Gotowe bibliografie tematyczne / Genetic methods for resistance detection

Gotowa bibliografia na temat „Genetic methods for resistance detection”

Autor: Grafiati

Data publikacji: 4 czerwca 2021

Data aktualizacji: 20 lutego 2023

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Artykuły w czasopismach na temat "Genetic methods for resistance detection"

SUNDSFJORD, ARNFINN, GUNNAR S. SIMONSEN, BJORG C. HALDORSEN, HAKON HAAHEIM, STIG-OVE HJELMEVOLL, PIA LITTAUER i KRISTIN H. DAHL. "Genetic methods for detection of antimicrobial resistance". APMIS 112, nr 11-12 (grudzień 2004): 815–37. http://dx.doi.org/10.1111/j.1600-0463.2004.apm11211-1208.x.

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Golovnin, A. V., A. L. Khanin i V. I. Golovnin. "THE SURGICAL STAGE OF PULMONARY TUBERCULOSIS TREATMENT USING MOLECULAR-GENETIC METHODS TO TEST SUSCEPTIBILITY TO RIFAMPICIN". Tuberculosis and Lung Diseases 97, nr 3 (3.04.2019): 31–34. http://dx.doi.org/10.21292/2075-1230-2019-97-3-31-34.

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The objective of the study: to analyze the frequency and patterns of drug resistance of Mycobacterium tuberculosis (MTB) according to the results of microbiological tests of surgical specimens of the patients who underwent surgery due to tuberculosis, and to compare them with the results of sputum tests done in the pre-operative period. Subjects and methods. The data of surgical specimens from 170 patients operated due to tuberculosis were analyzed. The surgical specimens were sent for histological and microbiological tests (detection of MTB DNA and rifampicin resistance by GeneXpert, culture on solid media with drug sensitivity testing). Results. The molecular genetic testing of surgical specimens by GeneXpert was highly effective for detection of rifampicin resistance; in 97.8% of cases, there was a match with the results of sputum culture with consecutive DST performed before the surgery. Molecular genetic tests of surgical specimens allowed detecting MTB DNA in 66.1% of patients in whom no MTB or MTB DNA was detected in sputum and bronchial washings prior to the surgery, and of them in 28.2% of cases, rifampicin resistance was detected, which was unknown before the surgery. These data allowed prescribing adequate chemotherapy immediately after surgery.

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Chroma, Magdalena, i Milan Kolar. "GENETIC METHODS FOR DETECTION OF ANTIBIOTIC RESISTANCE: FOCUS ON EXTENDED-SPECTRUM β-LACTAMASES". Biomedical Papers 154, nr 4 (1.12.2010): 289–96. http://dx.doi.org/10.5507/bp.2010.044.

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SHAMPUTA, I. C., L. RIGOUTS AND i F. PORTAELS. "Molecular genetic methods for diagnosis and antibiotic resistance detection of mycobacteria from clinical specimens". APMIS 112, nr 11-12 (grudzień 2004): 728–52. http://dx.doi.org/10.1111/j.1600-0463.2004.apm11211-1203.x.

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Eliseev, P. I., I. V. Tarasova i A. O. Mariandyshev. "MOLECULAR-GENETIC METHODS OF DETECTION OF TUBERCULOSIS AND ITS DRUG RESISTANCE IN ARKHANGELSK REGION IN 2017". Russian Journal of Infection and Immunity 8, nr 4 (16.01.2019): 567–68. http://dx.doi.org/10.15789/2220-7619-2018-4-6.14.

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Kolbert, C. P., J. Arruda, P. Varga-Delmore, X. Zheng, M. Lewis, J. Kolberg i D. H. Persing. "Branched-DNA Assay for Detection of themecA Gene in Oxacillin-Resistant and Oxacillin-Sensitive Staphylococci". Journal of Clinical Microbiology 36, nr 9 (1998): 2640–44. http://dx.doi.org/10.1128/jcm.36.9.2640-2644.1998.

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The identification of methicillin-resistant staphylococcus isolates in the clinical laboratory has typically been performed by using methods that detect phenotypic expression of resistance determinants. However, these methods may be difficult to interpret and some isolates do not express resistance until selective pressure is administered. Assays that detect genetic determinants are not subject to these limitations and have been effective in distinguishing isolates that are capable of expressing the resistance phenotype. In this study, a novel branched-DNA (bDNA) hybridization assay was used to test for themecA gene in 416 clinical staphylococcal isolates. The results were compared with those obtained by a PCR-based assay and oxacillin disk diffusion. For 155 Staphylococcus aureus and 261 coagulase-negative Staphylococcus isolates, the bDNA assay and PCR results were 100% concordant. Among the S. aureus isolates, 20 were MecA+ and 135 were MecA−. For the coagulase-negative staphylococci, 150 were MecA+ and 111 were MecA−. The results from the genotypic detection methods were compared with those obtained by oxacillin disk diffusion. No discrepancies were detected among theS. aureus isolates; however, 10 coagulase-negative isolates were MecA+ but oxacillin sensitive and 1 isolate was MecA− but oxacillin resistant. Oxacillin resistance was induced in 6 of the 10 MecA+ isolates previously classified as oxacillin sensitive. These results suggest that the bDNA method described here is a sensitive and efficient method for detection of methicillin resistance in staphylococci and that genetic detection methods may be useful for detection of potential methicillin resistance in the clinical laboratory.

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BEECH, R. N., P. SKUCE, D. J. BARTLEY, R. J. MARTIN, R. K. PRICHARD i J. S. GILLEARD. "Anthelmintic resistance: markers for resistance, or susceptibility?" Parasitology 138, nr 2 (9.09.2010): 160–74. http://dx.doi.org/10.1017/s0031182010001198.

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SUMMARYThe Consortium for Anthelmintic Resistance and Susceptibility (CARS) brings together researchers worldwide, with a focus of advancing knowledge of resistance and providing information on detection methods and treatment strategies. Advances in this field suggest mechanisms and features of resistance that are shared among different classes of anthelmintic. Benzimidazole resistance is characterized by specific amino acid substitutions in beta-tubulin. If present, these substitutions increase in frequency upon drug treatment and lead to treatment failure. In the laboratory, sequence substitutions in ion-channels can contribute to macrocyclic lactone resistance, but there is little evidence that they are significant in the field. Changes in gene expression are associated with resistance to several different classes of anthelmintic. Increased P-glycoprotein expression may prevent drug access to its site of action. Decreased expression of ion-channel subunits and the loss of specific receptors may remove the drug target. Tools for the identification and genetic analysis of parasitic nematodes and a new online database will help to coordinate research efforts in this area. Resistance may result from a loss of sensitivity as well as the appearance of resistance. A focus on the presence of anthelmintic susceptibility may be as important as the detection of resistance.

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Tsarev, V. N., E. V. Ippolitov i E. N. Nikolaeva. "PREVALENCE OF GENETIC MARKERS OF RESISTANCE TO ANTIBIOTICS IN BIOFILM-FORMING STRAINS OF OBLIGATE AND ELECTIVE ANAEROBES". Journal of microbiology epidemiology immunobiology, nr 2 (28.04.2017): 74–80. http://dx.doi.org/10.36233/0372-9311-2017-2-74-80.

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Aim. Comparative study of frequency of detection of genetic markers of resistance to antibiotics forming in anaerobic bacteria under the conditions of mixed biofilms in a clinical setting and comparison of data of phenotypic and genotypic methods of study. Materials and methods. 66 strains of bacteria forming biofilm with PCR detection of antibiotics were studied: Streptococcus sanguinis, Streptococcus salivarius, Staphylococcus aureus, Staphylococcus epidermidis, Enterococcus faecalis, Klebsiella pneumoniae, Pseudomonas aeruginosa and anaerobic pathogens - Porphyromonas gingivalis, Tannerella forsythia, Parvinonas micra, Prevotella intermedia. Modelling of microbial biofilms in vitro and scanning electron microscopy were carried out. Results. The studied strains of resident and pathogenic microbiota were established to have genes that code resistance to P-lactam antibiotics, carbapenems, macrolides, tetracyclines. Genetic markers of resistance to p-lactam antibiotics (STX-M и МЕСА - cepha-losporines), including carbapenems (VIM and NDM, but not Oxa-48), glycopeptides (VanA and VanB), macrolides (ERM), tetracycline (Tet) and QNRB plasmids (fluoroquinolones) were detected in strains by PCR. Conclusion. The most frequently used preparations in dental practice - metronidazole and lincomycin (for the last 20 - 30 years) have shown the highest number of resistant strains - 52.3 and 22.7%, respectively. The frequency of detection of genetic markers of resistance to other studied preparations did not exceed 2.5 - 11.4%. Minimal quantity of resistant strains of anaerobic bacteria was detected for carbapenems and fluoroquinolones.

