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Academic literature on the topic 'LAMP assay'

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Published: 10 December 2022
Last updated: 28 January 2023

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Journal articles on the topic "LAMP assay"

1

Lee, Jiwon, Youngbae Yoon, Eun Jin Kim, Donghyun Lee, Yeongjun Baek, Chika Takano, Bin Chang, et al. "23-valent polysaccharide vaccine (PPSV23)-targeted serotype-specific identification of Streptococcus pneumoniae using the loop-mediated isothermal amplification (LAMP) method." PLOS ONE 16, no. 2 (February 16, 2021): e0246699. http://dx.doi.org/10.1371/journal.pone.0246699.

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Reports of invasive disease due to Streptococcus pneumoniae have declined since the introduction of pneumococcal conjugate vaccines (PCV7 and PCV13). The incidence of invasive diseases due to S. pneumoniae that are not addressed by the vaccines, however, has increased in children and adults, creating a global public health problem. Previously, we established the loop-mediated isothermal amplification (LAMP) method for a PCV13 serotype-specific assay. In the current study, we developed a rapid, simple, and cost-effective assay to detect serotypes in the 23-valent pneumococcal polysaccharide vaccine (PPSV23) using the LAMP method. In this study, LAMP primer sets for serotypes 2, 8, 9N, 10A, 11A, 12F, 15B, 17F, 20, 22F, and 33F of S. pneumoniae were developed. The reactivity, specificity, and sensitivity of LAMP assays were determined and compared to those of conventional PCR. The feasibility of LAMP assays in clinical application in patients with invasive pneumococcal diseases was validated by defining the detection limit of the LAMP assay with bacterial genomic DNA-spiked blood specimens. The specificity of each LAMP assay was determined using 44 serotypes of pneumococcal strains. Their sensitivity was 100 copies per reaction versus 103 to 106 copies per reaction for PCR assays. Using DNA-spiked blood specimens, excluding the LAMP assay that targeted serotype 22F (103 copies per reaction), the limit of detection of the LAMP assay was similar to that with purified DNA as the template (102 copies per reaction), compared with 103 to >106 copies per reaction for PCR assays. In conclusion, a rapid and simple LAMP-based PPSV23-targeted serotype detection assay was developed for use in many countries. This study is the first report of a LAMP-based assay for identification of PPSV23 serotypes. Further evaluation of this assay is needed through surveillance and vaccine efficacy studies.
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Saito, Yuichi, Atsuka Matsui, Satoru Michiyuki, Hiroaki Morooka, Takayuki Ibi, Yoshikane Yamauchi, Nobumasa Takahashi, et al. "Loop-Mediated Isothermal Amplification as Point-of-Care Testing for EGFR-Mutated Lung Adenocarcinoma." Micromachines 13, no. 6 (June 6, 2022): 897. http://dx.doi.org/10.3390/mi13060897.

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Liquid biopsy has been adapted as a diagnostic test for EGFR mutations in patients with advanced or metastatic non-small cell lung cancer (NSCLC). Loop-mediated isothermal amplification (LAMP) has been widely used for the rapid detection of pathogens through DNA amplification. This study investigated the efficacy of an EGFR-LAMP assay using plasma samples of patients with resected NSCLC tumors. The EGFR status was investigated using both LAMP and next-generation sequencing (NGS) assays in cases that met the following criteria: (1) pulmonary adenocarcinoma with EGFR mutation detected by the Therascreen EGFR PCR Kit and (2) preoperative plasma samples contained enough DNA for the LAMP and NGS experiments. Among 51 specimens from patients with EGFR-mutated tumors or metastatic lymph nodes, the LAMP assay detected 1 EGFR mutation that was also detected in the NGS assay. However, a plasma sample that demonstrated EGFR wild type in the LAMP assay showed an EGFR mutant status in NGS. The detection rates (1.9% in LAMP and 3.9% in NGS) were very low in both assays, demonstrating a similar performance in detecting EGFR mutations in NSCLC tumors; therefore, it could be a more suitable test for the advanced stage, not the early stage. Notably, the LAMP assay was more time-saving, cost-effective, and straightforward. However, further investigation is required to develop a more sensitive assay.
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Yang, Zhu, Nicole Y. Liu, Zhiwei Zhu, Minmin Xiao, Shuzhi Zhong, Qiqi Xue, Lina Nie, and Jinhong Zhao. "Rapid and convenient detection of SARS-CoV-2 using a colorimetric triple-target reverse transcription loop-mediated isothermal amplification method." PeerJ 10 (October 10, 2022): e14121. http://dx.doi.org/10.7717/peerj.14121.

