water-soluble organic compounds (WSOCs) were extracted from corn stalk biochar produced at increasing pyrolysis temperatures (350-650 °C) and from the corresponding vapors, collected as bio-oil. WSOCs were characterized by gas chromatography (semivolatile fraction), negative electron spray ionization high resolution mass spectrometry (hydrophilic fraction) and fluorescence spectroscopy. The pattern of semivolatile WSOCs in bio-oil was dominated by aromatic products from lignocellulose, while in biochar was featured by saturated carboxylic acids from hemi/cellulose and lipids with concentrations decreasing with decreasing H/C ratios. Hydrophilic species in poorly carbonized biochar resembled those in bio-oil, but the increasing charring intensity caused a marked reduction in the molecular complexity and degree of aromaticity. Differences in the fluorescence spectra were attributed to the predominance of fulvic acid-like structures in biochar and lignin-like moieties in bio-oil. The divergence between pyrolysis vapors and biochar in the distribution of WSOCs with increasing carbonization was explained by the hydrophobic carbonaceous matrix acting like a filter favoring the release into water of carboxylic and fulvic acid-like components. The formation of these structures was confirmed in biochar produced by pilot plant pyrolysis units. Biochar affected differently shoot and root length of cress seedlings in germination tests highlighting its complex role on plant growth.

Identification of Brucella genus and eight Brucella species by Luminex bead-based suspension array.

PubMed

Lusk Pfefer, Tina S; Timme, Ruth; Kase, Julie A

2018-04-01

Globally, unpasteurized milk products are vehicles for the transmission of brucellosis, a zoonosis responsible for cases of foodborne illness in the United States and elsewhere. Existing PCR assays to detect Brucella species are restricted by the resolution of band sizes on a gel or the number of fluorescent channels in a single real-time system. The Luminex bead-based suspension array is performed in a 96-well plate allowing for high throughput screening of up to 100 targets in one sample with easily discernible results. We have developed an array using the Bio-Plex 200 to differentiate the most common Brucella species: B. abortus, B. melitensis, B. suis, B. suis bv5, B. canis, B. ovis, B. pinnipedia, and B. neotomae, as well as Brucella genus. All probes showed high specificity, with no cross-reaction with non-Brucella strains. We could detect pure DNA from B. abortus, B. melitensis, and genus-level Brucella at concentrations of ≤5 fg/μL. Pure DNA from all other species tested positive at concentrations well below 500 fg/μL and we positively identified B. neotomae in six artificially contaminated cheese and milk products. An intra-laboratory verification further demonstrated the assay's accuracy and robustness in the rapid screening (3-4 h including PCR) of DNA. Published by Elsevier Ltd.

Deconstruction of the beaten Path-Sidestep interaction network provides insights into neuromuscular system development

PubMed Central

Li, Hanqing; Watson, Ash; Olechwier, Agnieszka; Anaya, Michael; Sorooshyari, Siamak K; Harnett, Dermott P; Lee, Hyung-Kook (Peter); Vielmetter, Jost; Fares, Mario A; Garcia, K Christopher; Özkan, Engin

2017-01-01

An ‘interactome’ screen of all Drosophila cell-surface and secreted proteins containing immunoglobulin superfamily (IgSF) domains discovered a network formed by paralogs of Beaten Path (Beat) and Sidestep (Side), a ligand-receptor pair that is central to motor axon guidance. Here we describe a new method for interactome screening, the Bio-Plex Interactome Assay (BPIA), which allows identification of many interactions in a single sample. Using the BPIA, we ‘deorphanized’ four more members of the Beat-Side network. We confirmed interactions using surface plasmon resonance. The expression patterns of beat and side genes suggest that Beats are neuronal receptors for Sides expressed on peripheral tissues. side-VI is expressed in muscle fibers targeted by the ISNb nerve, as well as at growth cone choice points and synaptic targets for the ISN and TN nerves. beat-V genes, encoding Side-VI receptors, are expressed in ISNb and ISN motor neurons. PMID:28829740

Genetic profile of a multi-ethnic population from Guiné-Bissau (west African coast) using the new PowerPlex 16 System kit.

PubMed

Gonçalves, Rita; Jesus, José; Fernandes, Ana Teresa; Brehm, António

2002-09-10

Allele and haplotype frequencies of 15 chromosome STR loci included in the kit PowerPlex16 System from Promega, were determined in a sample of unrelated males from Guiné-Bissau, a country from the west African coast. All individuals were subjected to an interview in order to make sure that their ancestors belonged to the same ethnic group. This way we intended to look for possible inter-ethnic differences. PowerPlex 16 includes STRs not studied before in any multi-ethnic population. The kit includes two new allele markers (Penta D and Penta E), which are very useful either in forensics or population genetic studies. The Guinean population presents significant differences when compared with other African populations.

Quaternary ammonium isobaric tag for a relative and absolute quantification of peptides.

PubMed

Setner, Bartosz; Stefanowicz, Piotr; Szewczuk, Zbigniew

2018-02-01

Isobaric labeling quantification of peptides has become a method of choice for mass spectrometry-based proteomics studies. However, despite of wide variety of commercially available isobaric tags, none of the currently available methods offers significant improvement of sensitivity of detection during MS experiment. Recently, many strategies were applied to increase the ionization efficiency of peptides involving chemical modifications introducing quaternary ammonium fixed charge. Here, we present a novel quaternary ammonium-based isobaric tag for relative and absolute quantification of peptides (QAS-iTRAQ 2-plex). Upon collisional activation, the new stable benzylic-type cationic reporter ion is liberated from the tag. Deuterium atoms were used to offset the differential masses of a reporter group. We tested the applicability of QAS-iTRAQ 2-plex reagent on a series of model peptides as well as bovine serum albumin tryptic digest. Obtained results suggest usefulness of this isobaric ionization tag for relative and absolute quantification of peptides. Copyright © 2017 John Wiley & Sons, Ltd.

Effect of soil and water environment on typeability of PowerPlex Y (Promega) in selected tissue samples.

PubMed

Niemcunowicz-Janica, Anna; Pepinski, Witold; Janica, Jacek Robert; Skawronska, Malgorzata; Janica, Jerzy; Koc-Zorawska, Ewa; Stolyszewski, Ireneusz

2007-01-01

In cases of decomposed bodies Y chromosomal STR markers may be useful in identification of a male relative. The authors assessed typeability PowerPlex Y (Promega) loci in tissue material stored in water and soil environment. Tissue material was collected during autopsies of five persons aged 20-30 years with time of death determined within the limit of 14 hours. Heart muscle, liver and lung specimens were stored in pond water, sea water, sand and peat soil. DNA was extracted by organic method from tissue samples collected in 7-day intervals. Liver specimens were typeable in all PowerPlex Y loci within 100 days of storage in pond water with gradual decline at DYS392 in sea water. Heart muscle specimens stored in pond water exhibited allelic loss at DYS19, DYS385, DYS389II and DYS392, while all loci were typeable in sea water stored samples. For lung specimens allelic loss was noted throughout the profile. Storage of liver specimens in peat soil for more than 14 days resulted in allelic drop-out, and after 21 days no profiles were typeable. Heart muscle specimens were typeable in all PowerPlex Y systems after 35-day storage in sand, while allelic drop-out and subsequent lack of profiles were noted after 14 and 35 days respectively. Lung specimens stored in garden soil exhibited allelic drop-out and subsequent lack of profiles after 7 and 21 days, respectively. All PowerPlex Y loci were typeable in the latter material in sand up to day 35 with gradual decline of longer amplicons (DYS19, DYS385, DYS389II and DYS392).

MISSION LentiPlex pooled shRNA library screening in mammalian cells.

PubMed

Coussens, Matthew J; Corman, Courtney; Fischer, Ashley L; Sago, Jack; Swarthout, John

2011-12-21

RNA interference (RNAi) is an intrinsic cellular mechanism for the regulation of gene expression. Harnessing the innate power of this system enables us to knockdown gene expression levels in loss of gene function studies. There are two main methods for performing RNAi. The first is the use of small interfering RNAs (siRNAs) that are chemically synthesized, and the second utilizes short-hairpin RNAs (shRNAs) encoded within plasmids. The latter can be transfected into cells directly or packaged into replication incompetent lentiviral particles. The main advantages of using lentiviral shRNAs is the ease of introduction into a wide variety of cell types, their ability to stably integrate into the genome for long term gene knockdown and selection, and their efficacy in conducting high-throughput loss of function screens. To facilitate this we have created the LentiPlex pooled shRNA library. The MISSION LentiPlex Human shRNA Pooled Library is a genome-wide lentiviral pool produced using a proprietary process. The library consists of over 75,000 shRNA constructs from the TRC collection targeting 15,000+ human genes. Each library is tested for shRNA representation before product release to ensure robust library coverage. The library is provided in a ready-to-use lentiviral format at titers of at least 5 x 10(8) TU/ml via p24 assay and is pre-divided into ten subpools of approximately 8,000 shRNA constructs each. Amplification and sequencing primers are also provided for downstream target identification. Previous studies established a synergistic antitumor activity of TRAIL when combined with Paclitaxel in A549 cells, a human lung carcinoma cell line. In this study we demonstrate the application of a pooled LentiPlex shRNA library to rapidly conduct a positive selection screen for genes involved in the cytotoxicity of A549 cells when exposed to TRAIL and Paclitaxel. One barrier often encountered with high-throughput screens is the cost and difficulty in deconvolution; we also detail a cost-effective polyclonal approach utilizing traditional sequencing.

Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula.

PubMed

Moll, Karen M; Zhou, Peng; Ramaraj, Thiruvarangan; Fajardo, Diego; Devitt, Nicholas P; Sadowsky, Michael J; Stupar, Robert M; Tiffin, Peter; Miller, Jason R; Young, Nevin D; Silverstein, Kevin A T; Mudge, Joann

2017-08-04

Third generation sequencing technologies, with sequencing reads in the tens- of kilo-bases, facilitate genome assembly by spanning ambiguous regions and improving continuity. This has been critical for plant genomes, which are difficult to assemble due to high repeat content, gene family expansions, segmental and tandem duplications, and polyploidy. Recently, high-throughput mapping and scaffolding strategies have further improved continuity. Together, these long-range technologies enable quality draft assemblies of complex genomes in a cost-effective and timely manner. Here, we present high quality genome assemblies of the model legume plant, Medicago truncatula (R108) using PacBio, Dovetail Chicago (hereafter, Dovetail) and BioNano technologies. To test these technologies for plant genome assembly, we generated five assemblies using all possible combinations and ordering of these three technologies in the R108 assembly. While the BioNano and Dovetail joins overlapped, they also showed complementary gains in continuity and join numbers. Both technologies spanned repetitive regions that PacBio alone was unable to bridge. Combining technologies, particularly Dovetail followed by BioNano, resulted in notable improvements compared to Dovetail or BioNano alone. A combination of PacBio, Dovetail, and BioNano was used to generate a high quality draft assembly of R108, a M. truncatula accession widely used in studies of functional genomics. As a test for the usefulness of the resulting genome sequence, the new R108 assembly was used to pinpoint breakpoints and characterize flanking sequence of a previously identified translocation between chromosomes 4 and 8, identifying more than 22.7 Mb of novel sequence not present in the earlier A17 reference assembly. Adding Dovetail followed by BioNano data yielded complementary improvements in continuity over the original PacBio assembly. This strategy proved efficient and cost-effective for developing a quality draft assembly compared to traditional reference assemblies.

Whole genome amplification of DNA extracted from FFPE tissues.

PubMed

Bosso, Mira; Al-Mulla, Fahd

2011-01-01

Whole genome amplification systems were developed to meet the increasing research demands on DNA resources and to avoid DNA shortage. The technology enables amplification of nanogram amounts of DNA into microgram quantities and is increasingly used in the amplification of DNA from multiple origins such as blood, fresh frozen tissue, formalin-fixed paraffin-embedded tissues, saliva, buccal swabs, bacteria, and plant and animal sources. This chapter focuses on the use of GenomePlex(®) tissue Whole Genome Amplification Kit, to amplify DNA directly from archived tissue. In addition, this chapter documents our unique experience with the utilization of GenomePlex(®) amplified DNA using several molecular techniques including metaphase Comparative Genomic Hybridization, array Comparative Genomic Hybridization, and real-time quantitative polymerase chain reaction assays. GenomePlex(®) is a registered trademark of Rubicon Genomics Incorporation.

Development of a genetic tool for product regulation in the diverse British pig breed market.

PubMed

Wilkinson, Samantha; Archibald, Alan L; Haley, Chris S; Megens, Hendrik-Jan; Crooijmans, Richard P M A; Groenen, Martien A M; Wiener, Pamela; Ogden, Rob

2012-11-15

The application of DNA markers for the identification of biological samples from both human and non-human species is widespread and includes use in food authentication. In the food industry the financial incentive to substituting the true name of a food product with a higher value alternative is driving food fraud. This applies to British pork products where products derived from traditional pig breeds are of premium value. The objective of this study was to develop a genetic assay for regulatory authentication of traditional pig breed-labelled products in the porcine food industry in the United Kingdom. The dataset comprised of a comprehensive coverage of breed types present in Britain: 460 individuals from 7 traditional breeds, 5 commercial purebreds, 1 imported European breed and 1 imported Asian breed were genotyped using the PorcineSNP60 beadchip. Following breed-informative SNP selection, assignment power was calculated for increasing SNP panel size. A 96-plex assay created using the most informative SNPs revealed remarkably high genetic differentiation between the British pig breeds, with an average FST of 0.54 and Bayesian clustering analysis also indicated that they were distinct homogenous populations. The posterior probability of assignment of any individual of a presumed origin actually originating from that breed given an alternative breed origin was > 99.5% in 174 out of 182 contrasts, at a test value of log(LR) > 0. Validation of the 96-plex assay using independent test samples of known origin was successful; a subsequent survey of market samples revealed a high level of breed label conformity. The newly created 96-plex assay using selected markers from the PorcineSNP60 beadchip enables powerful assignment of samples to traditional breed origin and can effectively identify mislabelling, providing a highly effective tool for DNA analysis in food forensics.

Development of a genetic tool for product regulation in the diverse British pig breed market

PubMed Central

2012-01-01

Background The application of DNA markers for the identification of biological samples from both human and non-human species is widespread and includes use in food authentication. In the food industry the financial incentive to substituting the true name of a food product with a higher value alternative is driving food fraud. This applies to British pork products where products derived from traditional pig breeds are of premium value. The objective of this study was to develop a genetic assay for regulatory authentication of traditional pig breed-labelled products in the porcine food industry in the United Kingdom. Results The dataset comprised of a comprehensive coverage of breed types present in Britain: 460 individuals from 7 traditional breeds, 5 commercial purebreds, 1 imported European breed and 1 imported Asian breed were genotyped using the PorcineSNP60 beadchip. Following breed-informative SNP selection, assignment power was calculated for increasing SNP panel size. A 96-plex assay created using the most informative SNPs revealed remarkably high genetic differentiation between the British pig breeds, with an average FST of 0.54 and Bayesian clustering analysis also indicated that they were distinct homogenous populations. The posterior probability of assignment of any individual of a presumed origin actually originating from that breed given an alternative breed origin was > 99.5% in 174 out of 182 contrasts, at a test value of log(LR) > 0. Validation of the 96-plex assay using independent test samples of known origin was successful; a subsequent survey of market samples revealed a high level of breed label conformity. Conclusion The newly created 96-plex assay using selected markers from the PorcineSNP60 beadchip enables powerful assignment of samples to traditional breed origin and can effectively identify mislabelling, providing a highly effective tool for DNA analysis in food forensics. PMID:23150935

Development of a rapid 21-plex autosomal STR typing system for forensic applications.

PubMed

Yang, Meng; Yin, Caiyong; Lv, Yuexin; Yang, Yaran; Chen, Jing; Yu, Zailiang; Liu, Xu; Xu, Meibo; Chen, Feng; Wu, Huijuan; Yan, Jiangwei

2016-10-01

DNA-STR genotyping technology has been widely used in forensic investigations. Even with such success, there is a great need to reduce the analysis time. In this study, we established a new rapid 21-plex STR typing system, including 13 CODIS loci, Penta D, Penta E, D12S391, D2S1338, D6S1043, D19S433, D2S441 and Amelogenin loci. This system could shorten the amplification time to a minimum of 90 min and does not require DNA extraction from the samples. Validation of the typing system complied with the Scientific Working Group on DNA Analysis Methods (SWGDAM) and the Chinese National Standard (GA/T815-2009) guidelines. The results demonstrated that this 21-plex STR typing system was a valuable tool for rapid criminal investigation. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Further evidence for population specific differences in the effect of DNA markers and gender on eye colour prediction in forensics.

PubMed

Pośpiech, Ewelina; Karłowska-Pik, Joanna; Ziemkiewicz, Bartosz; Kukla, Magdalena; Skowron, Małgorzata; Wojas-Pelc, Anna; Branicki, Wojciech

2016-07-01

The genetics of eye colour has been extensively studied over the past few years, and the identified polymorphisms have been applied with marked success in the field of Forensic DNA Phenotyping. A picture that arises from evaluation of the currently available eye colour prediction markers shows that only the analysis of HERC2-OCA2 complex has similar effectiveness in different populations, while the predictive potential of other loci may vary significantly. Moreover, the role of gender in the explanation of human eye colour variation should not be neglected in some populations. In the present study, we re-investigated the data for 1020 Polish individuals and using neural networks and logistic regression methods explored predictive capacity of IrisPlex SNPs and gender in this population sample. In general, neural networks provided higher prediction accuracy comparing to logistic regression (AUC increase by 0.02-0.06). Four out of six IrisPlex SNPs were associated with eye colour in the studied population. HERC2 rs12913832, OCA2 rs1800407 and SLC24A4 rs12896399 were found to be the most important eye colour predictors (p < 0.007) while the effect of rs16891982 in SLC45A2 was less significant. Gender was found to be significantly associated with eye colour with males having ~1.5 higher odds for blue eye colour comparing to females (p = 0.002) and was ranked as the third most important factor in blue/non-blue eye colour determination. However, the implementation of gender into the developed prediction models had marginal and ambiguous impact on the overall accuracy of prediction confirming that the effect of gender on eye colour in this population is small. Our study indicated the advantage of neural networks in prediction modeling in forensics and provided additional evidence for population specific differences in the predictive importance of the IrisPlex SNPs and gender.

Performance of Identifiler Direct and PowerPlex 16 HS on the Applied Biosystems 3730 DNA Analyzer for processing biological samples archived on FTA cards.

PubMed

Laurin, Nancy; DeMoors, Anick; Frégeau, Chantal

2012-09-01

Direct amplification of STR loci from biological samples collected on FTA cards without prior DNA purification was evaluated using Identifiler Direct and PowerPlex 16 HS in conjunction with the use of a high throughput Applied Biosystems 3730 DNA Analyzer. In order to reduce the overall sample processing cost, reduced PCR volumes combined with various FTA disk sizes were tested. Optimized STR profiles were obtained using a 0.53 mm disk size in 10 μL PCR volume for both STR systems. These protocols proved effective in generating high quality profiles on the 3730 DNA Analyzer from both blood and buccal FTA samples. Reproducibility, concordance, robustness, sample stability and profile quality were assessed using a collection of blood and buccal samples on FTA cards from volunteer donors as well as from convicted offenders. The new developed protocols offer enhanced throughput capability and cost effectiveness without compromising the robustness and quality of the STR profiles obtained. These results support the use of these protocols for processing convicted offender samples submitted to the National DNA Data Bank of Canada. Similar protocols could be applied to the processing of casework reference samples or in paternity or family relationship testing. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Evaluation of advanced multiplex short tandem repeat systems in pairwise kinship analysis.

PubMed

Tamura, Tomonori; Osawa, Motoki; Ochiai, Eriko; Suzuki, Takanori; Nakamura, Takashi

2015-09-01

The AmpFLSTR Identifiler Kit, comprising 15 autosomal short tandem repeat (STR) loci, is commonly employed in forensic practice for calculating match probabilities and parentage testing. The conventional system exhibits insufficient estimation for kinship analysis such as sibship testing because of shortness of examined loci. This study evaluated the power of the PowerPlex Fusion System, GlobalFiler Kit, and PowerPlex 21 System, which comprise more than 20 autosomal STR loci, to estimate pairwise blood relatedness (i.e., parent-child, full siblings, second-degree relatives, and first cousins). The genotypes of all 24 STR loci in 10,000 putative pedigrees were constructed by simulation. The likelihood ratio for each locus was calculated from joint probabilities for relatives and non-relatives. The combined likelihood ratio was calculated according to the product rule. The addition of STR loci improved separation between relatives and non-relatives. However, these systems were less effectively extended to the inference for first cousins. In conclusion, these advanced systems will be useful in forensic personal identification, especially in the evaluation of full siblings and second-degree relatives. Moreover, the additional loci may give rise to two major issues of more frequent mutational events and several pairs of linked loci on the same chromosome. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Mass Spectrometry and Multiplex Antigen Assays to Assess Microbial Quality and Toxin Production of Staphylococcus aureus Strains Isolated from Clinical and Food Samples

PubMed Central

Attien, Paul; Sina, Haziz; Moussaoui, Wardi; Zimmermann-Meisse, Gaëlle; Dadié, Thomas; Keller, Daniel; Riegel, Philippe; Edoh, Vincent; Kotchoni, Simeon O.; Djè, Marcellin; Prévost, Gilles

2014-01-01

The aim of our study was to investigate the microbial quality of meat products and on some clinical samples in Abidjan focused on Staphylococcus genus and the toxin production profile of Staphylococcus aureus (S. aureus) isolated. Bacteria were collected from 240 samples of three meat products sold in Abidjan and 180 samples issued from clinical infections. The strains were identified by both microbiological and MALDI-TOF-MS methods. The susceptibility to antibiotics was determined by the disc diffusion method. The production of Panton-Valentine Leukocidin, LukE/D, and epidermolysins was screened using radial gel immunodiffusion. The production of staphylococcal enterotoxins and TSST-1 was screened by a Bio-Plex Assay. We observed that 96/240 of meat samples and 32/180 of clinical samples were contaminated by Staphylococcus. Eleven species were isolated from meats and 4 from clinical samples. Forty-two S. aureus strains were isolated from ours samples. Variability of resistance was observed for most of the tested antibiotics but none of the strains displays a resistance to imipenem and quinolones. We observed that 89% of clinical S. aureus were resistant to methicillin against 58% for those issued from meat products. All S. aureus isolates issued from meat products produce epidermolysins whereas none of the clinical strains produced these toxins. The enterotoxins were variably produced by both clinical and meat product samples. PMID:24987686

Cross-Linked Amylose Bio-Plastic: A Transgenic-Based Compostable Plastic Alternative

PubMed Central

Sagnelli, Domenico; Kemmer, Gerdi Christine; Holse, Mette; Hebelstrup, Kim H.; Bao, Jinsong; Stelte, Wolfgang; Bjerre, Anne-Belinda; Blennow, Andreas

2017-01-01

Bio-plastics and bio-materials are composed of natural or biomass derived polymers, offering solutions to solve immediate environmental issues. Polysaccharide-based bio-plastics represent important alternatives to conventional plastic because of their intrinsic biodegradable nature. Amylose-only (AO), an engineered barley starch with 99% amylose, was tested to produce cross-linked all-natural bioplastic using normal barley starch as a control. Glycerol was used as plasticizer and citrate cross-linking was used to improve the mechanical properties of cross-linked AO starch extrudates. Extrusion converted the control starch from A-type to Vh- and B-type crystals, showing a complete melting of the starch crystals in the raw starch granules. The cross-linked AO and control starch specimens displayed an additional wide-angle diffraction reflection. Phospholipids complexed with Vh-type single helices constituted an integrated part of the AO starch specimens. Gas permeability tests of selected starch-based prototypes demonstrated properties comparable to that of commercial Mater-Bi© plastic. The cross-linked AO prototypes had composting characteristics not different from the control, indicating that the modified starch behaves the same as normal starch. The data shows the feasibility of producing all-natural bioplastic using designer starch as raw material. PMID:28973963

Cross-Linked Amylose Bio-Plastic: A Transgenic-Based Compostable Plastic Alternative.

PubMed

Sagnelli, Domenico; Hooshmand, Kourosh; Kemmer, Gerdi Christine; Kirkensgaard, Jacob J K; Mortensen, Kell; Giosafatto, Concetta Valeria L; Holse, Mette; Hebelstrup, Kim H; Bao, Jinsong; Stelte, Wolfgang; Bjerre, Anne-Belinda; Blennow, Andreas

2017-09-30

Bio-plastics and bio-materials are composed of natural or biomass derived polymers, offering solutions to solve immediate environmental issues. Polysaccharide-based bio-plastics represent important alternatives to conventional plastic because of their intrinsic biodegradable nature. Amylose-only (AO), an engineered barley starch with 99% amylose, was tested to produce cross-linked all-natural bioplastic using normal barley starch as a control. Glycerol was used as plasticizer and citrate cross-linking was used to improve the mechanical properties of cross-linked AO starch extrudates. Extrusion converted the control starch from A-type to Vh- and B-type crystals, showing a complete melting of the starch crystals in the raw starch granules. The cross-linked AO and control starch specimens displayed an additional wide-angle diffraction reflection. Phospholipids complexed with Vh-type single helices constituted an integrated part of the AO starch specimens. Gas permeability tests of selected starch-based prototypes demonstrated properties comparable to that of commercial Mater-Bi © plastic. The cross-linked AO prototypes had composting characteristics not different from the control, indicating that the modified starch behaves the same as normal starch. The data shows the feasibility of producing all-natural bioplastic using designer starch as raw material.

Bio-oil upgrading strategies to improve PHA production from selected aerobic mixed cultures.

PubMed

Moita Fidalgo, Rita; Ortigueira, Joana; Freches, André; Pelica, João; Gonçalves, Magarida; Mendes, Benilde; Lemos, Paulo C

2014-06-25

Recent research on polyhydroxyalkanoates (PHAs) has focused on developing cost-effective production processes using low-value or industrial waste/surplus as substrate. One of such substrates is the liquid fraction resulting from pyrolysis processes, bio-oil. In this study, valorisation of bio-oil through PHA production was investigated. The impact of the complex bio-oil matrix on PHA production by an enriched mixed culture was examined. The performance of the direct utilization of pure bio-oil was compared with the utilization of three defined substrates contained in this bio-oil: acetate, glucose and xylose. When compared with acetate, bio-oil revealed lower capacity for polymer production as a result of a lower polymer yield on substrate and a lower PHA cell content. Two strategies for bio-oil upgrade were performed, anaerobic fermentation and vacuum distillation, and the resulting liquid streams were tested for polymer production. The first one was enriched in volatile fatty acids and the second one mainly on phenolic and long-chain fatty acids. PHA accumulation assays using the upgraded bio-oils attained polymer yields on substrate similar or higher than the one achieved with acetate, although with a lower PHA content. The capacity to use the enriched fractions for polymer production has yet to be optimized. The anaerobic digestion of bio-oil could also open-up the possibility to use the fermented bio-oil directly in the enrichment process of the mixed culture. This would increase the selective pressure toward an optimized PHA accumulating culture selection. Copyright © 2013 Elsevier B.V. All rights reserved.

First Evaluation of Glucose-6-Phosphate Dehydrogenase (G6PD) Deficiency in Vivax Malaria Endemic Regions in the Republic of Korea

PubMed Central

Goo, Youn-Kyoung; Ji, So-Young; Shin, Hyun-Il; Moon, Jun-Hye; Cho, Shin-Hyung; Lee, Won-Ja; Kim, Jung-Yeon

2014-01-01

Background Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common human enzyme defect and affects more than 400 million people worldwide. This deficiency is believed to protect against malaria because its global distribution is similar. However, this genetic disorder may be associated with potential hemolytic anemia after treatment with anti-malarials, primaquine or other 8-aminoquinolines. Although primaquine is used for malaria prevention, no study has previously investigated the prevalence of G6PD variants and G6PD deficiency in the Republic of Korea (ROK). Methods Two commercialized test kits (Trinity G-6-PDH and CareStart G6PD test) were used for G6PD deficiency screening. The seven common G6PD variants were investigated by DiaPlexC kit in blood samples obtained living in vivax malaria endemic regions in the ROK. Results Of 1,044 blood samples tested using the CareStart G6PD test, none were positive for G6PD deficiency. However, a slightly elevated level of G6PD activity was observed in 14 of 1,031 samples tested with the Trinity G-6-PDH test. Forty-nine of the 298 samples with non-specific amplification by DiaPlexC kit were confirmed by sequencing to be negative for the G6PD variants. Conclusions No G6PD deficiency was observed using phenotypic- or genetic-based tests in individuals residing in vivax malaria endemic regions in the ROK. Because massive chemoprophylaxis using primaquine has been performed in the ROK military to kill hypnozoites responsible for relapse and latent stage vivax malaria, further regular monitoring is essential for the safe administration of primaquine. PMID:24853873

First evaluation of glucose-6-phosphate dehydrogenase (G6PD) deficiency in vivax malaria endemic regions in the Republic of Korea.

PubMed

Goo, Youn-Kyoung; Ji, So-Young; Shin, Hyun-Il; Moon, Jun-Hye; Cho, Shin-Hyung; Lee, Won-Ja; Kim, Jung-Yeon

2014-01-01

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common human enzyme defect and affects more than 400 million people worldwide. This deficiency is believed to protect against malaria because its global distribution is similar. However, this genetic disorder may be associated with potential hemolytic anemia after treatment with anti-malarials, primaquine or other 8-aminoquinolines. Although primaquine is used for malaria prevention, no study has previously investigated the prevalence of G6PD variants and G6PD deficiency in the Republic of Korea (ROK). Two commercialized test kits (Trinity G-6-PDH and CareStart G6PD test) were used for G6PD deficiency screening. The seven common G6PD variants were investigated by DiaPlexC kit in blood samples obtained living in vivax malaria endemic regions in the ROK. Of 1,044 blood samples tested using the CareStart G6PD test, none were positive for G6PD deficiency. However, a slightly elevated level of G6PD activity was observed in 14 of 1,031 samples tested with the Trinity G-6-PDH test. Forty-nine of the 298 samples with non-specific amplification by DiaPlexC kit were confirmed by sequencing to be negative for the G6PD variants. No G6PD deficiency was observed using phenotypic- or genetic-based tests in individuals residing in vivax malaria endemic regions in the ROK. Because massive chemoprophylaxis using primaquine has been performed in the ROK military to kill hypnozoites responsible for relapse and latent stage vivax malaria, further regular monitoring is essential for the safe administration of primaquine.

Comparison of two suspension arrays for simultaneous detection of five biothreat bacterial in powder samples.

PubMed

Yang, Yu; Wang, Jing; Wen, Haiyan; Liu, Hengchuan

2012-01-01

We have developed novel Bio-Plex assays for simultaneous detection of Bacillus anthracis, Yersinia pestis, Brucella spp., Francisella tularensis, and Burkholderia pseudomallei. Universal primers were used to amplify highly conserved region located within the 16S rRNA amplicon, followed by hybridized to pathogen-specific probes for identification of these five organisms. The other assay is based on multiplex PCR to simultaneously amplify five species-specific pathogen identification-targeted regions unique to individual pathogen. Both of the two arrays are validated to be flexible and sensitive for simultaneous detection of bioterrorism bacteria. However, universal primer PCR-based array could not identify Bacillus anthracis, Yersinia pestis, and Brucella spp. at the species level because of the high conservation of 16S rDNA of the same genus. The two suspension arrays can be utilized to detect Bacillus anthracis sterne spore and Yersinia pestis EV76 from mimic "write powder" samples, they also proved that the suspension array system will be valuable tools for diagnosis of bacterial biothreat agents in environmental samples.

MSU-Northern Bio-Energy Center of Excellence

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

Kegel, Greg; Windy Boy, Jessica; Maglinao, Randy Latayan

The goal of this project was to establish the Bio-Energy Center (the Center) of Montana State University Northern (MSUN) as a Regional Research Center of Excellence in research, product development, and commercialization of non-food biomass for the bio-energy industry. A three-step approach, namely, (1) enhance the Center’s research and testing capabilities, (2) develop advanced biofuels from locally grown agricultural crops, and (3) educate the community through outreach programs for public understanding and acceptance of new technologies was identified to achieve this goal. The research activities aimed to address the obstacles concerning the production of biofuels and other bio-based fuel additivesmore » considering feedstock quality, conversion process, economic viability, and public awareness. First and foremost in enhancing the capabilities of the Center is the improvement of its laboratories and other physical facilities for investigating new biomass conversion technologies and the development of its manpower complement with expertise in chemistry, engineering, biology, and energy. MSUN renovated its Auto Diagnostics building and updated its mechanical and electrical systems necessary to house the state-of-the-art 525kW (704 hp) A/C Dynamometer. The newly renovated building was designated as the Advanced Fuels Building. Two laboratories, namely Biomass Conversion lab and Wet Chemistry lab were also added to the Center’s facilities. The Biomass Conversion lab was for research on the production of advanced biofuels including bio-jet fuel and bio-based fuel additives while the Wet Chemistry lab was used to conduct catalyst research. Necessary equipment and machines, such as gas chromatograph-mass spectrometry, were purchased and installed to help in research and testing. With the enhanced capabilities of the Center, research and testing activities were very much facilitated and more precise. New biofuels derived from Camelina sativa (camelina), a locally-grown oilseed crop was developed through a chemical process for converting the oil extracted into jet fuel. Promising methods of synthesizing heterogeneous metal complex catalyst that support the chemical conversion process were likewise developed. Breaking-down lignin to valuable chemicals using a metal complex catalyst was also investigated. Lignin is an organic polymer that binds around cellulose and hemicellulose fibers which strengthen cell walls in woody biomass. Test results showed promise and could lead to further exploration of using lignin for fuels and fuel additives. These findings could create another value-added product from lignin that can be sourced from beetle kill trees and product residues from cellulose ethanol plants. Coupled with these research discoveries was the provision of technical support to businesses in terms of product development and commercialization of bio-based products. This in turn opened new avenues for advancing the bio-energy industry in the region and helped support the regional agricultural-based economy through developing biofuels derived from feedstock that are grown locally. It assisted in developing biofuels that reduce exhaust emissions and improve engine performance.« less

[Analysis of genetic polymorphisms and mutations of 20 frequently used STR loci among ethnic Hans from Henan].

PubMed

Wang, Hongdan; Kang, Bing; Gao, Yue; Huo, Xiaodong; Li, Tao; Guo, Qiannan; Zhu, Bofeng; Liao, Shixiu

2017-04-10

To study the genetic polymorphisms and mutations of 20 frequently used autosomal microsatellites among ethnic Hans from Henan. Peripheral blood samples of 2604 individuals were collected. DNA was amplified and genotyped using a PowerPlex(TM) 21 system. The frequencies, forensic parameters and mutation rates of the 20 short tandem repeat (STR) loci were analyzed. A total of 323 alleles were found in this population and the allelic frequencies have ranged from 0.0003 to 0.5144. Except for D3S1358, TH01 and TPOX, mutations have been found in all of the remaining 17 STR loci, which totaled 47, with mutation rates ranging from 0 to 3.46 × 10 -3 . The 20 STR loci selected by the PowerPlex(TM) 21 system are highly polymorphic among ethnic Hans from Henan, and may be of great value in forensic and human population studies. As no similar study has been carried out previously, above results may be of great value for individual discrimination and paternal testing.

Concordance and population studies along with stutter and peak height ratio analysis for the PowerPlex ® ESX 17 and ESI 17 Systems.

PubMed

Hill, Carolyn R; Duewer, David L; Kline, Margaret C; Sprecher, Cynthia J; McLaren, Robert S; Rabbach, Dawn R; Krenke, Benjamin E; Ensenberger, Martin G; Fulmer, Patricia M; Storts, Douglas R; Butler, John M

2011-08-01

The PowerPlex(®) ESX 17 and ESI 17 Systems for short tandem repeat (STR) amplification were developed by the Promega Corporation to meet the European Network of Forensic Science Institutes (ENFSI) and the European DNA Profiling (EDNAP) Group recommendations for increasing the number of STR loci included in the European Standard Set (ESS). The PowerPlex ESX 17 and ESI 17 Systems utilize different PCR primer combinations to co-amplify the following 17 loci: D1S1656, D2S441, D2S1338, D3S1358, D8S1179, D10S1248, D12S391, D16S539, D18S51, D19S433, D21S11, D22S1045, FGA, TH01, vWA, SE33, and the sex-typing locus amelogenin. A total of 1443 U.S. population samples were evaluated with pre-commercialization versions of both kits. Stutter and heterozygote peak height ratios have been used to characterize kit performance. Typing results have been used to estimate the match probabilities provided by the chosen loci as well as in concordance studies. Full concordance between the typing results for the two kits was observed in 99.994% (49,055 out of 49,062) STR allele calls compared. All genotyping discrepancies were confirmed by DNA sequence analysis. As a result of these comparisons, a second forward primer for the D22S1045 locus has been added to the PowerPlex ESX 17 System to address a primer binding site mutation and the D1S1656 locus reverse primer in the PowerPlex ESI 17 System was modified to eliminate an amplification-efficiency reducing primer dimer. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Developmental validation of the PowerPlex(®) 21 System.

PubMed

Ensenberger, Martin G; Hill, Carolyn R; McLaren, Robert S; Sprecher, Cynthia J; Storts, Douglas R

2014-03-01

The PowerPlex(®) 21 System is a STR multiplex that has been optimized for casework samples while still being capable of database workflows including direct amplification. The loci included in the multiplex offer increasing overlap with core loci used in different countries and regions throughout the world. The PowerPlex(®) 21 System contains D1S1656, D2S1338, D3S1358, D5S818, D6S1043, D7S820, D8S1179, D12S391, D13S317, D16S539, D18S51, D19S433, D21S11, Amelogenin, CSF1PO, FGA, Penta D, Penta E, TH01, TPOX, and vWA. These loci represent all 13 core CODIS loci in addition to loci commonly used in Asia and Europe. A developmental validation study was completed to document performance capabilities and limitations of the PowerPlex(®) 21 System. Data from this validation work served as the basis for the following conclusions: genotyping of single-source samples was reliable across a range of template DNA concentrations with >95% alleles called at 50 pg. Direct amplification of samples from FTA(®) storage cards was successfully performed using the reagents provided with the system and modified cycling protocols provided in the technical manual. Mixture analysis showed that over 95% of minor alleles were detected at 1:9 ratios. Reaction conditions including volume and annealing temperature as well as the concentrations of primers, DNA polymerase, magnesium, and Master Mix were shown to be optimal and able to withstand moderate variations without affecting system performance. Reproducible results were generated by different users at different sites. Finally, concordance studies showed consistent results when comparing the PowerPlex(®) 21 System with other commercially available STR-genotyping systems. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Development of a new 26plex Y-STRs typing system for forensic application.

PubMed

Zhang, Suhua; Tian, Huaizhou; Wang, Zheng; Zhao, Shumin; Hu, Zhen; Li, Chengtao; Ji, Chaoneng

2014-11-01

In this study, 26plex Y-STRs typing system, including 17 Y-STRs (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4) recommended as YHRD standard loci and nine new highly discriminating Y-STRs (DYS549, DYS643, DYS388, DYS570, DYS533, DYS576, DYS460, DYS481 and DYS449), was established with 5-dye fluorescences labelling. Developmental validation indicated that the 26plex Y-STRs typing system was reproducible, accurate, sensitive and robust. The sensitivity of the system was such that a full profile was obtainable even with 125pg of male DNA. Specificity testing was demonstrated by the lack of cross-reactivity with a variety of commonly encountered animal species and bacteria. Also, the multiplex is suitable for mixture study. An average of above 97% of the minor alleles detected with the male/male mixture with 1:3 and 3:1 ratios, while an average of above 70% of the minor alleles detected with the male/male mixture with 1:19 and 19:1 ratios. Full profiles are consistently detected with 125pg of male DNA, even in the presence of excessive amounts of female DNA. In addition, the whole PCR amplification of the 26 Y-STRs can finish in 1h, making the multiplex system suitable for fast-detection. For the forensic evaluation of the multiplex system, 516 haplotypes were found among 517 unrelated males. HD of the multiplex system was 0.9999925 while DC was 0.9980658, which is suitable for forensic application. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Duchenne/Becker muscular dystrophy: A report on clinical, biochemical, and genetic study in Gujarat population, India

PubMed Central

Rao, Mandava V.; Sindhav, Gaurang M.; Mehta, Jitendra J.

2014-01-01

Objective: In India, various groups have studied different regions to find out deletion pattern of dystrophin gene. We have investigated its deletion pattern among Duchenne/Becker muscular dystrophy (D/BMD) patients across Gujarat. Moreover, in this study we also correlate the same with reading frame rule. However, we too consider various clinicopathological features to establish as adjunct indices when deletion detection fails. Materials and Methods: In this pilot study, a total of 88 D/BMD patients consulting at our centers in Gujarat, India were included. All patients were reviewed on basis of their clinical characteristics, tested by three primer sets of 10-plex, 9-plex, and 7-plex polymerase chain reaction (PCR) for genetic analysis; whereas, biochemical indices were measured using automated biochemical analyzers. Results: The diagnosis of D/BMD was confirmed by multiplex-PCR (M-PCR) in D/BMD patients. A number of 65 (73.86%) out of 88 patients showed deletion in dystrophin gene. The exon 50 (58.46%) was the most frequent deletion found in our study. The mean age of onset of DMD and BMD was 4.09 ± 0.15 and 7.14 ± 0.55 years, respectively. In patients, mean creatine phosphokinase (CPK), lactate dehydrogenase (LDH), and myoglobin levels were elevated significantly (P < 0.05) in comparison to controls. Addition to CPK, LDH and myoglobin are good adjunct when deletion detection failed. These data are further in accordance with world literature when correlated with frame rule. Conclusion: The analysis has been carried out for the first time for a total of 88 D/BMD patients particularly from Gujarat, India. More research is essential to elucidate specific mutation pattern in association with management and therapies of proband. PMID:25221400

Duchenne/Becker muscular dystrophy: A report on clinical, biochemical, and genetic study in Gujarat population, India.

PubMed

Rao, Mandava V; Sindhav, Gaurang M; Mehta, Jitendra J

2014-07-01

In India, various groups have studied different regions to find out deletion pattern of dystrophin gene. We have investigated its deletion pattern among Duchenne/Becker muscular dystrophy (D/BMD) patients across Gujarat. Moreover, in this study we also correlate the same with reading frame rule. However, we too consider various clinicopathological features to establish as adjunct indices when deletion detection fails. In this pilot study, a total of 88 D/BMD patients consulting at our centers in Gujarat, India were included. All patients were reviewed on basis of their clinical characteristics, tested by three primer sets of 10-plex, 9-plex, and 7-plex polymerase chain reaction (PCR) for genetic analysis; whereas, biochemical indices were measured using automated biochemical analyzers. The diagnosis of D/BMD was confirmed by multiplex-PCR (M-PCR) in D/BMD patients. A number of 65 (73.86%) out of 88 patients showed deletion in dystrophin gene. The exon 50 (58.46%) was the most frequent deletion found in our study. The mean age of onset of DMD and BMD was 4.09 ± 0.15 and 7.14 ± 0.55 years, respectively. In patients, mean creatine phosphokinase (CPK), lactate dehydrogenase (LDH), and myoglobin levels were elevated significantly (P < 0.05) in comparison to controls. Addition to CPK, LDH and myoglobin are good adjunct when deletion detection failed. These data are further in accordance with world literature when correlated with frame rule. The analysis has been carried out for the first time for a total of 88 D/BMD patients particularly from Gujarat, India. More research is essential to elucidate specific mutation pattern in association with management and therapies of proband.

Design of neural network model-based controller in a fed-batch microbial electrolysis cell reactor for bio-hydrogen gas production

NASA Astrophysics Data System (ADS)

Azwar; Hussain, M. A.; Abdul-Wahab, A. K.; Zanil, M. F.; Mukhlishien

2018-03-01

One of major challenge in bio-hydrogen production process by using MEC process is nonlinear and highly complex system. This is mainly due to the presence of microbial interactions and highly complex phenomena in the system. Its complexity makes MEC system difficult to operate and control under optimal conditions. Thus, precise control is required for the MEC reactor, so that the amount of current required to produce hydrogen gas can be controlled according to the composition of the substrate in the reactor. In this work, two schemes for controlling the current and voltage of MEC were evaluated. The controllers evaluated are PID and Inverse neural network (NN) controller. The comparative study has been carried out under optimal condition for the production of bio-hydrogen gas wherein the controller output is based on the correlation of optimal current and voltage to the MEC. Various simulation tests involving multiple set-point changes and disturbances rejection have been evaluated and the performances of both controllers are discussed. The neural network-based controller results in fast response time and less overshoots while the offset effects are minimal. In conclusion, the Inverse neural network (NN)-based controllers provide better control performance for the MEC system compared to the PID controller.

Targeted DNA delivery to cancer cells using a biotinylated chitosan carrier.

PubMed

Darvishi, Mohammad H; Nomani, Alireza; Hashemzadeh, Hadi; Amini, Mohsen; Shokrgozar, Mohammad A; Dinarvand, Rassoul

2017-05-01

A novel biotinylated chitosan-graft-polyethyleneimine (Bio-Chi-g-PEI) copolymer was synthesized and evaluated as a nonviral gene delivery carrier for improvement of the transfection efficiency, endosomal escape, and targeted gene delivery of a plasmid encoding green fluorescent protein N1 (pEGFP-N1) into two different biotin-overexpressing cell lines including HeLa and OVCAR-3 cells. The structure of the obtained copolymers was confirmed by 1 H nuclear magnetic resonance ( 1 H NMR) and Fourier transform infrared spectroscopy. Physicochemical properties of the Bio-Chi-g-PEI/plasmid DNA (pDNA) complexes such as complex stability, size, zeta potential, and their morphology were investigated at various weight ratios of copolymer to pDNA. Bio-Chi-g-PEI copolymers could effectively condense pDNA into small particles with average diameters less than 164 nm and the zeta potential of +34.8 mV at the N/P ratio of 40/1. As revealed by flow cytometry, Bio-Chi-g-PEI/pDNA complexes had lower cytotoxicity than that of PEI 25 kDa/pDNA complexes in both cell lines. In vitro experiments revealed that the Bio-Chi-gPEI/pDNA complexes not only had much lower cytotoxicity, but also displayed higher transfection efficiency than that of PEI 25kDa/pDNA complexes. High percentage of cancer cells was successfully transfected by Bio-Chi-g-PEI/pDNA and properly expressed GFP protein. This study indicates that this copolymer complex can be a promising gene delivery carrier. © 2016 International Union of Biochemistry and Molecular Biology, Inc.

LIMITED PHYTO-AND BIO-AVAILABILITY PREVENT RISK FROM CADMIUM IN REGULATED BIOSOLIDS (ABSTRACT)

EPA Science Inventory

Biosolids are a complex mixture which usually contain 100-times more Zn than Cd, and both inorganic and organic Cd adsorbents. Experiments were conducted to test the effect of persistent inorganic adsorbents in biosolids on phytoavailability of soil Cd to lettuce, and the role of...

LIMITED PHYTO- AND BIO-AVAILABILITY PREVENT RISK FROM CADMIUM IN REGULATED BIOSOLIDS

EPA Science Inventory

Biosolids are a complex mixture which usually contain 100-times more Zn than Cd, and both inorganic and organic Cd adsorbents. Experiments were conducted to test the effect of persistent inorganic adsorbents in biosolids on phytoavailability of soil Cd to lettuce, and the role of...

Identification of Skeletal Remains of Communist Armed Forces Victims During and After World War II: Combined Y-chromosome Short Tandem Repeat (STR) and MiniSTR Approach

PubMed Central

Marjanović, Damir; Durmić-Pašić, Adaleta; Kovačević, Lejla; Avdić, Jasna; Džehverović, Mirela; Haverić, Sanin; Ramić, Jasmin; Kalamujić, Belma; Bilela, Lada Lukić; Škaro, Vedrana; Projić, Petar; Bajrović, Kasim; Drobnič, Katja; Davoren, Jon; Primorac, Dragan

2009-01-01

Aim To report on the use of STR, Y-STRs, and miniSTRs typing methods in the identification of victims of revolutionary violence and crimes against humanity committed by the Communist Armed Forces during and after World War II in which bodies were exhumed from mass and individual graves in Slovenia. Methods Bone fragments and teeth were removed from human remains found in several small and closely located hidden mass graves in the Škofja Loka area (Lovrenska Grapa and Žolšče) and 2 individual graves in the Ljubljana area (Podlipoglav), Slovenia. DNA was isolated using the Qiagen DNA extraction procedure optimized for bone and teeth. Some DNA extracts required additional purification, such as N-buthanol treatment. The QuantifilerTM Human DNA Quantification Kit was used for DNA quantification. Initially, PowerPlex 16 kit was used to simultaneously analyze 15 short tandem repeat (STR) loci. The PowerPlex S5 miniSTR kit and AmpFℓSTR® MiniFiler PCR Amplification Kit was used for additional analysis if preliminary analysis yielded weak partial or no profiles at all. In 2 cases, when the PowerPlex 16 profiles indicated possible relatedness of the remains with reference samples, but there were insufficient probabilities to call the match to possible male paternal relatives, we resorted to an additional analysis of Y-STR markers. PowerPlex® Y System was used to simultaneously amplify 12 Y-STR loci. Fragment analysis was performed on an ABI PRISM 310 genetic analyzer. Matching probabilities were estimated using the DNA-View software. Results Following the Y-STR analysis, 1 of the “weak matches” previously obtained based on autosomal loci, was confirmed while the other 1 was not. Combined standard STR and miniSTR approach applied to bone samples from 2 individual graves resulted in positive identifications. Finally, using the same approach on 11 bone samples from hidden mass grave Žološče, we were able to obtain 6 useful DNA profiles. Conclusion The results of this study, in combination with previously obtained results, demonstrate that Y-chromosome testing and miniSTR methodology can contribute to the identification of human remains of victims of revolutionary violence from World War II. PMID:19480024

Whole-genome transcription and DNA methylation analysis of peripheral blood mononuclear cells identified aberrant gene regulation pathways in systemic lupus erythematosus.

PubMed

Zhu, Honglin; Mi, Wentao; Luo, Hui; Chen, Tao; Liu, Shengxi; Raman, Indu; Zuo, Xiaoxia; Li, Quan-Zhen

2016-07-13

Recent achievement in genetics and epigenetics has led to the exploration of the pathogenesis of systemic lupus erythematosus (SLE). Identification of differentially expressed genes and their regulatory mechanism(s) at whole-genome level will provide a comprehensive understanding of the development of SLE and its devastating complications, lupus nephritis (LN). We performed whole-genome transcription and DNA methylation analysis in PBMC of 30 SLE patients, including 15 with LN (SLE LN(+)) and 15 without LN (SLE LN(-)), and 25 normal controls (NC) using HumanHT-12 Beadchips and Illumina Human Methy450 chips. The serum proinflammatory cytokines were quantified using Bio-plex Human Cytokine 27-plex assay. Differentially expressed genes and differentially methylated CpG were analyzed with GenomeStudio, R, and SAM software. The association between DNA methylation and gene expression were tested. Gene interaction pathways of the differentially expressed genes were analyzed by IPA software. We identified 552 upregulated genes and 550 downregulated genes in PBMC of SLE. Integration of DNA methylation and gene expression profiling showed that 334 upregulated genes were hypomethylated, and 479 downregulated genes were hypermethylated. Pathway analysis on the differential genes in SLE revealed significant enrichment in interferon (IFN) signaling and toll-like receptor (TLR) signaling pathways. Nine IFN- and seven TLR-related genes were identified and displayed step-wise increase in SLE LN(-) and SLE LN(+). Hypomethylated CpG sites were detected on these genes. The gene expressions for MX1, GPR84, and E2F2 were increased in SLE LN(+) as compared to SLE LN(-) patients. The serum levels of inflammatory cytokines, including IL17A, IP-10, bFGF, TNF-α, IL-6, IL-15, GM-CSF, IL-1RA, IL-5, and IL-12p70, were significantly elevated in SLE compared with NC. The levels of IL-15 and IL1RA correlated with their mRNA expression. The upregulation of IL-15 may be regulated by hypomethylated CpG sites in the promotor region of the gene. Our study has demonstrated that significant number of differential genes in SLE were involved in IFN, TLR signaling pathways, and inflammatory cytokines. The enrichment of differential genes has been associated with aberrant DNA methylation, which may be relevant to the pathogenesis of SLE. Our observations have laid the groundwork for further diagnostic and mechanistic studies of SLE and LN.

Performance of the SNPforID 52 SNP-plex assay in paternity testing.

PubMed

Børsting, Claus; Sanchez, Juan J; Hansen, Hanna E; Hansen, Anders J; Bruun, Hanne Q; Morling, Niels

2008-09-01

The performance of a multiplex assay with 52 autosomal single nucleotide polymorphisms (SNPs) developed for human identification was tested on 124 mother-child-father trios. The typical paternity indices (PIs) were 10(5)-10(6) for the trios and 10(3)-10(4) for the child-father duos. Using the SNP profiles from the randomly selected trios and 700 previously typed individuals, a total of 83,096 comparisons between mother, child and an unrelated man were performed. On average, 9-10 mismatches per comparison were detected. Four mismatches were genetic inconsistencies and 5-6 mismatches were opposite homozygosities. In only two of the 83,096 comparisons did an unrelated man match perfectly to a mother-child duo, and in both cases the PI of the true father was much higher than the PI of the unrelated man. The trios were also typed for 15 short tandem repeats (STRs) and seven variable number of tandem repeats (VNTRs). The typical PIs based on 15 STRs or seven VNTRs were 5-50 times higher than the typical PIs based on 52 SNPs. Six mutations in tandem repeats were detected among the randomly selected trios. In contrast, there was not found any mutations in the SNP loci. The results showed that the 52 SNP-plex assay is a very useful alternative to currently used methods in relationship testing. The usefulness of SNP markers with low mutation rates in paternity and immigration casework is discussed.

Exploratory Investigation of Early Biomarkers for Chronic Fatigue in Prostate Cancer Patients Following Radiation Therapy

PubMed Central

Feng, Li Rebekah; Wolff, Brian S.; Lukkahatai, Nada; Espina, Alexandra; Saligan, Leorey N.

2016-01-01

Background Fatigue is one of the most debilitating side effects of cancer therapy. Identifying biomarkers early during cancer therapy may help us understand the biologic underpinnings of the persistence of fatigue following therapy. Objective We aimed to identify early biomarkers of fatigue by examining correlations of levels of cytokines during external beam radiation therapy (EBRT) with persistence of fatigue one year following treatment completion in men with non-metastatic prostate cancer (NM-PC). Methods A sample of 34 men with NM-PC scheduled to receive EBRT were followed at baseline (T1), midpoint of EBRT (T2), and one year following EBRT (T3). Demographic and clinical data were obtained by chart review. The Functional Assessment of Cancer Therapy-Fatigue (FACT-F) was administered to measure fatigue levels. Plasma cytokine levels were determined at T1 and T2 using the Bio-Rad Bio-Plex Cytokine Assay Kits. Results Significant correlations were observed between levels of IL-3, IL-8, IL-9, IL-10, IL-16, IP10, IFNα2, IFNγ, and SDF1α at T2 with worsening of fatigue from T1 to T3. Conclusions Immunological changes prior to chronic fatigue development may reflect the long term response to radiation therapy-induced damage. Implications for Practice Early biomarkers for chronic fatigue related to cancer therapy will help advance our understanding of the etiology of this distressing symptom and will help nurses identify patients at risk for developing chronic fatigue after cancer treatment. This information will also aide in patient education, as well as symptom management. PMID:27105468

Effect of inorganic or organic selenium supplementation on reproductive performance and tissue trace mineral concentrations in gravid first-parity gilts, fetuses, and nursing piglets.

PubMed

Ma, Y L; Lindemann, M D; Pierce, J L; Unrine, J M; Cromwell, G L

2014-12-01

The objective of this experiment was to evaluate 2 supplemental forms of Se on reproductive performance and tissue trace mineral concentration in fetus and first-parity gilts during pregnancy and their progeny. Crossbred gilts (n=100) were selected at 183±2.7 d and 137±10 kg BW and fed a common diet. After 1 mo, 8 gilts were sacrificed to establish baseline liver Se concentration and the remaining 92 gilts allotted to receive Se (0.3 mg/kg diet) as inorganic Se (Na2SeO3) or a Se supplement that contains organoselenium compounds (Sel-Plex; Alltech Inc., Nicholasville, KY). At 267±5.7 d (171±11 kg), gilts were estrus-synchronized and bred. Gilts were then slaughtered at defined time points throughout gestation (d 0, 43, 58, 73, 91, 101, or 108 of gestation; n=6 to 12 gilts/time point). A week before the expected farrowing day, 10 pregnant gilts (5 from each treatment) were moved to farrowing crates and monitored. Two pigs from each litter were randomly selected and euthanized at d 0 (within 2 h after birth; nursing deprived), 7, 14, and 21 from each litter. During the gestation phase, maternal liver, and fetal body and liver were collected for determination of trace mineral concentration by inductively coupled plasma mass spectrometry. Total number of fetus, crown-rump length, and corpora lutea of gilts were recorded as well. During the lactation phase, pigs (without liver and gastrointestinal tract) and associated liver were analyzed for Se concentration. The results demonstrated that the source of Se generally did not affect the maternal reproductive traits and fetal characteristics. Also, the source of Se supplemented to the maternal diet did not, in general, affect Cu, Fe, Mn, or Zn concentrations in the tissues evaluated other than the observation of a greater maternal liver Mn content (P<0.01) in gilts fed Sel-Plex and a greater amount of Fe accumulated in the entire litter (P<0.01) in gilts fed Sel-Plex. However, with regard to Se concentrations, Se in fetal body, fetal liver, and maternal liver were greater (P<0.01) when Sel-Plex was fed. Postnatal pigs from gilts fed Sel-Plex had greater (P<0.05) Se retention in body and liver with similar growth performance during the 21-d period. The results demonstrate Se form differences wherein Sel-Plex is associated with greater Se accumulation in both maternal and fetal tissues.

75 FR 5033 - Departmental Management; Public meeting on BioPreferredSM

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-01

...; Public meeting on BioPreferred\\SM\\ Complex Products and Assemblies Designation and Industry Training on... include: 1. Using BioPreferred tools to position your business to sell or increase sales to the Federal...: Ron Buckhalt, BioPreferred Manager, U.S. Department of Agriculture, Office of Procurement and Property...

The interaction between anti-Ro/SSA and anti-La/SSB autoantibodies and anti-infectious antibodies in a wide spectrum of auto-immune diseases: another angle of the autoimmune mosaic.

PubMed

Agmon-Levin, Nancy; Dagan, Amir; Peri, Yogev; Anaya, Juan-Manuel; Selmi, Carlo; Tincani, Angela; Bizzaro, Nicola; Stojanovich, Ljudmila; Damoiseaux, Jan; Cohen Tervaert, Jan Willem; Mosca, Marta; Cervera, Ricard; Shoenfeld, Yehuda

2017-01-01

The presence of anti-Ro/SSA and anti-La/SSB antibodies has been linked with autoimmunity in general and with several autoimmune diseases (AID) in particular. In the current study we evaluated these antibodies in a wide spectrum of AID as well as the links between them and anti-infectious antibodies. We examined 2082 sera from patients with 16 different AID compared to 524 sera from geographically-matched healthy controls, for the presence and titres of anti-Ro/SSA and anti-La/SSB. All samples were also tested for a variety of anti-infectious agents' antibodies using the BioPlex 2200-immunoassay (Bio-Rad, USA). Anti-Ro/SSA was more prevalent, with significantly higher titre in 5 autoimmune diseases namely Sjögren's syndrome (SS), systemic lupus erythematosus (SLE), antiphospholipid syndrome (APS) both primary and APS linked to SLE, systemic sclerosis (SSc) and primary biliary cirrhosis (PBC). Anti-La/SSB was more prevalent with higher titers in SS, SLE, APS linked to SLE and PBC. Prevalence, but not titers, of both antibodies were higher also in polymyositis (PM). Additionally, we found a correlation between anti-Ro/SSA antibodies and antibodies of the IgM and IgG subtypes directed at cytomegalovirus as well as IgG-antibodies directed at Epstein-Barr virus (EBV) and toxoplasma (p<0.001). Anti-La/SSB antibodies correlated with the presence of IgG antibodies against EBV early antigen (p<0.001). In a large cohort of patients with autoimmune diseases we found an association between anti-Ro/SSA and anti-La/SSB antibodies and 6 autoimmune diseases, amongst which primary APS and PM. Additionally, we observed linkages between these autoantibodies and anti-infectious antibodies directed at Epstein-Barr virus, toxoplasma and cytomegalovirus. Our findings support the concept of interplay between infectious agents and autoimmunity, such as the plausibility of an infectious agent that trigger the immune system to produce specific antibodies which will later result in a unique group of AID.

[Analysis of allele dropout at TH01 locus in paternity testing].

PubMed

Lai, Li; Shen, Xiao-li; Xue, Shi-jie; Hu, Jie

2013-10-01

To analyze allele dropout at TH01 locus in paternity testing in order to determine the accurate genotype. To use a two STR loci genotyping system to verify an abnormal genotype for the TH01 locus with PCR using specific primers, cloning and DNA sequencing. A rare allele at TH01 locus named 5.2, which was undetectable with PowerPlex 21 system, was detected with an Identifiler system. Genetic variations may result in rare alleles and loci loss. To avoid misjudgment, laboratories should have a variety of methods for detecting loci loss.

BioStar models of clinical and genomic data for biomedical data warehouse design

PubMed Central

Wang, Liangjiang; Ramanathan, Murali

2008-01-01

Biomedical research is now generating large amounts of data, ranging from clinical test results to microarray gene expression profiles. The scale and complexity of these datasets give rise to substantial challenges in data management and analysis. It is highly desirable that data warehousing and online analytical processing technologies can be applied to biomedical data integration and mining. The major difficulty probably lies in the task of capturing and modelling diverse biological objects and their complex relationships. This paper describes multidimensional data modelling for biomedical data warehouse design. Since the conventional models such as star schema appear to be insufficient for modelling clinical and genomic data, we develop a new model called BioStar schema. The new model can capture the rich semantics of biomedical data and provide greater extensibility for the fast evolution of biological research methodologies. PMID:18048122

Brucella BioR regulator defines a complex regulatory mechanism for bacterial biotin metabolism.

PubMed

Feng, Youjun; Xu, Jie; Zhang, Huimin; Chen, Zeliang; Srinivas, Swaminath

2013-08-01

The enzyme cofactor biotin (vitamin H or B7) is an energetically expensive molecule whose de novo biosynthesis requires 20 ATP equivalents. It seems quite likely that diverse mechanisms have evolved to tightly regulate its biosynthesis. Unlike the model regulator BirA, a bifunctional biotin protein ligase with the capability of repressing the biotin biosynthetic pathway, BioR has been recently reported by us as an alternative machinery and a new type of GntR family transcriptional factor that can repress the expression of the bioBFDAZ operon in the plant pathogen Agrobacterium tumefaciens. However, quite unusually, a closely related human pathogen, Brucella melitensis, has four putative BioR-binding sites (both bioR and bioY possess one site in the promoter region, whereas the bioBFDAZ [bio] operon contains two tandem BioR boxes). This raised the question of whether BioR mediates the complex regulatory network of biotin metabolism. Here, we report that this is the case. The B. melitensis BioR ortholog was overexpressed and purified to homogeneity, and its solution structure was found to be dimeric. Functional complementation in a bioR isogenic mutant of A. tumefaciens elucidated that Brucella BioR is a functional repressor. Electrophoretic mobility shift assays demonstrated that the four predicted BioR sites of Brucella plus the BioR site of A. tumefaciens can all interact with the Brucella BioR protein. In a reporter strain that we developed on the basis of a double mutant of A. tumefaciens (the ΔbioR ΔbioBFDA mutant), the β-galactosidase (β-Gal) activity of three plasmid-borne transcriptional fusions (bioBbme-lacZ, bioYbme-lacZ, and bioRbme-lacZ) was dramatically decreased upon overexpression of Brucella bioR. Real-time quantitative PCR analyses showed that the expression of bioBFDA and bioY is significantly elevated upon removal of bioR from B. melitensis. Together, we conclude that Brucella BioR is not only a negative autoregulator but also a repressor of expression of bioY and bio operons that separately function in biotin transport and the biosynthesis pathway.