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Bhattacharyya, Roby, Jamin Liu, Peijun Ma, Nirmalya Bandyopadhyay, Jonathan Livny i Deborah Hung. "Rapid Phenotypic Antibiotic Susceptibility Testing Through RNA Detection". Open Forum Infectious Diseases 4, suppl_1 (2017): S33. http://dx.doi.org/10.1093/ofid/ofx162.082.

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Abstract Background Culture-based antibiotic susceptibility testing, the gold standard, is too slow to guide early antibiotic selection, while newer genotypic methods require comprehensive knowledge of resistance mechanisms to predict phenotype. Quantitative measurement of key antibiotic-responsive transcripts offers a rapid, phenotypic assay for assessing antibiotic susceptibility, agnostic to the genetic basis for resistance. Methods We performed RNA-Seq on Klebsiella pneumoniae and Acinetobacter baumanii treated with ciprofloxacin, gentamicin, or meropenem for 0, 10, 30, and 60 minutes. For each, we identified 50 responsive transcripts whose expression levels differ most between susceptible and resistant organisms upon antibiotic exposure. We measured their expression using a multiplexed fluorescent RNA hybridization assay (NanoString) in 69 clinical isolates, including a “test set” of multidrug-resistant strains from the CDC, in an 8-hour assay. Gene expression data from test strains were compared against known susceptible and resistant isolates to generate a transcriptional susceptibility metric. We also designed NanoString probes to detect 5 carbapenemase genes (KPC-2, KPC-3, NDM-1, OXA-48, and CTX-M15). Results Across all bacteria-antibiotic pairs tested, a susceptibility metric derived from these transcriptional assays correctly grouped isolates in 167 of 173 tests (Table 1), with only 1 of 88 resistant isolates misclassified as susceptible. Five of six incorrectly grouped isolates were within one dilution of the breakpoint MIC, including the misclassified resistant isolate. Conclusion We demonstrate phenotypic antibiotic resistance detection based on fluorescent RNA detection in an 8-hour assay. We have previously published proof-of-concept studies that this assay may be run on a positive blood culture bottle with minimal sample processing. By coupling this phenotypic assay with detection of genetic resistance determinants (demonstrated for carbapenemases) in a single assay, strains with unexplained resistance can be prioritized for further study. Disclosures All authors: No reported disclosures.

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Gupta, Gunjan, Vibhor Tak i Purva Mathur. "Detection of AmpC β Lactamases in Gram-negative Bacteria". Journal of Laboratory Physicians 6, nr 01 (styczeń 2014): 001–6. http://dx.doi.org/10.4103/0974-2727.129082.

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ABSTRACT AmpC β-lactamases are clinically important cephalosporinases encoded on the chromosomes of many Enterobacteriaceae and a few other organisms, where they mediate resistance to cephalothin, cefazolin, cefoxitin, most penicillins, and β-lactamase inhibitor/β-lactam combinations. The increase in antibiotic resistance among Gram-negative bacteria is a notable example of how bacteria can procure, maintain and express new genetic information that can confer resistance to one or several antibiotics. Detection of organisms producing these enzymes can be difficult, because their presence does not always produce a resistant phenotype on conventional disc diffusion or automated susceptibility testing methods. These enzymes are often associated with potentially fatal laboratory reports of false susceptibility to β-lactams phenotypically. With the world-wide increase in the occurrence, types and rate of dissemination of these enzymes, their early detection is critical. AmpC β-lactamases show tremendous variation in geographic distribution. Thus, their accurate detection and characterization are important from epidemiological, clinical, laboratory, and infection control point of view. This document describes the methods for detection for AmpC β-lactamases, which can be adopted by routine diagnostic laboratories.

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Rozprawy doktorskie na temat "Genetic methods for resistance detection"

Thomas, Lee. "Genetic methods for Rapid Detection of Medically Important Nosocomial Bactera". Thesis, The University of Sydney, 2007. http://hdl.handle.net/2123/3575.

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The role of the microbiology laboratory is (1) to provide infection control information, so that highly transmissible isolates may be identified and appropriate control measures instigated as rapidly as possible and (2) to provide adequate information to the clinician enabling correct antibiotic choices to be made, particularly in the critically ill. Microbiological data is by definition slow as it is culture dependent: this study focused on the development of genetic, culture-independent methods for detection of resistance in nosocomial pathogens that could be introduced into the routine microbiology department and would fit into the routine workflow with a consequent reduction in time to result. Initially a duplex real-time polymerase chain reaction was developed for the rapid identification and detection of S. aureus and methicillin-resistance. This was optimised for immediate as-needs testing of positive blood cultures signalling with “Gram positive cocci, possibly staphylococcus” evident on Gram stain, on a random access real-time PCR platform. This technology, allowing early identification of S. aureus and its susceptibility to methicillin, by simple automated methodology, may soon become the standard for all microbiology laboratories servicing the critically ill. The second part of the study involved the development of a selective broth and multiplex PCR for detection of three important nosocomial isolates at this institution, methicillin-resistant S. aureus (MRSA), carbapenem-resistant Enterobacteriaceae, and multi-resistant Acinetobacter baumannii (MRAB). A multiplex PCR using four primer sets was designed to detect low colonisation levels of these isolates after overnight incubation in selective broth, significantly reducing the time to result and associated costs. This potentially useful epidemiological screening tool is practical, reproducible and sensitive with the potential of moving to an automated test (using real-time PCR, for example) in the future. The availability of early negative results judged by simple visual scanning (or by densitometry), means that the result is less operator-dependent, potentially reducing error rate. The last part of the study dealt with an important resistance phenotype, aminoglycoside resistance. There had been no recent comprehensive local surveys performed to determine the frequency of aminoglycoside resistance amongst the Enterobacteriaceae, or to identify the genetic determinants and their transmissibility. The isolates collected for the study were all resistant to at least one of gentamicin, tobramycin or amikacin. Identification of integron cassette arrays and use of specific internal primers identified at least one genetic determinant for gentamicin and tobramycin resistance in 22 of 23 isolates. Three isolates had two aminoglycoside resistance genes, and three isolates had three aminoglycoside resistance genes identified (Table 6.1). Transferable gentamicin-resistant plasmids were predominant amongst Klebsiella spp., but less so amongst Enterobacter spp. and E. coli. Gentamicin-resistant Klebsiella spp. were often ESBL positive, the genetic determinants of which were typically co-transferred on a conjugative plasmid. The importance of screening at a local level was demonstrated by the unexpected predominance of aac(6')-IIc amongst Enterobacter spp. and the detection of a new gene (aac(6')-LT). This part of the study has provided an understanding of the primary aminoglycoside resistance genes present in the local setting and their association with other resistances. This knowledge will allow development of assays for patient screening (clinical isolates and colonising flora), to better understand the epidemiology of aminoglycoside resistance and to allow better choice of antibiotic therapy related to presence or absence of these genes.

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Thomas, Lee. "Genetic methods for Rapid Detection of Medically Important Nosocomial Bactera". University of Sydney, 2007. http://hdl.handle.net/2123/3575.