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Coronavirus Disease 2019 (COVID-19) caused by SARS-CoV-2 poses a significant threat to global public health. Early detection with reliable, fast, and simple assays is crucial to contain the spread of SARS-CoV-2. The real-time reverse transcription-polymerase chain reaction (RT-PCR) assay is currently the gold standard for SARS-CoV-2 detection; however, the reverse transcription loop-mediated isothermal amplification method (RT-LAMP) assay may allow for faster, simpler and cheaper screening of SARS-CoV-2. In this study, the triple-target RT-LAMP assay was first established to simultaneously detect three different target regions (ORF1ab, N and E genes) of SARS-CoV-2. The results revealed that the developed triplex RT-LAMP assay was able to detect down to 11 copies of SARS-CoV-2 RNA per 25 µL reaction, with greater sensitivity than singleplex or duplex RT-LAMP assays. Moreover, two different indicators, hydroxy naphthol blue (HNB) and cresol red, were studied in the colorimetric RT-LAMP assay; our results suggest that both indicators are suitable for RT-LAMP reactions with an obvious color change. In conclusion, our developed triplex colorimetric RT-LAMP assay may be useful for the screening of COVID-19 cases in limited-resource areas.
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Lees, A. K., D. M. Roberts, J. Lynott, L. Sullivan, and J. L. Brierley. "Real-Time PCR and LAMP Assays for the Detection of Spores of Alternaria solani and Sporangia of Phytophthora infestans to Inform Disease Risk Forecasting." Plant Disease 103, no. 12 (December 2019): 3172–80. http://dx.doi.org/10.1094/pdis-04-19-0765-re.

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Real-time loop-mediated isothermal amplification (LAMP) assays for the detection of sporangia of the causal pathogen of late blight, Phytophthora infestans, and spores of the main causal pathogen of early blight, Alternaria solani, were developed to facilitate the in-field detection of airborne inoculum to improve disease forecasting. These assays were compared with an existing real-time PCR assay for P. infestans and a newly developed real-time PCR assay for A. solani. Primers were designed for real-time LAMP of P. infestans and A. solani. The specificity of the P. infestans real-time LAMP assay was similar to that of an existing real-time PCR assay: DNA of P. infestans was consistently amplified as was DNA of the taxonomically closely related species Phytophthora mirabilis, Phytophthora phaseoli, and Phytophthora ipomoea; no amplification of DNA from the potato pathogens Phytophthora erythroseptica or Phytophthora nicotianae occurred. Real-time LAMP and PCR assays were developed for A. solani, and the specificity was compared with an existing conventional PCR assay. Importantly, the A. solani real-time LAMP and PCR assays did not amplify the species Alternaria alternata. However, cross-reactivity with Alternaria dauci was observed with the real-time PCR assay and Alternaria brassicae with the real-time LAMP assay. The sensitivity of all assays for the detection of DNA extracted from sporangia/spores of the target pathogens was evaluated. The P. infestans real-time LAMP assay reliably detected 5 pg of DNA, equivalent to ∼1 sporangia per reaction. By comparison, 20 fg of DNA was detectable with the existing real-time PCR assay. In the case of A. solani, real-time LAMP detected 4.4 pg of DNA, equivalent to ∼1 spore per reaction, and real-time PCR detected 200 fg of DNA. In-field air samplers were deployed in two trial plots planted with potato: one infected with P. infestans, and the other infected with A. solani. Four additional samplers were located in commercial potato fields. Air samples were taken through the season, and detection of airborne inoculum of P. infestans and A. solani with both real-time PCR and LAMP was assessed.
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SABIKE, ISLAM IBRAHIM, and WATARU YAMAZAKI. "Improving the Detection Accuracy and Time for Campylobacter jejuni and Campylobacter coli in Naturally Infected Live and Slaughtered Chicken Broilers Using a Real-Time Fluorescent Loop-Mediated Isothermal Amplification Approach." Journal of Food Protection 82, no. 2 (January 22, 2019): 189–93. http://dx.doi.org/10.4315/0362-028x.jfp-18-179.

