Relevant bibliographies by topics / Molecular diagnostic tool

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Molecular diagnostic tool'

Author: Grafiati
Published: 6 September 2023

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Journal articles on the topic "Molecular diagnostic tool"

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Han, Su-Xia, Xi Jia, Jin-lu Ma, and Qing Zhu. "Molecular Beacons: A Novel Optical Diagnostic Tool." Archivum Immunologiae et Therapiae Experimentalis 61, no. 2 (January 5, 2013): 139–48. http://dx.doi.org/10.1007/s00005-012-0209-7.

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Pitt, T. L. "Molecular bacteriology: a diagnostic tool for the millennium." Journal of Clinical Pathology 53, no. 1 (January 1, 2000): 71–75. http://dx.doi.org/10.1136/jcp.53.1.71.

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Chiu, Rossa W. K. "Massively parallel sequencing as a molecular diagnostic tool." Pathology 44 (2012): S18. http://dx.doi.org/10.1016/s0031-3025(16)32643-5.

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Chiu, Rossa W. K. "Massively parallel sequencing as a molecular diagnostic tool." Pathology 44 (2012): S29—S30. http://dx.doi.org/10.1016/s0031-3025(16)32670-8.

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Kim, Seohyun, Sangmin Ji, and Hye Ran Koh. "CRISPR as a Diagnostic Tool." Biomolecules 11, no. 8 (August 6, 2021): 1162. http://dx.doi.org/10.3390/biom11081162.

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Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system has recently gained growing attention as a diagnostic tool due to its capability of specific gene targeting. It consists of Cas enzymes and a guide RNA (gRNA) that can cleave the target DNA or RNA based on the sequence of the gRNA, making it an attractive genetic engineering technique. In addition to the target-specific binding and cleavage, the trans-cleavage activity was reported for some Cas proteins, including Cas12a and Cas13a, which is to cleave the surrounding single-stranded DNA or RNA upon the target binding of Cas-gRNA complex. All these activities of the CRISPR-Cas system are based on its target-specific binding, making it applied to develop diagnostic methods by detecting the disease-related gene as well as microRNAs and the genetic variations such as single nucleotide polymorphism and DNA methylation. Moreover, it can be applied to detect the non-nucleic acids target such as proteins. In this review, we cover the various CRISPR-based diagnostic methods by focusing on the activity of the CRISPR-Cas system and the form of the target. The CRISPR-based diagnostic methods without target amplification are also introduced briefly.
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Netto, George J., and Rana Domiati Saad. "Diagnostic Molecular Pathology: An Increasingly Indispensable Tool for the Practicing Pathologist." Archives of Pathology & Laboratory Medicine 130, no. 9 (September 1, 2006): 1339–48. http://dx.doi.org/10.5858/2006-130-1339-dmpaii.

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Abstract Context.—Diagnostic molecular pathology is rapidly becoming an indispensable tool for anatomic pathologists. Familiarity with some of the technologic principles and current, as well as upcoming, molecular diagnostic applications is greatly advantageous for today's practice of pathology. Objectives.— To provide a discussion of the most common techniques currently used in molecular pathology laboratories and review their essential applications to diagnosis and management of neoplastic diseases. Data Sources.—A literature review and illustrative cases from the authors' molecular diagnostic practices. Conclusions.—Applications such as clonality assays, molecular cytogenetics, and chimerism analysis are providing us with accurate tools to resolve difficult diagnostic and management decisions in hemato-oncology. This should serve as a future model to expand molecular applications into the wider field of solid tumors.
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Monje, R. R., and S. Aalto. "Molecular Chemistry as Diagnostic tool for Starbursts and AGNs." EAS Publications Series 31 (2008): 81–84. http://dx.doi.org/10.1051/eas:0831016.

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McKerrell, Thomas D., Ignacio Varela, Nicolo Bolli, Postingl Hannes, Zemin Ning, German Tischler, Anthony Bench, et al. "R.I.S.C.L: A Holistic Molecular Diagnostic Tool for Myeloid Malignancies." Blood 124, no. 21 (December 6, 2014): 2342. http://dx.doi.org/10.1182/blood.v124.21.2342.2342.

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Abstract The genomic landscapes of acute myeloid leukemia (AML), myelodysplastic syndrome (MDS), myeloproliferative disorders (MPD) and other related myeloid malignancies are now amongst the best characterized cancer genomes. These malignancies share most of their somatic driver mutations, many of which have therapeutic and prognostic significance (Patel et al, NEJM 2012). Patient prognostication and clinical decision-making can be greatly facilitated by testing for these mutations in parallel with established diagnostic assays. Here, we describe and validate RISCL (Rearrangements, Indels, Substitutions, Copy number and Loss-of-heterozygosity), a novel methodological and bioinformatic tool for the molecular diagnosis of myeloid malignancies. This tool employs targeted DNA capture to simultaneously: 1) identify coding mutations in 49 genes, 2) detect the four most important translocations in AML and 3) derive genome-wide copy number and zygosity data. Samples & methods 1. Samples Genomic DNA was extracted from bone marrow samples of 62 patients with AML (n=86 samples, including 24 remission samples) and 68 patients with MDS; and from blood granulocytes and mononuclear cells from 5 cord blood samples and 18 adults with normal hematopoiesis. 2. cRNA baits and sequencing The bait library (Agilent) contained 53,613 probes to capture: 1) all exons from 49 genes 2) intronic breakpoint sites for PML-RARA, CBFb-MYH11 and RUNX1-RUNX1T1 and MLL breakpoints 3) 9958 SNPs (minor allele frequency 0.40-0.45) for genome wide copy number and zygosity analysis. Barcoded sequencing was performed using Illumina HiSeq 2000 (100bp paired-end). 3. Bioinformatic analysis We used bespoke bioinformatics for detecting coding substitutions and indels (MIDAS; Conte et al, Leukemia 2013), chromosomal translocations (SMALT-FIT), copy number analysis (Avadis software) and detection of specific mutations such as MLL-PTD and FLT3-ITD (in-house scripts). 4. Verification of results To validate the sensitivity and specificity of our approach, we compared our findings to conventional diagnostic data and are also validating 30% of randomly selected variants. Results A mean of 94% of targeted bases were covered at least by 30x. In AML samples, the four most common coding mutations identified affected NPM1 (n=10), CEBPA (n=8), IDH1 (n=8) and NRAS (n=7). By comparison to conventional diagnostics, we detected 5/5 IDH1R132, 4/4 CEBPA, 1/1 IDH2R172K and 8/9 NPM1 mutations. In MDS samples, the top four mutations affected TP53 (n=15), TET2 (n=13), SRSF2 (n=9), ASXL1 (n=8) and mutations affecting spliceosome genes (n=18) that were mutually exclusive, as previously described (Yoshida et al, Nature 2011). RISCL detected 100% of known translocations (28/28) in AML patients, namely CBFb-MYH11 (n=8/8), PML-RARA (n=9/9), RUNX1-RUNX1T1 (n=4/4) and rearrangements of MLL (n=7/7). In every case of MLL rearrangement the gene partner was identified and in one case with t(X;11) we identified a novel gene partner to MLL, DIAPH2. Furthermore, we identified one patient with an MLL rearrangement not identified at diagnosis. Copy number analysis efficiently detected known large chromosomal deletions or monosomies in chromosome 5 (18/18) and 7 (10/12). Overall 47/54 large deletions were detected using Avadis software. Furthermore in one MDS patient we were able to detect a submicroscopic heterozygous deletion in chromosome 4 which included TET2. However this method was much less sensitive for detecting trisomies (13/27 trisomies detected overall). The reasons for this disparity between detection of deletions and amplifications using a standardized depth of coverage algorithm are unclear, but may include subclonal mutations, selection of karyotypically abnormal cells during metaphase preparation or limitations of our bioinformatic analysis, which we are currently investigating. Figure 1 shows an example of the results of our holistic analysis using RISCL from an informative case of AML. In summary we describe RISCL, a novel powerful holistic NGS tool for detailed characterization of myeloid malignancies that can be used for patient stratification and a personalized approach to malignancy in the molecular era. The same approach can be extended to other malignancies. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.
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Klamminger, Gilbert Georg, Laurent Mombaerts, Karoline Klein, Finn Jelke, Giulia Mirizzi, Redouane Slimani, Jean-Jacques Gerardy, et al. "PATH-44. RAMAN SPECTROSCOPY AS A DIAGNOSTIC TOOL IN NEUROPATHOLOGY." Neuro-Oncology 23, Supplement_6 (November 2, 2021): vi125. http://dx.doi.org/10.1093/neuonc/noab196.496.