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Master of Science
The role of the microbiology laboratory is (1) to provide infection control information, so that highly transmissible isolates may be identified and appropriate control measures instigated as rapidly as possible and (2) to provide adequate information to the clinician enabling correct antibiotic choices to be made, particularly in the critically ill. Microbiological data is by definition slow as it is culture dependent: this study focused on the development of genetic, culture-independent methods for detection of resistance in nosocomial pathogens that could be introduced into the routine microbiology department and would fit into the routine workflow with a consequent reduction in time to result. Initially a duplex real-time polymerase chain reaction was developed for the rapid identification and detection of S. aureus and methicillin-resistance. This was optimised for immediate as-needs testing of positive blood cultures signalling with “Gram positive cocci, possibly staphylococcus” evident on Gram stain, on a random access real-time PCR platform. This technology, allowing early identification of S. aureus and its susceptibility to methicillin, by simple automated methodology, may soon become the standard for all microbiology laboratories servicing the critically ill. The second part of the study involved the development of a selective broth and multiplex PCR for detection of three important nosocomial isolates at this institution, methicillin-resistant S. aureus (MRSA), carbapenem-resistant Enterobacteriaceae, and multi-resistant Acinetobacter baumannii (MRAB). A multiplex PCR using four primer sets was designed to detect low colonisation levels of these isolates after overnight incubation in selective broth, significantly reducing the time to result and associated costs. This potentially useful epidemiological screening tool is practical, reproducible and sensitive with the potential of moving to an automated test (using real-time PCR, for example) in the future. The availability of early negative results judged by simple visual scanning (or by densitometry), means that the result is less operator-dependent, potentially reducing error rate. The last part of the study dealt with an important resistance phenotype, aminoglycoside resistance. There had been no recent comprehensive local surveys performed to determine the frequency of aminoglycoside resistance amongst the Enterobacteriaceae, or to identify the genetic determinants and their transmissibility. The isolates collected for the study were all resistant to at least one of gentamicin, tobramycin or amikacin. Identification of integron cassette arrays and use of specific internal primers identified at least one genetic determinant for gentamicin and tobramycin resistance in 22 of 23 isolates. Three isolates had two aminoglycoside resistance genes, and three isolates had three aminoglycoside resistance genes identified (Table 6.1). Transferable gentamicin-resistant plasmids were predominant amongst Klebsiella spp., but less so amongst Enterobacter spp. and E. coli. Gentamicin-resistant Klebsiella spp. were often ESBL positive, the genetic determinants of which were typically co-transferred on a conjugative plasmid. The importance of screening at a local level was demonstrated by the unexpected predominance of aac(6')-IIc amongst Enterobacter spp. and the detection of a new gene (aac(6')-LT). This part of the study has provided an understanding of the primary aminoglycoside resistance genes present in the local setting and their association with other resistances. This knowledge will allow development of assays for patient screening (clinical isolates and colonising flora), to better understand the epidemiology of aminoglycoside resistance and to allow better choice of antibiotic therapy related to presence or absence of these genes.

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Robberts, Frans Jacob Lourens. "Genetic investigations of pneumocystis jirovecii : detection, cotrimoxazole resistance and population structure". Thesis, Link to the online version, 2005. http://hdl.handle.net/10019.1/1304.

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Thomas, Lee Carolyn. "Genetic methods for rapid detection of medically important nosocomial bacteria". Connect to full text, 2007. http://hdl.handle.net/2123/3575.

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Thesis (M. Sc. Med.)--University of Sydney, 2007.
Title from title screen (viewed 15 October 2008). Submitted in fulfilment of the requirements for the degree of Master of Science in Medicine to the Discipline of Medicine, Faculty of Medicine. Includes bibliographical references. Also available in print form.

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Cohen, Joseph Paul. "Crater detection via genetic search methods to reduce image features". Thesis, University of Massachusetts Boston, 2014. http://pqdtopen.proquest.com/#viewpdf?dispub=1550596.

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Recent approaches to crater detection have been inspired by face detection's use of gray-scale texture features. Using gray-scale texture features for supervised machine learning crater detection algorithms provides better classification of craters in planetary images than previous methods. When using Haar features it is typical to generate thousands of numerical values from each candidate crater image. This magnitude of image features to extract and consider can spell disaster when the application is an entire planetary surface. One solution is to reduce the number of features extracted and considered in order to increase accuracy as well as speed. Feature subset selection provides the operational classifiers with a concise and denoised set of features by reducing irrelevant and redundant features. Feature subset selection is known to be NP-hard. To provide an efficient suboptimal solution, four genetic algorithms are proposed to use greedy selection, weighted random selection, and simulated annealing to distinguish discriminate features from indiscriminate features. Inspired by analysis regarding the relationship between subset size and accuracy, a squeezing algorithm is presented to shrink the genetic algorithm's chromosome cardinality during the genetic iterations. A significant increase in the classification performance of a Bayesian classifier in crater detection using image texture features is observed.

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Konstantinidis, Michalis. "Preimplantation genetic diagnosis : new methods for the detection of genetic abnormalities in human preimplantation embryos". Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:28611f65-7729-4293-9c3f-4fc3f0cc39d7.

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Preimplantation genetic diagnosis (PGD) refers to the testing of embryos produced through in vitro fertilization (IVF) in order to identify those unaffected by a specific genetic disorder or chromosomal abnormality. In this study, different methodologies were examined and developed for performance of PGD. Investigation of various whole genome amplification (WGA) methods identified multiple displacement amplification as a reliable method for genotyping single cells. Furthermore, this technology was shown to be compatible with subsequent analysis using single nucleotide polymorphism (SNP) microarrays. Compared to conventional methods used in this study to perform single cell diagnosis (e.g. multiplex PCR), WGA techniques were found to be advantageous since they streamline the development of PGD protocols for couples at high risk of transmitting an inherited disorder and simultaneously offer the possibility of comprehensive chromosome screening (CCS). This study also aimed to develop a widely applicable protocol for accurate typing of the human leukocyte antigen (HLA) region with the purpose of identifying embryos that will be HLA-identical to an existing sibling affected by a disorder that requires haematopoietic stem cell transplantation. Additionally, a novel microarray platform was developed that, apart from accurate CCS, was capable of reliably determining the relative quantity of mitochondrial DNA in polar bodies removed from oocytes and single cells biopsied from embryos. Mitochondria are known to play an important role in oogenesis and preimplantation embryogenesis and their measurement may therefore be of clinical relevance. Moreover, real-time PCR was used for development of protocols for CCS, DNA fingerprinting of sperm samples and embryos and the relative quantitation of telomere length in embryos (since shortened telomeres might be associated with reduced viability). As well as considering the role of genetics in terms of oocyte and embryo viability assessment and the diagnosis of inherited genetic disorders, attention was given to a specific gene (Phospholipase C zeta) of relevance to male infertility. A novel mutation affecting the function of the resulting protein was discovered highlighting the growing importance of DNA sequence variants in the diagnosis and treatment of infertility.

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Uygun, Sahra. "Development Of Analysis Methods For Cry1ac And Sam-k Gene Lines In Tomato Using Pcr And Real-time Pcr". Master's thesis, METU, 2010. http://etd.lib.metu.edu.tr/upload/3/12611991/index.pdf.

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Genetically modified organisms are entering the human diet in all over the world. In order to have transparency in the foods that are being consumed, there is a need to trace the genetically modified organisms (GMOs) in the market and consequently this need brings the necessity of analytical methods that are capable of detecting, identifying and quantifying the transgenic events. These analytical methods also form the basis of the labeling regulations that are tried to be formed regarding GMOs. The main aim of this study is to develop and apply the detection methods for the two of the tomato events, delayed ripening and insect resistant. Currently the only validated detection methods are mainly for the corn, soybean, and cotton. There is no validated detection method for tomato. Tomato is one of the most consumed food products in Turkey and it is also among the controversial organisms in terms of genetic modifications and labeling, therefore the analysis of the genetic modifications in tomato is crucial. In this study, DNA-based detection is performed, with PCR being the chosen method of study. In order to detect the GMO-derived DNA, the method of analysis includes the following studies: species-specific, screening, gene-specific, construct-specific and inverse PCR. In addition, the quantification method is developed using the real-time PCR. In order to develop the procedure of identification method, the reference samples are used and the unknown varieties that are to be analyzed using this method are expected to have similarities with the authorized transgenic events.

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Pecetti, Luciano. "Genetic resources and selection methods for drought and salinity resistance in durum wheat". Thesis, Bangor University, 1994. https://research.bangor.ac.uk/portal/en/theses/genetic-resources-and-selection-methods-for-drought-and-salinity-resistance-in-durum-wheat(119af68a-9751-4451-a54e-6c16fdb941ed).html.

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The relevance of drought and salinity stress under Mediterranean conditions is reviewed and prospects for crop improvement against these constraints are discussed. Field trials under severe drought in Syria highlighted the importance of earliness to ensure satisfactory yields. Peduncle length and frost tolerance were also important attributes. Under more favourable conditions in Sicily, the yield components per se (number of spikes, number of kernels and kernel weight) had greater influence on genotype performance. At both locations of evaluation high yields were attained through different architectures of traits. Durum wheat genetic resources proved very variable. Genotypes were identified which could be used as donors of adaptive characters in breeding programmes. The CERES-Wheat growth model was used for the two locations, using historical weather data and two genotypes of known adaptation to the region. Early heading was a positive attribute, particularly in Syria. At both sites, lengthening of the grain filling period resulted in higher yields. Three sowing dates were simulated. "Early" sowing (1 November) had the highest simulated yield in both environments, suggesting a possible agronomic means to improve yields under stress. Simulated yields were in most cases within 15% of measured values when a comparison was possible. The ability to adjust osmotically was sought in seedlings artificially exposed to drought stress during early development. One entry appeared to possess this feature. However, another genotype, of known tolerance under real conditions, did not show this ability. Therefore, osmotic adjustment during early stages of ontogeny does not seem unequivocally able to identify the best genotypes under drought. Salt tolerance of durum wheat genetic resources was assessed measuring early growth under controlled environment. The data indicated that the results may be somewhat experiment-specific when using different growing techniques such as hydroponics and sand-culture. Finding tolerant tetraploid entries in terms of plant survival and ion uptake seemed difficult. However, variability existed and some entries, less susceptible than others, were noted. They could be used for breeding. For instance, they could be valuable recipient for the introgression of identified resistance mechanisms from other taxa.