Brucella BioR Regulator Defines a Complex Regulatory Mechanism for Bacterial Biotin Metabolism

PubMed Central

Xu, Jie; Zhang, Huimin; Srinivas, Swaminath

2013-01-01

The enzyme cofactor biotin (vitamin H or B7) is an energetically expensive molecule whose de novo biosynthesis requires 20 ATP equivalents. It seems quite likely that diverse mechanisms have evolved to tightly regulate its biosynthesis. Unlike the model regulator BirA, a bifunctional biotin protein ligase with the capability of repressing the biotin biosynthetic pathway, BioR has been recently reported by us as an alternative machinery and a new type of GntR family transcriptional factor that can repress the expression of the bioBFDAZ operon in the plant pathogen Agrobacterium tumefaciens. However, quite unusually, a closely related human pathogen, Brucella melitensis, has four putative BioR-binding sites (both bioR and bioY possess one site in the promoter region, whereas the bioBFDAZ [bio] operon contains two tandem BioR boxes). This raised the question of whether BioR mediates the complex regulatory network of biotin metabolism. Here, we report that this is the case. The B. melitensis BioR ortholog was overexpressed and purified to homogeneity, and its solution structure was found to be dimeric. Functional complementation in a bioR isogenic mutant of A. tumefaciens elucidated that Brucella BioR is a functional repressor. Electrophoretic mobility shift assays demonstrated that the four predicted BioR sites of Brucella plus the BioR site of A. tumefaciens can all interact with the Brucella BioR protein. In a reporter strain that we developed on the basis of a double mutant of A. tumefaciens (the ΔbioR ΔbioBFDA mutant), the β-galactosidase (β-Gal) activity of three plasmid-borne transcriptional fusions (bioBbme-lacZ, bioYbme-lacZ, and bioRbme-lacZ) was dramatically decreased upon overexpression of Brucella bioR. Real-time quantitative PCR analyses showed that the expression of bioBFDA and bioY is significantly elevated upon removal of bioR from B. melitensis. Together, we conclude that Brucella BioR is not only a negative autoregulator but also a repressor of expression of bioY and bio operons that separately function in biotin transport and the biosynthesis pathway. PMID:23729648

One-step simultaneous detection of Ureaplasma parvum and genotypes SV1, SV3 and SV6 from clinical samples using PlexPCR technology.

PubMed

Payne, M S; Furfaro, L L; Tucker, R; Tan, L Y; Mokany, E

2017-08-01

Ureaplasma spp. are associated with preterm birth. In recent times, it has become apparent that Ureaplasma parvum, but not Ureaplasma urealyticum, is of most relevance. We recently demonstrated this in Australian pregnant women and using high-resolution melt (HRM) PCR, further showed that U. parvum genotype SV6 was of particular significance. However, our assay was unable to identify multiple genotypes in the same sample, required a separate species-level qPCR for low titre samples and was not ideal for diagnostic laboratories due to the nature of HRM PCR result interpretation. Consequently, our current study developed a novel, one-step PlexPCR assay capable of detecting U. parvum and genotypes SV1, SV3 and SV6 in a single reaction directly from clinical samples. We then validated this using vaginal swab DNA from our Australian cohort of pregnant women. The PlexPCR was highly sensitive, detecting all targets to between 0.4 × 10 -5  ng DNA (SV3) and 0.4 × 10 -6  ng DNA (U. parvum, SV1 and SV6). Compared to our HRM PCR, the PlexPCR defined genotype distribution in all seven cases previously reported as 'mixed', and detected another eight cases where multiple genotypes (two) were present in samples previously reported as single genotypes using HRM PCR. Ureaplasma spp. have been associated with prematurity for decades, however, only a minority of studies have examined this beyond the genus level. In those that have, Ureaplasma parvum has been strongly associated with preterm birth. We recently demonstrated this in Australian women and further showed that U. parvum genotype SV6 was of particular significance. Our PlexPCR assay allows rapid detection and concurrent genotyping of U. parvum in clinical samples and may be of particular interest to obstetricians, particularly those caring for women at a high risk of preterm birth, and any other disease phenotypes where U. parvum is of interest. © 2017 The Authors. Letters in Applied Microbiology published by John Wiley & Sons Ltd on behalf of The Society for Applied Microbiology.

Improved amplification results following episodes of failure to amplify at the Amelogenin Locus using PowerPlex® ESI 16 Fast System.

PubMed

Berlyne, Sigal; Oz, Carla; Einot, Naftaly; Avraham, Shlomit; Ram, Tanya; Goldberg, Miri D; Gafny, Ron

2017-07-01

In 2012 the Israel Police DNA Casework laboratory adopted the 16 STR PowerPlex ® ESI kit for routine use. The Promega Company updated this kit and developed the PowerPlex ® ESI 16 Fast System in which all autosomal primer pairs remained identical to the original set, except at the amelogenin site. The master mix was improved and optimized which allowed for direct, faster and more robust amplification. Prior to implementing the PowerPlex ® ESI 16 Fast System in our lab, we conducted a preliminary assay where 213 casework samples were amplified using the new kit. These samples had previously been extracted by one of two extraction kits employed by our lab. (the PrepFiler ExpressTM and PrepFiler BTATM Forensic DNA Extraction Kits). The amplification results from these samples were compared to samples amplified using the original PowerPlex ® ESI 16 kit. Multiple incidents of failure to amplify at the amelogenin locus were noted using the new system with the recommended protocol at a rate of 13% (28 of 213 samples). Experiments were performed to understand whether these amplification failures could be a result of primer binding site mutations, extraction method reagents and/or inhibitors. The conclusions reached following these experiments, in conjunction with consultation with the manufacturer, led to the trial of a modified amplification protocol where the suggested annealing temperature was reduced by 2 degrees. To evaluate the efficiency of this altered protocol, a comparison study was undertaken where 88 additional casework samples were chosen and amplified using both the modified 58°C and the recommended 60°C annealing temperatures. We concluded that the most effective method in our laboratory for achieving a consistent and balanced amplification at the amelogenin locus was to reduce the annealing temperature from the manufacturer's recommended 60°C to 58°C. This modification resulted in a reduction of the failure to amplify at the amelogenin locus from 13% (28/213) to 1.1% (1/88) without any observed changes to the autosomal STR amplification results. Copyright © 2017 Elsevier B.V. All rights reserved.

Paracoccus denitrificans possesses two BioR homologs having a role in regulation of biotin metabolism.

PubMed

Feng, Youjun; Kumar, Ritesh; Ravcheev, Dmitry A; Zhang, Huimin

2015-08-01

Recently, we determined that BioR, the GntR family of transcription factor, acts as a repressor for biotin metabolism exclusively distributed in certain species of α-proteobacteria, including the zoonotic agent Brucella melitensis and the plant pathogen Agrobacterium tumefaciens. However, the scenario is unusual in Paracoccus denitrificans, another closely related member of the same phylum α-proteobacteria featuring with denitrification. Not only does it encode two BioR homologs Pden_1431 and Pden_2922 (designated as BioR1 and BioR2, respectively), but also has six predictive BioR-recognizable sites (the two bioR homolog each has one site, whereas the two bio operons (bioBFDAGC and bioYB) each contains two tandem BioR boxes). It raised the possibility that unexpected complexity is present in BioR-mediated biotin regulation. Here we report that this is the case. The identity of the purified BioR proteins (BioR1 and BioR2) was confirmed with LC-QToF-MS. Phylogenetic analyses combined with GC percentage raised a possibility that the bioR2 gene might be acquired by horizontal gene transfer. Gel shift assays revealed that the predicted BioR-binding sites are functional for the two BioR homologs, in much similarity to the scenario seen with the BioR site of A. tumefaciens bioBFDAZ. Using the A. tumefaciens reporter system carrying a plasmid-borne LacZ fusion, we revealed that the two homologs of P. denitrificans BioR are functional repressors for biotin metabolism. As anticipated, not only does the addition of exogenous biotin stimulate efficiently the expression of bioYB operon encoding biotin transport/uptake system BioY, but also inhibits the transcription of the bioBFDAGC operon resembling the de novo biotin synthetic pathway. EMSA-based screening failed to demonstrate that the biotin-related metabolite is involved in BioR-DNA interplay, which is consistent with our former observation with Brucella BioR. Our finding defined a complex regulatory network for biotin metabolism in P. denitrificans by two BioR proteins. © 2015 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Paracoccus denitrificans possesses two BioR homologs having a role in regulation of biotin metabolism

PubMed Central

Feng, Youjun; Kumar, Ritesh; Ravcheev, Dmitry A; Zhang, Huimin

2015-01-01

Recently, we determined that BioR, the GntR family of transcription factor, acts as a repressor for biotin metabolism exclusively distributed in certain species of α-proteobacteria, including the zoonotic agent Brucella melitensis and the plant pathogen Agrobacterium tumefaciens. However, the scenario is unusual in Paracoccus denitrificans, another closely related member of the same phylum α-proteobacteria featuring with denitrification. Not only does it encode two BioR homologs Pden_1431 and Pden_2922 (designated as BioR1 and BioR2, respectively), but also has six predictive BioR-recognizable sites (the two bioR homolog each has one site, whereas the two bio operons (bioBFDAGC and bioYB) each contains two tandem BioR boxes). It raised the possibility that unexpected complexity is present in BioR-mediated biotin regulation. Here we report that this is the case. The identity of the purified BioR proteins (BioR1 and BioR2) was confirmed with LC-QToF-MS. Phylogenetic analyses combined with GC percentage raised a possibility that the bioR2 gene might be acquired by horizontal gene transfer. Gel shift assays revealed that the predicted BioR-binding sites are functional for the two BioR homologs, in much similarity to the scenario seen with the BioR site of A. tumefaciens bioBFDAZ. Using the A. tumefaciens reporter system carrying a plasmid-borne LacZ fusion, we revealed that the two homologs of P. denitrificans BioR are functional repressors for biotin metabolism. As anticipated, not only does the addition of exogenous biotin stimulate efficiently the expression of bioYB operon encoding biotin transport/uptake system BioY, but also inhibits the transcription of the bioBFDAGC operon resembling the de novo biotin synthetic pathway. EMSA-based screening failed to demonstrate that the biotin-related metabolite is involved in BioR-DNA interplay, which is consistent with our former observation with Brucella BioR. Our finding defined a complex regulatory network for biotin metabolism in P. denitrificans by two BioR proteins. PMID:26037461

Effect of non-tuberculous Mycobacteria on host biomarkers potentially relevant for tuberculosis management.

PubMed

Dhanasekaran, S; Jenum, Synne; Stavrum, Ruth; Wiker, Harald G; Kenneth, John; Vaz, Mario; Doherty, T Mark; Grewal, Harleen M S

2014-10-01

Non-tuberculous mycobacteria (NTM) are different from Mycobacterium tuberculosis (MTB) both in their ubiquitous environmental distribution and in their reduced capacity to cause disease. While often neglected in favour of other infectious diseases, NTM may interfere with important aspects of TB control and management, namely the efficacy of new anti-tuberculosis (TB) vaccines; the immuno-diagnostic Tuberculin skin test (TST) and QuantiFERON TB Gold In Tube assay (QFTGIT); and immune biomarkers explored for their diagnostic and/or predictive potential. Our objective was therefore to explore host immune biomarkers in children who had NTM isolated from respiratory and/or gastric specimens. The present study was nested within a prospective cohort study of BCG-vaccinated neonates in Southern India. In this setting, immune biomarkers from peripheral blood were analyzed in 210 children aged <3 years evaluated for TB using dual-colour-Reverse-Transcriptase-Multiple-Ligation-dependent-Probe-Amplification (dcRT-MLPA) and Bio-Plex assays. The children were classified based on clinical examination, chest X-rays and mycobacterial culture reports as either: 1) TB disease, 2) NTM present and 3) controls. The study shows a down-regulation of RAB33A (p<0.001) and up-regulation of TGFβ1, IL-2 and IL-6 (all p<0.05) in children with TB disease, and that RAB33A, TGFBR2 and IL-10 (all p<0.05) were differentially expressed in children with NTM present when compared to children that were culture negative for MTB and NTM (controls). Carriage of NTM may reduce the specificity of future diagnostic and predictive immune biomarkers relevant to TB management.

Analysis of the SNPforID 52-plex markers in four Native American populations from Venezuela.

PubMed

Ruiz, Y; Chiurillo, M A; Borjas, L; Phillips, C; Lareu, M V; Carracedo, Á

2012-09-01

The SNPforID 52-plex single nucleotide polymorphisms (SNPs) were analyzed in four native Venezuelan populations: Bari, Pemon, Panare and Warao. None of the population-locus combinations showed significant departure from Hardy-Weinberg equilibrium. Calculation of forensic and statistical parameters showed lower values of genetic diversity in comparison with African and European populations, as well as other, admixed populations of neighboring regions of Caribbean, Central and South America. Significant levels of divergence were observed between the four Native Venezuelan populations as well as with other previously studied populations. Analysis of the 52-plex SNP loci with Structure provided an optimum number of population clusters of three, corresponding to Africans, Europeans and Native Americans. Analysis of admixed populations indicated a range of membership proportions for ancestral populations consisting of Native American, African and European components. The genetic differences observed in the Native American groups suggested by the 52 SNPs typed in our study are in agreement with current knowledge of the demographic history of the Americas. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Retrograde Semaphorin-Plexin Signaling Drives Homeostatic Synaptic Plasticity

PubMed Central

Orr, Brian O.; Fetter, Richard D.; Davis, Graeme W.

2017-01-01

Homeostatic signaling systems ensure stable, yet flexible neural activity and animal behavior1–4. Defining the underlying molecular mechanisms of neuronal homeostatic signaling will be essential in order to establish clear connections to the causes and progression of neurological disease. Presynaptic homeostatic plasticity (PHP) is a conserved form of neuronal homeostatic signaling, observed in organisms ranging from Drosophila to human1,5. Here, we demonstrate that Semaphorin2b (Sema2b) is target-derived signal that acts upon presynaptic PlexinB (PlexB) receptors to mediate the retrograde, homeostatic control of presynaptic neurotransmitter release at the Drosophila neuromuscular junction. Sema2b-PlexB signaling regulates the expression of PHP via the cytoplasmic protein Mical and the oxoreductase-dependent control of presynaptic actin6,7. During neural development, Semaphorin-Plexin signaling instructs axon guidance and neuronal morphogenesis8–10. Yet, Semaphorins and Plexins are also expressed in the adult brain11–16. Here we demonstrate that Semaphorin-Plexin signaling controls presynaptic neurotransmitter release. We propose that Sema2b-PlexB signaling is an essential platform for the stabilization of synaptic transmission throughout life. PMID:28953869

Low-template methods yield limited extra information for PowerPlex® Fusion 6C profiling.

PubMed

Duijs, Francisca; van de Merwe, Linda; Sijen, Titia; Benschop, Corina C G

2018-06-01

Advances in autosomal DNA profiling systems enable analyzing increased numbers of short tandem repeat (STR) loci in one reaction. Increasing the number of STR loci increases the amount of information that may be obtained from a (crime scene) sample. In this study, we examined whether even more allelic information can be obtained by applying low-template methods. To this aim, the performance of the PowerPlex® Fusion 6C STR typing system was assessed when increasing the number of PCR cycles or enhancing the capillary electrophoresis (CE) injection settings. Results show that applying these low-template methods yields limited extra information and comes at cost of more background noise. In addition, the gain in detection of alleles was much smaller when compared to the gain when applying low-template methods to the 15-loci AmpFLSTR® NGM™ system. Consequently, the PowerPlex® Fusion 6C STR typing system was implemented using standard settings only; low-template methods were not implemented for our routine forensic casework. Copyright © 2018 Elsevier B.V. All rights reserved.

Requirements for the Development of Bacillus Anthracis Spore Reference Materials Used to Test Detection Systems

DTIC Science & Technology

2006-01-01

the sporangium) contributes the com- plex layers of the spore coats that encase the spore DNA. The mother cell dies and begins to fall apart at the end...spores. Bacillus spores contain a number of coat layers and some species posses an additional outermost layer called the exosporium. BA, B. cereus, and B...exosporium is the outermost layer of the BA spores, it likely contains important protein and carbohydrate markers that are recognized by antibodies

Profiling Bioactivity of the ToxCast Chemical Library Using BioMAP Primary Human Cell Systems

EPA Science Inventory

The complexity of human biology has made prediction of health effects as a consequence of exposure to environmental chemicals especially challenging. Complex cell systems, such as the Biologically Multiplexed Activity Profiling (BioMAP) primary, human, cell-based disease models, ...

X-ray absorption spectroscopy to watch catalysis by metalloenzymes: status and perspectives discussed for the water-splitting manganese complex of photosynthesis.

PubMed

Dau, Holger; Haumann, Michael

2003-01-01

Understanding structure-function relations is one of the main interests in the molecular biosciences. X-ray absorption spectroscopy of biological samples (BioXAS) has gained the status of a useful tool for characterization of the structure of protein-bound metal centers with respect to the electronic structure (oxidation states, orbital occupancies) and atomic structure (arrangement of ligand atoms). Owing to progress in the performance characteristics of synchrotron radiation sources and of experimental stations dedicated to the study of (ultra-dilute) biological samples, it is now possible to carry out new types of BioXAS experiments, which have been impracticable in the past. Of particular interest are approaches to follow biological catalysis at metal sites by characterization of functionally relevant structural changes. In this Article, the first steps towards the use of BioXAS to 'watch' biological catalysis are reviewed for the water-splitting reactions occurring at the manganese complex of photosynthesis. The following aspects are considered: the role of BioXAS in life sciences; methodological aspects of BioXAS; catalysis at the Mn complex of photosynthesis; combination of EXAFS and crystallographic information; the freeze-quench technique to capture semi-stable states; time-resolved BioXAS using a freeze-quench approach; room-temperature experiments and 'real-time' BioXAS; tasks and perspectives.

A Rapid and Inexpensive PCR-Based STR Genotyping Method for Identifying Forensic Specimens

DTIC Science & Technology

2006-06-01

this report) 20. Security Classif. (of this page) 21 . No. of Pages 22. Price Unclassified Unclassified 18 Form DOT F 1700.7 (8-72) Reproduction of...Promega PowerPlex 2.1 system (7) except that the buffer was 1x Amplitaq gold reaction buffer, 0.1% TritonX-100, and 0.2mM each dNTP in a 25µl final...electrophoresis were done using the PowerPlex 16 System (Promega Corp.; Madison, WI). rEsulTs ANd dIsCussION The goal of this study was to develop a simple DNA

Foliar application of microbial and plant based biostimulants increases growth and potassium uptake in almond (Prunus dulcis [Mill.] D. A. Webb).

PubMed

Saa, Sebastian; Olivos-Del Rio, Andres; Castro, Sebastian; Brown, Patrick H

2015-01-01

The use of biostimulants has become a common practice in agriculture. However, there is little peer-reviewed research on this topic. In this study we tested, under controlled and replicated conditions, the effect of one biostimulant derived from seaweed extraction (Bio-1) and another biostimulant derived from microbial fermentation (Bio-2). This experiment utilized 2-years-old almond plants over two growing seasons in a randomized complete design with a full 2 × 4 factorial structure with two soil potassium treatments (125 μg g(-1) of K vs. 5 μg g(-1)) and four foliar treatments (No spray, Foliar-K, Bio-1, Bio-2). Rubidium was utilized as a surrogate for short-term potassium uptake and plant growth, nutrient concentration, and final plant biomass were evaluated. There was a substantial positive effect of both biostimulant treatments on total shoot leaf area, and significant increases in shoot length and biomass under adequate soil potassium supply with a positive effect of Bio-1 only under low K supply. Rubidium uptake was increased by Bio-1 application an effect that was greater under the low soil K treatment. Though significant beneficial effects of the biostimulants used on plant growth were observed, it is not possible to determine the mode of action of these materials. The results presented here illustrate the promise and complexity of research involving biostimulants.

Structure and Properties of Melt-spun Bio-based Polyamide/Eu(TTA)3Phen Composite fibers

NASA Astrophysics Data System (ADS)

Li, Yunye; Lou, Pengfei; Jia, Qingxiu

2018-02-01

In this paper, the bio-based polyamide (PA ) was melt polymerized from four bio-based monomers. Composites of the bio-based PA and europium complex Eu(TTA)3Phen were prepared through solution mixing using N, N-Dimethylformamide (DMF) and formic acid as the mixed solvent, and then composite fibers were obtained by melt spinning method. The structure and properties of the melt-spun composite fibers were characterized by FTIR and SEM. The results indicated that the Eu(TTA)3Phen complex, with the average diameter below 300 nm, was homogeneously dispersed in the PA matrix. FTIR spectra indicated that the coordination bond between carbonyl of BDIS and Eu(TTA)3Phen complex formed, which was also confirmed by the mechanical properties. The initial modulus and breaking strength of these fibers can arrived at 2.5GPa and 0.3GPa, respectively.

Direct electronic probing of biological complexes formation

NASA Astrophysics Data System (ADS)

Macchia, Eleonora; Magliulo, Maria; Manoli, Kyriaki; Giordano, Francesco; Palazzo, Gerardo; Torsi, Luisa

2014-10-01

Functional bio-interlayer organic field - effect transistors (FBI-OFET), embedding streptavidin, avidin and neutravidin as bio-recognition element, have been studied to probe the electronic properties of protein complexes. The threshold voltage control has been achieved modifying the SiO2 gate diaelectric surface by means of the deposition of an interlayer of bio-recognition elements. A threshold voltage shift with respect to the unmodified dielectric surface toward more negative potential values has been found for the three different proteins, in agreement with their isoelectric points. The relative responses in terms of source - drain current, mobility and threshold voltage upon exposure to biotin of the FBI-OFET devices have been compared for the three bio-recognition elements.

Platelet lysate as a serum replacement for skin cell culture on biomimetic PCL nanofibers.

PubMed

Sovkova, Vera; Vocetkova, Karolina; Rampichova, Michala; Mickova, Andrea; Buzgo, Matej; Lukasova, Vera; Dankova, Jana; Filova, Eva; Necas, Alois; Amler, Evzen

2018-06-01

Platelets are a popular source of native growth factors for tissue engineering applications. The aim of the study was to verify the use of platelet lysate as a fetal bovine serum (FBS) replacement for skin cell culture. The cytokine content of the platelet lysate was characterized using the Bio-Plex system. The cells (fibroblasts, melanocytes, and keratinocytes) were cultured on PCL nanofibrous scaffolds to mimic their natural microenvironment. The cytokine content of the platelet lysate was determined, and to the cells, a medium containing platelet lysate or platelet lysate in combination with FBS was added. The results showed that 7% (v/v) platelet lysate was sufficient to supplement 10% (v/v) FBS in the culture of fibroblasts and keratinocytes. The combination of platelet lysate and FBS had a rather inhibitory effect on fibroblasts, in contrary to keratinocytes, where the effect was synergic. Platelet lysate did not sufficiently promote proliferation in melanocytes; however, the combination of FBS and platelet lysate yielded a better outcome and resulted in bipolar morphology of the cultured melanocytes. The data indicated that platelet lysate improved cell proliferation and metabolic activity and may be used as an additive to the cell culture media.

Web services-based text-mining demonstrates broad impacts for interoperability and process simplification.

PubMed

Wiegers, Thomas C; Davis, Allan Peter; Mattingly, Carolyn J

2014-01-01

The Critical Assessment of Information Extraction systems in Biology (BioCreAtIvE) challenge evaluation tasks collectively represent a community-wide effort to evaluate a variety of text-mining and information extraction systems applied to the biological domain. The BioCreative IV Workshop included five independent subject areas, including Track 3, which focused on named-entity recognition (NER) for the Comparative Toxicogenomics Database (CTD; http://ctdbase.org). Previously, CTD had organized document ranking and NER-related tasks for the BioCreative Workshop 2012; a key finding of that effort was that interoperability and integration complexity were major impediments to the direct application of the systems to CTD's text-mining pipeline. This underscored a prevailing problem with software integration efforts. Major interoperability-related issues included lack of process modularity, operating system incompatibility, tool configuration complexity and lack of standardization of high-level inter-process communications. One approach to potentially mitigate interoperability and general integration issues is the use of Web services to abstract implementation details; rather than integrating NER tools directly, HTTP-based calls from CTD's asynchronous, batch-oriented text-mining pipeline could be made to remote NER Web services for recognition of specific biological terms using BioC (an emerging family of XML formats) for inter-process communications. To test this concept, participating groups developed Representational State Transfer /BioC-compliant Web services tailored to CTD's NER requirements. Participants were provided with a comprehensive set of training materials. CTD evaluated results obtained from the remote Web service-based URLs against a test data set of 510 manually curated scientific articles. Twelve groups participated in the challenge. Recall, precision, balanced F-scores and response times were calculated. Top balanced F-scores for gene, chemical and disease NER were 61, 74 and 51%, respectively. Response times ranged from fractions-of-a-second to over a minute per article. We present a description of the challenge and summary of results, demonstrating how curation groups can effectively use interoperable NER technologies to simplify text-mining pipeline implementation. Database URL: http://ctdbase.org/ © The Author(s) 2014. Published by Oxford University Press.

Web services-based text-mining demonstrates broad impacts for interoperability and process simplification

PubMed Central

Wiegers, Thomas C.; Davis, Allan Peter; Mattingly, Carolyn J.

2014-01-01

The Critical Assessment of Information Extraction systems in Biology (BioCreAtIvE) challenge evaluation tasks collectively represent a community-wide effort to evaluate a variety of text-mining and information extraction systems applied to the biological domain. The BioCreative IV Workshop included five independent subject areas, including Track 3, which focused on named-entity recognition (NER) for the Comparative Toxicogenomics Database (CTD; http://ctdbase.org). Previously, CTD had organized document ranking and NER-related tasks for the BioCreative Workshop 2012; a key finding of that effort was that interoperability and integration complexity were major impediments to the direct application of the systems to CTD's text-mining pipeline. This underscored a prevailing problem with software integration efforts. Major interoperability-related issues included lack of process modularity, operating system incompatibility, tool configuration complexity and lack of standardization of high-level inter-process communications. One approach to potentially mitigate interoperability and general integration issues is the use of Web services to abstract implementation details; rather than integrating NER tools directly, HTTP-based calls from CTD's asynchronous, batch-oriented text-mining pipeline could be made to remote NER Web services for recognition of specific biological terms using BioC (an emerging family of XML formats) for inter-process communications. To test this concept, participating groups developed Representational State Transfer /BioC-compliant Web services tailored to CTD's NER requirements. Participants were provided with a comprehensive set of training materials. CTD evaluated results obtained from the remote Web service-based URLs against a test data set of 510 manually curated scientific articles. Twelve groups participated in the challenge. Recall, precision, balanced F-scores and response times were calculated. Top balanced F-scores for gene, chemical and disease NER were 61, 74 and 51%, respectively. Response times ranged from fractions-of-a-second to over a minute per article. We present a description of the challenge and summary of results, demonstrating how curation groups can effectively use interoperable NER technologies to simplify text-mining pipeline implementation. Database URL: http://ctdbase.org/ PMID:24919658

Myasthenia Gravis Impairment Index: Responsiveness, meaningful change, and relative efficiency.

PubMed

Barnett, Carolina; Bril, Vera; Kapral, Moira; Kulkarni, Abhaya V; Davis, Aileen M

2017-12-05

To study responsiveness and meaningful change of the Myasthenia Gravis Impairment Index (MGII) and its relative efficiency compared to other measures. We enrolled 95 patients receiving prednisone, IV immunoglobulin (IVIg), or plasma exchange (PLEX) and 54 controls. Patients were assessed with the MGII and other measures-including the Quantitative Myasthenia Gravis Score, Myasthenia Gravis Composite, and Myasthenia Gravis Activities of Daily Living-at baseline and 3-4 weeks after treatment. Statistical markers of responsiveness included between-groups and within-group differences, and we estimated the relative efficiency of the MGII compared to other measures. Patient-meaningful change was assessed with an anchor-based method, using the patient's impression of change. We determined the minimal detectable change (MDC) and the minimal important difference (MID) at the group and individual level. Treated patients had a higher change in MGII scores than controls (analysis of covariance p < 0.001). The ocular domain changed more with prednisone than with IVIg/PLEX (effect size 0.67 and 0.13, analysis of covariance p = 0.001). The generalized domain changed more with IVIg/PLEX than with prednisone (effect size 0.50 and 0.22, analysis of covariance p = 0.07). For the total MGII score, the individual MDC95 was 9.1 and the MID was 5.5 for individuals and 8.1 for groups. Relative efficiency ratios were >1 favoring the MGII. The MGII demonstrated responsiveness to prednisone, IVIg, and PLEX in patients with myasthenia. There is a differential response in ocular and generalized symptoms to type of therapy. The MGII has higher relative efficiency than comparison measures and is viable for use in clinical trials. Copyright © 2017 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of the American Academy of Neurology.

Inference of biogeographical ancestry across central regions of Eurasia.

PubMed

Bulbul, O; Filoglu, G; Zorlu, T; Altuncul, H; Freire-Aradas, A; Söchtig, J; Ruiz, Y; Klintschar, M; Triki-Fendri, S; Rebai, A; Phillips, C; Lareu, M V; Carracedo, Á; Schneider, P M

2016-01-01

The inference of biogeographical ancestry (BGA) can provide useful information for forensic investigators when there are no suspects to be compared with DNA collected at the crime scene or when no DNA database matches exist. Although public databases are increasing in size and population scope, there is a lack of information regarding genetic variation in Eurasian populations, especially in central regions such as the Middle East. Inhabitants of these regions show a high degree of genetic admixture, characterized by an allele frequency cline running from NW Europe to East Asia. Although a proper differentiation has been established between the cline extremes of western Europe and South Asia, populations geographically located in between, i.e, Middle East and Mediterranean populations, require more detailed study in order to characterize their genetic background as well as to further understand their demographic histories. To initiate these studies, three ancestry informative SNP (AI-SNP) multiplex panels: the SNPforID 34-plex, Eurasiaplex and a novel 33-plex assay were used to describe the ancestry patterns of a total of 24 populations ranging across the longitudinal axis from NW Europe to East Asia. Different ancestry inference approaches, including STRUCTURE, PCA, DAPC and Snipper Bayes analysis, were applied to determine relationships among populations. The structure results show differentiation between continental groups and a NW to SE allele frequency cline running across Eurasian populations. This study adds useful population data that could be used as reference genotypes for future ancestry investigations in forensic cases. The 33-plex assay also includes pigmentation predictive SNPs, but this study primarily focused on Eurasian population differentiation using 33-plex and its combination with the other two AI-SNP sets.

The Multi-factor Predictive Seis &Gis Model of Ecological, Genetical, Population Health Risk and Bio-geodynamic Processes In Geopathogenic Zones

NASA Astrophysics Data System (ADS)

Bondarenko, Y.

I. Goal and Scope. Human birth rate decrease, death-rate growth and increase of mu- tagenic deviations risk take place in geopathogenic and anthropogenic hazard zones. Such zones create unfavourable conditions for reproductive process of future genera- tions. These negative trends should be considered as a protective answer of the com- plex biosocial system to the appearance of natural and anthropogenic risk factors that are unfavourable for human health. The major goals of scientific evaluation and de- crease of risk of appearance of hazardous processes on the territory of Dnipropetrovsk, along with creation of the multi-factor predictive Spirit-Energy-Information Space "SEIS" & GIS Model of ecological, genetical and population health risk in connection with dangerous bio-geodynamic processes, were: multi-factor modeling and correla- tion of natural and anthropogenic environmental changes and those of human health; determination of indicators that show the risk of destruction structures appearance on different levels of organization and functioning of the city ecosystem (geophys- ical and geochemical fields, soil, hydrosphere, atmosphere, biosphere); analysis of regularities of natural, anthropogenic, and biological rhythms' interactions. II. Meth- ods. The long spatio-temporal researches (Y. Bondarenko, 1996, 2000) have proved that the ecological, genetic and epidemiological processes are in connection with de- velopment of dangerous bio-geophysical and bio-geodynamic processes. Mathemat- ical processing of space photos, lithogeochemical and geophysical maps with use of JEIS o and ERDAS o computer systems was executed at the first stage of forma- tion of multi-layer geoinformation model "Dnipropetrovsk ARC View GIS o. The multi-factor nonlinear correlation between solar activity and cosmic ray variations, geophysical, geodynamic, geochemical, atmospheric, technological, biological, socio- economical processes and oncologic case rate frequency, general and primary popula- tion sickness cases in Dnipropetrovsk City (1.2 million persons) are described by the multi-factor predictive SEIS & GIS model of geopathogenic zones that determines the human health risk and hazards. Results and Conclusions. We have created the SEIS system and multi-factor predictive SEIS model for the analysis of phase-metric spatio- 1 temporal nonlinear correlation and variations of rhythms of human health, ecological, genetic, epidemiological risks, demographic, socio-economic, bio-geophysical, bio- geodynamic processes in geopathogenic hazard zones. Cosmophotomaps "CPM" of vegetation index, anthropogenic-landscape and landscape-geophysical human health risk of Dnipropetrovsk City present synthesis-based elements of multi-layer GIS, which include multispectral images SPOT o, maps of different geophysical, geochem- ical, anthropogenic and citogenic risk factors, maps of integral oncologic case rate frequency, general and primary population sickness cases for administrative districts. Results of multi-layer spatio-temporal correlation of geophysical field parameters and variations of population sickness rate rhythms have enabled us to state grounds and to develop medico-biological and bio-geodynamic classification of geopathogenic zones. Bio-geodynamic model has served to define contours of anthropogenic-landscape and landscape-geophysical human health risk in Dnipropetrovsk City. Biorhythmic vari- ations give foundation for understanding physiological mechanisms of organism`s adaptation to extreme helio-geophysical and bio-geodynamic environmental condi- tions, which are dictated by changes in Multi-factor Correlation Stress Field "MCSF" with deformation of 5D SEIS. Interaction between organism and environment results in continuous superpositioning of external (exogenic) Nuclear-Molecular-Cristallic "NMC" MCSF rhythms on internal (endogenic) Nuclear-Molecular-Cellular "NMCl" MCSF rhythms. Their resonance wave (energy-information) integration and disinte- gration are responsible for structural and functional state of different physiological systems. Herewith, complex restructurization of defense functions blocks the adapta- tion process and may turn to be the primary reason for phase shifting, process and biorhythms hindering, appearance of different deseases. Interaction of biorhythms with natural and anthropogenic rhythms specify the peculiar features of environ- mental adaptation of living species. Such interaction results in correlation of sea- sonal rhythms in variations of thermo-baro-geodynamic "TBG" parameters of am- bient air with toxic concentration and human health risk in Dnipropetrovsk City. Bio-geodynamic analysis of medical and demographic situations has provided for search of spatio-temporal correlation between rhythms of general and primary pop- ulation sickness cases and oncologic case rate frequency, other medico-demographic rhythms, natural processes (helio-geophysical, thermodynamic, geodynamic) and an- thropogenic processes (industrial and houschold waste disposal, toxic emissions and their concentration in ambient air). The year of 1986, the year of minimum helio- geophysical activity "2G1dG1" and maximum anthropogenic processes associated with changes in sickness and death rates of the population of Earth were synchronized. With account of quantum character of SEIS rhythms, 5 reference levels of desyn- chronized helio-geophysical and bio-geodynamic processes affecting population sick- ness rate have been specified within bio-geodynamic models. The first reference level 2 of SEIS desynchronization includes rhythms with period of 22,5 years: ... 1958,2; 1980,7; 2003,2; .... The second reference level of SEIS desynchronization includes rhythms with period of 11,25 years: ... 1980,7; 1992; 2003,2;.... The third reference level covers 5,625-years periodic rhythms2:... 1980,7; 1986,3; 1992; 1997,6; 2003,2; .... The fourth quantum reference level includes rhythms 3 with period of 2,8125 years: ... 1980,7; 1983,5; 1986,3; 1989,1; 1992; 1994,8; 1997,6; 2000,4; 2003,2; .... Rhythms with 1,40625-years period fall is fifth reference level of SEIS desynchro- nization: ...1980,7; 1982,1; 1983,5; 1984,9; 1986,3; 1987,7; 1989,1; 1990,5; 1992; 1993,3; 1994,8; 1996,2; 1997,6; 1999; 2000,4; 2001,8; 2003,2;.... Analysis of alternat- ing medical and demographic situation in Ukraine (1981-1992)and in Dnipropetrovsk (1988-1995)has allowed to back up theoretical model of various-level rhythm quan- tum, with non-linear regularities due to phase-metric spatio-temporal deformation be- ing specified. Application of new technologies of Risk Analysis, Sinthesis and SEIS Modeling at the choice of a burial place for dangerous radioactive wastes in the zone of Chernobyl nuclear disaster (Shestopalov V., Bondarenko Y...., 1998) has shown their very high efficiency in comparison with GIS Analysis. IV.Recommendations and Outlook. In order to draw a conclusion regarding bio-geodynamic modeling of spatio-temporal structure of areas where common childhood sickness rate exists, it is necessary to mention that the only thing that can favour to exact predicting of where and when important catastrophes and epidemies will take place is correct and complex bio-geodynamic modeling. Imperfection of present GIS is the result of the lack of interactive facilities for multi-factor modeling of nonlinear natural and an- thropogenic processes. Equations' coefficients calculated for some areas are often irrelevant when applied to others. In this connection there arises a number of prob- lems concerning practical application and reliability of GIS-models that are used to carry out efficient ecological monitoring. References Bondarenko Y., 1997, Drawing up Cosmophotomaps and Multi-factor Forecasting of Hazard of Development of Dan- gerous Geodynamic Processes in Dnipropetrovsk,The Technically-Natural Problems of failures and catastrophes in connection with development of dangerous geological processes, Kiev, Ukraine, 1997. Bondarenko Y., 1997, The Methodology of a State the Value of Quality of the Ground and the House Level them Ecology-Genetic-Toxic of the human health risk based on multi-layer cartographical model", Experience of application GIS - Technologies for creating Cadastral Systems, Yalta, Ukraine, 1997, p. 39-40. Shestopalov V., Bondarenko Y., Zayonts I., Rudenko Y. , Bohuslavsky A., 1998, Complexation of Structural-Geodynamical and Hydrogeological Methods of Studying Areas to Reveal Geological Structural Perspectives for Deep Isolation of Radioactive Wastes, Field Testing and Associated Modeling of Potential High-Level Nuclear Waste Geologic Disposal Sites, Berkeley, USA, 1998, p.81-82. 3

[Observation and analysis on mutation of routine STR locus].

PubMed

Li, Qiu-yang; Feng, Wei-jun; Yang, Qin-gen

2005-05-01

To observe and analyze the characteristic of mutation at STR locus. 27 mutant genes observed in 1211 paternity testing cases were checked by PAGE-silver stained and PowerPlex 16 System Kit and validated by sequencing. Mutant genes locate on 15 loci. The pattern of mutation was accord with stepwise mutation model. The mutation ratio of male-to-female was 8:1 and correlated to the age of father. Mutation rate is correlated to the geometric mean of the number of homogeneous repeats of locus. The higher the mean, the higher the mutation rate. These loci are not so appropriate for use in paternity testing.

Querying and Computing with BioCyc Databases

PubMed Central

Krummenacker, Markus; Paley, Suzanne; Mueller, Lukas; Yan, Thomas; Karp, Peter D.

2006-01-01

Summary We describe multiple methods for accessing and querying the complex and integrated cellular data in the BioCyc family of databases: access through multiple file formats, access through Application Program Interfaces (APIs) for LISP, Perl and Java, and SQL access through the BioWarehouse relational database. Availability The Pathway Tools software and 20 BioCyc DBs in Tiers 1 and 2 are freely available to academic users; fees apply to some types of commercial use. For download instructions see http://BioCyc.org/download.shtml PMID:15961440

Foreword to 'Multiscale structural biology: biophysical principles and mechanisms underlying the action of bio-nanomachines', a special issue in Honour of Fumio Arisaka's 70th birthday.

PubMed

Hall, Damien; Takagi, Junichi; Nakamura, Haruki

2018-04-01

This issue of Biophysical Reviews, titled 'Multiscale structural biology: biophysical principles and mechanisms underlying the action of bio-nanomachines', is a collection of articles dedicated in honour of Professor Fumio Arisaka's 70th birthday. Initially, working in the fields of haemocyanin and actin filament assembly, Fumio went on to publish important work on the elucidation of structural and functional aspects of T4 phage biology. As his career has transitioned levels of complexity from proteins (hemocyanin) to large protein complexes (actin) to even more massive bio-nanomachinery (phage), it is fitting that the subject of this special issue is similarly reflective of his multiscale approach to structural biology. This festschrift contains articles spanning biophysical structure and function from the bio-molecular through to the bio-nanomachine level.

A Complex Between Biotin Synthase and The Iron-Sulfur Cluster Assembly Chaperone HscA That Enhances In Vivo Cluster Assembly†

PubMed Central

Reyda, Michael R.; Fugate, Corey J.; Jarrett, Joseph T.

2009-01-01

Biotin synthase (BioB) is an iron-sulfur enzyme that catalyzes the last step in biotin biosynthesis, the insertion of sulfur between the C6 and C9 carbons of dethiobiotin to complete the thiophane ring of biotin. Recent in vitro experiments suggest that the sulfur is derived from a [2Fe-2S]2+ cluster within BioB, and that the remnants of this cluster dissociate from the enzyme following each turnover. In order for BioB to catalyze multiple rounds of biotin synthesis, the [2Fe-2S]2+ cluster in BioB must be reassembled, a process that could be carried out in vivo by the ISC or SUF iron-sulfur cluster assembly systems. The bacterial ISC system includes HscA, an Hsp70-class molecular chaperone, whose yeast homolog has been shown to play an important but nonessential role in assembly of mitochondrial FeS clusters in S. cerevesiae. In the present work we show that in E. coli, HscA significantly improves the efficiency of the in vivo assembly of the [2Fe-2S]2+ cluster on BioB under conditions of low to moderate iron. In vitro, we show that HscA binds with increased affinity to BioB missing one or both FeS clusters, with a maximum of two HscA molecules per BioB dimer. BioB binds to HscA in an ATP/ADP-independent manner and a high affinity complex is also formed with a truncated form of HscA that lacks the nucleotide binding domain. Further, the BioB:HscA complex binds the FeS cluster scaffold protein IscU in a noncompetitive manner, generating a complex that contains all three proteins. We propose that HscA plays a role in facilitating the transfer of FeS clusters from IscU into the appropriate target apoproteins such as biotin synthase, perhaps by enhancing or prolonging the requisite protein:protein interaction. PMID:19821612

Fungicidal values of bio-oils and their lignin-rich fractions obtained from wood/bark fast pyrolysis.

PubMed

Mohan, Dinesh; Shi, Jenny; Nicholas, Darrel D; Pittman, Charles U; Steele, Philip H; Cooper, Jerome E

2008-03-01

Pine wood, pine bark, oak wood and oak bark were pyrolyzed in an auger reactor. A total of 16 bio-oils or pyrolytic oils were generated at different temperatures and residence times. Two additional pine bio-oils were produced at the National Renewable Energy Laboratory in a fluidized-bed reactor at different temperatures. All these bio-oils were fractionated to obtain lignin-rich fractions which consist mainly of phenols and neutrals. The pyrolytic lignin-rich fractions were obtained by liquid-liquid extraction. Whole bio-oils and their lignin-rich fractions were studied as potential environmentally benign wood preservatives to replace metal-based CCA and copper systems that have raised environmental concerns. Each bio-oil and several lignin-rich fractions were tested for antifungal properties. Soil block tests were conducted using one brown-rot fungus (Gloeophyllum trabeum) and one white-rot fungus (Trametes versicolor). The lignin-rich fractions showed greater fungal inhibition than whole bio-oils for a impregnation solution 10% concentration level. Water repellence tests were also performed to study wood wafer swelling behavior before and after bio-oil and lignin-rich fraction treatments. In this case, bio-oil fractions did not exhibit higher water repellency than whole bio-oils. Comparison of raw bio-oils in soil block tests, with unleached wafers, at 10% and 25% bio-oil impregnation solution concentration levels showed excellent wood preservation properties at the 25% level. The good performance of raw bio-oils at higher loading levels suggests that fractionation to generate lignin-rich fractions is unnecessary. At this more effective 25% loading level in general, the raw bio-oils performed similarly. Prevention of leaching is critically important for both raw bio-oils and their fractions to provide decay resistance. Initial tests of a polymerization chemical to prevent leaching showed some success.

Potency of bio-charcoal briquette from leather cassava tubers and industrial sludge

NASA Astrophysics Data System (ADS)

Citrasari, Nita; Pinatih, Tety A.; Kuncoro, Eko P.; Soegianto, Agoes; Salamun, Irawan, Bambang

2017-06-01

The purpose of this study was to determine the quality of the bio-charcoal briquette with materials from leather cassava tubers and sludge of wastewater treatment plant. The first, bio-charcoal briquette analized stability test and compressive strength. Then, bio-charcoal briquette with best value analyzed for parameter including moisture content, ash content, calorific content, and burned test. The result briquette quality based on compressive strength for bio-charcoal briquettes carbonated water content between 3.8%-4.5% and non-carbonated bio-charcoal briquettes between 5.2%-7.6%. Bio-charcoal carbonation briquette ash content was between 5.30%-7.40% and non-carbonated bio-charcoal briquettes was between 6.86%-7.46%. Bio-charcoal carbonation levels briquettes heated between 578.2 calories/g-1837.7 calories/g and non carbonatedbio-charcoal briquettes between 858.1 calories/g-891.1 calories/g. Carbonated bio-charcoal burned test was between 48-63 minutes and non-carbonated bio-charcoal was between 22-42 minutes. Emissions resulted from the bio-charcoal briquettes for carbonated and non carbonated composition according to the government regulations ESDM No. 047 of 2006 which, at 128 mg/Nm3 and 139 mg/Nm3.

Recognition of Y Fragment Deletion by Genotyping Graphs after Amplified by PowerPlex® 21 Detection Kit.

PubMed

Wang, S C; Ding, M M; Wei, X L; Zhang, T; Yao, F

2016-06-01

To recognize the possibility of Y fragment deletion of Amelogenin gene intuitively and simply according to the genotyping graphs. By calculating the ratio of total peak height of genotyping graphs, the statistics of equilibrium distribution between Amelogenin and D3S1358 loci, Amelogenin X-gene and Amelogenin Y-gene, and different alleles of D3S1358 loci from 1 968 individuals was analyzed after amplified by PowerPlex ® 21 detection kit. Sum of peak height of Amelogenin X allele was not less than 60% that of D3S1358 loci alleles in 90.8% female samples, and sum of peak height of Amelogenin X allele was not higher than 70% that of D3S1358 loci alleles in 94.9% male samples. The result of genotyping after amplified by PowerPlex ® 21 detection kit shows that the possibility of Y fragment deletion should be considered when only Amelogenin X-gene of Amelogenin is detected and the peak height of Amelogenin X-gene is not higher than 70% of the total peak height of D3S1358 loci. Copyright© by the Editorial Department of Journal of Forensic Medicine

Evaluation of the bioNexia Legionella Test, Including Impact of Incubation Time Extension, for Detection of Legionella pneumophila Serogroup 1 Antigen in Urine.

PubMed

Badoux, Paul; Euser, Sjoerd M; Bruin, Jacob P; Mulder, Patrick P G; Yzerman, Ed P F

2017-06-01

In this study, we compared the bioNexia test (bioMérieux, Marcy-l'Étoile, France), a new immunochromatographic assay for the detection of Legionella pneumophila serogroup 1 in urine, with the BinaxNOW urinary antigen test (Alere, Waltham, Massachusetts, USA). After 15 min of incubation (in accordance with the manufacturers' instructions), the sensitivities and specificities were, respectively, 76.5% and 97.2% for the bioNexia test and 87.1% and 100% for the BinaxNOW test. After a prolonged incubation time of 60 min, the sensitivities and specificities increased to, respectively, 89.4% and 97.2% for the bioNexia test and 91.8% and 100% for the BinaxNOW test. When the tests were read after 15 min, the concentration of discrepant urine samples increased the sensitivities to 94.1% for both tests. In conclusion, we found that although the bioNexia test showed lower sensitivity for the detection of L. pneumophila antigen in nonconcentrated urine compared to the BinaxNOW test, a prolonged incubation time as well as the use of concentrated samples showed comparable sensitivities for both tests. Copyright © 2017 American Society for Microbiology.

Foliar application of microbial and plant based biostimulants increases growth and potassium uptake in almond (Prunus dulcis [Mill.] D. A. Webb)

PubMed Central

Saa, Sebastian; Olivos-Del Rio, Andres; Castro, Sebastian; Brown, Patrick H.

2015-01-01

The use of biostimulants has become a common practice in agriculture. However, there is little peer-reviewed research on this topic. In this study we tested, under controlled and replicated conditions, the effect of one biostimulant derived from seaweed extraction (Bio-1) and another biostimulant derived from microbial fermentation (Bio-2). This experiment utilized 2-years-old almond plants over two growing seasons in a randomized complete design with a full 2 × 4 factorial structure with two soil potassium treatments (125 μg g-1 of K vs. 5 μg g-1) and four foliar treatments (No spray, Foliar-K, Bio-1, Bio-2). Rubidium was utilized as a surrogate for short-term potassium uptake and plant growth, nutrient concentration, and final plant biomass were evaluated. There was a substantial positive effect of both biostimulant treatments on total shoot leaf area, and significant increases in shoot length and biomass under adequate soil potassium supply with a positive effect of Bio-1 only under low K supply. Rubidium uptake was increased by Bio-1 application an effect that was greater under the low soil K treatment. Though significant beneficial effects of the biostimulants used on plant growth were observed, it is not possible to determine the mode of action of these materials. The results presented here illustrate the promise and complexity of research involving biostimulants. PMID:25755660

Apoptosis induction and anti-cancer activity of LeciPlex formulations.

PubMed

Dhawan, Vivek V; Joshi, Ganesh V; Jain, Ankitkumar S; Nikam, Yuvraj P; Gude, Rajiv P; Mulherkar, Rita; Nagarsenker, Mangal S

2014-10-01

Cationic agents have been reported to possess anti-neoplastic properties against various cancer cell types. However, their complexes with lipids appear to interact differently with different cancer cells. The purpose of this study was to (i) design and generate novel cationic lecithin nanoparticles, (ii) assess and understand the mechanism underlying their putative cytotoxicity and (iii) test their effect on cell cycle progression in various cancer-derived cell lines. In addition, we aimed to evaluate the in vivo potential of these newly developed nanoparticles in oral anti-cancer delivery. Cationic lecithin nanoparticles were generated using a single step nanoprecipitation method and they were characterized for particle size, zeta potential, stability and in vitro release. Their cytotoxic potential was assessed using a sulforhodamine B assay, and their effect on cell cycle progression was evaluated using flow cytometry. The nanoparticle systems were also tested in vivo for their anti-tumorigenic potential. In contrast to cationic agents alone, the newly developed nanoformulations showed a specific toxicity against cancer cells. The mechanism of toxic cell death included apoptosis, S and G2/M cell cycle phase arrest, depending on the type of cationic agent and the cancer-derived cell line used. Both blank and drug-loaded systems exhibited significant anti-cancer activity, suggesting a synergistic anti-tumorigenic effect of the drug and its delivery system. Both in vitro and in vivo data indicate that cationic agents themselves exhibit broad anti-neoplastic activities. Complex formation of the cationic agents with phospholipids was found to provide specificity to the anti-cancer activity. These formulations thus possess potential for the design of effective anti-cancer delivery systems.

AmericaPlex26: A SNaPshot Multiplex System for Genotyping the Main Human Mitochondrial Founder Lineages of the Americas

PubMed Central

Coutinho, Alexandra; Valverde, Guido; Fehren-Schmitz, Lars; Cooper, Alan; Barreto Romero, Maria Inés; Espinoza, Isabel Flores; Llamas, Bastien; Haak, Wolfgang

2014-01-01

Phylogeographic studies have described a reduced genetic diversity in Native American populations, indicative of one or more bottleneck events during the peopling and prehistory of the Americas. Classical sequencing approaches targeting the mitochondrial diversity have reported the presence of five major haplogroups, namely A, B, C, D and X, whereas the advent of complete mitochondrial genome sequencing has recently refined the number of founder lineages within the given diversity to 15 sub-haplogroups. We developed and optimized a SNaPshot assay to study the mitochondrial diversity in pre-Columbian Native American populations by simultaneous typing of 26 single nucleotide polymorphisms (SNPs) characterising Native American sub-haplogroups. Our assay proved to be highly sensitive with respect to starting concentrations of target DNA and could be applied successfully to a range of ancient human skeletal material from South America from various time periods. The AmericaPlex26 is a powerful assay with enhanced phylogenetic resolution that allows time- and cost-efficient mitochondrial DNA sub-typing from valuable ancient specimens. It can be applied in addition or alternative to standard sequencing of the D-loop region in forensics, ancestry testing, and population studies, or where full-resolution mitochondrial genome sequencing is not feasible. PMID:24671218

AmericaPlex26: a SNaPshot multiplex system for genotyping the main human mitochondrial founder lineages of the Americas.

PubMed

Coutinho, Alexandra; Valverde, Guido; Fehren-Schmitz, Lars; Cooper, Alan; Barreto Romero, Maria Inés; Espinoza, Isabel Flores; Llamas, Bastien; Haak, Wolfgang

2014-01-01

Phylogeographic studies have described a reduced genetic diversity in Native American populations, indicative of one or more bottleneck events during the peopling and prehistory of the Americas. Classical sequencing approaches targeting the mitochondrial diversity have reported the presence of five major haplogroups, namely A, B, C, D and X, whereas the advent of complete mitochondrial genome sequencing has recently refined the number of founder lineages within the given diversity to 15 sub-haplogroups. We developed and optimized a SNaPshot assay to study the mitochondrial diversity in pre-Columbian Native American populations by simultaneous typing of 26 single nucleotide polymorphisms (SNPs) characterising Native American sub-haplogroups. Our assay proved to be highly sensitive with respect to starting concentrations of target DNA and could be applied successfully to a range of ancient human skeletal material from South America from various time periods. The AmericaPlex26 is a powerful assay with enhanced phylogenetic resolution that allows time- and cost-efficient mitochondrial DNA sub-typing from valuable ancient specimens. It can be applied in addition or alternative to standard sequencing of the D-loop region in forensics, ancestry testing, and population studies, or where full-resolution mitochondrial genome sequencing is not feasible.

Unsteady bio-fluid dynamics in flying and swimming

NASA Astrophysics Data System (ADS)

Liu, Hao; Kolomenskiy, Dmitry; Nakata, Toshiyuki; Li, Gen

2017-08-01

Flying and swimming in nature present sophisticated and exciting ventures in biomimetics, which seeks sustainable solutions and solves practical problems by emulating nature's time-tested patterns, functions, and strategies. Bio-fluids in insect and bird flight, as well as in fish swimming are highly dynamic and unsteady; however, they have been studied mostly with a focus on the phenomena associated with a body or wings moving in a steady flow. Characterized by unsteady wing flapping and body undulation, fluid-structure interactions, flexible wings and bodies, turbulent environments, and complex maneuver, bio-fluid dynamics normally have challenges associated with low Reynolds number regime and high unsteadiness in modeling and analysis of flow physics. In this article, we review and highlight recent advances in unsteady bio-fluid dynamics in terms of leading-edge vortices, passive mechanisms in flexible wings and hinges, flapping flight in unsteady environments, and micro-structured aerodynamics in flapping flight, as well as undulatory swimming, flapping-fin hydrodynamics, body-fin interaction, C-start and maneuvering, swimming in turbulence, collective swimming, and micro-structured hydrodynamics in swimming. We further give a perspective outlook on future challenges and tasks of several key issues of the field.

Preparation of bio-deep eutectic solvent triggered cephalopod shaped silver chloride-DNA hybrid material having antibacterial and bactericidal activity.

PubMed

Bhatt, Jitkumar; Mondal, Dibyendu; Bhojani, Gopal; Chatterjee, Shruti; Prasad, Kamalesh

2015-11-01

2.5% w/w DNA (Salmon testes) was solubilized in a bio-deep eutectic solvent [(bio-DES), obtained by the complexation of choline chloride and ethylene glycol at 1:2 molar ratio] containing 1% w/w of silver chloride (AgCl) to yield a AgCl decorated DNA based hybrid material. Concentration dependent formation of AgCl crystals in the DES was observed and upon interaction with DNA it gave formation of a cephalopod shaped hybrid material. DNA was found to maintain its chemical and structural stability in the material. Further, AgCl microstructures were found to have orderly self assembled on the DNA helices indicating the electrostatic interaction between Ag(+) and phosphate side chain of DNA as a driving force for the formation of the material with ordered microstructural distribution of AgCl. Furthermore, the functionalized material exhibited excellent antibacterial and bactericidal activity against both Gram negative and Gram positive pathogenic bacteria. Copyright © 2015 Elsevier B.V. All rights reserved.

Biomarkers and Molecular Analysis to Improve Bloodstream Infection Diagnostics in an Emergency Care Unit

PubMed Central

Loonen, Anne J. M.; de Jager, Cornelis P. C.; Tosserams, Janna; Kusters, Ron; Hilbink, Mirrian; Wever, Peter C.; van den Brule, Adriaan J. C.

2014-01-01

Molecular pathogen detection from blood is still expensive and the exact clinical value remains to be determined. The use of biomarkers may assist in preselecting patients for immediate molecular testing besides blood culture. In this study, 140 patients with ≥ 2 SIRS criteria and clinical signs of infection presenting at the emergency department of our hospital were included. C-reactive protein (CRP), neutrophil-lymphocyte count ratio (NLCR), procalcitonin (PCT) and soluble urokinase plasminogen activator receptor (suPAR) levels were determined. One ml EDTA blood was obtained and selective pathogen DNA isolation was performed with MolYsis (Molzym). DNA samples were analysed for the presence of pathogens, using both the MagicPlex Sepsis Test (Seegene) and SepsiTest (Molzym), and results were compared to blood cultures. Fifteen patients had to be excluded from the study, leaving 125 patients for further analysis. Of the 125 patient samples analysed, 27 presented with positive blood cultures of which 7 were considered to be contaminants. suPAR, PCT, and NLCR values were significantly higher in patients with positive blood cultures compared to patients without (p < 0.001). Receiver operating characteristic curves of the 4 biomarkers for differentiating bacteremia from non-bacteremia showed the highest area under the curve (AUC) for PCT (0.806 (95% confidence interval 0.699–0.913)). NLCR, suPAR and CRP resulted in an AUC of 0.770, 0.793, and 0.485, respectively. When compared to blood cultures, the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) for SepsiTest and MagicPlex Sepsis Test were 11%, 96%, 43%, 80%, and 37%, 77%, 30%, 82%, respectively. In conclusion, both molecular assays perform poorly when one ml whole blood is used from emergency care unit patients. NLCR is a cheap, fast, easy to determine, and rapidly available biomarker, and therefore seems most promising in differentiating BSI from non-BSI patients for subsequent pathogen identification using molecular diagnostics. PMID:24475269

Biomarkers and molecular analysis to improve bloodstream infection diagnostics in an emergency care unit.

PubMed

Loonen, Anne J M; de Jager, Cornelis P C; Tosserams, Janna; Kusters, Ron; Hilbink, Mirrian; Wever, Peter C; van den Brule, Adriaan J C

2014-01-01

Molecular pathogen detection from blood is still expensive and the exact clinical value remains to be determined. The use of biomarkers may assist in preselecting patients for immediate molecular testing besides blood culture. In this study, 140 patients with ≥ 2 SIRS criteria and clinical signs of infection presenting at the emergency department of our hospital were included. C-reactive protein (CRP), neutrophil-lymphocyte count ratio (NLCR), procalcitonin (PCT) and soluble urokinase plasminogen activator receptor (suPAR) levels were determined. One ml EDTA blood was obtained and selective pathogen DNA isolation was performed with MolYsis (Molzym). DNA samples were analysed for the presence of pathogens, using both the MagicPlex Sepsis Test (Seegene) and SepsiTest (Molzym), and results were compared to blood cultures. Fifteen patients had to be excluded from the study, leaving 125 patients for further analysis. Of the 125 patient samples analysed, 27 presented with positive blood cultures of which 7 were considered to be contaminants. suPAR, PCT, and NLCR values were significantly higher in patients with positive blood cultures compared to patients without (p < 0.001). Receiver operating characteristic curves of the 4 biomarkers for differentiating bacteremia from non-bacteremia showed the highest area under the curve (AUC) for PCT (0.806 (95% confidence interval 0.699-0.913)). NLCR, suPAR and CRP resulted in an AUC of 0.770, 0.793, and 0.485, respectively. When compared to blood cultures, the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) for SepsiTest and MagicPlex Sepsis Test were 11%, 96%, 43%, 80%, and 37%, 77%, 30%, 82%, respectively. In conclusion, both molecular assays perform poorly when one ml whole blood is used from emergency care unit patients. NLCR is a cheap, fast, easy to determine, and rapidly available biomarker, and therefore seems most promising in differentiating BSI from non-BSI patients for subsequent pathogen identification using molecular diagnostics.

Bio-jETI: a service integration, design, and provisioning platform for orchestrated bioinformatics processes.

PubMed

Margaria, Tiziana; Kubczak, Christian; Steffen, Bernhard

2008-04-25

With Bio-jETI, we introduce a service platform for interdisciplinary work on biological application domains and illustrate its use in a concrete application concerning statistical data processing in R and xcms for an LC/MS analysis of FAAH gene knockout. Bio-jETI uses the jABC environment for service-oriented modeling and design as a graphical process modeling tool and the jETI service integration technology for remote tool execution. As a service definition and provisioning platform, Bio-jETI has the potential to become a core technology in interdisciplinary service orchestration and technology transfer. Domain experts, like biologists not trained in computer science, directly define complex service orchestrations as process models and use efficient and complex bioinformatics tools in a simple and intuitive way.

Spinal IL-33/ST2 Signaling Contributes to Neuropathic Pain via Neuronal CaMKII-CREB and Astroglial JAK2-STAT3 Cascades in Mice.

PubMed

Liu, Shenbin; Mi, Wen-Li; Li, Qian; Zhang, Meng-Ting; Han, Ping; Hu, Shan; Mao-Ying, Qi-Liang; Wang, Yan-Qing

2015-11-01

Emerging evidence indicates that nerve damage-initiated neuroinflammation and immune responses, which are evidenced by the up-regulation of proinflammatory cytokines, contribute to the development of neuropathic pain. This study investigated the role of spinal interleukin (IL)-33 and its receptor ST2 in spared nerve injury (SNI)-induced neuropathic pain. The von Frey test and acetone test were performed to evaluate neuropathic pain behaviors (n = 8 to 12), and Western blot (n = 4 to 6), immunohistochemistry, real-time polymerase chain reaction (n = 5), and Bio-Plex (n = 5) assays were performed to understand the molecular mechanisms. Intrathecal administration of ST2-neutralizing antibody or ST2 gene knockout (ST2) significantly attenuated the SNI-induced mechanical and cold allodynia. On the 7th day after SNI, the expression of spinal IL-33 and ST2 was increased by 255.8 ± 27.3% and 266.4 ± 83.5% (mean ± SD), respectively. Mechanistic studies showed that the increased expression of the spinal N-methyl-D-aspartate (NMDA) receptor subunit 1 after SNI was reduced by ST2 antibody administration or ST2. The induction of nociceptive behaviors in naive mice due to recombinant IL-33 was reversed by the noncompetitive NMDA antagonist MK-801. ST2 antibody administration or ST2 markedly inhibited the increased activation of the astroglial janus kinase 2 (JAK2)-signal transducer and activator of transcription 3 (STAT3) cascade and the neuronal calcium-calmodulin-dependent kinase II (CaMKII)-cyclic adenosine monophosphate response element-binding protein (CREB) cascade after SNI. Moreover, intrathecal pretreatment with the CaMKII inhibitor KN-93 or the JAK2-STAT3 cascade inhibitor AG490 attenuated recombinant IL-33-induced nociceptive behaviors and NMDA subunit 1 up-regulation in naive mice. Spinal IL-33/ST2 signaling contributes to neuropathic pain by activating the astroglial JAK2-STAT3 cascade and the neuronal CaMKII-CREB cascade.

Pepsi-SAXS: an adaptive method for rapid and accurate computation of small-angle X-ray scattering profiles.

PubMed

Grudinin, Sergei; Garkavenko, Maria; Kazennov, Andrei

2017-05-01

A new method called Pepsi-SAXS is presented that calculates small-angle X-ray scattering profiles from atomistic models. The method is based on the multipole expansion scheme and is significantly faster compared with other tested methods. In particular, using the Nyquist-Shannon-Kotelnikov sampling theorem, the multipole expansion order is adapted to the size of the model and the resolution of the experimental data. It is argued that by using the adaptive expansion order, this method has the same quadratic dependence on the number of atoms in the model as the Debye-based approach, but with a much smaller prefactor in the computational complexity. The method has been systematically validated on a large set of over 50 models collected from the BioIsis and SASBDB databases. Using a laptop, it was demonstrated that Pepsi-SAXS is about seven, 29 and 36 times faster compared with CRYSOL, FoXS and the three-dimensional Zernike method in SAStbx, respectively, when tested on data from the BioIsis database, and is about five, 21 and 25 times faster compared with CRYSOL, FoXS and SAStbx, respectively, when tested on data from SASBDB. On average, Pepsi-SAXS demonstrates comparable accuracy in terms of χ 2 to CRYSOL and FoXS when tested on BioIsis and SASBDB profiles. Together with a small allowed variation of adjustable parameters, this demonstrates the effectiveness of the method. Pepsi-SAXS is available at http://team.inria.fr/nano-d/software/pepsi-saxs.