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Abstract BACKGROUND Although microscopic assessment is still the diagnostic gold standard in pathology, non-light microscopic methods such as new imaging methods and molecular pathology have considerably contributed to more precise diagnostics. As an upcoming method, Raman spectroscopy (RS) offers a "molecular fingerprint" which could be used to differentiate tissue heterogeneity or diagnostic entities. RS has so far been successfully applied on fresh and frozen tissue, however more aggressively, chemically treated tissue such as formalin-fixed, paraffin-embedded (FFPE) samples are challenging for RS. METHODS To address this issue, we examined FFPE samples of a broad range of intracranial tumors (e.g. glioblastoma and primary CNS lymphoma) and also different areas of morphologically highly heterogeneous glioblastoma tumor tissue. The latter in order to classify not only the tumor entity but also histologically defined GBM areas according to their spectral properties. We applied linear and nonlinear machine learning algorithms (Logistic Regression, Random Forest, Support Vector Machine) on our spectroscopic data and compared statistical performance of resulting classifiers. RESULTS We found that Random Forest classification distinguished between glioblastoma and primary CNS lymphoma with a balanced accuracy of 94%, only using Raman measurements on FFPE tissue. Furthermore, our established support vector machine-based classifier identified distinct histological areas in glioblastoma such as tumor core and necroses with an overall accuracy of 70.5% and showed a clear separation between the areas of necrosis and peritumoral zone. CONCLUSIONS This relatively cheap and easy-to-apply tool may serve useful to complement histopathological and molecular diagnostics. It provides an unbiased approach to tumor diagnostics with very little requirements (e.g. histopathological feature completeness of the tumor entity) to the sample. As a conclusion, we propose RS as a potential future additional method in the (neuro)-pathological toolbox for tumor diagnostics.
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Ellis, David I., Warwick B. Dunn, Julian L. Griffin, J. William Allwood, and Royston Goodacre. "Metabolic fingerprinting as a diagnostic tool." Pharmacogenomics 8, no. 9 (September 2007): 1243–66. http://dx.doi.org/10.2217/14622416.8.9.1243.

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Dissertations / Theses on the topic "Molecular diagnostic tool"

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Mohamed, Moumin Neima. "DEVELOPING A MOLECULAR TOOL KIT FOR DIAGNOSTIC PCR." Thesis, Uppsala universitet, Institutionen för kvinnors och barns hälsa, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-392205.

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ABSTRACT The aim of this study is develop and test an inexpensive molecular tool kit to be used for diagnostic PCR for diseases such as Leber hereditary optic neuropathy (LHON) and Cystic fibrosis(CF). By developing and optimizing recombinant Taq polymerase and making a DNA size ladder from plasmids pPSU1 and pPSU2 the financial cost for the tool kit would be reduced significantly compared to the commercial components. With an inhouse method both the recombinant Taq polymerase and the pPSU1 and pPSU2 plasmids were purified from the E.coil strain DH5-α. Thereafter to analyse the components of the tool kit both conventional PCR and Real-time PCR to make sure that the tool kit would work for both types of PCRs.     The homemade Taq polymerase proved to be able to sustain in room temperature for at least 24 h and the polymerase also showed that it works with different primers such as LHON, CF and Beta-globin in both endpoint and probe base real-time PCR. The homemade size marker produced a reliable in agarose gel electrophoresis but requires optimization for continued usage for smaller PCR products.     In conclusion the homemade Taq polymerase will be used in future PCR analysis in the laboratory and the recombinant production process as well. Meanwhile the homemade size marker did not work sufficiency enough to be continuously used with gel electrophoresis in the laboratory without being further modified.
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Menmuir, Sheena. "Visible spectroscopy as a sensitive diagnostic tool for fusion plasmas." Licentiate thesis, KTH, Physics, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-572.

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To further the understanding and knowledge about fusion plasmas and their behaviour during different conditions, it is important to be able to collect information about the plasma and the processes occurring within it. Visible spectroscopy, or the study of the visible wavelength light emitted by the plasma, is a useful tool in this search for knowledge.

This thesis is based on experiments where visible wavelength light has been measured and analysed in order to determine quantities about the emitting source. Doppler shift measurements of spectral lines have been utilised to determine the toroidal rotation velocities of plasma impurity ions and to study the correlation with mode rotation and the effect of active feedback control of the resistive wall modes. Information on the impurities present in the plasma has been determined and the calibrated intensities of spectral lines has yielded impurity concentrations, particle fluxes and electron temperature and densities. Ion temperatures have been determined from Doppler broadening measurements.

The measured vibrational and rotational band structure of deuterium molecular spectra has been analysed in order to calculate rotational and vibrational temperatures, relative populations and molecular particle fluxes. The effect of the molecular flux on simple calculations of atomic flux has also been studied. Specific molecular states and transitions of deuterium have also been probed with synchrotron radiation to study the level and transition energies.

The measurement and analysis of visible wavelength light has been demonstrated to be a sensitive diagnostic tool in the quest for increased knowledge about fusion plasmas and molecular structure.

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Christopeit, Tony. "Protein Interaction Studies with Low Molecular Weight Ligands : Applications for Drug Discovery, Basic Research and Diagnostic Tool Design." Doctoral thesis, Uppsala universitet, Institutionen för kemi - BMC, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-188328.

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In this thesis, the interactions between different proteins and small ligands were characterized by surface plasmon resonance spectroscopy (SPR) and fluorescence resonance energy transfer (FRET) based assays.    For the C-reactive protein (CRP), a new type of artificial binder was identified which allows designing diagnostic assays superior to commonly used standard assays. Furthermore, an interaction study with the endogenous ligand phosphocholine revealed the importance of the avidity of pentameric CRP for the distinction of different types of lipid membranes. The interaction study with calcium showed how SPR based assays can be used to study ion-protein interactions despite the low atomic weight of ions.    The transmembrane protease BACE1, an important drug target for Alzheimer’s disease, was immobilized to an SPR biosensor surface and embedded into a lipid membrane. An interaction study with a set of known BACE1 inhibitors showed that the transmembrane region has only minor effects on the interactions. Furthermore the pH-dependencies of the interactions were investigated and revealed new important conclusions for inhibitor design. Computer aided modelling showed that the protonation state of the aspartic dyad is dependent on the interacting inhibitor which offers new perspectives for in silico screenings. The SPR assay developed for BACE1 was adapted to a more complex membrane protein, the pentameric β3 GABAA receptor. The assay allowed the pharmacological characterisation for histaminergic and GABAergic ligands and gave further evidence for cross-talk between the two signal transduction pathways. This study shows that the immobilisation method used for BACE1 and the ß3 GABAA receptor has the potential to become a standard method for handling membrane proteins.   The identification of new drug leads from natural sources is a common strategy for drug discovery. A combination of SPR and FRET based activity assays were explored to increase the efficiency of this process. For HIV-1 protease, secreted aspartic protease (SAP) 1, 2 and 3 extracts from a marine vertebrate were identified containing potent inhibitors which interacted with the active site of the enzymes. The studies in this thesis show that the investigation of protein interactions is crucial for understanding protein functions and can help to develop novel drugs for the treatment of different diseases.
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Flores, Carolina. "Cassava Bacterial Blight : development of a performant molecular detection tool and diversity analysis of Xanthomonas axonopodis pv. manihotis populations in Venezuela." Thesis, Montpellier, 2017. http://www.theses.fr/2017MONTT161.