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Jurstrand, Margaretha. "Detection of Chlamydia trachomatis and Mycoplasma genitalium by genetic and serological methods". Doctoral thesis, Örebro : Universitetsbiblioteket : Örebro University, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:oru:diva-793.

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Treuerne, Balazs Krisztina Eszter. "Methods for the surveillance of urgent drug-resistant bacterial threats". Thesis, University of Sydney, 2020. https://hdl.handle.net/2123/24498.

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Despite being a natural phenomenon, antibacterial resistance has been accelerated and the increasing rates of antibiotic therapy failure is now having a significant impact upon public health and the economy in every country of the world. As a result of declining investment and innovation in the development of novel antimicrobial agents, it is vitally important to preserve the currently effective agents through more regulated and tailored therapeutic interventions. In order to do so, rapid, robust, sensitive and specific diagnostic tests should be available to end-users. The incorporation of fluorogenic substrates into solid or liquid media could allow for the development of such tests, and the aim of this study was to investigate this relatively unexploited area of microbiology. Fluorogenic media for bacterial detection employ a non-fluorescent (fluorogenic) enzyme substrate, which is only converted to its fluorescent form when acted upon by a specific enzyme expressed by a bacterium of interest. In this research project, prolyl and pyroglutamyl aminopeptidase substrates were synthesized using coumarin fluorophores, which were linked to the enzyme targeting portions (proline or pyroglutamic acid) via self-immolative linkers. The fluorescence properties of the substrates were evaluated and compared with those of the respective fluorophores. The fluorescence intensity of the substrates was generally lower than that of the fluorophores, even at a 10-fold higher concentration, which is a key advantage for their use as diagnostic tools. A significant difference was observed between the fluorescence intensity of the different fluorophores, depending on their substituents. An ester linkage between the fluorophore and linker corresponded with a greater difference in fluorescence intensity from their corresponding fluorophore than for ether-linked substrates. However, ether-linked substrates generally showed greater differences in their emission wavelength maxima from the fluorophores, making them more suitable substrates for use in the detection of enzymatic activity. These enzyme substrates were then evaluated against a range of clinically relevant pathogenic bacteria in order to determine the sensitivity and specificity of these probes and their potential use in clinical diagnostics. Ester-linked substrates underwent spontaneous hydrolysis in aqueous media, while those with ether links remained stable and only produced fluorescence signals when acted upon by bacterial enzymes. Prolyl aminopeptidase substrates showed specificity to S. typhimurium and no enzyme activity was observed in clinically relevant species, including C. freundii, E. cloacae, Shigella spp., and S. typhi, however, their sensitivity for S. typhimurium remained low. Pyroglutamyl aminopeptidase substrates showed promising results against Enterobacteriaceae, and, exploiting the difference between their lactose fermentation rate, incorporating the substrate in MacConkey solid media proved to be a successful approach to distinguishing K. pneumoniae from other 3 clinically relevant enterobacter species, C. freundii, E. cloacae and S. marcescens with 91.7 % positive predictive and 95.2% negative predictive values based upon a 48-hour detection time. When combined with meropenem, and introducing the substrate in solution to overnight cultures, this method allowed the distinction of carbapenem-resistant K. pneumoniae from resistant E. coli, P. aeruginosa and A. baumannii in as little as 1 hour. In addition, a potential chromogenic ribosidase substrate was prepared and evaluated in growth media, however, this substrate showed poor stability in aqueous solution.

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Książki na temat "Genetic methods for resistance detection"

RNA detection and visualization: Methods and protocols. New York: Humana, 2011.

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Lupi, Claudio. Genetic engineering for plant protection: Methods, state of the art and applications. Basel: BATS, 1995.

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1948-, Luciw Paul A., i Steimer Kathelyn Sue 1948-, red. HIV detection by genetic engineering methods. New York: Dekker, 1989.

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Gerst, Jeffrey E. RNA Detection and Visualization: Methods and Protocols. Humana Press, 2016.

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Ali, Akhtar, Bright Agindotan, Xifeng Wang, Rajarshi Kumar Gaur, Xiaofei Cheng i Kristiina Mäkinen, red. Plant Viruses, Volume I: Detection Methods, Genetic Diversity and Evolution. Frontiers Media SA, 2022. http://dx.doi.org/10.3389/978-2-88974-129-8.

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Heller, Knut J. Genetically Engineered Food: Methods and Detection. Wiley-VCH, 2003.

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Heller, Knut J. Genetically Engineered Food: Methods and Detection. Wyd. 2. Wiley-VCH, 2007.

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Heinz, Hecker Karl, red. Genetic variance detection: Technologies for pharmacogenomics. [Eagleville, Pa.]: DNA Press, 2005.

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Genomic tests for ovarian cancer detection and management. Rockville, MD: U.S. Department of Health and Human Services, Public Health Service, Agency for Healthcare Research and Quality, 2006.

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Heller, Knut J. Genetically Engineered Food: Methods and Detection. Wiley & Sons, Limited, John, 2006.

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Części książek na temat "Genetic methods for resistance detection"

Jankowicz-Cieslak, Joanna, Ivan L. Ingelbrecht i Bradley J. Till. "Mutation Detection in Gamma-Irradiated Banana Using Low Coverage Copy Number Variation". W Efficient Screening Techniques to Identify Mutants with TR4 Resistance in Banana, 113–27. Berlin, Heidelberg: Springer Berlin Heidelberg, 2022. http://dx.doi.org/10.1007/978-3-662-64915-2_8.

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AbstractMutagenesis of in vitro propagated bananas is an efficient method to introduce novel alleles and broaden genetic diversity. The FAO/IAEA Plant Breeding and Genetics Laboratory previously established efficient methods for mutation induction of in vitro shoot tips in banana using physical and chemical mutagens as well as methods for the efficient discovery of ethyl methanesulphonate (EMS) induced single nucleotide mutations in targeted genes. Officially released mutant banana varieties have been created using gamma rays, a mutagen that can produce large genomic changes such as insertions and deletions (InDels). Such dosage mutations may be particularly important for generating observable phenotypes in polyploids such as banana. Here, we describe a Next Generation Sequencing (NGS) approach in Cavendish (AAA) bananas to identify large genomic InDels. The method is based on low coverage whole genome sequencing (LC-WGS) using an Illumina short-read sequencing platform. We provide details for sonication-mediated library preparation and the installation and use of freely available computer software to identify copy number variation in Cavendish banana. Alternative DNA library construction procedures and bioinformatics tools are briefly described. Example data is provided for the mutant variety Novaria and cv Grande Naine (AAA), but the methodology can be equally applied for triploid bananas with mixed genomes (A and B) and is useful for the characterization of putative Fusarium Wilt TR4 resistant mutant lines described elsewhere in this protocol book.

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Alexander, H. M., i P. J. Bramel-Cox. "Sustainability of Genetic Resistance". W Plant Breeding and Sustainable Agriculture: Considerations for Objectives and Methods, 11–27. Madison, WI, USA: Crop Science Society of America and American Society of Agronomy, 2015. http://dx.doi.org/10.2135/cssaspecpub18.c2.

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Posteraro, Brunella, Antonietta Vella, Elena De Carolis i Maurizio Sanguinetti. "Molecular Detection of Resistance to Echinocandins". W Methods in Molecular Biology, 413–21. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-6515-1_23.

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Lan, Caixia, Mandeep Singh Randhawa, Julio Huerta-Espino i Ravi P. Singh. "Genetic Analysis of Resistance to Wheat Rusts". W Methods in Molecular Biology, 137–49. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7249-4_12.

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Bruenn, Jeremy. "Novel Methods of Introducing Pest and Disease Resistance to Crop Plants". W Genetic Engineering, 11–22. Boston, MA: Springer US, 2000. http://dx.doi.org/10.1007/978-1-4615-4199-8_2.