Once-Daily Amikacin Dosing in Burn Patients Treated with Continuous Venovenous Hemofiltration

DTIC Science & Technology

2011-10-01

previously documented inaccuracies with the Vitek 2 instrument (1), all Acinetobacter baumannii isolates reported as susceptible to amikacin were confirmed...to the analysis. Bacteriology. Amikacin MICs were determined for Gram-negative blood- stream isolates using the Vitek 2 instrument (bioMérieux...al. 2010. Aminoglycoside resistance and susceptibility testing errors in Acinetobacter baumannii-calcoaceticus complex. J. Clin. Microbiol. 48:1132

Techniques and instrumental complex for research of influence of microwaves encoded by brain neural signals on biological objects’ psycho physiological state

NASA Astrophysics Data System (ADS)

Gurkovskiy, B. V.; Zhuravlev, B. V.; Onishchenko, E. M.; Simakov, A. B.; Trifonova, N. Yu; Voronov, Yu A.

2016-10-01

New instrumental technique for research of the psycho-physiological reactions of the bio-objects under the microwave electromagnetic radiation, modulated by interval patterns of neural activity in the brain registered under different biological motivations, are suggested. The preliminary results of these new tool tests in real psycho physiological experiments on rats are presented.

Diamond Nanoparticles Modify Curcumin Activity: In Vitro Studies on Cancer and Normal Cells and In Ovo Studies on Chicken Embryo Model

PubMed Central

Strojny, Barbara; Grodzik, Marta; Sawosz, Ewa; Winnicka, Anna; Kurantowicz, Natalia; Jaworski, Sławomir; Kutwin, Marta; Urbańska, Kaja; Hotowy, Anna; Wierzbicki, Mateusz; Chwalibog, André

2016-01-01

Curcumin has been studied broadly for its wide range of biological activities, including anticancer properties. The major problem with curcumin is its poor bioavailability, which can be improved by the addition of carriers, such as diamond nanoparticles (DN). They are carbon allotropes, and are therefore biocompatible and easily taken up by cells. DN are non-toxic and have antiangiogenic properties with potential applications in cancer therapy. Their large surface makes them promising compounds in a drug delivery system for bioactive agents, as DN create bio-complexes in a fast and simple process of self-organisation. We investigated the cytotoxicity of such bio-complexes against liver cancer cells and normal fibroblasts, revealing that conjugation of curcumin with DN significantly improves its activity. The experiment performed in a chicken embryo model demonstrated that neither curcumin nor DN nor bio-complexes affect embryo development, even though DN can form deposits in tissues. Preliminary results confirmed the applicability of DN as an efficient carrier of curcumin, which improves its performance against cancer cells in vitro, yet is not toxic to an organism, which makes the bio-complex a promising anticancer agent. PMID:27736939

Diamond Nanoparticles Modify Curcumin Activity: In Vitro Studies on Cancer and Normal Cells and In Ovo Studies on Chicken Embryo Model.

PubMed

Strojny, Barbara; Grodzik, Marta; Sawosz, Ewa; Winnicka, Anna; Kurantowicz, Natalia; Jaworski, Sławomir; Kutwin, Marta; Urbańska, Kaja; Hotowy, Anna; Wierzbicki, Mateusz; Chwalibog, André

2016-01-01

Curcumin has been studied broadly for its wide range of biological activities, including anticancer properties. The major problem with curcumin is its poor bioavailability, which can be improved by the addition of carriers, such as diamond nanoparticles (DN). They are carbon allotropes, and are therefore biocompatible and easily taken up by cells. DN are non-toxic and have antiangiogenic properties with potential applications in cancer therapy. Their large surface makes them promising compounds in a drug delivery system for bioactive agents, as DN create bio-complexes in a fast and simple process of self-organisation. We investigated the cytotoxicity of such bio-complexes against liver cancer cells and normal fibroblasts, revealing that conjugation of curcumin with DN significantly improves its activity. The experiment performed in a chicken embryo model demonstrated that neither curcumin nor DN nor bio-complexes affect embryo development, even though DN can form deposits in tissues. Preliminary results confirmed the applicability of DN as an efficient carrier of curcumin, which improves its performance against cancer cells in vitro, yet is not toxic to an organism, which makes the bio-complex a promising anticancer agent.

Effect of Non-tuberculous Mycobacteria on Host Biomarkers Potentially Relevant for Tuberculosis Management

PubMed Central

Dhanasekaran, S.; Jenum, Synne; Stavrum, Ruth; Wiker, Harald G.; Kenneth, John; Vaz, Mario; Doherty, T. Mark; Grewal, Harleen M. S.

2014-01-01

Background Non-tuberculous mycobacteria (NTM) are different from Mycobacterium tuberculosis (MTB) both in their ubiquitous environmental distribution and in their reduced capacity to cause disease. While often neglected in favour of other infectious diseases, NTM may interfere with important aspects of TB control and management, namely the efficacy of new anti-tuberculosis (TB) vaccines; the immuno-diagnostic Tuberculin skin test (TST) and QuantiFERON TB Gold In Tube assay (QFTGIT); and immune biomarkers explored for their diagnostic and/or predictive potential. Our objective was therefore to explore host immune biomarkers in children who had NTM isolated from respiratory and/or gastric specimens. Methodology and Principle Findings The present study was nested within a prospective cohort study of BCG-vaccinated neonates in Southern India. In this setting, immune biomarkers from peripheral blood were analyzed in 210 children aged <3 years evaluated for TB using dual-colour-Reverse-Transcriptase-Multiple-Ligation-dependent-Probe-Amplification (dcRT-MLPA) and Bio-Plex assays. The children were classified based on clinical examination, chest X-rays and mycobacterial culture reports as either: 1) TB disease, 2) NTM present and 3) controls. The study shows a down-regulation of RAB33A (p<0.001) and up-regulation of TGFβ1, IL-2 and IL-6 (all p<0.05) in children with TB disease, and that RAB33A, TGFBR2 and IL-10 (all p<0.05) were differentially expressed in children with NTM present when compared to children that were culture negative for MTB and NTM (controls). Conclusions and Significance Carriage of NTM may reduce the specificity of future diagnostic and predictive immune biomarkers relevant to TB management. PMID:25329719

Permanently Hypoxic Cell Culture Yields Rat Bone Marrow Mesenchymal Cells with Higher Therapeutic Potential in the Treatment of Chronic Myocardial Infarction.

PubMed

Liu, Yihua; Yang, Xiaoxi; Maureira, Pablo; Falanga, Aude; Marie, Vanessa; Gauchotte, Guillaume; Poussier, Sylvain; Groubatch, Frederique; Marie, Pierre-Yves; Tran, Nguyen

2017-01-01

The mismatch between traditional in vitro cell culture conditions and targeted chronic hypoxic myocardial tissue could potentially hamper the therapeutic effects of implanted bone marrow mesenchymal stem cells (BMSCs). This study sought to address (i) the extent of change to BMSC biological characteristics in different in vitro culture conditions and (ii) the effectiveness of permanent hypoxic culture for cell therapy in treating chronic myocardial infarction (MI) in rats. rat BMSCs were harvested and cultured in normoxic (21% O2, n=27) or hypoxic conditions (5% O2, n=27) until Passage 4 (P4). Cell growth tests, flow cytometry, and Bio-Plex assays were conducted to explore variations in the cell proliferation, phenotype, and cytokine expression, respectively. In the in vivo set-up, P3-BMSCs cultured in normoxia (n=6) or hypoxia (n=6) were intramyocardially injected into rat hearts that had previously experienced 1-month-old MI. The impact of cell therapy on cardiac segmental viability and hemodynamic performance was assessed 1 month later by 2-Deoxy-2[18F]fluoro-D-glucose (18F-FDG) positron emission tomography (PET) imaging and pressure-volume catheter, respectively. Additional histomorphological examinations were conducted to evaluate inflammation, fibrosis, and neovascularization. Hypoxic preconditioning significantly enhanced rat BMSC clonogenic potential and proliferation without altering the multipotency. Different profiles of inflammatory, fibrotic, and angiogenic cytokine secretion were also documented, with a marked correlation observed between in vitro and in vivo proangiogenic cytokine expression and tissue neovessels. Hypoxic-preconditioned cells presented a beneficial effect on the myocardial viability of infarct segments and intrinsic contractility. Hypoxic-preconditioned BMSCs were able to benefit myocardial perfusion and contractility, probably by modulating the inflammation and promoting angiogenesis. © 2017 The Author(s). Published by S. Karger AG, Basel.

Cytokine, chemokine, and growth factor profile of platelet-rich plasma.

PubMed

Mussano, F; Genova, T; Munaron, L; Petrillo, S; Erovigni, F; Carossa, S

2016-07-01

During wound healing, biologically active molecules are released from platelets. The rationale of using platelet-rich plasma (PRP) relies on the concentration of bioactive molecules and subsequent delivery to healing sites. These bioactive molecules have been seldom simultaneously quantified within the same PRP preparation. In the present study, the flexible Bio-Plex system was employed to assess the concentration of a large range of cytokines, chemokines, and growth factors in 16 healthy volunteers so as to determine whether significant baseline differences may be found. Besides IL-1b, IL-1ra, IL-4, IL-6, IL-8, IL-12, IL-13, IL-17, INF-γ, TNF-α, MCP-1, MIP-1a, RANTES, bFGF, PDGF, and VEGF that were already quantified elsewhere, the authors reported also on the presence of IL-2, IL-5, IL-7, IL-9, IL-10, IL-15 G-CSF, GM-CSF, Eotaxin, CXCL10 chemokine (IP-10), and MIP 1b. Among the most interesting results, it is convenient to mention the high concentrations of the HIV-suppressive and inflammatory cytokine RANTES and a statistically significant difference between males and females in the content of PDGF-BB. These data are consistent with previous reports pointing out that gender, diet, and test system affect the results of platelet function in healthy subjects, but seem contradictory when compared to other quantification assays in serum and plasma. The inconsistencies affecting the experimental results found in literature, along with the variability found in the content of bioactive molecules, urge further research, hopefully in form of randomized controlled clinical trials, in order to find definitive evidence of the efficacy of PRP treatment in various pathologic and regenerative conditions.

Evaluation of Machine Learning Algorithms for Classification of Primary Biological Aerosol using a new UV-LIF spectrometer

NASA Astrophysics Data System (ADS)

Ruske, S. T.; Topping, D. O.; Foot, V. E.; Kaye, P. H.; Stanley, W. R.; Morse, A. P.; Crawford, I.; Gallagher, M. W.

2016-12-01

Characterisation of bio-aerosols has important implications within Environment and Public Health sectors. Recent developments in Ultra-Violet Light Induced Fluorescence (UV-LIF) detectors such as the Wideband Integrated bio-aerosol Spectrometer (WIBS) and the newly introduced Multiparameter bio-aerosol Spectrometer (MBS) has allowed for the real time collection of fluorescence, size and morphology measurements for the purpose of discriminating between bacteria, fungal Spores and pollen. This new generation of instruments has enabled ever-larger data sets to be compiled with the aim of studying more complex environments, yet the algorithms used for specie classification remain largely invalidated. It is therefore imperative that we validate the performance of different algorithms that can be used for the task of classification, which is the focus of this study. For unsupervised learning we test Hierarchical Agglomerative Clustering with various different linkages. For supervised learning, ten methods were tested; including decision trees, ensemble methods: Random Forests, Gradient Boosting and AdaBoost; two implementations for support vector machines: libsvm and liblinear; Gaussian methods: Gaussian naïve Bayesian, quadratic and linear discriminant analysis and finally the k-nearest neighbours algorithm. The methods were applied to two different data sets measured using a new Multiparameter bio-aerosol Spectrometer. We find that clustering, in general, performs slightly worse than the supervised learning methods correctly classifying, at best, only 72.7 and 91.1 percent for the two data sets. For supervised learning the gradient boosting algorithm was found to be the most effective, on average correctly classifying 88.1 and 97.8 percent of the testing data respectively across the two data sets. We discuss the wider relevance of these results with regards to challenging existing classification in real-world environments.

Non-contact multi-frequency magnetic induction spectroscopy system for industrial-scale bio-impedance measurement

NASA Astrophysics Data System (ADS)

O'Toole, M. D.; Marsh, L. A.; Davidson, J. L.; Tan, Y. M.; Armitage, D. W.; Peyton, A. J.

2015-03-01

Biological tissues have a complex impedance, or bio-impedance, profile which changes with respect to frequency. This is caused by dispersion mechanisms which govern how the electromagnetic field interacts with the tissue at the cellular and molecular level. Measuring the bio-impedance spectra of a biological sample can potentially provide insight into the sample’s properties and its cellular structure. This has obvious applications in the medical, pharmaceutical and food-based industrial domains. However, measuring the bio-impedance spectra non-destructively and in a way which is practical at an industrial scale presents substantial challenges. The low conductivity of the sample requires a highly sensitive instrument, while the demands of industrial-scale operation require a fast high-throughput sensor of rugged design. In this paper, we describe a multi-frequency magnetic induction spectroscopy (MIS) system suitable for industrial-scale, non-contact, spectroscopic bio-impedance measurement over a bandwidth of 156 kHz-2.5 MHz. The system sensitivity and performance are investigated using calibration and known reference samples. It is shown to yield rapid and consistently sensitive results with good long-term stability. The system is then used to obtain conductivity spectra of a number of biological test samples, including yeast suspensions of varying concentration and a range of agricultural produce, such as apples, pears, nectarines, kiwis, potatoes, oranges and tomatoes.

PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactions.

PubMed

Dong, Jie; Yao, Zhi-Jiang; Zhang, Lin; Luo, Feijun; Lin, Qinlu; Lu, Ai-Ping; Chen, Alex F; Cao, Dong-Sheng

2018-03-20

With the increasing development of biotechnology and informatics technology, publicly available data in chemistry and biology are undergoing explosive growth. Such wealthy information in these data needs to be extracted and transformed to useful knowledge by various data mining methods. Considering the amazing rate at which data are accumulated in chemistry and biology fields, new tools that process and interpret large and complex interaction data are increasingly important. So far, there are no suitable toolkits that can effectively link the chemical and biological space in view of molecular representation. To further explore these complex data, an integrated toolkit for various molecular representation is urgently needed which could be easily integrated with data mining algorithms to start a full data analysis pipeline. Herein, the python library PyBioMed is presented, which comprises functionalities for online download for various molecular objects by providing different IDs, the pretreatment of molecular structures, the computation of various molecular descriptors for chemicals, proteins, DNAs and their interactions. PyBioMed is a feature-rich and highly customized python library used for the characterization of various complex chemical and biological molecules and interaction samples. The current version of PyBioMed could calculate 775 chemical descriptors and 19 kinds of chemical fingerprints, 9920 protein descriptors based on protein sequences, more than 6000 DNA descriptors from nucleotide sequences, and interaction descriptors from pairwise samples using three different combining strategies. Several examples and five real-life applications were provided to clearly guide the users how to use PyBioMed as an integral part of data analysis projects. By using PyBioMed, users are able to start a full pipelining from getting molecular data, pretreating molecules, molecular representation to constructing machine learning models conveniently. PyBioMed provides various user-friendly and highly customized APIs to calculate various features of biological molecules and complex interaction samples conveniently, which aims at building integrated analysis pipelines from data acquisition, data checking, and descriptor calculation to modeling. PyBioMed is freely available at http://projects.scbdd.com/pybiomed.html .

BIO::Phylo-phyloinformatic analysis using perl.

PubMed

Vos, Rutger A; Caravas, Jason; Hartmann, Klaas; Jensen, Mark A; Miller, Chase

2011-02-27

Phyloinformatic analyses involve large amounts of data and metadata of complex structure. Collecting, processing, analyzing, visualizing and summarizing these data and metadata should be done in steps that can be automated and reproduced. This requires flexible, modular toolkits that can represent, manipulate and persist phylogenetic data and metadata as objects with programmable interfaces. This paper presents Bio::Phylo, a Perl5 toolkit for phyloinformatic analysis. It implements classes and methods that are compatible with the well-known BioPerl toolkit, but is independent from it (making it easy to install) and features a richer API and a data model that is better able to manage the complex relationships between different fundamental data and metadata objects in phylogenetics. It supports commonly used file formats for phylogenetic data including the novel NeXML standard, which allows rich annotations of phylogenetic data to be stored and shared. Bio::Phylo can interact with BioPerl, thereby giving access to the file formats that BioPerl supports. Many methods for data simulation, transformation and manipulation, the analysis of tree shape, and tree visualization are provided. Bio::Phylo is composed of 59 richly documented Perl5 modules. It has been deployed successfully on a variety of computer architectures (including various Linux distributions, Mac OS X versions, Windows, Cygwin and UNIX-like systems). It is available as open source (GPL) software from http://search.cpan.org/dist/Bio-Phylo.

BIO::Phylo-phyloinformatic analysis using perl

PubMed Central

2011-01-01

Background Phyloinformatic analyses involve large amounts of data and metadata of complex structure. Collecting, processing, analyzing, visualizing and summarizing these data and metadata should be done in steps that can be automated and reproduced. This requires flexible, modular toolkits that can represent, manipulate and persist phylogenetic data and metadata as objects with programmable interfaces. Results This paper presents Bio::Phylo, a Perl5 toolkit for phyloinformatic analysis. It implements classes and methods that are compatible with the well-known BioPerl toolkit, but is independent from it (making it easy to install) and features a richer API and a data model that is better able to manage the complex relationships between different fundamental data and metadata objects in phylogenetics. It supports commonly used file formats for phylogenetic data including the novel NeXML standard, which allows rich annotations of phylogenetic data to be stored and shared. Bio::Phylo can interact with BioPerl, thereby giving access to the file formats that BioPerl supports. Many methods for data simulation, transformation and manipulation, the analysis of tree shape, and tree visualization are provided. Conclusions Bio::Phylo is composed of 59 richly documented Perl5 modules. It has been deployed successfully on a variety of computer architectures (including various Linux distributions, Mac OS X versions, Windows, Cygwin and UNIX-like systems). It is available as open source (GPL) software from http://search.cpan.org/dist/Bio-Phylo PMID:21352572

Constructing STR multiplex assays.

PubMed

Butler, John M

2005-01-01

Multiplex polymerase chain reaction (PCR) refers to the simultaneous amplification of multiple regions of deoxyribonucleic acid (DNA) using PCR. Commercial short tandem repeat (STR) assays that can coamplify as many as 16 different loci have become widely used in forensic DNA typing. This chapter will focus on some of the aspects of constructing robust STR multiplex assays, including careful design and quality control of PCR primers. Examples from the development of a cat STR 12plex and a human Y chromosome STR 20plex are used to illustrate the importance of various parts of the protocol. Primer design parameters and Internet-accessible resources are discussed, as are solutions to problems with residual dye artifacts that result from impure primers.

Photoelectrochemical Complexes of Fucoxanthin-Chlorophyll Protein for Bio-Photovoltaic Conversion with a High Open-Circuit Photovoltage.

PubMed

Zhang, Tianning; Liu, Cheng; Dong, Wenjing; Wang, Wenda; Sun, Yan; Chen, Xin; Yang, Chunhong; Dai, Ning

2017-12-05

Open-circuit photovoltage (V oc ) is among the critical parameters for achieving an efficient light-to-charge conversion in existing solar photovoltaic devices. Natural photosynthesis exploits light-harvesting chlorophyll (Chl) protein complexes to transfer sunlight energy efficiently. We describe the exploitation of photosynthetic fucoxanthin-chlorophyll protein (FCP) complexes for realizing photoelectrochemical cells with a high V oc . An antenna-dependent photocurrent response and a V oc up to 0.72 V are observed and demonstrated in the bio-photovoltaic devices fabricated with photosynthetic FCP complexes and TiO 2 nanostructures. Such high V oc is determined by fucoxanthin in FCP complexes, and is rarely found in photoelectrochemical cells with other natural light-harvesting antenna. We think that the FCP-based bio-photovoltaic conversion will provide an opportunity to fabricate environmental benign photoelectrochemical cells with high V oc , and also help improve the understanding of the essential physics behind the light-to-charge conversion in photosynthetic complexes. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Comparing the performance plateau in adult cochlear implant patients using HINT and AzBio.

PubMed

Massa, Sean T; Ruckenstein, Michael J

2014-04-01

This study aims to characterize the performance plateau in adult cochlear implant recipients after the initial postimplantation increase by using word recognition testing and an explicit definition of performance plateau. Retrospective review. Urban, tertiary referral center. One hundred twenty-five patients with 138 devices tested with AzBio were matched to 130 patients with 138 devices tested with HINT based on performed on CNC monosyllable tests. Patient's performance was measured overtime using AzBio and HINT tests to determine when and at what score their performance reached a plateau. Time from implantation to reach a performance plateau and plateau score with each test. Thirty-four devices reached a HINT plateau and 30 devices reached an AzBio plateau. Patients reached plateaus at similar times postoperatively using HINT and AzBio, 18.8 and 16.5 weeks, respectively (p = 0.476). Five patients tested with HINT plateaued at scores of 99% to 100%, whereas no patients plateaued above 92% with AzBio. Patients reached a plateau in performance at similar median times using AzBio and HINT, despite the ceiling effect of HINT in some patients. Most patients who reach a plateau did so within 4 months, but exactly when and if a patient's performance plateaus varies significantly among individuals. Further study is required to determine which test best reflects when a patient reaches his or her maximal performance in natural listening conditions.

Calixarenes in bio-medical researches.

PubMed

Rodik, Roman V; Boyko, Vyacheslav I; Kalchenko, Vitaly I

2009-01-01

Application of calixarene derivatives in bio-medical researches is reviewed in this article. Antiviral, bactericidal, antithrombothic, antituberculosis, anticancer activity as well as specific protein complexation, membranotropic properties and toxicity of modified calixarenes are discussed.

Bio-important antipyrine derived Schiff bases and their transition metal complexes: Synthesis, spectroscopic characterization, antimicrobial, anthelmintic and DNA cleavage investigation

NASA Astrophysics Data System (ADS)

Manjunath, M.; Kulkarni, Ajaykumar D.; Bagihalli, Gangadhar B.; Malladi, Shridhar; Patil, Sangamesh A.

2017-01-01

Spectroscopic (IR, NMR, UV-vis, ESR, ESI-mass), magnetic and TGA studies suggests octahedral geometry for all the CoII, NiII and CuII complexes of the Schiff bases, derived from 4-aminoantipyrine and 8-formyl-7-Hydroxy-4-methylcoumarin/5-formyl-6-hydroxycoumarin, coordinated through ONO donor sites. Antibacterial (Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa and Salmonella typhi), antifungal (Aspergillus niger, Aspergillus flavus and Cladosporium) and DNA cleavage properties of the metal complexes are investigated. The results suggested that some of the synthesized compounds are potential antimicrobials. The synthesized compounds tested for their anthelmintic activities and it was found that CoII and NiII complexes exhibited good anthelmintic properties.

Network and biosignature analysis for the integration of transcriptomic and metabolomic data to characterize leaf senescence process in sunflower.

PubMed

Moschen, Sebastián; Higgins, Janet; Di Rienzo, Julio A; Heinz, Ruth A; Paniego, Norma; Fernandez, Paula

2016-06-06

In recent years, high throughput technologies have led to an increase of datasets from omics disciplines allowing the understanding of the complex regulatory networks associated with biological processes. Leaf senescence is a complex mechanism controlled by multiple genetic and environmental variables, which has a strong impact on crop yield. Transcription factors (TFs) are key proteins in the regulation of gene expression, regulating different signaling pathways; their function is crucial for triggering and/or regulating different aspects of the leaf senescence process. The study of TF interactions and their integration with metabolic profiles under different developmental conditions, especially for a non-model organism such as sunflower, will open new insights into the details of gene regulation of leaf senescence. Weighted Gene Correlation Network Analysis (WGCNA) and BioSignature Discoverer (BioSD, Gnosis Data Analysis, Heraklion, Greece) were used to integrate transcriptomic and metabolomic data. WGCNA allowed the detection of 10 metabolites and 13 TFs whereas BioSD allowed the detection of 1 metabolite and 6 TFs as potential biomarkers. The comparative analysis demonstrated that three transcription factors were detected through both methodologies, highlighting them as potentially robust biomarkers associated with leaf senescence in sunflower. The complementary use of network and BioSignature Discoverer analysis of transcriptomic and metabolomic data provided a useful tool for identifying candidate genes and metabolites which may have a role during the triggering and development of the leaf senescence process. The WGCNA tool allowed us to design and test a hypothetical network in order to infer relationships across selected transcription factor and metabolite candidate biomarkers involved in leaf senescence, whereas BioSignature Discoverer selected transcripts and metabolites which discriminate between different ages of sunflower plants. The methodology presented here would help to elucidate and predict novel networks and potential biomarkers of leaf senescence in sunflower.

Bio-jETI: a service integration, design, and provisioning platform for orchestrated bioinformatics processes

PubMed Central

Margaria, Tiziana; Kubczak, Christian; Steffen, Bernhard

2008-01-01

Background With Bio-jETI, we introduce a service platform for interdisciplinary work on biological application domains and illustrate its use in a concrete application concerning statistical data processing in R and xcms for an LC/MS analysis of FAAH gene knockout. Methods Bio-jETI uses the jABC environment for service-oriented modeling and design as a graphical process modeling tool and the jETI service integration technology for remote tool execution. Conclusions As a service definition and provisioning platform, Bio-jETI has the potential to become a core technology in interdisciplinary service orchestration and technology transfer. Domain experts, like biologists not trained in computer science, directly define complex service orchestrations as process models and use efficient and complex bioinformatics tools in a simple and intuitive way. PMID:18460173

A Case Report of Recurrent Takotsubo Cardiomyopathy in a Patient during Myasthenia Crisis

PubMed Central

Battineni, Anusha; Mullaguri, Naresh; Thanki, Shail; Chockalingam, Anand

2017-01-01

Introduction Patients with myasthenia crisis can develop Takotsubo stress cardiomyopathy (SC) due to emotional or physical stress and high level of circulating catecholamines. We report a patient who developed recurrent Takotsubo cardiomyopathy during myasthenia crisis. Coexisting autoimmune disorders known to precipitate stress cardiomyopathy like Grave's disease need to be evaluated. Case Report A 69-year-old female with seropositive myasthenia gravis (MG), Grave's disease, and coronary artery disease on monthly infusion of intravenous immunoglobulin (IVIG), prednisone, pyridostigmine, and methimazole presented with shortness of breath and chest pain. Electrocardiogram (ECG) showed ST elevation in anterolateral leads with troponemia. Coronary angiogram was unremarkable for occlusive coronary disease with left ventriculogram showing reduced wall motion with apical and mid left ventricle (LV) hypokinesis suggestive of Takotsubo stress cardiomyopathy. Her symptoms were attributed to MG crisis. Her symptoms, ECG, and echocardiographic findings resolved after five cycles of plasma exchange (PLEX). She had another similar episode one year later during myasthenia crisis with subsequent resolution in 10 days after PLEX. Conclusion Takotsubo cardiomyopathy can be one of the manifestations of myasthenia crisis with or without coexisting Grave's disease. These patients might benefit from meticulous fluid status and cardiac monitoring while administering rescue treatments like IVIG and PLEX. PMID:29201468

Arsenic bio-accessibility and bioaccumulation in aged pesticide contaminated soils: A multiline investigation to understand environmental risk.

PubMed

Rahman, M S; Reichelt-Brushet, A J; Clark, M W; Farzana, T; Yee, L H

2017-03-01

Bio-accessibility and bioavailability of arsenic (As) in historically As-contaminated soils (cattle tick pesticide), and pristine soils were assessed using 3 different approaches. These approaches included human bio-accessibility using an extraction test replicating gastric conditions (in vitro physiologically-based extraction test); an operationally defined bioaccessibility extraction test - 1.0M HCl extraction; and a live organism bioaccumulation test using earthworms. A sequential extraction procedure revealed the soil As-pool that controls bio-accessibility and bioaccumulation of As. Findings show that As is strongly bound to historically contaminated soil with a lower degree of As bio-accessibility (<15%) and bioaccumulation (<9%) compared with freshly contaminated soil. Key to these lower degrees of bio-accessibility and bioaccumulation is the greater fraction of As associated with crystalline Fe/Al oxy-hydroxide and residual phases. The high bio-accessibility and bioaccumulation of freshly sorbed As in pristine soils were from the exchangeable and specifically sorbed As fractions. Arsenic bioaccumulation in earthworms correlates strongly with both the human bio-accessible, and the operationally defined bioavailable fractions. Hence, results suggest that indirect As bioavailability measures, such as accumulation by earthworm, can be used as complementary lines of evidence to reinforce site-wide trends in the bio-accessibility using in vitro physiologically-based extractions and/or operationally defined extraction test. Such detailed knowledge is useful for successful reclamation and management of the As contaminated soils. Copyright © 2017 Elsevier B.V. All rights reserved.

Results of the IEA Round Robin on Viscosity and Aging of Fast Pyrolysis Bio-oils: Long-Term Tests and Repeatability

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

Elliott, Douglas C.; Oasmaa, Anja; Meier, Dietrich

2012-11-06

An international round robin study of the viscosity and aging of fast pyrolysis bio-oil has been undertaken recently and this work is an outgrowth from that effort. Two bio-oil samples were distributed to the laboratories for aging tests and extended viscosity studies. The accelerated aging test was defined as the change in viscosity of a sealed sample of bio-oil held for 24 h at 80 °C. The test was repeated 10 times over consecutive days to determine the repeatability of the method. Other bio-oil samples were placed in storage at three temperatures, 21 °C, 4 °C and -17 °C formore » a period up to a year to evaluate the change in viscosity. The variation in the results of the aging test was shown to be low within a given laboratory. Storage of bio-oil under refrigeration can minimize the amount of change in viscosity. The accelerated aging test gives a measure of change similar to that of 6-12 months of storage at room temperature. These results can be helpful in setting standards for use of bio-oil, which is just coming into the marketplace.« less

Explorative search of distributed bio-data to answer complex biomedical questions

PubMed Central

2014-01-01

Background The huge amount of biomedical-molecular data increasingly produced is providing scientists with potentially valuable information. Yet, such data quantity makes difficult to find and extract those data that are most reliable and most related to the biomedical questions to be answered, which are increasingly complex and often involve many different biomedical-molecular aspects. Such questions can be addressed only by comprehensively searching and exploring different types of data, which frequently are ordered and provided by different data sources. Search Computing has been proposed for the management and integration of ranked results from heterogeneous search services. Here, we present its novel application to the explorative search of distributed biomedical-molecular data and the integration of the search results to answer complex biomedical questions. Results A set of available bioinformatics search services has been modelled and registered in the Search Computing framework, and a Bioinformatics Search Computing application (Bio-SeCo) using such services has been created and made publicly available at http://www.bioinformatics.deib.polimi.it/bio-seco/seco/. It offers an integrated environment which eases search, exploration and ranking-aware combination of heterogeneous data provided by the available registered services, and supplies global results that can support answering complex multi-topic biomedical questions. Conclusions By using Bio-SeCo, scientists can explore the very large and very heterogeneous biomedical-molecular data available. They can easily make different explorative search attempts, inspect obtained results, select the most appropriate, expand or refine them and move forward and backward in the construction of a global complex biomedical query on multiple distributed sources that could eventually find the most relevant results. Thus, it provides an extremely useful automated support for exploratory integrated bio search, which is fundamental for Life Science data driven knowledge discovery. PMID:24564278

Using an epiphytic moss to identify previously unknown sources of atmospheric cadmium pollution

Treesearch

Geoffrey H. Donovan; Sarah E. Jovan; Demetrios Gatziolis; Igor Burstyn; Yvonne L. Michael; Michael C. Amacher; Vicente J. Monleon

2016-01-01

Urban networks of air-quality monitors are often too widely spaced to identify sources of air pollutants, especially if they do not disperse far from emission sources. The objectives of this study were to test the use of moss bio-indicators to develop a fine-scale map of atmospherically-derived cadmium and to identify the sources of cadmium in a complex urban setting....

Multi-agent-based bio-network for systems biology: protein-protein interaction network as an example.

PubMed

Ren, Li-Hong; Ding, Yong-Sheng; Shen, Yi-Zhen; Zhang, Xiang-Feng

2008-10-01

Recently, a collective effort from multiple research areas has been made to understand biological systems at the system level. This research requires the ability to simulate particular biological systems as cells, organs, organisms, and communities. In this paper, a novel bio-network simulation platform is proposed for system biology studies by combining agent approaches. We consider a biological system as a set of active computational components interacting with each other and with an external environment. Then, we propose a bio-network platform for simulating the behaviors of biological systems and modelling them in terms of bio-entities and society-entities. As a demonstration, we discuss how a protein-protein interaction (PPI) network can be seen as a society of autonomous interactive components. From interactions among small PPI networks, a large PPI network can emerge that has a remarkable ability to accomplish a complex function or task. We also simulate the evolution of the PPI networks by using the bio-operators of the bio-entities. Based on the proposed approach, various simulators with different functions can be embedded in the simulation platform, and further research can be done from design to development, including complexity validation of the biological system.

Scout-MRM: Multiplexed Targeted Mass Spectrometry-Based Assay without Retention Time Scheduling Exemplified by Dickeya dadantii Proteomic Analysis during Plant Infection.

PubMed

Rougemont, Blandine; Bontemps Gallo, Sébastien; Ayciriex, Sophie; Carrière, Romain; Hondermarck, Hubert; Lacroix, Jean Marie; Le Blanc, J C Yves; Lemoine, Jérôme

2017-02-07

Targeted mass spectrometry of a surrogate peptide panel is a powerful method to study the dynamics of protein networks, but chromatographic time scheduling remains a major limitation for dissemination and implementation of robust and large multiplexed assays. We unveil a Multiple Reaction Monitoring method (Scout-MRM) where the use of spiked scout peptides triggers complex transition lists, regardless of the retention time of targeted surrogate peptides. The interest of Scout-MRM method regarding the retention time independency, multiplexing capability, reproducibility, and putative interest in facilitating method transfer was illustrated by a 782-peptide-plex relative assay targeting 445 proteins of the phytopathogen Dickeya dadantii during plant infection.

Effects of dietary supplementation with an organic source of selenium on characteristics of semen quality and in vitro fertility in boars.

PubMed

Speight, S M; Estienne, M J; Harper, A F; Crawford, R J; Knight, J W; Whitaker, B D

2012-03-01

Semen characteristics in boars fed organic or inorganic sources of Se were assessed in 3 experiments. Crossbred boars were randomly assigned at weaning to 1 of 3 dietary treatments: I) basal diets with no supplemental Se (control), II) basal diets with 0.3 mg/kg of supplemental Se from an organic source (Sel-Plex, Alltech Inc., Nicholasville, KY), and III) basal diets supplemented with 0.3 mg/kg of supplemental Se from sodium selenite (Premium Selenium 270, North American Nutrition Co. Inc., Lewisburg, OH). For Exp. 1, semen was collected from boars (n = 10/dietary treatment) on 5 consecutive days at 15 mo of age. Effects of treatment × day were detected for the proportions of progressively motile (P = 0.02) and rapidly moving (P = 0.03) spermatozoa, and measures of sperm velocity, including path velocity of the smoothed cell path (P = 0.05) and average velocity measured in a straight line from the beginning to the end of the track (P = 0.05). Negative effects of day of semen collection on sperm motility were least pronounced in boars fed Sel-Plex. Experiment 2 was conducted when boars were 17 mo of age, and semen was collected (n = 10 boars/dietary treatment), diluted in commercially available extenders, and stored at 18°C for 9 d. Effects of treatment × day were detected for percentages of motile (P = 0.01) and static (P = 0.01) spermatozoa, amplitude of lateral head displacement (P = 0.02), frequency with which the sperm track crossed the sperm path (P = 0.04), straightness (P = 0.01), and average size of all sperm heads (P = 0.03). In general, sperm cells from boars fed Sel-Plex were better able to maintain motility during liquid storage compared with boars fed sodium selenite. For Exp. 3, semen was collected from boars (n = 6/dietary treatment) at 23 mo of age, and spermatozoa were evaluated at d 1 and 8 after semen collection using in vitro fertilization procedures. There was a tendency for an effect (P = 0.11) of dietary treatment on fertilization rate with Sel-Plex-fed boars having the greatest value (70.7%). The results of this study suggest that there are positive effects of dietary supplementation with Sel-Plex on boar semen characteristics and that organic Se supplementation may help ameliorate the negative effects of semen storage on characteristics of sperm motility.

Targeted sequencing of clade-specific markers from skin microbiomes for forensic human identification.

PubMed

Schmedes, Sarah E; Woerner, August E; Novroski, Nicole M M; Wendt, Frank R; King, Jonathan L; Stephens, Kathryn M; Budowle, Bruce

2018-01-01

The human skin microbiome is comprised of diverse communities of bacterial, eukaryotic, and viral taxa and contributes millions of additional genes to the repertoire of human genes, affecting human metabolism and immune response. Numerous genetic and environmental factors influence the microbiome composition and as such contribute to individual-specific microbial signatures which may be exploited for forensic applications. Previous studies have demonstrated the potential to associate skin microbial profiles collected from touched items to their individual owner, mainly using unsupervised methods from samples collected over short time intervals. Those studies utilize either targeted 16S rRNA or shotgun metagenomic sequencing to characterize skin microbiomes; however, these approaches have limited species and strain resolution and susceptibility to stochastic effects, respectively. Clade-specific markers from the skin microbiome, using supervised learning, can predict individual identity using skin microbiomes from their respective donors with high accuracy. In this study the hidSkinPlex is presented, a novel targeted sequencing method using skin microbiome markers developed for human identification. The hidSkinPlex (comprised of 286 bacterial (and phage) family-, genus-, species-, and subspecies-level markers), initially was evaluated on three bacterial control samples represented in the panel (i.e., Propionibacterium acnes, Propionibacterium granulosum, and Rothia dentocariosa) to assess the performance of the multiplex. The hidSkinPlex was further evaluated for prediction purposes. The hidSkinPlex markers were used to attribute skin microbiomes collected from eight individuals from three body sites (i.e., foot (Fb), hand (Hp) and manubrium (Mb)) to their host donor. Supervised learning, specifically regularized multinomial logistic regression and 1-nearest-neighbor classification were used to classify skin microbiomes to their hosts with up to 92% (Fb), 96% (Mb), and 100% (Hp) accuracy. All samples (n=72) regardless of body site origin were correctly classified with up to 94% accuracy, and body site origin could be predicted with up to 86% accuracy. Finally, human short tandem repeat and single-nucleotide polymorphism profiles were generated from skin swab extracts from a single subject to highlight the potential to use microbiome profiling in conjunction with low-biomass samples. The hidSkinPlex is a novel targeted enrichment approach to profile skin microbiomes for human forensic identification purposes and provides a method to further characterize the utility of skin microflora for human identification in future studies, such as the stability and diversity of the personal skin microbiome. Copyright © 2017 Elsevier B.V. All rights reserved.

EU-approved rapid tests might underestimate bovine spongiform encephalopathy infection in goats.

PubMed

Meloni, Daniela; Bozzetta, Elena; Langeveld, Jan P M; Groschup, Martin H; Goldmann, Wilfred; Andrèoletti, Olivier; Lantier, Isabelle; Van Keulen, Lucien; Bossers, Alex; Pitardi, Danilo; Nonno, Romolo; Sklaviadis, Theodoros; Ingravalle, Francesco; Peletto, Simone; Colussi, Silvia; Acutis, Pier Luigi

2017-03-01

We report the diagnostic sensitivity of 3 EU-approved rapid tests (ELISAs; 1 from IDEXX and 2 from Bio-Rad) for the detection of transmissible spongiform encephalopathy diseases in goats. Ninety-eight goat brainstem samples were tested. All the rapid tests had 100% specificity and ≥80% sensitivity, with the IDEXX test significantly more sensitive than the 2 Bio-Rad tests. All tests detected 100% of samples from goats with clinical scrapie, but missed 8% (IDEXX) to 33% (Bio-Rad SG) of samples from preclinical goats. Importantly, only IDEXX picked up all samples from clinical bovine spongiform encephalopathy (BSE)-infected goats, whereas the other 2 rapid tests missed 15% (Bio-Rad SG) to 25% (Bio-Rad SAP). These results show that a fraction of preclinical scrapie infections are likely missed by EU surveillance, with sensitivity of detection strongly dependent on the choice of the rapid test. Moreover, a significant proportion of clinical BSE infections are underestimated by using either Bio-Rad test. Assuming that the same sensitivity on preclinical goats would also occur in BSE-infected goats, our data suggest that IDEXX is likely the most sensitive test for detecting preclinical field cases of BSE infection in goats, although with an 8% failure rate. These results raise some concerns about the reliability of current EU surveillance figures on BSE infection in goats.

Evaluation of physicochemical properties of root-end filling materials using conventional and Micro-CT tests.

PubMed

Torres, Fernanda Ferrari Esteves; Bosso-Martelo, Roberta; Espir, Camila Galletti; Cirelli, Joni Augusto; Guerreiro-Tanomaru, Juliane Maria; Tanomaru-Filho, Mario

2017-01-01

To evaluate solubility, dimensional stability, filling ability and volumetric change of root-end filling materials using conventional tests and new Micro-CT-based methods. 7. The results suggested correlated or complementary data between the proposed tests. At 7 days, BIO showed higher solubility and at 30 days, showed higher volumetric change in comparison with MTA (p<0.05). With regard to volumetric change, the tested materials were similar (p>0.05) at 7 days. At 30 days, they presented similar solubility. BIO and MTA showed higher dimensional stability than ZOE (p<0.05). ZOE and BIO showed higher filling ability (p<0.05). ZOE presented a higher dimensional change, and BIO had greater solubility after 7 days. BIO presented filling ability and dimensional stability, but greater volumetric change than MTA after 30 days. Micro-CT can provide important data on the physicochemical properties of materials complementing conventional tests.

Local and Systemic Inflammatory Responses to Experimentally Induced Gingivitis

PubMed Central

Leishman, Shaneen J.; Seymour, Gregory J.; Ford, Pauline J.

2013-01-01

This study profiled the local and systemic inflammatory responses to experimentally induced gingivitis. Eight females participated in a 21-day experimental gingivitis model followed by a 14-day resolution phase. Bleeding on probing and plaque index scores were assessed before, during, and after resolution of gingival inflammation, and samples of saliva, GCF, and plasma were collected. Samples were assessed for biomarkers of inflammation using the BioPlex platform and ELISA. There were no significant changes in GCF levels of cytokines during the experimental phase; however, individual variability in cytokine profiles was noted. During resolution, mean GCF levels of IL-2, IL-6, and TNF-α decreased and were significantly lower than baseline levels (P = 0.003, P = 0.025, and P = 0.007, resp.). Furthermore, changes in GCF levels of IL-2, IL-6, and TNF-α during resolution correlated with changes in plaque index scores (r = 0.88, P = 0.004; r = 0.72, P = 0.042; r = 0.79, P = 0.019, resp.). Plasma levels of sICAM-1 increased significantly during the experimental phase (P = 0.002) and remained elevated and significantly higher than baseline levels during resolution (P < 0.001). These results support the concept that gingivitis adds to the systemic inflammatory burden of an individual. PMID:24227893

Local and systemic inflammatory responses to experimentally induced gingivitis.

PubMed

Leishman, Shaneen J; Seymour, Gregory J; Ford, Pauline J

2013-01-01

This study profiled the local and systemic inflammatory responses to experimentally induced gingivitis. Eight females participated in a 21-day experimental gingivitis model followed by a 14-day resolution phase. Bleeding on probing and plaque index scores were assessed before, during, and after resolution of gingival inflammation, and samples of saliva, GCF, and plasma were collected. Samples were assessed for biomarkers of inflammation using the BioPlex platform and ELISA. There were no significant changes in GCF levels of cytokines during the experimental phase; however, individual variability in cytokine profiles was noted. During resolution, mean GCF levels of IL-2, IL-6, and TNF-α decreased and were significantly lower than baseline levels (P = 0.003, P = 0.025, and P = 0.007, resp.). Furthermore, changes in GCF levels of IL-2, IL-6, and TNF-α during resolution correlated with changes in plaque index scores (r = 0.88, P = 0.004; r = 0.72, P = 0.042; r = 0.79, P = 0.019, resp.). Plasma levels of sICAM-1 increased significantly during the experimental phase (P = 0.002) and remained elevated and significantly higher than baseline levels during resolution (P < 0.001). These results support the concept that gingivitis adds to the systemic inflammatory burden of an individual.

Correlation of interleukin-6 and monocyte chemotactic protein-1 concentrations with crescent formation and myeloperoxidase-specific anti-neutrophil cytoplasmic antibody titer in SCG/Kj mice by treatment with anti-interleukin-6 receptor antibody or mizoribine.

PubMed

Nagao, Tomokazu; Kusunoki, Reina; Iwamura, Chiaki; Kobayashi, Shigeto; Yumura, Wako; Kameoka, Yosuke; Nakayama, Toshinori; Suzuki, Kazuo

2013-09-01

Myeloperoxidase-specific anti-neutrophil cytoplasmic antibody (MPO-ANCA) is associated with rapidly progressive glomerulonephritis (RPGN) and glomerular crescent formation. Pathogenic factors in RPGN were analyzed by using SCG/Kj mice, which spontaneously develop MPO-ANCA-associated RPGN. The serum concentration of soluble IL-6R was determined by using ELISA and those of another 23 cytokines and chemokines by Bio-Plex analysis. Sections of frozen kidney tissue were examined by fluorescence microscopy and the CD3(+) B220(+) T cell subset in the spleen determined by a flow cytometry. Concentrations of IL-6 and monocyte chemotactic protein-1 were significantly correlated with the percentages of crescent formation. Anti-IL-6R antibody, which has been effective in patients with rheumatoid arthritis, was administered to SCG/Kj mice to elucidate the role of IL-6 in the development of RPGN. MPO-ANCA titers decreased after administration of anti-IL-6R antibody, but not titers of mizoribine, which is effective in Kawasaki disease model mice. These results suggest that IL-6-mediated signaling is involved in the production of MPO-ANCA. © 2013 The Societies and Wiley Publishing Asia Pty Ltd.

Comparison of PanBio Dengue Duo Enzyme-Linked Immunosorbent Assay (ELISA) and MRL Dengue Fever Virus Immunoglobulin M Capture ELISA for Diagnosis of Dengue Virus Infections in Southeast Asia

PubMed Central

Cuzzubbo, Andrea J.; Vaughn, David W.; Nisalak, Ananda; Solomon, Tom; Kalayanarooj, Siripen; Aaskov, John; Dung, Nguyen Minh; Devine, Peter L.

1999-01-01

The performances of the MRL dengue fever virus immunoglobulin M (IgM) capture enzyme-linked immunosorbent assay (ELISA) and the PanBio Dengue Duo IgM capture and IgG capture ELISA were compared. Eighty sera from patients with dengue virus infections, 24 sera from patients with Japanese encephalitis (JE), and 78 sera from patients with nonflavivirus infections, such as malaria, typhoid, leptospirosis, and scrub typhus, were used. The MRL test showed superior sensitivity for dengue virus infections (94 versus 89%), while the PanBio test showed superior specificity for JE (79 versus 25%) and other infections (100 versus 91%). The PanBio ELISA showed better overall performance, as assessed by the sum of sensitivity and specificity (F value). When dengue virus and nonflavivirus infections were compared, F values of 189 and 185 were obtained for the PanBio and MRL tests, respectively, while when dengue virus infections and JE were compared, F values of 168 and 119 were obtained. The results obtained with individual sera in the PanBio and MRL IgM ELISAs showed good correlation, but this analysis revealed that the cutoff value of the MRL test was set well below that of the PanBio test. Comparing the sensitivity and specificity of the tests at different cutoff values (receiver-operator analysis) revealed that the MRL and PanBio IgM ELISAs performed similarly in distinguishing dengue virus from nonflavivirus infections, although the PanBio IgM ELISA showed significantly better distinction between dengue virus infections and JE. The implications of these findings for the laboratory diagnosis of dengue are discussed. PMID:10473522

Energy Spectral Behaviors of Communication Networks of Open-Source Communities

PubMed Central

Yang, Jianmei; Yang, Huijie; Liao, Hao; Wang, Jiangtao; Zeng, Jinqun

2015-01-01

Large-scale online collaborative production activities in open-source communities must be accompanied by large-scale communication activities. Nowadays, the production activities of open-source communities, especially their communication activities, have been more and more concerned. Take CodePlex C # community for example, this paper constructs the complex network models of 12 periods of communication structures of the community based on real data; then discusses the basic concepts of quantum mapping of complex networks, and points out that the purpose of the mapping is to study the structures of complex networks according to the idea of quantum mechanism in studying the structures of large molecules; finally, according to this idea, analyzes and compares the fractal features of the spectra in different quantum mappings of the networks, and concludes that there are multiple self-similarity and criticality in the communication structures of the community. In addition, this paper discusses the insights and application conditions of different quantum mappings in revealing the characteristics of the structures. The proposed quantum mapping method can also be applied to the structural studies of other large-scale organizations. PMID:26047331

Direct amplification of casework bloodstains using the Promega PowerPlex(®) 21 PCR amplification system.

PubMed

Gray, Kerryn; Crowle, Damian; Scott, Pam

2014-09-01

A significant number of evidence items submitted to Forensic Science Service Tasmania (FSST) are blood swabs or bloodstained items. Samples from these items routinely undergo phenol:chloroform:isoamyl alcohol organic extraction and quantitative Polymerase Chain Reaction (qPCR) testing prior to PowerPlex(®) 21 amplification. This multi-step process has significant cost and timeframe implications in a fiscal climate of tightening government budgets, pressure towards improved operating efficiencies, and an increasing emphasis on rapid techniques better supporting intelligence-led policing. Direct amplification of blood and buccal cells on cloth and Whatman FTA™ card with PowerPlex(®) 21 has already been successfully implemented for reference samples, eliminating the requirement for sample pre-treatment. Scope for expanding this method to include less pristine casework blood swabs and samples from bloodstained items was explored in an endeavour to eliminate lengthy DNA extraction, purification and qPCR steps for a wider subset of samples. Blood was deposited onto a range of substrates including those historically found to inhibit STR amplification. Samples were collected with micro-punch, micro-swab, or both. The potential for further fiscal savings via reduced volume amplifications was assessed by amplifying all samples at full and reduced volume (25 and 13μL). Overall success rate data showed 80% of samples yielded a complete profile at reduced volume, compared to 78% at full volume. Particularly high success rates were observed for the blood on fabric/textile category with 100% of micro-punch samples yielding complete profiles at reduced volume and 85% at full volume. Following the success of this trial, direct amplification of suitable casework blood samples has been implemented at reduced volume. Significant benefits have been experienced, most noticeably where results from crucial items have been provided to police investigators prior to interview of suspects, and a coronial identification has been successfully completed in a short timeframe to avoid delay in the release of human remains to family members. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

[Polymorphism analysis of 20 autosomal short-tandem repeat loci in southern Chinese Han population].

PubMed

Chen, Ling; Lu, Hui-Jie; DU, Wei-An; Qiu, Ping-Ming; Liu, Chao

2016-02-20

To evaluate the value of PowerPlex ® 21 System (Promega) and study the genetic polymorphism of its 20 short-tandem repeat (STR) loci in southern Chinese Han population. We conducted genotyping experiments using PowerPlex ® 21 System on 20 autosomal STR loci (D3S1358, D1S1656, D6S1043, D13S317, Penta E, D16S539, D18S51, D2S1338, CSF1PO, Penta D, TH01, vWA, D21S11, D7S820, D5S818, TPOX, D8S1179, D12S391, D19S433 and FGA) in 2367 unrelated Chinese Han individuals living in South China. The allele frequencies and parameters commonly used in forensic science were statistically analyzed in these individuals and compared with the reported data of other populations. The PowerPlex ® 21 System had a power of discrimination (PD) ranging from 0.7839 to 0.9852 and a power of exclusion (PE) ranging from 0.2974 to 0.8099 for the 20 loci. No significant deviation from Hardy-Weinberg expectations was found for all the loci except for D5S818. This southern Chinese Han population had significant differences in the allele frequencies from 8 ethnic groups reported in China, and showed significant differences at 8 to 20 STR foci from 5 foreign populations. The allele frequency at the locus D1S1656 in this southern Chinese Han population differed significantly from those in the 5 foreign populations and from 3 reported Han populations in Beijing, Zhejiang Province and Fujian Province of China. The neighbor-joining phylogenetictree showed clustering of all the Asian populations in one branch, while the northern Italian and Argentina populations clustered in a separate branch. This southern Chinese Han population had the nearest affinity with the Yi ethnic population in Yunnan Province of China. The 20 STR loci are highly polymorphic in this southern Chinese Han population, suggesting the value of this set of STR loci in forensic personal identification, paternity testing and anthropological study.

A new biarticular actuator design facilitates control of leg function in BioBiped3.

PubMed

Sharbafi, Maziar Ahmad; Rode, Christian; Kurowski, Stefan; Scholz, Dorian; Möckel, Rico; Radkhah, Katayon; Zhao, Guoping; Rashty, Aida Mohammadinejad; Stryk, Oskar von; Seyfarth, Andre

2016-07-01

Bioinspired legged locomotion comprises different aspects, such as (i) benefiting from reduced complexity control approaches as observed in humans/animals, (ii) combining embodiment with the controllers and (iii) reflecting neural control mechanisms. One of the most important lessons learned from nature is the significant role of compliance in simplifying control, enhancing energy efficiency and robustness against perturbations for legged locomotion. In this research, we investigate how body morphology in combination with actuator design may facilitate motor control of leg function. Inspired by the human leg muscular system, we show that biarticular muscles have a key role in balancing the upper body, joint coordination and swing leg control. Appropriate adjustment of biarticular spring rest length and stiffness can simplify the control and also reduce energy consumption. In order to test these findings, the BioBiped3 robot was developed as a new version of BioBiped series of biologically inspired, compliant musculoskeletal robots. In this robot, three-segmented legs actuated by mono- and biarticular series elastic actuators mimic the nine major human leg muscle groups. With the new biarticular actuators in BioBiped3, novel simplified control concepts for postural balance and for joint coordination in rebounding movements (drop jumps) were demonstrated and approved.

Genetic polymorphisms of 20 autosomal STR loci in the Vietnamese population from Yunnan Province, Southwest China.

PubMed

Zhang, Xiufeng; Hu, Liping; Du, Lei; Nie, Aiting; Rao, Min; Pang, Jing Bo; Nie, Shengjie

2017-05-01

The genetic polymorphisms of 20 autosomal short tandem repeat (STR) loci included in the PowerPlex® 21 kit were evaluated in 522 healthy unrelated Vietnamese from Yunnan, China. All of the loci reached the Hardy-Weinberg equilibrium. These loci were examined to determine allele frequencies and forensic statistical parameters. The combined discrimination power and probability of excluding paternity of the 20 STR loci were 0.999999999999999999999991 26 and 0.999999975, respectively. Results suggested that the 20 STR loci are highly polymorphic, which is suitable for forensic personal identification and paternity testing.

Forensic genetic analysis of bio-geographical ancestry.

PubMed

Phillips, Chris

2015-09-01

With the great strides made in the last ten years in the understanding of human population variation and the detailed characterization of the genome, it is now possible to identify sets of ancestry informative markers suitable for relatively small-scale PCR-based assays and use them to analyze the ancestry of an individual from forensic DNA. This review outlines some of the current understanding of past human population structure and how it may have influenced the complex distribution of contemporary human diversity. A simplified description of human diversity can provide a suitable basis for choosing the best ancestry-informative markers, which is important given the constraints of multiplex sizes in forensic DNA tests. It is also important to decide the level of geographic resolution that is realistic to ensure the balance between informativeness and an over-simplification of complex human diversity patterns. A detailed comparison is made of the most informative ancestry markers suitable for forensic use and assessments are made of the data analysis regimes that can provide statistical inferences of a DNA donor's bio-geographical ancestry. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Null alleles and sequence variations at primer binding sites of STR loci within multiplex typing systems.

PubMed

Yao, Yining; Yang, Qinrui; Shao, Chengchen; Liu, Baonian; Zhou, Yuxiang; Xu, Hongmei; Zhou, Yueqin; Tang, Qiqun; Xie, Jianhui

2018-01-01

Rare variants are widely observed in human genome and sequence variations at primer binding sites might impair the process of PCR amplification resulting in dropouts of alleles, named as null alleles. In this study, 5 cases from routine paternity testing using PowerPlex ® 21 System for STR genotyping were considered to harbor null alleles at TH01, FGA, D5S818, D8S1179, and D16S539, respectively. The dropout of alleles was confirmed by using alternative commercial kits AGCU Expressmarker 22 PCR amplification kit and AmpFℓSTR ® . Identifiler ® Plus Kit, and sequencing results revealed a single base variation at the primer binding site of each STR locus. Results from the collection of previous reports show that null alleles at D5S818 were frequently observed in population detected by two PowerPlex ® typing systems and null alleles at D19S433 were mostly observed in Japanese population detected by two AmpFℓSTR™ typing systems. Furthermore, the most popular mutation type appeared the transition from C to T with G to A, which might have a potential relationship with DNA methylation. Altogether, these results can provide helpful information in forensic practice to the elimination of genotyping discrepancy and the development of primer sets. Copyright © 2017 Elsevier B.V. All rights reserved.

[Synthesis and characterization of polylactide-based thermosetting polyurethanes with shape memory properties].

PubMed

Shi, Shuo; Gu, Lin; Yang, Yihu; Yu, Haibin; Chen, Rui; Xiao, Xianglian; Qiu, Jun

2016-06-25

A series of bio-based thermosetting polyurethanes (Bio-PUs) were synthesized by the crosslinking reaction of polylactide and its copolymers diols with hexamethylene diisocyanate (HDI) trimer. The obtained Bio-PUs were characterized by Fourier Transform Infrared Spectroscopy (FTIR), Differential Scanning Calorimetry (DSC), Thermal Gravimetric Analysis (TGA), universal tensile testing machine and cytotoxicity test. Results indicate that the PLA copolymer (P(LA-co-CL)) diols reduced the glass transition temperature (Tg) of Bio-PUs and improved their thermal stability, compared with PLA diols. The Bio-PUs synthesized from P (LA-co-CL) diols exhibit better mechanical performance and shape memory properties. Especially, Young modulus and elongation at break of the obtained Bio-PUs were 277.7 MPa and 230% respectively; the shape recovery time of the obtained Bio-PUs at body temperature was only 93 s. Furthermore, alamar blue assay results showed that the obtained Bio-PUs had no cell toxicity.

KISS for STRAP: user extensions for a protein alignment editor.

PubMed

Gille, Christoph; Lorenzen, Stephan; Michalsky, Elke; Frömmel, Cornelius

2003-12-12

The Structural Alignment Program STRAP is a comfortable comprehensive editor and analyzing tool for protein alignments. A wide range of functions related to protein sequences and protein structures are accessible with an intuitive graphical interface. Recent features include mapping of mutations and polymorphisms onto structures and production of high quality figures for publication. Here we address the general problem of multi-purpose program packages to keep up with the rapid development of bioinformatical methods and the demand for specific program functions. STRAP was remade implementing a novel design which aims at Keeping Interfaces in STRAP Simple (KISS). KISS renders STRAP extendable to bio-scientists as well as to bio-informaticians. Scientists with basic computer skills are capable of implementing statistical methods or embedding existing bioinformatical tools in STRAP themselves. For bio-informaticians STRAP may serve as an environment for rapid prototyping and testing of complex algorithms such as automatic alignment algorithms or phylogenetic methods. Further, STRAP can be applied as an interactive web applet to present data related to a particular protein family and as a teaching tool. JAVA-1.4 or higher. http://www.charite.de/bioinf/strap/

The SNPforID Assay as a Supplementary Method in Kinship and Trace Analysis

PubMed Central

Schwark, Thorsten; Meyer, Patrick; Harder, Melanie; Modrow, Jan-Hendrick; von Wurmb-Schwark, Nicole

2012-01-01

Objective Short tandem repeat (STR) analysis using commercial multiplex PCR kits is the method of choice for kinship testing and trace analysis. However, under certain circumstances (deficiency testing, mutations, minute DNA amounts), STRs alone may not suffice. Methods We present a 50-plex single nucleotide polymorphism (SNP) assay based on the SNPs chosen by the SNPforID consortium as an additional method for paternity and for trace analysis. The new assay was applied to selected routine paternity and trace cases from our laboratory. Results and Conclusions Our investigation shows that the new SNP multiplex assay is a valuable method to supplement STR analysis, and is a powerful means to solve complicated genetic analyses. PMID:22851934

Structural Design and Monitoring Analysis of Foundation Pit Support in Yiwu Huishang Tiandi

NASA Astrophysics Data System (ADS)

Zhang, Chunsu

2017-08-01

Huishang Tiandi deep foundation pit in Yiwu is a two-story basement,which is located in the downtown area and adjacent to the city center main traffic trunk. The surrounding environment is too com-plex to slope. The excavation depth is large, the formation is weak and complex, and the groundwater level is high.In order to ensure the safety of the foundation wall and the surrounding environment, the deformation of the foundation pit support is strictly controlled, and the deformation and internal force of the foundation supporting structure and the surrounding building are monitored.The deformation law of the foundation pit is obtained through the analysis of the horizontal displacement, the deformation rate of the supporting struc-ture, the surrounding environment of the foundation pit and the internal force of the anchor cable. The relia-bility and rationality of the design of foundation pit support are verified. It is of reference value for the de-sign and construction of other deep foundation pit engineering in Yiwu area.

Promotion of hydrogen-rich gas and phenolic-rich bio-oil production from green macroalgae Cladophora glomerata via pyrolysis over its bio-char.

PubMed

Norouzi, Omid; Jafarian, Sajedeh; Safari, Farid; Tavasoli, Ahmad; Nejati, Behnam

2016-11-01

Conversion of Cladophora glomerata (C. glomerata) as a Caspian Sea's green macroalgae into gaseous, liquid and solid products was carried out via pyrolysis at different temperatures to determine its potential for bio-oil and hydrogen-rich gas production for further industrial utilization. Non-catalytic tests were performed to determine the optimum condition for bio-oil production. The highest portion of bio-oil was retrieved at 500°C. The catalytic test was performed using the bio-char derived at 500°C as a catalyst. Effect of the addition of the algal bio-char on the composition of the bio-oil and also gaseous products was investigated. Pyrolysis derived bio-char was characterized by BET, FESEM and ICP method to show its surface area, porosity, and presence of inorganic metals on its surface, respectively. Phenols were increased from 8.5 to 20.76area% by the addition of bio-char. Moreover, the hydrogen concentration and hydrogen selectivity were also enhanced by the factors of 1.37, 1.59 respectively. Copyright © 2016 Elsevier Ltd. All rights reserved.

Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms.

PubMed

Chen, DaYang; Zhen, HeFu; Qiu, Yong; Liu, Ping; Zeng, Peng; Xia, Jun; Shi, QianYu; Xie, Lin; Zhu, Zhu; Gao, Ya; Huang, GuoDong; Wang, Jian; Yang, HuanMing; Chen, Fang

2018-03-21

Research based on a strategy of single-cell low-coverage whole genome sequencing (SLWGS) has enabled better reproducibility and accuracy for detection of copy number variations (CNVs). The whole genome amplification (WGA) method and sequencing platform are critical factors for successful SLWGS (<0.1 × coverage). In this study, we compared single cell and multiple cells sequencing data produced by the HiSeq2000 and Ion Proton platforms using two WGA kits and then comprehensively evaluated the GC-bias, reproducibility, uniformity and CNV detection among different experimental combinations. Our analysis demonstrated that the PicoPLEX WGA Kit resulted in higher reproducibility, lower sequencing error frequency but more GC-bias than the GenomePlex Single Cell WGA Kit (WGA4 kit) independent of the cell number on the HiSeq2000 platform. While on the Ion Proton platform, the WGA4 kit (both single cell and multiple cells) had higher uniformity and less GC-bias but lower reproducibility than those of the PicoPLEX WGA Kit. Moreover, on these two sequencing platforms, depending on cell number, the performance of the two WGA kits was different for both sensitivity and specificity on CNV detection. The results can help researchers who plan to use SLWGS on single or multiple cells to select appropriate experimental conditions for their applications.