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Le manioc (Manihot esculenta L. Crantz) est cultivé dans toute la zone intertropicale. Compte tenu de ses utilisations potentielles, le développement de la culture du manioc a considérablement augmenté au niveau mondial, mais il est encore considéré comme une culture de subsistance en particulier dans les régions pauvres où il est cultivé par les petits producteurs. La production du manioc est fortement contrainte par des facteurs biotiques et abiotiques, dont la bactériose vasculaire du manioc (CBB) et la nécrose bactérienne du manioc (CBN) qui sont deux maladies causées par les bactéries Xanthomonas axonopodis pv. les manihotis (Xam) et X. cassavae (Xc), respectivement. CBB est considérée comme la principale maladie bactérienne, notamment au Venezuela où la CBB a été signalée pour la première fois dans les années 70. Dans les années 90, des études ont été menées pour élucider la variabilité génétique de Xam dans différentes régions du pays, au moyen d’outils moléculaires, mettant en évidence un degré élevé de polymorphisme parmi les souches analysés.Le sujet de cette thèse porte sur la situation de CBB au Venezuela 20 ans après. Quelle est la diversité génétique actuelle de Xam au Venezuela? Quelle est la structure génétique des populations de Xam dans ce pays, et comment diffèrent-elles des souches de Xam recueillies dans les années 90? En outre, étant donné que Xam et Xc provoquent des symptômes semblables sur feuilles de manioc et présentent des caractéristiques physiologiques et morphologiques similaires, nous avons également visé à développer un nouvel outil de diagnostic moléculaire permettant une détection rapide et fiable de Xam et de Xc tout étant capable de les discriminer l’une vis à vis de l’autre.Pour atteindre nos objectifs, nous avons d'abord établi une PCR-duplex comme outil de détection moléculaire des xanthomonades infectant le manioc. Sur la base de l'analyse in silico des séquences du génome de 66 souches de Xam et une de Xc, nous avons pu sélectionner 6 paires d'amorces candidates spécifiques de Xam et six autres pour Xc. Nous avons pu développer un test de PCR-duplex qui a été validé en testant 53 souches de Xam et 25 souches de Xc issues de différents pays, 18 souches non cibles contrôles et cinq souches épiphytes associées au manioc. Cette technique représente un outil utile pour détecter et différencier Xam et Xc provenant de cultures in vitro mais aussi fonctionnelle à partir de tissues de plantes infectés.Deuxièmement, nous avons donc évalué la diversité des populations de Xam à l’aide de l’étude de microsatellites (ou MLVA pour « Multiple loci VNTR analysis »). Une enquête de terrain menée dans six États du Venezuela a permis d'évaluer la présence de la maladie, son statut et nous a permis d'établir une collection de souches de Xam dont l’analyse détaillée de la diversité a pu être réalisée. Au total nous avons isolé 202 souches de Xam issues de six localités situées dans quatre états. À l'aide d'un schéma 14-MVLA, nous avons analysé 12 populations et mis en évidence un indice élevé de la diversité génétique au sein de ces populations et entre elles, et principalement dans l'est du pays.Le développement de ce type de recherche est essentiel pour une gestion raisonnée des cultures dans le monde. Conjugué aux politiques agricoles existantes, il nous permettra de mieux comprendre les agents pathogènes d'importance agricole et les mécanismes impliqués dans leur établissement dans le temps et à travers l’espace. L'objectif à long terme est d'appliquer des mesures de contrôle efficaces et durables, ce qui conduira à des mesures de quarantaine plus efficaces pour prévenir la propagation de la maladie
Cassava (Manihot esculenta L. Crantz) belongs to the group of roots and tubers and is cultivated in the tropics worldwide. This species is a nutritional alternative in many populations where no optimal crop production, general conditions nor technological support exist. Considering its potential uses, the global development of cassava crop has increased significantly but it is still considered a subsistence crop in poor regions lead by smallholder producers. Cassava is affected by biotic and abiotic factors during its life cycle, which heavily limiting its optimal performance. A variety of pests and diseases are known to affect cassava production. Among them are those caused by Xanthomonas axonopodis pv. manihotis (Xam) and Xanthomonas cassavae (Xc), causal agents of Cassava Bacterial Blight (CBB) and Cassava Bacterial Necrosis (CBN) diseases, respectively. CBB is considered the major bacterial disease that affects cassava crop worldwide which is also the case in Venezuela where it was first reported in the 70s. Since the 90s, studies were conducted to elucidate Xam genetic variability in different regions in the country, by means of different molecular tools available at that time. A high degree of polymorphism among the isolates was reported, whether collected from the same or different fields. The Xam population was distributed into eight clusters and no correlation was observed between genetic diversity and geographic origin.Our questions deal with the situation of CBB in Venezuela 20 years later : what is the current genetic diversity of Xam populations in Venezuela? what is the genetic structure of Xam populations and how do they differ with respect to Xam strains collected in 90s. Moreover, because Xam and Xc cause similar symptoms on cassava leaves and display similar physiological and morphological characteristics, we also aimed at developing a new molecular diagnostic tool allowing for fast and reliable detection of Xam and able to discriminate with Xc.To achieve our goals, we first established a duplex-PCR as a molecular detection tool of cassava-infecting xanthomonads. Based on in silico analysis of the genome sequences of 66 Xam and 1 Xc strains, we were able to select 6 Xam and 6 Xc primers pairs candidates, of which one set of primers for each was selected for further studies. We were able to develop a duplex-PCR assay that was validated upon testing 53 Xam strains and 25 Xc strains from different countries, 18 non-target strains, and 5 epiphytic strains associated to cassava, proving this technique a useful tool to detect and differentiate Xam and Xc from in vitro cultures and in planta.Secondly we assessed the diversity of Xam populations through a variable number of tandem repeat analysis (MLVA). A field survey conducted in six states in Venezuela enabled to evaluate the occurence of the disease, its status and allowed us to establish a strain collection for detailed diversity analysis. We isolated 202 Xam strains from six localities, localized in four states. Using a MVLA14-scheme, we analyzed 12 populations highlighting a high index of genetic diversity among and within populations, mainly in the east of the country.The development of this type of research is essential in the management of crops in the world and coupled with the existing agricultural policies, it will allow us to have a deeper understanding of pathogens of agricultural importance and the mechanisms involved in their establishment over time and across regions. The long-term objective of this is to apply control measures that are effective in time, thus establishing more stringent quarantine measures to prevent the spread of the disease
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CHIACCHIO, TERESA. "New molecular diagnostic and immunological tools for tuberculosis research." Doctoral thesis, Università degli Studi di Roma "Tor Vergata", 2009. http://hdl.handle.net/2108/916.

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Tuberculosis (TB) remains one of the world’s leading causes of mortality due to a single infectious agent, with approximately 1.5 million deaths and 9.2 million new cases per year as estimated in 2006. It is assumed that about 5-10% of individuals infected with M. tuberculosis develop TB and the remaining 90-95% contain M. tuberculosis through their immune systems, but have a latent tuberculosis infection (LTBI). To effectively control TB, it is essential to detect individuals with LTBI and to reliably diagnose active TB. Conventional TB diagnosis continues to rely on smear microscopy and culture that have several known limitations in terms of both speed and sensitivity that delay the diagnosis and, consequently, hold-up TB treatment and increase the spread of infection in the community. M. tuberculosis infection remains widespread, but the disease is generally limited to the primary infection stage. Patients with an immune defect or impaired immunity are more prone to develop the disease. In LTBI, the host immune response is capable of controlling the infection by the release of chemokines and cytokines produced by T helper (Th) cells, critical for the outcome of the infection. Several cells of the immune system are involved in the control of TB, from the macrophages and dendritic cells, called antigen presenting cells (APC) to the T cells, CD4, CD8, gamma delta T cells. Activation of these cells with excessive pro inflammatory responses can lead to tissue damage, with the need of mechanisms to counteract this, such as Th2 and T regulatory cells (Treg)-mediated responses. The optimal scenario would therefore seem to have balanced Th1, Th2 and Treg response, suited to the immune challenge. The balance between these types of response is reflected in the resultant host resistance against infection. Therefore the aims of the thesis were to find new approaches for diagnosis of active TB (First Part) and LTBI (Second Part). In this work we wanted to explore the immune mechanisms of TB pathogenesis with particular focus on the impact of Treg on suppressing M. tuberculosis-specific response (Third Part). For the diagnosis of active TB, we describe an alternative PCR methodology based on the amplification of small DNA fragments, originated from cells dying throughout the body (transrenal DNA; Tr-DNA) and detected in urine. It was found that small M. tuberculosis DNA fragments were specifically detected in the cell-free fraction of urine specimens from pulmonary TB patients. To detect LTBI, we compared the performances of two short-incubation interferon (IFN)-g release assays (IGRAs), the commercial QuantiFERON TB-Gold and the in-house whole blood stimulation with region of difference (RD)-1 proteins, with those of a 7-day whole blood stimulation and tuberculin skin test (TST). In an effort to find new markers for LTBI diagnosis, we also evaluated the production of pro-inflammatory cytokines [interleukin (IL)-1, IL-2, IL-6 and Tumor Necrosis Factor (TNF)-alfa], anti-inflammatory cytokines (IL-4, IL-10, IL-13) and chemokines [inducible protein (IP)-10, Macrophage Inflammatory Protein (MIP)-alfa, MIP-1beta, IL-8] after specific stimulation. The results raise the hypothesis that short-incubation IGRAs mainly detect recent or ongoing infection with M. tuberculosis, while prolonged-incubation IGRAs seem to be more sensitive for the diagnosis of past latent infection. Moreover we found that IL-2 and IP-10 may be additional markers for TB infection after RD1 specific stimulation. Finally we wanted to evaluate the impact of Treg on suppressing M. tuberculosis-specific response. Using classical markers for Treg recognition, discordant results were found in terms of Treg expansion during active TB disease. Recently CD39 has been shown to be an accurate marker for Treg detection. Objectives of this part of the thesis were: 1) to identify Treg expressing CD39 in patients with TB and to compare the results with those obtained by the standard phenotypic markers; 2) to evaluate if Treg are expanded in vitro by exogenous IL-2 or by antigen-specific stimulation; 3) to characterize Treg function on the modulation of antigen-specific responses. In this study we demonstrated that CD39 is a useful marker to detect Treg because within CD4+CD25high cells, it identifies a cell subset characterized by high production of transforming growth factor (TGF)-beta1 and the absence of IFN-gamma expression. Moreover, we showed that CD39+ Treg are expanded by M. tuberculosis-specific stimulation in patients with active TB disease.
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Ebai, Tonge. "Development of Enhanced Molecular Diagnostic Tools for Protein Detection and Analysis." Doctoral thesis, Uppsala universitet, Molekylära verktyg, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-320380.

