Academic literature on the topic 'Biologically Relevant Analytes'
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Journal articles on the topic "Biologically Relevant Analytes"
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Wu, Luling, Qingye Yang, Liyuan Liu, Adam C. Sedgwick, Alexander J. Cresswell, Steven D. Bull, Chusen Huang, and Tony D. James. "ESIPT-based fluorescence probe for the rapid detection of hypochlorite (HOCl/ClO−)." Chemical Communications 54, no. 61 (2018): 8522–25. http://dx.doi.org/10.1039/c8cc03717e.
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Xu, Yifei, and Marco Bonizzoni. "Discrimination and Quantitation of Biologically Relevant Carboxylate Anions Using A [Dye•PAMAM] Complex." Sensors 21, no. 11 (May 24, 2021): 3637. http://dx.doi.org/10.3390/s21113637.
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Carboxylate anions are analytical targets with environmental and biological relevance, whose detection is often challenging in aqueous solutions. We describe a method for discrimination and quantitation of carboxylates in water buffered to pH 7.4 based on their differential interaction with a supramolecular fluorescent sensor, self-assembled from readily available building blocks. A fifth-generation poly(amidoamine) dendrimer (PAMAM G5), bound to organic fluorophores (calcein or pyranine) through noncovalent interactions, forms a [dye•PAMAM] complex responsive to interaction with carboxylates. The observed changes in absorbance, and in fluorescence emission and anisotropy, were interpreted through linear discriminant analysis (LDA) and principal component analysis (PCA) to differentiate 10 structurally similar carboxylates with a limit of discrimination around 100 μM. The relationship between the analytes’ chemical structures and the system’s response was also elucidated. This insight allowed us to extend the system’s capabilities to the simultaneous identification of the nature and concentration of unknown analytes, with excellent structural identification results and good concentration recovery, an uncommon feat for a pattern-based sensing system.
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Dick, Jeffrey E., Adam T. Hilterbrand, Aliaksei Boika, Jason W. Upton, and Allen J. Bard. "Electrochemical detection of a single cytomegalovirus at an ultramicroelectrode and its antibody anchoring." Proceedings of the National Academy of Sciences 112, no. 17 (April 13, 2015): 5303–8. http://dx.doi.org/10.1073/pnas.1504294112.
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We report observations of stochastic collisions of murine cytomegalovirus (MCMV) on ultramicroelectrodes (UMEs), extending the observation of discrete collision events on UMEs to biologically relevant analytes. Adsorption of an antibody specific for a virion surface glycoprotein allowed differentiation of MCMV from MCMV bound by antibody from the collision frequency decrease and current magnitudes in the electrochemical collision experiments, which shows the efficacy of the method to size viral samples. To add selectivity to the technique, interactions between MCMV, a glycoprotein-specific primary antibody to MCMV, and polystyrene bead “anchors,” which were functionalized with a secondary antibody specific to the Fc region of the primary antibody, were used to affect virus mobility. Bead aggregation was observed, and the extent of aggregation was measured using the electrochemical collision technique. Scanning electron microscopy and optical microscopy further supported aggregate shape and extent of aggregation with and without MCMV. This work extends the field of collisions to biologically relevant antigens and provides a novel foundation upon which qualitative sensor technology might be built for selective detection of viruses and other biologically relevant analytes.
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Baker, Gary A., Chase A. Munson, Eric J. Bukowski, Sheila N. Baker, and Frank V. Bright. "Assessment of One- and Two-Photon Excited Luminescence for Directly Measuring O2, pH, Na+, Mg2+, or Ca2+ in Optically Dense and Biologically Relevant Samples." Applied Spectroscopy 56, no. 4 (April 2002): 455–63. http://dx.doi.org/10.1366/0003702021955114.
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We compare the emission spectra and analytical response profiles of several semiselective luminescent probes that are commonly used to quantify nonfluorescent analytes (ruthenium(II) tris(2,2′-bipyridyl) dication, tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dication, SNARF®-1, fluorescein, Rhodol Green™, and Sodium™, Magnesium™, and Calcium Green™) when they are excited under one- and two-photon excitation conditions in water, aqueous solutions of dyes or fluorophores, undiluted mouse or human serum, human urine, and mouse whole blood. The results from this work can be summarized as follows. First, in cases where the probes possess ground states that are composed of multiple species in equilibrium (e.g., acid and base forms of a luminophore), the analyte-dependent emission spectra can be significantly different under one- and two-photon excitation conditions due to differences in the relative one- and two-photon cross-sections associated with the individual ground-state species. Second, for those probes that exhibit one- and two-photon dependent emission spectra, an assessment of the analytical response vs. target analyte concentration profiles show that the response dynamic range can be improved by up to 100 fold, but the response sensitivity can decrease by up to 25% for two- vs. one-photon excitation. Third, two-photon excited luminescence provides a means to use these semiselective luminescent probes to quantify nonfluorescent analytes directly within optically dense mixtures, including solutions of dyes, mouse or human serum, human urine, and mouse whole blood. Finally, two-photon excited luminescence allows one to quantify nonfluorescent analytes in a spatially defined manner within complex samples.
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Terán-Alcocer, Álvaro, Francisco Bravo-Plascencia, Carlos Cevallos-Morillo, and Alex Palma-Cando. "Electrochemical Sensors Based on Conducting Polymers for the Aqueous Detection of Biologically Relevant Molecules." Nanomaterials 11, no. 1 (January 19, 2021): 252. http://dx.doi.org/10.3390/nano11010252.
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Electrochemical sensors appear as low-cost, rapid, easy to use, and in situ devices for determination of diverse analytes in a liquid solution. In that context, conducting polymers are much-explored sensor building materials because of their semiconductivity, structural versatility, multiple synthetic pathways, and stability in environmental conditions. In this state-of-the-art review, synthetic processes, morphological characterization, and nanostructure formation are analyzed for relevant literature about electrochemical sensors based on conducting polymers for the determination of molecules that (i) have a fundamental role in the human body function regulation, and (ii) are considered as water emergent pollutants. Special focus is put on the different types of micro- and nanostructures generated for the polymer itself or the combination with different materials in a composite, and how the rough morphology of the conducting polymers based electrochemical sensors affect their limit of detection. Polypyrroles, polyanilines, and polythiophenes appear as the most recurrent conducting polymers for the construction of electrochemical sensors. These conducting polymers are usually built starting from bifunctional precursor monomers resulting in linear and branched polymer structures; however, opportunities for sensitivity enhancement in electrochemical sensors have been recently reported by using conjugated microporous polymers synthesized from multifunctional monomers.
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Peltomaa, Riikka, Bettina Glahn-Martínez, Elena Benito-Peña, and María Moreno-Bondi. "Optical Biosensors for Label-Free Detection of Small Molecules." Sensors 18, no. 12 (November 24, 2018): 4126. http://dx.doi.org/10.3390/s18124126.
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Label-free optical biosensors are an intriguing option for the analyses of many analytes, as they offer several advantages such as high sensitivity, direct and real-time measurement in addition to multiplexing capabilities. However, development of label-free optical biosensors for small molecules can be challenging as most of them are not naturally chromogenic or fluorescent, and in some cases, the sensor response is related to the size of the analyte. To overcome some of the limitations associated with the analysis of biologically, pharmacologically, or environmentally relevant compounds of low molecular weight, recent advances in the field have improved the detection of these analytes using outstanding methodology, instrumentation, recognition elements, or immobilization strategies. In this review, we aim to introduce some of the latest developments in the field of label-free optical biosensors with the focus on applications with novel innovations to overcome the challenges related to small molecule detection. Optical label-free methods with different transduction schemes, including evanescent wave and optical fiber sensors, surface plasmon resonance, surface-enhanced Raman spectroscopy, and interferometry, using various biorecognition elements, such as antibodies, aptamers, enzymes, and bioinspired molecularly imprinted polymers, are reviewed.
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Crapnell, Robert, Alexander Hudson, Christopher Foster, Kasper Eersels, Bart Grinsven, Thomas Cleij, Craig Banks, and Marloes Peeters. "Recent Advances in Electrosynthesized Molecularly Imprinted Polymer Sensing Platforms for Bioanalyte Detection." Sensors 19, no. 5 (March 9, 2019): 1204. http://dx.doi.org/10.3390/s19051204.
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The accurate detection of biological materials has remained at the forefront of scientific research for decades. This includes the detection of molecules, proteins, and bacteria. Biomimetic sensors look to replicate the sensitive and selective mechanisms that are found in biological systems and incorporate these properties into functional sensing platforms. Molecularly imprinted polymers (MIPs) are synthetic receptors that can form high affinity binding sites complementary to the specific analyte of interest. They utilise the shape, size, and functionality to produce sensitive and selective recognition of target analytes. One route of synthesizing MIPs is through electropolymerization, utilising predominantly constant potential methods or cyclic voltammetry. This methodology allows for the formation of a polymer directly onto the surface of a transducer. The thickness, morphology, and topography of the films can be manipulated specifically for each template. Recently, numerous reviews have been published in the production and sensing applications of MIPs; however, there are few reports on the use of electrosynthesized MIPs (eMIPs). The number of publications and citations utilising eMIPs is increasing each year, with a review produced on the topic in 2012. This review will primarily focus on advancements from 2012 in the use of eMIPs in sensing platforms for the detection of biologically relevant materials, including the development of increased polymer layer dimensions for whole bacteria detection and the use of mixed monomer compositions to increase selectivity toward analytes.
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Redy-Keisar, Orit, Einat Kisin-Finfer, Shiran Ferber, Ronit Satchi-Fainaro, and Doron Shabat. "Synthesis and use of QCy7-derived modular probes for the detection and imaging of biologically relevant analytes." Nature Protocols 9, no. 1 (December 5, 2013): 27–36. http://dx.doi.org/10.1038/nprot.2013.166.
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González-Ruiz, Víctor, Jegathalaprathaban Rajesh, Ana I. Olives, Damiano Rocchi, Jorge Gómez-Carpintero, Juan F. González, Vellaisamy Sridharan, M. Antonia Martín, and J. Carlos Menéndez. "Antioxidants as Molecular Probes: Structurally Novel Dihydro-m-Terphenyls as Turn-On Fluorescence Chemodosimeters for Biologically Relevant Oxidants." Antioxidants 9, no. 7 (July 10, 2020): 605. http://dx.doi.org/10.3390/antiox9070605.
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One interesting aspect of antioxidant organic molecules is their use as probes for the detection and quantitation of biologically relevant reactive oxidant species (ROS). In this context, a small library of dihydroterphenyl derivatives has been synthesised and studied as fluorescent chemodosimeters for detecting reactive oxygen species and hypochlorite. The fluorescence quantum yields of these molecules are negligible, while the corresponding aromatized compounds formed upon oxidation show moderate to high native fluorescence, depending on their structures. The fluorescence signal is quickly developed in the presence of trace amounts of the probe and the analytes in acetonitrile media at room temperature, with good analytical figures. ROS detection in aqueous media required incubation at 37 °C in the presence of horseradish peroxidase, and was applied to glucose quantitation by coupling glucose oxidation by O2 to fluorescence detection of H2O2. The mild reaction conditions and sensitive fluorescent response lead us to propose dihydroterphenyls with an embedded anthranilate moiety as chemosensors/chemodosimeters for ROS detection.
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Granzhan, Anton, Heiko Ihmels, and Maoqun Tian. "The benzo[b]quinolizinium ion as a water-soluble platform for the fluorimetric detection of biologically relevant analytes." Arkivoc 2015, no. 6 (December 1, 2015): 494–523. http://dx.doi.org/10.3998/ark.5550190.p009.339.