BioCreative V track 4: a shared task for the extraction of causal network information using the Biological Expression Language.

PubMed

Rinaldi, Fabio; Ellendorff, Tilia Renate; Madan, Sumit; Clematide, Simon; van der Lek, Adrian; Mevissen, Theo; Fluck, Juliane

2016-01-01

Automatic extraction of biological network information is one of the most desired and most complex tasks in biological and medical text mining. Track 4 at BioCreative V attempts to approach this complexity using fragments of large-scale manually curated biological networks, represented in Biological Expression Language (BEL), as training and test data. BEL is an advanced knowledge representation format which has been designed to be both human readable and machine processable. The specific goal of track 4 was to evaluate text mining systems capable of automatically constructing BEL statements from given evidence text, and of retrieving evidence text for given BEL statements. Given the complexity of the task, we designed an evaluation methodology which gives credit to partially correct statements. We identified various levels of information expressed by BEL statements, such as entities, functions, relations, and introduced an evaluation framework which rewards systems capable of delivering useful BEL fragments at each of these levels. The aim of this evaluation method is to help identify the characteristics of the systems which, if combined, would be most useful for achieving the overall goal of automatically constructing causal biological networks from text. © The Author(s) 2016. Published by Oxford University Press.

Evaluation of physicochemical properties of root-end filling materials using conventional and Micro-CT tests

PubMed Central

TORRES, Fernanda Ferrari Esteves; BOSSO-MARTELO, Roberta; ESPIR, Camila Galletti; CIRELLI, Joni Augusto; GUERREIRO-TANOMARU, Juliane Maria; TANOMARU-FILHO, Mario

2017-01-01

Abstract Objective To evaluate solubility, dimensional stability, filling ability and volumetric change of root-end filling materials using conventional tests and new Micro-CT-based methods. Material and Methods 7 Results The results suggested correlated or complementary data between the proposed tests. At 7 days, BIO showed higher solubility and at 30 days, showed higher volumetric change in comparison with MTA (p<0.05). With regard to volumetric change, the tested materials were similar (p>0.05) at 7 days. At 30 days, they presented similar solubility. BIO and MTA showed higher dimensional stability than ZOE (p<0.05). ZOE and BIO showed higher filling ability (p<0.05). Conclusions ZOE presented a higher dimensional change, and BIO had greater solubility after 7 days. BIO presented filling ability and dimensional stability, but greater volumetric change than MTA after 30 days. Micro-CT can provide important data on the physicochemical properties of materials complementing conventional tests. PMID:28877275

Enhanced photocurrent production by bio-dyes of photosynthetic macromolecules on designed TiO2 film

PubMed Central

Yu, Daoyong; Wang, Mengfei; Zhu, Guoliang; Ge, Baosheng; Liu, Shuang; Huang, Fang

2015-01-01

The macromolecular pigment-protein complex has the merit of high efficiency for light-energy capture and transfer after long-term photosynthetic evolution. Here bio-dyes of A. platensis photosystem I (PSI) and spinach light-harvesting complex II (LHCII) are spontaneously sensitized on three types of designed TiO2 films, to assess the effects of pigment-protein complex on the performance of bio-dye sensitized solar cells (SSC). Adsorption models of bio-dyes are proposed based on the 3D structures of PSI and LHCII, and the size of particles and inner pores in the TiO2 film. PSI shows its merit of high efficiency for captured energy transfer, charge separation and transfer in the electron transfer chain (ETC), and electron injection from FB to the TiO2 conducting band. After optimization, the best short current (JSC) and photoelectric conversion efficiency (η) of PSI-SSC and LHCII-SSC are 1.31 mA cm-2 and 0.47%, and 1.51 mA cm-2 and 0.52%, respectively. The potential for further improvement of this PSI based SSC is significant and could lead to better utilization of solar energy. PMID:25790735

Bright luminescence from pure DNA-curcumin-based phosphors for bio hybrid light-emitting diodes

NASA Astrophysics Data System (ADS)

Reddy, M. Siva Pratap; Park, Chinho

2016-08-01

Recently, significant advances have occurred in the development of phosphors for bio hybrid light-emitting diodes (Bio-HLEDs), which have created brighter, metal-free, rare-earth phosphor-free, eco-friendly, and cost-competitive features for visible light emission. Here, we demonstrate an original approach using bioinspired phosphors in Bio-HLEDs based on natural deoxyribonucleic acid (DNA)-curcumin complexes with cetyltrimethylammonium (CTMA) in bio-crystalline form. The curcumin chromophore was bound to the DNA double helix structure as observed using field emission tunnelling electron microscopy (FE-TEM). Efficient luminescence occurred due to tightly bound curcumin chromophore to DNA duplex. Bio-HLED shows low luminous drop rate of 0.0551 s-1. Moreover, the solid bio-crystals confined the activating bright luminescence with a quantum yield of 62%, thereby overcoming aggregation-induced quenching effect. The results of this study herald the development of commercially viable large-scale hybrid light applications that are environmentally benign.

Technical note: developmental validation of a novel 6-dye typing system with 36 Y-STR loci.

PubMed

Du, Weian; Feng, Peipei; Huang, Hongyan; Wu, Weibin; Zhang, Lei; Guo, Yulin; Liu, Changhui; Liu, Hong; Liu, Chao; Chen, Ling

2018-05-30

Y-chromosomal short tandem repeats (Y-STRs) have proven to be very useful in investigating sexual assault cases and in paternity lineage differentiation. However, currently available commercial Y-STR multiplex amplification systems bear the limitations in the identification of related males from the same paternal lineage due to there being an insufficient number of loci in any single amplification kit. The aim of this study was to establish and validate a novel 6-dye, 36-plex Y-STR multiplex amplification system that incorporated all of the loci present in the Yfiler™ Plus kit (DYS19, DYS385a/b, DYF387S1, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS460, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, Y_GATA_H4) as well as a further nine highly polymorphic Y-STR loci (DYS388, DYS444, DYS447, DYS522, DYS527a/b, DYS549, DYS596, DYS643). The novel system was optimized and validated by a series of studies that tested the effect of different PCR-based conditions as well as the species specificity, sensitivity, stability, stutter precision, suitability for use on DNA mixtures, reproducibility, and parallel testing of the system, as well as its performance on casework samples and population analysis, according to the SWGDAM developmental validation guidelines. A total of 246 haplotypes were found for the 36 Y-STRs among 247 Guangdong Han unrelated males. Collectively, the results demonstrate that the developed 36-plex Y-STR system is sensitive, robust, reliable, and highly informative for use in forensic genetics.

Ehrlichia and Spotted Fever Group Rickettsiae Surveillance in Amblyomma americanum in Virginia Through Use of a Novel Six-Plex Real-Time PCR Assay

PubMed Central

Operario, Darwin J.; Stroup, Suzanne; Stromdahl, Ellen; Wright, Chelsea; Gaff, Holly; Broyhill, James; Smith, Joshua; Norris, Douglas E.; Henning, Tyler; Lucas, Agape; Houpt, Eric

2014-01-01

Abstract The population of the lone star tick Amblyomma americanum has expanded in North America over the last several decades. It is known to be an aggressive and nondiscriminatory biter and is by far the most common human-biting tick encountered in Virginia. Few studies of human pathogen prevalence in ticks have been conducted in our state since the mid-twentieth century. We developed a six-plex real-time PCR assay to detect three Ehrlichia species (E. chaffeensis, E. ewingii, and Panola Mountain Ehrlichia) and three spotted fever group Rickettsiae (SFGR; R. amblyommii, R. parkeri, and R. rickettsii) and used it to test A. americanum from around the state. Our studies revealed a presence of all three Ehrlichia species (0–24.5%) and a high prevalence (50–80%) of R. amblyommii, a presumptively nonpathogenic SFGR, in all regions surveyed. R. parkeri, previously only detected in Virginia's Amblyomma maculatum ticks, was found in A. americanum in several surveyed areas within two regions having established A. maculatum populations. R. rickettsii was not found in any sample tested. Our study provides the first state-wide screening of A. americanum ticks in recent history and indicates that human exposure to R. amblyommii and to Ehrlichiae may be common. The high prevalence of R. amblyommii, serological cross-reactivity of all SFGR members, and the apparent rarity of R. rickettsii in human biting ticks across the eastern United States suggest that clinical cases of tick-borne disease, including ehrlichiosis, may be commonly misdiagnosed as Rocky Mountain spotted fever, and that suspicion of other SFGR as well as Ehrlichia should be increased. These data may be of relevance to other regions where A. americanum is prevalent. PMID:24746145

Elevated cytokine and chemokine levels in the placenta are associated with in-utero HIV-1 mother-to-child transmission.

PubMed

Kumar, Surender B; Rice, Cara E; Milner, Danny A; Ramirez, Nilsa C; Ackerman, William E; Mwapasa, Victor; Turner, Abigail Norris; Kwiek, Jesse J

2012-03-27

To determine whether there is an association between cytokine and chemokine levels in plasma isolated from the placenta and HIV-1 mother-to-child transmission (MTCT). We designed a case-control study of HIV-infected, pregnant women enrolled in the Malaria and HIV in Pregnancy cohort. Participants were recruited in Blantyre, Malawi, from 2000 to 2004. Patients were women whose children were HIV-1 DNA-positive at birth (in-utero MTCT) or HIV-1 DNA-negative at birth and HIV-1 DNA-positive at 6 weeks postpartum (intrapartum MTCT); controls were women whose children were HIV-1 DNA-negative both at birth and 6 weeks postpartum. After delivery, blood was isolated from an incision on the basal plate of the placenta. We used a Bio-Plex human cytokine assay (Bio-Rad, Hercules, California USA) to simultaneously quantify 27 cytokines, chemokines and growth factors in placental plasma. HIV-1 RNA copies were quantified with the Roche Amplicor kit. Levels of interleukin (IL) 4, IL-5, IL-6, IL-7, IL-9, eotaxin, IL-1Ra and interferon gamma-induced protein 10 (IP-10) were significantly elevated in placental plasma isolated from cases of in-utero HIV-1 MTCT. In contrast, only granulocyte colony-stimulating factor was elevated in placental plasma isolated from cases of intrapartum MTCT. After adjusting for maternal age, gestational age and peripheral CD4(+) T-cell count, every log(10) increase in placental IP-10 was associated with a three-fold increase in the prevalence of in-utero HIV-1 MTCT. Elevated cytokine and chemokine levels in placental plasma were associated with in-utero and not intrapartum MTCT. IP-10, which is both a T-cell chemokine and potentiator of HIV-replication, was robustly and independently associated with prevalent, in-utero MTCT.

Semi-Targeted Analysis of Complex Matrices by ESI FT-ICR MS or How an Experimental Bias may be Used as an Analytical Tool.

PubMed

Hertzog, Jasmine; Carré, Vincent; Dufour, Anthony; Aubriet, Frédéric

2018-03-01

Ammonia is well suited to favor deprotonation process in electrospray ionization mass spectrometry (ESI-MS) to increase the formation of [M - H] - . Nevertheless, NH 3 may react with carbonyl compounds (aldehyde, ketone) and bias the composition description of the investigated sample. This is of significant importance in the study of complex mixture such as oil or bio-oil. To assess the ability of primary amines to form imines with carbonyl compounds during the ESI-MS process, two aldehydes (vanillin and cinnamaldehyde) and two ketones (butyrophenone and trihydroxyacetophenone) have been infused in an ESI source with ammonia and two different amines (aniline and 3-chloronaniline). The (+) ESI-MS analyses have demonstrated the formation of imine whatever the considered carbonyl compound and the used primary amine, the structure of which was extensively studied by tandem mass spectrometry. Thus, it has been established that the addition of ammonia, in the solution infused in an ESI source, may alter the composition description of a complex mixture and leads to misinterpretations due to the formation of imines. Nevertheless, this experimental bias can be used to identify the carbonyl compounds in a pyrolysis bio-oil. As we demonstrated, infusion of the bio-oil with 3-chloroaniline in ESI source leads to specifically derivatized carbonyl compounds. Thanks to their chlorine isotopic pattern and the high mass measurement accuracy, (+) ESI Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) unambiguously highlighted them from the numerous C x H y O z bio-oil components. These results offer a new perspective into the detailed molecular structure of complex mixtures such as bio-oils. Graphical Abstract ᅟ.

Semi-Targeted Analysis of Complex Matrices by ESI FT-ICR MS or How an Experimental Bias may be Used as an Analytical Tool

NASA Astrophysics Data System (ADS)

Hertzog, Jasmine; Carré, Vincent; Dufour, Anthony; Aubriet, Frédéric

2018-03-01

Ammonia is well suited to favor deprotonation process in electrospray ionization mass spectrometry (ESI-MS) to increase the formation of [M - H]-. Nevertheless, NH3 may react with carbonyl compounds (aldehyde, ketone) and bias the composition description of the investigated sample. This is of significant importance in the study of complex mixture such as oil or bio-oil. To assess the ability of primary amines to form imines with carbonyl compounds during the ESI-MS process, two aldehydes (vanillin and cinnamaldehyde) and two ketones (butyrophenone and trihydroxyacetophenone) have been infused in an ESI source with ammonia and two different amines (aniline and 3-chloronaniline). The (+) ESI-MS analyses have demonstrated the formation of imine whatever the considered carbonyl compound and the used primary amine, the structure of which was extensively studied by tandem mass spectrometry. Thus, it has been established that the addition of ammonia, in the solution infused in an ESI source, may alter the composition description of a complex mixture and leads to misinterpretations due to the formation of imines. Nevertheless, this experimental bias can be used to identify the carbonyl compounds in a pyrolysis bio-oil. As we demonstrated, infusion of the bio-oil with 3-chloroaniline in ESI source leads to specifically derivatized carbonyl compounds. Thanks to their chlorine isotopic pattern and the high mass measurement accuracy, (+) ESI Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) unambiguously highlighted them from the numerous CxHyOz bio-oil components. These results offer a new perspective into the detailed molecular structure of complex mixtures such as bio-oils. [Figure not available: see fulltext.

WE-H-BRA-04: Biological Geometries for the Monte Carlo Simulation Toolkit TOPASNBio

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

McNamara, A; Held, K; Paganetti, H

2016-06-15

Purpose: New advances in radiation therapy are most likely to come from the complex interface of physics, chemistry and biology. Computational simulations offer a powerful tool for quantitatively investigating radiation interactions with biological tissue and can thus help bridge the gap between physics and biology. The aim of TOPAS-nBio is to provide a comprehensive tool to generate advanced radiobiology simulations. Methods: TOPAS wraps and extends the Geant4 Monte Carlo (MC) simulation toolkit. TOPAS-nBio is an extension to TOPAS which utilizes the physics processes in Geant4-DNA to model biological damage from very low energy secondary electrons. Specialized cell, organelle and molecularmore » geometries were designed for the toolkit. Results: TOPAS-nBio gives the user the capability of simulating biological geometries, ranging from the micron-scale (e.g. cells and organelles) to complex nano-scale geometries (e.g. DNA and proteins). The user interacts with TOPAS-nBio through easy-to-use input parameter files. For example, in a simple cell simulation the user can specify the cell type and size as well as the type, number and size of included organelles. For more detailed nuclear simulations, the user can specify chromosome territories containing chromatin fiber loops, the later comprised of nucleosomes on a double helix. The chromatin fibers can be arranged in simple rigid geometries or within factual globules, mimicking realistic chromosome territories. TOPAS-nBio also provides users with the capability of reading protein data bank 3D structural files to simulate radiation damage to proteins or nucleic acids e.g. histones or RNA. TOPAS-nBio has been validated by comparing results to other track structure simulation software and published experimental measurements. Conclusion: TOPAS-nBio provides users with a comprehensive MC simulation tool for radiobiological simulations, giving users without advanced programming skills the ability to design and run complex simulations.« less

Pyrolysis of waste animal fats in a fixed-bed reactor: Production and characterization of bio-oil and bio-char

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

Ben Hassen-Trabelsi, A., E-mail: aidabenhassen@yahoo.fr; Kraiem, T.; Département de Géologie, Université de Tunis, 2092, Tunis

Highlights: • Produced bio-fuels (bio-oil and bio-char) from some animal fatty wastes. • Investigated the effects of main parameters on pyrolysis products distribution. • Determined the suitable conditions for the production of the maximum of bio-oil. • Characterized bio-oils and bio-chars obtained from several animal fatty wastes. - Abstract: Several animal (lamb, poultry and swine) fatty wastes were pyrolyzed under nitrogen, in a laboratory scale fixed-bed reactor and the main products (liquid bio-oil, solid bio-char and syngas) were obtained. The purpose of this study is to produce and characterize bio-oil and bio-char obtained from pyrolysis of animal fatty wastes. Themore » maximum production of bio-oil was achieved at a pyrolysis temperature of 500 °C and a heating rate of 5 °C/min. The chemical (GC–MS analyses) and spectroscopic analyses (FTIR analyses) of bio-oil showed that it is a complex mixture consisting of different classes of organic compounds, i.e., hydrocarbons (alkanes, alkenes, cyclic compounds…etc.), carboxylic acids, aldehydes, ketones, esters,…etc. According to fuel properties, produced bio-oils showed good properties, suitable for its use as an engine fuel or as a potential source for synthetic fuels and chemical feedstock. Obtained bio-chars had low carbon content and high ash content which make them unattractive for as renewable source energy.« less

Pacifiplex: an ancestry-informative SNP panel centred on Australia and the Pacific region.

PubMed

Santos, Carla; Phillips, Christopher; Fondevila, Manuel; Daniel, Runa; van Oorschot, Roland A H; Burchard, Esteban G; Schanfield, Moses S; Souto, Luis; Uacyisrael, Jolame; Via, Marc; Carracedo, Ángel; Lareu, Maria V

2016-01-01

The analysis of human population variation is an area of considerable interest in the forensic, medical genetics and anthropological fields. Several forensic single nucleotide polymorphism (SNP) assays provide ancestry-informative genotypes in sensitive tests designed to work with limited DNA samples, including a 34-SNP multiplex differentiating African, European and East Asian ancestries. Although assays capable of differentiating Oceanian ancestry at a global scale have become available, this study describes markers compiled specifically for differentiation of Oceanian populations. A sensitive multiplex assay, termed Pacifiplex, was developed and optimized in a small-scale test applicable to forensic analyses. The Pacifiplex assay comprises 29 ancestry-informative marker SNPs (AIM-SNPs) selected to complement the 34-plex test, that in a combined set distinguish Africans, Europeans, East Asians and Oceanians. Nine Pacific region study populations were genotyped with both SNP assays, then compared to four reference population groups from the HGDP-CEPH human diversity panel. STRUCTURE analyses estimated population cluster membership proportions that aligned with the patterns of variation suggested for each study population's currently inferred demographic histories. Aboriginal Taiwanese and Philippine samples indicated high East Asian ancestry components, Papua New Guinean and Aboriginal Australians samples were predominantly Oceanian, while other populations displayed cluster patterns explained by the distribution of divergence amongst Melanesians, Polynesians and Micronesians. Genotype data from Pacifiplex and 34-plex tests is particularly well suited to analysis of Australian Aboriginal populations and when combined with Y and mitochondrial DNA variation will provide a powerful set of markers for ancestry inference applied to modern Australian demographic profiles. On a broader geographic scale, Pacifiplex adds highly informative data for inferring the ancestry of individuals from Oceanian populations. The sensitivity of Pacifiplex enabled successful genotyping of population samples from 50-year-old serum samples obtained from several Oceanian regions that would otherwise be unlikely to produce useful population data. This indicates tests primarily developed for forensic ancestry analysis also provide an important contribution to studies of populations where useful samples are in limited supply. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Hybrid deterministic/stochastic simulation of complex biochemical systems.

PubMed

Lecca, Paola; Bagagiolo, Fabio; Scarpa, Marina

2017-11-21

In a biological cell, cellular functions and the genetic regulatory apparatus are implemented and controlled by complex networks of chemical reactions involving genes, proteins, and enzymes. Accurate computational models are indispensable means for understanding the mechanisms behind the evolution of a complex system, not always explored with wet lab experiments. To serve their purpose, computational models, however, should be able to describe and simulate the complexity of a biological system in many of its aspects. Moreover, it should be implemented by efficient algorithms requiring the shortest possible execution time, to avoid enlarging excessively the time elapsing between data analysis and any subsequent experiment. Besides the features of their topological structure, the complexity of biological networks also refers to their dynamics, that is often non-linear and stiff. The stiffness is due to the presence of molecular species whose abundance fluctuates by many orders of magnitude. A fully stochastic simulation of a stiff system is computationally time-expensive. On the other hand, continuous models are less costly, but they fail to capture the stochastic behaviour of small populations of molecular species. We introduce a new efficient hybrid stochastic-deterministic computational model and the software tool MoBioS (MOlecular Biology Simulator) implementing it. The mathematical model of MoBioS uses continuous differential equations to describe the deterministic reactions and a Gillespie-like algorithm to describe the stochastic ones. Unlike the majority of current hybrid methods, the MoBioS algorithm divides the reactions' set into fast reactions, moderate reactions, and slow reactions and implements a hysteresis switching between the stochastic model and the deterministic model. Fast reactions are approximated as continuous-deterministic processes and modelled by deterministic rate equations. Moderate reactions are those whose reaction waiting time is greater than the fast reaction waiting time but smaller than the slow reaction waiting time. A moderate reaction is approximated as a stochastic (deterministic) process if it was classified as a stochastic (deterministic) process at the time at which it crosses the threshold of low (high) waiting time. A Gillespie First Reaction Method is implemented to select and execute the slow reactions. The performances of MoBios were tested on a typical example of hybrid dynamics: that is the DNA transcription regulation. The simulated dynamic profile of the reagents' abundance and the estimate of the error introduced by the fully deterministic approach were used to evaluate the consistency of the computational model and that of the software tool.

BioPig: a Hadoop-based analytic toolkit for large-scale sequence data.

PubMed

Nordberg, Henrik; Bhatia, Karan; Wang, Kai; Wang, Zhong

2013-12-01

The recent revolution in sequencing technologies has led to an exponential growth of sequence data. As a result, most of the current bioinformatics tools become obsolete as they fail to scale with data. To tackle this 'data deluge', here we introduce the BioPig sequence analysis toolkit as one of the solutions that scale to data and computation. We built BioPig on the Apache's Hadoop MapReduce system and the Pig data flow language. Compared with traditional serial and MPI-based algorithms, BioPig has three major advantages: first, BioPig's programmability greatly reduces development time for parallel bioinformatics applications; second, testing BioPig with up to 500 Gb sequences demonstrates that it scales automatically with size of data; and finally, BioPig can be ported without modification on many Hadoop infrastructures, as tested with Magellan system at National Energy Research Scientific Computing Center and the Amazon Elastic Compute Cloud. In summary, BioPig represents a novel program framework with the potential to greatly accelerate data-intensive bioinformatics analysis.

Safety Aspects of Bio-Based Nanomaterials.

PubMed

Catalán, Julia; Norppa, Hannu

2017-12-01

Moving towards a bio-based and circular economy implies a major focus on the responsible and sustainable utilization of bio-resources. The emergence of nanotechnology has opened multiple possibilities, not only in the existing industrial sectors, but also for completely novel applications of nanoscale bio-materials, the commercial exploitation of which has only begun during the last few years. Bio-based materials are often assumed not to be toxic. However, this pre-assumption is not necessarily true. Here, we provide a short overview on health and environmental aspects associated with bio-based nanomaterials, and on the relevant regulatory requirements. We also discuss testing strategies that may be used for screening purposes at pre-commercial stages. Although the tests presently used to reveal hazards are still evolving, regarding modifi-cations required for nanomaterials, their application is needed before the upscaling or commercialization of bio-based nanomaterials, to ensure the market potential of the nanomaterials is not delayed by uncertainties about safety issues.

BioFed: federated query processing over life sciences linked open data.

PubMed

Hasnain, Ali; Mehmood, Qaiser; Sana E Zainab, Syeda; Saleem, Muhammad; Warren, Claude; Zehra, Durre; Decker, Stefan; Rebholz-Schuhmann, Dietrich

2017-03-15

Biomedical data, e.g. from knowledge bases and ontologies, is increasingly made available following open linked data principles, at best as RDF triple data. This is a necessary step towards unified access to biological data sets, but this still requires solutions to query multiple endpoints for their heterogeneous data to eventually retrieve all the meaningful information. Suggested solutions are based on query federation approaches, which require the submission of SPARQL queries to endpoints. Due to the size and complexity of available data, these solutions have to be optimised for efficient retrieval times and for users in life sciences research. Last but not least, over time, the reliability of data resources in terms of access and quality have to be monitored. Our solution (BioFed) federates data over 130 SPARQL endpoints in life sciences and tailors query submission according to the provenance information. BioFed has been evaluated against the state of the art solution FedX and forms an important benchmark for the life science domain. The efficient cataloguing approach of the federated query processing system 'BioFed', the triple pattern wise source selection and the semantic source normalisation forms the core to our solution. It gathers and integrates data from newly identified public endpoints for federated access. Basic provenance information is linked to the retrieved data. Last but not least, BioFed makes use of the latest SPARQL standard (i.e., 1.1) to leverage the full benefits for query federation. The evaluation is based on 10 simple and 10 complex queries, which address data in 10 major and very popular data sources (e.g., Dugbank, Sider). BioFed is a solution for a single-point-of-access for a large number of SPARQL endpoints providing life science data. It facilitates efficient query generation for data access and provides basic provenance information in combination with the retrieved data. BioFed fully supports SPARQL 1.1 and gives access to the endpoint's availability based on the EndpointData graph. Our evaluation of BioFed against FedX is based on 20 heterogeneous federated SPARQL queries and shows competitive execution performance in comparison to FedX, which can be attributed to the provision of provenance information for the source selection. Developing and testing federated query engines for life sciences data is still a challenging task. According to our findings, it is advantageous to optimise the source selection. The cataloguing of SPARQL endpoints, including type and property indexing, leads to efficient querying of data resources over the Web of Data. This could even be further improved through the use of ontologies, e.g., for abstract normalisation of query terms.

PCR-free quantitative detection of genetically modified organism from raw materials – A novel electrochemiluminescence-based bio-barcode method

PubMed Central

Zhu, Debin; Tang, Yabing; Xing, Da; Chen, Wei R.

2018-01-01

Bio-barcode assay based on oligonucleotide-modified gold nanoparticles (Au-NPs) provides a PCR-free method for quantitative detection of nucleic acid targets. However, the current bio-barcode assay requires lengthy experimental procedures including the preparation and release of barcode DNA probes from the target-nanoparticle complex, and immobilization and hybridization of the probes for quantification. Herein, we report a novel PCR-free electrochemiluminescence (ECL)-based bio-barcode assay for the quantitative detection of genetically modified organism (GMO) from raw materials. It consists of tris-(2’2’-bipyridyl) ruthenium (TBR)-labele barcode DNA, nucleic acid hybridization using Au-NPs and biotin-labeled probes, and selective capture of the hybridization complex by streptavidin-coated paramagnetic beads. The detection of target DNA is realized by direct measurement of ECL emission of TBR. It can quantitatively detect target nucleic acids with high speed and sensitivity. This method can be used to quantitatively detect GMO fragments from real GMO products. PMID:18386909

PCR-free quantitative detection of genetically modified organism from raw materials. An electrochemiluminescence-based bio bar code method.

PubMed

Zhu, Debin; Tang, Yabing; Xing, Da; Chen, Wei R

2008-05-15

A bio bar code assay based on oligonucleotide-modified gold nanoparticles (Au-NPs) provides a PCR-free method for quantitative detection of nucleic acid targets. However, the current bio bar code assay requires lengthy experimental procedures including the preparation and release of bar code DNA probes from the target-nanoparticle complex and immobilization and hybridization of the probes for quantification. Herein, we report a novel PCR-free electrochemiluminescence (ECL)-based bio bar code assay for the quantitative detection of genetically modified organism (GMO) from raw materials. It consists of tris-(2,2'-bipyridyl) ruthenium (TBR)-labeled bar code DNA, nucleic acid hybridization using Au-NPs and biotin-labeled probes, and selective capture of the hybridization complex by streptavidin-coated paramagnetic beads. The detection of target DNA is realized by direct measurement of ECL emission of TBR. It can quantitatively detect target nucleic acids with high speed and sensitivity. This method can be used to quantitatively detect GMO fragments from real GMO products.

A bio-hybrid DNA rotor-stator nanoengine that moves along predefined tracks

NASA Astrophysics Data System (ADS)

Valero, Julián; Pal, Nibedita; Dhakal, Soma; Walter, Nils G.; Famulok, Michael

2018-06-01

Biological motors are highly complex protein assemblies that generate linear or rotary motion, powered by chemical energy. Synthetic motors based on DNA nanostructures, bio-hybrid designs or synthetic organic chemistry have been assembled. However, unidirectionally rotating biomimetic wheel motors with rotor-stator units that consume chemical energy are elusive. Here, we report a bio-hybrid nanoengine consisting of a catalytic stator that unidirectionally rotates an interlocked DNA wheel, powered by NTP hydrolysis. The engine consists of an engineered T7 RNA polymerase (T7RNAP-ZIF) attached to a dsDNA nanoring that is catenated to a rigid rotating dsDNA wheel. The wheel motor produces long, repetitive RNA transcripts that remain attached to the engine and are used to guide its movement along predefined ssDNA tracks arranged on a DNA nanotube. The simplicity of the design renders this walking nanoengine adaptable to other biological nanoarchitectures, facilitating the construction of complex bio-hybrid structures that achieve NTP-driven locomotion.

A bio-hybrid DNA rotor-stator nanoengine that moves along predefined tracks.

PubMed

Valero, Julián; Pal, Nibedita; Dhakal, Soma; Walter, Nils G; Famulok, Michael

2018-06-01

Biological motors are highly complex protein assemblies that generate linear or rotary motion, powered by chemical energy. Synthetic motors based on DNA nanostructures, bio-hybrid designs or synthetic organic chemistry have been assembled. However, unidirectionally rotating biomimetic wheel motors with rotor-stator units that consume chemical energy are elusive. Here, we report a bio-hybrid nanoengine consisting of a catalytic stator that unidirectionally rotates an interlocked DNA wheel, powered by NTP hydrolysis. The engine consists of an engineered T7 RNA polymerase (T7RNAP-ZIF) attached to a dsDNA nanoring that is catenated to a rigid rotating dsDNA wheel. The wheel motor produces long, repetitive RNA transcripts that remain attached to the engine and are used to guide its movement along predefined ssDNA tracks arranged on a DNA nanotube. The simplicity of the design renders this walking nanoengine adaptable to other biological nanoarchitectures, facilitating the construction of complex bio-hybrid structures that achieve NTP-driven locomotion.

Aspergillus oryzae–Saccharomyces cerevisiae Consortium Allows Bio-Hybrid Fuel Cell to Run on Complex Carbohydrates

PubMed Central

Jahnke, Justin P.; Hoyt, Thomas; LeFors, Hannah M.; Sumner, James J.; Mackie, David M.

2016-01-01

Consortia of Aspergillus oryzae and Saccharomyces cerevisiae are examined for their abilities to turn complex carbohydrates into ethanol. To understand the interactions between microorganisms in consortia, Fourier-transform infrared spectroscopy is used to follow the concentrations of various metabolites such as sugars (e.g., glucose, maltose), longer chain carbohydrates, and ethanol to optimize consortia conditions for the production of ethanol. It is shown that with proper design A. oryzae can digest food waste simulants into soluble sugars that S. cerevisiae can ferment into ethanol. Depending on the substrate and conditions used, concentrations of 13% ethanol were achieved in 10 days. It is further shown that a direct alcohol fuel cell (FC) can be coupled with these A. oryzae-enabled S. cerevisiae fermentations using a reverse osmosis membrane. This “bio-hybrid FC” continually extracted ethanol from an ongoing consortium, enhancing ethanol production and allowing the bio-hybrid FC to run for at least one week. Obtained bio-hybrid FC currents were comparable to those from pure ethanol—water mixtures, using the same FC. The A. oryzae–S. cerevisiae consortium, coupled to a bio-hybrid FC, converted food waste simulants into electricity without any pre- or post-processing. PMID:27681904

Aspergillus oryzae-Saccharomyces cerevisiae Consortium Allows Bio-Hybrid Fuel Cell to Run on Complex Carbohydrates.

PubMed

Jahnke, Justin P; Hoyt, Thomas; LeFors, Hannah M; Sumner, James J; Mackie, David M

2016-02-04

Consortia of Aspergillus oryzae and Saccharomyces cerevisiae are examined for their abilities to turn complex carbohydrates into ethanol. To understand the interactions between microorganisms in consortia, Fourier-transform infrared spectroscopy is used to follow the concentrations of various metabolites such as sugars (e.g., glucose, maltose), longer chain carbohydrates, and ethanol to optimize consortia conditions for the production of ethanol. It is shown that with proper design A. oryzae can digest food waste simulants into soluble sugars that S. cerevisiae can ferment into ethanol. Depending on the substrate and conditions used, concentrations of 13% ethanol were achieved in 10 days. It is further shown that a direct alcohol fuel cell (FC) can be coupled with these A. oryzae-enabled S. cerevisiae fermentations using a reverse osmosis membrane. This "bio-hybrid FC" continually extracted ethanol from an ongoing consortium, enhancing ethanol production and allowing the bio-hybrid FC to run for at least one week. Obtained bio-hybrid FC currents were comparable to those from pure ethanol-water mixtures, using the same FC. The A. oryzae-S. cerevisiae consortium, coupled to a bio-hybrid FC, converted food waste simulants into electricity without any pre- or post-processing.

Synergistic effects of bioremediation and electrokinetics in the remediation of petroleum-contaminated soil.

PubMed

Guo, Shuhai; Fan, Ruijuan; Li, Tingting; Hartog, Niels; Li, Fengmei; Yang, Xuelian

2014-08-01

The present study evaluated the coupling interactions between bioremediation (BIO) and electrokinetics (EK) in the remediation of total petroleum hydrocarbons (TPH) by using bio-electrokinetics (BIO-EK) with a rotatory 2-D electric field. The results demonstrated an obvious positive correlation between the degradation extents of TPH and electric intensity both in the EK and BIO-EK tests. The use of BIO-EK showed a significant improvement in degradation of TPH as compared to BIO or EK alone. The actual degradation curve in BIO-EK tests fitted well with the simulated curve obtained by combining the degradation curves in BIO- and EK-only tests during the first 60 d, indicating a superimposed effect of biological degradation and electrochemical stimulation. The synergistic effect was particularly expressed during the later phase of the experiment, concurrent with changes in the microbial community structure. The community composition changed mainly according to the duration of the electric field, leading to a reduction in diversity. No significant spatial shifts in microbial community composition and bacterial numbers were detected among different sampling positions. Soil pH was uniform during the experimental process, soil temperature showed no variations between the soil chambers with and without an electric field. Copyright © 2014 Elsevier Ltd. All rights reserved.

[Research progress on the technique and materials for three-dimensional bio-printing].

PubMed

Yang, Runhuai; Chen, Yueming; Ma, Changwang; Wang, Huiqin; Wang, Shuyue

2017-04-01

Three-dimensional (3D) bio-printing is a novel engineering technique by which the cells and support materials can be manufactured to a complex 3D structure. Compared with other 3D printing methods, 3D bio-printing should pay more attention to the biocompatible environment of the printing methods and the materials. Aimed at studying the feature of the 3D bio-printing, this paper mainly focuses on the current research state of 3D bio-printing, with the techniques and materials of the bio-printing especially emphasized. To introduce current printing methods, the inkjet method, extrusion method, stereolithography skill and laser-assisted technique are described. The printing precision, process, requirements and influence of all the techniques on cell status are compared. For introduction of the printing materials, the cross-link, biocompatibility and applications of common bio-printing materials are reviewed and compared. Most of the 3D bio-printing studies are being remained at the experimental stage up to now, so the review of 3D bio-printing could improve this technique for practical use, and it could also contribute to the further development of 3D bio-printing.

Time-lapse imaging assay using the BioStation CT: A sensitive drug-screening method for three-dimensional cell culture

PubMed Central

Sakamoto, Ruriko; Rahman, M Mamunur; Shimomura, Manami; Itoh, Manabu; Nakatsura, Tetsuya

2015-01-01

Three-dimensional (3D) cell culture is beneficial for physiological studies of tumor cells, due to its potential to deliver a high quantity of cell culture information that is representative of the cancer microenvironment and predictive of drug responses in vivo. Currently, gel-associated or matrix-associated 3D cell culture is comprised of intricate procedures that often result in experimental complexity. Therefore, we developed an innovative anti-cancer drug sensitivity screening technique for 3D cell culture on NanoCulture Plates (NCP) by employing the imaging device BioStation CT. Here, we showed that the human breast cancer cell lines BT474 and T47D form multicellular spheroids on NCP plates and compared their sensitivity to the anti-cancer drugs trastuzumab and paclitaxel using the BioStation CT. The anticancer drugs reduced spheroid migration velocity and suppressed spheroid fusion. In addition, primary cells derived from the human breast cancer tissues B58 and B61 grown on NCP plates also exhibited similar drug sensitivity. These results were in good agreement with the conventional assay method using ATP quantification. We confirmed the antitumor effects of the drugs on cells seeded in 96-well plates using the BioStation CT imaging technique. We expect this method to be useful in research for new antitumor agents and for drug sensitivity tests in individually-tailored cancer treatments. PMID:25865675

DeviceEditor visual biological CAD canvas

PubMed Central

2012-01-01

Background Biological Computer Aided Design (bioCAD) assists the de novo design and selection of existing genetic components to achieve a desired biological activity, as part of an integrated design-build-test cycle. To meet the emerging needs of Synthetic Biology, bioCAD tools must address the increasing prevalence of combinatorial library design, design rule specification, and scar-less multi-part DNA assembly. Results We report the development and deployment of web-based bioCAD software, DeviceEditor, which provides a graphical design environment that mimics the intuitive visual whiteboard design process practiced in biological laboratories. The key innovations of DeviceEditor include visual combinatorial library design, direct integration with scar-less multi-part DNA assembly design automation, and a graphical user interface for the creation and modification of design specification rules. We demonstrate how biological designs are rendered on the DeviceEditor canvas, and we present effective visualizations of genetic component ordering and combinatorial variations within complex designs. Conclusions DeviceEditor liberates researchers from DNA base-pair manipulation, and enables users to create successful prototypes using standardized, functional, and visual abstractions. Open and documented software interfaces support further integration of DeviceEditor with other bioCAD tools and software platforms. DeviceEditor saves researcher time and institutional resources through correct-by-construction design, the automation of tedious tasks, design reuse, and the minimization of DNA assembly costs. PMID:22373390

Using arm and hand gestures to command robots during stealth operations

NASA Astrophysics Data System (ADS)

Stoica, Adrian; Assad, Chris; Wolf, Michael; You, Ki Sung; Pavone, Marco; Huntsberger, Terry; Iwashita, Yumi

2012-06-01

Command of support robots by the warfighter requires intuitive interfaces to quickly communicate high degree-offreedom (DOF) information while leaving the hands unencumbered. Stealth operations rule out voice commands and vision-based gesture interpretation techniques, as they often entail silent operations at night or in other low visibility conditions. Targeted at using bio-signal inputs to set navigation and manipulation goals for the robot (say, simply by pointing), we developed a system based on an electromyography (EMG) "BioSleeve", a high density sensor array for robust, practical signal collection from forearm muscles. The EMG sensor array data is fused with inertial measurement unit (IMU) data. This paper describes the BioSleeve system and presents initial results of decoding robot commands from the EMG and IMU data using a BioSleeve prototype with up to sixteen bipolar surface EMG sensors. The BioSleeve is demonstrated on the recognition of static hand positions (e.g. palm facing front, fingers upwards) and on dynamic gestures (e.g. hand wave). In preliminary experiments, over 90% correct recognition was achieved on five static and nine dynamic gestures. We use the BioSleeve to control a team of five LANdroid robots in individual and group/squad behaviors. We define a gesture composition mechanism that allows the specification of complex robot behaviors with only a small vocabulary of gestures/commands, and we illustrate it with a set of complex orders.

Using Arm and Hand Gestures to Command Robots during Stealth Operations

NASA Technical Reports Server (NTRS)

Stoica, Adrian; Assad, Chris; Wolf, Michael; You, Ki Sung; Pavone, Marco; Huntsberger, Terry; Iwashita, Yumi

2012-01-01

Command of support robots by the warfighter requires intuitive interfaces to quickly communicate high degree-of-freedom (DOF) information while leaving the hands unencumbered. Stealth operations rule out voice commands and vision-based gesture interpretation techniques, as they often entail silent operations at night or in other low visibility conditions. Targeted at using bio-signal inputs to set navigation and manipulation goals for the robot (say, simply by pointing), we developed a system based on an electromyography (EMG) "BioSleeve", a high density sensor array for robust, practical signal collection from forearm muscles. The EMG sensor array data is fused with inertial measurement unit (IMU) data. This paper describes the BioSleeve system and presents initial results of decoding robot commands from the EMG and IMU data using a BioSleeve prototype with up to sixteen bipolar surface EMG sensors. The BioSleeve is demonstrated on the recognition of static hand positions (e.g. palm facing front, fingers upwards) and on dynamic gestures (e.g. hand wave). In preliminary experiments, over 90% correct recognition was achieved on five static and nine dynamic gestures. We use the BioSleeve to control a team of five LANdroid robots in individual and group/squad behaviors. We define a gesture composition mechanism that allows the specification of complex robot behaviors with only a small vocabulary of gestures/commands, and we illustrate it with a set of complex orders.

9 CFR 147.6 - Procedure for determining the status of flocks reacting to tests for Mycoplasma gallisepticum...

Code of Federal Regulations, 2010 CFR

2010-01-01

... Agency may examine reactors by the in vivo bio-assay, PCR-based procedures, and/or culture procedures before final determination of the flock status is made. (13) If the in vivo bio-assay, PCR-based... classification for which it was tested. (14) If the in vivo bio-assay, PCR-based procedures, or culture...

Hydrocarbon liquid production via the bioCRACK process and catalytic hydroprocessing of the product oil

DOE PAGES

Schwaiger, Nickolaus; Elliott, Douglas C.; Ritzberger, Jurgen; ...

2015-01-01

Continuous hydroprocessing of liquid phase pyrolysis bio-oil, provided by BDI-BioEnergy International bioCRACK pilot plant at OMV Refinery in Schwechat/Vienna Austria was investigated. These hydroprocessing tests showed promising results using catalytic hydroprocessing strategies developed for unfractionated bio-oil. A sulfided base metal catalyst (CoMo on Al2O3) was evaluated. The bed of catalyst was operated at 400 °C in a continuous-flow reactor at a pressure of 12.1 MPa with flowing hydrogen. The condensed liquid products were analyzed and found that the hydrocarbon liquid was significantly hydrotreated so that nitrogen and sulfur were below the level of detection (<0.05), while the residual oxygen rangedmore » from 0.7 to 1.2%. The density of the products varied from 0.71 g/mL up to 0.79 g/mL with a correlated change of the hydrogen to carbon atomic ratio from 2.1 down to 1.9. The product quality remained high throughout the extended tests suggesting minimal loss of catalyst activity through the test. These tests provided the data needed to assess the quality of liquid fuel products obtained from the bioCRACK process as well as the activity of the catalyst for comparison with products obtained from hydrotreated fast pyrolysis bio-oils from fluidized-bed operation.« less

Serological Diagnosis of Acute Scrub Typhus in Southern India: Evaluation of InBios Scrub Typhus Detect IgM Rapid Test and Comparison with other Serological Tests.

PubMed

Anitharaj, Velmurugan; Stephen, Selvaraj; Pradeep, Jothimani; Park, Sungman; Kim, Seung-Han; Kim, Young Jin; Kim, Eun-Ye; Kim, Yoon-Won

2016-11-01

Scrub Typhus (ST) is being reported from different parts of India in the recent past. However, the diagnosis and confirmation of ST cases require specific serological and molecular diagnostic tests. Both rapid and conventional ELISA tests need to be properly evaluated. Evaluation of a new ST IgM Immunochromatography (ICT) test kit (InBios Scrub Typhus Detect IgM Rapid Test) and compare it with another rapid kit, conventional ELISA kit and Weil-Felix (WF) test. This prospective study was carried out in Mahatma Gandhi Medical College and Research Institute, Puducherry, during November 2015 to June 2016. Clinically suspected 220 ST patients were examined by a new kit, InBios Scrub Typhus Detect IgM Rapid Test, taking the conventional InBios Scrub Typhus Detect IgM ELISA as reference. Additional comparison was made with ImmuneMed Scrub Typhus Rapid, and WF test (single OXK titers ≥1:320). Statistical analysis was performed (Chi-square, Spearman's correlation and Kappa) using IBM SPSS Statistics 17 for Windows (SPSS Inc; Chicago, USA). Percentage Sensitivity, Specificity, Positive Predictive and Negative Predictive Values for InBios, ImmuneMed and WF were 99.25, 93.02, 95.68, 98.77; 94.87, 94.19, 96.21, 92.05 and 50.38, 95.51, 94.29, 56.67 respectively. A total of 134 patients were positive in reference standard InBios IgM ELISA. This new rapid ST IgM kit validated for the first time in India, showed good sensitivity and specificity. As a Point-of-Care (PoC) test, the kit would be helpful in both urban and remote rural parts of India.

Serological Diagnosis of Acute Scrub Typhus in Southern India: Evaluation of InBios Scrub Typhus Detect IgM Rapid Test and Comparison with other Serological Tests

PubMed Central

Anitharaj, Velmurugan; Pradeep, Jothimani; Park, Sungman; Kim, Seung-Han; Kim, Young Jin; Kim, Eun-Ye; Kim, Yoon-Won

2016-01-01

Introduction Scrub Typhus (ST) is being reported from different parts of India in the recent past. However, the diagnosis and confirmation of ST cases require specific serological and molecular diagnostic tests. Both rapid and conventional ELISA tests need to be properly evaluated. Aim Evaluation of a new ST IgM Immunochromatography (ICT) test kit (InBios Scrub Typhus Detect IgM Rapid Test) and compare it with another rapid kit, conventional ELISA kit and Weil-Felix (WF) test. Materials and Methods This prospective study was carried out in Mahatma Gandhi Medical College and Research Institute, Puducherry, during November 2015 to June 2016. Clinically suspected 220 ST patients were examined by a new kit, InBios Scrub Typhus Detect IgM Rapid Test, taking the conventional InBios Scrub Typhus Detect IgM ELISA as reference. Additional comparison was made with ImmuneMed Scrub Typhus Rapid, and WF test (single OXK titers ≥1:320). Statistical analysis was performed (Chi-square, Spearman’s correlation and Kappa) using IBM SPSS Statistics 17 for Windows (SPSS Inc; Chicago, USA). Results Percentage Sensitivity, Specificity, Positive Predictive and Negative Predictive Values for InBios, ImmuneMed and WF were 99.25, 93.02, 95.68, 98.77; 94.87, 94.19, 96.21, 92.05 and 50.38, 95.51, 94.29, 56.67 respectively. A total of 134 patients were positive in reference standard InBios IgM ELISA. Conclusion This new rapid ST IgM kit validated for the first time in India, showed good sensitivity and specificity. As a Point-of-Care (PoC) test, the kit would be helpful in both urban and remote rural parts of India. PMID:28050364

Bright luminescence from pure DNA-curcumin–based phosphors for bio hybrid light-emitting diodes

PubMed Central

Reddy, M. Siva Pratap; Park, Chinho

2016-01-01

Recently, significant advances have occurred in the development of phosphors for bio hybrid light-emitting diodes (Bio-HLEDs), which have created brighter, metal-free, rare-earth phosphor-free, eco-friendly, and cost-competitive features for visible light emission. Here, we demonstrate an original approach using bioinspired phosphors in Bio-HLEDs based on natural deoxyribonucleic acid (DNA)-curcumin complexes with cetyltrimethylammonium (CTMA) in bio-crystalline form. The curcumin chromophore was bound to the DNA double helix structure as observed using field emission tunnelling electron microscopy (FE-TEM). Efficient luminescence occurred due to tightly bound curcumin chromophore to DNA duplex. Bio-HLED shows low luminous drop rate of 0.0551 s−1. Moreover, the solid bio-crystals confined the activating bright luminescence with a quantum yield of 62%, thereby overcoming aggregation-induced quenching effect. The results of this study herald the development of commercially viable large-scale hybrid light applications that are environmentally benign. PMID:27572113

Protein bio-corona: critical issue in immune nanotoxicology.

PubMed

Neagu, Monica; Piperigkou, Zoi; Karamanou, Konstantina; Engin, Ayse Basak; Docea, Anca Oana; Constantin, Carolina; Negrei, Carolina; Nikitovic, Dragana; Tsatsakis, Aristidis

2017-03-01

With the expansion of the nanomedicine field, the knowledge focusing on the behavior of nanoparticles in the biological milieu has rapidly escalated. Upon introduction to a complex biological system, nanomaterials dynamically interact with all the encountered biomolecules and form the protein "bio-corona." The decoration with these surface biomolecules endows nanoparticles with new properties. The present review will address updates of the protein bio-corona characteristics as influenced by nanoparticle's physicochemical properties and by the particularities of the encountered biological milieu. Undeniably, bio-corona generation influences the efficacy of the nanodrug and guides the actions of innate and adaptive immunity. Exploiting the dynamic process of protein bio-corona development in combination with the new engineered horizons of drugs linked to nanoparticles could lead to innovative functional nanotherapies. Therefore, bio-medical nanotechnologies should focus on the interactions of nanoparticles with the immune system for both safety and efficacy reasons.

BioInt: an integrative biological object-oriented application framework and interpreter.

PubMed

Desai, Sanket; Burra, Prasad

2015-01-01

BioInt, a biological programming application framework and interpreter, is an attempt to equip the researchers with seamless integration, efficient extraction and effortless analysis of the data from various biological databases and algorithms. Based on the type of biological data, algorithms and related functionalities, a biology-specific framework was developed which has nine modules. The modules are a compilation of numerous reusable BioADTs. This software ecosystem containing more than 450 biological objects underneath the interpreter makes it flexible, integrative and comprehensive. Similar to Python, BioInt eliminates the compilation and linking steps cutting the time significantly. The researcher can write the scripts using available BioADTs (following C++ syntax) and execute them interactively or use as a command line application. It has features that enable automation, extension of the framework with new/external BioADTs/libraries and deployment of complex work flows.

Synthetic biology routes to bio-artificial intelligence

PubMed Central

Zaikin, Alexey; Saka, Yasushi; Romano, M. Carmen; Giuraniuc, Claudiu V.; Kanakov, Oleg; Laptyeva, Tetyana

2016-01-01

The design of synthetic gene networks (SGNs) has advanced to the extent that novel genetic circuits are now being tested for their ability to recapitulate archetypal learning behaviours first defined in the fields of machine and animal learning. Here, we discuss the biological implementation of a perceptron algorithm for linear classification of input data. An expansion of this biological design that encompasses cellular ‘teachers’ and ‘students’ is also examined. We also discuss implementation of Pavlovian associative learning using SGNs and present an example of such a scheme and in silico simulation of its performance. In addition to designed SGNs, we also consider the option to establish conditions in which a population of SGNs can evolve diversity in order to better contend with complex input data. Finally, we compare recent ethical concerns in the field of artificial intelligence (AI) and the future challenges raised by bio-artificial intelligence (BI). PMID:27903825

Chemicals derived from pyrolysis bio-oils as antioxidants in fuels and lubricants

USDA-ARS?s Scientific Manuscript database

Softwood and hardwood lignins and hardwood were pyrolyzed to produce bio-oils to produce lignin-derived bio-oils of which phenols were the major component. These bio-oils were extracted with alkali to yield a range of lignin-related phenols having molecular weights (MWs) from 110 to 344. When tested...

Induction by TNF-α of IL-6 and IL-8 in cystic fibrosis bronchial IB3-1 epithelial cells encapsulated in alginate microbeads.

PubMed

Borgatti, Monica; Mazzitelli, Stefania; Breveglieri, Giulia; Gambari, Roberto; Nastruzzi, Claudio

2010-01-01

We have developed a microencapsulation procedure for the entrapment and manipulation of IB3-1 cystic fibrosis cells. The applied method is based on generation of monodisperse droplets by a vibrational nozzle. Different experimental parameters were analyzed, including frequency and amplitude of vibration, polymer pumping rate and distance between the nozzle and the gelling bath. We have found that the microencapsulation procedure does not alter the viability of the encapsulated IB3-1 cells. The encapsulated IB3-1 cells were characterized in term of secretomic profile, analyzing the culture medium by Bio-Plex strategy. The experiments demonstrated that most of the analyzed proteins, were secreted both by the free and encapsulated cells, even if in a different extent. In order to determine the biotechnological applications of this procedure, we determined whether encapsulated IB3-1 cells could be induced to pro-inflammatory responses, after treatment with TNF-α. In this experimental set-up, encapsulated and free IB3-1 cells were treated with TNF-α, thereafter the culture media from both cell populations were collected. As expected, TNF-α induced a sharp increase in the secretion of interleukins, chemokines and growth factors. Of great interest was the evidence that induction of interleukin-6 and interleukin-8 occurs also by encapsulated IB3-1 cells.

David Brandner | NREL

Science.gov Websites

chemical reaction engineering and transport phenomena Analytical analysis of complex bio-derived samples and Lignin Areas of Expertise Analytical analysis of complex samples Chemical reaction engineering and

Evaluation of the internal and external biofidelity of current rear impact ATDs to response targets developed from moderate-speed rear impacts of PMHS.

PubMed

Moorhouse, Kevin; Donnelly, Bruce; Kang, Yun-Seok; Bolte, John H; Herriott, Rodney

2012-10-01

The goal of this study is to evaluate both the internal and external biofidelity of existing rear impact anthropomorphic test devices (BioRID II, RID3D, Hybrid III 50th) in two moderate-speed rear impact sled test conditions (8.5g, 17 km/h; 10.5g, 24 km/h) by quantitatively comparing the ATD responses to biomechanical response targets developed from PMHS testing in a corresponding study. The ATDs and PMHS were tested in an experimental seat system that is capable of simulating the dynamic seat back rotation response of production seats. The experimental seat contains a total of fourteen load cells installed such that external loads from the ATDs and PMHS can be measured to evaluate external biofidelity. The PMHS were instrumented to correspond to the instrumentation contained in the ATDs so that direct comparison between ATDs and PMHS could be made to evaluate internal biofidelity. The NHTSA Biofidelity Ranking system was used to quantitatively evaluate the biofidelity of the ATDs and an additional tool was introduced and utilized which allows for the biofidelity score to be partitioned into components of amplitude, phase, and shape. For internal biofidelity, the BioRID II and RID3D were more biofidelic than the Hybrid III in the 17 km/h test, and the BioRID II was most biofidelic in the 24 km/h test. For external biofidelity, the BioRID II was most biofidelic in the 17 km/h test, while both the BioRID II and the RID3D were more biofidelic than the Hybrid III in the 24 km/h test. Overall, the BioRID II demonstrated the best biofidelity in both the 17 km/h and 24 km/h tests.

Integration of motor proteins - towards an ATP fueled soft actuator.

PubMed

Kakugo, Akira; Shikinaka, Kazuhiro; Gong, Jian Ping

2008-09-01

We present a soft bio-machine constructed from biological motors (actin/myosin). We have found that chemically cross-linked polymer-actin complex gel filaments can move on myosin coated surfaces with a velocity as high as that of native F-actin, by coupling to ATP hydrolysis. Additionally, it is shown that the velocity of polymer-actin complex gel depends on the species of polycations binding to the F-actins. Since the design of functional actuators of well-defined size and morphology is important, the structural behavior of polymer-actin complexes has been investigated. Our results show that the morphology and growth size of polymer-actin complex can be controlled by changes in the electrostatic interactions between F-actins and polycations. Our results indicate that bio actuators with desired shapes can be created by using a polymer-actin complex.

Custom oligonucleotide array-based CGH: a reliable diagnostic tool for detection of exonic copy-number changes in multiple targeted genes

PubMed Central

Vasson, Aurélie; Leroux, Céline; Orhant, Lucie; Boimard, Mathieu; Toussaint, Aurélie; Leroy, Chrystel; Commere, Virginie; Ghiotti, Tiffany; Deburgrave, Nathalie; Saillour, Yoann; Atlan, Isabelle; Fouveaut, Corinne; Beldjord, Cherif; Valleix, Sophie; Leturcq, France; Dodé, Catherine; Bienvenu, Thierry; Chelly, Jamel; Cossée, Mireille

2013-01-01

The frequency of disease-related large rearrangements (referred to as copy-number mutations, CNMs) varies among genes, and search for these mutations has an important place in diagnostic strategies. In recent years, CGH method using custom-designed high-density oligonucleotide-based arrays allowed the development of a powerful tool for detection of alterations at the level of exons and made it possible to provide flexibility through the possibility of modeling chips. The aim of our study was to test custom-designed oligonucleotide CGH array in a diagnostic laboratory setting that analyses several genes involved in various genetic diseases, and to compare it with conventional strategies. To this end, we designed a 12-plex CGH array (135k; 135 000 probes/subarray) (Roche Nimblegen) with exonic and intronic oligonucleotide probes covering 26 genes routinely analyzed in the laboratory. We tested control samples with known CNMs and patients for whom genetic causes underlying their disorders were unknown. The contribution of this technique is undeniable. Indeed, it appeared reproducible, reliable and sensitive enough to detect heterozygous single-exon deletions or duplications, complex rearrangements and somatic mosaicism. In addition, it improves reliability of CNM detection and allows determination of boundaries precisely enough to direct targeted sequencing of breakpoints. All of these points, associated with the possibility of a simultaneous analysis of several genes and scalability ‘homemade' make it a valuable tool as a new diagnostic approach of CNMs. PMID:23340513

Challenges in Bio-fabrication of Organoid Cultures.

PubMed

Peng, Weijie; Datta, Pallab; Wu, Yang; Dey, Madhuri; Ayan, Bugra; Dababneh, Amer; Ozbolat, Ibrahim T

2018-06-01

Three-dimensional (3D) organoids have shown advantages in cell culture over traditional two-dimensional (2D) culture, and have great potential in various applications of tissue engineering. However, there are limitations in current organoid fabrication technologies, such as uncontrolled size, poor reproductively, and inadequate complexity of organoids. In this chapter, we present the existing techniques and discuss the major challenges for 3D organoid biofabrication. Future perspectives on organoid bioprinting are also discussed, where bioprinting technologies are expected to make a major contribution in organoid fabrication, such as realizing mass production and constructing complex heterotypic tissues, and thus further advance the translational application of organoids in tissue engineering and regenerative medicine as well drug testing and pharmaceutics.

Fixed site neutralization model programmer's manual. Volume II

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

Engi, D.; Chapman, L.D.; Judnick, W.

This report relates to protection of nuclear materials at nuclear facilities. This volume presents the source listings for the Fixed Site Neutralization Model and its supporting modules, the Plex Preprocessor and the Data Preprocessor. (DLC)

Upgrading of bio-oil from the pyrolysis of biomass over the rice husk ash catalysts

NASA Astrophysics Data System (ADS)

Sutrisno, B.; Hidayat, A.

2016-11-01

The pyrolysis oils are complex mixtures of organic compounds that exhibit a wide spectrum of chemical functionality, and generally contain some water. Their direct use as fuels may present some difficulties due to their high viscosity, poor heating value, corrosiveness and instability. For possible future use as replacements for hydrocarbon chemical feedstocks and fuels, the liquids will require considerable upgrading to improve its characteristics. By esterification of the bio oil as the upgrading method, the properties of the bio-oil could be improved. In the paper, the upgrading of a bio-oil obtained by pyrolysis was studied over rice husk ash catalysts. The raw bio-oil was produced by pyrolysis of rice husk.From the experiment results, it can be concluded that the densities of upgraded bio-oil were reduced from 1.24 to 0.95 g.cm-3, and the higherheating value increased from 16.0 to 27.2 MJ/kg and the acidity of upgraded bio-oil was also alleviated from 2.3 to 4.4. The results of gas chromatography-mass spectrometry (GC-MS) and FT-IR analysis showed that the ester compounds in the upgraded bio-oil increased. It is possible to improve the properties of bio-oil by esterifying the raw bio-oil.

Hydrocarbon Liquid Production from Biomass via Hot-Vapor-Filtered Fast Pyrolysis and Catalytic Hydroprocessing of the Bio-oil

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

Elliott, Douglas C.; Wang, Huamin; French, Richard

2014-08-14

Hot-vapor filtered bio-oils were produced from two different biomass feedstocks, oak and switchgrass, and the oils were evaluated in hydroprocessing tests for production of liquid hydrocarbon products. Hot-vapor filtering reduced bio-oil yields and increased gas yields. The yields of fuel carbon as bio-oil were reduced by ten percentage points by hot-vapor filtering for both feedstocks. The unfiltered bio-oils were evaluated alongside the filtered bio-oils using a fixed bed catalytic hydrotreating test. These tests showed good processing results using a two-stage catalytic hydroprocessing strategy. Equal-sized catalyst beds, a sulfided Ru on carbon catalyst bed operated at 220°C and a sulfided CoMomore » on alumina catalyst bed operated at 400°C were used with the entire reactor at 100 atm operating pressure. The products from the four tests were similar. The light oil phase product was fully hydrotreated so that nitrogen and sulfur were below the level of detection, while the residual oxygen ranged from 0.3 to 2.0%. The density of the products varied from 0.80 g/ml up to 0.86 g/ml over the period of the test with a correlated change of the hydrogen to carbon atomic ratio from 1.79 down to 1.57, suggesting some loss of catalyst activity through the test. These tests provided the data needed to assess the suite of liquid fuel products from the process and the activity of the catalyst in relationship to the existing catalyst lifetime barrier for the technology.« less

Combination of bioremediation and electrokinetics for the in-situ treatment of diesel polluted soil: A comparison of strategies.

PubMed

Mena Ramírez, Esperanza; Villaseñor Camacho, José; Rodrigo, Manuel A; Cañizares, Pablo

2015-11-15

The aim of this work is to compare different strategies based on electrokinetic soil flushing and bioremediation for the remediation of diesel-polluted soil. Four options were tested at the laboratory scale: single bioremediation (Bio), performed as a control test; a direct combination of electrokinetic soil flushing and biological technologies (EKSF-Bio); EKSF-Bio with daily polarity reversal of the electric field (PR-EKSF-Bio); and a combination of electrokinetic soil flushing and a permeable reactive biological barrier (EKSF-BioPRB). Four batch experiments of 14 days duration were carried out for comparing technologies at room temperature with an electric field of 1.0 V cm(-1) (in EKSF). A diesel degrading microbial consortium was used. The experimental procedure and some specific details, such as the flushing fluids used, varied depending on the strategy. When using the EKSF-Bio option, a high buffer concentration was required to control the pH, causing soil heating, which negatively affected the biological growth and thus the diesel removal. The PR-EKSF-Bio and the EKSF-BioPRB options attained suitable operating conditions and improved the transport processes for biological growth. Polarity reversal was an efficient option for pH, moisture and temperature control. Homogeneous microbial growth was observed, and approximately 20% of the diesel was removed. The BioPRB option was not as efficient as PR-EKSF-Bio in controlling the operating conditions, but the central biobarrier protected the biological activity. Microbial growth was observed not only in the biobarrier but also in a large portion of the soil, and 29% of the diesel was removed in the short remediation test. Copyright © 2015 Elsevier B.V. All rights reserved.

[A novel tissue-engineered bone constructed by using human adipose-derived stem cells and biomimetic calcium phosphate scaffold coprecipitated with bone morphogenetic protein-2].