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ABSTRACT Rapid and accurate identification of Campylobacter-positive broiler flocks and carcasses expedites separation and control interventions before release into the food supply chain and directly facilitates a reduction in the prevalence of human campylobacteriosis. In this study, the diagnostic performance of fluorescent loop-mediated isothermal amplification (LAMP) assays for the direct detection of Campylobacter jejuni and Campylobacter coli in broiler cloacal and cecal samples were evaluated and compared with that of turbidimetric LAMP approaches investigated previously. The duplex fluorescent LAMP assay had significantly higher (P < 0.05) diagnostic sensitivity (93.1%, 54 of 58 samples) than did the turbidimetric LAMP assay (82.8%, 48 of 58 samples) for detecting C. jejuni and C. coli in broiler cloacal samples, whereas the singleplex fluorescent LAMP assay had equivalent diagnostic sensitivity. For cecal samples, the diagnostic sensitivity of the fluorescent LAMP assay (100%, 38 of 38 samples) was the same as that of the turbidimetric LAMP. Fluorescent LAMP significantly reduced (P < 0.05) the maximum detection time for Campylobacter-positive cloacal and cecal samples to 28 and 11 min, respectively, and reduced the influence of amplification inhibitors responsible for most false-negative results obtained for cloacal samples with the turbidimetric LAMP assay. The diagnostic accuracy of the fluorescent LAMP assay for the direct detection of C. jejuni and C. coli in cloacal and cecal samples was 97.7 and 100%, respectively. These findings indicate that fluorescent LAMP assays are robust, highly accurate, and field-applicable methods for the identification of C. jejuni and C. coli, which will allow more accurate monitoring of food safety at various stages of the food supply chain at farms and slaughter facilities.
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Kaushik, D., M. H. Halabi, P. Barua, and P. D. Nath. "Real-Time loop-mediated isothermal amplification assay for rapid detection of Banana bunchy top virus in North-east India." Journal of Environmental Biology 43, no. 6 (November 15, 2022): 873–78. http://dx.doi.org/10.22438/jeb/43/6/mrn-2043.

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Aim: The study aims to standardize a Real-Time LAMP assay for effective, highly sensitive, and rapid detection of BBTV in North-east India. Methodology: Forty samples of banana showing BBTV like symptoms were collected from Assam, India and subjected to conventional PCR for confirmation. Six sets of BBTV LAMP primers were designed and the PCR positive samples were subjected to Real-Time LAMP assay for detection of BBTV. Finally, a sensitivity test of BBTV LAMP assay and comparison of BBTV LAMP assay with conventional PCR was done using seven 10-fold dilutions of total genomic DNA of leaf samples with the highest dilution starting from 100 ng µl-1. Results: Initially a total of twenty six out of forty banana samples were tested positive for BBTV with conventional PCR method. The Real-Time LAMP assay for BBTV detection resulted in typical sigmoidal amplification curves with the peak values ranging between 8.00 to 12.15 min and annealing derivatives ranging between 83.3oC to 84.3oC in the tested samples. Sensitivity testing and comparison of BBTV Real-Time LAMP assay with conventional PCR revealed that the BBTV LAMP assay could efficiently detect up to 0.0001ng µl-1 of total DNA against 0.01ng µl-1 in conventional PCR. Interpretation: The findings highlight rapid, sensitive, accurate and effective diagnosis of BBTV using Real-Time LAMP method. This method can be preferred over conventional diagnostic techniques like PCR or ELISA for rapid large scale detection of BBTV in banana plants in North-east India. Key words: Banana, Banana bunchy top virus, Rapid detection, Real-Time LAMP assay
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Kumagai, Takashi, Emilie Louise Akiko Matsumoto-Takahashi, Hirofumi Ishikawa, Sengdeuane Keomalaphet, Phonepadith Khattignavong, Pheovaly Soundala, Bouasy Hongvanthong, et al. "Detection of Schistosoma mekongi DNA in Human Stool and Intermediate Host Snail Neotricula aperta via Loop-Mediated Isothermal Amplification Assay in Lao PDR." Pathogens 11, no. 12 (November 24, 2022): 1413. http://dx.doi.org/10.3390/pathogens11121413.