Full textDissertations / Theses on the topic "Biologically Relevant Analytes"
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Palisi, Angelica. "NMR-based metabolomic analysis of biological fluids to monitor relevant unsolved diseases." Doctoral thesis, Universita degli studi di Salerno, 2017. http://hdl.handle.net/10556/2565.
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2015 - 2016Metabolomics and metabonomics encompass the comprehensive profiling of multiple metabolite concentrations and their cellular and systemic fluctuations in response to drugs, diet, lifestyle, environment, stimuli and genetic modulations, in order to characterize the beneficial and adverse effects of such interactions. In the context of biomedical applications, metabolomics will have a preferential role with respect to the other "Omics" sciences for its ability to detect in real time the response of the organisms to pathological stressors. The application of the NMR technique for the metabolomics analysis was applied to bio-fluids deriving from populations of patients respectively affected by salivary gland tumor, antiphospholipid autoimmune syndrome and altered lipid profile. This NMR metabolomic screening was aimed i) at the definition of a metabolomic profile that may be patognomonic of the disease under scrutiny and ii) at the identification of biomarkers to be used with diagnostic and prognostic scope. In the present work, we present a NMR-based metabolomic study of saliva of patients suffering of salivary gland tumors. Our data show that individuals suffering parotid tumor have a characteristic metabolomic profile with abnormalities associated to the metabolism of acetate, alanine, lactate, methanol, phenylalanine, propionate, succinate. We have identified for the first time the metabolomic fingerprint characterizing parotid tumor patients disease having potential application to improve timely diagnosis and appropriate therapeutic approaches. Salivary gland tumor, as many other cancers, is a complex disease, resulting from an interdependent series of biochemical alterations, rather than a single disruptive event. In this case our approach aimed at the identification of a panel of metabolite markers rather than a single biomarker, will improve the sensitivity and specificity for detection. Integrating the protocols of tumor grading and histological classification. Our NMR-based metabolomic study revealed different metabolomic profiles in saliva of male patients affected by salivary gland tumors compared with the profiles of age, gender, and sampling-date matched control individuals. Our approach provide preliminary data for the identification of metabolites that can be used as metabolomics fingerprint of salivary gland tumor. Determination of metabolomics fingerprint, rather than single metabolic biomarker, may fully reflect the multifactorial nature of oncogenesis and the heterogeneity of oncogenic pathways, providing precious elements to integrate diagnostic laboratory and clinical tests. Antiphospholipid syndrome (APS) is a rheumatic inflammatory chronic autoimmune disease inducing hypercoagulable state associated with vascular thrombosis and pregnancy loss in women. Cardiac, cerebral and vascular strokes in these patients are responsible for reduction in life expectancy. Timely diagnosis and accurate monitoring of disease is decisive to improve the accuracy of therapy. In the present work, we present a NMR-based metabolomic study of blood sera of APS patients. Our data show that individuals suffering APS have a characteristic metabolomic profile with abnormalities associated to the metabolism of methyl group donors, ketone bodies and amino acids. We have identified for the first time the metabolomic fingerprint characterizing APS disease having potential application to improve APS timely diagnosis and appropriate therapeutic approaches. The first stratification of APS patients according to the gender offers preliminary indications for the management of the disease according to the gender oriented medicinal approach. Human serum includes a large number of components which derive from endogenous metabolism and nutritional intake. Serum components vary in response to diet. Serum lipid composition is probably the most important benchmark in assessing cardiovascular risk and disease progression. Serum components, also derived from nutritional intake, can affect general metabolism and, more specifically, affect molecular mechanisms and pathways linking nutritional intake and chronic disease risk. To identify the effect exerted by altered lipid composition on the genome expression pattern, response of gene expression to serum samples from hypercholesterolemic and normocholesterolemic male subjects was previously studied. In the present part of my PhD thesis, using a NMR metabolomics approach I studied the metabolomics profile of the aforementioned hypercholesterolemic and normocholesterolemic sera to correlate the previously identified trascriptomic signature of human hepatoma cells to the relative metabolomics profile. Hypercholesterolemic sera previously proved to increase in human hepatoma cells, the mRNA expression of HMGCS2, an enzyme involved in the pathway of keton bodies. Our NMR based metabolomics analysis evidences abnormal concentrations of metabolites involved in the keton bodies pathway. This indicates a correlation between the trascriptomic profile of hepatoma cells treated with hypercholesterolemic sera, and the metabolomics profile of the same sera. [edited by author]
La metabolomica e la metabonomica comprendono il profilo completo di numerosi metaboliti con riferimento alle varie concentrazioni e fluttuazioni sia cellulari che sistemiche in risposta a farmaci, dieta, stile di vita, influenza dell'ambiente, stimoli e modulazioni genetiche, al fine di caratterizzare gli effetti benefici e negativi di tali interazioni. Nel contesto delle applicazioni biomediche, la metabolomica avrà in futuro un ruolo preferenziale rispetto alle altre scienze 'omiche' per la possibilità di rilevare in tempo reale la risposta degli organismi agli stress patologici. L' applicazione della tecnica NMR è stata utilizzata per l' analisi metabolomica di bio-fluidi derivanti da popolazioni di pazienti affetti rispettivamente da tumore delle ghiandole salivari; da sindrome da antifosfolipidi; pazineti con profilo lipidico alterato. Questo screening metabolomico NMR è mirato i) alla definizione di un profilo metabolomico che potrebbe essere patognomonico delle malatte monitorate e ii) l'identificazione di biomarcatori da utilizzare in ambito diagnostico e prognostico. In questo studio metabolomico basato su analisi NMR della saliva di pazienti affetti dai tumori delle ghiandole salivari i nostri dati mostrano caratteristiche anomalie nel profilo metabolomico connesse con il metabolismo di acetato , alanina, lattato, metanolo, fenilalanina, propionato, succinato. Abbiamo identificato per la prima volta l'impronta digitale metabolomica che caratterizza pazienti con tumori della parotide con una potenziale applicazione per migliorare la diagnosi tempestiva ed un approccio terapeutico adeguato. I tumori alle ghiandole salivari, come molti altri tipi di cancro, sono patologie complesse, risultanti da una serie interdipendente di alterazioni biochimiche, piuttosto che un singolo evento dirompente. In questo caso, con un approccio rivolto all'identificazione di un panel di metaboliti marcatori, piuttosto che ad un singolo biomarcatore, miglioreranno ed aumenteranno la sensibilità e la specificità per il rilevament, integrando i protocolli diagnostici classici e la classificazione istologica. Il nostro studio metabolomico NMR-based ha rivelato diversi profili nella saliva di pazienti affetti da tumori delle ghiandole salivari, confrontati in base all' età e al sesso, abbinati con i controlli. Il “finger print”, piuttosto che i singoli biomarkers, può riflettere in pieno la natura multifattoriale ed etrogenea della oncogenesi , fornendo preziosi elementi per integrare i test diagnostici clinici e di laboratorio. La sindrome antifosfolipidi (APS) è una malattia autoimmune, reumatica, infiammatoria cronica associata ad uno stato di ipercoagulabilità: inducendo trombosi vascolari ed aborti spontaeni nelle donne. Ictus cerebrali e vascolari in questi pazienti sono responsabili della riduzione della aspettativa di vita: una diagnosi tempestiva ed un accurato monitoraggio della malattia è determinante per migliorare la precisione della terapia. Nel presente lavoro, vi presentiamo uno studio di metabolomica NMR su siero di pazienti affetti da APS. I nostri dati mostrano che gli individui che soffrono di APS hanno un profilo metabolomico caratteristico con anomalie del metabolismo associate ai donatori di gruppi metilici, di aminoacidi e corpi chetonici. Abbiamo identificato per la prima volta il “finger print” della sindrome da APS con la potenziale applicazione di migliorare la diagnosi tempestiva e favorire un approccio terapeutico adeguato. La prima stratificazione di pazienti APS pazienti in base al sesso offre indicazioni per la gestione della malattia secondo un approccio medico gender oriented. Il siero umano comprende un gran numero di componenti derivanti sia dal metabolismo endogeno sia dall' apporto nutrizionale i quali variano in risposta alla dieta. La composizione lipidica del siero è probabilmente il punto di riferimento più importante nella valutazione del rischio cardiovascolare e della progressione della malattia. Inoltre la composizione lipidica può influenzare il metabolismo e più in particolare, i percorsi molecolari che collegano l' apporto nutrizionale ed rischio di malattia cronica. L'effetto esercitato dalla composizione lipidica modificata sul pattern genomico in risposta all' espressione su campioni di siero da sogetti maschi ipercolesterolemici, confrontati con normocholesterolemici è stato oggetto di un precedente studio. Nell' ultimaparte di questa tesi di dottorato, utilizzando l'approccio metabolomico NMR ho studiato il profilo dei supramenzionati ipercolesterolemici e normocholesterolemici per correlare il profilo trascrittomico ottenuto dalle cellule epatiche umane con il profilo metabolomico del siero umano utilizzato per la cultura, mostrando una aumentata espressione di mRNA di HMGCS2, un enzima coinvolto nel percorso di corpi chetonici. Dall' analisi NMR sono emerse concentrazioni alterate di metaboliti coinvolti della via biosintetica dei corpi chetonici. Questo indica una correlazione tra il profilo trascriptomico di cellule epatiche trattate con sieri ipercolesterolemici, e il profilo metabolomica dei sieri stessi. [a cura dell'autore]
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Goolsby, Brian James. "Techniques for improved mass spectrometric analysis of biologically relevant molecules produced by MALDI and ESI in the quadrupole ion trap /." Full text (PDF) from UMI/Dissertation Abstracts International, 2000. http://wwwlib.umi.com/cr/utexas/fullcit?p3004273.
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Giacopelli, Brian John. "Global DNA methylation analysis of chronic lymphocytic leukemia and acute myeloid leukemia reveals distinct clinically relevant biological subtypes." The Ohio State University, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=osu1591114255694166.
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Michel, Yvonne [Verfasser], and Reinhard [Akademischer Betreuer] Bredehorst. "Structural and functional analyses of IgE epitopes and their biological relevance / Yvonne Michel. Betreuer: Reinhard Bredehorst." Hamburg : Staats- und Universitätsbibliothek Hamburg, 2012. http://d-nb.info/1024772802/34.
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Karaminkov, Rosen. "Conformations and fragmentation of biologically relevant molecules and their binary complexes with water probed by high resolution UV and mass analyzed threshold ionization spectroscopy." kostenfrei, 2009. https://mediatum2.ub.tum.de/node?id=821610.
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Stevens, Anna L. (Anna Lea). "Mechanical injury and inflammatory cytokines affect cartilage integrity and tissue homeostasis : a mass spectrometric analysis of proteins with relevance to arthritis." Thesis, Massachusetts Institute of Technology, 2006. http://hdl.handle.net/1721.1/37956.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Biological Engineering Division, 2006.Includes bibliographical references.