PubMed

Jiang, W R; Zhang, X; Liu, Y S; Wu, G; Ge, Y J; Zhou, Y S

2017-02-18

To construct a novel biomimetic calcium phosphate (BioCaP) scaffold loaded with bone morphogenetic protein-2 (BMP-2), and to investigate its role in the osteogenesis of human adipose-derived stem cells (hASCs) in vitro and in vivo. The BioCaP scaffold coprecipitated with BMP-2 (BMP-2-BioCaP) was constructed in this study. Field emission scanning electron microscopy (SEM) was used to analyze the morphology of the surfaces. The release kinetics was measured to evaluate the slow-release characteristics in vitro. BMP-2-BioCaP was immersed in proliferation medium (PM) or osteogenic medium (OM), respectively. The supernatants were collected and used to culture hASCs in vitro. Cell numbers were determined using the cell-counting kit-8 (CCK-8) to assess the cell proliferation. After 7 and 14 days, alkaline phosphatase (ALP) staining and quantification were performed to test the activity of ALP. After 14 and 21 days, the calcification deposition was determined by alizarin red S (ARS) staining and quantification. The expressions of the osteoblast-related genes were tested on day 4 and day 14. In the in vivo study, 6 nude mice were used and implanted subcutaneously into the back of the nude mice for 4 groups: (1) BioCaP scaffold only, (2) BioCaP scaffold+hASCs, (3) BMP-2-BioCaP scaffold, (4) BMP-2-BioCaP scaffold+hASCs (test group). After 4 weeks of implantation, hematoxylin-eosin (HE) staining was performed to evaluate the in vivo osteogenesis of hASCs. SEM observations showed that BioCaP and BMP-2-BioCaP scaffold were entirely composed of straight, plate-like and sharp-edged crystal units, and the length of the crystal units varied between 5 and 10 μm. Release kinetics analysis demonstrated that BMP-2 incorporated with BioCaP could be released at certain concentration and last for more than 21 days, and the accumulative protein release could reach 20%. CCK-8 assays showed that cell proliferation was not significantly affected by BMP-2-BioCaP. ALP activity was higher by the induction of OM+BMP-2-BioCaP than of the other groups (P<0.01). More mineralization deposition and more expressions of osteoblast-related genes such as Runt-related transcription factor 2 (RUNX2), ALP, osteopontin (OPN) and osteocalcin (OC) were determined in the OM+BMP-2-BioCaP group at different time points (P<0.01). HE staining showed that, in the test group and BMP-2-BioCaP scaffold group, the extracellular matrix (ECM) with eosinophilic staining were observed around hASCs, and newly-formed bone-like tissues could be found in ECM around the scaffold materials. Moreover, compared with the BMP-2-BioCaP scaffold group, more bone-like tissues could be observed in ECM with typical structure of bone tissue in the test groups. No obvious positive results were found in the other groups. BMP-2-BioCaP scaffold could achieve slow-release of BMP-2 and promote the osteogenic differentiation of hASCs in vitro and in vivo. The novel tissue-engineered bone composed of hASCs and BMP-2-BioCaPis promising for the repair of bone defect.

Bio-oil Analysis Using Negative Electrospray Ionization: Comparative Study of High-Resolution Mass Spectrometers and Phenolic versus Sugaric Components

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

Smith, Erica A.; Park, Soojin; Klein, Adam T.

2012-05-16

We have previously demonstrated that a petroleomic analysis could be performed for bio-oils and revealed the complex nature of bio-oils for the nonvolatile phenolic compounds (Smith, E.; Lee, Y. J. Energy Fuels 2010, 24, 5190−5198). As a subsequent study, we have adapted electrospray ionization in negative-ion mode to characterize a wide variety of bio-oil compounds. A comparative study of three common high-resolution mass spectrometers was performed to validate the methodology and to investigate the differences in mass discrimination and resolution. The mass spectrum is dominated by low mass compounds with m/z of 100–250, with some compounds being analyzable by gasmore » chromatography–mass spectrometry (GC–MS). We could characterize over 800 chemical compositions, with only about 40 of them being previously known in GC–MS. This unveiled a much more complex nature of bio-oils than typically shown by GC–MS. The pyrolysis products of cellulose and hemicellulose, particularly polyhydroxy cyclic hydrocarbons (or what we call “sugaric” compounds), such as levoglucosan, could be effectively characterized with this approach. Phenolic compounds from lignin pyrolysis could be clearly distinguished in a contour map of double bond equivalent (DBE) versus the number of carbons from these sugaric compounds.« less

Fate and wetting potential of bio-refractory organics in membrane distillation for coke wastewater treatment.

PubMed

Ren, Jing; Li, Jianfeng; Chen, Zuliang; Cheng, Fangqin

2018-06-02

Membrane distillation (MD) has been hindered in industrial applications due to the potential wetting or fouling caused by complicated organic compositions. This study investigated the correlations between the fate and wetting potential of bio-refractory organics in the MD process, where three coke wastewater samples pre-treated with bio-degradation and coagulation served as feed solutions. Results showed that although most of the bio-refractory organics in coke wastewater were rejected by the hydrophobic membrane, some volatile aromatic organics including benzenes, phenols, quinolines and naphthalenes passed through the membrane during the MD process. Interestingly, membrane wetting occurred coincidently with the penetration of phenolic and heterocyclic organics. The wetting rate was obviously correlated with the feed composition and membrane surface properties. Ultimately, novel insights into the anti-wetting strategy of MD with bio-refractory organics was proposed, illustrating that the polyaluminum chloride/polyacrylamide coagulation not only removed contaminants which could accelerate membrane wetting, but also retarded membrane wetting by the complexation with organics. The deposition of these complexes on the membrane surface introduced a secondary hydrophilic layer on the hydrophobic substrate, which established a composite membrane structure with superior wetting resistance. These new findings would be beneficial to wetting control in membrane distillation for wastewater treatment. Copyright © 2018 Elsevier Ltd. All rights reserved.

Electrical study on Carboxymethyl Cellulose-Polyvinyl alcohol based bio-polymer blend electrolytes

NASA Astrophysics Data System (ADS)

Saadiah, M. A.; Samsudin, A. S.

2018-04-01

The present work deals with the formulation of bio-materials namely carboxymethyl cellulose (CMC) and polyvinyl alcohol (PVA) for bio-polymer blend electrolytes (BBEs) system which was successfully carried out with different ratio of polymer blend. The biopolymer blend was prepared via economical & classical technique that is solution casting technique and was characterized by using impedance spectroscopy (EIS). The ionic conductivity was achieved to optimum value 9.12 x 10-6 S/cm at room temperature for sample containing ratio 80:20 of CMC:PVA. The highest conducting sample was found to obey the Arrhenius behaviour with a function of temperature. The electrical properties were analyzed using complex permittivity ε* and complex electrical modulus M* for BBEs system and it shows the non-Debye characteristics where no single relaxation time has observed.

Highly Stable Lyophilized Homogeneous Bead-Based Immunoassays for On-Site Detection of Bio Warfare Agents from Complex Matrices.

PubMed

Mechaly, Adva; Marx, Sharon; Levy, Orly; Yitzhaki, Shmuel; Fisher, Morly

2016-06-21

This study shows the development of dry, highly stable immunoassays for the detection of bio warfare agents in complex matrices. Thermal stability was achieved by the lyophilization of the complete, homogeneous, bead-based immunoassay in a special stabilizing buffer, resulting in a ready-to-use, simple assay, which exhibited long shelf and high-temperature endurance (up to 1 week at 100 °C). The developed methodology was successfully implemented for the preservation of time-resolved fluorescence, Alexa-fluorophores, and horse radish peroxidase-based bead assays, enabling multiplexed detection. The multiplexed assay was successfully implemented for the detection of Bacillus anthracis, botulinum B, and tularemia in complex matrices.

A brief review of extrusion-based tissue scaffold bio-printing.

PubMed

Ning, Liqun; Chen, Xiongbiao

2017-08-01

Extrusion-based bio-printing has great potential as a technique for manipulating biomaterials and living cells to create three-dimensional (3D) scaffolds for damaged tissue repair and function restoration. Over the last two decades, advances in both engineering techniques and life sciences have evolved extrusion-based bio-printing from a simple technique to one able to create diverse tissue scaffolds from a wide range of biomaterials and cell types. However, the complexities associated with synthesis of materials for bio-printing and manipulation of multiple materials and cells in bio-printing pose many challenges for scaffold fabrication. This paper presents an overview of extrusion-based bio-printing for scaffold fabrication, focusing on the prior-printing considerations (such as scaffold design and materials/cell synthesis), working principles, comparison to other techniques, and to-date achievements. This paper also briefly reviews the recent development of strategies with regard to hydrogel synthesis, multi-materials/cells manipulation, and process-induced cell damage in extrusion-based bio-printing. The key issue and challenges for extrusion-based bio-printing are also identified and discussed along with recommendations for future, aimed at developing novel biomaterials and bio-printing systems, creating patterned vascular networks within scaffolds, and preserving the cell viability and functions in scaffold bio-printing. The address of these challenges will significantly enhance the capability of extrusion-based bio-printing. Copyright © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

BioJazz: in silico evolution of cellular networks with unbounded complexity using rule-based modeling.

PubMed

Feng, Song; Ollivier, Julien F; Swain, Peter S; Soyer, Orkun S

2015-10-30

Systems biologists aim to decipher the structure and dynamics of signaling and regulatory networks underpinning cellular responses; synthetic biologists can use this insight to alter existing networks or engineer de novo ones. Both tasks will benefit from an understanding of which structural and dynamic features of networks can emerge from evolutionary processes, through which intermediary steps these arise, and whether they embody general design principles. As natural evolution at the level of network dynamics is difficult to study, in silico evolution of network models can provide important insights. However, current tools used for in silico evolution of network dynamics are limited to ad hoc computer simulations and models. Here we introduce BioJazz, an extendable, user-friendly tool for simulating the evolution of dynamic biochemical networks. Unlike previous tools for in silico evolution, BioJazz allows for the evolution of cellular networks with unbounded complexity by combining rule-based modeling with an encoding of networks that is akin to a genome. We show that BioJazz can be used to implement biologically realistic selective pressures and allows exploration of the space of network architectures and dynamics that implement prescribed physiological functions. BioJazz is provided as an open-source tool to facilitate its further development and use. Source code and user manuals are available at: http://oss-lab.github.io/biojazz and http://osslab.lifesci.warwick.ac.uk/BioJazz.aspx. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Inventory-based landscape-scale simulation of management effectiveness and economic feasibility with BioSum

Treesearch

Jeremy S. Fried; Larry D. Potts; Sara M. Loreno; Glenn A. Christensen; R. Jamie Barbour

2017-01-01

The Forest Inventory and Analysis (FIA)-based BioSum (Bioregional Inventory Originated Simulation Under Management) is a free policy analysis framework and workflow management software solution. It addresses complex management questions concerning forest health and vulnerability for large, multimillion acre, multiowner landscapes using FIA plot data as the initial...

Wet air oxidation induced enhanced biodegradability of distillery effluent.

PubMed

Malik, S N; Saratchandra, T; Tembhekar, P D; Padoley, K V; Mudliar, S L; Mudliar, S N

2014-04-01

The present study reports the feasibility of Wet Air Oxidation (WAO) as a pretreatment option for enhanced biodegradation of complex distillery effluent. Initially, the distillery effluent was pretreated by WAO at different process conditions (pressure, temperature and time) to facilitate enhancement in the biodegradability index (BI = BOD5: COD ratio). The biodegradability of WAO pretreated effluent was evaluated by subjecting it to aerobic biodegradation and anaerobic followed by aerobic biodegradation. Aerobic biodegradation of pretreated effluent with enhanced biodegradability index (BI = 0.4-0.8) showed enhanced COD reduction of up to 67.7%, whereas the untreated effluent (BI = 0.17) indicated poor COD reduction of only 22.5%. Anaerobic followed by aerobic biodegradation of pretreated effluent has shown up to 87.9% COD reduction, while the untreated effluent has shown only 43.1% COD reduction. Bio-kinetic parameters also confirmed the increased rate of bio-oxidation at enhanced BIs. The results indicate that the WAO pretreatment facilitates enhanced bio-oxidation/bio-degradation of complex effluents like the distillery spent wash. Copyright © 2014 Elsevier Ltd. All rights reserved.

BioLayout(Java): versatile network visualisation of structural and functional relationships.

PubMed

Goldovsky, Leon; Cases, Ildefonso; Enright, Anton J; Ouzounis, Christos A

2005-01-01

Visualisation of biological networks is becoming a common task for the analysis of high-throughput data. These networks correspond to a wide variety of biological relationships, such as sequence similarity, metabolic pathways, gene regulatory cascades and protein interactions. We present a general approach for the representation and analysis of networks of variable type, size and complexity. The application is based on the original BioLayout program (C-language implementation of the Fruchterman-Rheingold layout algorithm), entirely re-written in Java to guarantee portability across platforms. BioLayout(Java) provides broader functionality, various analysis techniques, extensions for better visualisation and a new user interface. Examples of analysis of biological networks using BioLayout(Java) are presented.

Bio-Aerosol Testkamer: Ontwikkeling van Protocollen (Bio Aerosol Test Chamber: Development of Protocols)

DTIC Science & Technology

2007-07-01

testfaciliteit detector met de drie simulanten getest beschikbaar gekomen voor het testen van Beschrijving van de worden volgens gangbare internationale bio...2005 werd de Bio-Adrosol Testkamer (BAT-kamer) geplaatst door de firma Dycor Technologies Ltd., Canada. In de BAT-kamner kan een bio-ai5rosol...bestaande ruimte past. In beide gevallen bleek de firma Dycor Technologies Ltd in Canada (http://www.dycor.com) de beste leverancier te zijn, en voor beide

[Biological evaluation within a risk management process].

PubMed

Zhuang, Fei; Ding, Biao

2007-07-01

Bio-evaluation within the medical device quality/risk management system is a risk analyzing and assessing process. On the basis of data from characterization of materials, scientific literatures, application history, bio-toxicology testing and so on, weighing the benefit and the risk, bio-evaluation does a conclusion to "take" or "quit" the product design. There is no "zero risk" though "no toxicity" always is the most desirable conclusion in a testing report. The application history data is the most comprehensive among the information available, since no testing system can "clone" the human body. In addition, the capital cost has to be taken into account when bringing the sophisticated testing technologies into the evaluating system. Investigating the #G95-1 of FDA CDRH and the changes of ISO 10993-1, the trend to integrate bio-evaluation into a quality/risk management process can be figured out.

D-Amino acid oxidase bio-functionalized platforms: Toward an enhanced enzymatic bio-activity

NASA Astrophysics Data System (ADS)

Herrera, Elisa; Valdez Taubas, Javier; Giacomelli, Carla E.

2015-11-01

The purpose of this work is to study the adsorption process and surface bio-activity of His-tagged D-amino acid oxidase (DAAO) from Rhodotorula gracilis (His6-RgDAAO) as the first step for the development of an electrochemical bio-functionalized platform. With such a purpose this work comprises: (a) the His6-RgDAAO bio-activity in solution determined by amperometry, (b) the adsorption mechanism of His6-RgDAAO on bare gold and carboxylated modified substrates in the absence (substrate/COO-) and presence of Ni(II) (substrate/COO- + Ni(II)) determined by reflectometry, and (c) the bio-activity of the His6-RgDAAO bio-functionalized platforms determined by amperometry. Comparing the adsorption behavior and bio-activity of His6-RgDAAO on these different solid substrates allows understanding the contribution of the diverse interactions responsible for the platform performance. His6-RgDAAO enzymatic performance in solution is highly improved when compared to the previously used pig kidney (pk) DAAO. His6-RgDAAO exhibits an amperometrically detectable bio-activity at concentrations as low as those expected on a bio-functional platform; hence, it is a viable bio-recognition element of D-amino acids to be coupled to electrochemical platforms. Moreover, His6-RgDAAO bio-functionalized platforms exhibit a higher surface activity than pkDAAO physically adsorbed on gold. The platform built on Ni(II) modified substrates present enhanced bio-activity because the surface complexes histidine-Ni(II) provide with site-oriented, native-like enzymes. The adsorption mechanism responsible of the excellent performance of the bio-functionalized platform takes place in two steps involving electrostatic and bio-affinity interactions whose prevalence depends on the degree of surface coverage.

Three-dimensional bio-printing.

PubMed

Gu, Qi; Hao, Jie; Lu, YangJie; Wang, Liu; Wallace, Gordon G; Zhou, Qi

2015-05-01

Three-dimensional (3D) printing technology has been widely used in various manufacturing operations including automotive, defence and space industries. 3D printing has the advantages of personalization, flexibility and high resolution, and is therefore becoming increasingly visible in the high-tech fields. Three-dimensional bio-printing technology also holds promise for future use in medical applications. At present 3D bio-printing is mainly used for simulating and reconstructing some hard tissues or for preparing drug-delivery systems in the medical area. The fabrication of 3D structures with living cells and bioactive moieties spatially distributed throughout will be realisable. Fabrication of complex tissues and organs is still at the exploratory stage. This review summarize the development of 3D bio-printing and its potential in medical applications, as well as discussing the current challenges faced by 3D bio-printing.

Performance of the fourth-generation Bio-Rad GS HIV Combo Ag/Ab enzyme immunoassay for diagnosis of HIV infection in Southern Africa

PubMed Central

Piwowar-Manning, Estelle; Fogel, Jessica M.; Richardson, Paul; Wolf, Shauna; Clarke, William; Marzinke, Mark A.; Fiamma, Agnès; Donnell, Deborah; Kulich, Michal; Mbwambo, Jessie K.K.; Richter, Linda; Gray, Glenda; Sweat, Michael; Coates, Thomas J.; Eshleman, Susan H.

2015-01-01

Background Fourth-generation HIV assays detect both antigen and antibody, facilitating detection of acute/early HIV infection. The Bio-Rad GS HIV Combo Ag/Ab assay (Bio-Rad Combo) is an enzyme immunoassay that simultaneously detects HIV p24 antigen and antibodies to HIV-1 and HIV-2 in serum or plasma. Objective To evaluate the performance of the Bio-Rad Combo assay for detection of HIV infection in adults from Southern Africa. Study design Samples were obtained from adults in Soweto and Vulindlela, South Africa and Dar es Salaam, Tanzania (300 HIV-positive samples; 300 HIV-negative samples; 12 samples from individuals previously classified as having acute/early HIV infection). The samples were tested with the Bio-Rad Combo assay. Additional testing was performed to characterize the 12 acute/early samples. Results All 300 HIV-positive samples were reactive using the Bio-Rad Combo assay; false positive test results were obtained for 10 (3.3%) of the HIV-negative samples (sensitivity: 100%, 95% confidence interval [CI]: 98.8–100%); specificity: 96.7%, 95% CI: 94.0–98.4%). The assay detected 10 of the 12 infections classified as acute/early. The two infections that were not detected had viral loads < 400 copies/mL; one of those samples contained antiretroviral drugs consistent with antiretroviral therapy. Conclusions The Bio-Rad Combo assay correctly classified the majority of study specimens. The specificity reported here may be higher than that seen in other settings, since HIV-negative samples were pre-screened using a different fourth-generation test. The assay also had high sensitivity for detection of acute/early infection. False-negative test results may be obtained in individuals who are virally suppressed. PMID:25542477

Enhanced photoluminescence from single nitrogen-vacancy defects in nanodiamonds coated with phenol-ionic complexes

NASA Astrophysics Data System (ADS)

Bray, Kerem; Previdi, Rodolfo; Gibson, Brant C.; Shimoni, Olga; Aharonovich, Igor

2015-03-01

Fluorescent nanodiamonds are attracting major attention in the field of bio-sensing and bio-labeling. In this work we demonstrate a robust approach to achieve an encapsulation of individual nanodiamonds with phenol-ionic complexes that enhance the photoluminescence from single nitrogen vacancy (NV) centers. We show that single NV centres in the coated nanodiamonds also exhibit shorter lifetimes, opening another channel for high resolution sensing. We propose that the nanodiamond encapsulation reduces the non-radiative decay pathways of the NV color centers. Our results provide a versatile and assessable way to enhance photoluminescence from nanodiamond defects that can be used in a variety of sensing and imaging applications.Fluorescent nanodiamonds are attracting major attention in the field of bio-sensing and bio-labeling. In this work we demonstrate a robust approach to achieve an encapsulation of individual nanodiamonds with phenol-ionic complexes that enhance the photoluminescence from single nitrogen vacancy (NV) centers. We show that single NV centres in the coated nanodiamonds also exhibit shorter lifetimes, opening another channel for high resolution sensing. We propose that the nanodiamond encapsulation reduces the non-radiative decay pathways of the NV color centers. Our results provide a versatile and assessable way to enhance photoluminescence from nanodiamond defects that can be used in a variety of sensing and imaging applications. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr07510b

Short term endurance results on a single cylinder diesel engine fueled with upgraded bio oil biodiesel emulsion

NASA Astrophysics Data System (ADS)

Prakash, R.; Murugan, S.

2017-11-01

This paper deliberates the endurance test outcomes obtained from a single cylinder, diesel engine fueled with an upgraded bio oil biodiesel emulsion. In this investigation a bio oil obtained by pyrolysis of woody biomass was upgraded with acid treatment. The resulted bio oil was emulsified with addition of biodiesel and suitable surfactant which is termed as ATJOE15. The main objective of the endurance test was to evaluate the wear characteristics of the engine components and lubrication oil properties, when the engine is fueled with the ATJOE15 emulsion. The photographic views taken before and after the end of 100 hrs endurance test, and visual inspection of the engine components, wear and carbon deposit results, are discussed in this paper.

A Powerful Molecular Engineering Tool Provided Efficient Chlamydomonas Mutants as Bio-Sensing Elements for Herbicides Detection

PubMed Central

Lambreva, Maya D.; Giardi, Maria Teresa; Rambaldi, Irene; Antonacci, Amina; Pastorelli, Sandro; Bertalan, Ivo; Husu, Ivan; Johanningmeier, Udo; Rea, Giuseppina

2013-01-01

This study was prompted by increasing concerns about ecological damage and human health threats derived by persistent contamination of water and soil with herbicides, and emerging of bio-sensing technology as powerful, fast and efficient tool for the identification of such hazards. This work is aimed at overcoming principal limitations negatively affecting the whole-cell-based biosensors performance due to inadequate stability and sensitivity of the bio-recognition element. The novel bio-sensing elements for the detection of herbicides were generated exploiting the power of molecular engineering in order to improve the performance of photosynthetic complexes. The new phenotypes were produced by an in vitro directed evolution strategy targeted at the photosystem II (PSII) D1 protein of Chlamydomonas reinhardtii, using exposures to radical-generating ionizing radiation as selection pressure. These tools proved successful to identify D1 mutations conferring enhanced stability, tolerance to free-radical-associated stress and competence for herbicide perception. Long-term stability tests of PSII performance revealed the mutants capability to deal with oxidative stress-related conditions. Furthermore, dose-response experiments indicated the strains having increased sensitivity or resistance to triazine and urea type herbicides with I50 values ranging from 6×10−8 M to 2×10−6 M. Besides stressing the relevance of several amino acids for PSII photochemistry and herbicide sensing, the possibility to improve the specificity of whole-cell-based biosensors, via coupling herbicide-sensitive with herbicide-resistant strains, was verified. PMID:23613953

Cyclic biomechanical testing of biocomposite lateral row knotless anchors in a human cadaveric model.

PubMed

Barber, F Alan; Bava, Eric D; Spenciner, David B; Piccirillo, Justin

2013-06-01

The purpose of this study was to assess the mechanical performance of biocomposite knotless lateral row anchors based on both anchor design and the direction of pull. Two lateral row greater tuberosity insertion sites (anterior and posterior) were identified in matched pairs of fresh-frozen human cadaveric shoulders DEXA (dual energy X-ray absorptiometry) scanned to verify comparability. The humeri were stripped of all soft tissue and 3 different biocomposite knotless lateral row anchors: HEALIX Knotless BR (DePuy Mitek, Raynham MA), BioComposite PushLock (Arthrex, Naples, FL), and Bio-SwiveLock (Arthrex). Fifty-two anchors were distributed among the insertion locations and tested them with either an anatomic or axial pull. A fixed-gauge loop (15 mm) of 2 high-strength sutures from each anchor was created. After a 10-Nm preload, anchors were cycled from 10 to 45 Nm at 0.5 Hz for 200 cycles and tested to failure at 4.23 mm/second. The load to reach 3 mm and 5 mm displacement, ultimate failure load, displacement at ultimate failure, and failure mode were recorded. Threaded anchors (Bio-SwiveLock, P = .03; HEALIX Knotless, P = .014) showed less displacement with anatomic testing than did the nonthreaded anchor (BioComposite PushLock), and the HEALIX Knotless showed less overall displacement than did the other 2 anchors. The Bio-SwiveLock exhibited greater failure loads than did the other 2 anchors (P < .05). Comparison of axial and anatomic loading showed no maximum load differences for all anchors as a whole (P = .1084). Yet, anatomic pulling produced higher failure loads than did axial pulling for the Bio-SwiveLock but not for the BioComposite PushLock or the HEALIX Knotless. The nonthreaded anchor (BioComposite PushLock) displayed lower failure loads than did both threaded anchors with axial pulling. Threaded biocomposite anchors (HEALIX Knotless BR and Bio-SwiveLock) show less anatomic loading displacement and higher axial failure loads than do the nonthreaded (BioComposite PushLock) anchor. The HEALIX Knotless BR anchor showed less displacement than did the BioComposite PushLock and Bio-SwiveLock anchors. Neither axial nor anatomic loading had an effect on overall anchor displacement. Because of the strength profiles exhibited, this study supports the use of biocomposite anchors, which have definite advantages over polyetheretherketone (PEEK) and metal products. However, the nonthreaded BioComposite PushLock anchor cannot be recommended. Copyright © 2013 Arthroscopy Association of North America. All rights reserved.

In vitro comparison of two widely used surgical sealants for treating alveolar air leak.

PubMed

Zhang, Ruoyu; Bures, Maximilian; Höffler, Klaus; Jonigk, Danny; Haverich, Axel; Krueger, Marcus

2014-12-01

Controversies surrounding the efficacy of sealants against alveolar air leak (AAL) are abundant in the literature. We sought to test the widely used sealants, TachoSil (Takeda Pharmaceutical Company Limited, Osaka, Japan) and BioGlue (CryoLife Europa Ltd., Surrey, United Kingdom) in an in vitro model. Materials and After creation of a focal superficial defect (40 × 25 mm) in swine lungs (n=40), AAL was assessed with increasing inspired tidal volume (TVi). Upon sealant application in a randomized order, AAL was assessed in the same way until sealant burst. At TVi =400, 500, 600, and 700 mL, BioGlue achieved sealing in 19, 19, 16, and 14 tests, while TachoSil sealed in 19, 14, 4, and no test, respectively. The maximally tolerated pressure of BioGlue was higher than TachoSil (40.3 ± 3.0 vs. 36.0 ± 4.9 cm H2O, p=0.003). Cohesive and adhesive failures were found in 10 and 1 tests of BioGlue, respectively, while all burst failures of TachoSil were adhesive. Concerning elasticity, TachoSil allowed more expansion of the covered defect than BioGlue (6.3 ± 3.9 vs. 1.4 ± 1.0 mm, p<0.001). The tested sealants demonstrated high sealing efficacy. While BioGlue was superior in resisting higher ventilation pressure, TachoSil possessed better elasticity. Georg Thieme Verlag KG Stuttgart · New York.

Integration of functional myotubes with a Bio-MEMS device for non-invasive interrogation.

PubMed

Wilson, Kerry; Molnar, Peter; Hickman, James

2007-07-01

We have developed a biological micro-electromechanical system (Bio-MEMS) device consisting of surface-modified microfabricated silicon cantilevers and an AFM detection apparatus for the study of cultured myotubes. With this system we are able to selectively stimulate the myotubes as well as report on a variety of physiological properties of the myotubes in real time and in a high-throughput manner. This system will serve as the foundation for future work integrating multiple tissue types for the creation of Bio-MEMS analogues of complex tissues and biological circuits.

BioImageXD: an open, general-purpose and high-throughput image-processing platform.

PubMed

Kankaanpää, Pasi; Paavolainen, Lassi; Tiitta, Silja; Karjalainen, Mikko; Päivärinne, Joacim; Nieminen, Jonna; Marjomäki, Varpu; Heino, Jyrki; White, Daniel J

2012-06-28

BioImageXD puts open-source computer science tools for three-dimensional visualization and analysis into the hands of all researchers, through a user-friendly graphical interface tuned to the needs of biologists. BioImageXD has no restrictive licenses or undisclosed algorithms and enables publication of precise, reproducible and modifiable workflows. It allows simple construction of processing pipelines and should enable biologists to perform challenging analyses of complex processes. We demonstrate its performance in a study of integrin clustering in response to selected inhibitors.

Measuring the activity of BioBrick promoters using an in vivo reference standard

PubMed Central

Kelly, Jason R; Rubin, Adam J; Davis, Joseph H; Ajo-Franklin, Caroline M; Cumbers, John; Czar, Michael J; de Mora, Kim; Glieberman, Aaron L; Monie, Dileep D; Endy, Drew

2009-01-01

Background The engineering of many-component, synthetic biological systems is being made easier by the development of collections of reusable, standard biological parts. However, the complexity of biology makes it difficult to predict the extent to which such efforts will succeed. As a first practical example, the Registry of Standard Biological Parts started at MIT now maintains and distributes thousands of BioBrick™ standard biological parts. However, BioBrick parts are only standardized in terms of how individual parts are physically assembled into multi-component systems, and most parts remain uncharacterized. Standardized tools, techniques, and units of measurement are needed to facilitate the characterization and reuse of parts by independent researchers across many laboratories. Results We found that the absolute activity of BioBrick promoters varies across experimental conditions and measurement instruments. We choose one promoter (BBa_J23101) to serve as an in vivo reference standard for promoter activity. We demonstrated that, by measuring the activity of promoters relative to BBa_J23101, we could reduce variation in reported promoter activity due to differences in test conditions and measurement instruments by ~50%. We defined a Relative Promoter Unit (RPU) in order to report promoter characterization data in compatible units and developed a measurement kit so that researchers might more easily adopt RPU as a standard unit for reporting promoter activity. We distributed a set of test promoters to multiple labs and found good agreement in the reported relative activities of promoters so measured. We also characterized the relative activities of a reference collection of BioBrick promoters in order to further support adoption of RPU-based measurement standards. Conclusion Relative activity measurements based on an in vivoreference standard enables improved measurement of promoter activity given variation in measurement conditions and instruments. These improvements are sufficient to begin to support the measurement of promoter activities across many laboratories. Additional in vivo reference standards for other types of biological functions would seem likely to have similar utility, and could thus improve research on the design, production, and reuse of standard biological parts. PMID:19298678

40 CFR 265.314 - Special requirements for bulk and containerized liquids.

Code of Federal Regulations, 2012 CFR

2012-07-01

... (iii) Mixtures of these non-bio-degrad-a-ble materials. (2) Tests for non-bio-degrad-a-ble sorbents. (i) The sorbent material is determined to be non-bio-degrad-a-ble under ASTM Method G21-70 (1984a...

40 CFR 265.314 - Special requirements for bulk and containerized liquids.

Code of Federal Regulations, 2013 CFR

2013-07-01

... (iii) Mixtures of these non-bio-degrad-a-ble materials. (2) Tests for non-bio-degrad-a-ble sorbents. (i) The sorbent material is determined to be non-bio-degrad-a-ble under ASTM Method G21-70 (1984a...

40 CFR 265.314 - Special requirements for bulk and containerized liquids.

Code of Federal Regulations, 2014 CFR

2014-07-01

... (iii) Mixtures of these non-bio-degrad-a-ble materials. (2) Tests for non-bio-degrad-a-ble sorbents. (i) The sorbent material is determined to be non-bio-degrad-a-ble under ASTM Method G21-70 (1984a...

40 CFR 265.314 - Special requirements for bulk and containerized liquids.

Code of Federal Regulations, 2010 CFR

2010-07-01

... (iii) Mixtures of these non-bio-degrad-a-ble materials. (2) Tests for non-bio-degrad-a-ble sorbents. (i) The sorbent material is determined to be non-bio-degrad-a-ble under ASTM Method G21-70 (1984a...

Cyclic load testing of biodegradable suture anchors containing 2 high-strength sutures.

PubMed

Barber, F Alan; Coons, David A; Ruiz-Suarez, Michell

2007-04-01

The purpose of this study was to test 4 different biodegradable suture anchors threaded with 2 high-strength sutures under cyclic loading conditions in humeral cadaveric specimens divided into 2 different age groups. Thirty-two paired human cadaveric humeri were stripped of all soft tissue. Two groups were studied: group 1, in which the mean age was 54 years, and group 2, in which the mean age was 70 years. We placed 1 suture anchor at 3 humeral sites per bone (anterior, middle, and posterior greater tuberosity). We tested 24 specimens using each of 4 anchors: TwinFix AB (Smith & Nephew Endoscopy, Andover, MA), BioZip (Stryker Endoscopy, San Jose, CA), Bio-Corkscrew FT (Arthrex, Naples, FL), and SpiraLok (DePuy Mitek, Raynham, MA). The anchor's sutures were grasped with an Instron clamp (Instron, Canton, MA), preloaded, and cycled from 10 to 60 N 500 times, followed by destructive testing. The mean displacement at 500 cycles, yield loads, failure modes, and ultimate loads were recorded. Most cyclic motion occurred during the first 100 cycles. More motion occurred in older bones than in younger bones (P < .05). The mean yield loads were greater for the young group for the SpiraLok anchors than for Bio-Corkscrew FT anchors in the young and old groups (P < .001), TwinFix anchors in the old group (P < .05), and BioZip anchors in the old group (P < .05). The ultimate failure loads for SpiraLok anchors in the young group were greater than for Bio-Corkscrew FT anchors in the young and old groups and BioZip anchors in the old group (P < .05). In group 1 TwinFix AB (P = .01) and BioZip (P = .02) ultimate loads were statistically greater than that for Bio-Corkscrew FT. The TwinFix AB failed by anchor pullout. The Bio-Corkscrew FT failed by eyelet pullout. The BioZip and SpiraLok pulled out in older bone and experienced eyelet breakage in younger bone. None of the 4 anchors reached 5 mm of displacement even after 500 loading cycles. Most of the displacement occurred in the first 100 cycles. Of all anchors tested, the Bio-Corkscrew FT recorded the lowest displacement after 500 cycles (P < .05). The SpiraLok had the highest ultimate load of all anchors tested (P < .01). Rotator cuff anchors perform differently in younger humeral bone than in older humeral bone. Most displacement with cyclic loading occurring between the anchor and bone takes place in the first 100 cycles. Anchors in older bones can be expected to fail at lower loads.

Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal

PubMed Central

Gao, Jianjiong; Aksoy, Bülent Arman; Dogrusoz, Ugur; Dresdner, Gideon; Gross, Benjamin; Sumer, S. Onur; Sun, Yichao; Jacobsen, Anders; Sinha, Rileen; Larsson, Erik; Cerami, Ethan; Sander, Chris; Schultz, Nikolaus

2014-01-01

The cBioPortal for Cancer Genomics (http://cbioportal.org) provides a Web resource for exploring, visualizing, and analyzing multidimensional cancer genomics data. The portal reduces molecular profiling data from cancer tissues and cell lines into readily understandable genetic, epigenetic, gene expression, and proteomic events. The query interface combined with customized data storage enables researchers to interactively explore genetic alterations across samples, genes, and pathways and, when available in the underlying data, to link these to clinical outcomes. The portal provides graphical summaries of gene-level data from multiple platforms, network visualization and analysis, survival analysis, patient-centric queries, and software programmatic access. The intuitive Web interface of the portal makes complex cancer genomics profiles accessible to researchers and clinicians without requiring bioinformatics expertise, thus facilitating biological discoveries. Here, we provide a practical guide to the analysis and visualization features of the cBioPortal for Cancer Genomics. PMID:23550210

Bio-Response Operational Testing and Evaluation (BOTE) ...

EPA Pesticide Factsheets

Report and technical brief and informational video The Bio-response Operational Testing and Evaluation (BOTE) Project was a multi-agency effort designed to operationally test and evaluate, at the scale of a moderately sized building, a response to a B. anthracis spore release from initial public health and law enforcement investigation through environmental remediation.

Design, Development, and Preliminary Validation for a BioContainment System for MSR

NASA Astrophysics Data System (ADS)

Fumagalli, A.; Spagnoli, B.; Terribile, A.; Indrigo, D.; Romstedt, J.; Vjendran, S.; Kminek, G.

2018-04-01

A bio-containment system was conceived, designed, and tested by Leonardo S.p.A. and partners under ESA development contract. Results achieved so far are presented, including reports of the several tests performed on development hardware.

Cyanobacteria: A Precious Bio-resource in Agriculture, Ecosystem, and Environmental Sustainability.

PubMed

Singh, Jay Shankar; Kumar, Arun; Rai, Amar N; Singh, Devendra P

2016-01-01

Keeping in view, the challenges concerning agro-ecosystem and environment, the recent developments in biotechnology offers a more reliable approach to address the food security for future generations and also resolve the complex environmental problems. Several unique features of cyanobacteria such as oxygenic photosynthesis, high biomass yield, growth on non-arable lands and a wide variety of water sources (contaminated and polluted waters), generation of useful by-products and bio-fuels, enhancing the soil fertility and reducing green house gas emissions, have collectively offered these bio-agents as the precious bio-resource for sustainable development. Cyanobacterial biomass is the effective bio-fertilizer source to improve soil physico-chemical characteristics such as water-holding capacity and mineral nutrient status of the degraded lands. The unique characteristics of cyanobacteria include their ubiquity presence, short generation time and capability to fix the atmospheric N2. Similar to other prokaryotic bacteria, the cyanobacteria are increasingly applied as bio-inoculants for improving soil fertility and environmental quality. Genetically engineered cyanobacteria have been devised with the novel genes for the production of a number of bio-fuels such as bio-diesel, bio-hydrogen, bio-methane, synga, and therefore, open new avenues for the generation of bio-fuels in the economically sustainable manner. This review is an effort to enlist the valuable information about the qualities of cyanobacteria and their potential role in solving the agricultural and environmental problems for the future welfare of the planet.

Cyanobacteria: A Precious Bio-resource in Agriculture, Ecosystem, and Environmental Sustainability

PubMed Central

Singh, Jay Shankar; Kumar, Arun; Rai, Amar N.; Singh, Devendra P.

2016-01-01

Keeping in view, the challenges concerning agro-ecosystem and environment, the recent developments in biotechnology offers a more reliable approach to address the food security for future generations and also resolve the complex environmental problems. Several unique features of cyanobacteria such as oxygenic photosynthesis, high biomass yield, growth on non-arable lands and a wide variety of water sources (contaminated and polluted waters), generation of useful by-products and bio-fuels, enhancing the soil fertility and reducing green house gas emissions, have collectively offered these bio-agents as the precious bio-resource for sustainable development. Cyanobacterial biomass is the effective bio-fertilizer source to improve soil physico-chemical characteristics such as water-holding capacity and mineral nutrient status of the degraded lands. The unique characteristics of cyanobacteria include their ubiquity presence, short generation time and capability to fix the atmospheric N2. Similar to other prokaryotic bacteria, the cyanobacteria are increasingly applied as bio-inoculants for improving soil fertility and environmental quality. Genetically engineered cyanobacteria have been devised with the novel genes for the production of a number of bio-fuels such as bio-diesel, bio-hydrogen, bio-methane, synga, and therefore, open new avenues for the generation of bio-fuels in the economically sustainable manner. This review is an effort to enlist the valuable information about the qualities of cyanobacteria and their potential role in solving the agricultural and environmental problems for the future welfare of the planet. PMID:27148218

Draft Genome Sequence of the Mycobacterium tuberculosis Complex Pathogen M. mungi, Identified in a Banded Mongoose (Mungos mungo) in Northern Botswana.

PubMed

Alexander, Kathleen A; Larsen, Michelle H; Robbe-Austerman, Suelee; Stuber, Tod P; Camp, Patrick M

2016-07-28

Mycobacterium mungi, a Mycobacterium tuberculosis complex pathogen, has emerged in banded mongoose in northern Botswana and Northwest Zimbabwe. The pathogen is transmitted through infected secretions used in olfactory communication behavior (K. A. Alexander, C. E. Sanderson, M. H. Larsen, S. Robbe-Austerman, M. C. Williams, and M. V. Palmer, mBio 7(3):e00281-16, 2016, http://dx.doi.org/10.1128/mBio.00281-16). We announce here the draft genome sequence of this emerging pathogen. Copyright © 2016 Alexander et al.

Bioengineering strategies to generate artificial protein complexes.

PubMed

Kim, Heejae; Siu, Ka-Hei; Raeeszadeh-Sarmazdeh, Maryam; Sun, Qing; Chen, Qi; Chen, Wilfred

2015-08-01

For many applications, increasing synergy between distinct proteins through organization is important for the specificity, regulation, and overall reaction efficiency. Although there are many examples of protein complexes in nature, a generalized method to create these complexes remains elusive. Many conventional techniques such as random chemical conjugation, physical adsorption onto surfaces, and encapsulation within matrices are imprecise approaches and can lead to deactivation of protein native functionalities. More "bio-friendly" approaches such as genetically fused proteins and biological scaffolds often can result in low yields and low complex stability. Alternatively, site-specific protein conjugation or ligation can generate artificial protein complexes that preserve the native functionalities of protein domains and maintain stability through covalent bonds. In this review, we describe three distinct methods to synthesize artificial protein complexes (genetic incorPoration of unnatural amino acids to introduce bio-orthogonal azide and alkyne groups to proteins, split-intein based expressed protein ligation, and sortase mediated ligation) and highlight interesting applications for each technique. © 2015 Wiley Periodicals, Inc.

Biomacromolecular quantitative structure-activity relationship (BioQSAR): a proof-of-concept study on the modeling, prediction and interpretation of protein-protein binding affinity.

PubMed

Zhou, Peng; Wang, Congcong; Tian, Feifei; Ren, Yanrong; Yang, Chao; Huang, Jian

2013-01-01

Quantitative structure-activity relationship (QSAR), a regression modeling methodology that establishes statistical correlation between structure feature and apparent behavior for a series of congeneric molecules quantitatively, has been widely used to evaluate the activity, toxicity and property of various small-molecule compounds such as drugs, toxicants and surfactants. However, it is surprising to see that such useful technique has only very limited applications to biomacromolecules, albeit the solved 3D atom-resolution structures of proteins, nucleic acids and their complexes have accumulated rapidly in past decades. Here, we present a proof-of-concept paradigm for the modeling, prediction and interpretation of the binding affinity of 144 sequence-nonredundant, structure-available and affinity-known protein complexes (Kastritis et al. Protein Sci 20:482-491, 2011) using a biomacromolecular QSAR (BioQSAR) scheme. We demonstrate that the modeling performance and predictive power of BioQSAR are comparable to or even better than that of traditional knowledge-based strategies, mechanism-type methods and empirical scoring algorithms, while BioQSAR possesses certain additional features compared to the traditional methods, such as adaptability, interpretability, deep-validation and high-efficiency. The BioQSAR scheme could be readily modified to infer the biological behavior and functions of other biomacromolecules, if their X-ray crystal structures, NMR conformation assemblies or computationally modeled structures are available.

Mixed Contaminants Removal Efficiency Using Bio-FeS Nanoparticles.

PubMed

Seo, Hyunhee; Roh, Yul

2018-02-01

Advances in nanotechnology has provided diverse industrial applications including an environmental remediation field. In particular, bio-nanotechnology gives extended eco-friendly remediation practice. Among diverse bio-nanoparticles synthesized by microorganisms, the iron based nanoparticles (NPs) are of great interest because of their availability, low cost and toxicity to human health and the environment. In this study, iron based nanoparticles were biologically synthesized and mineralogically identified. Also, the removal efficiency of mixed contaminants, high As(III)-low Cr(VI) and high As(V)-low Cr(VI), using these bio-nanoparticles were conducted. As a result, biologically synthesized NPs were identified as FeS complex and their catalytic capacity showed highly effective to immobilize more than 97% of mixed contaminants by adsorption/mineralization.

Detailed characterization of bio-oil from pyrolysis of non-edible seed-cakes by Fourier Transform Infrared Spectroscopy (FTIR) and gas chromatography mass spectrometry (GC-MS) techniques.

PubMed

Sugumaran, Vatsala; Prakash, Shanti; Ramu, Emmandi; Arora, Ajay Kumar; Bansal, Veena; Kagdiyal, Vivekanand; Saxena, Deepak

2017-07-15

Bio-oil obtained from pyrolysis is highly complicated mixture with valued chemicals. In order to reduce the complexity for unambiguous characterization of components present in bio-oil, solvent extractions using different solvents with increasing polarity have been adopted. The fractions have been analyzed by Fourier transform infrared (FTIR) spectroscopy for identifying the functional groups and Gas chromatography-mass spectrometry (GC-MS), for detailed characterization of components present in various fractions, thereby providing in-depth information at molecular level of various components in bio-oil. This paper reveals the potential of the analytical techniques in identification and brings out the similarities as well as differences in the components present in the bio-oil obtained from two non-edible oil seed-cakes, viz., Jatropha and Karanjia. Copyright © 2017 Elsevier B.V. All rights reserved.

Recirculation: A New Concept to Drive Innovation in Sustainable Product Design for Bio-Based Products.

PubMed

Sherwood, James; Clark, James H; Farmer, Thomas J; Herrero-Davila, Lorenzo; Moity, Laurianne

2016-12-29

Bio-based products are made from renewable materials, offering a promising basis for the production of sustainable chemicals, materials, and more complex articles. However, biomass is not a limitless resource or one without environmental and social impacts. Therefore, while it is important to use biomass and grow a bio-based economy, displacing the unsustainable petroleum basis of energy and chemical production, any resource must be used effectively to reduce waste. Standards have been developed to support the bio-based product market in order to achieve this aim. However, the design of bio-based products has not received the same level of attention. Reported here are the first steps towards the development of a framework of understanding which connects product design to resource efficiency. Research and development scientists and engineers are encouraged to think beyond simple functionality and associate value to the potential of materials in their primary use and beyond.

Quantum Information Biology: From Theory of Open Quantum Systems to Adaptive Dynamics

NASA Astrophysics Data System (ADS)

Asano, Masanari; Basieva, Irina; Khrennikov, Andrei; Ohya, Masanori; Tanaka, Yoshiharu; Yamato, Ichiro

This chapter reviews quantum(-like) information biology (QIB). Here biology is treated widely as even covering cognition and its derivatives: psychology and decision making, sociology, and behavioral economics and finances. QIB provides an integrative description of information processing by bio-systems at all scales of life: from proteins and cells to cognition, ecological and social systems. Mathematically QIB is based on the theory of adaptive quantum systems (which covers also open quantum systems). Ideologically QIB is based on the quantum-like (QL) paradigm: complex bio-systems process information in accordance with the laws of quantum information and probability. This paradigm is supported by plenty of statistical bio-data collected at all bio-scales. QIB re ects the two fundamental principles: a) adaptivity; and, b) openness (bio-systems are fundamentally open). In addition, quantum adaptive dynamics provides the most generally possible mathematical representation of these principles.

SpaceX CRS-14 What's On Board Science Briefing

NASA Image and Video Library

2018-04-01

Dan Close, chief scientific officer at 490 BioTech, discusses the company's Metabolic Tracking investigation to evaluate the use of a new method to test, in microgravity, the metabolic impacts of pharmaceutical drugs. This is one of the scientific materials that will be aboard a Dragon spacecraft scheduled for liftoff from Cape Canaveral Air Force Station's Space Launch Complex 40 at 4:30 p.m. EST, on April 2, 2018. The SpaceX Falcon 9 rocket will launch the company's 14th Commercial Resupply Services mission to the space station.

SNPflow: A Lightweight Application for the Processing, Storing and Automatic Quality Checking of Genotyping Assays

PubMed Central

Schönherr, Sebastian; Neuner, Mathias; Forer, Lukas; Specht, Günther; Kloss-Brandstätter, Anita; Kronenberg, Florian; Coassin, Stefan

2013-01-01

Single nucleotide polymorphisms (SNPs) play a prominent role in modern genetics. Current genotyping technologies such as Sequenom iPLEX, ABI TaqMan and KBioscience KASPar made the genotyping of huge SNP sets in large populations straightforward and allow the generation of hundreds of thousands of genotypes even in medium sized labs. While data generation is straightforward, the subsequent data conversion, storage and quality control steps are time-consuming, error-prone and require extensive bioinformatic support. In order to ease this tedious process, we developed SNPflow. SNPflow is a lightweight, intuitive and easily deployable application, which processes genotype data from Sequenom MassARRAY (iPLEX) and ABI 7900HT (TaqMan, KASPar) systems and is extendible to other genotyping methods as well. SNPflow automatically converts the raw output files to ready-to-use genotype lists, calculates all standard quality control values such as call rate, expected and real amount of replicates, minor allele frequency, absolute number of discordant replicates, discordance rate and the p-value of the HWE test, checks the plausibility of the observed genotype frequencies by comparing them to HapMap/1000-Genomes, provides a module for the processing of SNPs, which allow sex determination for DNA quality control purposes and, finally, stores all data in a relational database. SNPflow runs on all common operating systems and comes as both stand-alone version and multi-user version for laboratory-wide use. The software, a user manual, screenshots and a screencast illustrating the main features are available at http://genepi-snpflow.i-med.ac.at. PMID:23527209

Comparison of Knee and Ankle Dynamometry between NASA's X1 Exoskeleton and Biodex System 4

NASA Technical Reports Server (NTRS)

English, K. L.; Newby, N. J.; Hackney, K. J.; DeWitt, J. K.; Beck, C. E.; Rovekamp, R. N.; Rea, R. L.; Ploutz-Snyder, L. L.

2014-01-01

Pre- and post-flight dynamometry is performed on International Space Station crewmembers to characterize microgravity-induced strength changes. Strength is not assessed in flight due to hardware limitations and there is poor understanding of the time course of in-flight changes. PURPOSE: To assess the reliability of a prototype dynamometer, the X1 Exoskeleton (EXO) and its agreement with a Biodex System 4 (BIO). METHODS: Eight subjects (4 M/4 F) completed 2 counterbalanced testing sessions of knee extension/flexion (KE/KF), 1 with BIO and 1 with EXO, with repeated measures within each session in normal gravity. Test-retest reliability (test 1 and 2) and device agreement (BIO vs. EXO) were evaluated. Later, to assess device agreement for ankle plantarflexion (PF), 10 subjects (4 M/6 F) completed 3 test conditions (BIO, EXO, and BIOEXO); BIOEXO was a hybrid condition comprised of the Biodex dynamometer motor and the X1 footplate and ankle frame. Ankle comparisons were: BIO vs. BIOEXO (footplate differences), BIOEXO vs. EXO (motor differences), and BIO vs. EXO (all differences). Reliability for KE/KF was determined by intraclass correlation (ICC). Device agreement was assessed with: 1) repeated measures ANOVA, 2) a measure of concordance (rho), and 3) average difference. RESULTS: ICCs for KE/KF were 0.99 for BIO and 0.96 to 0.99 for EXO. Agreement was high for KE (concordance: 0.86 to 0.95; average differences: -7 to +9 Nm) and low to moderate for KF (concordance: 0.64 to 0.78; average differences: -4 to -29 Nm, P<0.05). BIO vs. BIOEXO PF concordance ranged from 0.89 to 0.92 and mean differences ranged from -9 to +3 Nm (BIO < BIOEXO). BIOEXO vs. EXO PF concordance ranged from 0.73 to 0.80 while mean differences were -18 to -36 Nm (BIOEXO < EXO, P<0.05). PF concordance for BIO vs. EXO was slightly lower (0.61 to 0.84) and mean differences were greater (-27 to -33 Nm; BIO < EXO, P<0.05). CONCLUSION: BIO and EXO were similarly reliable for KE and KF. KE measures produced high agreement between devices; KF did not. For ankle PF, torque differences due to the two footplates were small. However, the X1 motor reports greater torques than the Biodex motor during PF. This first prototype provides proof of concept for a reliable, robotic-based exoskeleton to perform portable dynamometry for large muscle groups of the lower body.

Test-retest reliability and smallest detectable change of the Bristol Impact of Hypermobility (BIoH) questionnaire.

PubMed

Palmer, S; Manns, S; Cramp, F; Lewis, R; Clark, E M

2017-12-01

The Bristol Impact of Hypermobility (BIoH) questionnaire is a patient-reported outcome measure developed in conjunction with adults with Joint Hypermobility Syndrome (JHS). It has demonstrated strong concurrent validity with the Short Form-36 (SF-36) physical component score but other psychometric properties have yet to be established. This study aimed to determine its test-retest reliability and smallest detectable change (SDC). A test-retest reliability study. Participants were recruited from the Hypermobility Syndromes Association, a patient organisation in the United Kingdom. Recruitment packs were sent to 1080 adults who had given permission to be contacted about research. BIoH and SF-36 questionnaires were administered at baseline and repeated two weeks later. An 11-point global rating of change scale (-5 to +5) was also administered at two weeks. Test-retest analysis and calculation of the SDC was conducted on 'stable' patients (defined as global rating of change -1 to +1). 462 responses were received. 233 patients reported a 'stable' condition and were included in analysis (95% women; mean (SD) age 44.5 (13.9) years; BIoH score 223.6 (54.0)). The BIoH questionnaire demonstrated excellent test-retest reliability (ICC 0.923, 95% CI 0.900-0.940). The SDC was 42 points (equivalent to 19% of the mean baseline score). The SF-36 physical and mental component scores demonstrated poorer test-retest reliability and larger SDCs (as a proportion of the mean baseline scores). The results provide further evidence of the potential of the BIoH questionnaire to underpin research and clinical practice for people with JHS. Copyright © 2017 Elsevier Ltd. All rights reserved.

Clinical evaluation of the BioFire FilmArray® BioThreat-E test for the diagnosis of Ebola Virus Disease in Guinea.

PubMed

Gay-Andrieu, Françoise; Magassouba, N'Fally; Picot, Valentina; Phillips, Cynthia L; Peyrefitte, Christophe N; Dacosta, Brigitte; Doré, Ahmadou; Kourouma, Fode; Ligeon-Ligeonnet, Véronique; Gauby, Corentin; Longuet, Christophe; Scullion, Matt; Faye, Ousmane; Machuron, Jean Louis; Miller, Mark

2017-07-01

The recent West Africa Ebola outbreak highlighted the need to provide access to rapid, safe and reliable Ebola Virus Disease diagnostics. The objective of this field study was to assess the clinical performance of the FilmArray ® BioThreat-E test for the detection of Ebola Zaïre virus in whole blood in symptomatic patients suspected of Ebola Virus Disease in Conakry (Guinea) from March to July 2015. The BioThreat-E test was compared to the two RT-PCRs, using serum, implemented at Donka Hospital in the emergency context: an in-house developed quantitative one-step RT-PCR adapted from the Weidmann technique, and the RealStar ® Filovirus RT-PCR Kit 1.0 (Altona-Diagnostics). We also assessed the performance of this assay in noninvasive specimens (urine and saliva) to detect infected patients. Of 135 patients enrolled and eligible for performance assessment on whole blood, the sensitivity was 95.7% [95% CI: 85.5-99.5] and specificity 100% [95% CI: 95.9-100]. Of the 37 symptomatic infected patients able to provide saliva and/or urine samples, 34 of the 35 saliva samples and all 3 of the urine samples were positive with the BioThreat-E test. This study showed that the FilmArray BioThreat-E test performs comparably to conventional molecular tests under field conditions, providing results and interpretation in approximately 1h. Due to its operational characteristics, it can be easily deployed in the field during an epidemic and could also be a useful tool for post-outbreak surveillance. Copyright © 2017 Elsevier B.V. All rights reserved.

LSP/MAO composite bio-coating on AZ80 magnesium alloy for biomedical application.

PubMed

Xiong, Ying; Hu, Qiang; Song, Renguo; Hu, Xiaxia

2017-06-01

A composite bio-coating was fabricated on AZ80 magnesium (Mg) alloy by using micro-arc oxidation (MAO) under the pretreatment of laser shock peening (LSP) in order to improve the bio-corrosion resistance and the mechanical integrity. LSP treatment could induce grain refinement and compressive residual stress field on the surface of material. MAO bio-coating was grown in alkaline electrolyte with hydroxyapatite (HA, Ca 10 (PO4) 6 (OH) 2 ) to improve the biological properties of the material. The microstructure, element and phase composition for untreated based material (BM) and treated samples (LSP layer, MAO bio-coating and LSP/MAO composite bio-coating) were investigated by transmission electron microscopy (TEM), scanning electron microscope (SEM), energy dispersion spectroscopy (EDS) and X-ray diffraction (XRD). Electrochemical tests and slow strain rate tensile (SSRT) tests were used to evaluate the corrosion resistance and the stress corrosion susceptibility in simulated body fluid (SBF). The results indicated that LSP/MAO composite bio-coating can not only improve the corrosion resistance of Mg alloy substrate evidently but also increase the mechanical properties in SBF compared to LSP layer and MAO bio-coating. Mg alloy treated by LSP/MAO composite technique should be better suited as biodegradable orthopedic implants. Copyright © 2017 Elsevier B.V. All rights reserved.

Bio-cellulose Production by Beijerinckia fluminensis WAUPM53 and Gluconacetobacter xylinus 0416 in Sago By-product Medium.

PubMed

Voon, W W Y; Muhialdin, B J; Yusof, N L; Rukayadi, Y; Meor Hussin, A S

2018-06-19

Bio-cellulose is the microbial extracellular cellulose that is produced by growing several microorganisms on agriculture by-products, and it is used in several food applications. This study aims to utilize sago by-product, coconut water, and the standard medium Hestrin-Schramm as the carbon sources in the culture medium for bio-cellulose production. The bacteria Beijerinkia fluminensis WAUPM53 and Gluconacetobacter xylinus 0416 were selected based on their bio-cellulose production activity. The structure was determined by Fourier transform infrared spectroscopy and scanning electron microscopy, while the toxicity safety was evaluated by brine shrimp lethality test. The results of Fourier transform infrared spectroscopy showed that the bio-cellulose produced by B. fluminensis cultivated in sago by-products was of high quality. The bio-cellulose production by B. fluminensis in the sago by-product medium was slightly higher than that in the coconut water medium and was comparable with the production in the Hestrin-Schramm medium. Brine shrimp lethality test confirmed that the bio-cellulose produced by B. fluminensis in the sago by-product medium has no toxicity, which is safe for applications in the food industry. This is the first study to determine the high potential of sago by-product to be used as a new carbon source for the bio-cellulose production.

Elaborating European Pharmacopoeia monographs for biotherapeutic proteins using substances from a single source.

PubMed

Buda, M; Wicks, S; Charton, E

2016-01-01

For more than twenty years, the European Pharmacopoeia (Ph. Eur.) monographs for biotherapeutic proteins have been elaborated using the multisource approach (Procedure 1), which has led to robust quality standards for many of the first-generation biotherapeutics. In 2008, the Ph. Eur. opened up the way towards an alternative mechanism for the elaboration of monographs (Procedure 4-BIO pilot phase), which is applied to substances still under patent protection, based on a close collaboration with the Innovator company, to ensure a harmonised global standard and strengthen the quality of the upcoming products. This article describes the lessons learned during the P4-BIO pilot phase and addresses the current thinking on monograph elaboration in the field of biotherapeutics. Case studies are described to illustrate the standardisation challenges associated with the complexity of biotherapeutics and of analytical procedures, as well as the approaches that help ensure expectations are met when setting monograph specifications and allow for compatibility with the development of biosimilars. Emphasis is put on monograph flexibility, notably by including tests that measure process-dependent microheterogeneity (e.g. glycosylation) in the Production section of the monograph. The European Pharmacopoeia successfully concluded the pilot phase of the P4-BIO during its 156 th session on 22-23 November 2016.

Field-Control, Phase-Transitions, and Life’s Emergence

PubMed Central

Mitra-Delmotte, Gargi; Mitra, A. N.

2012-01-01

Instances of critical-like characteristics in living systems at each organizational level (bio-molecules to ecosystems) as well as the spontaneous emergence of computation (Langton), do suggest the relevance of self-organized criticality (SOC). But extrapolating complex bio-systems to life’s origins, brings up a paradox: how could simple organics – lacking the “soft-matter” response properties of today’s complex bio-molecules – have dissipated energy from primordial reactions (eventually reducing CO2) in a controlled manner for their “ordering”? Nevertheless, a causal link of life’s macroscopic irreversible dynamics to the microscopic reversible laws of statistical mechanics is indicated via the “functional-takeover” of a soft magnetic scaffold by organics (c.f. Cairns-Smith’s “crystal-scaffold”). A field-controlled structure offers a mechanism for boot-strapping – bottom-up assembly with top-down control: its super-paramagnetic colloidal components obey reversible dynamics, but its dissipation of magnetic (H)-field energy for aggregation breaks time-reversal symmetry. The responsive adjustments of the controlled (host) mineral system to environmental changes would bring about mutual coupling between random organic sets supported by it; here the generation of long-range correlations within organic (guest) networks could include SOC-like mechanisms. And, such cooperative adjustments enable the selection of the functional configuration by altering the inorganic dipolar network’s capacity to assist a spontaneous process. A non-equilibrium dynamics could now drive the kinetically oriented system (trimming the phase-space via sterically coupled organics) toward a series of phase-transitions with appropriate organic replacements “taking-over” its functions. Where available, experiments are cited in support of these speculations and for designing appropriate tests. PMID:23060803

Whole Genome Amplification of Labeled Viable Single Cells Suited for Array-Comparative Genomic Hybridization.

PubMed

Kroneis, Thomas; El-Heliebi, Amin

2015-01-01

Understanding details of a complex biological system makes it necessary to dismantle it down to its components. Immunostaining techniques allow identification of several distinct cell types thereby giving an inside view of intercellular heterogeneity. Often staining reveals that the most remarkable cells are the rarest. To further characterize the target cells on a molecular level, single cell techniques are necessary. Here, we describe the immunostaining, micromanipulation, and whole genome amplification of single cells for the purpose of genomic characterization. First, we exemplify the preparation of cell suspensions from cultured cells as well as the isolation of peripheral mononucleated cells from blood. The target cell population is then subjected to immunostaining. After cytocentrifugation target cells are isolated by micromanipulation and forwarded to whole genome amplification. For whole genome amplification, we use GenomePlex(®) technology allowing downstream genomic analysis such as array-comparative genomic hybridization.

Development of a supercritical fluid chromatography method with ultraviolet and mass spectrometry detection for the characterization of biomass fast pyrolysis bio oils.

PubMed

Crepier, Julien; Le Masle, Agnès; Charon, Nadège; Albrieux, Florian; Heinisch, Sabine

2017-08-11

The characterization of complex mixtures is a challenging issue for the development of innovative processes dedicated to biofuels and bio-products production. The huge number of compounds present in biomass fast pyrolysis oils combined with the large diversity of chemical functions represent a bottleneck as regards analytical technique development. For the extensive characterization of complex samples, supercritical fluid chromatography (SFC) can be alternative to usual separation techniques such as gas (GC) or liquid chromatography (LC). In this study, an approach is proposed to define the best conditions for the SFC separation of a fast pyrolysis bio-oil. This approach was based on SFC data obtained directly from the bio-oil itself instead of selecting model compounds as usually done. SFC conditions were optimized by using three specific, easy-to-use and quantitative criteria aiming at maximizing the separation power. Polar stationary phases (ethylpyridine bonded silica) associated to a mix of acetonitrile and water as polarity modifier provided the best results, with more than 120 peaks detected in SFC-UV. Copyright © 2017 Elsevier B.V. All rights reserved.

Integrative Bioengineering Institute

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

Eddington, David; Magin,L,Richard; Hetling, John

2009-01-09

Microfabrication enables many exciting experimental possibilities for medicine and biology that are not attainable through traditional methods. However, in order for microfabricated devices to have an impact they must not only provide a robust solution to a current unmet need, but also be simple enough to seamlessly integrate into standard protocols. Broad dissemination of bioMEMS has been stymied by the common aim of replacing established and well accepted protocols with equally or more complex devices, methods, or materials. The marriage of a complex, difficult to fabricate bioMEMS device with a highly variable biological system is rarely successful. Instead, the designmore » philosophy of my lab aims to leverage a beneficial microscale phenomena (e.g. fast diffusion at the microscale) within a bioMEMS device and adapt to established methods (e.g. multiwell plate cell culture) and demonstrate a new paradigm for the field (adapt instead of replace). In order for the field of bioMEMS to mature beyond novel proof-of-concept demonstrations, researchers must focus on developing systems leveraging these phenomena and integrating into standard labs, which have largely been ignored. Towards this aim, the Integrative Bioengineering Institute has been established.« less

Simultaneous Detection of Antibodies against Apx Toxins ApxI, ApxII, ApxIII, and ApxIV in Pigs with Known and Unknown Actinobacillus pleuropneumoniae Exposure Using a Multiplexing Liquid Array Platform

PubMed Central

Giménez-Lirola, Luis G.; Jiang, Yong-Hou; Sun, Dong; Hoang, Hai; Yoon, Kyoung-Jin; Halbur, Patrick G.