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Schistosomiasis mekongi infection represents a public health concern in Laos and Cambodia. While both countries have made significant progress in disease control over the past few decades, eradication has not yet been achieved. Recently, several studies reported the application of loop-mediated isothermal amplification (LAMP) for detecting Schistosoma DNA in low-transmission settings. The objective of this study was to develop a LAMP assay for Schistosoma mekongi using a simple DNA extraction method. In particular, we evaluated the utility of the LAMP assay for detecting S. mekongi DNA in human stool and snail samples in endemic areas in Laos. We then used the LAMP assay results to develop a risk map for monitoring schistosomiasis mekongi and preventing epidemics. A total of 272 stool samples were collected from villagers on Khon Island in the southern part of Laos in 2016. DNA for LAMP assays was extracted via the hot-alkaline method. Following the Kato-Katz method, we determined that 0.4% (1/272) of the stool samples were positive for S. mekongi eggs, as opposed to 2.9% (8/272) for S. mekongi DNA based on the LAMP assays. Snail samples (n = 11,762) were annually collected along the riverside of Khon Island from 2016 to 2018. DNA was extracted from pooled snails as per the hot-alkaline method. The LAMP assay indicated that the prevalence of S. mekongi in snails was 0.26% in 2016, 0.08% in 2017, and less than 0.03% in 2018. Based on the LAMP assay results, a risk map for schistosomiasis with kernel density estimation was created, and the distribution of positive individuals and snails was consistent. In a subsequent survey of residents, schistosomiasis prevalence among villagers with latrines at home was lower than that among villagers without latrines. This is the first study to develop and evaluate a LAMP assay for S. mekongi detection in stools and snails. Our findings indicate that the LAMP assay is an effective method for monitoring pathogen prevalence and creating risk maps for schistosomiasis.
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Lu, Chenchen, Bi Song, HaiFeng Zhang, YuanChao Wang, and XiaoBo Zheng. "Rapid Diagnosis of Soybean Seedling Blight Caused by Rhizoctonia solani and Soybean Charcoal Rot Caused by Macrophomina phaseolina Using LAMP Assays." Phytopathology® 105, no. 12 (December 2015): 1612–17. http://dx.doi.org/10.1094/phyto-01-15-0023-r.

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A new method of direct detection of pathogenic fungi in infected soybean tissues has been reported here. The method rapidly diagnoses soybean seedling blight caused by Rhizoctonia solani and soybean charcoal rot caused by Macrophomina phaseolina, and features loop-mediated isothermal amplification (LAMP). The primers were designed and screened using internal transcribed spacers (ITS) as target DNAs of both pathogens. An ITS-Rs-LAMP assay for R. solani and an ITS-Mp-LAMP assay for M. phaseolina that can detect the pathogen in diseased soybean tissues in the field have been developed. Both LAMP assays efficiently amplified the target genes over 60 min at 62°C. A yellow-green color (visible to the naked eye) or intense green fluorescence (visible under ultraviolet light) was only observed in the presence of R. solani or M. phaseolina after addition of SYBR Green I. The detection limit of the ITS-Rs-LAMP assay was 10 pg μl–1 of genomic DNA; and that of the ITS-Mp-LAMP assay was 100 pg μl–1 of genomic DNA. Using the two assays described here, we successfully and rapidly diagnosed suspect diseased soybean samples collected in the field from Jiangsu and Anhui provinces.
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Dao Thi, Viet Loan, Konrad Herbst, Kathleen Boerner, Matthias Meurer, Lukas PM Kremer, Daniel Kirrmaier, Andrew Freistaedter, et al. "A colorimetric RT-LAMP assay and LAMP-sequencing for detecting SARS-CoV-2 RNA in clinical samples." Science Translational Medicine 12, no. 556 (July 27, 2020): eabc7075. http://dx.doi.org/10.1126/scitranslmed.abc7075.