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Arunkumar, C. G., K. S. Jagadish i T. D. Nidheesh. "Genetic Tools for Insecticide Resistance Management". W Genetic Methods and Tools for Managing Crop Pests, 569–77. Singapore: Springer Nature Singapore, 2022. http://dx.doi.org/10.1007/978-981-19-0264-2_23.

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Posteraro, Brunella, Antonietta Vella, Elena De Carolis i Maurizio Sanguinetti. "Molecular Detection of Resistance to Azole Components". W Methods in Molecular Biology, 423–35. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-6515-1_24.

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Maslov, Sergei, i Kim Sneppen. "Detection of Topological Patterns in Protein Networks". W Genetic Engineering: Principles and Methods, 33–47. Boston, MA: Springer US, 2004. http://dx.doi.org/10.1007/978-0-306-48573-2_4.

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Anjum, Muna F., Ea Zankari i Henrik Hasman. "Molecular Methods for Detection of Antimicrobial Resistance". W Antimicrobial Resistance in Bacteria from Livestock and Companion Animals, 33–50. Washington, DC, USA: ASM Press, 2018. http://dx.doi.org/10.1128/9781555819804.ch3.

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Aarts, Henk J. M., Beatriz Guerra i Burkhard Malorny. "Molecular Methods for Detection of Antibiotic Resistance". W Antimicrobial Resistance in Bacteria of Animal Origin, 37–48. Washington, DC, USA: ASM Press, 2019. http://dx.doi.org/10.1128/9781555817534.ch4.

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Streszczenia konferencji na temat "Genetic methods for resistance detection"

Mital, Manu, i E. P. Scott. "Thermal Detection of Embedded Tumors Using Infrared Imaging". W ASME 2004 International Mechanical Engineering Congress and Exposition. ASMEDC, 2004. http://dx.doi.org/10.1115/imece2004-62260.

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Breast cancer is the most common cancer among women. Statistics released by American Cancer Society (1999) show that every 1 in every 8 women in the United States is likely to get breast cancer during her lifetime. Thermography, also known as thermal or infrared imaging, is a procedure to determine if an abnormality is present in the breast tissue temperature distribution, which may indicate the presence of an embedded tumor. In the year 1982, United States Food and Drug Administration (FDA) approved thermography as an adjunct method of detecting breast cancer, which could be combined with other established techniques like mammography. Although thermography is currently used to indicate the presence of an abnormality, there are no standard protocols to interpret the abnormal thermal images and determine the size and location of an embedded tumor. This research explores the relationship between the physical characteristics of an embedded tumor and the resulting temperature distributions on the skin surface. Experiments were conducted using a resistance heater that was embedded in agar in order to simulate the heat produced by a tumor in the biological tissue. The resulting temperature distribution on the surface was imaged using an infrared camera. In order to estimate the location and heat generation rate of the source from these temperature distributions, a genetic algorithm was used as the estimation method. The genetic algorithm utilizes a finite difference scheme for the direct solution of Pennes bioheat equation. It was determined that a genetic algorithm based approach is well suited for the estimation problem and that thermography can prove to be a valuable tool in locating tumors if combined with such an algorithm.

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Ramirez, Abelardo, William Daily, Andrew Binley i Douglas LaBrecque. "Tank Leak Detection Using Electrical Resistance Methods". W 9th EEGS Symposium on the Application of Geophysics to Engineering and Environmental Problems. European Association of Geoscientists & Engineers, 1996. http://dx.doi.org/10.3997/2214-4609-pdb.205.1996_083.

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Ramirez, Abelardo, William Daily, Andrew Binley i Douglas LaBrecque. "Tank Leak Detection Using Electrical Resistance Methods". W Symposium on the Application of Geophysics to Engineering and Environmental Problems 1996. Environment and Engineering Geophysical Society, 1996. http://dx.doi.org/10.4133/1.2922341.

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"Molecular genetic methods for assessing drought resistance of spring barley". W Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Novosibirsk ICG SB RAS 2021, 2021. http://dx.doi.org/10.18699/plantgen2021-142.

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Pizzuti, Clara, i Annalisa Socievole. "An Effective Resistance based Genetic Algorithm for Community Detection". W 13th International Conference on Evolutionary Computation Theory and Applications. SCITEPRESS - Science and Technology Publications, 2021. http://dx.doi.org/10.5220/0010644300003063.

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Mitina, Irina, Aighiuni Bahsiev, Valentin Mitin i Irina Zamorzaeva. "QPCR detection and quantification of ‘Candidatus phytoplasma solani’ in tomato with primers targeting CPN60 gene". W VIIth International Scientific Conference “Genetics, Physiology and Plant Breeding”. Institute of Genetics, Physiology and Plant Protection, Republic of Moldova, 2021. http://dx.doi.org/10.53040/gppb7.2021.20.

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Tomato is one of the most economically important crops in Republic of Moldova. However, it is affected by a number of pathogens. One of the wide spread diseases is stolbur caused by the infection agent ‘Candidatus Phytoplasma solani’. Accurate diagnostics of the disease at an early stage is essential for successful control of the disease. In this work, we describe detection and quantification of ‘Candida-tus Phytoplasma solani’ in tomato by real-time PCR, as well as suitability of the method for assessing resistance of different tomato varieties to Phytoplasma infection.

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Greco, Annalisa, Francesco Cannizzaro i Alessandro Pluchino. "ON THE USE OF GENETIC ALGORITHMS TO ASSESS THE SEISMIC RESISTANCE OF PLANAR FRAME STRUCTURES". W 6th International Conference on Computational Methods in Structural Dynamics and Earthquake Engineering Methods in Structural Dynamics and Earthquake Engineering. Athens: Institute of Structural Analysis and Antiseismic Research School of Civil Engineering National Technical University of Athens (NTUA) Greece, 2017. http://dx.doi.org/10.7712/120117.5706.18227.

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Hauptman, Ami. "Are Evolutionary Computation-Based Methods Comparable to State-of-the-art non-Evolutionary Methods for Community Detection?" W GECCO '16: Genetic and Evolutionary Computation Conference. New York, NY, USA: ACM, 2016. http://dx.doi.org/10.1145/2908961.2931643.

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Alwan, Salwan, Jean-Marc Caillec i Gerard Meur. "Detection of Primitives in Engineering Drawing using Genetic Algorithm". W 8th International Conference on Pattern Recognition Applications and Methods. SCITEPRESS - Science and Technology Publications, 2019. http://dx.doi.org/10.5220/0007248802770282.

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Dobos, Daniel, Tien Thanh Nguyen, John McCall, Allan Wilson, Phil Stockton i Helen Corbett. "Weighted ensemble of gross error detection methods based on particle swarm optimization". W GECCO '21: Genetic and Evolutionary Computation Conference. New York, NY, USA: ACM, 2021. http://dx.doi.org/10.1145/3449726.3459415.

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Raporty organizacyjne na temat "Genetic methods for resistance detection"

Levisohn, Sharon, Mark Jackwood i Stanley Kleven. New Approaches for Detection of Mycoplasma iowae Infection in Turkeys. United States Department of Agriculture, luty 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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Slezak, T., R. Lenhoff, J. Allen, M. Borucki, E. Vitalis i S. Gardner. TMTI Task 1.6 Genetic Engineering Methods and Detection. Office of Scientific and Technical Information (OSTI), grudzień 2009. http://dx.doi.org/10.2172/972121.

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Jorgensen, Frieda, Andre Charlett, Craig Swift, Anais Painset i Nicolae Corcionivoschi. A survey of the levels of Campylobacter spp. contamination and prevalence of selected antimicrobial resistance determinants in fresh whole UK-produced chilled chickens at retail sale (non-major retailers). Food Standards Agency, czerwiec 2021. http://dx.doi.org/10.46756/sci.fsa.xls618.