2014-01-01

Surveillance for the presence of Actinobacillus pleuropneumoniae infection in a population plays a central role in controlling the disease. In this study, a 4-plex fluorescent microbead-based immunoassay (FMIA), developed for the simultaneous detection of IgG antibodies to repeat-in-toxin (RTX) toxins (ApxI, ApxII, ApxIII, and ApxIV) of A. pleuropneumoniae, was evaluated using (i) blood serum samples from pigs experimentally infected with each of the 15 known A. pleuropneumoniae serovars or with Actinobacillus suis, (ii) blood serum samples from pigs vaccinated with a bacterin containing A. pleuropneumoniae serovar 1, 3, 5, or 7, and (iii) blood serum samples from pigs with an unknown A. pleuropneumoniae exposure status. The results were compared to those obtained in a previous study where a dual-plate complement fixation test (CFT) and three commercially available enzyme-linked immunosorbent assays (ELISAs) were conducted on the same sample set. On samples from experimentally infected pigs, the 4-plex Apx FMIA detected specific seroconversion to Apx toxins as early as 7 days postinfection in a total of 29 pigs inoculated with 14 of the 15 A. pleuropneumoniae serovars. Seroconversion to ApxII and ApxIII was detected by FMIA in pigs inoculated with A. suis. The vaccinated pigs showed poor humoral responses against ApxI, ApxII, ApxIII, and ApxIV. In the field samples, the humoral response to ApxIV and the A. pleuropneumoniae seroprevalence increased with age. This novel FMIA (with a sensitivity of 82.7% and a specificity of 100% for the anti-ApxIV antibody) was found to be more sensitive and accurate than current tests (sensitivities, 9.5 to 56%; specificity, 100%) and is potentially an improved tool for the surveillance of disease and for monitoring vaccination compliance. PMID:24226091

Genetic analysis of 15 autosomal and 12 Y-STR loci in the Espirito Santo State population, Brazil.

PubMed

Wolfgramm, Eldamária de Vargas; Silva, Beatriz Candida; Aguiar, Vitor Resende da Costa; Malta, Frederico Scott Varela; de Castro, Amanda Mafia; Ferreira, Alessandro Clayton de Souza; Prezoti, Alessandra Nunes Loureiro; de Paula, Flavia; Louro, Iúri Drumond

2011-06-01

This study provides population genetic data for individuals of Vitoria, Espirito Santo, Brazil, a location not yet characterized for STR frequencies used for genetic identification studies. Allelic frequencies and other population data analysis are reported for the 15 autosomal-STR loci included in the PowerPlex(®)16 kit (CSF1PO, D13S317, D16S539, D18S51, D21S11, D3S1358, D5S818, D7S820, D8S1179, FGA, Penta D, Penta E, TPOX, TH01 and vWA). Allele and haplotype frequencies, gene diversity and discrimination capacity were also estimated for the PowerPlex(®) Y System (DYS19, DYS385, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439). Blood samples were obtained from 226 unrelated volunteers (135 males and 91 females) residents in the city of Vitoria, representing a typical sample of the mixed ethnicity present in the Espirito Santo State, Brazil. Within the tested population, the total number of individuals typed for specific markers is: 226 for D13S317, D21S11, D3S1358, D7S820, D8S1179 and FGA; 225 for D16S539 and D5S818; 224 for D18S51; 223 for CSF1PO; 222 for Penta D and vWA; 220 for Penta E; 207 for TPOX and 142 for TH01. Y-STR haplotypes were analyzed for 102 unrelated males, being 71 of them present in the 135 autosomal-STR sample, and 31 new males tested only for Y-STR markers. All autosomal markers were in Hardy-Weinberg Equilibrium. Y-STR analysis identified 101 haplotypes, being 100 of them unique. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Benchtop Antigen Detection Technique using Nanofiltration and Fluorescent Dyes

NASA Technical Reports Server (NTRS)

Scardelletti, Maximilian C.; Varaljay, Vanessa

2009-01-01

The designed benchtop technique is primed to detect bacteria and viruses from antigenic surface marker proteins in solutions, initially water. This inclusive bio-immunoassay uniquely combines nanofiltration and near infrared (NIR) dyes conjugated to antibodies to isolate and distinguish microbial antigens, using laser excitation and spectrometric analysis. The project goals include detecting microorganisms aboard the International Space Station, space shuttle, Crew Exploration Vehicle (CEV), and human habitats on future Moon and Mars missions, ensuring astronaut safety. The technique is intended to improve and advance water contamination testing both commercially and environmentally as well. Lastly, this streamlined technique poses to greatly simplify and expedite testing of pathogens in complex matrices, such as blood, in hospital and laboratory clinics.

Core ethical values: EuropaBio.

PubMed

2002-01-01

EuropaBio, the European Association for BioIndustries, represents 40 companies operating world wide and 14 national association (totaling around 600 small and medium-sized enterprises) involved in the research, development, testing, manufacturing, marketing, sales and distribution of biotechnology products and services in the fields of healthcare, agriculture, food and the environment.

Deconstruction of lignocellulosic biomass with hydrated cerium (III) chloride in water and ethanol

DOE PAGES

Akalin, Mehmet K.; Das, Parthapratim; Alper, Koray; ...

2017-08-08

Lignocellulosic biomass was decomposed to produce crude bio-oil in water and ethanol using hydrated cerium (III) chloride as a catalyst. Use of the catalyst affected not only the yield of crude bio-oil but also the composition of bio-crude for both water and ethanol. The catalyst had a detrimental effect on the crude bio-oil yields obtained from water processing for all runs. However, in ethanol, use of the catalyst improved the crude bio-oil yields in all tested runs. The solid residue yields decreased with the catalyst use in the runs with water but increased in all studies with ethanol, except thosemore » with the shortest tested residence time of 10 min. The highest crude bio-oil yield of 48.2 wt% was obtained at 300 °C using 5 mmol of hydrated cerium (III) chloride at a residence time of 90 min in ethanol. The heating values of the crude bio-oils increased with the catalyst use for both water and ethanol processing. In conclusion, the highest heating value of 33.3 MJ kg –1 was obtained with hydrated cerium (III) chloride at 300 °C and a residence time of 120 min.« less

Deconstruction of lignocellulosic biomass with hydrated cerium (III) chloride in water and ethanol

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

Akalin, Mehmet K.; Das, Parthapratim; Alper, Koray

Lignocellulosic biomass was decomposed to produce crude bio-oil in water and ethanol using hydrated cerium (III) chloride as a catalyst. Use of the catalyst affected not only the yield of crude bio-oil but also the composition of bio-crude for both water and ethanol. The catalyst had a detrimental effect on the crude bio-oil yields obtained from water processing for all runs. However, in ethanol, use of the catalyst improved the crude bio-oil yields in all tested runs. The solid residue yields decreased with the catalyst use in the runs with water but increased in all studies with ethanol, except thosemore » with the shortest tested residence time of 10 min. The highest crude bio-oil yield of 48.2 wt% was obtained at 300 °C using 5 mmol of hydrated cerium (III) chloride at a residence time of 90 min in ethanol. The heating values of the crude bio-oils increased with the catalyst use for both water and ethanol processing. In conclusion, the highest heating value of 33.3 MJ kg –1 was obtained with hydrated cerium (III) chloride at 300 °C and a residence time of 120 min.« less

Stabilization of Bio-Oil Fractions for Insertion into Petroleum Refineries

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

Brown, Robert C.; Smith, Ryan; Wright, Mark

This project is part of a collaboration effort between Iowa State University (ISU), University of Oklahoma (OK) and Pacific Northwest National Laboratory (PNNL). The purpose of this project is to stabilize bio-oil fractions and improve their suitability for insertion into petroleum refineries. Bio-oil from fast pyrolysis of biomass is a complex mixture of unstable organic compounds. These organic compounds react under standard room conditions resulting in increases in bio-oil viscosity and water content – both detrimental for bio-oil storage and transportation. This study employed fractionation and upgrading systems to improve the stability of bio-oil. The fractionation system consists of amore » series of condensers, and electrostatic precipitators designed to separate bio-oil into five fractions: soluble carbohydrates (SF1&2), clean phenolic oligomers (CPO) and middle fraction (SF3&4), light oxygenates (SF5). A two-stage upgrading process was designed to process bio-oil stage fractions into stable products that can be inserted into a refinery. In the upgrading system, heavy and middle bio-oil fractions were upgraded into stable oil via cracking and subsequent hydrodeoxygenation. The light oxygenate fraction was steam reformed to provide a portion of requisite hydrogen for hydroprocessing. Hydrotreating and hydrocracking employed hydrogen from natural gas, fuel gas and light oxygenates reforming. The finished products from this study consist of gasoline- and diesel-blend stock fuels.« less

Combination of electrospray ionization, atmospheric pressure photoionization and laser desorption ionization Fourier transform ion cyclotronic resonance mass spectrometry for the investigation of complex mixtures - Application to the petroleomic analysis of bio-oils.

PubMed

Hertzog, Jasmine; Carré, Vincent; Le Brech, Yann; Mackay, Colin Logan; Dufour, Anthony; Mašek, Ondřej; Aubriet, Frédéric

2017-05-29

The comprehensive description of complex mixtures such as bio-oils is required to understand and improve the different processes involved during biological, environmental or industrial operation. In this context, we have to consider how different ionization sources can improve a non-targeted approach. Thus, the Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) has been coupled to electrospray ionization (ESI), laser desorption ionization (LDI) and atmospheric pressure photoionization (APPI) to characterize an oak pyrolysis bio-oil. Close to 90% of the all 4500 compound formulae has been attributed to C x H y O z with similar oxygen class compound distribution. Nevertheless, their relative abundance in respect with their double bound equivalent (DBE) value has evidenced significant differences depending on the ion source used. ESI has allowed compounds with low DBE but more oxygen atoms to be ionized. APPI has demonstrated the efficient ionization of less polar compounds (high DBE values and less oxygen atoms). The LDI behavior of bio-oils has been considered intermediate in terms of DBE and oxygen amounts but it has also been demonstrated that a significant part of the features are specifically detected by this ionization method. Thus, the complementarity of three different ionization sources has been successfully demonstrated for the exhaustive characterization by petroleomic approach of a complex mixture. Copyright © 2017 Elsevier B.V. All rights reserved.

Extracellular polymeric substances govern the surface charge of biogenic elemental selenium nanoparticles.

PubMed

Jain, Rohan; Jordan, Norbert; Weiss, Stephan; Foerstendorf, Harald; Heim, Karsten; Kacker, Rohit; Hübner, René; Kramer, Herman; van Hullebusch, Eric D; Farges, François; Lens, Piet N L

2015-02-03

The origin of the organic layer covering colloidal biogenic elemental selenium nanoparticles (BioSeNPs) is not known, particularly in the case when they are synthesized by complex microbial communities. This study investigated the presence of extracellular polymeric substances (EPS) on BioSeNPs. The role of EPS in capping the extracellularly available BioSeNPs was also examined. Fourier transform infrared (FT-IR) spectroscopy and colorimetric measurements confirmed the presence of functional groups characteristic of proteins and carbohydrates on the BioSeNPs, suggesting the presence of EPS. Chemical synthesis of elemental selenium nanoparticles in the presence of EPS, extracted from selenite fed anaerobic granular sludge, yielded stable colloidal spherical selenium nanoparticles. Furthermore, extracted EPS, BioSeNPs, and chemically synthesized EPS-capped selenium nanoparticles had similar surface properties, as shown by ζ-potential versus pH profiles and isoelectric point measurements. This study shows that the EPS of anaerobic granular sludge form the organic layer present on the BioSeNPs synthesized by these granules. The EPS also govern the surface charge of these BioSeNPs, thereby contributing to their colloidal properties, hence affecting their fate in the environment and the efficiency of bioremediation technologies.

Plasmonic bio-sensing for the Fenna-Matthews-Olson complex

NASA Astrophysics Data System (ADS)

Chen, Guang-Yin; Lambert, Neill; Shih, Yen-An; Liu, Meng-Han; Chen, Yueh-Nan; Nori, Franco

2017-01-01

We study theoretically the bio-sensing capabilities of metal nanowire surface plasmons. As a specific example, we couple the nanowire to specific sites (bacteriochlorophyll) of the Fenna-Matthews-Olson (FMO) photosynthetic pigment protein complex. In this hybrid system, we find that when certain sites of the FMO complex are subject to either the suppression of inter-site transitions or are entirely disconnected from the complex, the resulting variations in the excitation transfer rates through the complex can be monitored through the corresponding changes in the scattering spectra of the incident nanowire surface plasmons. We also find that these changes can be further enhanced by changing the ratio of plasmon-site couplings. The change of the Fano lineshape in the scattering spectra further reveals that “site 5” in the FMO complex plays a distinct role from other sites. Our results provide a feasible way, using single photons, to detect mutation-induced, or bleaching-induced, local defects or modifications of the FMO complex, and allows access to both the local and global properties of the excitation transfer in such systems.

Molecular dynamics investigations of BioH protein substrate specificity for biotin synthesis.

PubMed

Xue, Qiao; Cui, Ying-Lu; Zheng, Qing-Chuan; Zhang, Hong-Xing

2016-05-01

BioH, an enzyme of biotin synthesis, plays an important role in fatty acid synthesis which assembles the pimelate moiety. Pimeloyl-acyl carrier protein (ACP) methyl ester, which is long known to be a biotin precursor, is the physiological substrate of BioH. Azelayl methyl ester, which has a longer chain than pimeloyl methyl ester, conjugated to ACP is also indeed accepted by BioH with very low rate of hydrolysis. To date, the substrate specificity for BioH and the molecular origin for the experimentally observed rate changes of hydrolysis by the chain elongation have remained elusive. To this end, we have investigated chain elongation effects on the structures by using the fully atomistic molecular dynamics simulations combined with binding free energy calculations. The results indicate that the substrate specificity is determined by BioH together with ACP. The added two methylenes would increase the structural flexibility by protein motions at the interface of ACP and BioH, instead of making steric clashes with the side chains of the BioH hydrophobic cavity. On the other hand, the slower hydrolysis of azelayl substrate is suggested to be associated with the loose of contacts between BioH and ACP, and with the lost electrostatic interactions of two ionic/hydrogen bonding networks at the interface of the two proteins. The present study provides important insights into the structure-function relationships of the complex of BioH with pimeloyl-ACP methyl ester, which could contribute to further understanding about the mechanism of the biotin synthetic pathway, including the catalytic role of BioH.

ValiRx plc.

PubMed

Eccleston, Mark; Morris, George

2008-09-01

ValiRx plc is a therapeutics and diagnostics company developing an integrated approach to the diagnosis, treatment and prognosis of cancer through its two subsidiaries; ValiPharma and ValiBio. Over 95% of cellular DNA is tightly packaged into a complex structure called chromatin, with only 1% available to be read by cell's machinery. ValiRx's two proprietary technology platforms exploit this epigenomic structure. ValiBio is developing low-cost, rapid, high-throughput, noninvasive screening tests for the early detection, differential diagnosis and prognosis of cancer using its patented Hypergenomics™ and Nucleosomics™ technology. Its therapeutics subsidiary, ValiPharma, is developing novel gene-silencing therapeutics based on its GeneICE™ technology platform, which works by repackaging specific open areas of DNA, resulting in targeted gene deactivation. HyperGenomics and GeneICE are synergistic but independent business areas based on the company's core patent portfolio. ValiRx intends to facilitate early, optimal personalized treatment regimes by correlating 'hypersensitive' site profiles within the genome to specific types of cancer.

Exploring blocking assays using Octet, ProteOn, and Biacore biosensors.

PubMed

Abdiche, Yasmina N; Malashock, Dan S; Pinkerton, Alanna; Pons, Jaume

2009-03-15

We demonstrate the use of label-free real-time optical biosensors in competitive binding assays by epitope binning a panel of antibodies. We describe three assay orientations that we term in tandem, premix, and classical sandwich blocking, and we perform each of them on three platforms: ForteBio's Octet QK, Bio-Rad's ProteOn XPR36, and GE Healthcare's Biacore 3000. By testing whether antibodies block one another's binding to their antigen in a pairwise fashion, we establish a blocking profile for each antibody relative to the others in the panel. The blocking information is then used to create "bins" of antibodies with similar epitopes. The advantages and disadvantages of each biosensor, factors to consider when deciding on the most appropriate blocking assay orientation for a particular interaction system, and tips for dealing with ambiguous data are discussed. The data from our different assay orientations and biosensors agree very well, establishing these machines as valuable tools for characterizing antibody epitopes and multiprotein complexes of biological significance.

Development ceramic composites based on Al2O3, SiO2 and IG-017 additive

NASA Astrophysics Data System (ADS)

Kurovics, E.; Shmakova, A.; Kanev, B.; Gömze, L. A.

2017-02-01

Based on high purity alumina and quartz powders and IG-017 bio-original additives the authors have developed new ceramic composite materials for different industrial purposes. The main goal was to fine a material and morphological structures of high performance ceramic composites as frames for development complex materials for extreme consumptions in the future. For this the mixed powders of Al2O3 , SiO2 and IG-017 bio-original additive were uniaxially pressed at different compaction pressures into disc shapes and were sintered in electric kiln under air (1) and nitrogrn (2) atmosphere. The grain size distributions of the raw materials were determined by laser granulometry. There thermo-physical properties were also determined by derivatography. The prepared and sintered specimens were tested on geometrical sizes, microstructure and morphology by scanning electron microscopy, porosity and water absorption. In this work the authors present the results of their research and investigation.

Novel High Integrity Bio-Inspired Systems with On-Line Self-Test and Self-Repair Properties

NASA Astrophysics Data System (ADS)

Samie, Mohammad; Dragffy, Gabriel; Pipe, Tony

2011-08-01

Since the beginning of life nature has been developing some remarkable solutions to the problem of creating reliable systems that can operate under difficult environmental and fault conditions. Yet, no matter how sophisticated our systems are, we are still unable to match the high degree of reliability that biological organisms posses. Since the early '90s attempts have been made to adapt biological properties and processes to the design of electronic systems but the results have always been unduly complex.This paper, proposes a novel model using a radically new approach to construct highly reliable electronic systems with online fault repair properties. It uses the characteristics and behaviour of unicellular bacteria and bacterial communities to achieve this. The result is a configurable bio-inspired cellular array architecture that, with built-in self-diagnostic and self-repair properties, can implement any application specific electronic system but is particularly suited for safety critical environments, such as space.

Astronaut Bonnie Dunbar preparing to perform bio-medical test

NASA Image and Video Library

1985-10-30

61A-18-001A (30 Oct-6 Nov 1985) --- Her head equipped with a sensor device, astronaut Bonnie J. Dunbar, 61-A mission specialist, talks to earthbound investigators while participating in a bio-medical test. A 35mm camera was used to expose the frame.

Highly variable sensitivity of five binding and two bio-assays for TSH-receptor antibodies.

PubMed

Diana, T; Wüster, C; Kanitz, M; Kahaly, G J

2016-10-01

TSH-receptor (TSHR) antibodies (Ab) can be measured with binding or bio-assays. Sensitivity and specificity of five binding and two bio-assays were compared. TSHR-blocking (TBAb) and TSHR-stimulating (TSAb) Ab were measured with reporter bio-assays. Blocking activity was defined as percent inhibition of luciferase expression relative to induction with bTSH alone. TSAb was reported as percentage of specimen-to-reference ratio (SRR%). TSHR-binding inhibitory immunoglobulins (TBII) were measured with Kronus, Dynex, Kryptor, Cobas, and Immulite. Sixty patients with Graves' disease (GD), 20 with Hashimoto's thyroiditis (HT), and 20 healthy controls (C) were included. C tested negative in all assays (specificity 100 %) while all 60 hyperthyroid GD patients tested positive in the TSAb bio-assay (sensitivity 100 %). Among these 60 GD patients, 20 had low TSAb positivity (SRR% 140-279), but were TBII positive in only 20 (100 %), 7 (35 %), 9 (45 %), 11 (55 %), and 18 (90 %) using the Kronus, Dynex, Kryptor, Cobas, and Immulite, respectively. In 20 moderate TSAb-positive (SRR% 280-420) patients, TBII tested positive in 20 (100 %), 14 (70 %), 13 (65 %), 16 (80 %), and 19 (95 %), respectively. The high (SRR% > 420) TSAb-positive patients were all TBII positive. All 20 hypothyroid HT patients tested TBAb positive (sensitivity 100 %) in the bio-assay while they tested TBII positive in 20 (100 %), 18 (90 %), 20, 20, and 18, respectively. Results obtained with two luminometers correlated for TSAb positive (r = 0.99, p < 0.001), TBAb positive (r = 0.88, p < 0.001), and C (r = 0.86, p < 0.001). None of the binding assays differentiated between TSAb and TBAb. Sensitivity is highly variable between binding and bio-assays for TSHR-Abs.

Christmas tree worms of Indo-Pacific coral reefs: untangling the Spirobranchus corniculatus (Grube, 1862) complex

NASA Astrophysics Data System (ADS)

Willette, Demian A.; Iñiguez, Abril R.; Kupriyanova, Elena K.; Starger, Craig J.; Varman, Tristan; Toha, Abdul Hamid; Maralit, Benedict A.; Barber, Paul H.

2015-09-01

Christmas tree worm is the common name of a group of colorful serpulid polychaetes from the genus Spirobranchus that are symbionts of hermatypic corals. As is increasingly common with reef-associated organisms, Spirobranchus is arranged as a complex of species with overlapping geographic ranges. Current species delimitations based largely on opercular morphology are problematic because of high intraspecific variation. Here, a multi-gene phylogeny of the Spirobranchus corniculatus complex, which tentatively includes S. corniculatus, S. cruciger, and S. gaymardi, sampled from the Coral Triangle, Australia, and Fiji, was reconstructed to test whether the complex includes three genetically distinct lineages identifiable by their opercula. Maximum-likelihood analyses of nuclear and mitochondrial markers revealed a single, monophyletic clade for the S. corniculatus complex. Furthermore, the genetic and morphological variation observed is not geographically based, indicating that the former S. corniculatus complex of three morphospecies is a single, morphologically variable species across the Central Indo-Pacific. Resolving the taxonomy of S. corniculatus presents novel opportunities to utilize this tentative bio-indicator species for monitoring reef health.

Potential relationship between single nucleotide polymorphisms used in forensic genetics and diseases or other traits in European population.

PubMed

Pombar-Gomez, Maria; Lopez-Lopez, Elixabet; Martin-Guerrero, Idoia; Garcia-Orad Carles, Africa; de Pancorbo, Marian M

2015-05-01

Single nucleotide polymorphisms (SNPs) are an interesting option to facilitate the analysis of highly degraded DNA by allowing the reduction of the size of the DNA amplicons. The SNPforID 52-plex panel is a clear example of the use of non-coding SNPs in forensic genetics. However, nonstop advances in studies of genetic polymorphisms are leading to the discovery of new associations between SNPs and diseases. The aim of this study was to perform a comprehensive review of the state of association between the 52 SNPs in the 52-plex panel and diseases or other traits related to their treatment, such as drug response characters. In order to achieve this goal, we have conducted a bioinformatic search for each SNP included in the panel and the SNPs in linkage disequilibrium (LD) with them in the European population (r (2)  > 0.8). A total of 424 SNPs (52 in the panel and 372 in LD) were investigated in PubMed, Scopus, and dbSNP databases. Our results show that three SNPs in the SNPforID 52-plex panel (rs2107612, rs1979255, rs1463729) have been associated with diseases such as hypertension or macular degeneration, as well as drug response. Similarly, three out of the 372 SNPs in LD (rs2107614, r (2)  = 0.859; rs765250, r (2)  = 0.858; rs11064560, r (2)  = 0,887) are also associated with various pathologies. In view of these results, we propose the need for a periodic review of the SNPs used in forensic genetics in order to keep their associations with diseases or related phenotypes updated and to evaluate their continuity in forensic panels for avoiding legal and ethical conflicts.

Concurrent uptake and metabolism of dyestuffs through bio-assisted phytoremediation: a symbiotic approach.

PubMed

Tahir, Uruj; Sohail, Sana; Khan, Umair Hassan

2017-10-01

Manipulation of bio-technological processes in treatment of dyestuffs has attracted considerable attention, because a large proportion of these synthetic dyes enter into natural environment during synthesis and dyeing operations that contaminates different ecosystems. Moreover, these dyestuffs are toxic and difficult to degrade because of their synthetic origin, durability, and complex aromatic molecular structures. Hence, bio-assisted phytoremediation has recently emerged as an innovative cleanup approach in which microorganisms and plants work together to transform xenobiotic dyestuffs into nontoxic or less harmful products. This manuscript will focus on competence and potential of plant-microbe synergistic systems for treatment of dyestuffs, their mixtures and real textile effluents, and effects of symbiotic relationship on plant performances during remediation process and will highlight their metabolic activities during bio-assisted phytodegradation and detoxification.

Analytical characterization of products obtained from slow pyrolysis of Calophyllum inophyllum seed cake: study on performance and emission characteristics of direct injection diesel engine fuelled with bio-oil blends.

PubMed

Rajamohan, Sakthivel; Kasimani, Ramesh

2018-04-01

This paper aims to analyse the characteristics and properties of the fractions obtained from slow pyrolysis of non-edible seed cake of Calophyllum inophyllum (CI). The gas, bio-oil and biochar obtained from the pyrolysis carried out at 500 °C in a fixed bed batch type reactor at a heating rate of 30 °C/min were characterized by various analytical techniques. Owing to the high volatile content of CI biomass (72.61%), it was selected as the raw material in this present investigation. GC-MS and FT-IR analysis of bio-oil showed the presence of higher amount of oxygenated compounds, phenol derivatives, esters, acid and furans. The physicochemical properties of the bio-oil were tested as per ASTM norms which imply that bio-oil is a highly viscous liquid with lower heating value as compared to that of diesel fuel. The chemical composition of evolved gas was analysed by using GC testing which revealed the presence of combustible components. The FT-IR characterization of biochar showed the presence of aliphatic and aromatic hydrocarbons whereas the elevated amount of carbon in biochar indicates its potential to be used as solid fuel. The performance and emission characteristics of CI engine were assessed with different CI bio-oil blends and compared with baseline diesel fuel. The results showed that addition of bio-oil leads to decreased brake thermal efficiency and increased brake specific energy consumption. Meanwhile, increase in blend ratio reduces harmful pollutants such as oxides of nitrogen and smoke in the exhaust. From the engine testing, it is suggested to employ 20% of CI bio-oil blends in CI engine to obtain better operation.

Bio-based coatings as potential barriers to chemical contaminants from recycled paper and board for food packaging.

PubMed

Guazzotti, V; Marti, A; Piergiovanni, L; Limbo, S

2014-01-01

Partition and diffusion experiments were carried out with paper and board samples coated with different biopolymers. The aim was to evaluate the physicochemical behaviour and barrier properties of bio-coatings against migration of typical contaminants from recycled paper packaging. Focus was directed towards water-based, renewable biopolymers, such as modified starches (cationic starch and cationic waxy starch), plant and animal proteins (gluten and gelatine), poured onto paper with an automatic applicator. Additionally, a comparison with polyethylene-laminated paper was performed. Microstructural observations of the bio-coated paper allowed the characterisation of samples. From the partitioning studies, considerable differences in the adsorption behaviour of the selected contaminants between bio-coated or uncoated paper and air were highlighted. For both the polar and non-polar compounds considered (benzophenone and diisobutyl phthalate, respectively), the lowest values of partition coefficients were found when paper was bio-coated, making it evident that biopolymers acted as chemical/physical barriers towards these contaminants. These findings are discussed considering the characteristics of the tested biopolymers. Diffusion studies into the solid food simulant poly 2,6-diphenyl-p-phenylene oxide, also known as Tenax(®), confirmed that all the tested biopolymers slowed down migration. The Weibull kinetic model was fitted to the experimental data to compare migration from paper and bio-coated paper. Values found for β, an index determining the pattern of curvature, ranged from 1.1 to 1.7 for uncoated and polyethylene paper, whereas for bio-coated papers they ranged from 2.2 to 4.9, corresponding to the presence of an evident lag phase due to barrier properties of the tested bio-coatings.

Time-lapse imaging assay using the BioStation CT: a sensitive drug-screening method for three-dimensional cell culture.

PubMed

Sakamoto, Ruriko; Rahman, M Mamunur; Shimomura, Manami; Itoh, Manabu; Nakatsura, Tetsuya

2015-06-01

Three-dimensional (3D) cell culture is beneficial for physiological studies of tumor cells, due to its potential to deliver a high quantity of cell culture information that is representative of the cancer microenvironment and predictive of drug responses in vivo. Currently, gel-associated or matrix-associated 3D cell culture is comprised of intricate procedures that often result in experimental complexity. Therefore, we developed an innovative anti-cancer drug sensitivity screening technique for 3D cell culture on NanoCulture Plates (NCP) by employing the imaging device BioStation CT. Here, we showed that the human breast cancer cell lines BT474 and T47D form multicellular spheroids on NCP plates and compared their sensitivity to the anti-cancer drugs trastuzumab and paclitaxel using the BioStation CT. The anticancer drugs reduced spheroid migration velocity and suppressed spheroid fusion. In addition, primary cells derived from the human breast cancer tissues B58 and B61 grown on NCP plates also exhibited similar drug sensitivity. These results were in good agreement with the conventional assay method using ATP quantification. We confirmed the antitumor effects of the drugs on cells seeded in 96-well plates using the BioStation CT imaging technique. We expect this method to be useful in research for new antitumor agents and for drug sensitivity tests in individually-tailored cancer treatments. © 2015 The Authors. Cancer Science published by Wiley Publishing Asia Pty Ltd on behalf of Japanese Cancer Association.

Design for Additive Bio-Manufacturing: From Patient-Specific Medical Devices to Rationally Designed Meta-Biomaterials.

PubMed

Zadpoor, Amir A

2017-07-25

Recent advances in additive manufacturing (AM) techniques in terms of accuracy, reliability, the range of processable materials, and commercial availability have made them promising candidates for production of functional parts including those used in the biomedical industry. The complexity-for-free feature offered by AM means that very complex designs become feasible to manufacture, while batch-size-indifference enables fabrication of fully patient-specific medical devices. Design for AM (DfAM) approaches aim to fully utilize those features for development of medical devices with substantially enhanced performance and biomaterials with unprecedented combinations of favorable properties that originate from complex geometrical designs at the micro-scale. This paper reviews the most important approaches in DfAM particularly those applicable to additive bio-manufacturing including image-based design pipelines, parametric and non-parametric designs, metamaterials, rational and computationally enabled design, topology optimization, and bio-inspired design. Areas with limited research have been identified and suggestions have been made for future research. The paper concludes with a brief discussion on the practical aspects of DfAM and the potential of combining AM with subtractive and formative manufacturing processes in so-called hybrid manufacturing processes.

Design for Additive Bio-Manufacturing: From Patient-Specific Medical Devices to Rationally Designed Meta-Biomaterials

PubMed Central

Zadpoor, Amir A.

2017-01-01

Recent advances in additive manufacturing (AM) techniques in terms of accuracy, reliability, the range of processable materials, and commercial availability have made them promising candidates for production of functional parts including those used in the biomedical industry. The complexity-for-free feature offered by AM means that very complex designs become feasible to manufacture, while batch-size-indifference enables fabrication of fully patient-specific medical devices. Design for AM (DfAM) approaches aim to fully utilize those features for development of medical devices with substantially enhanced performance and biomaterials with unprecedented combinations of favorable properties that originate from complex geometrical designs at the micro-scale. This paper reviews the most important approaches in DfAM particularly those applicable to additive bio-manufacturing including image-based design pipelines, parametric and non-parametric designs, metamaterials, rational and computationally enabled design, topology optimization, and bio-inspired design. Areas with limited research have been identified and suggestions have been made for future research. The paper concludes with a brief discussion on the practical aspects of DfAM and the potential of combining AM with subtractive and formative manufacturing processes in so-called hybrid manufacturing processes. PMID:28757572

Operant conditioning: a minimal components requirement in artificial spiking neurons designed for bio-inspired robot's controller

PubMed Central

Cyr, André; Boukadoum, Mounir; Thériault, Frédéric

2014-01-01

In this paper, we investigate the operant conditioning (OC) learning process within a bio-inspired paradigm, using artificial spiking neural networks (ASNN) to act as robot brain controllers. In biological agents, OC results in behavioral changes learned from the consequences of previous actions, based on progressive prediction adjustment from rewarding or punishing signals. In a neurorobotics context, virtual and physical autonomous robots may benefit from a similar learning skill when facing unknown and unsupervised environments. In this work, we demonstrate that a simple invariant micro-circuit can sustain OC in multiple learning scenarios. The motivation for this new OC implementation model stems from the relatively complex alternatives that have been described in the computational literature and recent advances in neurobiology. Our elementary kernel includes only a few crucial neurons, synaptic links and originally from the integration of habituation and spike-timing dependent plasticity as learning rules. Using several tasks of incremental complexity, our results show that a minimal neural component set is sufficient to realize many OC procedures. Hence, with the proposed OC module, designing learning tasks with an ASNN and a bio-inspired robot context leads to simpler neural architectures for achieving complex behaviors. PMID:25120464

Operant conditioning: a minimal components requirement in artificial spiking neurons designed for bio-inspired robot's controller.

PubMed

Cyr, André; Boukadoum, Mounir; Thériault, Frédéric

2014-01-01

In this paper, we investigate the operant conditioning (OC) learning process within a bio-inspired paradigm, using artificial spiking neural networks (ASNN) to act as robot brain controllers. In biological agents, OC results in behavioral changes learned from the consequences of previous actions, based on progressive prediction adjustment from rewarding or punishing signals. In a neurorobotics context, virtual and physical autonomous robots may benefit from a similar learning skill when facing unknown and unsupervised environments. In this work, we demonstrate that a simple invariant micro-circuit can sustain OC in multiple learning scenarios. The motivation for this new OC implementation model stems from the relatively complex alternatives that have been described in the computational literature and recent advances in neurobiology. Our elementary kernel includes only a few crucial neurons, synaptic links and originally from the integration of habituation and spike-timing dependent plasticity as learning rules. Using several tasks of incremental complexity, our results show that a minimal neural component set is sufficient to realize many OC procedures. Hence, with the proposed OC module, designing learning tasks with an ASNN and a bio-inspired robot context leads to simpler neural architectures for achieving complex behaviors.

Broncho-Vaxom attenuates allergic airway inflammation by restoring GSK3β-related T regulatory cell insufficiency.

PubMed

Fu, Ran; Li, Jian; Zhong, Hua; Yu, Dehong; Zeng, Xianping; Deng, Mengxia; Sun, Yueqi; Wen, Weiping; Li, Huabin

2014-01-01

Oral administration of bacterial extracts (eg, Broncho-Vaxom (BV)) has been proposed to attenuate asthma through modulating Treg cells. However, the underlying mechanism has not been fully characterized. This study sought to assess the effects of oral administration of BV on GSK-3β expression and Treg cells in ovalbumin (OVA)-induced asthmatic mice models. Asthmatic mice models were established with OVA challenge and treated with oral administration of BV. Next, infiltration of inflammatory cells including eosinophil and neutrophils, mucous metaplasia, levels of Th1/Th2/Treg-typed cytokines and expression of GSK3β and Foxp3 were examined in asthmatic mice models by histological analysis, Bio-Plex and western blot, respectively. Moreover, the frequencies of Treg cells were evaluated in cultured splenocytes by flow cytometry in the presence of BV or GSK3β siRNA interference. We found significant decrease of infiltrated inflammatory cells in bronchoalveolar lavage fluid (BALF) in asthmatic mice models after oral administration of BV. Oral administration of BV was shown to significantly suppress mucus metaplasia, Th2-typed cytokine levels and GSK3β expression while increasing Foxp3 production in asthmatic mice models. Moreover, BV significantly enhanced GSK3β-related expansion of Treg cells in cultured spleen cells in vitro. Our findings provide evidence that oral administration of BV is capable of attenuating airway inflammation in asthmatic mice models, which may be associated with GSK3β-related expansion of Treg cells.

Identification of neutrophil-derived proteases and angiotensin II as biomarkers of cancer cachexia

PubMed Central

Penafuerte, Claudia A; Gagnon, Bruno; Sirois, Jacinthe; Murphy, Jessica; MacDonald, Neil; Tremblay, Michel L

2016-01-01

Background: Cachexia is a metabolic disorder characterised by muscle wasting, diminished response to anti-cancer treatments and poor quality of life. Our objective was to identify blood-based biomarkers of cachexia in advanced cancer patients. Hence, we characterised the plasma cytokine and blood cell mRNA profiles of patients grouped in three cohorts: patients with cachexia, pre-cachexia (no cachexia but high CRP levels: ⩾5 mg l−1) and no cachexia (no cachexia and CRP: <5 mg l−1). Methods: A total of 122 newly diagnosed cancer patients with seven cancer types were studied prior to their initial therapy. Plasma levels of 22 cytokines were quantified using the bio-plex technology. mRNAs isolated from whole blood and expression profiles were determined by the chip array technology and Ingenuity Pathway Analysis (IPA) software. Results: In comparison with non-cachectic individuals, both pre-cachectic and cachectic patients showed an increase (⩾1.5-folds) in mRNA expression of neutrophil-derived proteases (NDPs) and significantly elevated angiotensin II (Ang II) (P=0.005 and P=0.02, respectively), TGFβ1 (P=0.042 and P<0.0001, respectively) and CRP (both P<0.0001) in the plasma. Moreover, cachectic patients displayed a significant increase in IL-6 (P=0.005), IL-8 (P=0.001) and absolute neutrophil counts (P=0.007). Conclusions: Ang II, TGFβ1, CRP and NDP are blood biomarkers for cancer cachexia. These findings contribute to early diagnosis and prevention of cachexia. PMID:26954714

Vaginal cytokines do not correlate with postmenopausal vulvovaginal symptoms.

PubMed

Kollmann, Zahraa; Bersinger, Nick; von Wolff, Michael; Thurman, Andrea R; Archer, David F; Stute, Petra

2015-04-01

Exploratory pilot study to determine the correlation between postmenopausal vulvovaginal symptoms and vaginal cytokine levels. Postmenopausal women (n = 34) not using menopausal hormone therapy and presenting with or without symptoms of vulvovaginal irritation were screened. Each participant underwent a vaginal examination and screening for vaginitis. A cervicovaginal lavage (CVL) with sterile saline and a peripheral blood sample were obtained. Main outcome measures were assessed by Luminex® X-map method on the Bio-Plex® platform. Main outcome measures were cervicovaginal and serum interleukin (IL)-4, IL-5, IL-10, IL-12, IL-13, TNF-α, GM-CSF, MIP-1-alpha and RANTES level. Cervicovaginal cytokines were adjusted to total protein concentration [pg/mcg protein]. Twenty-six postmenopausal women were enrolled (symptomatic: n = 15; asymptomatic: n = 11). There were no significant differences between groups: age, age at menopause, vaginal pH and all CVL and serum cytokines (IL-4, IL-5, IL-10, IL-12, IL-13, TNF-α, GM-CSF, MIP-1-alpha and RANTES). GM-CSF was the most abundant vaginal cytokine (symptomatic: 146.5 ± 165.6 pg/mcg protein; asymptomatic: 146.0 ± 173.5 pg/mcg protein; p = 0.99). Postmenopausal vulvovaginal symptoms did not correlate with vaginal inflammatory marker. There was no difference in serum or CVL cytokines between symptomatic and asymptomatic postmenopasual women. Vaginal symptoms after menopause are not related to the vaginal cytokine changes associated with loss of estrogen.

Geophysical and Geotechnical Characterization of Beta-1,3/1,6-glucan Biopolymer treated Soil

NASA Astrophysics Data System (ADS)

Chang, I.; Cho, G.

2012-12-01

Bacteria or microbes in soil excrete hydrocarbon (e.g. polysaccharide) by-products which are called biopolymers. These biopolymers (or sometime biofilms) recently begun to make a mark on soil erosion control, aggregate stabilization, and drilling enhancement. However, the biological effect on soil behavior (e.g. bio-clogging or bio-cementation) has been poorly understood. In this study, the bio-cementation and bio-clogging effect induced by the existence of β-1,3/1,6-glucan biopolymers in soil were evaluated through a series of geophysical and geotechnical characterization tests in laboratory. According to the experimental test results, as the β-1,3/1,6-glucan content in soil increases, the compressive strength and shear wave velocity increase (i.e., bio-cementation) while the hydraulic conductivity decreases (i.e., bio-clogging) but the electrical conductivity increases due to the high electrical conductivity characteristic of β-1,3/1,6-glucan fibers. Coefficient of consolidation variation with the increases of β-1,3/1,6-glucan content in soil. SEM image of β-1,3/1,6-glucan treated soil. Fibers are form matices with soil particles.

Visible light induced electropolymerization of suspended hydrogel bioscaffolds in a microfluidic chip.

PubMed

Li, Pan; Yu, Haibo; Liu, Na; Wang, Feifei; Lee, Gwo-Bin; Wang, Yuechao; Liu, Lianqing; Li, Wen Jung

2018-05-23

The development of microengineered hydrogels co-cultured with cells in vitro could advance in vivo bio-systems in both structural complexity and functional hierarchy, which holds great promise for applications in regenerative tissues or organs, drug discovery and screening, and bio-sensors or bio-actuators. Traditional hydrogel microfabrication technologies such as ultraviolet (UV) laser or multiphoton laser stereolithography and three-dimensional (3D) printing systems have advanced the development of 3D hydrogel micro-structures but need either expensive and complex equipment, or harsh material selection with limited photoinitiators. Herein, we propose a simple and flexible hydrogel microfabrication method based on a ubiquitous visible-light projection system combined with a custom-designed photosensitive microfluidic chip, to rapidly (typically several to tens of seconds) fabricate various two-dimensional (2D) hydrogel patterns and 3D hydrogel constructs. A theoretical layer-by-layer model that involves continuous polymerizing-delaminating-polymerizing cycles is presented to explain the polymerization and structural formation mechanism of hydrogels. A large area of hydrogel patterns was efficiently fabricated without the usage of costly laser systems or photoinitiators, i.e., a stereoscopic mesh-like hydrogel network with intersecting hydrogel micro-belts was fabricated via a series of dynamic-changing digital light projections. The pores and gaps of the hydrogel network are tunable, which facilitates the supply of nutrients and discharge of waste in the construction of 3D thick bio-models. Cell co-culture experiments showed the effective regulation of cell spreading by hydrogel scaffolds fabricated by the new method presented here. This visible light enabled hydrogel microfabrication method may provide new prospects for designing cell-based units for advanced biomedical studies, e.g., for 3D bio-models or bio-actuators in the future.

Statistical methods for quantitative mass spectrometry proteomic experiments with labeling.

PubMed

Oberg, Ann L; Mahoney, Douglas W

2012-01-01

Mass Spectrometry utilizing labeling allows multiple specimens to be subjected to mass spectrometry simultaneously. As a result, between-experiment variability is reduced. Here we describe use of fundamental concepts of statistical experimental design in the labeling framework in order to minimize variability and avoid biases. We demonstrate how to export data in the format that is most efficient for statistical analysis. We demonstrate how to assess the need for normalization, perform normalization, and check whether it worked. We describe how to build a model explaining the observed values and test for differential protein abundance along with descriptive statistics and measures of reliability of the findings. Concepts are illustrated through the use of three case studies utilizing the iTRAQ 4-plex labeling protocol.

ARSENIC CONTAMINATION AT THE INDUSTRI-PLEX SUPERFUND SITE, WOBURN, MA

EPA Science Inventory

Arsenate coprecipitated with hydrous ferric oxide (HFO) was stabilized against dissolution during transformation of HFO to more crystalline iron (hydr)oxides. The rate of arsenate stabilization approximately coincided with the rate of HFO transformation at pH 6 and 40 ?C. Compa...

CASE STUDY: SITE CONCEPTUAL MODEL FOR ENHANCED MNA OF ARSENIC

EPA Science Inventory

Field investigations have been conducted to understand the fate of arsenic in contaminated ground water during discharge into the Halls Brook Holding Area (HBHA) Pond at the Industri-Plex Superfund Site in Massachusetts. The ground water plume contains elevated levels of arsenic...

Bio-prospecting of distillery yeasts as bio-control and bio-remediation agents.

PubMed

Ubeda, Juan F; Maldonado, María; Briones, Ana I; Francisco, J Fernández; González, Francisco J

2014-05-01

This work constitutes a preliminary study in which the capacity of non-Saccharomyces yeasts isolated from ancient distilleries as bio-control agents against moulds and in the treatment of waste waters contaminated by heavy metals-i.e. bio-remediation-is shown. In the first control assays, antagonist effect between non-Saccharomyces yeasts, their extracts and supernatants against some moulds, analysing the plausible (not exhaustive) involved factors were qualitatively verified. In addition, two enzymatic degrading properties of cell wall plant polymers, quitinolitic and pectinolitic, were screened. Finally, their use as agents of bio-remediation of three heavy metals (cadmium, chromium and lead) was analysed semi-quantitatively. The results showed that all isolates belonging to Pichia species effectively inhibited all moulds assayed. Moreover, P. kudriavzevii is a good candidate for both bio-control and bio-remediation because it inhibited moulds and accumulated the major proportion of the three tested metals.

Results for five sets of forensic genetic markers studied in a Greek population sample.

PubMed

Tomas, C; Skitsa, I; Steinmeier, E; Poulsen, L; Ampati, A; Børsting, C; Morling, N

2015-05-01

A population sample of 223 Greek individuals was typed for five sets of forensic genetic markers with the kits NGM SElect™, SNPforID 49plex, DIPplex®, Argus X-12 and PowerPlex® Y23. No significant deviation from Hardy-Weinberg expectations was observed for any of the studied markers after Holm-Šidák correction. Statistically significant (P<0.05) levels of linkage disequilibrium were observed between markers within two of the studied X-chromosome linkage groups. AMOVA analyses of the five sets of markers did not show population structure when the individuals were grouped according to their geographic origin. The Greek population grouped closely to the other European populations measured by F(ST)(*) distances. The match probability ranged from a value of 1 in 2×10(7) males by using haplotype frequencies of four X-chromosome haplogroups in males to 1 in 1.73×10(21) individuals for 16 autosomal STRs. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Bio-layer interferometry for measuring kinetics of protein-protein interactions and allosteric ligand effects.

PubMed

Shah, Naman B; Duncan, Thomas M

2014-02-18

We describe the use of Bio-layer Interferometry to study inhibitory interactions of subunit ε with the catalytic complex of Escherichia coli ATP synthase. Bacterial F-type ATP synthase is the target of a new, FDA-approved antibiotic to combat drug-resistant tuberculosis. Understanding bacteria-specific auto-inhibition of ATP synthase by the C-terminal domain of subunit ε could provide a new means to target the enzyme for discovery of antibacterial drugs. The C-terminal domain of ε undergoes a dramatic conformational change when the enzyme transitions between the active and inactive states, and catalytic-site ligands can influence which of ε's conformations is predominant. The assay measures kinetics of ε's binding/dissociation with the catalytic complex, and indirectly measures the shift of enzyme-bound ε to and from the apparently nondissociable inhibitory conformation. The Bio-layer Interferometry signal is not overly sensitive to solution composition, so it can also be used to monitor allosteric effects of catalytic-site ligands on ε's conformational changes.

BioClips of symmetric and asymmetric cell division.

PubMed

Lu, Fong-Mei; Eliceiri, Kevin W; White, John G

2007-05-01

Animations have long been used as tools to illustrate complex processes in such diverse fields as mechanical engineering, astronomy, bacteriology and physics. Animations in biology hold particular educational promise for depicting complex dynamic processes, such as photosynthesis, motility, viral replication and cellular respiration, which cannot be easily explained using static two-dimensional images. However, these animations have often been restrictive in scope, having been created for a specific classroom or research audience. In recent years, a new type of animation has emerged called the BioClip (http://www.bioclips.com) that strives to present science in an interactive multimedia format, which is, at once, informative and entertaining, by combining animations, text descriptions and music in one portable cross-platform document. In the present article, we illustrate the educational value of this new electronic resource by reviewing in depth two BioClips our group has created which describe the processes of symmetric and asymmetric cell division (http://www.wormclassroom.org/cb/bioclip).

A comparative study of bio-inspired protective scales using 3D printing and mechanical testing.

PubMed

Martini, Roberto; Balit, Yanis; Barthelat, Francois

2017-06-01

Flexible natural armors from fish, alligators or armadillo are attracting an increasing amount of attention for their unique combinations of hardness, flexibility and light weight. The extreme contrast of stiffness between hard scales and surrounding soft tissues gives rise to unusual and attractive mechanisms, which now serve as models for the design of bio-inspired armors. Despite this growing interest, there is little guideline for the choice of materials, optimum thickness, size, shape and arrangement for the protective scales. In this work, we explore how the geometry and arrangement of hard scales can be tailored to promote scale-scale interactions. We use 3D printing to fabricate arrays of scales with increasingly complex geometries and arrangements, from simple squares with no overlap to complex ganoid-scales with overlaps and interlocking features. We performed puncture tests and flexural tests on each of the 3D printed materials, and we report the puncture resistance - compliance characteristics of each design on an Ashby chart. The interactions between the scales can significantly increase the resistance to puncture, and these interactions can be maximized by tuning the geometry and arrangement of the scales. Interestingly, the designs that offer the best combinations of puncture resistance and flexural compliance are similar to the geometry and arrangement of natural teleost and ganoid scales, which suggests that natural evolution has shaped these systems to maximize flexible protection. This study yields new insights into the mechanisms of natural dermal armor, and also suggests new designs for personal protective systems. Flexible natural armors from fishes, alligators or armadillos are attracting an increasing amount of attention for their unique and attractive combinations of hardness, flexibility and low weight. Despite a growing interest in bio-inspired flexible protection, there is still little guideline for the choice of materials, optimum thickness, size, shape and arrangement of the protective scales. In this work, we explore how the geometry and arrangement of hard scales affect puncture resistance and flexural compliance, using 3D printing and mechanical testing. Our main finding is that the performance of the scaled skin in terms of puncture resistance can be significantly improved by slight changes in their geometry and arrangement. Our results also suggest that natural evolution has shaped scaled skins to maximize flexible protection. This study yields new insights into the mechanics of natural dermal armors, and also suggests new designs for personal protective systems. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Bio-Inspired Metal-Coordination Dynamics: A Unique Tool for Engineering Soft Matter Mechanics

NASA Astrophysics Data System (ADS)

Holten-Andersen, Niels

Growing evidence supports a critical role of metal-coordination in soft biological material properties such as self-healing, underwater adhesion and autonomous wound plugging. Using bio-inspired metal-binding polymers, initial efforts to mimic these properties with metal-coordination crosslinked polymer materials have shown promise. In addition, with polymer network mechanics strongly coupled to coordinate crosslink dynamics material properties can be easily tuned from visco-elastic fluids to solids. Given their exploitation in desirable material applications in Nature, bio-inspired metal-coordinate complex crosslinking provides an opportunity to further advance synthetic polymer materials design. Early lessons from this pursuit are presented.

‘GREENER’ SURFACTANTS FROM BIO-BASED WASTE AS EFFICIENT ALTERNATIVES TO NONYLPHENOL ETHOXYLATES

EPA Science Inventory

All bio-based surfactants synthesized over the course of the project will be tested for their ability to lower the surface tension at the air-water interface using a Du Nüoy ring tensiometer. The cleaning efficiency of the surfactants will be tested at the Toxics Use Reduc...

Natural Materials and Systems

DTIC Science & Technology

2013-03-07

distribution is unlimited 7 Program Trends – BRI is biggest impact • Chromophores/Bioluminescence – Bio-X STT phase 1 focus. One of its discoveries are...C) Tm ( ferritin ) Tm (nAl) Bio-thermite complex nAl only nAl FeO(OH) TGA/DSC profile (~40-44 cages/nAl...stabilize reactive components, interact with nAl, and quickly deliver components to the surface. • Ferritin used in a single or multi-layer

Bio-repository of post-clinical test samples at the national cancer center hospital (NCCH) in Tokyo.

PubMed

Furuta, Koh; Yokozawa, Karin; Takada, Takako; Kato, Hoichi

2009-08-01

We established the Bio-repository at the National Cancer Center Hospital in October 2002. The main purpose of this article is to show the importance and usefulness of a bio-repository of post-clinical test samples not only for translational cancer research but also for routine clinical oncology by introducing the experience of setting up such a facility. Our basic concept of a post-clinical test sample is not as left-over waste, but rather as frozen evidence of a patient's pathological condition at a particular point. We can decode, if not all, most of the laboratory data from a post-clinical test sample. As a result, the bio-repository is able to provide not only the samples, but potentially all related laboratory data upon request. The areas of sample coverage are the following: sera after routine blood tests; sera after cross-match tests for transfusion; serum or plasma submitted at a patient's clinically important time period by the physician; and samples collected by the individual investigator. The formats of stored samples are plasma or serum, dried blood spot (DBS) and buffy coat. So far, 150 218 plasmas or sera, 35 253 DBS and 536 buffy coats have been registered for our bio-repository system. We arranged to provide samples to various concerned parties under strict legal and ethical agreements. Although the number of the utilized samples was initially limited, the inquiries for sample utilization are now increasing steadily from both research and clinical sources. Further efforts to increase the benefits of the repository are intended.

Chemical and ecotoxicological properties of three bio-oils from pyrolysis of biomasses.

PubMed

Campisi, Tiziana; Samorì, Chiara; Torri, Cristian; Barbera, Giuseppe; Foschini, Anna; Kiwan, Alisar; Galletti, Paola; Tagliavini, Emilio; Pasteris, Andrea

2016-10-01

In view of the potential use of pyrolysis-based technologies, it is crucial to understand the environmental hazards of pyrolysis-derived products, in particular bio-oils. Here, three bio-oils were produced from fast pyrolysis of pine wood and intermediate pyrolysis of corn stalk and poultry litter. They were fully characterized by chemical analysis and tested for their biodegradability and their ecotoxicity on the crustacean Daphnia magna and the green alga Raphidocelis subcapitata. These tests were chosen as required by the European REACH regulation. These three bio-oils were biodegradable, with 40-60% of biodegradation after 28 days, and had EC50 values above 100mgL(-1) for the crustacean and above 10mgL(-1) for the alga, showing low toxicity to the aquatic life. The toxic unit approach was applied to verify whether the observed toxicity could be predicted from the data available for the substances detected in the bio-oils. The predicted values largely underestimated the experimental values. Copyright © 2016 Elsevier Inc. All rights reserved.

Quantum-dot-based suspension microarray for multiplex detection of lung cancer markers: preclinical validation and comparison with the Luminex xMAP® system

NASA Astrophysics Data System (ADS)

Bilan, Regina; Ametzazurra, Amagoia; Brazhnik, Kristina; Escorza, Sergio; Fernández, David; Uríbarri, María; Nabiev, Igor; Sukhanova, Alyona

2017-03-01

A novel suspension multiplex immunoassay for the simultaneous specific detection of lung cancer markers in bronchoalveolar lavage fluid (BALF) clinical samples based on fluorescent microspheres having different size and spectrally encoded with quantum dots (QDEM) was developed. The designed suspension immunoassay was validated for the quantitative detection of three lung cancer markers in BALF samples from 42 lung cancer patients and 10 control subjects. Tumor markers were detected through simultaneous formation of specific immune complexes consisting of a capture molecule, the target antigen, and biotinylated recognition molecule on the surface of the different QDEM in a mixture. The immune complexes were visualized by fluorescently labeled streptavidin and simultaneously analyzed using a flow cytometer. Preclinical validation of the immunoassay was performed and results were compared with those obtained using an alternative 3-plex immunoassay based on Luminex xMAP® technology, developed on classical organic fluorophores. The comparison showed that the QDEM and xMAP® assays yielded almost identical results, with clear discrimination between control and clinical samples. Thus, developed QDEM technology can become a good alternative to xMAP® assays permitting analysis of multiple protein biomarkers using conventional flow cytometers.

Sentiment Diffusion of Public Opinions about Hot Events: Based on Complex Network

PubMed Central

Hao, Xiaoqing; An, Haizhong; Zhang, Lijia; Li, Huajiao; Wei, Guannan

2015-01-01

To study the sentiment diffusion of online public opinions about hot events, we collected people’s posts through web data mining techniques. We calculated the sentiment value of each post based on a sentiment dictionary. Next, we divided those posts into five different orientations of sentiments: strongly positive (P), weakly positive (p), neutral (o), weakly negative (n), and strongly negative (N). These sentiments are combined into modes through coarse graining. We constructed sentiment mode complex network of online public opinions (SMCOP) with modes as nodes and the conversion relation in chronological order between different types of modes as edges. We calculated the strength, k-plex clique, clustering coefficient and betweenness centrality of the SMCOP. The results show that the strength distribution obeys power law. Most posts’ sentiments are weakly positive and neutral, whereas few are strongly negative. There are weakly positive subgroups and neutral subgroups with ppppp and ooooo as the core mode, respectively. Few modes have larger betweenness centrality values and most modes convert to each other with these higher betweenness centrality modes as mediums. Therefore, the relevant person or institutes can take measures to lead people’s sentiments regarding online hot events according to the sentiment diffusion mechanism. PMID:26462230

Quantum-dot-based suspension microarray for multiplex detection of lung cancer markers: preclinical validation and comparison with the Luminex xMAP® system

PubMed Central

Bilan, Regina; Ametzazurra, Amagoia; Brazhnik, Kristina; Escorza, Sergio; Fernández, David; Uríbarri, María; Nabiev, Igor; Sukhanova, Alyona

2017-01-01

A novel suspension multiplex immunoassay for the simultaneous specific detection of lung cancer markers in bronchoalveolar lavage fluid (BALF) clinical samples based on fluorescent microspheres having different size and spectrally encoded with quantum dots (QDEM) was developed. The designed suspension immunoassay was validated for the quantitative detection of three lung cancer markers in BALF samples from 42 lung cancer patients and 10 control subjects. Tumor markers were detected through simultaneous formation of specific immune complexes consisting of a capture molecule, the target antigen, and biotinylated recognition molecule on the surface of the different QDEM in a mixture. The immune complexes were visualized by fluorescently labeled streptavidin and simultaneously analyzed using a flow cytometer. Preclinical validation of the immunoassay was performed and results were compared with those obtained using an alternative 3-plex immunoassay based on Luminex xMAP® technology, developed on classical organic fluorophores. The comparison showed that the QDEM and xMAP® assays yielded almost identical results, with clear discrimination between control and clinical samples. Thus, developed QDEM technology can become a good alternative to xMAP® assays permitting analysis of multiple protein biomarkers using conventional flow cytometers. PMID:28300171

Evaluation of a joint Bioinformatics and Medical Informatics international course in Peru

PubMed Central

Curioso, Walter H; Hansen, Jacquelyn R; Centurion-Lara, Arturo; Garcia, Patricia J; Wolf, Fredric M; Fuller, Sherrilynne; Holmes, King K; Kimball, Ann Marie

2008-01-01

Background New technologies that emerge at the interface of computational and biomedical science could drive new advances in global health, therefore more training in technology is needed among health care workers. To assess the potential for informatics training using an approach designed to foster interaction at this interface, the University of Washington and the Universidad Peruana Cayetano Heredia developed and assessed a one-week course that included a new Bioinformatics (BIO) track along with an established Medical/Public Health Informatics track (MI) for participants in Peru. Methods We assessed the background of the participants, and measured the knowledge gained by track-specific (MI or BIO) 30-minute pre- and post-tests. Participants' attitudes were evaluated both by daily evaluations and by an end-course evaluation. Results Forty-three participants enrolled in the course – 20 in the MI track and 23 in the BIO track. Of 20 questions, the mean % score for the MI track increased from 49.7 pre-test (standard deviation or SD = 17.0) to 59.7 (SD = 15.2) for the post-test (P = 0.002, n = 18). The BIO track mean score increased from 33.6 pre-test to 51.2 post-test (P < 0.001, n = 21). Most comments (76%) about any aspect of the course were positive. The main perceived strength of the course was the quality of the speakers, and the main perceived weakness was the short duration of the course. Overall, the course acceptability was very good to excellent with a rating of 4.1 (scale 1–5), and the usefulness of the course was rated as very good. Most participants (62.9%) expressed a positive opinion about having had the BIO and MI tracks come together for some of the lectures. Conclusion Pre- and post-test results and the positive evaluations by the participants indicate that this first joint Bioinformatics and Medical/Public Health Informatics (MI and BIO) course was a success. PMID:18194533

Evaluation of a joint Bioinformatics and Medical Informatics international course in Peru.

PubMed

Curioso, Walter H; Hansen, Jacquelyn R; Centurion-Lara, Arturo; Garcia, Patricia J; Wolf, Fredric M; Fuller, Sherrilynne; Holmes, King K; Kimball, Ann Marie

2008-01-14

New technologies that emerge at the interface of computational and biomedical science could drive new advances in global health, therefore more training in technology is needed among health care workers. To assess the potential for informatics training using an approach designed to foster interaction at this interface, the University of Washington and the Universidad Peruana Cayetano Heredia developed and assessed a one-week course that included a new Bioinformatics (BIO) track along with an established Medical/Public Health Informatics track (MI) for participants in Peru. We assessed the background of the participants, and measured the knowledge gained by track-specific (MI or BIO) 30-minute pre- and post-tests. Participants' attitudes were evaluated both by daily evaluations and by an end-course evaluation. Forty-three participants enrolled in the course - 20 in the MI track and 23 in the BIO track. Of 20 questions, the mean % score for the MI track increased from 49.7 pre-test (standard deviation or SD = 17.0) to 59.7 (SD = 15.2) for the post-test (P = 0.002, n = 18). The BIO track mean score increased from 33.6 pre-test to 51.2 post-test (P < 0.001, n = 21). Most comments (76%) about any aspect of the course were positive. The main perceived strength of the course was the quality of the speakers, and the main perceived weakness was the short duration of the course. Overall, the course acceptability was very good to excellent with a rating of 4.1 (scale 1-5), and the usefulness of the course was rated as very good. Most participants (62.9%) expressed a positive opinion about having had the BIO and MI tracks come together for some of the lectures. Pre- and post-test results and the positive evaluations by the participants indicate that this first joint Bioinformatics and Medical/Public Health Informatics (MI and BIO) course was a success.

Forensic validation of the PowerPlex® ESI 16 STR Multiplex and comparison of performance with AmpFlSTR® SGM Plus®.

PubMed

Tucker, Valerie C; Kirkham, Amanda J; Hopwood, Andrew J

2012-05-01

We describe the forensic validation of Promega's PowerPlex® European Standard Investigator 16 (ESI 16) multiplex kit and compare results generated with the AmpFlSTR® SGM Plus® (SGM+) multiplex. ESI 16 combines the loci contained within the SGM+ multiplex with five additional loci: D2S441, D10S1248, D22S1045, D1S1656, and D12S391. A relative reduction in amplicon size of the SGM+ loci facilitates an increased robustness and amplification success of these amplicons with degraded DNA samples. Tests performed herein supplement ESI 16 data published previously with sensitivity, profile quality, mock casework, inhibitor and mixture study data collected in our laboratories in alignment with our internal technical and quality guidelines and those issued by the Scientific Working Group on DNA Analysis Methods (SWGDAM), the DNA Advisory Board (DAB) and the DNA working group (DNAWG) of the European Network of Forensic Science Institutes (ENFSI). Full profiles were routinely generated from a fully heterozygous single source DNA template using 62.5 pg for ESI 16 and 500 pg for SGM+. This increase in sensitivity has a consequent effect on mixture analyses and the detection of minor mixture components. The improved PCR chemistry confers enhanced tolerance to high levels of laboratory prepared inhibitors compared with SGM+ results. In summary, our results demonstrate that the ESI 16 multiplex kit is more robust and sensitive compared with SGM+ and will be a suitable replacement system for the analysis of forensic DNA samples providing compliance with the European standard set of STR loci.

Injection Drug Users’ Involvement In Drug Economy: Dynamics of Sociometric and Egocentric Social Networks

PubMed Central

Yang, Cui; Latkin, Carl; Muth, Stephen Q.; Rudolph, Abby

2014-01-01

The purpose of this analysis was to examine the effect of social network cohesiveness on drug economy involvement, and to test whether this relationship is mediated by drug support network size in a sample of active injection drug users. Involvement in the drug economy was defined by self-report of participation in at least one of the following activities: selling drugs, holding drugs or money for drugs, providing street security for drug sellers, cutting/packaging/cooking drugs, selling or renting drug paraphernalia (e.g., pipes, tools, rigs), and injecting drugs in others’ veins. The sample consists of 273 active injection drug users in Baltimore, Maryland who reported having injected drugs in the last 6 months and were recruited through either street outreach or by their network members. Egocentric drug support networks were assessed through a social network inventory at baseline. Sociometric networks were built upon the linkages by selected matching characteristics, and k-plex rank was used to characterize the level of cohesiveness of the individual to others in the social network. Although no direct effect was observed, structural equation modeling indicated k-plex rank was indirectly associated with drug economy involvement through drug support network size. These findings suggest the effects of large-scale sociometric networks on injectors’ drug economy involvement may occur through their immediate egocentric networks. Future harm reduction programs for injection drug users (IDUs) should consider providing programs coupled with economic opportunities to those drug users within a cohesive network subgroup. Moreover, individuals with a high connectivity to others in their network may be optimal individuals to train for diffusing HIV prevention messages. PMID:25309015

Comparative sensitivity and inhibitor tolerance of GlobalFiler® PCR Amplification and Investigator® 24plex QS kits for challenging samples.