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Improved diagnosis, prognosis and disease follow-up is a fundamental procedure and a constant challenge in medicine.  Among the different molecular biomarkers, proteins are the essential regulatory component in blood; hence, by developing enhanced specific and sensitive molecular tools will gives great insight into the different processes in disease treatment.  In this thesis, we build on the proximity ligation assay to develop and apply new adaptable methods to facilitate protein detection. In paper I, I present a variant of the proximity ligation assay (we call PLARCA) using micro titer plate for detection and quantification of protein using optical density as readout in the fluorometer. PLARCA detected femtomolar levels of these proteins in patient samples, which was considerably below the detection threshold for ELISA. In paper II, we developed and adapted a new method into the in situ PLA methods for detection and identification of extracellular vesicles (EVs) using flow cytometry as readout (a method we call ExoPLA).  We identified five target proteins on the surface of the Evs and using three colors, we identified the EV using flow cytometer. In paper III, we aim to improve the efficiency of in situ PLA by creating and developing new designs and versions of the assay we called Unfold probes Through comparison of detection of protein using in situ PLA versus Unfold probes, we observed considerable decrease in non-specific signals, and also a lower detection threshold. In paper IV, we describe the development of a solid phase proximity extension (sp-PEA) assay for protein detection and quantification. We compared detection of IL-8, TNF-alpha, IL-10 and IL-6 using spPEA and PEA; spPEA demonstrations over 2 orders of magnitudes in the lower detection concentrations by decreased in background noise.
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Fluegel, Amanda M. "Validation of diagnostic assays and development of molecular epidemiological tools for brucellosis." Laramie, Wyo. : University of Wyoming, 2008. http://proquest.umi.com/pqdweb?did=1594477821&sid=1&Fmt=2&clientId=18949&RQT=309&VName=PQD.

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Holzapfel, Marion. "De l’épidémiologie moléculaire aux analyses fonctionnelles de Brucella chez les ruminants, une approche intégrée pour l’identification et l’étude de la diversité phénotypique d’un genre génétiquement homogène." Thesis, Paris Est, 2018. http://www.theses.fr/2018PESC1141.

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La brucellose est une zoonose causée par le genre bactérien Brucella (B.) dont l’incidence mondiale est estimée à 500 000 cas humains par an. Le réservoir est animal, touchant principalement les espèces de rente. Les espèces les plus importantes pour l’Homme sont B. melitensis, B. abortus et B. suis qui partagent plus de 90% d’identité de séquence. Bien qu’elles soient très apparentées sur le plan génétique, elles présentent une diversité de caractéristiques phénotypiques, de préférence d’hôte et de pathogénicité. L’homogénéité génétique de ces espèces peut apparaître comme un atout pour le développement d’outils de diagnostic universels robustes. En revanche, il s’agit d’un challenge pour les distinguer, rendant difficile la caractérisation précise des isolats issus d’un même foyer. Dans le cadre de cette thèse, un outil de diagnostic moléculaire de PCR en temps réel ciblant le genre Brucella a été développé et optimisé. L’outil a été évalué sur des prélèvements de lait de ruminants, ces prélèvements peuvent être une source importante de Brucella et peuvent être utiles au dépistage de la maladie à l’échelle du troupeau. Basée sur la détection de l’élément d’insertion IS711, une séquence présente en plusieurs exemplaires dans le génome, cette méthode affiche des valeurs de sensibilité et de spécificité qui la rendent intéressante pour un schéma global de lutte contre la brucellose. D’autre part, en vue d’améliorer la compréhension de la stabilité génétique de B. melitensis, un panel original de souches isolées dans le cadre d’un foyer et impliquant 4 espèces d’hôtes différentes a été comparé. Ainsi à l’aide de différentes approches complémentaires, leurs séquences génomiques, les caractères phénotypiques ainsi que leurs comportements dans un modèle in vitro ont été comparés. Nos résultats n’ont pas mis en évidence marqueurs qui laisserait à penser que des mutations dans le génome soient indispensables pour s’adapter à un nouvel hôte
Brucellosis is a zoonotic disease caused by the bacterial genus Brucella (B.), whose global incidence is estimated at 500,000 human cases per year. The reservoir is animal, affecting mainly livestock. The most important species for humans are B. melitensis, B. abortus and B. suis, which share more than 90% sequence identity. Although highly genetically related, Brucella spp. exhibit a variety of phenotypic characteristics, host preference and pathogenicity. The genetic homogeneity of these species may appear as an asset for the development of robust universal diagnostic tools. On the other hand, it is a challenge to distinguish them, making it difficult to precisely characterize isolates from the same outbreak. As part of this thesis, a real-time PCR molecular diagnostic tool targeting the genus Brucella was developed and optimized. The method has been evaluated on ruminant milk samples; these samples may be an important source of Brucella and may be useful for herd-scale disease screening. Based on the detection of the IS711 insertion element, a sequence present in several copies within the genome, this method displays sensitivity and specificity values that make it interesting for a global scheme to fight against brucellosis. On the other hand, in order to improve the understanding of the genetic stability of B. melitensis, an original panel of strains isolated in an outbreak and involving four different host species was compared. Thus, using different complementary approaches, their genomic sequences, phenotypic characteristics and their behavior in an in vitro model were compared. Our results did not highlight markers that would suggest that mutations in the genome are essential to adapt to a new host
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Lopes, Jéssica Sousa. "FTIR, a potential tool to dementia diagnosis trough analysis of plasma." Master's thesis, Universidade de Aveiro, 2016. http://hdl.handle.net/10773/16149.