Osteoarthritis is characterized by synovial joint degeneration, and its cardinal pathological feature is degeneration and loss of the articular cartilage joint surface. While the aetiology of osteoarthritis is unknown, risk factors include gender, age, obesity, and prior joint injury. Joint injuries, including tears of the anterior cruciate ligament (ACL) and meniscus, increase the risk for the development of OA and involve both mechanical damage to cartilage, meniscus and synovial tissues, and tissue degradation associated with cytokine-induced inflammation. While the role of inflammatory cytokines in OA is still controversial, their role in rheumatoid arthritis is evidenced by the successful use of anti-TNF-ca and anti-IL-1 therapies to abrogate disease symptoms and progression. In vitro, both IL-13 and TNF-ca promote chondrocyte-mediated matrix degradation and inhibit cartilage matrix synthesis, while mechanical damage causes cell death, matrix damage, and decreased cell biosynthesis. Understanding the similarities and differences in cartilage responses to inflammatory cytokines and mechanical injury is important in understanding the catabolic-anabolic shifts that typify OA progression. Therefore, the objectives of this thesis were (1) to identify the role of TNF-a and IL-1 induced nitric oxide (NO) as a mediator of cartilage tissue damage;
(cont.) (2) to characterize and compare the regulation by IL- 1 P, TNF-cc, and mechanical injury of secreted factors, matrix degradation, and mechanisms of chondrocyte cell death using an SDS-PAGE-LC/MS/MS protein profiling approach; and (3) to further quantify the effects of IL-1 3, TNF-ca and injury using an isobaric isotope labeling (iTRAQ) based 2D-LC/MS/MS approach. Together these studies were designed to provide better understanding of matrix degradation, cell death, immune response, and evidence of cell-mediated repair processes. NO is produced by chondrocytes in response to inflammatory cytokines TNF-a, IL-1 3 and IL-17, and can mediate cellular and extracellular events through cGMP signaling, protein modifications (e.g., S-nitrosation or tyrosine nitration), altered transcript stability, and altered sugar and lipid chemistry. Cartilage was treated with IL-13 or TNF-ca left untreated in the presence or absence of the NO synthase inhibitor, L-N-methylarginine (L-NMA), and changes in gene expression and matrix breakdown were measured. We found that L-NMA treatment partially inhibited TNF-a-induced, aggrecanase-mediated aggrecan degradation as indicated by a decrease in sGAG loss to the medium and by an increase in the generation of aggrecanase-specific aggrecan fragments.
(cont.) No change was observed upon addition of L-NMA to IL- 1P treated explants, but addition of L-NMA to combined IL-1 3 and TNF-a treated explants increased sGAG loss, suggesting that the effects of NO may be contextual. We hypothesized that this might be due to differences in aggrecanase expression (ADAMTS4 vs. ADAMTS5) or post-translational modification, but no aggrecanase was consistently identified in the samples. No difference in MMP expression or activation was noted following addition of L-NMA, and no change in NO chemistry between IL-1 3 and TNF-a treatment was evident by nitrate and nitrite production. Gene expression analysis was conducted on a battery of 32 genes, including matrix proteins, inflammatory mediators, proteases, cytokines and growth factors, and housekeeping proteins. While IL-113 and TNF-a both increased the expression of proteases and inflammatory mediators, addition of L-NMA did not significantly affect expression of the genes tested. We concluded that the effects of TNF-a and IL-1 p-induced NO production may depend on differences in cellular responses to each of these cytokines and possibly to differences in signaling or aggrecanase expression.
(cont.) In the second study, newborn bovine calf cartilage explants were treated with 10 ng/ml IL-1 p, 100 ng/ml TNF-a, radially-unconfined injurious compression (strain: 50%; strain rate 1000/o/sec), or no treatment, and cultured for five days. Pooled medium was subjected to SDS-PAGE-LC/MS/MS, and data were analyzed by Spectrum Mill proteomics software, focusing on protein identification, differences between treatments and matrix protein proteolysis. Over 250 proteins were identified among the four protein groups including CD 109, platelet derived growth factor like protein, and scrapie responsive protein, which have not been previously identified in cartilage. IL-13 and TNF-a caused an increase in YKL39, YKL40, complement factor B, MMP-3, ECM-1, haptoglobin, serum amyloid A3, and clusterin. Injurious compression caused the release of intracellular proteins including GRP58, GRP78, alpha 4 actinin, pyruvate kinase, and vimentin, suggesting a loss of membrane integrity in a population of chondrocytes. Data on actin release within the first 24 hours suggested that this loss of membrane integrity occurred by mechanical cell disruption. Injurious compression also caused proteolysis of collagen type VI subunits, collagen type II, and COMP. Thrombospondin 1 fragments were seen in all treatment groups, and aggrecan proteolysis was predominant with cytokine treatment.
(cont.) Cartilage explants subjected to injurious compression released intracellular proteins and showed enhanced degradation of matrix proteins, while explants subjected to IL- 13 or TNF-ct released proteins involved in innate immunity and stress response. In the third study, cartilage explants were subjected to injurious compression, TNF-a (100 ng/ml) or IL-13 (10 ng/ml), or no treatment, cultured in equal volumes of medium, and the medium was collected, pooled and the proteins deglycosylated by treatment with chondroitinase ABC. The proteins were subjected to trypsinization, and the peptides were labeled with one of four iTRAQ labels each containing a unique signature ion. The labeled peptides were subjected to nano-2D-LC/MS/MS on a QStar, quadrupole time of flight instrument. The study was done in analytical replicate on a pooled sample of greater than 70 explants from a total of 6-12 different animals. Data were analyzed by ProQuant to obtain a ProGroup peptide report containing identified spectra, which were combined to achieve a peptide, and then a protein level output of mean ratios, standard deviations of those ratios, and significance based on either Wilcoxan sign rank or Student's t-test both corrected for multiple comparisons.
(cont.) Because of our interest in catabolic and anabolic shifts, a targeted data analysis approach was taken in addition to a systems level PCA and K-means clustering approach. By focusing on particular protein domains, we identified a decrease in the synthesis of most fibrillar collagen subunits (p<0.05), and an increase in the release of the aggrecan G2 and G3 domains with IL-13 and TNF-ta treatment (p<0.05). We also noted a significant increase in MMP-1, MMP-3, MMP-9, and MMP-13 in at least one condition and, in most cases, all conditions compared to the untreated sample. Increases in proteins involved in innate immunity and immune cell recruitment were noted with IL-1 [3 and TNF-a treatment, while an increase in intracellular protein release was seen most dramatically with mechanical compression injury. Since anabolic effects are often driven by the insulin-like growth factor family and the TGF-[3 superfamily, we specifically identified members of these pathways to understand which factors may mediate early repair processes.
(cont.) At the systems level, 2 principal components were sufficient to describe 97% of the covariance in the data. IL- 1 and TNF-a caused a similar response in proteins identified; in contrast, a 'Y'-shaped distribution was observed upon projection of proteins based on their response injury vs. cytokine treatment. K-means clustering revealed six main clusters to further characterize the biology of mechanical injury versus cytokine effects on cartilage.
by Anna L. Stevens.
Ph.D.
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Georgiev, Stoyan G. [Verfasser], Hans Jürgen [Akademischer Betreuer] Neusser, and Klaus [Akademischer Betreuer] Köhler. "Mass Analyzed Threshold Ionization Studies and Quantum-Chemical Calculations of Biologically Relevant Molecules and Hydrogen-Bonded Complexes / Stoyan Georgiev. Gutachter: Klaus Köhler. Betreuer: Hans Jürgen Neusser." München : Universitätsbibliothek der TU München, 2011. http://d-nb.info/101959005X/34.
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Ferhatosmanoglu, Nilgun. "Optimal design of experiments for emerging biological and computational applications." Columbus, Ohio : Ohio State University, 2007. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1179177867.
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Martins, Joana Mafalda Nunes Paulo Silva. "Supramolecular Sensors and Actuators for Biologically Relevant Analytes." Master's thesis, 2020. http://hdl.handle.net/10362/111125.
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Tese de Mestrado parcialmente desenvolvida e suportada pelo projeto “Verão com Ciência”, aquando da participação na Escola de Verão do Laboratório Associado para a Química Verde (LAQV-REQUIMTE), que decorreu de 27 de julho até 30 de outubro de 2020, na Faculdade de Ciências e Tecnologia.In the field of biochemistry, the study of peptides is of great interest, not only due to the variety of functions these molecules present in biological systems (e.g. in signalling, neuromodulation, immune response and metabolism) but also as tools in biotechnology and as pharmaco-logical agents, as is the case of antimicrobial cell-penetrating peptides. Supramolecular receptors have had a rising application in the transport, modulation and sensing of these biomolecules, due to the strong interactions they can establish with affinities up to the nM range. In this thesis, a group of supramolecular dual emission sensors and a light-controlled transporter for cationic peptides were synthesized and characterized. These consist of a modular amphiphilic system based on a p-sulfonatocalix[4]arene receptor, monosubstituted in its lower rim with different functional groups, depending on the target application. The sensors SCnPy present an aliphatic chain of variable size (n = 4, 6), with a pyrene fluorescent moiety at its end, while the transporter SC6Azo presents a six-carbon aliphatic chain with an azobenzene moiety. SCnPy have shown to have the pyrene’s characteristic monomer emission at low concentration and, when at high enough concentrations or in the presence of organic cations, they can form ground state dimers that emit at higher wavelengths. The variation of chain length successfully modulated the capacity of the SCnPy sensors to aggregate. SC4Py showed this dual emission for polyarginines of four or more residues, presenting a critical aggregation concentration (CAC) of 9.8 μΜ for a 1:2 molar ratio of sensor to a six-residue polyarginine. SC6Py is able to aggregate in the presence of peptides with only 3 cationic residues, with CAC of 0.11 μM, with the same peptide and in the same conditions as for SC4Py. Furthermore, SC6Py showed selectivity for a fragment of the peptide Humanin, over a similar sequence of another mitochondrial signaling peptide, SHLP4, all the while presenting a dual emission that enables the correction of the measurement for instrumental factors and sensor concentration variations. Other phenomena and modes of detection (resonance energy transfer and dye displacement assays) were also explored for the SCnPy system. The light-controlled transporter, SC6Azo, also binds to polyarginines and presents an efficient light induced isomerization, with quantitative photochemical conversion from trans to cis, when irradiated at 382 nm, and reaching 73% of maximum conversion for the reverse reaction, upon irradiation at 500 nm. This enabled a great decrease in polarity of the tail, when irradiating the cis isomer and converting it to trans, showing a maximum increase of peptide transport in phosphatidylcholine liposomes of, approximately, 30%.
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Dey, Nilanjan. "Engaging Small Organic Molecules and Self-Assemblies for ‘Label-Free’ Recognition of Biologically Relevant Analytes." Thesis, 2016. https://etd.iisc.ac.in/handle/2005/4908.
Full textAbstract:
The thesis entitled ‘Engaging Small Organic Molecules and Self-Assemblies for
‘Label-Free’ Recognition of Biologically Relevant Analytes’ mainly deals with design and
synthesis of various types of small molecular probes or molecular assemblies for
fluorometric recognition of a large number of biologically relevant analytes in water.
The first chapter begins with the general overview of various types of biosensors and their
working principles. Then we discussed about various small organic molecules or molecular
assemblies based systems in optical biosensing. The strategies for designing these sensors
have also been discussed in connection with frequently encountered photophysical
interactions. Finally, the design principles of some biosensors were highlighted on the basis
of the structural aspects of the concerned analytes.
The second chapter describes the design and synthesis of various optical probes for
selective detections of different warfare materials in water.
Chapter 2A: Cyanide Mediated Facile Michael Addition Reaction: A Simple Protocol to
Distinguish ‘Tabun Mimic’ DCNP in Solution as well as in Vapor Phase
Figure 1. Structures of the molecular probes used in chapter 2A.
This chapter discussed about involvement of a series of water soluble bis-indolyl compounds
for selective detection of nerve gas mimicking agent, DCNP (Diethyl Cyanophosphonate) at
pH 8.0 in water. The mechanism of interaction was proposed as the bis-indole assisted
hydrolysis of phosphoester nerve gas agents through hydrogen bonding interaction. Then the
Michael addition of the liberated CN- ion to the electron deficient C=C bond of the bisindolyl
moiety. This led to a remarkable color change from red to colorless at ambient
condition. Further the protocol was exploited in vapor phase detection of DCNP (Tabun
mimic) below its toxic level.