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Campylobacter spp. are the most common bacterial cause of foodborne illness in the UK, with chicken considered to be the most important vehicle for this organism. The UK Food Standards Agency (FSA) agreed with industry to reduce Campylobacter spp. contamination in raw chicken and issued a target to reduce the prevalence of the most contaminated chickens (those with more than 1000 cfu per g chicken neck skin) to below 10 % at the end of the slaughter process, initially by 2016. To help monitor progress, a series of UK-wide surveys were undertaken to determine the levels of Campylobacter spp. on whole UK-produced, fresh chicken at retail sale in the UK. The data obtained for the first four years was reported in FSA projects FS241044 (2014/15) and FS102121 (2015 to 2018). The FSA has indicated that the retail proxy target for the percentage of highly contaminated raw whole retail chickens should be less than 7% and while continued monitoring has demonstrated a sustained decline for chickens from major retailer stores, chicken on sale in other stores have yet to meet this target. This report presents results from testing chickens from non-major retailer stores (only) in a fifth survey year from 2018 to 2019. In line with previous practise, samples were collected from stores distributed throughout the UK (in proportion to the population size of each country). Testing was performed by two laboratories - a Public Health England (PHE) laboratory or the Agri-Food & Biosciences Institute (AFBI), Belfast. Enumeration of Campylobacter spp. was performed using the ISO 10272-2 standard enumeration method applied with a detection limit of 10 colony forming units (cfu) per gram (g) of neck skin. Antimicrobial resistance (AMR) to selected antimicrobials in accordance with those advised in the EU harmonised monitoring protocol was predicted from genome sequence data in Campylobacter jejuni and Campylobacter coli isolates The percentage (10.8%) of fresh, whole chicken at retail sale in stores of smaller chains (for example, Iceland, McColl’s, Budgens, Nisa, Costcutter, One Stop), independents and butchers (collectively referred to as non-major retailer stores in this report) in the UK that are highly contaminated (at more than 1000 cfu per g) with Campylobacter spp. has decreased since the previous survey year but is still higher than that found in samples from major retailers. 8 whole fresh raw chickens from non-major retailer stores were collected from August 2018 to July 2019 (n = 1009). Campylobacter spp. were detected in 55.8% of the chicken skin samples obtained from non-major retailer shops, and 10.8% of the samples had counts above 1000 cfu per g chicken skin. Comparison among production plant approval codes showed significant differences of the percentages of chicken samples with more than 1000 cfu per g, ranging from 0% to 28.1%. The percentage of samples with more than 1000 cfu of Campylobacter spp. per g was significantly higher in the period May, June and July than in the period November to April. The percentage of highly contaminated samples was significantly higher for samples taken from larger compared to smaller chickens. There was no statistical difference in the percentage of highly contaminated samples between those obtained from chicken reared with access to range (for example, free-range and organic birds) and those reared under standard regime (for example, no access to range) but the small sample size for organic and to a lesser extent free-range chickens, may have limited the ability to detect important differences should they exist. Campylobacter species was determined for isolates from 93.4% of the positive samples. C. jejuni was isolated from the majority (72.6%) of samples while C. coli was identified in 22.1% of samples. A combination of both species was found in 5.3% of samples. C. coli was more frequently isolated from samples obtained from chicken reared with access to range in comparison to those reared as standard birds. C. jejuni was less prevalent during the summer months of June, July and August compared to the remaining months of the year. Resistance to ciprofloxacin (fluoroquinolone), erythromycin (macrolide), tetracycline, (tetracyclines), gentamicin and streptomycin (aminoglycosides) was predicted from WGS data by the detection of known antimicrobial resistance determinants. Resistance to ciprofloxacin was detected in 185 (51.7%) isolates of C. jejuni and 49 (42.1%) isolates of C. coli; while 220 (61.1%) isolates of C. jejuni and 73 (62.9%) isolates of C. coli isolates were resistant to tetracycline. Three C. coli (2.6%) but none of the C. jejuni isolates harboured 23S mutations predicting reduced susceptibility to erythromycin. Multidrug resistance (MDR), defined as harbouring genetic determinants for resistance to at least three unrelated antimicrobial classes, was found in 10 (8.6%) C. coli isolates but not in any C. jejuni isolates. Co-resistance to ciprofloxacin and erythromycin was predicted in 1.7% of C. coli isolates. 9 Overall, the percentages of isolates with genetic AMR determinants found in this study were similar to those reported in the previous survey year (August 2016 to July 2017) where testing was based on phenotypic break-point testing. Multi-drug resistance was similar to that found in the previous survey years. It is recommended that trends in AMR in Campylobacter spp. isolates from retail chickens continue to be monitored to realise any increasing resistance of concern, particulary to erythromycin (macrolide). Considering that the percentage of fresh, whole chicken from non-major retailer stores in the UK that are highly contaminated (at more than 1000 cfu per g) with Campylobacter spp. continues to be above that in samples from major retailers more action including consideration of interventions such as improved biosecurity and slaughterhouse measures is needed to achieve better control of Campylobacter spp. for this section of the industry. The FSA has indicated that the retail proxy target for the percentage of highly contaminated retail chickens should be less than 7% and while continued monitoring has demonstrated a sustained decline for chickens from major retailer stores, chicken on sale in other stores have yet to meet this target.

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Hovav, Ran, Peggy Ozias-Akins i Scott A. Jackson. The genetics of pod-filling in peanut under water-limiting conditions. United States Department of Agriculture, styczeń 2012. http://dx.doi.org/10.32747/2012.7597923.bard.

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Pod-filling, an important yield-determining stage is strongly influenced by water stress. This is particularly true for peanut (Arachishypogaea), wherein pods are developed underground and are directly affected by the water condition. Pod-filling in peanut has a significant genetic component as well, since genotypes are considerably varied in their pod-fill (PF) and seed-fill (SF) potential. The goals of this research were to: Examine the effects of genotype, irrigation, and genotype X irrigation on PF and SF. Detect global changes in mRNA and metabolites levels that accompany PF and SF. Explore the response of the duplicate peanut pod transcriptome to drought stress. Study how entire duplicated PF regulatory processes are networked within a polyploid organism. Discover locus-specific SNP markers and map pod quality traits under different environments. The research included genotypes and segregating populations from Israel and US that are varied in PF, SF and their tolerance to water deficit. Initially, an extensive field trial was conducted to investigate the effects of genotype, irrigation, and genotype X irrigation on PF and SF. Significant irrigation and genotypic effect was observed for the two main PF related traits, "seed ratio" and "dead-end ratio", demonstrating that reduction in irrigation directly influences the developing pods as a result of low water potential. Although the Irrigation × Genotype interaction was not statistically significant, one genotype (line 53) was found to be more sensitive to low irrigation treatments. Two RNAseq studies were simultaneously conducted in IL and the USA to characterize expression changes that accompany shell ("source") and seed ("sink") biogenesis in peanut. Both studies showed that SF and PF processes are very dynamic and undergo very rapid change in the accumulation of RNA, nutrients, and oil. Some genotypes differ in transcript accumulation rates, which can explain their difference in SF and PF potential; like cvHanoch that was found to be more enriched than line 53 in processes involving the generation of metabolites and energy at the beginning of seed development. Interestingly, an opposite situation was found in pericarp development, wherein rapid cell wall maturation processes were up-regulated in line 53. Although no significant effect was found for the irrigation level on seed transcriptome in general, and particularly on subgenomic assignment (that was found almost comparable to a 1:1 for A- and B- subgenomes), more specific homoeologous expression changes associated with particular biosynthesis pathways were found. For example, some significant A- and B- biases were observed in particular parts of the oil related gene expression network and several candidate genes with potential influence on oil content and SF were further examined. Substation achievement of the current program was the development and application of new SNP detection and mapping methods for peanut. Two major efforts on this direction were performed. In IL, a GBS approach was developed to map pod quality traits on Hanoch X 53 F2/F3 generations. Although the GBS approach was found to be less effective for our genetic system, it still succeeded to find significant mapping locations for several traits like testa color (linkage A10), number of seeds/pods (A5) and pod wart resistance (B7). In the USA, a SNP array was developed and applied for peanut, which is based on whole genome re-sequencing of 20 genotypes. This chip was used to map pod quality related traits in a Tifrunner x NC3033 RIL population. It was phenotyped for three years, including a new x-ray method to phenotype seed-fill and seed density. The total map size was 1229.7 cM with 1320 markers assigned. Based on this linkage map, 21 QTLs were identified for the traits 16/64 weight, kernel percentage, seed and pod weight, double pod and pod area. Collectively, this research serves as the first fundamental effort in peanut for understanding the PF and SF components, as a whole, and as influenced by the irrigation level. Results of the proposed study will also generate information and materials that will benefit peanut breeding by facilitating selection for reduced linkage drag during introgression of disease resistance traits into elite cultivars. BARD Report - Project4540 Page 2 of 10

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Ramirez, A., i W. Daily. Detection of leaks in underground storage tanks using electrical resistance methods: 1996 results. Office of Scientific and Technical Information (OSTI), październik 1996. http://dx.doi.org/10.2172/479070.