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Mestrado em Biomedicina Molecular
Nowadays it is still difficult to perform an early and accurate diagnosis of dementia, therefore many research focus on the finding of new dementia biomarkers that can aid in that purpose. So scientists try to find a noninvasive, rapid, and relatively inexpensive procedures for early diagnosis purpose. Several studies demonstrated that the utilization of spectroscopic techniques, such as Fourier Transform Infrared Spectroscopy (FTIR) and Raman spectroscopy could be an useful and accurate procedure to diagnose dementia. As several biochemical mechanisms related to neurodegeneration and dementia can lead to changes in plasma components and others peripheral body fluids, blood-based samples and spectroscopic analyses can be used as a more simple and less invasive technique. This work is intended to confirm some of the hypotheses of previous studies in which FTIR was used in the study of plasma samples of possible patient with AD and respective controls and verify the reproducibility of this spectroscopic technique in the analysis of such samples. Through the spectroscopic analysis combined with multivariate analysis it is possible to discriminate controls and demented samples and identify key spectroscopic differences between these two groups of samples which allows the identification of metabolites altered in this disease. It can be concluded that there are three spectral regions, 3500-2700 cm -1, 1800-1400 cm-1 and 1200-900 cm-1 where it can be extracted relevant spectroscopic information. In the first region, the main conclusion that is possible to take is that there is an unbalance between the content of saturated and unsaturated lipids. In the 1800-1400 cm-1 region it is possible to see the presence of protein aggregates and the change in protein conformation for highly stable parallel β-sheet. The last region showed the presence of products of lipid peroxidation related to impairment of membranes, and nucleic acids oxidative damage. FTIR technique and the information gathered in this work can be used in the construction of classification models that may be used for the diagnosis of cognitive dysfunction.
Atualmente, não é possível fazer um diagnóstico precoce e diferencial da doença de Alzheimer, deste modo, é necessário encontrar biomarcadores que o permitam. Para isso, os cientistas tentam encontrar um procedimento nãoinvasivo, rápido, e relativamente barato. Os resultados de vários estudos demonstraram que a utilização de técnicas espectroscópicas, tais como a Espectroscopia de Infravermelho Transformada de Fourier (FTIR) e / ou espectroscopia de Raman, podem ser ferramentas úteis para diagnosticar a DA. Uma vez que, na DA, alguns mecanismos bioquímicos podem levar a mudanças em componentes do plasma, podem então ser utilizadas amostras de sangue nas análises espectroscópicas o que torna a técnica simples e menos invasiva. Com este trabalho pretende-se confirmar algumas das hipóteses de estudos anteriores em que o FTIR foi usado no estudo de amostras de plasma de possíveis doentes com DA e respetivos controlos e verificar a reprodutibilidade desta técnica espectroscópica na análise deste tipo de amostras. Através da análise espectroscopia combinada com análise multivariada é possível discriminar as amostras controlos e dementes e identificar as principais diferenças espectroscópicas entre estes dois grupos de amostras que permitem identificar os metabolitos alterados nesta patologia. Pode-se concluir que existem três regiões espectrais, 3500-2700 cm-1, 18001400 cm-1 e 1200-900 cm-1 onde se pode extrair informação espectroscópica relevante. Na primeira região, a principal conclusão que é possível tirar é que há um desequilíbrio entre o teor de lípidos saturados e insaturados. Na região entre 1800-1400 cm-1, é possível observar a presença de agregados de proteínas e a alteração na conformação das proteínas para folha β paralela altamente estável. A última região revelou a presença de produtos de peroxidação lipídica relacionados com a insuficiência de membranas, e danos oxidativos nos ácidos nucleicos. A técnica de FTIR e a informação reunida neste trabalho pode ser utilizada na construção de modelos de classificação que possam vir a ser utilizados para o diagnóstico de disfunções cognitivas.
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Englund, Stina. "Molecular biology techniques as a tool for detection and characterisation of Mycobacterium avium subsp. paratuberculosis /." Uppsala : Dept. of Veterinary Microbiology, Swedish Univ. of Agricultural Sciences ([Institutionen för veterinärmedicinsk mikrobiologi], Sveriges lantbruksuniv.), 2002. http://epsilon.slu.se/avh/2002/91-576-6366-1.pdf.

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Books on the topic "Molecular diagnostic tool"

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Licha, Kai, and Alexei Bogdanov. Molecular Imaging: An Essential Tool in Preclinical Research, Diagnostic Imaging, and Therapy. Springer Berlin / Heidelberg, 2014.

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Licha, Kai, and Alexei Bogdanov. Molecular Imaging: An Essential Tool in Preclinical Research, Diagnostic Imaging, and Therapy. Springer London, Limited, 2007.

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(Editor), A. A: Bogdanov, and K. Licha (Editor), eds. Molecular Imaging: An Essential Tool in Preclinical Research, Diagnostic Imaging, and Therapy (Ernst Schering Foundation Symposium Proceedings). Springer, 2004.

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Veedu, Rakesh N. Aptamers: Tools for Nanotherapy and Molecular Imaging. Jenny Stanford Publishing, 2017.

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Witt, Michal, Malgorzata Dawidowska, and Tomasz Szczepanski. Molecular Aspects of Hematologic Malignancies: Diagnostic Tools and Clinical Applications. Springer London, Limited, 2012.

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Molecular Aspects Of Hematologic Malignancies Diagnostic Tools And Clinical Applications. Springer, 2012.

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Witt, Michal, Malgorzata Dawidowska, and Tomasz Szczepanski. Molecular Aspects of Hematologic Malignancies: Diagnostic Tools and Clinical Applications. Springer, 2015.

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Molecular Diagnostics and Biological Safety 2021. COVID-19: Epidemiology, Diagnosis and Prophylaxis: Conference Abstracts. Central Research Institute for Epidemiology, 2021. http://dx.doi.org/10.36233/978-5-6045286-2-4.

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The pandemic of the new coronavirus infection has spread to more than 200 countries. To date, over 130 million people have been affected and over 2.8 million have died. COVID-19 infection has a number of specific epidemiological and clinical features. In severe cases of the disease, acute respiratory distress syndrome develops, which is often fatal. The SARS-CoV-2 virus is susceptible to mutations, which alarms the scientific community all over the world. Therefore, scientific research in the field of COVID-19, the search for new diagnostic tools, methods for nonspecific and specific prevention and treatment are central topics today.This collection contains abstracts submitted by leading experts in the field of epidemiology, clinics of infectious diseases, molecular diagnostics, young researchers and medical practitioners. Published materials contain data on the methods of molecular diagnostics of COVID-19, se-quencing of the SARS-CoV-2 genome, epidemiology of new coronavirus infection, immuno-pathogenesis of COVID-19, clinical features of infection and treatment options, as well as the study of post-infectious and post-vaccination immunity and examples of complex measures for nonspecific prevention of COVID-19.The materials of the Congress are of interest to doctors and researchers of all specialties, teachers of secondary and higher educational institutions.
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Aptamers: Tools for Nanotherapy and Molecular Imaging. Taylor & Francis Group, 2016.

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Veedu, Rakesh N. Aptamers: Tools for Nanotherapy and Molecular Imaging. Jenny Stanford Publishing, 2017.

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Book chapters on the topic "Molecular diagnostic tool"

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Sędek, Łukasz, Juan Flores-Montero, Joanna Bulsa, Susana Barrena, Julia Almeida, Alberto Orfao, and Tomasz Szczepański. "Flow Cytometric Immunophenotyping as Diagnostic Tool of Hematopoietic Malignancies." In Molecular Aspects of Hematologic Malignancies, 143–60. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-642-29467-9_9.

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Bastian, Boris C. "Molecular Cytogenetics as a Diagnostic Tool for Typing Melanocytic Tumors." In Cancers of the Skin, 92–99. Berlin, Heidelberg: Springer Berlin Heidelberg, 2002. http://dx.doi.org/10.1007/978-3-642-59410-6_13.

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Adams, Ian P., Rachel H. Glover, Wendy A. Monger, Richard Thwaites, Rick Mumford, Elena Jackeviciene, Meletele Navalinskiene, Marija Samuitiene, and Neil Boonham. "Next-Generation Sequencing and Metagenomic Analysis: A Universal Diagnostic Tool in Plant Pathology." In Handbook of Molecular Microbial Ecology II, 63–72. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2011. http://dx.doi.org/10.1002/9781118010549.ch7.

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Cottrell, Isabel, Asma Khan, Sidra Maqsood, Jemma Thornes, and Paul Eggleton. "Meta-analysis as a Diagnostic Tool for Predicting Disease Onset and/or Activity in Systemic Lupus Erythematosus." In Methods in Molecular Biology, 249–59. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-0326-9_19.

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Leary, Scot C. "Blue Native Polyacrylamide Gel Electrophoresis: A Powerful Diagnostic Tool for the Detection of Assembly Defects in the Enzyme Complexes of Oxidative Phosphorylation." In Methods in Molecular Biology, 195–206. Totowa, NJ: Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-504-6_13.

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Izumi, Takuma. "AGN Feedback on the CND-Scale Molecular Gas: Submillemeter HCN Enhancement as a New Extinction Free Energy Diagnostic Tool." In Springer Theses, 29–69. Singapore: Springer Singapore, 2018. http://dx.doi.org/10.1007/978-981-10-7910-8_2.

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Castagnone-Sereno, Philippe, Andrea Skantar, and Lee Robertson. "Molecular Tools for Diagnostics." In Genomics and Molecular Genetics of Plant-Nematode Interactions, 443–64. Dordrecht: Springer Netherlands, 2011. http://dx.doi.org/10.1007/978-94-007-0434-3_21.

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Ruiz, Blanca Iciar Indave. "Improving the WHO Classification of Tumours by an Evidence-Based Approach: A New Online/Blended Learning Training Program." In Improving Oncology Worldwide, 43–53. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-030-96053-7_6.