Chapter 2B: Selective and Efficient Detection of Nitro-Aromatic Explosives in Multiple
Media including Water, Micelles, Organogel, and Solid Support
Figure 2. Structures of the molecular probes used in chapter 2B.
This chapter demonstrated development of phenylenevinylene based optical probes for the
selective detection of both DNP (2,4-Dinitrophenol) and TNP (2,4,6-Trinitrophenol) in pure
water as well as in micellar medium. The mechanistic investigation suggested that the initial
proton transfer caused electrostatic association between the picrate anions and the protonated
pyridine ends, which could further promote electron transfer from the electron-rich
fluorophore moiety to the electron-deficient nitroaromatics (NACs). Thus the selectivity
depends on the pKa of the probe molecules as well as the NACs under consideration. Further
portable test strips were made successfully for rapid on-sight detection purpose.
The third chapter describes identification of different enzymes in water as well as in
biological fluids via disaggregation of template mediated molecular assemblies.
Chapter 3A: Employment of ATP-Sensitive Lanthanide Ensemble for the Estimation of
Creatine Kinase Level in Blood Serum and Live Cell Imaging
Figure 3. Structures of the molecular probes used in chapter 3A.
This chapter presents the use of in-situ generated luminescent lanthanide complexes in
sensing of adenosine triphosphate (ATP) in water. The indicator tetracarboxylate salt showed
rapid quenching in green molecular emission upon coordination with highly paramagnetic
lanthanide ion (Gd3+). The addition of ATP could displace the lanthanide ion from the
vicinity of the compound and retrieved its original emission. Further this selective ‘Turn-On’
response of the probe towards ATP was utilized to discriminate between the live and dead
cells depending upon their ATP/ADP content. Moreover, excellent selectivity of the probe
for ATP over ADP was utilized for the detection of Creatine Kinase in human blood serum
samples.
Chapter 3B: Estimation of Albumin Content in Different Biological Fluids and
Monitoring Trypsin Mediated Digestion of HSA
Figure 4. Structures of the molecular probes used in chapter 3B.
This chapter describes design of several amphipathic carbazole dyes, which could form
thermo sensitive, pH dependent fluorescent nano-aggregates in water. This facile
nanoclustering behavior of the compounds was then utilized for detection of human serum
albumin (HSA). The site-specific nature of the interaction was appeared to be the key reason
for the unique selectivity of the probes towards HSA over other structurally resembled
albumin proteins. Further the estimation of HSA was achieved in different biological fluids
like human urine, blood serum and saliva etc. Finally the protease mediated digestion of
protein template was applied as an alternative strategy for detection of trypsin.
The fourth chapter describes fluorometric detection of different physiologically relevant
monosaccharides by exploiting multi-point hydrogen bonding network.
Chapter 4A: Analyte Induced Alteration in the Aggregation Property of Fluorescent
Organic Nano-particles: A Simple Recognition Strategy for D-(-)-Ribose in Water
Figure 5. Structures of the molecular probes used in chapter 4A.
This chapter demonstrated selective detection of D(-)-ribose and ribose containing
biomolecules (Adenosine, riboflavin etc.) in water via hydrogen bonding interactions from
aceylhydrazone and pyridine units. The interaction with ribose was found to be responsible
for dissociation of the preformed molecular assemblies, resulting drastic quenching in
luminescent signal. Finally determination of ribose was also performed in presence of
complex biological matrix like human urine.
Chapter 4B: Restriction in Keto-Enol Tatumerization through Multipoint Hydrogen
Bonding Network with D-(+)-Glucosamine
Figure 6. Structures of the molecular probes used in chapter 4B.
This chapter presents design and synthesis of different chromogenic probes by connecting
nicotinic hydrazide with different -hydroxy aromatic aldehydes via carbonyl-nucleophile
addition protocol. Addition of D-glucosamine was found to modulate the keto-enol
tatumerization of the molecules via formation of multi-point hydrogen bonding network. The
rapid change in color from bright yellow to colorless with prominent emission quenching led
detection of up to 5.3 mg/L of glucosamine in water. Then monitoring of glucosamine level
was also achieved in human blood serum as well as pharmaceutical formulations. Moreover,
the probes were found to be competent in detection of glucosamine even in intracellular
condition.
The fifth chapter describes development of new fluorometric probes for identifying
different inflammatory-response markers in water.
Chapter 5A: Heparin Triggered Multicolor Emission Switching in Water: A Convenient
Protocol for Heparinase I Assay
Figure 7. Structures of the molecular probes used in chapter 5A.
In this chapter, conjugated bis-pyridinium salts of phenylenevinylene (PPV) have been used
for selective detection of heparin in water. The unique dose-dependent emission switching
ability of the probes ensured quantitiative estimation of heparin without involving any
sofisticated facilities. The higher negative charge density and preferential conformation of
sugar dimers faciliated interaction between compounds and heparin. Finally, the heparin
induced reversible aggregate formation was utilized to develop an alternative easy-to-operate
heparinase I assay protocol.
Chapter 5B: Application of Neurotransmitter Induced Emission Switching for
Histamine Detection in Biological Fluids and Macrophage Cells
Figure 8. Structures of the molecular probes used in chapter 5B.
This chapter presents the involvement of well-known fluorescein aldehyde dyes in
recognition of histamine below nanomolar concentration in water. Here, the dual mode of
detection of histamine was achieved at pH 7.0 without involving any toxic metal ions. The
selective response towards histamine was confirmed through secondary hydrogen bonding
interaction followed by imine formation. Then the probes were also employed for detection
of histamine in different biological fluid matrices (human urine and blood serum). Finally,
the rise in endogenous histamine level in macrophage RAW 264.7 was identified under
stimuli-responsive condition (treatement with thapsigargin).
The sixth chapter describes fluorometric detection of purine alkaloids via their preferential
stacking over the electron rich planer dye molecules.
Chapter 6A: Hydrogen Bonding Triggered Crumbling of Pyrene Excimer: A Simple
Method for Detection of Uric Acid in Human Serum and Infested Grain Extracts
This chapter deals with design and synthesis of different amphipathic pyrene molecules for
nanomolar detection of uric acid in water. Hydrogen bonding interaction of uric acid with
amide functional groups found to push two adjacent pyrene units away from each other,
resulting into quenching of blue excimer emission. The optimized liposomal formulation
derived from the doping of probe molecules into soya lecithin vesicles was further utilized
for estimating uric acid content in blood serum samples. Finally, the present protocol was
used for identifying the rise in uric acid content in insect-infested grain samples.
Figure 9. Structures of the molecular probes used in chapter 6A.
Chapter 6B: Caffeine Modulated Dissociation of Carbazole Based FONs in Water:
Excitation Triggered Alteration in Sensing Property
Figure 10. Structures of the molecular probes used in chapter 6B.
This chapter deals with self aggregation properties of a series of carbazole based ampiphilic
dyes, which could be modulated by the micro polarity of the local environment and
electronic influence from the functional groups attached to the core organic scaffold. In
comparison to other structurally related purine analogs, caffeine exerted most prominent
emission response due to its planar electron deficient structure. An optimal balance between
selectivity and sensitivity was achieved by varying the excitation wavelengths or electron
density over the carbazole core. In application, the sensor was successfully exploited to
address diverse real-life problems ranging from applications in ‘dope-analysis in human
urine’ to carbonated drinks.
Books on the topic "Biologically Relevant Analytes"
1
E, Merian, ed. Metals and their compoundsin the environment: Occurrence, analysis, and biological relevance. Weinheim: VCH, 1991.
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E, Merian, and Clarkson Thomas W, eds. Metals and their compounds in the environment: Occurrence, analysis, and biological relevance. Weinheim: VCH, 1991.
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3
Anke, M. Elements and their compounds in the environment: Occurrence, analysis and biological relevance. 2nd ed. Weinheim: Wiley-VCH, 2004.
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M, Anke, Ihnat M, and Stoeppler M. 1927-, eds. Elements and their compounds in the environment: Occurence, analysis and biological relevance. 2nd ed. Weinheim: Wiley-VCH, 2004.
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Dovigi, Stephanie. An Analysis of the performance of molecular mechanics methods in the study of some biologically relevant hydrogen-bonded systems. Sudbury, Ont: Laurentian University, 1993.
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6
Smetanin, Anatoliy. Formation and structure of the biota of Kamchatka's natural ecosystems. ru: INFRA-M Academic Publishing LLC., 2021. http://dx.doi.org/10.12737/1316649.
Full textAbstract:
The formation of the modern flora and fauna of Kamchatka, paleogeography, natural ecosystems are considered. The biological diversity of the most important groups of biota is analyzed: vascular plants, mollusks, echinoderms, crustaceans, insects, fish, birds, mammals. The most prominent representatives, including economically significant ones, are highlighted. Brief information on paleodendroflora is given, a brief analysis of currently flourishing vascular plants is given. The fossil forms of extinct and currently living animals inhabiting the natural ecosystems of Kamchatka are described. A polytomic analysis of the biota was performed and its functional structure was established.
For researchers in the field of ecology and nature protection, teachers and students of relevant academic disciplines, as well as for a wide range of readers in order to learn about the nature of the region and environmental education.
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Agafonov, Vyacheslav, Sergey Bogolyubov, Liya Vasil'eva, Galina Vyphanova, Dmitriy Gorohov, Natal'ya Zhavoronkova, Inna Ignat'eva, et al. Sources of environmental law. ru: INFRA-M Academic Publishing LLC., 2022. http://dx.doi.org/10.12737/1913253.
Full textAbstract:
The monograph summarizes new relevant materials and topics. The study of the sources (forms) of environmental and natural resource law, legislation on environmental assessment and environmental control (supervision), provisions of land and other codes as forms of law, mechanisms for regulating environmental management, as well as the evolution of sources of law in the field of agriculture.
The complex nature of environmental law is demonstrated, the constitutional, legislative, and political foundations of environmental development, the unified state environmental policy of the Russian Federation and a number of foreign states are outlined. The genesis and systematization of forms of atmospheric air protection, specially protected natural territories of Russia, Belarus and Kazakhstan, legal regulation of waste management, international and national measures of adaptation to climate change are reflected.
The legislation on land reclamation, land management, subsoil use, forest management, water use, fishing and conservation of aquatic biological resources in the system of sources of environmental law is analyzed; the issues of intersectoral communication of environmental, urban planning, information, energy, civil legislation and law are considered.
Examples from the field of law enforcement are given. The idea of ecologization of sources (forms), institutions, categories, norms of branches of Russian law is being developed.
For lawyers — scientists and practitioners, teachers, postgraduates, masters, law students, and other specialists interested in the theory and practice of lawmaking and the application of environmental law.
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Merian, Ernest. Metals and Their Compounds in the Environment: Occurrence, Analysis, and Biological Relevance. Wiley-VCH, 1990.
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(Editor), Ernest Merian, Manfred Anke (Editor), Milan Ihnat (Editor), and Markus Stoeppler (Editor), eds. Elements and their Compounds in the Environment: Occurrence, Analysis and Biological Relevance. 2nd ed. Wiley-VCH, 2004.
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Lentzos, Filippa. Genetic Engineering and Biological Risks. Edited by Roger Brownsword, Eloise Scotford, and Karen Yeung. Oxford University Press, 2017. http://dx.doi.org/10.1093/oxfordhb/9780199680832.013.66.