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The coronavirus disease 2019 (COVID-19) pandemic caused by the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) coronavirus is a major public health challenge. Rapid tests for detecting existing SARS-CoV-2 infections and assessing virus spread are critical. Approaches to detect viral RNA based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) have potential as simple, scalable, and broadly applicable testing methods. Compared to RT quantitative polymerase chain reaction (RT-qPCR)–based methods, RT-LAMP assays require incubation at a constant temperature, thus eliminating the need for sophisticated instrumentation. Here, we tested a two-color RT-LAMP assay protocol for detecting SARS-CoV-2 viral RNA using a primer set specific for the N gene. We tested our RT-LAMP assay on surplus RNA samples isolated from 768 pharyngeal swab specimens collected from individuals being tested for COVID-19. We determined the sensitivity and specificity of the RT-LAMP assay for detecting SARS-CoV-2 viral RNA. Compared to an RT-qPCR assay using a sensitive primer set, we found that the RT-LAMP assay reliably detected SARS-CoV-2 RNA with an RT-qPCR cycle threshold (CT) number of up to 30, with a sensitivity of 97.5% and a specificity of 99.7%. We also developed a swab–to–RT-LAMP assay that did not require a prior RNA isolation step, which retained excellent specificity (99.5%) but showed lower sensitivity (86% for CT < 30) than the RT-LAMP assay. In addition, we developed a multiplexed sequencing protocol (LAMP-sequencing) as a diagnostic validation procedure to detect and record the outcome of RT-LAMP reactions.
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Azizi, Mohammad Malek Faizal, Han Yih Lau, Norliza Abu Bakar, Sohana Romeli, Muhammad Fairuz Mohd Yusof, Rafidah Badrun, and Nur Sulastri Jaffar. "Development of a Highly Sensitive Loop-Mediated Isothermal Amplification Incorporated with Flocculation of Carbon Particles for Rapid On-Site Diagnosis of Blood Disease Bacterium Banana." Horticulturae 8, no. 5 (May 5, 2022): 406. http://dx.doi.org/10.3390/horticulturae8050406.

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Bananas are one of the most crucial fruit crops worldwide and significantly contribute to food security in developing countries. However, blood disease of bananas caused by Ralstonia syzygii subspecies celebensensis has become a threat to banana production. Rapid and accurate diagnosis of BDB for on-site detection is pivotal at an early stage for an effective disease control strategy. This study developed LAMP with specific primers targeting BDB, followed by a flocculation assay for visualising positive amplification in the LAMP assay. The assay was sensitive to picogram amounts of gDNA (0.5 pg). LAMP assay on BDB gDNA showed flocculation, but negative results on Fusarium oxysporus cubense and Ralstonia solanacaerum confirming the specificity of the assays. Field testing conducted at MARDI headquarters and Taman Pertanian Universiti discovered that the LAMP-flocculation assays were successful in detecting BDB on symptomatic samples as well as on samples from a healthy plot with no symptom observed at the sampling stage, revealing that this assay can detect BDB at an early infection stage. The validation results showed that the LAMP-flocculation assay was comparable with the PCR technique. This newly developed technique is highly specific and sensitive for the early detection of BDB for the adoption of precautionary control measures.
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Dissertations / Theses on the topic "LAMP assay"

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Lasota, Tomasz. "Enhanced molecular assays using strand-displacing polymerases and loop-mediated amplification (LAMP) with Bioluminescent Assay in Real Time (BART)." Thesis, Cardiff University, 2017. http://orca.cf.ac.uk/111111/.

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Real-time reverse transcription loop-mediated isothermal amplification (RT-LAMP) is becoming a widely accepted method for use in the field of molecular diagnostics. This method makes use of a highly robust core enzymology’s that are tolerant to sample derived inhibitors, along with a priming mechanisms that permit impeccable amplification sensitivities and specificities. These are well documented attributes associated with LAMP, but little is known about factors that drive and interfere with the reverse transcription of RT-LAMP assays. This study aims to address a number of factors that affect RNA amplification, including impedance of priming related to template structure, inhibition of polymerase activities by sample derived inhibitors and the general effect of assay chemistry and primer function with respect to reverse transcription. In addition to the chemistry optimisation and choice of polymerase (DNA / RT), the secondary structure innate within RNA, could significantly affect the efficiency of RT. Priming position and design would also need to be seriously considered with respect to the folding nature of these targets. Overtly, RT-LAMP showed an increased sensitivity to inhibition compared to its DNA counterpart. Similar observations of impeded RNA transcription were made during the development of an internal amplification control (IAC), which was designed to determine the exact inhibitory nature of any tested samples, in tandem with the RT-LAMP. This report clearly discloses that RT amplification controls must be synthesised ‘free of contaminating DNA’, to avoid poor characterisation of first strand DNA synthesis. Alternative ‘non-enzymatic methods’ of reporting amplification in real-time were compared to the bioluminescent assay real-time (BART) reporter; a well-established method of nucleic acid detection and quantification developed and patented by Lumora Ltd, Cambridgeshire (Fortes et al., 2013). Despite BARTs track record for detection of LAMP, its 4 indiscriminate reporting of amplification is of little use for duplexed assay characterisation, such as the IAC / RT-LAMP combined assay. Thus, methods of specific sequence detection were designed that could target single stranded elements of amplified products (STEMs and LOOP structures). It was demonstrated that the mechanism for RT-LAMP fluorescent probing ‘presented here’ was unique to this Thesis and does not fall under the guise of Taqman or other molecular beacon detection mechanisms. Together with BART, this new form of probing was successfully deployed to distinguish between true RT-LAMP and IAC afflicted amplifications. The possibility of utilising the LAMP/BART technologies for microRNA (miRNA) detection was also explored. Even though it is well known that miRNAs have crucial roles in responding to and regulating a wide range of biological and cellular processes, no real headway has been made in developing highly sensitive, low resource methods for their detection. Here we develop novel methods of miRNA detection capable of sensing picomolar levels that also make use of the LAMP and BART chemistry.
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Wong, Ting-yin, and 王婷妍. "HPV 16 and HPV 18 detection in cytology sample of follicular cervicitis using LAMP assay." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2011. http://hub.hku.hk/bib/B46632761.