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AbstractThe WHO Classification of Tumours (WCT) is a series of authoritative and concise reference books for the histological and molecular classification of tumors that underpins treatment and care of cancer patients, as well as research into cancer epidemiology, prevention, diagnosis, and treatment, and is essential for cancer diagnosis worldwide. This classification relies traditionally on consensus of pathological expert opinions as basis for cancer classification, but the understanding of cancer at a molecular level advances in prognosis, and other related fields have moved the WCT to find ways of translating diagnostic research into evidence synthesis that can effectively inform decisions relevant to the classification. Systematic reviews represent the top of the hierarchy of scientific evidence and allow to summarize evidence from many publications to inform decisions. This evidence-based approach is the cornerstone of evidence-based medicine and well established in many medical specialties. However, uptake of these principles within pathology has been slow, and such high-quality reviews of available evidence are not easily available for authors contributing to the WCT. In an effort to overcome reluctance in the field to adopt these methods, a collaborative project between the Advanced Oncology program of the University of Ulm in Germany, the Cochrane Netherlands, the Universidad de Campinas in Brazil, and the WCT has been started. This project called Evi-Pat (Evidence-Based Pathology Training Initiative) aims to develop and evaluate an online training for oncologists and pathologists to train them in the application of evidence-based practice to pathology and related specialties, thereby addressing and overcoming challenges in this, and to pathology, novel approach. Scientific and didactic evaluation of such an effective training tool for online-educated pathologists and oncologists will improve the evidence base in pathology and hence provide a solid foundation for diagnostic and prognostic decision-making. We believe that an evidence-based approach to informing key decisions that feed into tumor classification will allow the WCT editorial board to mitigate the potential inclusion of biased decisions into the classification and also benefit authors by providing structured, transparent, and reliable methods for the synthesis of available evidence for each tumor type, as the same time training to apply these methodologies.
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Uno, Naoki, and Katsunori Yanagihara. "Rapid Diagnosis of Influenza Viral Infection: What Are the Rapid Diagnostic Tests and Molecular Diagnosis?" In Respiratory Disease Series: Diagnostic Tools and Disease Managements, 69–77. Singapore: Springer Singapore, 2020. http://dx.doi.org/10.1007/978-981-15-9109-9_7.

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Garg, Shivanshu, P. R. Shashank, Naresh M. Meshram, and S. N. Bhagyashree. "Modern Molecular Tools for Insect Diagnostics." In Genetic Methods and Tools for Managing Crop Pests, 45–67. Singapore: Springer Nature Singapore, 2022. http://dx.doi.org/10.1007/978-981-19-0264-2_3.

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Conference papers on the topic "Molecular diagnostic tool"

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Schweitzer, Dietrich, Matthias Klemm, Stefan Schenke, Silvio Quick, Lydia Deutsch, Susanne Jentsch, and Martin Hammer. "FLIM in Ophthalmology - a Diagnostic Tool for Metabolic Mapping." In Optical Molecular Probes, Imaging and Drug Delivery. Washington, D.C.: OSA, 2011. http://dx.doi.org/10.1364/omp.2011.otub2.

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Wanichapichart, Pikul, Tanawat Wongluksanapan, and Leang Khooburat. "Electrorotation: Diagnostic Tool for Abnormality of Marine Phytoplankton Cells." In 2007 2nd IEEE International Conference on Nano/Micro Engineered and Molecular Systems. IEEE, 2007. http://dx.doi.org/10.1109/nems.2007.352213.

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Larsen, A., J. Hughes, and T. Frazier. "Molecular Breast Imaging as a Cost Effective Diagnostic Tool for Breast Cancer." In Abstracts: Thirty-Second Annual CTRC‐AACR San Antonio Breast Cancer Symposium‐‐ Dec 10‐13, 2009; San Antonio, TX. American Association for Cancer Research, 2009. http://dx.doi.org/10.1158/0008-5472.sabcs-09-5014.

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Jacobsen, Martha Rolland, Harsh Dongre, Israa Ahmed, Vidisha Tuljaurkar, Prathamesh S. Pai, Asawari Patil, Dipak Sapkota, et al. "Abstract 45: Development of a molecular diagnostic tool for more precise diagnosis of oral squamous cell carcinoma." In Abstracts: AACR-AHNS Head and Neck Cancer Conference: Optimizing Survival and Quality of Life through Basic, Clinical, and Translational Research; April 23-25, 2017; San Diego, CA. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1557-3265.aacrahns17-45.

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Facciotti, M., P. S. Amaro, R. C. D. Brown, P. L. Lewin, J. A. Pilgrim, G. Wilson, and P. N. Jarman. "SSIMS molecular selective imaging: A new diagnostic tool to investigate metal passivators in scrapped transformers." In 2015 IEEE Electrical Insulation Conference. IEEE, 2015. http://dx.doi.org/10.1109/icacact.2014.7223492.

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Suarthana, Eva, Olivier Vandenplas, Mahsa Taghiakbari, Jacques A. Pralong, Paramita Saha-Chaudhuri, Gregory Moullec, Roberto Castano, et al. "Diagnostic model for occupational asthma induced by high-molecular-weight agents: A tertiary prevention tool." In ERS International Congress 2021 abstracts. European Respiratory Society, 2021. http://dx.doi.org/10.1183/13993003.congress-2021.pa1908.

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Lunak, M., Z. Chobola, J. Vanek, and E. Hulicius. "Low noise as a diagnostic tool for GaSb based laser diodes prepared by Molecular Beam Epitaxy." In 2012 28th International Conference on Microelectronics (MIEL 2012). IEEE, 2012. http://dx.doi.org/10.1109/miel.2012.6222870.

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Matsuda, Yu, Hiroki Yamaguchi, Yasuhiro Egami, and Tomohide Niimi. "Pressure-Sensitive Molecular Film for Experimental Analyses of Micro Gas-Flows." In ASME 2011 9th International Conference on Nanochannels, Microchannels, and Minichannels. ASMEDC, 2011. http://dx.doi.org/10.1115/icnmm2011-58259.

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Pressure-sensitive paint (PSP) is an optical measurement technique based on the photo-chemical reaction between oxygen and luminescent molecules, and has potential as a diagnostic tool for pressure measurement in the high Knudsen number regime. However, the application of PSP to micro flow measurement is not straightforward, because conventional PSPs are too thick owing to their polymer binder. In our previous work, we fabricated pressure-sensitive molecular film (PSMF) by using the Langmuir-Blodgett (LB) technique. In this study, we investigated the temperature dependency of Pt(II) Mesoporphyrin IX (PtMP) based PSMF, and found that the temperature dependency of the pressure sensitivity is very small. Moreover, we have applied PSMF to the pressure measurement of micro gas flows through the 170μm width micro channel and the 100μm width micro nozzle, and the pressure distributions were successfully obtained.
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Lucht, Robert P., Michael S. Brown, and Larry A. Rahn. "Effects of Doppler Broadening and Unequal Pump Intensities in Saturated Degenerate Four-Wave Mixing Spectroscopy." In Laser Applications to Chemical Analysis. Washington, D.C.: Optica Publishing Group, 1994. http://dx.doi.org/10.1364/laca.1994.fb.2.

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Degenerate four-wave mixing (DFWM) is a technique that shows great promise for sensitive measurements of transient gas-phase species, and diagnostic applications of DFWM are being pursued actively at laboratories throughout the world. Applications of DFWM as a combustion diagnostic and as a tool for molecular spectroscopy are reviewed in a recent article by Farrow and Rakestraw (1992). However, significant questions remain regarding strategies for quantitative concentration measurements using DFWM.
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Hussein Ayoub AL-JABISH, Bassam, Ibtisam N. AL-ASSAF, and Iman Radha JASIM. "SIMILARITY AND DISSIMILARITY OF PHENOTYPIC AND GENOTYPIC CHARACTERISTICS OF PRUNUS DEMOSTICA (L.) ROSACEAE IN NORTH OF IRAQ (NINAVAH)." In VI.International Scientific Congress of Pure,Applied and Technological Sciences. Rimar Academy, 2022. http://dx.doi.org/10.47832/minarcongress6-20.

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Prunus domestica is recognized as a species of fruit tree grown all over the world. It is used locally for various commercial purposes. In this research, we determined of the morphological and genetic diversity present for 5 samples of P. domestica cultivars from the governorate of Ninavah (Northern,Iraq).Five categorical fruit properties assist us to detect the varieties under phenotypic study. Five plum cultivars identified, they referred by P. domistica Santa Rosa(SR),P. domistica,Black Diamond(BD);P. domistica, Black Beauty(BB);P. domistica Angeleno(AG) and P. domistica Red Heart(RH). Morphological diagnosis were included shape, diameter, color and indumentum for fruits were depended to differentiate among the cultivars in this study, molecular diversity was detected by using universal primers represent mtK(Maturase) gene. The results showed that there were significant difference among the specimens morphologically, whereas alleles of maturase K(matK)gene, revealed significance outcomes for detection of each cultivar with specific amplification products(BD-mtK414bp.,SR-mtK344bp.,AG-mtK271 bp., RH-mtK263bp.andBB-mtK 258bp).We concluded that molecular screening is a significance diagnostic and confirmative tool for classify of economic fruited trees.
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Reports on the topic "Molecular diagnostic tool"

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Levisohn, Sharon, Maricarmen Garcia, David Yogev, and Stanley Kleven. Targeted Molecular Typing of Pathogenic Avian Mycoplasmas. United States Department of Agriculture, January 2006. http://dx.doi.org/10.32747/2006.7695853.bard.