Full textAbstract:
This chapter serves three objectives. First, it provides a narrative account of key developments in core bioengineering technologies. Second, it critically interrogates the emergence and evolution of regulatory regimes aimed at responding to perceived risks associated with these technological capabilities, highlighting how these have primarily relied on establishing ‘soft’ forms of control rather than hard edged legal frameworks backed by coercive sanctions, largely in the form of self-regulation by the scientific research community (with some notification provisions to keep the relevant government informed). Third, it provides an analysis of this regulatory evolution, focusing on the narrow construction of risk, and flagging up the possibility of alternative framings, which might have generated more inclusive and deliberative approaches to standard-setting and oversight.
Book chapters on the topic "Biologically Relevant Analytes"
1
Głowacki, Rafał, Justyna Piechocka, Edward Bald, and Grażyna Chwatko. "Application of Separation Techniques in Analytics of Biologically Relevant Sulfur Compounds." In Handbook of Bioanalytics, 233–56. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-030-95660-8_11.
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Głowacki, Rafał, Justyna Piechocka, Edward Bald, and Grażyna Chwatko. "Application of Separation Techniques in Analytics of Biologically Relevant Sulfur Compounds." In Handbook of Bioanalytics, 1–24. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-030-63957-0_11-1.
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Ooi, Chia Huey, Madhu Chetty, and Shyh Wei Teng. "Relevance, Redundancy and Differential Prioritization in Feature Selection for Multiclass Gene Expression Data." In Biological and Medical Data Analysis, 367–78. Berlin, Heidelberg: Springer Berlin Heidelberg, 2005. http://dx.doi.org/10.1007/11573067_37.
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Tashiro, Hironori, Manabu Fukumoto, Kohji Miyazaki, and Hitoshi Okamura. "Biological Relevance and Analysis of c-myc Gene Expression in Normal Human Ovary." In Molecular Basis of Reproductive Endocrinology, 243–49. New York, NY: Springer New York, 1993. http://dx.doi.org/10.1007/978-1-4613-9260-6_20.
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Wang, Yajie, Lufeng Wang, Chuanjiang Dong, Li Li, Mengqi Tang, Weizhong Sun, and Yao Wu. "Evaluation of Uncertainty for Determination of Trace Uranium in Biology by Laser Fluorescence Method." In Springer Proceedings in Physics, 549–66. Singapore: Springer Nature Singapore, 2023. http://dx.doi.org/10.1007/978-981-99-1023-6_48.
Full textAbstract:
AbstractLarge amounts of uranium-containing radioactive waste are generated in reactor operation and in the research and manufacture of nuclear fuel elements. At present, there are various uranium enrichment and separation methods such as reduction precipitation method, ion exchange method, solvent extraction method, membrane filtration method, adsorption method, and microorganism method to treat the uranium-containing radioactive waste generated in the related processes of nuclear facilities. However, the airborne effluent or liquid effluent discharged after treatment may still contain radioactive uranium. It is well known that uranium is a radioactive heavy metal element, and its radioactive and chemical toxicity cannot be ignored. Uranium in the environment enters the human body through the food route, and its long half-life can make the human body suffer from continuous radioactive internal radiation damage. As an environmental medium, organisms are closely related to the entry of uranium into the human body through food. Therefore, it is of great significance to carry out accurate measurement of uranium content in environmental-grade biological samples around nuclear facilities, however, complete and accurate measurement results include measurement data and uncertainty. Laser fluorescence method is a method for rapid analysis of uranium content in environmental samples. It has the advantages of high sensitivity, simple sample pretreatment, and wide measurement range, which has been widely used in nuclear industry, environmental monitoring and scientific research. At present, there is a lack of relevant reports on the uncertainty of the measurement of total uranium content in environmental-grade biological samples by laser fluorescence method. It is of great significance to accurately measure the uranium content in biological samples by evaluating the uncertainty of this method. In this paper, the WGJ-III trace uranium analyzer was used to analyze the uncertainty source of total uranium in environmental-grade biological samples by laser fluorescence method. The uncertainty measurement model was established, the uncertainty components were quantified, and the expanded uncertainty of the measurement of total uranium content in environmental biological samples was calculated. The evaluation results showed that the expanded uncertainty of a 0.05 g environmental biological sample is 10.8% (k = 2) without dilution, and the dominant uncertainty component is derived from the measurement uncertainty of sample fluorescence counting.
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Kodali, Surya T., Philip Kauffman, Sainath R. Kotha, Anita Yenigalla, Rengasayee Veeraraghavan, Sonal R. Pannu, Thomas J. Hund, et al. "Oxidative Lipidomics: Analysis of Oxidized Lipids and Lipid Peroxidation in Biological Systems with Relevance to Health and Disease." In Measuring Oxidants and Oxidative Stress in Biological Systems, 61–92. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-47318-1_5.
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Dissmeyer, Nico, and Arp Schnittger. "Use of Phospho-Site Substitutions to Analyze the Biological Relevance of Phosphorylation Events in Regulatory Networks." In Methods in Molecular Biology, 93–138. Totowa, NJ: Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-264-9_6.
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Jamrozik, Euzebiusz, and Michael J. Selgelid. "Drug-Resistant Infection: Causes, Consequences, and Responses." In Ethics and Drug Resistance: Collective Responsibility for Global Public Health, 3–18. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-27874-8_1.
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Abstract This chapter provides an overview of the causes and consequences of, and possible policy responses to, the problem of drug resistance. Throughout, we highlight the ways that ethical and conceptual analyses can help to clarify relevant issues and improve policy, especially in public health, broadly conceived. Drug resistant pathogens arise, persist, spread, and produce harm due to a complex set of causes: biological processes (e.g., related to microbial evolution, the transmission of genetic determinants of resistance between microbes, and human host immunity) as well as human behaviors (e.g., antimicrobial use and hygiene practices) and other social factors (e.g., access to clean water, sanitation, healthcare, and antimicrobials). Furthermore, the ethically salient consequences of drug resistance include not only morbidity and mortality from untreatable infections (that are often inequitably distributed), but also broader effects on human freedom, privacy, and well-being. Public health ethicists are ideally placed to identify and weigh the values that might be promoted or compromised by potential policies and/or interventions that aim to address the problem of drug resistance. This chapter concludes by discussing potential policy responses, including those related to surveillance, research, animal and human antimicrobial use, the broader social determinants of health, infection control practices, and vaccination.
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Moosavi, Sanaz Rahimi, and Arman Izadifar. "End-to-End Security Scheme for E-Health Systems Using DNA-Based ECC." In Silicon Valley Cybersecurity Conference, 77–89. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-030-96057-5_6.
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AbstractToday, the amount of data produced and stored in computing Internet of Things (IoT) devices is growing. Massive volumes of sensitive information are exchanged between these devices making it critical to ensure the security of these data. Cryptography is a widely used method for ensuring data security. Many lightweight cryptographic algorithms have been developed to address the limitations of resources on the IoT devices. Such devices have limited processing capabilities in terms of memory, processing power, storage, etc. The primary goal of exploiting cryptographic technique is to send data from the sender to the receiver in the most secure way to prevent eavesdropping of the content of the original data. In this paper, we propose an end-to-end security scheme for IoT system. The proposed scheme consists of (i) a secure and efficient mutual authentication scheme based on the Elliptic Curve Cryptography (ECC) and the Quark lightweight hash design, and (ii) a secure end-to-end communication based on Deoxyribonucleic Acid (DNA) and ECC. DNA Cryptography is the cryptographic technique to encrypt and decrypt the original data using DNA sequences based on its biological processes. It is a novel technique to hide data from unauthorized access with the help of DNA. The security analysis of the proposed scheme reveals that it is secure against the relevant threat models and provides a higher security level than the existing related work in the literature.
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Hale, Robert C., Meredith E. Seeley, Ashley E. King, and Lehuan H. Yu. "Analytical Chemistry of Plastic Debris: Sampling, Methods, and Instrumentation." In Microplastic in the Environment: Pattern and Process, 17–67. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-78627-4_2.
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AbstractApproaches for the collection and analysis of plastic debris in environmental matrices are rapidly evolving. Such plastics span a continuum of sizes, encompassing large (macro-), medium (micro-, typically defined as particles between 1 μm and 5 mm), and smaller (nano-) plastics. All are of environmental relevance. Particle sizes are dynamic. Large plastics may fragment over time, while smaller particles may agglomerate in the field. The diverse morphologies (fragment, fiber, sphere) and chemical compositions of microplastics further complicate their characterization. Fibers are of growing interest and present particular analytical challenges due to their narrow profiles. Compositional classes of emerging concern include tire wear, paint chips, semisynthetics (e.g., rayon), and bioplastics. Plastics commonly contain chemical additives and fillers, which may alter their toxicological potency, behavior (e.g., buoyancy), or detector response (e.g., yield fluorescence) during analysis. Field sampling methods often focus on >20 μm and even >300 μm sized particles and will thus not capture smaller microplastics (which may be most abundant and bioavailable). Analysis of a limited subgroup (selected polymer types, particle sizes, or shapes) of microplastics, while often operationally necessary, can result in an underestimation of actual sample content. These shortcomings complicate calls for toxicological studies of microplastics to be based on “environmentally relevant concentrations.” Sample matrices of interest include water (including wastewater, ice, snow), sediment (soil, dust, wastewater sludge), air, and biota. Properties of the environment, and of the particles themselves, may concentrate plastic debris in select zones (e.g., gyres, shorelines, polar ice, wastewater sludge). Sampling designs should consider such patchy distributions. Episodic releases due to weather and anthropogenic discharges should also be considered. While water grab samples and sieving are commonplace, novel techniques for microplastic isolation, such as continuous flow centrifugation, show promise. The abundance of nonplastic particulates (e.g., clay, detritus, biological material) in samples interferes with microplastic detection and characterization. Their removal is typically accomplished using a combination of gravity separation and oxidative digestion (including strong bases, peroxide, enzymes); unfortunately, aggressive treatments may damage more labile plastics. Microscope-based infrared or Raman detection is often applied to provide polymer chemistry and morphological data for individual microplastic particles. However, the sheer number of particles in many samples presents logistical hurdles. In response, instruments have been developed that employ detector arrays and rapid scanning lasers. The addition of dyes to stain particulates may facilitate spectroscopic detection of some polymer types. Most researchers provide microplastic data in the form of the abundances of polymer types within particle size, polymer, and morphology classes. Polymer mass data in samples remain rare but are essential to elucidating fate. Rather than characterizing individual particles in samples, solvent extraction (following initial sample prep, such as sediment size class sorting), combined with techniques such as thermoanalysis (e.g., pyrolysis), has been used to generate microplastic mass data. However, this may obviate the acquisition of individual particle morphology and compositional information. Alternatively, some techniques (e.g., electron and atomic force microscopy and matrix-assisted laser desorption mass spectrometry) are adept at providing highly detailed data on the size, morphology, composition, and surface chemistry of select particles. Ultimately, the analyst must select the approach best suited for their study goals. Robust quality control elements are also critical to evaluate the accuracy and precision of the sampling and analysis techniques. Further, improved efforts are required to assess and control possible sample contamination due to the ubiquitous distribution of microplastics, especially in indoor environments where samples are processed.
Conference papers on the topic "Biologically Relevant Analytes"
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Quesada-Moreno, María, Melanie Schnell, and Anna Krin. "CHIRAL ANALYSIS OF BIOLOGICALLY RELEVANT SAMPLES USING BROADBAND ROTATIONAL SPECTROSCOPY." In 73rd International Symposium on Molecular Spectroscopy. Urbana, Illinois: University of Illinois at Urbana-Champaign, 2018. http://dx.doi.org/10.15278/isms.2018.tc05.