PubMed

Elwick, Kyleen; Mayes, Carrie; Hughes-Stamm, Sheree

2018-05-01

In cases such as mass disasters or missing persons, human remains are challenging to identify as they may be fragmented, burnt, been buried, decomposed, and/or contain inhibitory substances. This study compares the performance of a relatively new STR kit in the US market (Investigator® 24plex QS kit; Qiagen) with the GlobalFiler® PCR Amplification kit (Thermo Fisher Scientific) when genotyping highly inhibited and low level DNA samples. In this study, DNA samples ranging from 1 ng to 7.8 pg were amplified to define the sensitivity of two systems. In addition, DNA (1 ng and 0.1 ng input amounts) was spiked with various concentrations of five inhibitors common to human remains (humic acid, melanin, hematin, collagen, calcium). Furthermore, bone (N = 5) and tissue samples from decomposed human remains (N = 6) were used as mock casework samples for comparative analysis with both STR kits. The data suggest that the GlobalFiler® kit may be slightly more sensitive than the Investigator® kit. On average STR profiles appeared to be more balanced and average peak heights were higher when using the GlobalFiler® kit. However, the data also show that the Investigator® kit may be more tolerant to common PCR inhibitors. While both STR kits showed a decrease in alleles as the inhibitor concentration increased, more complete profiles were obtained when the Investigator® kit was used. Of the 11 bone and decomposed tissue samples tested, 8 resulted in more complete and balanced STR profiles when amplified with the GlobalFiler® kit. Copyright © 2018 Elsevier B.V. All rights reserved.

Forensic ancestry analysis with two capillary electrophoresis ancestry informative marker (AIM) panels: Results of a collaborative EDNAP exercise.

PubMed

Santos, C; Fondevila, M; Ballard, D; Banemann, R; Bento, A M; Børsting, C; Branicki, W; Brisighelli, F; Burrington, M; Capal, T; Chaitanya, L; Daniel, R; Decroyer, V; England, R; Gettings, K B; Gross, T E; Haas, C; Harteveld, J; Hoff-Olsen, P; Hoffmann, A; Kayser, M; Kohler, P; Linacre, A; Mayr-Eduardoff, M; McGovern, C; Morling, N; O'Donnell, G; Parson, W; Pascali, V L; Porto, M J; Roseth, A; Schneider, P M; Sijen, T; Stenzl, V; Court, D Syndercombe; Templeton, J E; Turanska, M; Vallone, P M; Oorschot, R A H van; Zatkalikova, L; Carracedo, Á; Phillips, C

2015-11-01

There is increasing interest in forensic ancestry tests, which are part of a growing number of DNA analyses that can enhance routine profiling by obtaining additional genetic information about unidentified DNA donors. Nearly all ancestry tests use single nucleotide polymorphisms (SNPs), but these currently rely on SNaPshot single base extension chemistry that can fail to detect mixed DNA. Insertion-deletion polymorphism (Indel) tests have been developed using dye-labeled primers that allow direct capillary electrophoresis detection of PCR products (PCR-to-CE). PCR-to-CE maintains the direct relationship between input DNA and signal strength as each marker is detected with a single dye, so mixed DNA is more reliably detected. We report the results of a collaborative inter-laboratory exercise of 19 participants (15 from the EDNAP European DNA Profiling group) that assessed a 34-plex SNP test using SNaPshot and a 46-plex Indel test using PCR-to-CE. Laboratories were asked to type five samples with different ancestries and detect an additional mixed DNA sample. Statistical inference of ancestry was made by participants using the Snipper online Bayes analysis portal plus an optional PCA module that analyzes the genotype data alongside calculation of Bayes likelihood ratios. Exercise results indicated consistent genotyping performance from both tests, reaching a particularly high level of reliability for the Indel test. SNP genotyping gave 93.5% concordance (compared to the organizing laboratory's data) that rose to 97.3% excluding one laboratory with a large number of miscalled genotypes. Indel genotyping gave a higher concordance rate of 99.8% and a reduced no-call rate compared to SNP analysis. All participants detected the mixture from their Indel peak height data and successfully assigned the correct ancestry to the other samples using Snipper, with the exception of one laboratory with SNP miscalls that incorrectly assigned ancestry of two samples and did not obtain informative likelihood ratios for a third. Therefore, successful ancestry assignments were achieved by participants in 92 of 95 Snipper analyses. This exercise demonstrates that ancestry inference tests based on binary marker sets can be readily adopted by laboratories that already have well-established CE regimes in place. The Indel test proved to be easy to use and allowed all exercise participants to detect the DNA mixture as well as achieving complete and concordant profiles in nearly all cases. Lastly, two participants successfully ran parallel next-generation sequencing analyses (each using different systems) and achieved high levels of genotyping concordance using the exercise PCR primer mixes unmodified. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Enhanced photoluminescence from single nitrogen-vacancy defects in nanodiamonds coated with phenol-ionic complexes.

PubMed

Bray, Kerem; Previdi, Rodolfo; Gibson, Brant C; Shimoni, Olga; Aharonovich, Igor

2015-03-21

Fluorescent nanodiamonds are attracting major attention in the field of bio-sensing and bio-labeling. In this work we demonstrate a robust approach to achieve an encapsulation of individual nanodiamonds with phenol-ionic complexes that enhance the photoluminescence from single nitrogen vacancy (NV) centers. We show that single NV centres in the coated nanodiamonds also exhibit shorter lifetimes, opening another channel for high resolution sensing. We propose that the nanodiamond encapsulation reduces the non-radiative decay pathways of the NV color centers. Our results provide a versatile and assessable way to enhance photoluminescence from nanodiamond defects that can be used in a variety of sensing and imaging applications.

Highly Preorganized Ligand 1,10-Phenanthroline-2,9-dicarboxylic Acid for the Selective Recovery of Uranium from Seawater in the Presence of Competing Vanadium Species

DOE PAGES

Lashley, Mark A.; Ivanov, Alexander S.; Bryantsev, Vyacheslav S.; ...

2016-09-30

Studies of the complexation of new promising ligands with uranyl (UO 2 2+) and other seawater cations can aid the development of more efficient, selective, and robust sorbents for the recovery of uranium from seawater. Here, we propose that the ligand design principles based on structural preorganization can be successfully applied to obtain a dramatic enhancement in UO 2 2+ ion binding affinity and selectivity. This concept is exemplified through the investigation of the com-plexes of UO 2 2+, VO 2+, and VO 2+ with the highly preorganized ligand PDA (1,10-phenanthroline-2,9-dicarboxylic acid) using a combination of fluores-cence and absorbance techniques,more » along with den-sity functional theory (DFT) calculations. Moreover, the measured stability constant value, log K1, of 16.5 for the UO 2 2+/PDA complex is very high compared to uranyl complexes with other dicarboxylic ligands. Moreover, PDA exhibits strong selectivity for uranyl over vanadium ions, since the determined sta-bility constant values of the PDA complexes of the vanadium ions are quite low (V(IV) log K1 = 7.4, V(V) = 7.3). Finally, the structures of the corresponding UO 2 2+, VO 2+, and VO 2+ complexes with PDA were identified by systematic DFT calculations, and helped to interpret the stronger binding affinity for uranium over the vanadium ions. Due to its high chemical stability, selectivity, and structural preor-ganization for UO 2 2+ complexation, PDA is a very promising candidate that can be potentially used in the development of novel adsorbent materials for the selective extraction of uranium from sea-water.« less

Highly Preorganized Ligand 1,10-Phenanthroline-2,9-dicarboxylic Acid for the Selective Recovery of Uranium from Seawater in the Presence of Competing Vanadium Species

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

Lashley, Mark A.; Ivanov, Alexander S.; Bryantsev, Vyacheslav S.

Studies of the complexation of new promising ligands with uranyl (UO 2 2+) and other seawater cations can aid the development of more efficient, selective, and robust sorbents for the recovery of uranium from seawater. Here, we propose that the ligand design principles based on structural preorganization can be successfully applied to obtain a dramatic enhancement in UO 2 2+ ion binding affinity and selectivity. This concept is exemplified through the investigation of the com-plexes of UO 2 2+, VO 2+, and VO 2+ with the highly preorganized ligand PDA (1,10-phenanthroline-2,9-dicarboxylic acid) using a combination of fluores-cence and absorbance techniques,more » along with den-sity functional theory (DFT) calculations. Moreover, the measured stability constant value, log K1, of 16.5 for the UO 2 2+/PDA complex is very high compared to uranyl complexes with other dicarboxylic ligands. Moreover, PDA exhibits strong selectivity for uranyl over vanadium ions, since the determined sta-bility constant values of the PDA complexes of the vanadium ions are quite low (V(IV) log K1 = 7.4, V(V) = 7.3). Finally, the structures of the corresponding UO 2 2+, VO 2+, and VO 2+ complexes with PDA were identified by systematic DFT calculations, and helped to interpret the stronger binding affinity for uranium over the vanadium ions. Due to its high chemical stability, selectivity, and structural preor-ganization for UO 2 2+ complexation, PDA is a very promising candidate that can be potentially used in the development of novel adsorbent materials for the selective extraction of uranium from sea-water.« less

Oil recovery test using bio surfactants of indigenous bacteria in variation concentration of carbon source

NASA Astrophysics Data System (ADS)

Yudono, B.; Purwaningrum, W.; Estuningsih, S. P.; Kaffah, S.

2017-05-01

Recovery tests of crude oil by using bio surfactant of indigenous bacteria Pseudomonas peli, Pseudomonas citronellolis, Burkholderia glumae and Bacillus firmus. The bio surfactants were prepared with the variation concentrations of molasses carbon source; 0, 5, 10, 15, 20, and 25 %. The results showed that 10 g samples, which concentration 18.64% TPH could be dissolved in the bio surfactant 10%. Optimally in the molasses carbon source concentrations for each bacterium at 5, 10, 20 and 15 % with oil recovery as much as 31.92, 17.65, 22.32, and 14.38 % respectively. Oil components which extracted by bio surfactant were analyzed by using GLC (Gas Liquid Chromatography). The bio surfactants of Pseudomonas peli could dissolve oil fraction temperatures; 139.85; 144.69; 149.98; 1.55.03: 174.22 °C, Pseudomonas citronellolis could dissolve oil fraction temperatures; 139.13; 142.64;147.99; 155.03; 159.85; 164.50 °C, Burkholderia glumae could dissolve oil fraction temperatures 144.69; 149.98; 155.03; 159.85; 164.50 °C, and Bacillus firmus could dissolve oil fraction temperatures; 149.98; 155.03; 158.46; 164.50 °C.

Rapid Quadrupole-Time-of-Flight Mass Spectrometry Method Quantifies Oxygen-Rich Lignin Compound in Complex Mixtures

NASA Astrophysics Data System (ADS)

Boes, Kelsey S.; Roberts, Michael S.; Vinueza, Nelson R.

2018-03-01

Complex mixture analysis is a costly and time-consuming task facing researchers with foci as varied as food science and fuel analysis. When faced with the task of quantifying oxygen-rich bio-oil molecules in a complex diesel mixture, we asked whether complex mixtures could be qualitatively and quantitatively analyzed on a single mass spectrometer with mid-range resolving power without the use of lengthy separations. To answer this question, we developed and evaluated a quantitation method that eliminated chromatography steps and expanded the use of quadrupole-time-of-flight mass spectrometry from primarily qualitative to quantitative as well. To account for mixture complexity, the method employed an ionization dopant, targeted tandem mass spectrometry, and an internal standard. This combination of three techniques achieved reliable quantitation of oxygen-rich eugenol in diesel from 300 to 2500 ng/mL with sufficient linearity (R2 = 0.97 ± 0.01) and excellent accuracy (percent error = 0% ± 5). To understand the limitations of the method, it was compared to quantitation attained on a triple quadrupole mass spectrometer, the gold standard for quantitation. The triple quadrupole quantified eugenol from 50 to 2500 ng/mL with stronger linearity (R2 = 0.996 ± 0.003) than the quadrupole-time-of-flight and comparable accuracy (percent error = 4% ± 5). This demonstrates that a quadrupole-time-of-flight can be used for not only qualitative analysis but also targeted quantitation of oxygen-rich lignin molecules in complex mixtures without extensive sample preparation. The rapid and cost-effective method presented here offers new possibilities for bio-oil research, including: (1) allowing for bio-oil studies that demand repetitive analysis as process parameters are changed and (2) making this research accessible to more laboratories. [Figure not available: see fulltext.

Rapid Quadrupole-Time-of-Flight Mass Spectrometry Method Quantifies Oxygen-Rich Lignin Compound in Complex Mixtures

NASA Astrophysics Data System (ADS)

Boes, Kelsey S.; Roberts, Michael S.; Vinueza, Nelson R.

2017-12-01

Complex mixture analysis is a costly and time-consuming task facing researchers with foci as varied as food science and fuel analysis. When faced with the task of quantifying oxygen-rich bio-oil molecules in a complex diesel mixture, we asked whether complex mixtures could be qualitatively and quantitatively analyzed on a single mass spectrometer with mid-range resolving power without the use of lengthy separations. To answer this question, we developed and evaluated a quantitation method that eliminated chromatography steps and expanded the use of quadrupole-time-of-flight mass spectrometry from primarily qualitative to quantitative as well. To account for mixture complexity, the method employed an ionization dopant, targeted tandem mass spectrometry, and an internal standard. This combination of three techniques achieved reliable quantitation of oxygen-rich eugenol in diesel from 300 to 2500 ng/mL with sufficient linearity (R2 = 0.97 ± 0.01) and excellent accuracy (percent error = 0% ± 5). To understand the limitations of the method, it was compared to quantitation attained on a triple quadrupole mass spectrometer, the gold standard for quantitation. The triple quadrupole quantified eugenol from 50 to 2500 ng/mL with stronger linearity (R2 = 0.996 ± 0.003) than the quadrupole-time-of-flight and comparable accuracy (percent error = 4% ± 5). This demonstrates that a quadrupole-time-of-flight can be used for not only qualitative analysis but also targeted quantitation of oxygen-rich lignin molecules in complex mixtures without extensive sample preparation. The rapid and cost-effective method presented here offers new possibilities for bio-oil research, including: (1) allowing for bio-oil studies that demand repetitive analysis as process parameters are changed and (2) making this research accessible to more laboratories. [Figure not available: see fulltext.

Rapid Quadrupole-Time-of-Flight Mass Spectrometry Method Quantifies Oxygen-Rich Lignin Compound in Complex Mixtures.

PubMed

Boes, Kelsey S; Roberts, Michael S; Vinueza, Nelson R

2018-03-01

Complex mixture analysis is a costly and time-consuming task facing researchers with foci as varied as food science and fuel analysis. When faced with the task of quantifying oxygen-rich bio-oil molecules in a complex diesel mixture, we asked whether complex mixtures could be qualitatively and quantitatively analyzed on a single mass spectrometer with mid-range resolving power without the use of lengthy separations. To answer this question, we developed and evaluated a quantitation method that eliminated chromatography steps and expanded the use of quadrupole-time-of-flight mass spectrometry from primarily qualitative to quantitative as well. To account for mixture complexity, the method employed an ionization dopant, targeted tandem mass spectrometry, and an internal standard. This combination of three techniques achieved reliable quantitation of oxygen-rich eugenol in diesel from 300 to 2500 ng/mL with sufficient linearity (R 2 = 0.97 ± 0.01) and excellent accuracy (percent error = 0% ± 5). To understand the limitations of the method, it was compared to quantitation attained on a triple quadrupole mass spectrometer, the gold standard for quantitation. The triple quadrupole quantified eugenol from 50 to 2500 ng/mL with stronger linearity (R 2 = 0.996 ± 0.003) than the quadrupole-time-of-flight and comparable accuracy (percent error = 4% ± 5). This demonstrates that a quadrupole-time-of-flight can be used for not only qualitative analysis but also targeted quantitation of oxygen-rich lignin molecules in complex mixtures without extensive sample preparation. The rapid and cost-effective method presented here offers new possibilities for bio-oil research, including: (1) allowing for bio-oil studies that demand repetitive analysis as process parameters are changed and (2) making this research accessible to more laboratories. Graphical Abstract ᅟ.

Glyphing Decolonial Love through Urban Flash Mobbing and "Walking with Our Sisters"

ERIC Educational Resources Information Center

Recollet, Karyn

2015-01-01

This article contributes to understanding multi-plexed Indigenous resistance through examining spatial tags. As symbolic, moving critiques, spatial tagging intervenes normative structures of settler colonialism and provides the space through which radical decolonial love can emerge. This discussion of the production of spatial glyphs has…

Structure and Properties of Intercalated Graphite Fiber-Polymer Composites.

DTIC Science & Technology

1983-07-07

resistivities of all com- nal graphite. Experimental evidence (1,2) in- plexes were determined both before and after dicated that the electrophilic N02...others show promise as fluorinating agents in chemical synthesisI21. At this point, however, so little is Known of processing parameters and long-term

An online model composition tool for system biology models

PubMed Central

2013-01-01

Background There are multiple representation formats for Systems Biology computational models, and the Systems Biology Markup Language (SBML) is one of the most widely used. SBML is used to capture, store, and distribute computational models by Systems Biology data sources (e.g., the BioModels Database) and researchers. Therefore, there is a need for all-in-one web-based solutions that support advance SBML functionalities such as uploading, editing, composing, visualizing, simulating, querying, and browsing computational models. Results We present the design and implementation of the Model Composition Tool (Interface) within the PathCase-SB (PathCase Systems Biology) web portal. The tool helps users compose systems biology models to facilitate the complex process of merging systems biology models. We also present three tools that support the model composition tool, namely, (1) Model Simulation Interface that generates a visual plot of the simulation according to user’s input, (2) iModel Tool as a platform for users to upload their own models to compose, and (3) SimCom Tool that provides a side by side comparison of models being composed in the same pathway. Finally, we provide a web site that hosts BioModels Database models and a separate web site that hosts SBML Test Suite models. Conclusions Model composition tool (and the other three tools) can be used with little or no knowledge of the SBML document structure. For this reason, students or anyone who wants to learn about systems biology will benefit from the described functionalities. SBML Test Suite models will be a nice starting point for beginners. And, for more advanced purposes, users will able to access and employ models of the BioModels Database as well. PMID:24006914

Antibodies to biotinylated red blood cells in adults and infants: improved detection, partial characterization, and dependence on red blood cell-biotin dose.

PubMed

Schmidt, Robert L; Mock, Donald M; Franco, Robert S; Cohen, Robert M; North, Anne K; Cancelas, José A; Geisen, Christof; Strauss, Ronald G; Vlaar, Alexander P; Nalbant, Demet; Widness, John A

2017-06-01

Biotin-labeled red blood cells (BioRBCs) are used for in vivo kinetic studies. Because BioRBC dosing occasionally induces antibodies, a sensitive and specific anti-BioRBC detection assay is needed. Aims were to 1) develop a gel card assay to evaluate existing, naturally occurring and BioRBC-induced plasma antibodies, 2) compare gel card and tube agglutination detection results, and 3) test for a relationship of antibody induction and BioRBC dose. Reagent BioRBCs were prepared using sulfo-NHS biotin ranging from densities 18 (BioRBC-18) to 1458 (BioRBC-1458) µg/mL RBCs. Among BioRBC-exposed subjects, gel card and tube agglutination results were concordant in 21 of 22 adults and all 19 infant plasma samples. Gel card antibody detection sensitivity was more than 10-fold greater than tube agglutination. Twelve to 16 weeks after BioRBC exposure, induced anti-antibodies were detected by gel card in three of 26 adults (12%) at reagent densities BioRBC-256 or less, but in none of 41 infants. Importantly, induced anti-BioRBC antibodies were associated with higher BioRBC dose (p = 0.008); no antibodies were detected in 18 subjects who received BioRBC doses less than or equal to BioRBC-18. For noninduced BioRBC antibodies, six of 1125 naïve adults (0.3%) and none of 46 naïve infants demonstrated existing anti-BioRBC antibodies using reagent BioRBC-140 or -162. Existing anti-BioRBCs were all neutralized by biotin compounds, while induced antibodies were not. The gel card assay is more sensitive than the tube agglutination assay. We recommend reagent BioRBC-256 for identifying anti-BioRBCs. Use of a low total RBC biotin label dose (≤ BioRBC-18) may minimize antibody induction. © 2017 AABB.

Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area.

PubMed

Nakano, Kazuma; Shiroma, Akino; Shimoji, Makiko; Tamotsu, Hinako; Ashimine, Noriko; Ohki, Shun; Shinzato, Misuzu; Minami, Maiko; Nakanishi, Tetsuhiro; Teruya, Kuniko; Satou, Kazuhito; Hirano, Takashi

2017-07-01

PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II's sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions. Moreover, PacBio RS II is ideal for whole genome sequencing, targeted sequencing, complex population analysis, RNA sequencing, and epigenetics characterization. With PacBio RS II, we have sequenced and analyzed the genomes of many species, from viruses to humans. Herein, we summarize and review some of our key genome sequencing projects, including full-length viral sequencing, complete bacterial genome and almost-complete plant genome assemblies, and long amplicon sequencing of a disease-associated gene region. We believe that PacBio RS II is not only an effective tool for use in the basic biological sciences but also in the medical/clinical setting.

Analytical considerations and dimensionless analysis for a description of particle interactions in high pressure processes

NASA Astrophysics Data System (ADS)

Rauh, Cornelia; Delgado, Antonio

2010-12-01

High pressures of up to several hundreds of MPa are utilized in a wide range of applications in chemical, bio-, and food engineering, aiming at selective control of (bio-)chemical reactions. Non-uniformity of process conditions may threaten the safety and quality of the resulting products because processing conditions such as pressure, temperature, and treatment history are crucial for the course of (bio-)chemical reactions. Therefore, thermofluid-dynamical phenomena during the high pressure process have to be examined, and numerical tools to predict process uniformity and to optimize the processes have to be developed. Recently applied mathematical models and numerical simulations of laboratory and industrial scale high pressure processes investigating the mentioned crucial phenomena are based on continuum balancing models of thermofluid dynamics. Nevertheless, biological systems are complex fluids containing the relevant (bio-)chemical compounds (enzymes and microorganisms). These compounds are particles that interact with the surrounding medium and between each other. This contribution deals with thermofluid-dynamical interactions of the relevant particulate (bio-)chemical compounds (enzymes and microorganisms) with the surrounding fluid. By consideration of characteristic time and length scales and particle forces, the motion of the (bio-)chemical compounds is characterized.

Bio-oil production from fast pyrolysis of waste furniture sawdust in a fluidized bed.

PubMed

Heo, Hyeon Su; Park, Hyun Ju; Park, Young-Kwon; Ryu, Changkook; Suh, Dong Jin; Suh, Young-Woong; Yim, Jin-Heong; Kim, Seung-Soo

2010-01-01

The amount of waste furniture generated in Korea was over 2.4 million tons in the past 3 years, which can be used for renewable energy or fuel feedstock production. Fast pyrolysis is available for thermo-chemical conversion of the waste wood mostly into bio-oil. In this work, fast pyrolysis of waste furniture sawdust was investigated under various reaction conditions (pyrolysis temperature, particle size, feed rate and flow rate of fluidizing medium) in a fluidized-bed reactor. The optimal pyrolysis temperature for increased yields of bio-oil was 450 degrees C. Excessively smaller or larger feed size negatively affected the production of bio-oil. Higher flow and feeding rates were more effective for the production of bio-oil, but did not greatly affect the bio-oil yields within the tested ranges. The use of product gas as the fluidizing medium had a potential for increased bio-oil yields.

Biomimetic cellular metals-using hierarchical structuring for energy absorption.

PubMed

Bührig-Polaczek, A; Fleck, C; Speck, T; Schüler, P; Fischer, S F; Caliaro, M; Thielen, M

2016-07-19

Fruit walls as well as nut and seed shells typically perform a multitude of functions. One of the biologically most important functions consists in the direct or indirect protection of the seeds from mechanical damage or other negative environmental influences. This qualifies such biological structures as role models for the development of new materials and components that protect commodities and/or persons from damage caused for example by impacts due to rough handling or crashes. We were able to show how the mechanical properties of metal foam based components can be improved by altering their structure on various hierarchical levels inspired by features and principles important for the impact and/or puncture resistance of the biological role models, rather than by tuning the properties of the bulk material. For this various investigation methods have been established which combine mechanical testing with different imaging methods, as well as with in situ and ex situ mechanical testing methods. Different structural hierarchies especially important for the mechanical deformation and failure behaviour of the biological role models, pomelo fruit (Citrus maxima) and Macadamia integrifolia, were identified. They were abstracted and transferred into corresponding structural principles and thus hierarchically structured bio-inspired metal foams have been designed. A production route for metal based bio-inspired structures by investment casting was successfully established. This allows the production of complex and reliable structures, by implementing and combining different hierarchical structural elements found in the biological concept generators, such as strut design and integration of fibres, as well as by minimising casting defects. To evaluate the structural effects, similar investigation methods and mechanical tests were applied to both the biological role models and the metallic foams. As a result an even deeper quantitative understanding of the form-structure-function relationship of the biological concept generators as well as the bio-inspired metal foams was achieved, on deeper hierarchical levels and overarching different levels.

Study on EM-parameters and EM-wave absorption properties of materials with bio-flaky particles added

NASA Astrophysics Data System (ADS)

Zhang, Wenqiang; Zhang, Deyuan; Xu, Yonggang; McNaughton, Ryan

2016-01-01

Bio-flaky particles, fabricated through deposition of carbonyl iron on the surface of disk shaped diatomite, demonstrated beneficial performance on electromagnetic parameters. This paper will detail the improvements to the electromagnetic parameters and absorbing properties of traditional absorbing material generated by the addition of bio-flaky particles. Composites' electromagnetic parameters were measured using the transmission method. Calculated test results confirmed with bio-flaky particles were added, composites' permittivity increased due to the high permeability of bio-flaky particles. Secondly, the permeability of composites increased as a result of the increased volume content of iron particles. Composites with bio-flaky particles added exhibited superlative absorption properties at 0.5 mm thickness, with a maximum reflection loss of approximately -5.1 dB at 14.4 GHz.

BioVLAB-MMIA: a cloud environment for microRNA and mRNA integrated analysis (MMIA) on Amazon EC2.

PubMed

Lee, Hyungro; Yang, Youngik; Chae, Heejoon; Nam, Seungyoon; Choi, Donghoon; Tangchaisin, Patanachai; Herath, Chathura; Marru, Suresh; Nephew, Kenneth P; Kim, Sun

2012-09-01

MicroRNAs, by regulating the expression of hundreds of target genes, play critical roles in developmental biology and the etiology of numerous diseases, including cancer. As a vast amount of microRNA expression profile data are now publicly available, the integration of microRNA expression data sets with gene expression profiles is a key research problem in life science research. However, the ability to conduct genome-wide microRNA-mRNA (gene) integration currently requires sophisticated, high-end informatics tools, significant expertise in bioinformatics and computer science to carry out the complex integration analysis. In addition, increased computing infrastructure capabilities are essential in order to accommodate large data sets. In this study, we have extended the BioVLAB cloud workbench to develop an environment for the integrated analysis of microRNA and mRNA expression data, named BioVLAB-MMIA. The workbench facilitates computations on the Amazon EC2 and S3 resources orchestrated by the XBaya Workflow Suite. The advantages of BioVLAB-MMIA over the web-based MMIA system include: 1) readily expanded as new computational tools become available; 2) easily modifiable by re-configuring graphic icons in the workflow; 3) on-demand cloud computing resources can be used on an "as needed" basis; 4) distributed orchestration supports complex and long running workflows asynchronously. We believe that BioVLAB-MMIA will be an easy-to-use computing environment for researchers who plan to perform genome-wide microRNA-mRNA (gene) integrated analysis tasks.

Cancer mortality risk among biology research workers in France: first results of two retrospective cohorts studies.

PubMed

Guseva Canu, Irina; Rogel, Agnès; Samson, Eric; Benhamou, Simone; Laplanche, Agnès; Tirmarche, Margot

2008-05-01

To investigate all-cause and cancer mortality of biological research laboratories workers of the French Atomic Energy Commission (CEA) and the National Institute of Health and Medical Research (INSERM). Two cohorts, bioCEA (N = 3,509) and bioINSERM (N = 4,966) were followed from 1968 to 1994 and 1980 to 1993, respectively. The mortality of each cohort was compared with that of the French population by computation of the standardized mortality ratio (SMR) with their 90% confidence interval (90% CI). Trend and heterogeneity tests were computed in order to study SMRs variation by job characteristics. In the bioCEA cohort individual dosimetry data being available, a trend test was also computed according to ionizing radiation cumulative dose. The SMRs were significantly below one in both cohorts for all-cause mortality (bioCEA: SMR = 0.52 [0.46-0.59], bioINSERM: SMR = 0.56 [0.46-0.67]) and for all-cancer mortality (bioCEA: SMR = 0.66 [0.54-0.80], bioINSERM: SMR = 0.55 [0.39-0.75]). There were some specific cancer sites for which the SMR was higher than 1, but not significantly. In the bioCEA cohort a positive trend was observed between ionizing radiation cumulative doses and all-cause as well as all-cancer SMRs. This study on two French cohorts of biological research workers found a favorable mortality pattern. These findings are consistent with recent publications. The positive trend of cancer mortality according to ionizing radiation exposure among bioCEA cohort needs to be confirmed with more precise assessment of exposures and information on individual risk factors.

Finding complex biological relationships in recent PubMed articles using Bio-LDA.

PubMed

Wang, Huijun; Ding, Ying; Tang, Jie; Dong, Xiao; He, Bing; Qiu, Judy; Wild, David J

2011-03-23

The overwhelming amount of available scholarly literature in the life sciences poses significant challenges to scientists wishing to keep up with important developments related to their research, but also provides a useful resource for the discovery of recent information concerning genes, diseases, compounds and the interactions between them. In this paper, we describe an algorithm called Bio-LDA that uses extracted biological terminology to automatically identify latent topics, and provides a variety of measures to uncover putative relations among topics and bio-terms. Relationships identified using those approaches are combined with existing data in life science datasets to provide additional insight. Three case studies demonstrate the utility of the Bio-LDA model, including association predication, association search and connectivity map generation. This combined approach offers new opportunities for knowledge discovery in many areas of biology including target identification, lead hopping and drug repurposing.

Direct conversion of bio-ethanol to isobutene on nanosized Zn(x)Zr(y)O(z) mixed oxides with balanced acid-base sites.

PubMed

Sun, Junming; Zhu, Kake; Gao, Feng; Wang, Chongmin; Liu, Jun; Peden, Charles H F; Wang, Yong

2011-07-27

We report the design and synthesis of nanosized Zn(x)Zr(y)O(z) mixed oxides for direct and high-yield conversion of bio-ethanol to isobutene (~83%). ZnO is addded to ZrO(2) to selectively passivate zirconia's strong Lewis acidic sites and weaken Brönsted acidic sites, while simultaneously introducing basicity. As a result, the undesired reactions of bio-ethanol dehydration and acetone polymerization/coking are suppressed. Instead, a surface basic site-catalyzed ethanol dehydrogenation to acetaldehyde, acetaldehyde to acetone conversion via a complex pathway including aldol-condensation/dehydrogenation, and a Brönsted acidic site-catalyzed acetone-to-isobutene reaction pathway dominates on the nanosized Zn(x)Zr(y)O(z) mixed oxide catalyst, leading to a highly selective process for direct conversion of bio-ethanol to isobutene.

Finding Complex Biological Relationships in Recent PubMed Articles Using Bio-LDA

PubMed Central

Wang, Huijun; Ding, Ying; Tang, Jie; Dong, Xiao; He, Bing; Qiu, Judy; Wild, David J.

2011-01-01

The overwhelming amount of available scholarly literature in the life sciences poses significant challenges to scientists wishing to keep up with important developments related to their research, but also provides a useful resource for the discovery of recent information concerning genes, diseases, compounds and the interactions between them. In this paper, we describe an algorithm called Bio-LDA that uses extracted biological terminology to automatically identify latent topics, and provides a variety of measures to uncover putative relations among topics and bio-terms. Relationships identified using those approaches are combined with existing data in life science datasets to provide additional insight. Three case studies demonstrate the utility of the Bio-LDA model, including association predication, association search and connectivity map generation. This combined approach offers new opportunities for knowledge discovery in many areas of biology including target identification, lead hopping and drug repurposing. PMID:21448266

BioFET-SIM web interface: implementation and two applications.

PubMed

Hediger, Martin R; Jensen, Jan H; De Vico, Luca

2012-01-01

We present a web interface which allows us to conveniently set up calculations based on the BioFET-SIM model. With the interface, the signal of a BioFET sensor can be calculated depending on its parameters, as well as the signal dependence on pH. As an illustration, two case studies are presented. In the first case, a generic peptide with opposite charges on both ends is inverted in orientation on a semiconducting nanowire surface leading to a corresponding change in sign of the computed sensitivity of the device. In the second case, the binding of an antibody/antigen complex on the nanowire surface is studied in terms of orientation and analyte/nanowire surface distance. We demonstrate how the BioFET-SIM web interface can aid in the understanding of experimental data and postulate alternative ways of antibody/antigen orientation on the nanowire surface.

A basis for a visual language for describing, archiving and analyzing functional models of complex biological systems

PubMed Central

Cook, Daniel L; Farley, Joel F; Tapscott, Stephen J

2001-01-01

Background: We propose that a computerized, internet-based graphical description language for systems biology will be essential for describing, archiving and analyzing complex problems of biological function in health and disease. Results: We outline here a conceptual basis for designing such a language and describe BioD, a prototype language that we have used to explore the utility and feasibility of this approach to functional biology. Using example models, we demonstrate that a rather limited lexicon of icons and arrows suffices to describe complex cell-biological systems as discrete models that can be posted and linked on the internet. Conclusions: Given available computer and internet technology, BioD may be implemented as an extensible, multidisciplinary language that can be used to archive functional systems knowledge and be extended to support both qualitative and quantitative functional analysis. PMID:11305940

Biological removal of NOx from flue gas.

PubMed

Kumaraswamy, R; Muyzer, G; Kuenen, J G; Loosdrecht, M C M

2004-01-01

BioDeNOx is a novel integrated physico-chemical and biological process for the removal of nitrogen oxides (NOx) from flue gas. Due to the high temperature of flue gas the process is performed at a temperature between 50-55 degrees C. Flue gas containing CO2, O2, SO2 and NOx, is purged through Fe(II)EDTA2- containing liquid. The Fe(II)EDTA2- complex effectively binds the NOx; the bound NOx is converted into N2 in a complex reaction sequence. In this paper an overview of the potential microbial reactions in the BioDeNOx process is discussed. It is evident that though the process looks simple, due to the large number of parallel potential reactions and serial microbial conversions, it is much more complex. There is a need for a detailed investigation in order to properly understand and optimise the process.

Using AberOWL for fast and scalable reasoning over BioPortal ontologies.

PubMed

Slater, Luke; Gkoutos, Georgios V; Schofield, Paul N; Hoehndorf, Robert

2016-08-08

Reasoning over biomedical ontologies using their OWL semantics has traditionally been a challenging task due to the high theoretical complexity of OWL-based automated reasoning. As a consequence, ontology repositories, as well as most other tools utilizing ontologies, either provide access to ontologies without use of automated reasoning, or limit the number of ontologies for which automated reasoning-based access is provided. We apply the AberOWL infrastructure to provide automated reasoning-based access to all accessible and consistent ontologies in BioPortal (368 ontologies). We perform an extensive performance evaluation to determine query times, both for queries of different complexity and for queries that are performed in parallel over the ontologies. We demonstrate that, with the exception of a few ontologies, even complex and parallel queries can now be answered in milliseconds, therefore allowing automated reasoning to be used on a large scale, to run in parallel, and with rapid response times.

tmBioC: improving interoperability of text-mining tools with BioC.

PubMed

Khare, Ritu; Wei, Chih-Hsuan; Mao, Yuqing; Leaman, Robert; Lu, Zhiyong

2014-01-01

The lack of interoperability among biomedical text-mining tools is a major bottleneck in creating more complex applications. Despite the availability of numerous methods and techniques for various text-mining tasks, combining different tools requires substantial efforts and time owing to heterogeneity and variety in data formats. In response, BioC is a recent proposal that offers a minimalistic approach to tool interoperability by stipulating minimal changes to existing tools and applications. BioC is a family of XML formats that define how to present text documents and annotations, and also provides easy-to-use functions to read/write documents in the BioC format. In this study, we introduce our text-mining toolkit, which is designed to perform several challenging and significant tasks in the biomedical domain, and repackage the toolkit into BioC to enhance its interoperability. Our toolkit consists of six state-of-the-art tools for named-entity recognition, normalization and annotation (PubTator) of genes (GenNorm), diseases (DNorm), mutations (tmVar), species (SR4GN) and chemicals (tmChem). Although developed within the same group, each tool is designed to process input articles and output annotations in a different format. We modify these tools and enable them to read/write data in the proposed BioC format. We find that, using the BioC family of formats and functions, only minimal changes were required to build the newer versions of the tools. The resulting BioC wrapped toolkit, which we have named tmBioC, consists of our tools in BioC, an annotated full-text corpus in BioC, and a format detection and conversion tool. Furthermore, through participation in the 2013 BioCreative IV Interoperability Track, we empirically demonstrate that the tools in tmBioC can be more efficiently integrated with each other as well as with external tools: Our experimental results show that using BioC reduces >60% in lines of code for text-mining tool integration. The tmBioC toolkit is publicly available at http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/tmTools/. Database URL: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/tmTools/. Published by Oxford University Press 2014. This work is written by US Government employees and is in the public domain in the US.

Mechanical and optical characterization of bio-nanocomposite from pineapple leaf fiber material for food packaging

NASA Astrophysics Data System (ADS)

Nikmatin, Siti; Rudwiyanti, Jerry R.; Prasetyo, Kurnia W.; Yedi, Dwi A.

2015-01-01

The utilization of Bio-nanocomposite material that was derived from pineapple leaf fiber as filler and tapioca starch with plasticizer glycerol as a matrix for food packaging can reduce the use of plastic that usually was made from petroleum materials. It is important to develop and producethis environmental friendly plastic because of limited availability of petroleum nowadays. The process of synthesize and characterization tapioca starch with the plasticizer glycerol bionanocomposites using print method had been conducted. There were 3 samples with different filler concentration variation; 3%, 4% and 5%.The results of mechanical test from each sample showed that bio-nanocomposite with 5% filler concentration was the optimum sample with 4.6320 MPa for tensile strength test and 24.87% for the elongation test. Based on the result of optical test for each sample was gained that along with the increasing of concentration filler would make the absorbance value of the sample became decreased, bio-nanocomposite with 5% filler concentration had several peaks with low absorbance values. The first peak was in 253 nm of wavelength regionwith absorbance of 0.131%, and the second peak was in 343 nmwavelength region and absorbance was 0.087%.

Development of a Laminar Flame Test Facility for Bio-Diesel Characterization

NASA Astrophysics Data System (ADS)

Tan, Giam

2009-11-01

The relevance of applying testing standards established for diesel fuels to evaluate bio-diesel fuels motivates the design and fabrication of a vertical combustion chamber to be able to measure flame speeds of the varying strains of bio-diesel fuels and to attain more detailed kinetics information for biodiesel fuel. Extensive research is ongoing to understand the impact of fundamental combustion properties such as ignition characteristics, laminar flame speed, strain sensitivity and extinction strain rates on emission and stability characteristics of the combustor. It is envisioned that further flame studies will provide key kinetics validation data for biodiesel-like molecules -- the current test rig was developed with provisions for optical access and for future spectroscopic measurements. The current work focuses on laminar flame speeds since this important parameter contains fundamental information regarding reactivity, diffusivity, and exothermicity of the fuel mixture. It has a significant impact upon the propensity of a flame to flashback and blowoff and also serves as a key scaling parameter for other important combustion characteristics, such as the turbulent flame structure, turbulent flame speed and flame's spatial distribution etc. The flame experiments are challenging as the tested bio-fuel must be uniformly atomized and uniformly dispersed.

Standardization of chemical analytical techniques for pyrolysis bio-oil: history, challenges, and current status of methods

DOE PAGES

Ferrell, Jack R.; Olarte, Mariefel V.; Christensen, Earl D.; ...

2016-07-05

Here, we discuss the standardization of analytical techniques for pyrolysis bio-oils, including the current status of methods, and our opinions on future directions. First, the history of past standardization efforts is summarized, and both successful and unsuccessful validation of analytical techniques highlighted. The majority of analytical standardization studies to-date has tested only physical characterization techniques. In this paper, we present results from an international round robin on the validation of chemical characterization techniques for bio-oils. Techniques tested included acid number, carbonyl titrations using two different methods (one at room temperature and one at 80 °C), 31P NMR for determination ofmore » hydroxyl groups, and a quantitative gas chromatography–mass spectrometry (GC-MS) method. Both carbonyl titration and acid number methods have yielded acceptable inter-laboratory variabilities. 31P NMR produced acceptable results for aliphatic and phenolic hydroxyl groups, but not for carboxylic hydroxyl groups. As shown in previous round robins, GC-MS results were more variable. Reliable chemical characterization of bio-oils will enable upgrading research and allow for detailed comparisons of bio-oils produced at different facilities. Reliable analytics are also needed to enable an emerging bioenergy industry, as processing facilities often have different analytical needs and capabilities than research facilities. We feel that correlations in reliable characterizations of bio-oils will help strike a balance between research and industry, and will ultimately help to -determine metrics for bio-oil quality. Lastly, the standardization of additional analytical methods is needed, particularly for upgraded bio-oils.« less

Standardization of chemical analytical techniques for pyrolysis bio-oil: history, challenges, and current status of methods

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

Ferrell, Jack R.; Olarte, Mariefel V.; Christensen, Earl D.

Here, we discuss the standardization of analytical techniques for pyrolysis bio-oils, including the current status of methods, and our opinions on future directions. First, the history of past standardization efforts is summarized, and both successful and unsuccessful validation of analytical techniques highlighted. The majority of analytical standardization studies to-date has tested only physical characterization techniques. In this paper, we present results from an international round robin on the validation of chemical characterization techniques for bio-oils. Techniques tested included acid number, carbonyl titrations using two different methods (one at room temperature and one at 80 °C), 31P NMR for determination ofmore » hydroxyl groups, and a quantitative gas chromatography–mass spectrometry (GC-MS) method. Both carbonyl titration and acid number methods have yielded acceptable inter-laboratory variabilities. 31P NMR produced acceptable results for aliphatic and phenolic hydroxyl groups, but not for carboxylic hydroxyl groups. As shown in previous round robins, GC-MS results were more variable. Reliable chemical characterization of bio-oils will enable upgrading research and allow for detailed comparisons of bio-oils produced at different facilities. Reliable analytics are also needed to enable an emerging bioenergy industry, as processing facilities often have different analytical needs and capabilities than research facilities. We feel that correlations in reliable characterizations of bio-oils will help strike a balance between research and industry, and will ultimately help to -determine metrics for bio-oil quality. Lastly, the standardization of additional analytical methods is needed, particularly for upgraded bio-oils.« less

[Comparison of commercial HIV-1 viral load tests by using proficiency test results in China, 2013- 2015].

PubMed

Zhang, L; Jin, C; Jiang, Z; Tang, T; Jiang, Y; Pan, P L

2017-09-10

Objective: To compare the bio-equivalence among commercial HIV-1 viral load tests, including EasyQ HIV-1 v2.0 (EasyQ) from bioMerieux NucliSens of France; VERSANT HIV-1 RNA 3.0 assay (bDNA) from Siemens Healthcare Diagnostics of USA; COBAS AmpliPrep/COBAS TaqMan HIV-1 test (Taqman) from Roche Molecular Diagnosis of USA; Abbott Real Time HIV-1 Kit (M2000) from Abbott Molecular of USA and two domestic HIV-1 viral load test kits (domestic kit) from DaAn Gene Company of Sun Yat-Sen University and Liaoning Bio-Pharmaceutical company of Northeast pharmaceutical group, by using proficiency test results in China from 2013 to 2015. Methods: A total of 2 954 proficiency test results, obtained from 22 positive samples of 6 proficiency tests in 155 laboratories conducted by China CDC were analyzed during 2013-2015. The results from each sample were first logarithmic transformed and then grouped according to the method used, the mean value of logarithmic results was calculated. Subsequently, 22 clusters of mean values were analyzed by Bland-Altman analysis for the consistency, and linear regression analysis for the interdependency. Results: The results indicated that, by taking Taqman as the reference, EasyQ, M2000, bDNA and domestic kit had good consistency (90 % -100 % ) and interdependency. Conclusion: All the viral load tests were bio-equivalent. Moreover, according to the conversion formula derived from domestic proficiency test results, all the viral load results could be converted, which is critical for epidemiological analysis.

Vegetable Fibers for Composite Materials In Constructive Sector

NASA Astrophysics Data System (ADS)

Giglio, Francesca; Savoja, Giulia

2017-08-01

The aim of the research is to study and to test bio-mixture for laminas to use in construction field components. Composite materials are becoming more common in different sectors, but their embodied energy is an environmental problem. For this, in recent years, the researchers investigate new mixtures for composites, in particular with vegetable fibers and bio-based epoxy resin. The research carried out different laboratory tests for material and mechanical characterization, starting from the analysis of vegetable fibers, and arriving to test different kind of laminas with sundry fabrics and bio-based epoxy resin. In the most general organization of the theme, the research has the overall objective to contribute to reduce composites environmental impacts, with the promotion of local production chains about innovative materials from renewable and sustainable sources.

Enhancement of poly(3-hydroxybutyrate) thermal and processing stability using a bio-waste derived additive.

PubMed

Persico, Paola; Ambrogi, Veronica; Baroni, Antonio; Santagata, Gabriella; Carfagna, Cosimo; Malinconico, Mario; Cerruti, Pierfrancesco

2012-12-01

Poly(3-hydroxybutyrate) (PHB) is a biodegradable polymer, whose applicability is limited by its brittleness and narrow processing window. In this study a pomace extract (EP), from the bio-waste of winery industry, was used as thermal and processing stabilizer for PHB, aimed to engineer a totally bio-based system. The results showed that EP enhanced the thermal stability of PHB, which maintained high molecular weights after processing. This evidence was in agreement with the slower decrease in viscosity over time observed by rheological tests. EP also affected the melt crystallization kinetics and the overall crystallinity extent. Finally, dynamic mechanical and tensile tests showed that EP slightly improved the polymer ductility. The results are intriguing, in view of the development of sustainable alternatives to synthetic polymer additives, thus increasing the applicability of bio-based materials. Moreover, the reported results demonstrated the feasibility of the conversion of an agro-food by-product into a bio-resource in an environmentally friendly and cost-effective way. Copyright © 2012 Elsevier B.V. All rights reserved.

Sensors Based on Bio and Biomimetic Receptors in Medical Diagnostic, Environment, and Food Analysis.

PubMed

Kozitsina, Alisa N; Svalova, Tatiana S; Malysheva, Natalia N; Okhokhonin, Andrei V; Vidrevich, Marina B; Brainina, Khiena Z

2018-04-01

Analytical chemistry is now developing mainly in two areas: automation and the creation of complexes that allow, on the one hand, for simultaneously analyzing a large number of samples without the participation of an operator, and on the other, the development of portable miniature devices for personalized medicine and the monitoring of a human habitat. The sensor devices, the great majority of which are biosensors and chemical sensors, perform the role of the latter. That last line is considered in the proposed review. Attention is paid to transducers, receptors, techniques of immobilization of the receptor layer on the transducer surface, processes of signal generation and detection, and methods for increasing sensitivity and accuracy. The features of sensors based on synthetic receptors and additional components (aptamers, molecular imprinted polymers, biomimetics) are discussed. Examples of bio- and chemical sensors' application are given. Miniaturization paths, new power supply means, and wearable and printed sensors are described. Progress in this area opens a revolutionary era in the development of methods of on-site and in-situ monitoring, that is, paving the way from the "test-tube to the smartphone".

Synthetic biology routes to bio-artificial intelligence.

PubMed

Nesbeth, Darren N; Zaikin, Alexey; Saka, Yasushi; Romano, M Carmen; Giuraniuc, Claudiu V; Kanakov, Oleg; Laptyeva, Tetyana

2016-11-30

The design of synthetic gene networks (SGNs) has advanced to the extent that novel genetic circuits are now being tested for their ability to recapitulate archetypal learning behaviours first defined in the fields of machine and animal learning. Here, we discuss the biological implementation of a perceptron algorithm for linear classification of input data. An expansion of this biological design that encompasses cellular 'teachers' and 'students' is also examined. We also discuss implementation of Pavlovian associative learning using SGNs and present an example of such a scheme and in silico simulation of its performance. In addition to designed SGNs, we also consider the option to establish conditions in which a population of SGNs can evolve diversity in order to better contend with complex input data. Finally, we compare recent ethical concerns in the field of artificial intelligence (AI) and the future challenges raised by bio-artificial intelligence (BI). © 2016 The Author(s). This is an open access article published by Portland Press Limited on behalf of the Biochemical Society and distributed under the Creative Commons Attribution License 4.0 (CC BY).

Visualization, documentation, analysis, and communication of large scale gene regulatory networks

PubMed Central

Longabaugh, William J.R.; Davidson, Eric H.; Bolouri, Hamid

2009-01-01

Summary Genetic regulatory networks (GRNs) are complex, large-scale, and spatially and temporally distributed. These characteristics impose challenging demands on computational GRN modeling tools, and there is a need for custom modeling tools. In this paper, we report on our ongoing development of BioTapestry, an open source, freely available computational tool designed specifically for GRN modeling. We also outline our future development plans, and give some examples of current applications of BioTapestry. PMID:18757046

Miniaturized soft bio-hybrid robotics: a step forward into healthcare applications.

PubMed

Patino, T; Mestre, R; Sánchez, S

2016-10-07

Soft robotics is an emerging discipline that employs soft flexible materials such as fluids, gels and elastomers in order to enhance the use of robotics in healthcare applications. Compared to their rigid counterparts, soft robotic systems have flexible and rheological properties that are closely related to biological systems, thus allowing the development of adaptive and flexible interactions with complex dynamic environments. With new technologies arising in bioengineering, the integration of living cells into soft robotic systems offers the possibility of accomplishing multiple complex functions such as sensing and actuating upon external stimuli. These emerging bio-hybrid systems are showing promising outcomes and opening up new avenues in the field of soft robotics for applications in healthcare and other fields.

Catalytic Hydrogenation of Bio-Oil for Chemicals and Fuels

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

Elliott, Douglas C.

2006-02-14

The scope of work includes optimizing processing conditions and demonstrating catalyst lifetime for catalyst formulations that are readily scaleable to commercial operations. We use a bench-scale, continuous-flow, packed-bed, catalytic, tubular reactor, which can be operated in the range of 100-400 mL/hr., from 50-400 C and up to 20MPa (see Figure 1). With this unit we produce upgraded bio-oil from whole bio-oil or useful bio-oil fractions, specifically pyrolytic lignin. The product oils are fractionated, for example by distillation, for recovery of chemical product streams. Other products from our tests have been used in further testing in petroleum refining technology at UOPmore » and fractionation for product recovery in our own lab. Further scale-up of the technology is envisioned and we will carry out or support process design efforts with industrial partners, such as UOP.« less

Tumor Immunotherapy by Gene-circuit Recruited Immunomodulatory Systems (TIGRIS) for Prostate Cancer

DTIC Science & Technology

2017-09-01

Fu, X., Huang, W., and Cai, Z. (2014). Syn- thesizing AND gate genetic circuits based on CRISPR -Cas9 for identification of bladder cancer cells. Nat...and Lu, T.K. (2014). Multi- plexed and programmable regulation of gene networks with an integrated RNA and CRISPR /Cas toolkit in human cells. Mol

Multiplex Allele-Specific Amplification from Whole Blood for Detecting Multiple Polymorphisms Simultaneously

PubMed Central

Zhu, Jianjie; Chen, Lanxin; Mao, Yong; Zhou, Huan

2013-01-01

Allele-specific amplification on the basis of polymerase chain reaction (PCR) has been widely used for single-nucleotide polymorphism (SNP) genotyping. However, the extraction of PCR-compatible genomic DNA from whole blood is usually required. This process is complicated and tedious, and is prone to cause cross-contamination between samples. To facilitate direct PCR amplification from whole blood without the extraction of genomic DNA, we optimized the pH value of PCR solution and the concentrations of magnesium ions and facilitator glycerol. Then, we developed multiplex allele-specific amplifications from whole blood and applied them to a case–control study. In this study, we successfully established triplex, five-plex, and eight-plex allele-specific amplifications from whole blood for determining the distribution of genotypes and alleles of 14 polymorphisms in 97 gastric cancer patients and 141 healthy controls. Statistical analysis results showed significant association of SNPs rs9344, rs1799931, and rs1800629 with the risk of gastric cancer. This method is accurate, time-saving, cost-effective, and easy-to-do, especially suitable for clinical prediction of disease susceptibility. PMID:23072573

Multiplex analysis of pro-inflammatory cytokines in serum of Actinobacillus pleuropneumoniae-infected pigs.

PubMed

Wyns, H; Croubels, S; Vandekerckhove, M; Demeyere, K; De Backer, P; Goddeeris, B M; Meyer, E

2015-10-01

Porcine pleuropneumonia is a severe respiratory disease caused by Actinobacillus (A.) pleuropneumoniae. The aim of the present study was to analyze serum samples of A. pleuropneumoniae-infected pigs for TNF-α, IL-1β and IL-6 using a cytometric bead array (CBA) 3-plex assay and additionally for IL-6 using ELISA. The CBA 3-plex assay was successfully validated for use in serum. The limits of detection varied between 0.012 and 0.333 ng/mL, and the inter- and inter-assay coefficients of variation were <5% and <10%, respectively. Increased levels were observed for all 3 cytokines following experimental infection with A. pleuropneumoniae. Mean peak concentrations of TNF-α and IL-6 were recorded at 12h and at 10h p.i., respectively. For IL-6, similar concentration-time profiles were observed with CBA and ELISA. It is proposed that this immuno-assay can be applied for the screening of immunomodulatory properties of drugs and vaccine adjuvants in infection, inflammation and vaccination. Copyright © 2015 Elsevier Ltd. All rights reserved.

DNA Identification of Commingled Human Remains from the Cemetery Relocated by Flooding in Central Bosnia and Herzegovina.

PubMed

Čakar, Jasmina; Pilav, Amela; Džehverović, Mirela; Ahatović, Anesa; Haverić, Sanin; Ramić, Jasmin; Marjanović, Damir

2018-01-01

The floods in Bosnia and Herzegovina in May 2014 caused landslides all over the country. In the small village of Šerići, near the town of Zenica, a landslide destroyed the local cemetery, relocated graves, and commingled skeletal remains. As the use of other physical methods of identification (facial recognition, fingerprint analysis, dental analysis, etc.) was not possible, DNA analysis was applied. DNA was isolated from 20 skeletal remains (bone and tooth samples) and six reference samples (blood from living relatives) and amplified using PowerPlex ® Fusion and PowerPlex ® Y23 kits. DNA profiles were generated for all reference samples and 17 skeletal remains. A statistical analysis (calculation of paternity, maternity, and sibling indexes and matching probabilities) resulted in 10 positive identifications. In this study, 5 individuals were identified based on one reference sample. This has once again demonstrated the significance of DNA analysis in resolving the most complicated cases, such as the identification of commingled human skeletal remains. © 2017 American Academy of Forensic Sciences.

Generation of miniaturized planar ecombinant antibody arrays using a microcantilever-based printer

NASA Astrophysics Data System (ADS)

Petersson, Linn; Berthet Duroure, Nathalie; Auger, Angèle; Dexlin-Mellby, Linda; Borrebaeck, Carl AK; Ait Ikhlef, Ali; Wingren, Christer

2014-07-01

Miniaturized (Ø 10 μm), multiplexed (>5-plex), and high-density (>100 000 spots cm-2) antibody arrays will play a key role in generating protein expression profiles in health and disease. However, producing such antibody arrays is challenging, and it is the type and range of available spotters which set the stage. This pilot study explored the use of a novel microspotting tool, BioplumeTM—consisting of an array of micromachined silicon cantilevers with integrated microfluidic channels—to produce miniaturized, multiplexed, and high-density planar recombinant antibody arrays for protein expression profiling which targets crude, directly labelled serum. The results demonstrated that 16-plex recombinant antibody arrays could be produced—based on miniaturized spot features (78.5 um2, Ø 10 μm) at a 7-125-times increased spot density (250 000 spots cm-2), interfaced with a fluorescent-based read-out. This prototype platform was found to display adequate reproducibility (spot-to-spot) and an assay sensitivity in the pM range. The feasibility of the array platform for serum protein profiling was outlined.

GOTHiC, a probabilistic model to resolve complex biases and to identify real interactions in Hi-C data.

PubMed

Mifsud, Borbala; Martincorena, Inigo; Darbo, Elodie; Sugar, Robert; Schoenfelder, Stefan; Fraser, Peter; Luscombe, Nicholas M

2017-01-01

Hi-C is one of the main methods for investigating spatial co-localisation of DNA in the nucleus. However, the raw sequencing data obtained from Hi-C experiments suffer from large biases and spurious contacts, making it difficult to identify true interactions. Existing methods use complex models to account for biases and do not provide a significance threshold for detecting interactions. Here we introduce a simple binomial probabilistic model that resolves complex biases and distinguishes between true and false interactions. The model corrects biases of known and unknown origin and yields a p-value for each interaction, providing a reliable threshold based on significance. We demonstrate this experimentally by testing the method against a random ligation dataset. Our method outperforms previous methods and provides a statistical framework for further data analysis, such as comparisons of Hi-C interactions between different conditions. GOTHiC is available as a BioConductor package (http://www.bioconductor.org/packages/release/bioc/html/GOTHiC.html).

In-vitro characterization of stress corrosion cracking of aluminium-free magnesium alloys for temporary bio-implant applications.

PubMed

Choudhary, Lokesh; Singh Raman, R K; Hofstetter, Joelle; Uggowitzer, Peter J

2014-09-01

The complex interaction between physiological stresses and corrosive human body fluid may cause premature failure of metallic biomaterials due to the phenomenon of stress corrosion cracking. In this study, the susceptibility to stress corrosion cracking of biodegradable and aluminium-free magnesium alloys ZX50, WZ21 and WE43 was investigated by slow strain rate tensile testing in a simulated human body fluid. Slow strain rate tensile testing results indicated that each alloy was susceptible to stress corrosion cracking, and this was confirmed by fractographic features of transgranular and/or intergranular cracking. However, the variation in alloy susceptibility to stress corrosion cracking is explained on the basis of their electrochemical and microstructural characteristics. Copyright © 2014 Elsevier B.V. All rights reserved.

ENVIRONMENTAL TECHNOLOGY VERIFICATION: JOINT (NSF-EPA) VERIFICATION STATEMENT AND REPORT FOR THE REDUCTION OF NITROGEN IN DOMESTIC WASTEWATER FROM INDIVIDUAL HOMES, BIO-MICROBICS, INC., MODEL RETROFAST ®0.375

EPA Science Inventory

Verification testing of the Bio-Microbics RetroFAST® 0.375 System to determine the reduction of nitrogen in residential wastewater was conducted over a twelve-month period at the Mamquam Wastewater Technology Test Facility, located at the Mamquam Wastewater Treatment Plant. The R...

Programmable bio-nano-chip system for saliva diagnostics

NASA Astrophysics Data System (ADS)

Christodoulides, Nicolaos; De La Garza, Richard; Simmons, Glennon W.; McRae, Michael P.; Wong, Jorge; Kosten, Thomas R.; Miller, Craig S.; Ebersole, Jeffrey L.; McDevitt, John

2014-06-01

This manuscript describes programmable Bio-Nano-Chip (p-BNC) approach that serves as miniaturized assay platform designed for the rapid detection and quantitation of multiple analytes in biological fluids along with the specific applications in salivary diagnostics intended for the point of need (PON). Included here are oral fluid-based tests for local periodontal disease, systemic cardiac disease and multiplexed tests for drugs of abuse.

Biorefining of precious metals from wastes: an answer to manufacturing of cheap nanocatalysts for fuel cells and power generation via an integrated biorefinery?

PubMed

Yong, Ping; Mikheenko, Iryna P; Deplanche, Kevin; Redwood, Mark D; Macaskie, Lynne E

2010-12-01

Bio-manufacturing of nano-scale palladium was achieved via enzymatically-mediated deposition of Pd from solution using Desulfovibrio desulfuricans, Escherichia coli and Cupriavidus metallidurans. Dried 'Bio-Pd' materials were sintered, applied onto carbon papers and tested as anodes in a proton exchange membrane (PEM) fuel cell for power production. At a Pd(0) loading of 25% by mass the fuel cell power using Bio-Pd( D. desulfuricans ) (positive control) and Bio-Pd( E. coli ) (negative control) was ~140 and ~30 mW respectively. Bio-Pd( C. metallidurans ) was intermediate between these with a power output of ~60 mW. An engineered strain of E. coli (IC007) was previously reported to give a Bio-Pd that was >3-fold more active than Bio-Pd of the parent E. coli MC4100 (i.e. a power output of >110 mW). Using this strain, a mixed metallic catalyst was manufactured from an industrial processing waste. This 'Bio-precious metal' ('Bio-PM') gave ~68% of the power output as commercial Pd(0) and ~50% of that of Bio-Pd( D. desulfuricans ) when used as fuel cell anodic material. The results are discussed in relation to integrated bioprocessing for clean energy.

Investigation on Thermal Properties of Kenaf Fibre Reinforced Polyurethane Bio-Composites

NASA Astrophysics Data System (ADS)

Athmalingam, Mathan; Vicki, W. V.

2018-01-01

This research focuses on the effect of Kenaf fibre on thermal properties of Polyurethane (PU) reinforced kenaf bio-composites. The samples were prepared using the polymer casting method with different percentages of kenaf fibre content (5 wt%, 10 wt%, 15 wt%). The thermal properties of Kenaf/PU bio-composite are determined through the Thermogravimetric Analysis and Differential Scanning Calorimeter test. The TGA results revealed that 10 wt% Kenaf/PU bio-composite appeared to be more stable. DSC results show that the glass transition temperature (Tg) value of 10 wt% Kenaf/PU composite is significant to pure polyurethane. It can be said that the thermal stability of 10 wt% Kenaf/PU bio-composite exhibits higher thermal stability compared to other samples.

[Current and future ecological niche of Leishmaniasis (Kinetoplastida: Trypanosomatidae) in the Neotropical region].

PubMed

Moo-Llanes, David A

2016-09-01

The leishmaniasis is a complex disease system, caused by the protozoan parasite Leishmania and transmitted to humans by the vector Lutzomyia spp. Since it is listed as a neglected disease according to the World Health Organization, the aim of this study was to determine the current and future niche of cutaneous and visceral leishmaniasis in the Neotropical region. We built the ecological niche model (ENM) of cutaneous (N= 2 910 occurrences) and visceral (N= 851 occurrences) leishmaniasis using MaxEnt algorithm. Nine bioclimatic variables (BIO1, BIO4, BIO5, BIO6, BIO7, BIO12, BIO13, BIO14, BIO15 (downloaded from the Worldclim) and disease occurrences data were used for the construction of ENM for three periods (current, 2050 and 2070) and four climate change scenarios (RCP 2.6, 4.5, 6.0 y 8.5). We analyzed the number of pixels occupied, identity niche, modified niche (stable, loss, and gain) and seasonality. Our analyses indicated the expansion for cutaneous leishmaniasis (CL), a comparison for visceral leishmaniasis (VL). We rejected the null hypothesis of niche identity between CL and VL with Hellinger’s index = 0.91 (0.92-0.98) and Schoener’s Index = 0.67 (0.85-1.00) but with an overlap niche of 56.3 %. The differences between the two leishmaniasis types were detected in relation to RCP scenarios and niche shifts (area gained / loss). Seasonality was more important for CL. We provided a current picture of CL and VL distributions and the predicted distributional changes associated to different climate change scenarios for the Neotropical region. We can anticipate that increasing range is likely although it will depend locally on the future trends in weather seasonality.