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Intraspecies identification (DNA "fingerprinting") of pathogenic avian mycoplasmas is a powerful tool for epidemiological studies and monitoring strain identity. However the only widely method available for Mycoplasma gallisepticum (MG) and M. synoviae (MS)wasrandom amplified polymorphic DNA (RAPD). This project aimed to develop alternative and supplementary typing methods that will overcome the major constraints of RAPD, such as the need for isolation of the organism in pure culture and the lack of reproducibility intrinsic in the method. Our strategy focussed on recognition of molecular markers enabling identification of MG and MS vaccine strains and, by extension, pathogenic potential of field isolates. Our first aim was to develop PCR-based systems which will allow amplification of specific targeted genes directly from clinical material. For this purpose we evaluated the degree of intraspecies heterogeneity in genes encoding variable surface antigens uniquely found in MG all of which are putative pathogenicity factors. Phylogenic analysis of targeted sequences of selected genes (pvpA, gapA, mgc2, and lp) was employed to determine the relationship among MG strains.. This method, designated gene targeted sequencing (GTS), was successfully employed to identify strains and to establish epidemiologically-linked strain clusters. Diagnostic PCR tests were designed and validated for each of the target genes, allowing amplification of specific nucleotide sequences from clinical samples. An mgc2-PCR-RFLP test was designed for rapid differential diagnosis of MG vaccine strains in Israel. Addressing other project goals, we used transposon mutagenesis and in vivo and in vitro models for pathogenicity to correlated specific changes in target genes with biological properties that may impact the course of infection. An innovative method for specific detection and typing of MS strains was based on the hemagglutinin-encoding gene vlhA, uniquely found in this species. In parallel, we evaluated the application of amplified fragment length polymorphism (AFLP) in avian mycoplasmas. AFLP is a highly discriminatory method that scans the entire genome using infrequent restriction site PCR. As a first step the method was found to be highly correlated with other DNA typing methods for MG species and strain differentiation. The method is highly reproducible and relatively rapid, although it is necessary to isolate the strain to be tested. Both AFLP and GTS are readily to amenable to computer-assisted analysis of similarity and construction of a data-base resource. The availability of improved and diverse tools will help realize the full potential of molecular typing of avian mycoplasmas as an integral and essential part of mycoplasma control programs.
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Levisohn, Sharon, Mark Jackwood, and Stanley Kleven. New Approaches for Detection of Mycoplasma iowae Infection in Turkeys. United States Department of Agriculture, February 1995. http://dx.doi.org/10.32747/1995.7612834.bard.

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Mycoplasma iowae (Mi) is a pathogenic avian mycoplasma which causes mortality in turkey embryos and as such has clinical and economic significance for the turkey breeder industry. Control of Mi infection is severely hampered by lack of adequate diagnostic tests, together with resistance to most antibiotics and resilience to environment. A markedly high degree of intra-species antigenic variation also contributes to difficulties in detection and control of infection. In this project we have designed an innovative gene-based diagnostic test based on specific amplification of the 16S rRNA gene of Mi. This reaction, designed Multi-species PCR-RFLP test, also amplifies the DNA of the pathogenic avian mycoplasmas M. gallisepticum (Mg) and M. synoviae (Ms). This test detects DNA equivalent to about 300 cfu Mi or either of the other two target mycoplasmas, individually or in mixed infection. It is a quick test, applicable to a wide variety of clinical samples, such as allantoic fluid or tracheal or cloacal swab suspensions. Differential diagnosis is carried out by gel electro-phoresis of the PCR amplicon digested with selected restriction enzymes (Restriction Fragment Length Polymorphism). This can also be readily accomplished by using a simple Dot-Blot hybridization assay with digoxigenin-labeled oligonucleotide probes reacting specifically with unique Mi, Mg or Ms sequences in the PCR amplicon. The PCR/OLIGO test increased sensitivity by at least 10-fold with a capacity for rapid testing of large numbers of samples. Experimental infection trials were carried out to evaluate the diagnostic tools and to study pathogenesis of Mi infection. Field studies and experimental infection of embryonated eggs indicated both synergistic and competitive interaction of mycoplasma pathogens in mixed infection. The value of the PCR diagnostic tests for following the time course of egg transmission was shown. A workable serological test (Dot Immunobinding Assay) was also developed but there was no clear-cut evidence that infected turkeys develop an immune response. Typing of a wide spectrum of Mi field isolates by a variety of gene-based molecular techniques indicated a higher degree of genetic homogeneity than predicted on the basis of the phenotypic variability. All known strains of Mi were detected by the method developed. Together with an M. meleagridis-PCR test based on the same gene, the Multi-species PCR test is a highly valuable tool for diagnosis of pathogenic mycoplasmas in single or mixed infection. The further application of this rapid and specific test as a part of Mi and overall mycoplasma control programs will be dependent on developments in the turkey industry.
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Osburn, Bennie, Marius Ianconescu, Geoffrey Akita, and Rozalia Kaufman. Rapid, Sensitive Bluetongue Virus Serogroup and Serotype Detection Using Polymerase Chain Reaction. United States Department of Agriculture, September 1995. http://dx.doi.org/10.32747/1995.7612836.bard.

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The objectives of this proposal were to enhance animal health by 1) development of a BTV serogroup diagnostic assay using polymerase chain reaction (PCR) and 2) development of a BTV serotype specific diagnostic PCR assay. A PCR assay for diagnosis of bluetongue virus (BTV) serogroup from clinical samples meeting the criteria of objective 1 was developed. This PCR assay is more sensitive than virus isolation and has been adopted by both the U.S. and Israeli collaborating laboratories of this project, as well as at least one other U.S. laboratory for routine diagnosis of BTV infection in ruminants. The basic BTV PCR protocol has also become an essential tool in BTV molecular research in both collaborating laboratories. During development of the BTV serotype specific PCR we had the opportunity to investigate a nationwide outbreak of abortions and fatal disease in dogs in the U.S. purportedly due to BTV infection via a BTV contaminated canine vaccine. The BTV serogroup PCR was integral in confirming BTV in tissues from affected dogs and in lots of the suspect vaccine. This led to the first published report of BTV infection in dogs. We discovered that BTV can produce silent persistent infection in canine cell culture. This indicated a need for more stringent screening of biologics for occult BTV infection. A novel mixed cell culture method was developed to identify occult BTV and other occult viral infection cell cultures. Serotype specific primers for PCR detection of all U.S. BTV serotypes and two Israel serotypes (BTV-2 and 10) have been evaluated and are available. A subsequent collaboration would logically include sequencing of the L2 genes of Israel BTV-4, 6 and 16, allowing incorporation of these Israel BTV serotypes into a multiplex PCR assay.
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Yogev, David, Ricardo Rosenbusch, Sharon Levisohn, and Eitan Rapoport. Molecular Pathogenesis of Mycoplasma bovis and Mycoplasma agalactiae and its Application in Diagnosis and Control. United States Department of Agriculture, April 2000. http://dx.doi.org/10.32747/2000.7573073.bard.