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Vattam, Swaroop S., and Ashok K. Goel. "Foraging for Inspiration: Understanding and Supporting the Online Information Seeking Practices of Biologically Inspired Designers." In ASME 2011 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2011. http://dx.doi.org/10.1115/detc2011-48238.
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Finding suitable biological systems to emulate is one of the key initial steps in biologically inspired design. Designers often turn to online information environments such as the World Wide Web to seek biological sources of inspiration, which poses its own set of challenges. The focus of our research is to understand and address those challenges. In this paper, we first present an information-processing model of the task of seeking bio-inspiration in online information environments based on our observations of designers engaged in biologically inspired design. Then, we analyze the information foraging behavior of designers that is encapsulated in this model to understand the costs associated with this task. Next, we propose an approach for enhancing information environments to better support the task of seeking bio-inspiration. Our approach augments individual information resources within an information environment with conceptual models to make the task of finding relevant information resources more efficient. Finally, we describe an interactive online information environment called Biologue that realizes this approach.
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Celli, Jonathan P., Imran Rizvi, Adam R. Blanden, Adnan O. Abu-Yousif, Bryan Q. Spring, and Tayyaba Hasan. "Biologically relevant 3D tumor arrays: imaging-based methods for quantification of reproducible growth and analysis of treatment response." In SPIE BiOS, edited by David H. Kessel and Tayyaba Hasan. SPIE, 2011. http://dx.doi.org/10.1117/12.876149.
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Sevinsky, Chris, Alberto Santamaria-Pang, Jingyu Zhang, Christina Lowes, Dipen Sangurdekar, Beverly Falcon, Qing Li, et al. "Abstract 1709: Quantification of biologically relevant vascular phenotypes in human prostate cancer: automated image analysis using hyperplexed immunofluorescence." In Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1538-7445.am2015-1709.
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Semenov, V. G. "THE RELEVANCE OF THE APPLICATION OF BIOLOGICALLY ACTIVE COMPLEXES IN THE NEONATAL PERIOD IN CALVES GROWING." In DIGEST OF ARTICLES ALL-RUSSIAN (NATIONAL) SCIENTIFIC AND PRACTICAL CONFERENCE "CURRENT ISSUES OF VETERINARY MEDICINE: EDUCATION, SCIENCE, PRACTICE", DEDICATED TO THE 190TH ANNIVERSARY FROM THE BIRTH OF A.P. Stepanova. Publishing house of RGAU - MSHA, 2021. http://dx.doi.org/10.26897/978-5-9675-1853-9-2021-21.
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The article presents the results of the analysis of scientific works related to biologically active complexes, in particular, probiotics used to increase the efficiency of raising calves in the early stages of postnatal ontogenesis and maintaining their productive health.
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Shen, Zhuohua, and Justin Seipel. "A Simple Analytical Tool for Legged Robot Design." In ASME 2012 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2012. http://dx.doi.org/10.1115/detc2012-71452.
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Although legged locomotion is better at tackling complicated terrains compared with wheeled locomotion, legged robots are rare, in part, because of the lack of simple design tools. The dynamics governing legged locomotion are generally nonlinear and hybrid (piecewise-continuous) and so require numerical simulation for analysis and are not easily applied to robot designs. During the past decade, a few approximated analytical solutions of Spring-Loaded Inverted Pendulum (SLIP), a canonical model in legged locomotion, have been developed. However, SLIP is energy conserving and cannot predict the dynamical stability of real-world legged locomotion. To develop new analytical tools for legged robot designs, we first analytically solved SLIP in a new way. Then based on SLIP solution, we developed an analytical solution of a hip-actuated Spring-Loaded Inverted Pendulum (hip-actuated-SLIP) model, which is more biologically relevant and stable than the canonical energy conserving SLIP model. The analytical approximations offered here for SLIP and the hip actuated-SLIP solutions compare well with the numerical simulations of each. The analytical solutions presented here are simpler in form than those resulting from existing analytical approximations. The analytical solutions of SLIP and the hip actuated-SLIP can be used as tools for robot design or for generating biological hypotheses.
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Holt, Jeremiah R., Heejoon Jo, Vonn Walter, Xiaobei Zhao, David Neil Hayes, and Yoon Ho Ko. "Abstract 5448: Integrative analysis of microRNA expression identifies two biologically distinct and clinically relevant subtypes of head and neck squamous cell carcinoma." In Proceedings: AACR Annual Meeting 2020; April 27-28, 2020 and June 22-24, 2020; Philadelphia, PA. American Association for Cancer Research, 2020. http://dx.doi.org/10.1158/1538-7445.am2020-5448.
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James, Angela. "BIOLOGICAL SCIENCES PRE-SERVICE TEACHERS' EXPERIENCES OF COVID-19 AS AN ENABLER FOR THEIR SERVICE-LEARNING PROJECTS." In SCIENCE AND TECHNOLOGY EDUCATION: DEVELOPING A GLOBAL PERSPECTIVE. Scientia Socialis Ltd., 2021. http://dx.doi.org/10.33225/balticste/2021.86.
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The newspaper headlines in July 2020, reflected the context of COVID-19 and the challenges in the education sector in South Africa. Pre-service teachers completing a Biological Sciences for Educations Research and Service-Learning module conducted their Service-Learning in their home contexts, which under normal times, they would do so in the neighbouring university contexts. The research question: Why did the Biological Sciences pre-service teachers' experience COVID-19 as an enabler for their Service-Learning projects. An interpretive, qualitative case study was adopted to explore the pre-service teacher’s experiences of their projects undertaken. The data gathering methods included document analysis (pre-service teacher’s reflective diaries); observation of module reflective sessions and seminar presentations and visual methodology (pre-service teachers made videos). The data analysis using descriptive content analysis. The research rigour of credibility and dependability were worked with, and the research ethics were considered. The results indicated that during the learning about the project, the pre-service teachers had emotional experiences of fear, excitement and even confusion. During the planning for the project, they had concerns about Covid-19 restrictions and access to placement sites, what to do, who to work with and the nature of the projects planned. The action of the Service-Learning indicated the collaboration and teamwork, imagination and creativity, including the contextually relevant problem-solving actions that were undertaken. Pre-service teachers were in their own communities where they excelled and built relationships and valued their community members. Service-Learning should be completed in the pre-service teacher’s home contexts for greater relevance, value and connectedness with their community. Keywords: biological sciences, case study, COVID-19 pandemic, pre-service-teacher education, service-learning
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Cooper, Kathryn, Prasuna Vemuri, and Hesham Ali. "On the comparison of state- and transition-based analysis of biological relevance in gene co-expression networks." In 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2015. http://dx.doi.org/10.1109/bibm.2015.7359852.
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Almeida, Henrique A., and Paulo J. Ba´rtolo. "The Use of Schwartz Geometries for Scaffold Design in Tissue Engineering Applications." In ASME 2010 10th Biennial Conference on Engineering Systems Design and Analysis. ASMEDC, 2010. http://dx.doi.org/10.1115/esda2010-25385.
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Additive biomanufacturing processes are increasingly recognised as ideal techniques to produce scaffolds for tissue engineering applications. Scaffolds provide a temporary mechanical and vascular support for tissue regeneration while shaping the in-growth tissues. These scaffolds must be biocompatible, biodegradable, with appropriate porosity, pore structure and pore distribution and optimal vascularisation, with both surface and structural compatibility. Surface compatibility means a chemical, biological and physical suitability to the host tissue. Structural compatibility corresponds to an optimal adaptation to the mechanical behaviour of the host tissue. Recent advances in the tissue engineering field are increasingly relying on modelling and simulation. The design of optimised scaffolds based on the fundamental knowledge of its microstructure is a relevant topic of research. This paper proposes the use of novel geometric structures based on the Triple Periodic Minimal Surfaces formulation, namely the Schwartz primitives, one of the a sub-classes of Triple Periodic Minimal Surfaces. Schwartz primitives enables the design of vary high surface-to-volume ratio structures with high porosity and mechanical/vascular properties. With the use of a computational tool combining structural, computational fluid dynamics and topological optimisation schemes, it is possible to predict and optimise both mechanical and vascular behaviour of scaffolds for soft and hard tissue applications, with different topological architectures and levels of porosity. This tool is particularly important to quantify the structural heterogeneity and scaffold mechanical properties with a designed microstructure subjected to either a single or a multiple load distribution. This computational tool enables the simulation of biological flows in vascular passages of scaffolds. The blood flow considered in this study is a complex fluid comprising a suspension of red blood cells, white blood cells and platelets within a newtonian plasma.
Reports on the topic "Biologically Relevant Analytes"
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Jones, Robert, Molly Creagar, Michael Musty, Randall Reynolds, Scott Slone, and Robyn Barbato. A 𝘬-means analysis of the voltage response of a soil-based microbial fuel cell to an injected military-relevant compound (urea). Engineer Research and Development Center (U.S.), November 2022. http://dx.doi.org/10.21079/11681/45940.
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Biotechnology offers new ways to use biological processes as environmental sensors. For example, in soil microbial fuel cells (MFCs), soil electro-genic microorganisms are recruited to electrodes embedded in soil and produce electricity (measured by voltage) through the breakdown of substrate. Because the voltage produced by the electrogenic microbes is a function of their environment, we hypothesize that the voltage may change in a characteristic manner given environmental disturbances, such as the contamination by exogenous material, in a way that can be modelled and serve as a diagnostic. In this study, we aimed to statistically analyze voltage from soil MFCs injected with urea as a proxy for gross contamination. Specifically, we used 𝘬-means clustering to discern between voltage output before and after the injection of urea. Our results showed that the 𝘬-means algorithm recognized 4–6 distinctive voltage regions, defining unique periods of the MFC voltage that clearly identify pre- and postinjection and other phases of the MFC lifecycle. This demonstrates that 𝘬-means can identify voltage patterns temporally, which could be further improve the sensing capabilities of MFCs by identifying specific regions of dissimilarity in voltage, indicating changes in the environment.
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Wang, Xiaoyue, Hui Lu, Zhihao Liang, Liang Wang, and Ji Ma. Ixazomib combined with autologous stem cell transplantation for POEMS syndrome: a case report and meta‑analysis. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, July 2022. http://dx.doi.org/10.37766/inplasy2022.7.0061.
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Review question / Objective: POEMS syndrome is a rare monoclonal plasma cell proliferation disorder. At present, there is no unified treatment for POEMS syndrome. Here, we describe one case with POEMS syndrome. And we made a metaanalysis to assess the efficacy of treatment strategies in recent ten years. Search strategy: We searched relevant articles in PubMed, Embase and MEDLINE database for the period up to July 2021.The search strategy included the keywords: POEMS, Therapy, Drug Therapy, Biological Therapy, Combined Modality Therapy, Hematopoietic Stem Cell Transplantation, Immunotherapy, Molecular Targeted Therapy, Chemoradiotherapy, Salvage Therapy, Controlled Clinical Trial, Randomized Controlled Trial et al. In addition, we checked all the references of eligible articles that our search retrieved to identify potentially eligible papers.
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Savosko, V., I. Komarova, Yu Lykholat, E. Yevtushenko, and T. Lykholat. Predictive model of heavy metals inputs to soil at Kryvyi Rih District and its use in the training for specialists in the field of Biology. IOP Publishing, 2021. http://dx.doi.org/10.31812/123456789/4511.