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Wisniewski, Michael E., Samir Droby, John L. Norelli, Noa Sela i Elena Levin. Genetic and transcriptomic analysis of postharvest decay resistance in Malus sieversii and the characterization of pathogenicity effectors in Penicillium expansum. United States Department of Agriculture, styczeń 2014. http://dx.doi.org/10.32747/2014.7600013.bard.

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Blue mold of apple caused by Penicilliumexpansumis a major postharvest disease. Selection for postharvest disease resistance in breeding programs has been ignored in favor of fruit quality traits such as size, color, taste, etc. The identification of postharvest disease resistance as a heritable trait would represent a significant accomplishment and has not been attempted in apple. Furthermore, insight into the biology of the pathogenicity of P. expansumin apple could provide new approaches to postharvest decay management. Hypothesis: Postharvest resistance of apple to P. expansumcan be mapped to specific genetic loci and significant quantitative-trait-loci (QTLs) can be identified that account for a major portion of the population variance. Susceptibility of apple fruit to P. expansumis dependent on the ability of the pathogen to produce LysM effectors that actively suppress primary and/or secondary resistance mechanisms in the fruit. Objectives: 1) Identify QTL(s) and molecular markers for blue mold resistance in GMAL4593 mapping population (‘Royal Gala’ X MalussieversiiPI613981), 2) Characterize the transcriptome of the host and pathogen (P. expansum) during the infection process 3) Determine the function of LysM genes in pathogenicity of P. expansum. Methods: A phenotypic evaluation of blue mold resistance in the GMAL4593 mapping population, conducted in several different years, will be used for QTL analysis (using MapQTL 6.0) to identify loci associated with blue mold resistance. Molecular markers will be developed for the resistance loci. Transcriptomic analysis by RNA-seq will be used to conduct a time course study of gene expression in resistant and susceptible apple GMAL4593 genotypes in response to P. expansum, as well as fungal responses to both genotypes. Candidate resistance genes identified in the transcriptomic study and or bioinformatic analysis will be positioned in the ‘Golden Delicious’ genome to identify markers that co-locate with the identified QTL(s). A functional analysis of LysM genes on pathogenicity will be conducted by eliminating or reducing the expression of individual effectors by heterologous recombination and silencing technologies. LysMeffector genes will also be expressed in a yeast expression system to study protein function. Expected Results: Identification of postharvest disease resistance QTLs and tightly-linked genetic markers. Increased knowledge of the role of effectors in blue mold pathogenic

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Sessa, Guido, i Gregory Martin. MAP kinase cascades activated by SlMAPKKKε and their involvement in tomato resistance to bacterial pathogens. United States Department of Agriculture, styczeń 2012. http://dx.doi.org/10.32747/2012.7699834.bard.

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The research problem: Pseudomonas syringae pv. tomato (Pst) and Xanthomonas campestrispv. vesicatoria (Xcv) are the causal agents of tomato bacterial speck and spot diseases, respectively. These pathogens colonize the aerial parts of the plant and cause economically important losses to tomato yield worldwide. Control of speck and spot diseases by cultural practices or chemicals is not effective and genetic sources of resistance are very limited. In previous research supported by BARD, by gene expression profiling we identified signaling components involved in resistance to Xcvstrains. Follow up experiments revealed that a tomato gene encoding a MAP kinase kinase kinase (MAPKKKe) is required for resistance to Xcvand Pststrains. Goals: Central goal of this research was to investigate the molecular mechanisms by which MAPKKKεand associated MAP kinase cascades regulate host resistance. Specific objectives were to: 1. Determine whether MAPKKKεplays a broad role in defense signaling in plants; 2. Identify components of MAP kinase cascades acting downstream of MAPKKKε; 3. Determine the role of phosphorylation-related events in the function of MAPKKKε; 4. Isolate proteins directly activated by MAPKKKε-associatedMAPK modules. Our main achievements during this research program are in the following major areas: 1. Characterization of MAPKKKεas a positive regulator of cell death and dissection of downstream MAP kinase cascades (Melech-Bonfil et al., 2010; Melech-Bonfil and Sessa, 2011). The MAPKKKεgene was found to be required for tomato resistance to Xcvand Pstbacterial strains and for hypersensitive response cell death triggered by different R gene/effector gene pairs. In addition, overexpression analysis demonstrated that MAPKKKεis a positive regulator of cell death, whose activity depends on an intact kinase catalytic domain. Epistatic experiments delineated a signaling cascade downstream of MAPKKKεand identified SIPKK as a negative regulator of MAPKKKε-mediated cell death. Finally, genes encoding MAP kinase components downstream of MAPKKKεwere shown to contribute to tomato resistance to Xcv. 2. Identification of tomato proteins that interact with MAPKKKεand play a role in plant immunity (Oh et al., 2011). We identified proteins that interact with MAPKKKε. Among them, the 14-3-3 protein TFT7 was required for cell death mediated by several R proteins. In addition, TFT7 interacted with the MAPKK SlMKK2 and formed homodimersin vivo. Thus, TFT7 is proposed to recruit SlMKK2 and MAPKKK client proteins for efficient signal transfer. 3. Development of a chemical genetic approach to identify substrates of MAPKKKε-activated MAP kinase cascades (Salomon et al., 2009, 2011). This approach is based on engineering the kinase of interest to accept unnatural ATP analogs. For its implementation to identify substrates of MAPKKKε-activated MAP kinase modules, we sensitized the tomato MAP kinase SlMPK3 to ATP analogs and verified its ability to use them as phosphodonors. By using the sensitized SlMPK3 and radiolabeled N6(benzyl)ATP it should be possible to tag direct substrates of this kinase. 4. Development of methods to study immunity triggered by pathogen-associated molecular patterns (PAMPs) in tomato and N. benthamiana plants (Kim et al., 2009; Nguyen et al. 2010). We developed protocols for measuring various PTI-associatedphenotypes, including bacterial populations after pretreatment of leaves with PAMPs, induction of reporter genes, callose deposition at the cell wall, activation of MAP kinases, and a luciferase-based reporter system for use in protoplasts. Scientific and agricultural significance: Our research activities discovered and characterized a signal transduction pathway mediating plant immunity to bacterial pathogens. Increased understanding of molecular mechanisms of immunity will allow them to be manipulated by both molecular breeding and genetic engineering to produce plants with enhanced natural defense against disease. In addition, we successfully developed new biochemical and molecular methods that can be implemented in the study of plant immunity and other aspects of plant biology.

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Sessa, Guido, i Gregory B. Martin. molecular link from PAMP perception to a MAPK cascade associated with tomato disease resistance. United States Department of Agriculture, styczeń 2012. http://dx.doi.org/10.32747/2012.7597918.bard.

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The research problem: The detection of pathogen-associated molecular patterns (PAMPs) by plant pattern recognition receptors (PRRs) is a key mechanism by which plants activate an effective immune response against pathogen attack. MAPK cascades are important signaling components downstream of PRRs that transduce the PAMP signal to activate various defense responses. Preliminary experiments suggested that the receptor-like cytoplasmickinase (RLCK) Mai5 plays a positive role in pattern-triggered immunity (PTI) and interacts with the MAPKKK M3Kε. We thus hypothesized that Mai5, as other RLCKs, functions as a component PRR complexes and acts as a molecular link between PAMP perception and activation of MAPK cascades. Original goals: The central goal of this research was to investigate the molecular mechanisms by which Mai5 and M3Kε regulate plant immunity. Specific objectives were to: 1. Determine the spectrum of PAMPs whose perception is transmitted by M3Kε; 2. Identify plant proteins that act downstream of M3Kε to mediate PTI; 3. Investigate how and where Mai5 interacts with M3Kε in the plant cell; 4. Examine the mechanism by which Mai5 contributes to PTI. Changes in research directions: We did not find convincing evidence for the involvement of M3Kε in PTI signaling and substituted objectives 1 and 3 with research activities aimed at the analysis of transcriptomic profiles of tomato plants during the onset of plant immunity, isolation of the novel tomato PRR FLS3, and investigation of the involvement of the RLCKBSKs in PTI. Main achievements during this research program are in the following major areas: 1. Functional characterization of Mai5. The function of Mai5 in PTI signaling was demonstrated by testing the effect of silencing the Mai5 gene by virus-induced gene silencing (VIGS) experiments and in cell death assays. Domains of Mai5 that interact with MAPKKKs and subcellular localization of Mai5 were analyzed in detail. 2. Analysis of transcriptional profiles during the tomato immune responses to Pseudomonas syringae (Pombo et al., 2014). We identified tomato genes whose expression is induced specifically in PTI or in effector-triggered immunity (ETI). Thirty ETI-specific genes were examined by VIGS for their involvement in immunity and the MAPKKK EPK1, was found to be required for ETI. 3. Dissection of MAP kinase cascades downstream of M3Kε (Oh et al., 2013; Teper et al., 2015). We identified genes that encode positive (SGT and EDS1) and negative (WRKY1 and WRKY2) regulators of the ETI-associated cell death mediated by M3Kε. In addition, the MKK2 MAPKK, which acts downstream of M3Kε, was found to interact with the MPK3 MAPK and specific MPK3 amino acids involved interaction were identified and found to be required for induction of cell death. We also identified 5 type III effectors of the bacterial pathogen Xanthomonaseuvesicatoria that inhibited cell death induced by components of ETI-associated MAP kinase cascades. 4. Isolation of the tomato PRR FLS3 (Hind et al., submitted). FLS3, a novel PRR of the LRR-RLK family that specifically recognizes the flagellinepitope flgII-28 was isolated. FLS3 was shown to bind flgII-28, to require kinase activity for function, to act in concert with BAK1, and to enhance disease resistance to Pseudomonas syringae. 5. Functional analysis of RLCKs of the brassinosteroid signaling kinase (BSK) family.Arabidopsis and tomato BSKs were found to interact with PRRs. In addition, certain ArabidospsisBSK mutants were found to be impaired in PAMP-induced resistance to Pseudomonas syringae. Scientific and agricultural significance: Our research activities discovered and characterized new molecular components of signaling pathways mediating recognition of invading pathogens and activation of immune responses against them. Increased understanding of molecular mechanisms of immunity will allow them to be manipulated by both molecular breeding and genetic engineering to produce plants with enhanced natural defense against disease.