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Hardinge, Patrick. "Low copy number quantification of DNA utilising Loop-mediated Amplification (LAMP) with Bioluminescent Assay in Real-Time (BART) reporter." Thesis, Cardiff University, 2014. http://orca.cf.ac.uk/66189/.

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iv Abstract Low Copy Number Quantification of DNA Utilising Loop - mediated Amplification (LAMP) with Biolumines cent Assay in Real - Time (BART) Reporter Real time quantitative PCR is the benchmark technology of molecular diagnostics in a wide range of fields including forensic science, clinical diagnosis and the detection of genetically modified (GM) c rops. T here is a requirement for rapid, cheap and simple portable quantitative and specific diagnostics . Quantitative PCR is limited by a number of factors in this regard: t he complex hardware is often expensive and largely laboratory limited. Bioluminescent Assay in Re al Time (BART) is a nucleic acid amplification detection system that converts inorganic pyrophosphate (PPi) , a by - product of DNA synthesis , into light output. The pyrophosphate is converted into ATP which is utilised by a thermostable luciferase to convert luciferin to oxyluciferin with the emission of light. The development of isothermal amplification techniques that use the strand displacement properties of certain DNA polymerases enables the BART detection to be utilised in simple and cheap hardware at a single temperature. Loop - mediated amplification (LAMP) is an isothermal amplification method which is highly specific to the DNA target sequence and produ ces high concentrations of PPi.
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Odari, Eddy Okoth. "Establishment and evaluation of a loop-mediated isothermal assay (LAMP) for the semi-quantitative detection of HIV-1 group M virus in blood and plasma." Diss., Ludwig-Maximilians-Universität München, 2015. http://nbn-resolving.de/urn:nbn:de:bvb:19-180624.

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The past decade has witnessed a dramatic increase of anti-retroviral treatment of Human Immunodeficiency Virus (HIV) infected patients in many African countries. Due to costs and sophistication of currently available commercial viral load assays, little attention has been paid to therapy monitoring through measurement of plasma viral load, a challenge that could reverse achievements already made against HIV/AIDS infection. Loop-mediated isothermal amplification (LAMP) has been shown to be simple, rapid and cost-effective, characteristics which make this assay ideal for viral load monitoring in resource limited settings. The aim of this study was to establish and evaluate LAMP for quantitative detection of HIV-1 group M virus in blood and plasma. Cell culture supernatants of HIV-1 subtype B (IIIB and MVP899-87) viruses were used to optimize reaction conditions and to test primer suitability. Together with HIV-1 M non-B subtypes, HIV-1 group O and HIV-2, the cell culture supernatants were used to evaluate the performance of LAMP, to generate a model for viral load estimation and to establish the limits of the assay. A panel of 467 clinical samples was analyzed (282 plasmas and 121 dry blood spots from Kenya and 112 plasmas from Germany) and the results obtained by LAMP were compared to those generated by the Abbott Real Time HIV-1 assay, an established commercial viral load quantification test. A linear regression equation was generated from time to detection values and used to estimate the viral loads of the samples by the LAMP assay. Kenyan samples were tested in Nairobi and Munich. LAMP primers targeting the integrase of the pol gene were found to be the most suitable compared to further 3 primer sets tested. Lower limit of detection (LLOD) of 1,200 copies/mL and lower limit of quantification (LLOQ) of 9,800 copies/mL were determined as suitable thresholds for quantitative estimations of the LAMP viral loads. Sensitivities of 82 and 86% (Kenyan samples) and 93% (German samples) and specificities of 99 and 100% were realized with plasma samples. The study also realized a sensitivity of 76% and specificity of 77% with dry blood spot samples from Kenya. In conclusion, LAMP assay shows obvious potential for diagnostic application in semi-quantification of HIV-1 group M viral load in resource limited countries. However there is a need for further improvement of primers in respect to detection of HIV-1 non-B viruses and evaluation of dry blood spot samples to ensure that more reliable results are obtained.
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Odari, Eddy Okoth [Verfasser], and Ulrich [Akademischer Betreuer] Koszinowski. "Establishment and evaluation of a loop-mediated isothermal assay (LAMP) for the semi-quantitative detection of HIV-1 group M virus in blood and plasma / Eddy Okoth Odari. Betreuer: Ulrich Koszinowski." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2015. http://d-nb.info/1069743437/34.