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The importance of our research is due to the need to introduce into modern biological education methods of predictive modeling which are based on relevant factual material. Such an actual material may be the entry of natural and anthropic heavy metals into the soil at industrial areas. The object of this work: (i) to work out a predictive model of the total heavy metals inputs to soil at the Kryvyi Rih ore-mining & metallurgical District and (ii) to identify ways to use this model in biological education. Our study areas are located in the Kryvyi Rih District (Dnipropetrovsk region, Central Ukraine). In this work, classical scientific methods (such as analysis and synthesis, induction and deduction, analogy and formalization, abstraction and concretization, classification and modelling) were used. By summary the own research results and available scientific publications, the heavy metals total inputs to soils at Kryvyi Rih District was predicted. It is suggested that the current heavy metals content in soils of this region due to 1) natural and 2) anthropogenic flows, which are segmented into global and local levels. Predictive calculations show that heavy metals inputs to the soil of this region have the following values (mg ⋅ m2/year): Fe – 800-80 000, Mn – 125-520, Zn – 75-360, Ni – 20-30, Cu – 15-50, Pb – 7.5-120, Cd – 0.30-0.70. It is established that anthropogenic flows predominate in Fe and Pb inputs (60-99 %), natural flows predominate in Ni and Cd inputs (55-95 %). While, for Mn, Zn, and Cu inputs the alternate dominance of natural and anthropogenic flows are characterized. It is shown that the predictive model development for heavy metals inputs to soils of the industrial region can be used for efficient biological education (for example in bachelors of biologists training, discipline "Computer modelling in biology").
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Савосько, Василь Миколайович, Ірина Олександрівна Комарова, Юрій Васильович Лихолат, Едуард Олексійович Євтушенко,, and Тетяна Юріївна Лихолат. Predictive Model of Heavy Metals Inputs to Soil at Kryvyi Rih District and its Use in the Training for Specialists in the Field of Biology. IOP Publishing, 2021. http://dx.doi.org/10.31812/123456789/4266.
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The importance of our research is due to the need to introduce into modern biological education methods of predictive modeling which are based on relevant factual material. Such an actual material may be the entry of natural and anthropic heavy metals into the soil at industrial areas. The object of this work: (i) to work out a predictive model of the total heavy metals inputs to soil at the Kryvyi Rih ore-mining & metallurgical District and (ii) to identify ways to use this model in biological education. Our study areas are located in the Kryvyi Rih District (Dnipropetrovsk region, Central Ukraine). In this work, classical scientific methods (such as analysis and synthesis, induction and deduction, analogy and formalization, abstraction and concretization, classification and modelling) were used. By summary the own research results and available scientific publications, the heavy metals total inputs to soils at Kryvyi Rih District was predicted. It is suggested that the current heavy metals content in soils of this region due to 1) natural and 2) anthropogenic flows, which are segmented into global and local levels. Predictive calculations show that heavy metals inputs to the soil of this region have the following values ( mg ∙ m ଶ year ⁄ ): Fe – 800-80 000, Mn – 125-520, Zn – 75-360, Ni – 20-30, Cu – 15-50, Pb – 7.5-120, Cd – 0.30-0.70. It is established that anthropogenic flows predominate in Fe and Pb inputs (60-99 %), natural flows predominate in Ni and Cd inputs (55-95 %). While, for Mn, Zn, and Cu inputs the alternate dominance of natural and anthropogenic flows are characterized. It is shown that the predictive model development for heavy metals inputs to soils of the industrial region can be used for efficient biological education (for example in bachelors of biologists training, discipline “Computer modelling in biology”).
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Belkin, Shimshon, Sylvia Daunert, and Mona Wells. Whole-Cell Biosensor Panel for Agricultural Endocrine Disruptors. United States Department of Agriculture, December 2010. http://dx.doi.org/10.32747/2010.7696542.bard.
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Objectives: The overall objective as defined in the approved proposal was the development of a whole-cell sensor panel for the detection of endocrine disruption activities of agriculturally relevant chemicals. To achieve this goal several specific objectives were outlined: (a) The development of new genetically engineered wholecell sensor strains; (b) the combination of multiple strains into a single sensor panel to effect multiple response modes; (c) development of a computerized algorithm to analyze the panel responses; (d) laboratory testing and calibration; (e) field testing. In the course of the project, mostly due to the change in the US partner, three modifications were introduced to the original objectives: (a) the scope of the project was expanded to include pharmaceuticals (with a focus on antibiotics) in addition to endocrine disrupting chemicals, (b) the computerized algorithm was not fully developed and (c) the field test was not carried out. Background: Chemical agents, such as pesticides applied at inappropriate levels, may compromise water quality or contaminate soils and hence threaten human populations. In recent years, two classes of compounds have been increasingly implicated as emerging risks in agriculturally-related pollution: endocrine disrupting compounds (EDCs) and pharmaceuticals. The latter group may reach the environment by the use of wastewater effluents, whereas many pesticides have been implicated as EDCs. Both groups pose a threat in proportion to their bioavailability, since that which is biounavailable or can be rendered so is a priori not a threat; bioavailability, in turn, is mediated by complex matrices such as soils. Genetically engineered biosensor bacteria hold great promise for sensing bioavailability because the sensor is a live soil- and water-compatible organism with biological response dynamics, and because its response can be genetically “tailored” to report on general toxicity, on bioavailability, and on the presence of specific classes of toxicants. In the present project we have developed a bacterial-based sensor panel incorporating multiple strains of genetically engineered biosensors for the purpose of detecting different types of biological effects. The overall objective as defined in the approved proposal was the development of a whole-cell sensor panel for the detection of endocrine disruption activities of agriculturally relevant chemicals. To achieve this goal several specific objectives were outlined: (a) The development of new genetically engineered wholecell sensor strains; (b) the combination of multiple strains into a single sensor panel to effect multiple response modes; (c) development of a computerized algorithm to analyze the panel responses; (d) laboratory testing and calibration; (e) field testing. In the course of the project, mostly due to the change in the US partner, three modifications were introduced to the original objectives: (a) the scope of the project was expanded to include pharmaceuticals (with a focus on antibiotics) in addition to endocrine disrupting chemicals, (b) the computerized algorithm was not fully developed and (c) the field test was not carried out. Major achievements: (a) construction of innovative bacterial sensor strains for accurate and sensitive detection of agriculturally-relevant pollutants, with a focus on endocrine disrupting compounds (UK and HUJ) and antibiotics (HUJ); (b) optimization of methods for long-term preservation of the reporter bacteria, either by direct deposition on solid surfaces (HUJ) or by the construction of spore-forming Bacillus-based sensors (UK); (c) partial development of a computerized algorithm for the analysis of sensor panel responses. Implications: The sensor panel developed in the course of the project was shown to be applicable for the detection of a broad range of antibiotics and EDCs. Following a suitable development phase, the panel will be ready for testing in an agricultural environment, as an innovative tool for assessing the environmental impacts of EDCs and pharmaceuticals. Furthermore, while the current study relates directly to issues of water quality and soil health, its implications are much broader, with potential uses is risk-based assessment related to the clinical, pharmaceutical, and chemical industries as well as to homeland security.
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Mawassi, Munir, and Valerian Dolja. Role of RNA Silencing Suppression in the Pathogenicity and Host Specificity of the Grapevine Virus A. United States Department of Agriculture, January 2010. http://dx.doi.org/10.32747/2010.7592114.bard.
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RNA silencing is a defense mechanism that functions against virus infection and involves sequence-specific degradation of viral RNA. Diverse RNA and DNA viruses of plants encode RNA silencing suppressors (RSSs), which, in addition to their role in viral counterdefense, were implicated in the efficient accumulation of viral RNAs, virus transport, pathogenesis, and determination of the virus host range. Despite rapidly growing understanding of the mechanisms of RNA silencing suppression, systematic analysis of the roles played by diverse RSSs in virus biology and pathology is yet to be completed. Our research was aimed at conducting such analysis for two grapevine viruses, Grapevine virus A (GVA) and Grapevine leafroll-associated virus-2 (GLRaV- 2). Our major achievements on the previous cycle of BARD funding are as follows. 1. GVA and GLRaV-2 were engineered into efficient gene expression and silencing vectors for grapevine. The efficient techniques for grapevine infection resulting in systemic expression or silencing of the recombinant genes were developed. Therefore, GVA and GLRaV-2 were rendered into powerful tools of grapevine virology and functional genomics. 2. The GVA and GLRaV-2 RSSs, p10 and p24, respectively, were identified, and their roles in viral pathogenesis were determined. In particular, we found that p10 functions in suppression and pathogenesis are genetically separable. 3. We revealed that p10 is a self-interactive protein that is targeted to the nucleus. In contrast, p24 mechanism involves binding small interfering RNAs in the cytoplasm. We have also demonstrated that p10 is relatively weak, whereas p24 is extremely strong enhancer of the viral agroinfection. 4. We found that, in addition to the dedicated RSSs, GVA and GLRaV-2 counterdefenses involve ORF1 product and leader proteases, respectively. 5. We have teamed up with Dr. Koonin and Dr. Falnes groups to study the evolution and function of the AlkB domain presents in GVA and many other plant viruses. It was demonstrated that viral AlkBs are RNA-specific demethylases thus providing critical support for the biological relevance of the novel process of AlkB-mediated RNA repair.
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Gottlieb, Yuval, Bradley Mullens, and Richard Stouthamer. investigation of the role of bacterial symbionts in regulating the biology and vector competence of Culicoides vectors of animal viruses. United States Department of Agriculture, June 2015. http://dx.doi.org/10.32747/2015.7699865.bard.
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Symbiotic bacteria have been shown to influence host reproduction and defense against biotic and abiotic stressors, and this relates to possible development of a symbiont-based control strategy. This project was based on the hypothesis that symbionts have a significant impact on Culicoides fitness and vector competence for animal viruses. The original objectives in our proposal were: 1. Molecular identification and localization of the newly-discovered symbiotic bacteria within C. imicola and C. schultzei in Israel and C. sonorensis in California. 2. Determination of the prevalence of symbiotic bacteria within different vector Culicoides populations. 3. Documentation of specific symbiont effects on vector reproduction and defense: 3a) test for cytoplasmic incompatibility in Cardinium-infected species; 3b) experimentally evaluate the role of the symbiont on infection or parasitism by key Culicoides natural enemies (iridescent virus and mermithid nematode). 4. Testing the role(s) of the symbionts in possible protection against infection of vector Culicoides by BTV. According to preliminary findings and difficulties in performing experimental procedures performed in other insect symbiosis systems where insect host cultures are easily maintained, we modified the last two objectives as follows: Obj. 3, we tested how symbionts affected general fitness of Israeli Culicoides species, and thoroughly described and evaluated the correlation between American Culicoides and their bacterial communities in the field. We also tried alternative methods to test symbiont-Culicoides interactions and launched studies to characterize low-temperature stress tolerances of the main US vector, which may be related to symbionts. Obj. 4, we tested the correlation between EHDV (instead of BTV) aquisition and Cardinium infection. Culicoides-bornearboviral diseases are emerging or re-emerging worldwide, causing direct and indirect economic losses as well as reduction in animal welfare. One novel strategy to reduce insects’ vectorial capacity is by manipulating specific symbionts to affect vector fitness or performance of the disease agent within. Little was known on the bacterial tenants occupying various Culicoides species, and thus, this project was initiated with the above aims. During this project, we were able to describe the symbiont Cardinium and whole bacterial communities in Israeli and American Culicoides species respectively. We showed that Cardinium infection prevalence is determined by land surface temperature, and this may be important to the larval stage. We also showed no patent significant effect of Cardinium on adult fitness parameters. We showed that the bacterial community in C. sonorensis varies significantly with the host’s developmental stage, but it varies little across multiple wastewater pond environments. This may indicate some specific biological interactions and allowed us to describe a “core microbiome” for C. sonorensis. The final set of analyses that include habitat sample is currently done, in order to separate the more intimately-associated bacteria from those inhabiting the gut contents or cuticle surface (which also could be important). We were also able to carefully study other biological aspects of Culicoides and were able to discriminate two species in C. schultzei group in Israel, and to investigate low temperature tolerances of C. sonorensis that may be related to symbionts. Scientific implications include the establishment of bacterial identification and interactions in Culicoides (our work is cited in other bacteria-Culicoides studies), the development molecular identification of C. schultzei group, and the detailed description of the microbiome of the immature and matched adult stages of C. sonorensis. Agricultural implications include understanding of intrinsic factors that govern Culicoides biology and population regulation, which may be relevant for vector control or reduction in pathogen transmission. Being able to precisely identify Culicoides species is central to understanding Culicoides borne disease epidemiology.