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Sela, Hanan, Eduard Akhunov i Brian J. Steffenson. Population genomics, linkage disequilibrium and association mapping of stripe rust resistance genes in wild emmer wheat, Triticum turgidum ssp. dicoccoides. United States Department of Agriculture, styczeń 2014. http://dx.doi.org/10.32747/2014.7598170.bard.

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The primary goals of this project were: (1) development of a genetically characterized association panel of wild emmer for high resolution analysis of the genetic basis of complex traits; (2) characterization and mapping of genes and QTL for seedling and adult plant resistance to stripe rust in wild emmer populations; (3) characterization of LD patterns along wild emmer chromosomes; (4) elucidation of the multi-locus genetic structure of wild emmer populations and its correlation with geo-climatic variables at the collection sites. Introduction In recent years, Stripe (yellow) rust (Yr) caused by Pucciniastriiformis f. sp. tritici(PST) has become a major threat to wheat crops in many parts of the world. New races have overcome most of the known resistances. It is essential, therefore, that the search for new genes will continue, followed by their mapping by molecular markers and introgression into the elite varieties by marker-assisted selection (MAS). The reservoir of genes for disease and pest resistance in wild emmer wheat (Triticumdicoccoides) is an important resource that must be made available to wheat breeders. The majority of resistance genes that were introgressed so far in cultivated wheat are resistance (R) genes. These genes, though confering near-immunity from the seedling stage, are often overcome by the pathogen in a short period after being deployed over vast production areas. On the other hand, adult-plant resistance (APR) is usually more durable since it is, in many cases, polygenic and confers partial resistance that may put less selective pressure on the pathogen. In this project, we have screened a collection of 480 wild emmer accessions originating from Israel for APR and seedling resistance to PST. Seedling resistance was tested against one Israeli and 3 North American PST isolates. APR was tested on accessions that did not have seedling resistance. The APR screen was conducted in two fields in Israel and in one field in the USA over 3 years for a total of 11 replicates. We have found about 20 accessions that have moderate stripe rust APR with infection type (IT<5), and about 20 additional accessions that have novel seedling resistance (IT<3). We have genotyped the collection using genotyping by sequencing (GBS) and the 90K SNP chip array. GBS yielded a total 341K SNP that were filtered to 150K informative SNP. The 90K assay resulted in 11K informative SNP. We have conducted a genome-wide association scan (GWAS) and found one significant locus on 6BL ( -log p >5). Two novel loci were found for seedling resistance. Further investigation of the 6BL locus and the effect of Yr36 showed that the 6BL locus and the Yr36 have additive effect and that the presence of favorable alleles of both loci results in reduction of 2 grades in the IT score. To identify alleles conferring adaption to extreme climatic conditions, we have associated the patterns of genomic variation in wild emmer with historic climate data from the accessions’ collection sites. The analysis of population stratification revealed four genetically distinct groups of wild emmer accessions coinciding with their geographic distribution. Partitioning of genomic variance showed that geographic location and climate together explain 43% of SNPs among emmer accessions with 19% of SNPs affected by climatic factors. The top three bioclimatic factors driving SNP distribution were temperature seasonality, precipitation seasonality, and isothermality. Association mapping approaches revealed 57 SNPs associated with these bio-climatic variables. Out of 21 unique genomic regions controlling heading date variation, 10 (~50%) overlapped with SNPs showing significant association with at least one of the three bioclimatic variables. This result suggests that a substantial part of the genomic variation associated with local adaptation in wild emmer is driven by selection acting on loci regulating flowering. Conclusions: Wild emmer can serve as a good source for novel APR and seedling R genes for stripe rust resistance. APR for stripe rust is a complex trait conferred by several loci that may have an additive effect. GWAS is feasible in the wild emmer population, however, its detection power is limited. A panel of wild emmer tagged with more than 150K SNP is available for further GWAS of important traits. The insights gained by the bioclimatic-gentic associations should be taken into consideration when planning conservation strategies.

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Breiman, Adina, Jan Dvorak, Abraham Korol i Eduard Akhunov. Population Genomics and Association Mapping of Disease Resistance Genes in Israeli Populations of Wild Relatives of Wheat, Triticum dicoccoides and Aegilops speltoides. United States Department of Agriculture, grudzień 2011. http://dx.doi.org/10.32747/2011.7697121.bard.

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Wheat is the most widely grown crop on earth, together with rice it is second to maize in total global tonnage. One of the emerging threats to wheat is stripe (yellow) rust, especially in North Africa, West and Central Asia and North America. The most efficient way to control plant diseases is to introduce disease resistant genes. However, the pathogens can overcome rapidly the effectiveness of these genes when they are wildly used. Therefore, there is a constant need to find new resistance genes to replace the non-effective genes. The resistance gene pool in the cultivated wheat is depleted and there is a need to find new genes in the wild relative of wheat. Wild emmer (Triticum dicoccoides) the progenitor of the cultivated wheat can serve as valuable gene pool for breeding for disease resistance. Transferring of novel genes into elite cultivars is highly facilitated by the availability of information of their chromosomal location. Therefore, our goals in this study was to find stripe rust resistant and susceptible genotypes in Israeli T. dicoccoides population, genotype them using state of the art genotyping methods and to find association between genetic markers and stripe rust resistance. We have screened 129 accessions from our collection of wild emmer wheat for resistance to three isolates of stripe rust. About 30% of the accessions were resistant to one or more isolates, 50% susceptible, and the rest displayed intermediate response. The accessions were genotyped with Illumina'sInfinium assay which consists of 9K single nucleotide polymorphism (SNP) markers. About 13% (1179) of the SNPs were polymorphic in the wild emmer population. Cluster analysis based on SNP diversity has shown that there are two main groups in the wild population. A big cluster probably belongs to the Horanum ssp. and a small cluster of the Judaicum ssp. In order to avoid population structure bias, the Judaicum spp. was removed from the association analysis. In the remaining group of genotypes, linkage disequilibrium (LD) measured along the chromosomes decayed rapidly within one centimorgan. This is the first time when such analysis is conducted on a genome wide level in wild emmer. Such a rapid decay in LD level, quite unexpected for a selfer, was not observed in cultivated wheat collection. It indicates that wild emmer populations are highly suitable for association studies yielding a better resolution than association studies in cultivated wheat or genetic mapping in bi-parental populations. Significant association was found between an SNP marker located in the distal region of chromosome arm 1BL and resistance to one of the isolates. This region is not known in the literature to bear a stripe rust resistance gene. Therefore, there may be a new stripe rust resistance gene in this locus. With the current fast increase of wheat genome sequence data, genome wide association analysis becomes a feasible task and efficient strategy for searching novel genes in wild emmer wheat. In this study, we have shown that the wild emmer gene pool is a valuable source for new stripe rust resistance genes that can protect the cultivated wheat.

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