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Denschlag, Carla [Verfasser], Rudi F. [Akademischer Betreuer] Vogel, and Michael W. [Akademischer Betreuer] Pfaffl. "Rapid diagnosis of Fusarium contamination in cereals using group-specific loop-mediated isothermal amplification (LAMP) assays / Carla Denschlag. Gutachter: Michael W. Pfaffl ; Rudi F. Vogel. Betreuer: Rudi F. Vogel." München : Universitätsbibliothek der TU München, 2014. http://d-nb.info/1057000612/34.

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Luo, Jie [Verfasser], Rudi F. [Akademischer Betreuer] Vogel, and Karl-Heinz [Akademischer Betreuer] Engel. "Detection, identification, and quantification of aflatoxin producing fungi in food raw materials using loop-mediated isothermal amplification (LAMP) assays / Jie Luo. Gutachter: Karl-Heinz Engel ; Rudi F. Vogel. Betreuer: Rudi F. Vogel." München : Universitätsbibliothek der TU München, 2014. http://d-nb.info/1051935296/34.

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Bo-Chuan, Tsou, and 鄒博全. "Detection of Food Allergens by Loop-mediatedIsothermal Amplification Assay (LAMP)." Thesis, 2016. http://ndltd.ncl.edu.tw/handle/92748983689493040276.

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Su, Sheng-Yuan, and 蘇聖淵. "Development of rapid colorimetric assay and real-time duplex LAMP method to detect viral nucleic acid." Thesis, 2012. http://ndltd.ncl.edu.tw/handle/48596477047745340466.

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碩士
國立臺灣大學
醫學檢驗暨生物技術學研究所
100
Loop-mediated isothermal amplification (LAMP) was established by Notomi et al. (2000). It uses 4-6 specific primers to recognize the target gene sequence and rapidly amplify under isothermal condition. Using this technique, we established a rapid colorimetric assay and a real-time duplex LAMP (dLAMP) method for viral nucleic acid detection. We anticipated that these two assays could be applied in blood screening, clinical diagnosis, and epidemiological investigation in the future. In the rapid colorimetric assay, we first optimized and validated the HCMV-LAMP reaction, the viral detection limit was about 30 copies per reaction. Furthermore, we mixed colloidal gold with LAMP products. Gold nanoparticles (AuNPs) became accumulated and solution color changed from red to blue quickly in HCMV-LAMP negative situation. But in positive situation, the solution color kept in red more longer. This phenomenon might be based on decreasing the ionic strength along with increasing DNA numbers of the solution after the HCMV-LAMP reaction. For the dLAMP method, HBV and HCV were detected simultaneously. The viral detection limits were 50 copies for HBV and 60 copies for HCV. In viral identification, we first collected clinical samples containing HBV or HCV strains of different genotypes or subtypes, respectively. By post-dLAMP melting curve analysis, HBV and HCV had different and non-overlapped Tm confidence intervals as 85.49±1.34°C and 88.90±0.81°C, respectively. We also tested the possibility of clinical application of the dLAMP and Tm analysis in detection and differentiation of HBV and HCV. The positive predictive value (PPV) of dLAMP method was 88 %. The accuracy of Tm differentiation of HBV and HCV was 88.64 %, that of HBV was 83.72 %, HCV 93.33 %. In conclusion, the specificity and sensitivity of colorimetric assay were similar to those of turbidimetry. Reading colors by naked-eye was simple and easy. This end-point assay is suitable for rapid qualitative analysis. However, the duplex LAMP detected the viral nucleic acid in real-time manner and differentiated HBV and HCV conveniently by melting temperature analysis. But the efficiency and accuracy rate were not satisfactory, and further improvement is required.
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Chapuy, Björn. "Analyse der putativen AP-3-Funktion für die Vesikelbildung am Trans-Golgi-Netzwerk." Doctoral thesis, 2005. http://hdl.handle.net/11858/00-1735-0000-0006-B322-4.