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Lers, Amnon, Majid R. Foolad, and Haya Friedman. genetic basis for postharvest chilling tolerance in tomato fruit. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7600014.bard.
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ABSTRACT Postharvest losses of fresh produce are estimated globally to be around 30%. Reducing these losses is considered a major solution to ensure global food security. Storage at low temperatures is an efficient practice to prolong postharvest performance of crops with minimal negative impact on produce quality or human health and the environment. However, many fresh produce commodities are susceptible to chilling temperatures, and the application of cold storage is limited as it would cause physiological chilling injury (CI) leading to reduced produce quality. Further, the primary CI becomes a preferred site for pathogens leading to decay and massive produce losses. Thus, chilling sensitive crops should be stored at higher minimal temperatures, which curtails their marketing life and in some cases necessitates the use of other storage strategies. Development of new knowledge about the biological basis for chilling tolerance in fruits and vegetables should allow development of both new varieties more tolerant to cold, and more efficient postharvest storage treatments and storage conditions. In order to improve the agricultural performance of modern crop varieties, including tomato, there is great potential in introgression of marker-defined genomic regions from wild species onto the background of elite breeding lines. To exploit this potential for improving tomato fruit chilling tolerance during postharvest storage, we have used in this research a recombinant inbred line (RIL) population derived from a cross between the red-fruited tomato wild species SolanumpimpinellifoliumL. accession LA2093 and an advanced Solanum lycopersicumL. tomato breeding line NCEBR-1, developed in the laboratory of the US co-PI. The original specific objectives were: 1) Screening of RIL population resulting from the cross NCEBR1 X LA2093 for fruit chilling response during postharvest storage and estimation of its heritability; 2) Perform a transcriptopmic and bioinformatics analysis for the two parental lines following exposure to chilling storage. During the course of the project, we learned that we could measure greater differences in chilling responses among specific RILs compared to that observed between the two parental lines, and thus we decided not to perform transcriptomic analysis and instead invest our efforts more on characterization of the RILs. Performing the transcriptomic analysis for several RILs, which significantly differ in their chilling tolerance/sensitivity, at a later stage could result with more significant insights. The RIL population, (172 lines), was used in field experiment in which fruits were examined for chilling sensitivity by determining CI severity. Following the field experiments, including 4 harvest days and CI measurements, two extreme tails of the response distribution, each consisting of 11 RILs exhibiting either high sensitivity or tolerance to chilling stress, were identified and were further examined for chilling response in greenhouse experiments. Across the RILs, we found significant (P < 0.01) correlation between field and greenhouse grown plants in fruit CI. Two groups of 5 RILs, whose fruits exhibited reproducible chilling tolerant/sensitive phenotypes in both field and greenhouse experiments, were selected for further analyses. Numerous genetic, physiological, biochemical and molecular variations were investigated in response to postharvest chilling stress in the selected RILs. We confirmed the differential response of the parental lines of the RIL population to chilling stress, and examined the extent of variation in the RIL population in response to chilling treatment. We determined parameters which would be useful for further characterization of chilling response in the RIL population. These included chlorophyll fluorescence Fv/Fm, water loss, total non-enzymatic potential of antioxidant activity, ascorbate and proline content, and expression of LeCBF1 gene, known to be associated with cold acclimation. These parameters could be used in continuation studies for the identification and genetic mapping of loci contributing to chilling tolerance in this population, and identifying genetic markers associated with chilling tolerance in tomato. Once genetic markers associated with chilling tolerance are identified, the trait could be transferred to different genetic background via marker-assisted selection (MAS) and breeding. The collaborative research established in this program has resulted in new information and insights in this area of research and the collaboration will be continued to obtain further insights into the genetic, molecular biology and physiology of postharvest chilling tolerance in tomato fruit. The US Co-PI, developed the RIL population that was used for screening and measurement of the relevant chilling stress responses and conducted statistical analyses of the data. Because we were not able to grow the RIL population under field conditions in two successive generations, we could not estimate heritability of response to chilling temperatures. However, we plan to continue the research, grow the RIL progeny in the field again, and determine heritability of chilling tolerance in a near future. The IS and US investigators interacted regularly and plan to continue and expand on this study, since combing the expertise of the Co-PI in genetics and breeding with that of the PI in postharvest physiology and molecular biology will have great impact on this line of research, given the significant findings of this one-year feasibility project.
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Avni, Adi, and Gitta L. Coaker. Proteomic investigation of a tomato receptor like protein recognizing fungal pathogens. United States Department of Agriculture, January 2015. http://dx.doi.org/10.32747/2015.7600030.bard.
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Maximizing food production with minimal negative effects on the environment remains a long-term challenge for sustainable food production. Microbial pathogens cause devastating diseases, minimizing crop losses by controlling plant diseases can contribute significantly to this goal. All plants possess an innate immune system that is activated after recognition of microbial-derived molecules. The fungal protein Eix induces defense responses in tomato and tobacco. Plants recognize Eix through a leucine-rich-repeat receptor- like-protein (LRR-RLP) termed LeEix. Despite the knowledge obtained from studies on tomato, relatively little is known about signaling initiated by RLP-type immune receptors. The focus of this grant proposal is to generate a foundational understanding of how the tomato xylanase receptor LeEix2 signals to confer defense responses. LeEix2 recognition results in pattern triggered immunity (PTI). The grant has two main aims: (1) Isolate the LeEix2 protein complex in an active and resting state; (2) Examine the biological function of the identified proteins in relation to LeEix2 signaling upon perception of the xylanase elicitor Eix. We used two separate approaches to isolate receptor interacting proteins. Transgenic tomato plants expressing LeEix2 fused to the GFP tag were used to identify complex components at a resting and activated state. LeEix2 complexes were purified by mass spectrometry and associated proteins identified by mass spectrometry. We identified novel proteins that interact with LeEix receptor by proteomics analysis. We identified two dynamin related proteins (DRPs), a coiled coil – nucleotide binding site leucine rich repeat (SlNRC4a) protein. In the second approach we used the split ubiquitin yeast two hybrid (Y2H) screen system to identified receptor-like protein kinase At5g24010-like (SlRLK-like) (Solyc01g094920.2.1) as an interactor of LeEIX2. We examined the role of SlNRC4a in plant immunity. Co-immunoprecipitation demonstrates that SlNRC4a is able to associate with different PRRs. Physiological assays with specific elicitors revealed that SlNRC4a generally alters PRR-mediated responses. SlNRC4a overexpression enhances defense responses while silencing SlNRC4 reduces plant immunity. We propose that SlNRC4a acts as a non-canonical positive regulator of immunity mediated by diverse PRRs. Thus, SlNRC4a could link both intracellular and extracellular immune perception. SlDRP2A localizes at the plasma membrane. Overexpression of SlDRP2A increases the sub-population of LeEIX2 inVHAa1 endosomes, and enhances LeEIX2- and FLS2-mediated defense. The effect of SlDRP2A on induction of plant immunity highlights the importance of endomembrane components and endocytosis in signal propagation during plant immune . The interaction of LeEIX2 with SlRLK-like was verified using co- immunoprecipitation and a bimolecular fluorescence complementation assay. The defence responses induced by EIX were markedly reduced when SlRLK-like was over-expressed, and mutation of slrlk-likeusing CRISPR/Cas9 increased EIX- induced ethylene production and SlACSgene expression in tomato. Co-expression of SlRLK-like with different RLPs and RLKs led to their degradation, apparently through an endoplasmic reticulum-associated degradation process. We provided new knowledge and expertise relevant to expression of specific be exploited to enhance immunity in crops enabling the development of novel environmentally friendly disease control strategies.
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Shmulevich, Itzhak, Shrini Upadhyaya, Dror Rubinstein, Zvika Asaf, and Jeffrey P. Mitchell. Developing Simulation Tool for the Prediction of Cohesive Behavior Agricultural Materials Using Discrete Element Modeling. United States Department of Agriculture, October 2011. http://dx.doi.org/10.32747/2011.7697108.bard.
Full textAbstract:
The underlying similarity between soils, grains, fertilizers, concentrated animal feed, pellets, and mixtures is that they are all granular materials used in agriculture. Modeling such materials is a complex process due to the spatial variability of such media, the origin of the material (natural or biological), the nonlinearity of these materials, the contact phenomenon and flow that occur at the interface zone and between these granular materials, as well as the dynamic effect of the interaction process. The lack of a tool for studying such materials has limited the understanding of the phenomena relevant to them, which in turn has led to energy loss and poor quality products. The objective of this study was to develop a reliable prediction simulation tool for cohesive agricultural particle materials using Discrete Element Modeling (DEM). The specific objectives of this study were (1) to develop and verify a 3D cohesionless agricultural soil-tillage tool interaction model that enables the prediction of displacement and flow in the soil media, as well as forces acting on various tillage tools, using the discrete element method; (2) to develop a micro model for the DEM formulation by creating a cohesive contact model based on liquid bridge forces for various agriculture materials; (3) to extend the model to include both plastic and cohesive behavior of various materials, such as grain and soil structures (e.g., compaction level), textures (e.g., clay, loam, several grains), and moisture contents; (4) to develop a method to obtain the parameters for the cohesion contact model to represent specific materials. A DEM model was developed that can represent both plastic and cohesive behavior of soil. Soil cohesive behavior was achieved by considering tensile force between elements. The developed DEM model well represented the effect of wedge shape on soil behavior and reaction force. Laboratory test results showed that wedge penetration resistance in highly compacted soil was two times greater than that in low compacted soil, whereas DEM simulation with parameters obtained from the test of low compacted soil could not simply be extended to that of high compacted soil. The modified model took into account soil failure strength that could be changed with soil compaction. A three dimensional representation composed of normal displacement, shear failure strength and tensile failure strength was proposed to design mechanical properties between elements. The model based on the liquid bridge theory. An inter particle tension force measurement tool was developed and calibrated A comprehensive study of the parameters of the contact model for the DEM taking into account the cohesive/water-bridge was performed on various agricultural grains using this measurement tool. The modified DEM model was compared and validated against the test results. With the newly developed model and procedure for determination of DEM parameters, we could reproduce the high compacted soil behavior and reaction forces both qualitatively and quantitatively for the soil conditions and wedge shapes used in this study. Moreover, the effect of wedge shape on soil behavior and reaction force was well represented with the same parameters. During the research we made use of the commercial PFC3D to analyze soil tillage implements. An investigation was made of three different head drillers. A comparison of three commonly used soil tillage systems was completed, such as moldboard plow, disc plow and chisel plow. It can be concluded that the soil condition after plowing by the specific implement can be predicted by the DEM model. The chisel plow is the most economic tool for increasing soil porosity. The moldboard is the best tool for soil manipulation. It can be concluded that the discrete element simulation can be used as a reliable engineering tool for soil-implement interaction quantitatively and qualitatively.