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Mycoplasma bovis and M. agalactiae are two phylogenetically related mycoplasmas which cause economically significant diseases in their respective bovine or small ruminant hosts. These organisms cause persistent asymptomatic infections that can result in severe outbreaks upon introduction of carrier animals into susceptible herds. Little is known about the mechanisms underlying mycoplasma-host interaction, variation in virulence, or of the factors enabling avoidance of the host immune system. In recent years it has become apparent that the ability of pathogenic microorganisms to rapidly alter surface antigenic structures and to fine tune their antigenicity, a phenomena called antigenic variation, is one of the most effective strategies used to escape immune destruction and to establish chronic infections. Our discovery of a novel genetic system, mediating antigenic variation in M. bovis (vsp) as well as in M. agalactiae (avg) served as a starting point for our proposal which included the following objectives: (i) Molecular and functional characterization of the variable surface lipoproteins (Vsp) system of M. bovis and comparison with the Vsp-counterpart in M. agalactiae (ii) Determination of the role of Vsp proteins in the survival of M. bovis when confronted by host defense factors, (iii) Assessment of Vsp-based genetic and antigenic typing of M. bovis and M. agalactiae for epidemiology of infection and (iv) Improvement of diagnostic tests for M. bovis and M. agalactiae based on the vsp-and vsp-analogous systems. We have carried out an extensive molecular characterization of the vsp system and unravelled the precise molecular mechanism responsible for the generation of surface antigenic variation in M. bovis. Our data clearly demonstrated that the two pathogenic mycoplasma species possess large gene families encoding variable lipoprotein antigens that apparently play an important role in immune evasion and in pathogen-host interaction during infection. Phase variable production of these antigens was found to be mediated by a novel molecular mechanism utilizing double site-specific DNA inversions via an intermediate vsp configuration. Studies in model systems indicate that phase variation of VspA is relevant in interaction between M. bovis and macrophages or monocytes, a crucial stage in pathogenesis. Using an ELISA test with captured VspA as an antigen, phase variation was shown to occur in vivo and under field conditions. Genomic rearrangements in the avg gene family of M. agalactiae were shown to occur in vivo and may well have a role in evasion of host defences and establishment of chronic infection. An epidemiological study indicated that patterns of vsp-related antigenic variation diverge rapidly in an M. bovis infected herd. Marked divergence was also found with avg-based genomic typing of M. agalactiae in chronically infected sheep. However, avg-genomic fingerprints were found to be relatively homogeneous in different animals during acute stages of an outbreak of Contagious Agalactiae, and differ between unrelated outbreaks. These data support the concept of vsp-based genomic typing but indicate the necessity for further refinement of the methodology. The molecular knowledge on these surface antigens and their encoding genes provides the basis for generating specific recombinant tools and serological methods for serodiagnosis and epidemiological purposes. Utilization of these methods in the field may allow differentiating acutely infected herds from chronic herds and disease-free herds. In addition the highly immunogenic nature of these lipoproteins may facilitate the design of protective vaccine against mycoplasma infections.
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Rajarajan, Kunasekaran, Alka Bharati, Hirdayesh Anuragi, Arun Kumar Handa, Kishor Gaikwad, Nagendra Kumar Singh, Kamal Prasad Mohapatra, et al. Status of perennial tree germplasm resources in India and their utilization in the context of global genome sequencing efforts. World Agroforestry, 2020. http://dx.doi.org/10.5716/wp20050.pdf.

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Tree species are characterized by their perennial growth habit, woody morphology, long juvenile period phase, mostly outcrossing behaviour, highly heterozygosity genetic makeup, and relatively high genetic diversity. The economically important trees have been an integral part of the human life system due to their provision of timber, fruit, fodder, and medicinal and/or health benefits. Despite its widespread application in agriculture, industrial and medicinal values, the molecular aspects of key economic traits of many tree species remain largely unexplored. Over the past two decades, research on forest tree genomics has generally lagged behind that of other agronomic crops. Genomic research on trees is motivated by the need to support genetic improvement programmes mostly for food trees and timber, and develop diagnostic tools to assist in recommendation for optimum conservation, restoration and management of natural populations. Research on long-lived woody perennials is extending our molecular knowledge and understanding of complex life histories and adaptations to the environment, enriching a field that has traditionally drawn its biological inference from a few short-lived herbaceous species. These concerns have fostered research aimed at deciphering the genomic basis of complex traits that are related to the adaptive value of trees. This review summarizes the highlights of tree genomics and offers some priorities for accelerating progress in the next decade.
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McCarthy, Noel, Eileen Taylor, Martin Maiden, Alison Cody, Melissa Jansen van Rensburg, Margaret Varga, Sophie Hedges, et al. Enhanced molecular-based (MLST/whole genome) surveillance and source attribution of Campylobacter infections in the UK. Food Standards Agency, July 2021. http://dx.doi.org/10.46756/sci.fsa.ksj135.

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This human campylobacteriosis sentinel surveillance project was based at two sites in Oxfordshire and North East England chosen (i) to be representative of the English population on the Office for National Statistics urban-rural classification and (ii) to provide continuity with genetic surveillance started in Oxfordshire in October 2003. Between October 2015 and September 2018 epidemiological questionnaires and genome sequencing of isolates from human cases was accompanied by sampling and genome sequencing of isolates from possible food animal sources. The principal aim was to estimate the contributions of the main sources of human infection and to identify any changes over time. An extension to the project focussed on antimicrobial resistance in study isolates and older archived isolates. These older isolates were from earlier years at the Oxfordshire site and the earliest available coherent set of isolates from the national archive at Public Health England (1997/8). The aim of this additional work was to analyse the emergence of the antimicrobial resistance that is now present among human isolates and to describe and compare antimicrobial resistance in recent food animal isolates. Having identified the presence of bias in population genetic attribution, and that this was not addressed in the published literature, this study developed an approach to adjust for bias in population genetic attribution, and an alternative approach to attribution using sentinel types. Using these approaches the study estimated that approximately 70% of Campylobacter jejuni and just under 50% of C. coli infection in our sample was linked to the chicken source and that this was relatively stable over time. Ruminants were identified as the second most common source for C. jejuni and the most common for C. coli where there was also some evidence for pig as a source although less common than ruminant or chicken. These genomic attributions of themselves make no inference on routes of transmission. However, those infected with isolates genetically typical of chicken origin were substantially more likely to have eaten chicken than those infected with ruminant types. Consumption of lamb’s liver was very strongly associated with infection by a strain genetically typical of a ruminant source. These findings support consumption of these foods as being important in the transmission of these infections and highlight a potentially important role for lamb’s liver consumption as a source of Campylobacter infection. Antimicrobial resistance was predicted from genomic data using a pipeline validated by Public Health England and using BIGSdb software. In C. jejuni this showed a nine-fold increase in resistance to fluoroquinolones from 1997 to 2018. Tetracycline resistance was also common, with higher initial resistance (1997) and less substantial change over time. Resistance to aminoglycosides or macrolides remained low in human cases across all time periods. Among C. jejuni food animal isolates, fluoroquinolone resistance was common among isolates from chicken and substantially less common among ruminants, ducks or pigs. Tetracycline resistance was common across chicken, duck and pig but lower among ruminant origin isolates. In C. coli resistance to all four antimicrobial classes rose from low levels in 1997. The fluoroquinolone rise appears to have levelled off earlier and among animals, levels are high in duck as well as chicken isolates, although based on small sample sizes, macrolide and aminoglycoside resistance, was substantially higher than for C. jejuni among humans and highest among pig origin isolates. Tetracycline resistance is high in isolates from pigs and the very small sample from ducks. Antibiotic use following diagnosis was relatively high (43.4%) among respondents in the human surveillance study. Moreover, it varied substantially across sites and was highest among non-elderly adults compared to older adults or children suggesting opportunities for improved antimicrobial stewardship. The study also found evidence for stable lineages over time across human and source animal species as well as some tighter genomic clusters that may represent outbreaks. The genomic dataset will allow extensive further work beyond the specific goals of the study. This has been made accessible on the web, with access supported by data visualisation tools.
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Safeguarding through science: Center for Plant Health Science and Technology 2009 Accomplishments. U.S. Department of Agriculture, Animal and Plant Health Inspection Service, February 2011. http://dx.doi.org/10.32747/2011.7296843.aphis.

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The Center for Plant Health Science and Technology (CPHST) provides scientific support for the regulatory decisions and operations of the Animal and Plant Health Inspection Service’s (APHIS) Plant Protection and Quarantine (PPQ) program in order to safeguard U.S. agriculture and natural resources. CPHST is responsible for ensuring that PPQ has the information, tools, and technology to make the most scientifically valid regulatory and policy decisions possible. In addition, CPHST ensures that PPQ’s operations have the most scientifically viable and practical tools for pest exclusion, detection, and management. This 2009 CPHST Annual Report is intended to offer an in-depth look at the status of our programs and the progress CPHST has made toward the Center’s long-term strategic goals. CPHST's work is organized into six National Science Programs: Agricultural Quarantine Inspection and Port Technology; Risk and Pathway Analysis; Domestic Surveillance, Detection, and Identification; Emergency Response; Response and Recovery Systems Technology - Arthropods; and Response and Recovery Systems Technology - Plant Pathogens and Weeds. the scientists of CPHST provide leadership and expertise in a wide range of fields, including risk assessments that support trade, commodity quarantine treatments, pest survey and detection methods, molecular diagnostics, biological control techniques, integrated pest management, and mass rearing of insects. Some highlights of significant CPHST efforts in 2009 include: Establishment of the National Ornamentals Research Site at Dominican University of California, Established LBAM Integrated Pest Management and Survey Methods, Continue to develop Citrus Greening/Huanglongbing Management Tools, and further European Grapevine Moth (EGVM) Response.
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