Biocoder: A programming language for standardizing and automating biology protocols

PubMed Central

2010-01-01

Background Published descriptions of biology protocols are often ambiguous and incomplete, making them difficult to replicate in other laboratories. However, there is increasing benefit to formalizing the descriptions of protocols, as laboratory automation systems (such as microfluidic chips) are becoming increasingly capable of executing them. Our goal in this paper is to improve both the reproducibility and automation of biology experiments by using a programming language to express the precise series of steps taken. Results We have developed BioCoder, a C++ library that enables biologists to express the exact steps needed to execute a protocol. In addition to being suitable for automation, BioCoder converts the code into a readable, English-language description for use by biologists. We have implemented over 65 protocols in BioCoder; the most complex of these was successfully executed by a biologist in the laboratory using BioCoder as the only reference. We argue that BioCoder exposes and resolves ambiguities in existing protocols, and could provide the software foundations for future automation platforms. BioCoder is freely available for download at http://research.microsoft.com/en-us/um/india/projects/biocoder/. Conclusions BioCoder represents the first practical programming system for standardizing and automating biology protocols. Our vision is to change the way that experimental methods are communicated: rather than publishing a written account of the protocols used, researchers will simply publish the code. Our experience suggests that this practice is tractable and offers many benefits. We invite other researchers to leverage BioCoder to improve the precision and completeness of their protocols, and also to adapt and extend BioCoder to new domains. PMID:21059251

Development of Bio-Based Foams Prepared from Pbat/Pla Reinforced with Bio-Calcium Carbonate Compatibilized by Electron-Beam Radiation

NASA Astrophysics Data System (ADS)

Cardoso, Elizabeth Carvalho L.; Seixas, Marcus Vinicius S.; Wiebeck, Helio; Oliveira, René R.; Machado, Glauson Aparecido F.; Moura, Esperidiana A. B.

In Brazil, the food industry generates every year huge amounts of avian eggshell waste, an industrial byproduct containing 95% of calcium carbonate, and its disposal constitutes a serious environmental hazard. This study aims to the development of bio-foams from PBAT/PLA blends reinforced with bio-calcium carbonate from eggshells. Composites were obtained by melting extrusion process, blending PBAT/PLA (50/50) with 25% of bio-calcium carbonate, PBAT/PLA (50/45) with 25% of bio-calcium carbonate and 5 % of pre-irradiated PLA and PBAT/PLA (50/40) with 25% of bio-calcium carbonate and 10 % of pre-irradiated PLA. PLA was previously e-beam irradiated at 150kGy in air and used as compatibilizer agent. The composites were then extruded in a Rheomex 332p single special screw for foaming. Samples were submitted to Tensile and Compression tests, MFI, DSC, TGA, XRD and FEG/SEM, analyses.

Inhibitors removal from bio-oil aqueous fraction for increased ethanol production.

PubMed

Sukhbaatar, Badamkhand; Li, Qi; Wan, Caixia; Yu, Fei; Hassan, El-Barbary; Steele, Philip

2014-06-01

Utilization of 1,6-anhydro-β-d-glucopyranose (levoglucosan) present (11% w/v) in the water fraction of bio-oil for ethanol production will facilitate improvement in comprehensive utilization of total carbon in biomass. One of the major challenges for conversion of anhydrous sugars from the bio-oil water fraction to bio-ethanol is the presence of inhibitory compounds that slow or impede the microbial fermentation process. Removal of inhibitory compounds was first approached by n-butanol extraction. Optimal ratio of n-butanol and bio-oil water fraction was 1.8:1. Removal of dissolved n-butanol was completed by evaporation. Concentration of sugars in the bio-oil water fraction was performed by membrane filtration and freeze drying. Fermentability of the pyrolytic sugars was tested by fermentation of hydrolyzed sugars with Saccharomyces pastorianus lager yeast. The yield of ethanol produced from pyrolytic sugars in the bio-oil water fraction reached a maximum of 98% of the theoretical yield. Copyright © 2014 Elsevier Ltd. All rights reserved.

Quantitative investigation of free radicals in bio-oil and their potential role in condensed-phase polymerization.

PubMed

Kim, Kwang Ho; Bai, Xianglan; Cady, Sarah; Gable, Preston; Brown, Robert C

2015-03-01

We report on the quantitative analysis of free radicals in bio-oils produced from pyrolysis of cellulose, organosolv lignin, and corn stover by EPR spectroscopy. Also, we investigated their potential role in condensed-phase polymerization. Bio-oils produced from lignin and cellulose show clear evidence of homolytic cleavage reactions during pyrolysis that produce free radicals. The concentration of free radicals in lignin bio-oil was 7.5×10(20)  spin g(-1), which was 375 and 138 times higher than free-radical concentrations in bio-oil from cellulose and corn stover. Pyrolytic lignin had the highest concentration in free radicals, which could be a combination of carbon-centered (benzyl radicals) and oxygen-centered (phenoxy radicals) organic species because they are delocalized in a π system. Free-radical concentrations did not change during accelerated aging tests despite increases in molecular weight of bio-oils, suggesting that free radicals in condensed bio-oils are stable. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Serum amyloid A induction of cytokines in monocytes/macrophages and lymphocytes.

PubMed

Song, Changjie; Hsu, Kenneth; Yamen, Eric; Yan, Weixing; Fock, Jianyi; Witting, Paul K; Geczy, Carolyn L; Freedman, S Ben

2009-12-01

Serum amyloid A (SAA) is a biomarker of inflammation. Elevated blood levels in cardiovascular disease and local deposition in atheroma implies a role of SAA as a mediator rather than just a marker of inflammation. This study explored SAA-induced cytokine production and secretion by mononuclear cells. RT-PCR showed that SAA time-dependently induced cytokine mRNAs in peripheral blood mononuclear cells (PBMC) and THP-1 monocytoid cells, and dramatically increased IL-1beta, MCP-1, IL-6, IL-8, IL-10, GM-CSF, TNF, and MIP-1alpha secretion by PBMC to levels 28 to 25,000 fold above baseline, as measured with Bio-Plex kits; monocytes were the principle source. SAA induction of cytokines in monocyte-derived macrophages (MDM) was significantly higher than from monocytes from the same donors. SAA time-dependently induced transient and significant upregulation of NF-kappaB1 mRNA; inhibitor studies indicate that activation of NF-kappaB through the ERK1/2, p38 and JNK MAPKs and the PI3K pathway was involved. PBMC from 10 patients with coronary artery disease (CAD) spontaneously secreted higher levels of IL-6 and MIP-1alpha after 24h incubation than PBMC from normal controls, whereas SAA-induced levels of all cytokines were similar to controls. Aortic and coronary sinus sampling in 23 CAD patients indicated significant SAA release into the coronary circulation, not evident in 11 controls. SAA can increase monocyte and macrophage cytokine production, possibly at sites of atherosclerosis, thereby contributing to the pro-inflammatory state in coronary artery disease.

Fibromyalgia: anti-inflammatory and stress responses after acute moderate exercise.

PubMed

Bote, Maria Elena; Garcia, Juan Jose; Hinchado, Maria Dolores; Ortega, Eduardo

2013-01-01

Fibromyalgia (FM) is characterized in part by an elevated inflammatory status, and "modified exercise" is currently proposed as being a good therapeutic help for these patients. However, the mechanisms involved in the exercise-induced benefits are still poorly understood. The objective was to evaluate the effect of a single bout of moderate cycling (45 min at 55% VO2 max) on the inflammatory (serum IL-8; chemotaxis and O2 (-) production by neutrophils; and IL-1β, TNF-α, IL-6, IL-10, and IL-18 release by monocytes) and stress (cortisol; NA; and eHsp72) responses in women diagnosed with FM compared with an aged-matched control group of healthy women (HW). IL-8, NA, and eHsp72 were determined by ELISA. Cytokines released by monocytes were determined by Bio-Plex® system (LUMINEX). Cortisol was determined by electrochemoluminiscence, chemotaxis was evaluated in Boyden chambers and O2 (-) production by NBT reduction. In the FM patients, the exercise induced a decrease in the systemic concentration of IL-8, cortisol, NA, and eHsp72; as well as in the neutrophil's chemotaxis and O2 (-) production and in the inflammatory cytokine release by monocytes. This was contrary to the completely expected exercise-induced increase in all those biomarkers in HW. In conclusion, single sessions of moderate cycling can improve the inflammatory status in FM patients, reaching values close to the situation of aged-matched HW at their basal status. The neuroendocrine mechanism seems to be an exercise-induced decrease in the stress response of these patients.

Broncho-Vaxom Attenuates Allergic Airway Inflammation by Restoring GSK3β-Related T Regulatory Cell Insufficiency

PubMed Central

Zhong, Hua; Yu, Dehong; Zeng, Xianping; Deng, Mengxia; Sun, Yueqi; Wen, Weiping; Li, Huabin

2014-01-01

Background Oral administration of bacterial extracts (eg, Broncho-Vaxom (BV)) has been proposed to attenuate asthma through modulating Treg cells. However, the underlying mechanism has not been fully characterized. This study sought to assess the effects of oral administration of BV on GSK-3β expression and Treg cells in ovalbumin (OVA)-induced asthmatic mice models. Method Asthmatic mice models were established with OVA challenge and treated with oral administration of BV. Next, infiltration of inflammatory cells including eosinophil and neutrophils, mucous metaplasia, levels of Th1/Th2/Treg-typed cytokines and expression of GSK3β and Foxp3 were examined in asthmatic mice models by histological analysis, Bio-Plex and western blot, respectively. Moreover, the frequencies of Treg cells were evaluated in cultured splenocytes by flow cytometry in the presence of BV or GSK3β siRNA interference. Results We found significant decrease of infiltrated inflammatory cells in bronchoalveolar lavage fluid (BALF) in asthmatic mice models after oral administration of BV. Oral administration of BV was shown to significantly suppress mucus metaplasia, Th2-typed cytokine levels and GSK3β expression while increasing Foxp3 production in asthmatic mice models. Moreover, BV significantly enhanced GSK3β-related expansion of Treg cells in cultured spleen cells in vitro. Conclusion Our findings provide evidence that oral administration of BV is capable of attenuating airway inflammation in asthmatic mice models, which may be associated with GSK3β-related expansion of Treg cells. PMID:24667347

Reduced immune responses to purified protein derivative and Candida albicans in oral lichen planus.

PubMed

Simark-Mattsson, Charlotte; Eklund, Christina

2013-10-01

Impairment of cellular immunity is reported in lichen planus, an autoimmune disease affecting mucosae and skin. Our aim was to investigate immune responses directed against a set of microbial antigens in patients with oral lichen planus and in matched controls. Venous blood was obtained, and the mononuclear cells were enriched by density gradient centrifugation. The proliferation of peripheral blood mononuclear cells was assessed, following stimulation with purified protein derivative (PPD), Candida albicans, phytohemagglutinin or when cells were left unstimulated, after three or six days of cell culture. The production of interleukin-1ß (IL-1ß), IL-2, IL-4, IL-5, IL-6, IL-10, IL-12, IL-13, IL-17, interferon-γ (IFN-γ), tumour necrosis factor-α (TNF-α), G-CSF, GM-CSF, MCP-1, MIP-ß was assessed in supernatants using the Bio-plex(®) assay and was complemented with ELISA for selected cytokines. Patients with oral lichen planus demonstrated reduced proliferative responses against PPD (P < 0.05) and C. albicans (P < 0.05). The majority of investigated cytokines, including the pro-inflammatory, IFN-γ and TNF-α were expressed at reduced levels in PPD-stimulated supernatants from patients with oral lichen planus. Collectively, the findings suggested that memory lymphocytes from patients with oral lichen planus (OLP) may have an impaired functional ability to react against certain recall antigens, as part of a generalized response, which may reflect immune regulatory processes. Further studies are needed to clarify the mechanisms of down-regulation in OLP pathogenesis and progression. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Comparison of low-abundance biomarker levels in capillary-collected nonstimulated tears and washout tears of aqueous-deficient and normal patients.

PubMed

Guyette, Nicole; Williams, Larezia; Tran, My-Tho; Than, Tammy; Bradley, John; Kehinde, Lucy; Edwards, Clara; Beasley, Mark; Fullard, Roderick

2013-05-01

Low tear volume limits the use of nonstimulated (NS) microcapillary tear collection in aqueous-deficient (AD) patients. Adding a small amount of "washout" fluid to the eye prior to tear collection is a potentially viable alternative method for abundant proteins, but is relatively untested for low-abundance biomarkers. This study determined the feasibility of the washout (WO) method as an NS alternative for low-abundance biomarkers. NS and WO biomarker profiles were compared between AD patients and non-AD controls to determine if the two methods identify the same intergroup differences. Matching NS and WO tears were collected from 48 patients by micropipette, the WO sample after instillation of 10 μL saline. Tear cytokine levels were measured by 27-Plex Bio-Rad assay. Bland-Altman analyses for each biomarker determined the agreement between tear sample types. Patients were grouped as AD or non-AD based on Schirmer score to determine if NS profile between-group differences were preserved in WO tears. Bland-Altman plots showed good biomarker level agreement between NS and WO tears for most cytokines. Five biomarkers, among those most often cited as differing in AD dry eye, differed significantly between non-AD and AD groups in both tear types. Additional biomarker differences were seen in NS tears only. The WO tear collection method is a viable alternative to NS tears for many low-abundance biomarkers and is able to replicate major NS tear differences between dry eye groups. More subtle intergroup differences are lost in WO samples because of reduced statistical power.

Relation of sensory peripheral neuropathy in Sjögren syndrome to anti-Ro/SSA.

PubMed

Scofield, Amanda Kyle; Radfar, Lida; Ice, John A; Vista, Evan; Anaya, Juan-Manuel; Houston, Glen; Lewis, David; Stone, Donald U; Chodosh, James; Hefner, Kimberly; Lessard, Christopher J; Moser, Kathy L; Scofield, Robert Hal

2012-09-01

Sjögren syndrome is a common, chronic autoimmune disease that typically produces inflammation and poor function of the salivary and lacrimal glands. Other organs can be affected, including the nervous system. Sensory peripheral neuropathy is a common manifestation of the disease. Eight-eight patients attending a dry eyes-dry mouth clinic were diagnosed to have primary Sjögren syndrome and underwent a neurological examination. Anti-Ro (or SSA) and anti-La (or SSB) were determined using immunodiffusion as well as Inno-Lia and BioPlex ANA screen. Serum vitamin B(12) levels were determined using an enzyme-linked microtiter plate assay. Twenty-seven (31%) of the 88 patients had peripheral neuropathy as defined by loss of light touch, proprioception, or vibratory sensation. Anti-Ro and anti-La were found by immunodiffusion in 12 patients, and 8 of these 12 had neuropathy (χ(2) = 8.46, P = 0.0036, odds ratio = 6.0 compared to those without precipitating anti-Ro and anti-La). Of the 27 patients with only anti-Ro by immunodiffusion, 13 (48.1%) had neuropathy (χ(2) = 5.587, P = 0.018, compared to those without anti-Ro). There was no relationship of the other, more sensitive measures of anti-Ro and anti-La to neuropathy. In addition, we found no association of serum vitamin B(12) levels to neuropathy among these patients with Sjögren syndrome. Sensory peripheral neuropathy is common among patients with Sjögren syndrome and is associated with the presence of anti-Ro and anti-La when determined by immunodiffusion.

Biomarkers and insulin sensitivity in women with Polycystic Ovary Syndrome: Characteristics and predictive capacity.

PubMed

Cassar, Samantha; Teede, Helena J; Harrison, Cheryce L; Joham, Anju E; Moran, Lisa J; Stepto, Nigel K

2015-07-01

Polycystic ovary syndrome (PCOS) is a common endocrine disorder associated with metabolic complications. Metabolic biomarkers with roles in obesity, glycaemic control and lipid metabolism are potentially relevant in PCOS. The aim was to investigate metabolic biomarkers in lean and overweight women with and without PCOS and to determine whether any biomarker was able to predict insulin resistance in PCOS. Cross-sectional study. Eighty-four women (22 overweight and 22 lean women with PCOS, 18 overweight and 22 lean women without PCOS) were recruited from the community and categorized based on PCOS and BMI status. Primary outcomes were metabolic biomarkers [ghrelin, resistin, visfatin, glucagon-like peptide-1 (GLP-1), leptin, plasminogen activator inhibitor -1 (PAI-1), glucose-dependent insulinotropic polypeptide (GIP) and C-Peptide] measured using the Bio-Plex Pro Diabetes assay and insulin sensitivity as assessed by glucose infusion rate on euglycaemic-hyperinsulinaemic clamp. The biomarkers C-peptide, leptin, ghrelin and visfatin were different between overweight and lean women, irrespective of PCOS status. The concentration of circulating biomarkers did not differ between women with PCOS diagnosed by the Rotterdam criteria or National Institute of Health criteria. PAI-1 was the only biomarker that significantly predicted insulin resistance in both control women (P = 0.04) and women with PCOS (P = 0.01). Biomarkers associated with metabolic diseases appear more strongly associated with obesity rather than PCOS status. PAI-1 may also be a novel independent biomarker and predictor of insulin resistance in women with and without PCOS. © 2014 John Wiley & Sons Ltd.

The transport phase of pyrolytic oil exiting a fast fluidized bed reactor

NASA Astrophysics Data System (ADS)

Daugaard, Daren Einar

An unresolved and debated aspect in the fast pyrolysis of biomass is whether the bio-oil exits as a vapor or as an aerosol from the pyrolytic reactor. The determination of the bio-oil transport phase will have direct and significant impact on the design of fast pyrolysis systems. Optimization of both the removal of particulate matter and collection of bio-oil will require this information. In addition, the success of catalytic reforming of bio-oil to high-value chemicals will depend upon this transport phase. A variety of experimental techniques were used to identify the transport phase. Some tests were as simple as examining the catch of an inline filter while others attempted to deduce whether vapor or aerosol predominated by examining the pressure drop across a flow restriction. In supplementary testing, the effect of char on aerosol formation and the potential impact of cracking during direct contact filtering are evaluated. The study indicates that for pyrolysis of red oak approximately 90 wt-% of the collected bio-oil existed as a liquid aerosol. Conversely, the pyrolysis of corn starch produced bio-oil predominately in the vapor phase at the exit of the reactor. Furthermore, it was determined that the addition of char promotes the production of aerosols during pyrolysis of corn starch. Direct contact filtering of the product stream did not collect any liquids and the bio-oil yield was not significantly reduced indicating measurable cracking or coking did not occur.

Multi-Dimensional Measurement of Antibody-Mediated Heterosubtypic Immunity to Influenza.

PubMed

Wang, Jiong; Hilchey, Shannon P; Hyrien, Ollivier; Huertas, Nelson; Perry, Sheldon; Ramanunninair, Manojkumar; Bucher, Doris; Zand, Martin S

2015-01-01

The human immune response to influenza vaccination depends in part on preexisting cross-reactive (heterosubtypic) immunity from previous infection by, and/or vaccination with, influenza strains that share antigenic determinants with the vaccine strains. However, current methods for assessing heterosubtypic antibody responses against influenza, including the hemagglutination-inhibition (HAI) assay and ELISA, are time and labor intensive, and require moderate amounts of serum and reagents. To address these issues we have developed a fluorescent multiplex assay, mPlex-Flu, that rapidly and simultaneously measures strain specific IgG, IgA, and IgM antibodies against influenza hemagglutinin (HA) from multiple viral strains. We cloned, expressed and purified HA proteins from 12 influenza strains, and coupled them to multiplex beads. Assay validation showed that minimal sample volumes (<5 μl of serum) were needed, and the assay had a linear response over a four Log10 range. The assay detected nanogram levels of anti-influenza specific antibodies, had high accuracy and reproducibility, with an average percentage coefficient of variation (%CV) of 9.06 for intra-assay and 12.94 for inter-assay variability. Pre- and post-intramuscular trivalent influenza vaccination levels of virus specific Ig were consistent with HAI titer and ELISA measurements. A significant advantage of the mPLEX-Flu assay over the HAI assay is the ability to perform antigenic cartography, determining the antigenic distances between influenza HA's, without mathematical correction for HAI data issues. For validation we performed antigenic cartography on 14 different post-influenza infection ferret sera assayed against 12 different influenza HA's. Results were in good agreement with a phylogenetic tree generated from hierarchical clustering of the genomic HA sequences. This is the first report of the use of a multiplex method for antigenic cartography using ferret sera. Overall, the mPlex-Flu assay provides a powerful tool to rapidly assess the influenza antibody repertoire in large populations and to study heterosubtypic immunity induced by influenza vaccination.

Factors Predicting Risk for Antibody-mediated Rejection and Graft Loss in Highly Human Leukocyte Antigen Sensitized Patients Transplanted After Desensitization.

PubMed

Vo, Ashley A; Sinha, Aditi; Haas, Mark; Choi, Jua; Mirocha, James; Kahwaji, Joseph; Peng, Alice; Villicana, Rafael; Jordan, Stanley C

2015-07-01

Desensitization with intravenous immunoglobulin and rituximab (I+R) significantly improves transplant rates in highly sensitized patients, but antibody-mediated rejection (ABMR) remains a concern. Between July 2006 and December 2012, 226 highly sensitized patients received transplants after desensitization. Most received alemtuzumab induction and standard immunosuppression. Two groups were examined: ABMR (n = 181) and ABMR (n = 45, 20%). Risk factors for ABMR, pathology, and outcomes were assessed. Significant risks for ABMR included previous transplants and pregnancies as sensitizing events, donor-specific antibody (DSA) relative intensity scores greater than 17, presence of both class I and II DSAs at transplant and time on waitlist. The ABMR showed a significant benefit for graft survival and glomerular filtration rate at 5 years (P < 0.0001). Banff pathology characteristics for ABMR patients with or without graft loss did not differ. C4d versus C4d ABMR did not predict graft loss (P = 0.086). Thrombotic microangiopathy (TMA) significantly predicted graft failure (P = 0.045). The ABMR episodes were treated with I+R (n = 25), or, in more severe ABMR, plasma exchange (PLEX)+I+R (n = 20). Graft survival for patients treated with I+R was superior (P = 0.028). Increased mortality was seen in ABMR patients experiencing graft loss after ABMR treatment (P = 0.004). The PLEX + Eculizumab improved graft survival for TMA patients (P = 0.036). Patients desensitized with I+R who remain ABMR have long-term graft and patient survival. The ABMR patients have significantly reduced graft survival and glomerular filtration rate at 5 years, especially TMA. Severe ABMR episodes benefit from treatment with PLEX + Eculizumab. The DSA-relative intensity scores at transplant was a strong predictor of ABMR. Donor-specific antibody avoidance and reduction strategies before transplantation are critical to avoiding ABMR and improving long-term outcomes.

Multi-Dimensional Measurement of Antibody-Mediated Heterosubtypic Immunity to Influenza

PubMed Central

Wang, Jiong; Hilchey, Shannon P.; Hyrien, Ollivier; Huertas, Nelson; Perry, Sheldon; Ramanunninair, Manojkumar; Bucher, Doris; Zand, Martin S.

2015-01-01

The human immune response to influenza vaccination depends in part on preexisting cross-reactive (heterosubtypic) immunity from previous infection by, and/or vaccination with, influenza strains that share antigenic determinants with the vaccine strains. However, current methods for assessing heterosubtypic antibody responses against influenza, including the hemagglutination-inhibition (HAI) assay and ELISA, are time and labor intensive, and require moderate amounts of serum and reagents. To address these issues we have developed a fluorescent multiplex assay, mPlex-Flu, that rapidly and simultaneously measures strain specific IgG, IgA, and IgM antibodies against influenza hemagglutinin (HA) from multiple viral strains. We cloned, expressed and purified HA proteins from 12 influenza strains, and coupled them to multiplex beads. Assay validation showed that minimal sample volumes (<5 μl of serum) were needed, and the assay had a linear response over a four Log10 range. The assay detected nanogram levels of anti-influenza specific antibodies, had high accuracy and reproducibility, with an average percentage coefficient of variation (%CV) of 9.06 for intra-assay and 12.94 for inter-assay variability. Pre- and post-intramuscular trivalent influenza vaccination levels of virus specific Ig were consistent with HAI titer and ELISA measurements. A significant advantage of the mPLEX-Flu assay over the HAI assay is the ability to perform antigenic cartography, determining the antigenic distances between influenza HA’s, without mathematical correction for HAI data issues. For validation we performed antigenic cartography on 14 different post-influenza infection ferret sera assayed against 12 different influenza HA’s. Results were in good agreement with a phylogenetic tree generated from hierarchical clustering of the genomic HA sequences. This is the first report of the use of a multiplex method for antigenic cartography using ferret sera. Overall, the mPlex-Flu assay provides a powerful tool to rapidly assess the influenza antibody repertoire in large populations and to study heterosubtypic immunity induced by influenza vaccination. PMID:26103163

Environmental Baseline Survey for Proposed Land Use Permit Modification for Expansion of the Dynamic Explosive Test Site (DETS) 9940 Main Complex Parking Lot.

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

Peek, Dennis W.

The approach was to perform a document search, supplemented by a visual site inspection, to identify potential environmental contamination associated with the property. Factors evaluated included hazardous substances; petroleum products and derivatives; environmental restoration sites; areas of concern; storage tanks; oil/water separators; grease traps; wash racks; waste tanks; pesticides; military munitions/ordnance; medical or bio-hazardous waste; radioactive waste; solid/municipal waste; indoor air quality; groundwater; wastewater treatment, collection, and disposal/discharge; drinking water quality; utilities; asbestos; polychlorinated biphenyls (PCBs); radon; lead-based paint; cultural resources; floodplains; and natural/biological resources.

Bioreactor Technology in Cardiovascular Tissue Engineering

NASA Astrophysics Data System (ADS)

Mertsching, H.; Hansmann, J.

Cardiovascular tissue engineering is a fast evolving field of biomedical science and technology to manufacture viable blood vessels, heart valves, myocar-dial substitutes and vascularised complex tissues. In consideration of the specific role of the haemodynamics of human circulation, bioreactors are a fundamental of this field. The development of perfusion bioreactor technology is a consequence of successes in extracorporeal circulation techniques, to provide an in vitro environment mimicking in vivo conditions. The bioreactor system should enable an automatic hydrodynamic regime control. Furthermore, the systematic studies regarding the cellular responses to various mechanical and biochemical cues guarantee the viability, bio-monitoring, testing, storage and transportation of the growing tissue.

PicoGreen dye as an active medium for plastic lasers

NASA Astrophysics Data System (ADS)

Pradeep, C.; Vallabhan, C. P. G.; Radhakrishnan, P.; Nampoori, V. P. N.

2015-08-01

Deoxyribonucleic acid lipid complex thin films are used as a host material for laser dyes. We tested PicoGreen dye, which is commonly used for the quantification of single and double stranded DNA, for its applicability as lasing medium. PicoGreen dye exhibits enhanced fluorescence on intercalation with DNA. This enormous fluorescence emission is amplified in a planar microcavity to achieve yellow lasing. Here the role of DNA is not only a host medium, but also as a fluorescence dequencher. With the obtained results we have ample reasons to propose PicoGreen dye as a lasing medium, which can lead to the development of DNA based bio-lasers.

Ultra-high performance supercritical fluid chromatography hyphenated to atmospheric pressure chemical ionization high resolution mass spectrometry for the characterization of fast pyrolysis bio-oils.

PubMed

Crepier, Julien; Le Masle, Agnès; Charon, Nadège; Albrieux, Florian; Duchene, Pascal; Heinisch, Sabine

2018-06-01

Extensive characterization of complex mixtures requires the combination of powerful analytical techniques. A Supercritical Fluid Chromatography (SFC) method was previously developed, for the specific case of fast pyrolysis bio oils, as an alternative to gas chromatography (GC and GC × GC) or liquid chromatography (LC and LC × LC), both separation methods being generally used prior to mass spectrometry (MS) for the characterization of such complex matrices. In this study we investigated the potential of SFC hyphenated to high resolution mass spectrometry (SFC-HRMS) for this characterization using Negative ion Atmospheric Pressure Chemical ionization ((-)APCI) for the ionization source. The interface between SFC and (-)APCI/HRMS was optimized from a mix of model compounds with the objective of maximizing the signal to noise ratio. The main studied parameters included both make-up flow-rate and make-up composition. A methodology for the treatment of APCI/HRMS data is proposed. This latter allowed for the identification of molecular formulae. Both SFC-APCI/HRMS method and data processing method were applied to a mixture of 36 model compounds, first analyzed alone and then spiked in a bio-oil. In both cases, 19 compounds could be detected. Among them 9 could be detected in a fast pyrolysis bio-oil by targeted analysis. The whole procedure was applied to the characterization of a bio-oil using helpful representations such as mass-plots, van Krevelen diagrams and heteroatom class distributions. Finally the results were compared with those obtained with a Fourier Transform ion-cyclotron resonance mass spectrometer (FT-ICR/MS). Copyright © 2018 Elsevier B.V. All rights reserved.

Paternity testing in case of brother-sister incest.

PubMed

Macan, Marijana; Uvodić, Petra; Botica, Vladimir

2003-06-01

We performed a paternity test in a case of incest between brother and sister. DNA from blood samples of the alleged parents and their two children was obtained with Chelex DNA extraction method and quantified with Applied Biosystems QuantiBlot quantitation kit. Polymerase chain reaction (PCR) amplification of DNA samples was performed with AmpFlSTR SGM Plus PCR amplification kit and GenePrint PowerPlex PCR amplification kit. The amplified products were separated and detected by using the Perkin Elmer's ABI PRISM trade mark 310 Genetic Analyser. DNA and data analysis of 17 loci and Amelogenin confirmed the suspicion of brother-sister incest. Since both children had inherited all of the obligate alleles from the alleged father, we could confirm with certainty of 99.999999% that the oldest brother in the family was the biological father of both children. Calculated data showed that even in a case of brother-sister incest, paternity could be proved by the analysis of Amelogenin and 17 DNA loci.

Demise of Polymerase Chain Reaction/Electrospray Ionization-Mass Spectrometry as an Infectious Diseases Diagnostic Tool.

PubMed

Özenci, Volkan; Patel, Robin; Ullberg, Måns; Strålin, Kristoffer

2018-01-18

Although there are several US Food and Drug Administration (FDA)-approved/cleared molecular microbiology diagnostics for direct analysis of patient samples, all are single target or panel-based tests. There is no FDA-approved/cleared diagnostic for broad microbial detection. Polymerase chain reaction (PCR)/electrospray ionization-mass spectrometry (PCR/ESI-MS), commercialized as the IRIDICA system (Abbott) and formerly PLEX-ID, had been under development for over a decade and had become CE-marked and commercially available in Europe in 2014. Capable of detecting a large number of microorganisms, it was under review at the FDA when, in April 2017, Abbott discontinued it. This turn of events represents not only the loss of a potential diagnostic tool for infectious diseases but may be a harbinger of similar situations with other emerging and expensive microbial diagnostics, especially genomic tests. © The Author(s) 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

NETTAB 2012 on "Integrated Bio-Search"

PubMed Central

2014-01-01

The NETTAB 2012 workshop, held in Como on November 14-16, 2012, was devoted to "Integrated Bio-Search", that is to technologies, methods, architectures, systems and applications for searching, retrieving, integrating and analyzing data, information, and knowledge with the aim of answering complex bio-medical-molecular questions, i.e. some of the most challenging issues in bioinformatics today. It brought together about 80 researchers working in the field of Bioinformatics, Computational Biology, Biology, Computer Science and Engineering. More than 50 scientific contributions, including keynote and tutorial talks, oral communications, posters and software demonstrations, were presented at the workshop. This preface provides a brief overview of the workshop and shortly introduces the peer-reviewed manuscripts that were accepted for publication in this Supplement. PMID:24564635

Bio-chemo-mechanics of thoracic aortic aneurysms.

PubMed

Wagenseil, Jessica E

2018-03-01

Most thoracic aortic aneurysms (TAAs) occur in the ascending aorta. This review focuses on the unique bio-chemo-mechanical environment that makes the ascending aorta susceptible to TAA. The environment includes solid mechanics, fluid mechanics, cell phenotype, and extracellular matrix composition. Advances in solid mechanics include quantification of biaxial deformation and complex failure behavior of the TAA wall. Advances in fluid mechanics include imaging and modeling of hemodynamics that may lead to TAA formation. For cell phenotype, studies demonstrate changes in cell contractility that may serve to sense mechanical changes and transduce chemical signals. Studies on matrix defects highlight the multi-factorial nature of the disease. We conclude that future work should integrate the effects of bio-chemo-mechanical factors for improved TAA treatment.

Simultaneous assessment of iodine, iron, vitamin A, malarial antigenemia, and inflammation status biomarkers via a multiplex immunoassay method on a population of pregnant women from Niger.

PubMed

Brindle, Eleanor; Lillis, Lorraine; Barney, Rebecca; Hess, Sonja Y; Wessells, K Ryan; Ouédraogo, Césaire T; Stinca, Sara; Kalnoky, Michael; Peck, Roger; Tyler, Abby; Lyman, Christopher; Boyle, David S

2017-01-01

Deficiencies of vitamin A, iron, and iodine are major public health concerns in many low- and middle-income countries, but information on their status in populations is often lacking due to high costs and logistical challenges associated with assessing micronutrient status. Accurate, user-friendly, and low-cost analytical tools are needed to allow large-scale population surveys on micronutrient status. We present the expansion of a 7-plex protein microarray tool for the simultaneous measurement of up to seven biomarkers with relevance to the assessment of the key micronutrients iron, iodine, and vitamin A, and inflammation and malaria biomarkers: α-1-acid glycoprotein, C-reactive protein, ferritin, retinol binding protein 4, soluble transferrin receptor, thyroglobulin, and histidine-rich protein II. Assay performance was assessed using international reference standards and then verified by comparing the multiplexed and conventional immunoassay results on a training panel of plasma samples collected from US adults. These data were used to assign nominal concentrations to the calibrators of the assay to further improve performance which was then assessed by interrogating plasma samples from a cohort of pregnant women from Niger. The correlation between assays for each biomarker measured from this cohort was typically good, with the exception of thyroglobulin, and the sensitivity ranged from 74% to 93%, and specificity from 81% to 98%. The 7-Plex micronutrient assay has the potential for use as an affordable tool for population surveillance of vitamin A, iron, and iodine deficiencies as well as falciparum malarial parasitemia infectivity and inflammation. The assay is easy-to-use, requires minimal sample volume, and is scalable, rapid, and accurate-needing only a low-cost reader and basic equipment present in most reference laboratory settings and so may be employed by low and middle income countries for micronutrient surveillance to inform on status in key populations. Micronutrient deficiencies including iron, iodine, and vitamin A affect a significant portion of the world's population. Efforts to assess the prevalence of these deficiencies in vulnerable populations are challenging, partly due to measurement tools that are inadequate for assessing multiple micronutrients in large-scale population surveys. We have developed a 7-plex immunoassay for the simultaneous measurement of seven biomarkers relevant to assessing iodine, iron, and vitamin A status, inflammation and Plasmodium falciparum parasitemia by measuring levels of thyroglobulin, ferritin, soluble transferrin receptor, retinol binding protein 4, α-1-acid glycoprotein, C-reactive protein, and histidine-rich protein II. This 7-plex immunoassay technique has potential as a rapid and effective tool for use in large-scale surveys and assessments of nutrition intervention programs in low- and middle-income countries.

Assessment of Human Lung Macrophages After Exposure to Multi-Walled Carbon Nanotubes. Part 1. Cytotoxicity

DTIC Science & Technology

2011-01-01

animals) to gain a better understanding between their physicochemical properties and bio -effects. Keywords: U937 Cell, MWNTs, MWNT-COOH, ROS. 1...complex (i.e., cells vs. whole animals) to gain a better understanding between their physicochemical properties and bio -effects. 4. MATERIAL AND METHODS...Roach, G. A. M. Reynolds, and T. R. Webb, Tox. Sci. 77, 117 (2004). 3. C. W. Lam, J. T. James , R. McCluskey, and R. L. Hunter, Toxicol. Lett. 77, 126

Bio-Orthogonal Mediated Nucleic Acid Transfection of Cells via Cell Surface Engineering.

PubMed

O'Brien, Paul J; Elahipanah, Sina; Rogozhnikov, Dmitry; Yousaf, Muhammad N

2017-05-24

The efficient delivery of foreign nucleic acids (transfection) into cells is a critical tool for fundamental biomedical research and a pillar of several biotechnology industries. There are currently three main strategies for transfection including reagent, instrument, and viral based methods. Each technology has significantly advanced cell transfection; however, reagent based methods have captured the majority of the transfection market due to their relatively low cost and ease of use. This general method relies on the efficient packaging of a reagent with nucleic acids to form a stable complex that is subsequently associated and delivered to cells via nonspecific electrostatic targeting. Reagent transfection methods generally use various polyamine cationic type molecules to condense with negatively charged nucleic acids into a highly positively charged complex, which is subsequently delivered to negatively charged cells in culture for association, internalization, release, and expression. Although this appears to be a straightforward procedure, there are several major issues including toxicity, low efficiency, sorting of viable transfected from nontransfected cells, and limited scope of transfectable cell types. Herein, we report a new strategy (SnapFect) for nucleic acid transfection to cells that does not rely on electrostatic interactions but instead uses an integrated approach combining bio-orthogonal liposome fusion, click chemistry, and cell surface engineering. We show that a target cell population is rapidly and efficiently engineered to present a bio-orthogonal functional group on its cell surface through nanoparticle liposome delivery and fusion. A complementary bio-orthogonal nucleic acid complex is then formed and delivered to which chemoselective click chemistry induced transfection occurs to the primed cell. This new strategy requires minimal time, steps, and reagents and leads to superior transfection results for a broad range of cell types. Moreover the transfection is efficient with high cell viability and does not require a postsorting step to separate transfected from nontransfected cells in the cell population. We also show for the first time a precision transfection strategy where a single cell type in a coculture is target transfected via bio-orthogonal click chemistry.

Visual detection of nucleic acids based on Mie scattering and the magnetophoretic effect.

PubMed

Zhao, Zichen; Chen, Shan; Ho, John Kin Lim; Chieng, Ching-Chang; Chen, Ting-Hsuan

2015-12-07

Visual detection of nucleic acid biomarkers is a simple and convenient approach to point-of-care applications. However, issues of sensitivity and the handling of complex bio-fluids have posed challenges. Here we report on a visual method detecting nucleic acids using Mie scattering of polystyrene microparticles and the magnetophoretic effect. Magnetic microparticles (MMPs) and polystyrene microparticles (PMPs) were surface-functionalised with oligonucleotide probes, which can hybridise with target oligonucleotides in juxtaposition and lead to the formation of MMPs-targets-PMPs sandwich structures. Using an externally applied magnetic field, the magnetophoretic effect attracts the sandwich structure to the sidewall, which reduces the suspended PMPs and leads to a change in the light transmission via the Mie scattering. Based on the high extinction coefficient of the Mie scattering (∼3 orders of magnitude greater than that of the commonly used gold nanoparticles), our results showed the limit of detection to be 4 pM using a UV-Vis spectrometer or 10 pM by direct visual inspection. Meanwhile, we also demonstrated that this method is compatible with multiplex assays and detection in complex bio-fluids, such as whole blood or a pool of nucleic acids, without purification in advance. With a simplified operation procedure, low instrumentation requirement, high sensitivity and compatibility with complex bio-fluids, this method provides an ideal solution for visual detection of nucleic acids in resource-limited settings.

SOIL RX

EPA Pesticide Factsheets

Technical product bulletin: aka BIO-REGEN HYDROCARBON, this bioremediation agent (microbiological culture, nutrient additive) used in oil spill cleanups is a liquid formulation of humic acid, hydrocarbon-oxidizing bacteria, and amino acid complex.

Negated bio-events: analysis and identification

PubMed Central

2013-01-01

Background Negation occurs frequently in scientific literature, especially in biomedical literature. It has previously been reported that around 13% of sentences found in biomedical research articles contain negation. Historically, the main motivation for identifying negated events has been to ensure their exclusion from lists of extracted interactions. However, recently, there has been a growing interest in negative results, which has resulted in negation detection being identified as a key challenge in biomedical relation extraction. In this article, we focus on the problem of identifying negated bio-events, given gold standard event annotations. Results We have conducted a detailed analysis of three open access bio-event corpora containing negation information (i.e., GENIA Event, BioInfer and BioNLP’09 ST), and have identified the main types of negated bio-events. We have analysed the key aspects of a machine learning solution to the problem of detecting negated events, including selection of negation cues, feature engineering and the choice of learning algorithm. Combining the best solutions for each aspect of the problem, we propose a novel framework for the identification of negated bio-events. We have evaluated our system on each of the three open access corpora mentioned above. The performance of the system significantly surpasses the best results previously reported on the BioNLP’09 ST corpus, and achieves even better results on the GENIA Event and BioInfer corpora, both of which contain more varied and complex events. Conclusions Recently, in the field of biomedical text mining, the development and enhancement of event-based systems has received significant interest. The ability to identify negated events is a key performance element for these systems. We have conducted the first detailed study on the analysis and identification of negated bio-events. Our proposed framework can be integrated with state-of-the-art event extraction systems. The resulting systems will be able to extract bio-events with attached polarities from textual documents, which can serve as the foundation for more elaborate systems that are able to detect mutually contradicting bio-events. PMID:23323936

Assessment of geometry in 2D immune systems using high accuracy laser-based bioprinting techniques (Conference Presentation)

NASA Astrophysics Data System (ADS)

Lauzurica, Sara; Márquez, Andrés.; Molpeceres, Carlos; Notario, Laura; Gómez-Fontela, Miguel; Lauzurica, Pilar

2017-02-01

The immune system is a very complex system that comprises a network of genetic and signaling pathways subtending a network of interacting cells. The location of the cells in a network, along with the gene products they interact with, rules the behavior of the immune system. Therefore, there is a great interest in understanding properly the role of a cell in such networks to increase our knowledge of the immune system response. In order to acquire a better understanding of these processes, cell printing with high spatial resolution emerges as one of the promising approaches to organize cells in two and three-dimensional patterns to enable the study the geometry influence in these interactions. In particular, laser assisted bio-printing techniques using sub-nanosecond laser sources have better characteristics for application in this field, mainly due to its higher spatial resolution, cell viability percentage and process automation. This work presents laser assisted bio-printing of antigen-presenting cells (APCs) in two-dimensional geometries, placing cellular components on a matrix previously generated on demand, permitting to test the molecular interactions between APCs and lymphocytes; as well as the generation of two-dimensional structures designed ad hoc in order to study the mechanisms of mobilization of immune system cells. The use of laser assisted bio-printing, along with APCs and lymphocytes emulate the structure of different niches of the immune system so that we can analyse functional requirement of these interaction.

Simulating surface oil transport during the Deepwater Horizon oil spill: Experiments with the BioCast system

NASA Astrophysics Data System (ADS)

Jolliff, Jason Keith; Smith, Travis A.; Ladner, Sherwin; Arnone, Robert A.

2014-03-01

The U.S. Naval Research Laboratory (NRL) is developing nowcast/forecast software systems designed to combine satellite ocean color data streams with physical circulation models in order to produce prognostic fields of ocean surface materials. The Deepwater Horizon oil spill in the Gulf of Mexico provided a test case for the Bio-Optical Forecasting (BioCast) system to rapidly combine the latest satellite imagery of the oil slick distribution with surface circulation fields in order to produce oil slick transport scenarios and forecasts. In one such sequence of experiments, MODIS satellite true color images were combined with high-resolution ocean circulation forecasts from the Coupled Ocean-Atmosphere Mesoscale Prediction System (COAMPS®) to produce 96-h oil transport simulations. These oil forecasts predicted a major oil slick landfall at Grand Isle, Louisiana, USA that was subsequently observed. A key driver of the landfall scenario was the development of a coastal buoyancy current associated with Mississippi River Delta freshwater outflow. In another series of experiments, longer-term regional circulation model results were combined with oil slick source/sink scenarios to simulate the observed containment of surface oil within the Gulf of Mexico. Both sets of experiments underscore the importance of identifying and simulating potential hydrodynamic conduits of surface oil transport. The addition of explicit sources and sinks of surface oil concentrations provides a framework for increasingly complex oil spill modeling efforts that extend beyond horizontal trajectory analysis.

Predicting ready biodegradability of premanufacture notice chemicals.

PubMed

Boethling, Robert S; Lynch, David G; Thom, Gary C

2003-04-01

Chemical substances other than pesticides, drugs, and food additives are regulated by the U.S. Environmental Protection Agency (U.S. EPA) under the Toxic Substances Control Act (TSCA), but the United States does not require that new substances be tested automatically for such critical properties as biodegradability. The resulting lack of submitted data has fostered the development of estimation methods, and the BioWIN models for predicting biodegradability from chemical structure have played a prominent role in premanufacture notice (PMN) review. Until now, validation efforts have used only the Japanese Ministry of International Trade and Industry (MITI) test data and have not included all models. To assess BioWIN performance with PMN substances, we assembled a database of PMNs for which ready biodegradation data had been submitted over the period 1995 through 2001. The 305 PMN structures are highly varied and pose major challenges to chemical property estimation. Despite the variability of ready biodegradation tests, the use of at least six different test methods, and widely varying quality of submitted data, accuracy of four of six BioWIN models (MITI linear, MITI nonlinear, survey ultimate, survey primary) was in the 80+% range for predicting ready biodegradability. Greater accuracy (>90%) can be achieved by using model estimates only when the four models agree (true for 3/4 of the PMNs). The BioWIN linear and nonlinear probability models did not perform as well even when classification criteria were optimized. The results suggest that the MITI and survey BioWIN models are suitable for use in screening-level applications.

Ecotoxicological assessment of biosolids by microcosms.

PubMed

Groth, Vitor Avelar; Carvalho-Pereira, Ticiana; da Silva, Eduardo Mendes; Niemeyer, Júlia Carina

2016-10-01

Biosolids have been applied as soil amendments to improve and maintain the soil fertility and faster plant growth. In spite of its beneficial use, the potential risks of land disposal should be analyzed, considering potential ecological receptors in soil and water. This work describes the use of an early warning laboratory microcosm system to evaluate the integrated ecotoxicological potential of two biosolids: BIO-1 and BIO-2 (18 and 28 months after landfarming, respectively), from an effluent treatment station in a petrochemical and industrial district. The endpoints related to habitat function were: a) germination, growth and biomass of Phaseolus vulgaris; b) survival, biomass and number of cocoons of Eisenia andrei (Oligochaeta) and; c) reproduction of Folsomia candida (Collembola). The retention function was evaluated by testing the leachates using the tropical cladoceran Latonopsis australis (Cladocera) in a 48-h acute toxicity test, and growth of the aquatic plant Lemna minor in a 7-d chronic test. Tropical artificial soil (TAS) and a natural soil (NS) from the region were used as control soils. Results showed no chronic toxicity of BIO-1 and BIO-2 to the soil organisms tested, but acute toxicity of BIO-1 in the leachate for 50% of L. australis, and chronic toxicity of both biosolid leachates to L. minor (inhibition of growth rate), indicating potential risks to aquatic ecosystems. The results confirmed the ability of this microcosm system as a rapid tool to assess biosolid toxicity over time and its potential for hazardous waste characterization in environmental risk assessment, in a screening phase. Copyright © 2016 Elsevier Ltd. All rights reserved.

Optical bio-sniffer for methyl mercaptan in halitosis.

PubMed

Mitsubayashi, Kohji; Minamide, Takeshi; Otsuka, Kimio; Kudo, Hiroyuki; Saito, Hirokazu

2006-07-28

An optical bio-sniffer for methyl mercaptan (MM) one of major odorous chemicals in halitosis (bad breath) was constructed by immobilizing monoamine oxidase type A (MAO-A) onto a tip of a fiber optic oxygen sensor (od: 1.59 mm) with an oxygen sensitive ruthenium organic complex (excitation: 470 nm, fluorescent: 600 nm). A flow cell for circulating buffer solution was applied to rinse and clean the tip of the device like nasal mucosa. In order to amplify the bio-sniffer output, a substrate regeneration cycle caused by coupling MAO-A with l-ascorbic acid (AsA) as reducing reaction with reagent system was applied to the sensor system. After evaluating the sensor characteristics using a gas flow measurement system with a gas generator, the optical bio-sniffer was applied to expired gases from healthy male volunteers for halitosis analysis as a physiological application. The optical bio-sniffer was applied to detect the oxygen consumption induced by MAO-A enzymatic reaction (and AsA chemical reduction) with gaseous MM application. The bio-sniffer was calibrated against MM vapor from 8.7 to 11500 ppb with correlation coefficient of 0.977, including a MM threshold (200 ppb) of pathologic halitosis and the human sense of smell level 3.5 (10.0 ppb), with good gas-selectivity based on the MAO-A substrate specificity. As the result of the physiological application, the optical bio-sniffer could successfully monitor the MM level change in breath samples during daytime, which is consistent with the previously reported results.

Superhard Transparent Coatings

DTIC Science & Technology

1975-04-01

alcohol has OH groups and polymethacrylic acid has carboxyl COOH groups. These form a clear suspension with the sub- micron hydrophilic particles...PHOSPHORIC ACID /SILICA/PVA 38 SYSTEM 3: ALON/POLYSILICIC ACID /BORACIC ACID 38 SYSTEM 4: ALON/SILICA/CYMEL - MOH HARDNESS VS...60 POLYSILICIC ACID 60 Methods for the Preparation of a Polystllcate/ Alon Suspension 61 Compositions 62 STRETCHED PLEX 63 OPTIMUM COMPOSITIONS

Novel features and enhancements in BioBin, a tool for the biologically inspired binning and association analysis of rare variants

PubMed Central

Byrska-Bishop, Marta; Wallace, John; Frase, Alexander T; Ritchie, Marylyn D

2018-01-01

Abstract Motivation BioBin is an automated bioinformatics tool for the multi-level biological binning of sequence variants. Herein, we present a significant update to BioBin which expands the software to facilitate a comprehensive rare variant analysis and incorporates novel features and analysis enhancements. Results In BioBin 2.3, we extend our software tool by implementing statistical association testing, updating the binning algorithm, as well as incorporating novel analysis features providing for a robust, highly customizable, and unified rare variant analysis tool. Availability and implementation The BioBin software package is open source and freely available to users at http://www.ritchielab.com/software/biobin-download Contact mdritchie@geisinger.edu Supplementary information Supplementary data are available at Bioinformatics online. PMID:28968757

RTD fluxgate performance for application in magnetic label-based bioassay: preliminary results.

PubMed

Ando, B; Ascia, A; Baglio, S; Bulsara, A R; Trigona, C; In, V

2006-01-01

Magnetic bioassay is becoming of great interest in several application including magnetic separation, drug delivery, hyperthermia treatments, magnetic resonance imaging (MRI) and magnetic labelling. The latter can be used to localize bio-entities (e.g. cancer tissues) by using magnetic markers and high sensitive detectors. To this aim SQUIDs can be adopted, however this result in a quite sophisticated and complex method involving high cost and complex set-up. In this paper, the possibility to adopt RTD fluxgate magnetometers as alternative low cost solution to perform magnetic bio-sensing is investigated. Some experimental results are shown that encourage to pursue this approach in order to obtain simple devices that can detect a certain number of magnetic particles accumulated onto a small surface such to be useful for diagnosis purposes.

Bio-Photoelectrochemical Solar Cells Incorporating Reaction Center and Reaction Center Plus Light Harvesting Complexes

NASA Astrophysics Data System (ADS)

Yaghoubi, Houman

Harvesting solar energy can potentially be a promising solution to the energy crisis now and in the future. However, material and processing costs continue to be the most important limitations for the commercial devices. A key solution to these problems might lie within the development of bio-hybrid solar cells that seeks to mimic photosynthesis to harvest solar energy and to take advantage of the low material costs, negative carbon footprint, and material abundance. The bio-photoelectrochemical cell technologies exploit biomimetic means of energy conversion by utilizing plant-derived photosystems which can be inexpensive and ultimately the most sustainable alternative. Plants and photosynthetic bacteria harvest light, through special proteins called reaction centers (RCs), with high efficiency and convert it into electrochemical energy. In theory, photosynthetic RCs can be used in a device to harvest solar energy and generate 1.1 V open circuit voltage and ~1 mA cm-2 short circuit photocurrent. Considering the nearly perfect quantum yield of photo-induced charge separation, efficiency of a protein-based solar cell might exceed 20%. In practice, the efficiency of fabricated devices has been limited mainly due to the challenges in the electron transfer between the protein complex and the device electrodes as well as limited light absorption. The overarching goal of this work is to increase the power conversion efficiency in protein-based solar cells by addressing those issues (i.e. electron transfer and light absorption). This work presents several approaches to increase the charge transfer rate between the photosynthetic RC and underlying electrode as well as increasing the light absorption to eventually enhance the external quantum efficiency (EQE) of bio-hybrid solar cells. The first approach is to decrease the electron transfer distance between one of the redox active sites in the RC and the underlying electrode by direct attachment of the of protein complex onto Au electrodes via surface exposed cysteine residues. This resulted in photocurrent densities as large as ~600 nA cm-2 while still the incident photon to generated electron quantum efficiency was as low as %3 x 10-4. 2- The second approach is to immobilize wild type RCs of Rhodobacter sphaeroides on the surface of a Au underlying electrode using self-assembled monolayers of carboxylic acid terminated oligomers and cytochrome c charge mediating layers, with a preferential orientation from the primary electron donor site. This approach resulted in EQE of up to 0.06%, which showed 200 times efficiency improvement comparing to the first approach. In the third approach, instead of isolated protein complexes, RCs plus light harvesting (LH) complexes were employed for a better photon absorption. Direct attachment of RC-LH1 complexes on Au working electrodes, resulted in 0.21% EQE which showed 3.5 times efficiency improvement over the second approach (700 times higher than the first approach). The main impact of this work is the harnessing of biological RCs for efficient energy harvesting in man-made structures. Specifically, the results in this work will advance the application of RCs in devices for energy harvesting and will enable a better understanding of bio and nanomaterial interfaces, thereby advancing the application of biological materials in electronic devices. At the end, this work offers general guidelines that can serve to improve the performance of bio-hybrid solar cells.

Biological satellite scientific devices

NASA Astrophysics Data System (ADS)

Perepech, B. L.; Rumiantsev, V. P.; Galkin, V. M.; Shakhvorostov, S. V.; Rvachev, S. S.

1991-02-01

The paper describes the NA SBS 9 systems developed for the ninth Cosmos-2044 biological test mission. The NA SBS 9 life support systems designed for monkeys and rats follow standard design of BIOS-Vivarium and BIOS-Primate units. The main features of NA SBS 9 include the use of a recently developed HF physiological data recorder Skat-3; the incorporation into BIOS-Primate of two units intended for biorhythmic studies (the BBI-Zh system for studying beetles and the VITALOG developed by NASA for studies on monkeys); and a new version of BIOS-Primate system incorporating a capacitance-link and an inductance-link temperature transmitters and a brain tissue oxygen tension control channel.

Alternative Bio-Derived JP-8 Class Fuel and JP-8 Fuel: Flame Tube Combustor Test Results Compared using a GE TAPS Injector Configuration

NASA Technical Reports Server (NTRS)

Hicks, Yolanda R.; Anderson, Robert; Tedder, Sarah

2016-01-01

This paper presents results from tests in a NASA Glenn Research Center (GRC) flame tube facility, where a bio-derived alternate fuel was compared with JP-8 for emissions and general combustion performance. A research version of General Electric Aviation (GE) TAPS injector was used for the tests. Results include 2D, planar laser-based imaging as well as basic flow visualization of the flame. Four conditions were selected that simulate various engine power conditions relevant to NASA Fundamental Aeronautics Supersonics and Environmentally Responsible Aviation Projects were tested.

The non-linear response of a muscle in transverse compression: assessment of geometry influence using a finite element model.

PubMed

Gras, Laure-Lise; Mitton, David; Crevier-Denoix, Nathalie; Laporte, Sébastien

2012-01-01

Most recent finite element models that represent muscles are generic or subject-specific models that use complex, constitutive laws. Identification of the parameters of such complex, constitutive laws could be an important limit for subject-specific approaches. The aim of this study was to assess the possibility of modelling muscle behaviour in compression with a parametric model and a simple, constitutive law. A quasi-static compression test was performed on the muscles of dogs. A parametric finite element model was designed using a linear, elastic, constitutive law. A multi-variate analysis was performed to assess the effects of geometry on muscle response. An inverse method was used to define Young's modulus. The non-linear response of the muscles was obtained using a subject-specific geometry and a linear elastic law. Thus, a simple muscle model can be used to have a bio-faithful, biomechanical response.

Medium Effects are as Important as Catalyst Design for Selectivity in Electrocatalytic Oxygen Reduction by Iron-porphyrin Complexes

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

Rigsby, Matthew L.; Wasylenko, Derek J.; Pegis, Michael L.

2015-04-08

Several substituted iron porphyrin com-plexes were evaluated for oxygen reduction reaction (ORR) electrocatalysis in different homogeneous and heterogeneous media. The selectivity for 4-electron re-duction to H2O vs. 2-electron reduction to H2O2 varies substantially from one medium to another for a given catalyst. In many cases, the influence of the medium in which the catalyst is evaluated has a larger effect on the observed selectivity than the factors attributable to chemical modification of the catalyst. For instance, introduction of potential proton relays has variable effects depending on the catalyst medium. Thus, comparisons of ORR selectivity results need to be interpreted withmore » caution, as the catalysis is a property not just of the catalyst, but also of the larger mesoscale environment be-yond the catalyst. Still, in all the direct pairwise comparisons in the same medium, the catalysts with potential proton relays have similar or better selectivity for the preferred 4e– path. This work was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences.« less

Self-assembled hierarchically structured organic-inorganic composite systems.

PubMed

Tritschler, Ulrich; Cölfen, Helmut

2016-05-13

Designing bio-inspired, multifunctional organic-inorganic composite materials is one of the most popular current research objectives. Due to the high complexity of biocomposite structures found in nacre and bone, for example, a one-pot scalable and versatile synthesis approach addressing structural key features of biominerals and affording bio-inspired, multifunctional organic-inorganic composites with advanced physical properties is highly challenging. This article reviews recent progress in synthesizing organic-inorganic composite materials via various self-assembly techniques and in this context highlights a recently developed bio-inspired synthesis concept for the fabrication of hierarchically structured, organic-inorganic composite materials. This one-step self-organization concept based on simultaneous liquid crystal formation of anisotropic inorganic nanoparticles and a functional liquid crystalline polymer turned out to be simple, fast, scalable and versatile, leading to various (multi-)functional composite materials, which exhibit hierarchical structuring over several length scales. Consequently, this synthesis approach is relevant for further progress and scientific breakthrough in the research field of bio-inspired and biomimetic materials.

A bio-enabled maximally mild layer-by-layer Kapton surface modification approach for the fabrication of all-inkjet-printed flexible electronic devices

PubMed Central

Fang, Yunnan; Hester, Jimmy G. D.; Su, Wenjing; Chow, Justin H.; Sitaraman, Suresh K.; Tentzeris, Manos M.

2016-01-01

A bio-enabled, environmentally-friendly, and maximally mild layer-by-layer approach has been developed to surface modify inherently hydrophobic Kapton HN substrates to allow for great printability of both water- and organic solvent-based inks thus facilitating the full-inkjet-printing of flexible electronic devices. Different from the traditional Kapton surface modification approaches which are structure-compromising and use harsh conditions to target, and oxidize and/or remove part of, the surface polyimide of Kapton, the present Kapton surface modification approach targeted the surface electric charges borne by its additive particles, and was not only the first to utilize environmentally-friendly clinical biomolecules to build up a thin film of protamine-heparin complex on Kapton, but also the first to be conducted under minimally destructive and maximally mild conditions. Besides, for electrically charged ink particles, the present surface modification method can enhance the uniformity of the inkjet-printed films by reducing the “coffee ring effect”. As a proof-of-concept demonstration, reduced graphene oxide-based gas sensors, which were flexible, ultra-lightweight, and miniature-sized, were fully-inkjet-printed on surface modified Kapton HN films and tested for their sensitivity to dimethyl methylphosphonate (a nerve agent simulant). Such fabricated sensors survived a Scotch-tape peel test and were found insensitive to repeated bending to a small 0.5 cm radius. PMID:28008987

A bio-enabled maximally mild layer-by-layer Kapton surface modification approach for the fabrication of all-inkjet-printed flexible electronic devices

NASA Astrophysics Data System (ADS)

Fang, Yunnan; Hester, Jimmy G. D.; Su, Wenjing; Chow, Justin H.; Sitaraman, Suresh K.; Tentzeris, Manos M.

2016-12-01

A bio-enabled, environmentally-friendly, and maximally mild layer-by-layer approach has been developed to surface modify inherently hydrophobic Kapton HN substrates to allow for great printability of both water- and organic solvent-based inks thus facilitating the full-inkjet-printing of flexible electronic devices. Different from the traditional Kapton surface modification approaches which are structure-compromising and use harsh conditions to target, and oxidize and/or remove part of, the surface polyimide of Kapton, the present Kapton surface modification approach targeted the surface electric charges borne by its additive particles, and was not only the first to utilize environmentally-friendly clinical biomolecules to build up a thin film of protamine-heparin complex on Kapton, but also the first to be conducted under minimally destructive and maximally mild conditions. Besides, for electrically charged ink particles, the present surface modification method can enhance the uniformity of the inkjet-printed films by reducing the “coffee ring effect”. As a proof-of-concept demonstration, reduced graphene oxide-based gas sensors, which were flexible, ultra-lightweight, and miniature-sized, were fully-inkjet-printed on surface modified Kapton HN films and tested for their sensitivity to dimethyl methylphosphonate (a nerve agent simulant). Such fabricated sensors survived a Scotch-tape peel test and were found insensitive to repeated bending to a small 0.5 cm radius.

Targeting of polyplex to human hepatic cells by bio-nanocapsules, hepatitis B virus surface antigen L protein particles.

PubMed

Somiya, Masaharu; Yoshimoto, Nobuo; Iijima, Masumi; Niimi, Tomoaki; Dewa, Takehisa; Jung, Joohee; Kuroda, Shun'ichi

2012-06-15

We have previously demonstrated that lipoplex, a complex of cationic liposomes and DNA, could be targeted to human hepatic cells in vitro and in vivo by conjugation with bio-nanocapsules (BNCs) comprising hepatitis B virus (HBV) surface antigen L protein particles. Because the BNC-lipoplex complexes were endowed with the human hepatic cell-specific infection machinery from HBV, the complexes showed excellent specific transfection efficiency in human hepatic cells. In this study, we have found that polyplex (a complex of polyethyleneimine (PEI) and DNA) could form stable complexes with BNCs spontaneously. The diameter and ζ-potential of BNC-polyplex complexes are about 240 nm and +3.54 mV, respectively, which make them more suitable for in vivo use than polyplex alone. BNC-polyplex complexes with an N/P ratio (the molar ratio of the amine group of PEI to the phosphate group of DNA) of 40 showed excellent transfection efficiency in human hepatic cells. When acidification of endosomes was inhibited by bafilomycin A1, the complexes showed higher transfection efficiency than polyplex itself, strongly suggesting that the complexes escaped from endosomes by both fusogenic activity of BNCs and proton sponge activity of polyplex. Furthermore, the cytotoxicity is comparable to that of polyplex of the same N/P value. Thus, BNC-polyplex complexes would be a promising gene delivery carrier for human liver-specific gene therapy. Copyright © 2012 Elsevier Ltd. All rights reserved.

Performance Assessment of the CapitalBio Mycobacterium Identification Array System for Identification of Mycobacteria

PubMed Central

Liu, Jingbo; Yan, Zihe; Han, Min; Han, Zhijun; Jin, Lingjie; Zhao, Yanlin

2012-01-01

The CapitalBio Mycobacterium identification microarray system is a rapid system for the detection of Mycobacterium tuberculosis. The performance of this system was assessed with 24 reference strains, 486 Mycobacterium tuberculosis clinical isolates, and 40 clinical samples and then compared to the “gold standard” of DNA sequencing. The CapitalBio Mycobacterium identification microarray system showed highly concordant identification results of 100% and 98.4% for Mycobacterium tuberculosis complex (MTC) and nontuberculous mycobacteria (NTM), respectively. The sensitivity and specificity of the CapitalBio Mycobacterium identification array for identification of Mycobacterium tuberculosis isolates were 99.6% and 100%, respectively, for direct detection and identification of clinical samples, and the overall sensitivity was 52.5%. It was 100% for sputum, 16.7% for pleural fluid, and 10% for bronchoalveolar lavage fluid, respectively. The total assay was completed in 6 h, including DNA extraction, PCR, and hybridization. The results of this study confirm the utility of this system for the rapid identification of mycobacteria and suggest that the CapitalBio Mycobacterium identification array is a molecular diagnostic technique with high sensitivity and specificity that has the capacity to quickly identify most mycobacteria. PMID:22090408

Bio-Inspired Assembly of Artificial Photosynthetic Antenna Complexes for Development of Nanobiodevices

DTIC Science & Technology

2011-06-24

extensively studied by ultrafast laser spectroscopy. More recently the structures of the LH2 complexes has revealed the nonameric and octameric arrangement of...Scheme 1). 4 Scheme 1. Compartimentalization of light harvesting and charge separation. The antenna complexes( LH2 ,LH1-RC) efficiently...realize various photosynthetic functions using cofactors (BChl a and carotenoid) assembled into the apoproteins (LH1 and LH2 ). The light-harvesting