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Book chapters on the topic "LAMP assay"

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Hardinge, Patrick. "Optimized Loop-Mediated Isothermal Amplification (LAMP) Allows Single Copy Detection Using Bioluminescent Assay in Real Time (BART)." In Bioluminescence, 107–17. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2453-1_8.

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Ghosh, Dilip Kumar, Ashish Warghane, and Kajal Kumar Biswas. "Rapid and Sensitive Detection of Citrus tristeza virus Using Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) Assay." In Methods in Molecular Biology, 143–50. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9558-5_10.

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Hsu, Ren-Jun, and Huai-Jen Tsai. "Performing the Labeled microRNA Pull-Down (LAMP) Assay System: An Experimental Approach for High-Throughput Identification of microRNA-Target mRNAs." In Methods in Molecular Biology, 241–47. Totowa, NJ: Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-188-8_16.

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Lopez-Jimena, Benjamin, Mohammed Bakheit, Michaël Bekaert, Graham Harold, Sieghard Frischmann, Cheikh Fall, Cheikh Tidiane Diagne, et al. "Development and Validation of Real-Time RT-LAMP Assays for the Specific Detection of Zika Virus." In Methods in Molecular Biology, 147–64. New York, NY: Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-0581-3_13.

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Storari, Michelangelo, and Giovanni A. L. Broggini. "Identification of Ochratoxin A-Producing Black Aspergilli from Grapes Using Loop-Mediated Isothermal Amplification (LAMP) Assays." In Methods in Molecular Biology, 337–43. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-6707-0_22.

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Kaewphinit, Thongchai, Somchai Santiwatanakul, and Kosum Chansiri. "The Detection of Tuberculosis by Loop-Mediated Isothermal Amplification (LAMP) Combined with a Lateral Flow Dipstick." In Handbook of Research on Diverse Applications of Nanotechnology in Biomedicine, Chemistry, and Engineering, 269–300. IGI Global, 2015. http://dx.doi.org/10.4018/978-1-4666-6363-3.ch013.

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Tuberculosis (TB) is an airborne infectious disease caused by the bacterium Mycobacterium Tuberculosis (MTB) and is a persistent problem in developing countries. Present methods for its detection include normal or nested Polymerase Chain Reaction (PCR) followed by electrophoresis, real-time PCR, Ziehl-Neelsen staining, and culture assay. These techniques entail various disadvantages such as high cost, long assay time and use of toxic substances. Novel loop-mediated isothermal amplification (LAMP) permits DNA to be amplified rapidly under constant temperature. The combination of LAMP and chromatographic Lateral Flow Dipstick (LAMP-LFD) by using biotinylated LAMP amplicon hybridized with Fluorescein Isothiocyanate (FITC)-labeled probes are allowed to detect MTB without electrophoresis and interpreted within 3-5 min. LAMP-LFD is as highly sensitive as PCR-electrophoresis method. Based on its sensitivity, specificity, rapidity, cost effectiveness, ease of use, and convenience, LAMP-LFD could be suitable for use in early MTB detection.
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Shivakumar, Prakruthi, and Kavitha Sunil Shettigar. "Tuberculosis Diagnosis: Updates and Challenges." In Mycobacterium - Epidemiology, Prevention, Diagnostic, and Management [Working Title]. IntechOpen, 2022. http://dx.doi.org/10.5772/intechopen.107168.

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Tuberculosis (TB) is caused by a single infectious agent, Mycobacterium tuberculosis, and a public health concern due to increased cases of drug-resistance and high mortality rates. Rapid identification of tuberculosis is necessary for its early treatment and to prevent the emergence of drug-resistant strains. For effective management of patients, rapid, cost-effective, and point-of-care (POC) diagnostic methods are required. The commonly used screening and identification methods are clinical examination, radiography, sputum smear microscopy, culture method, serological method, and tuberculin skin test. In addition, several molecular methods such as NAAT based GeneXpert, loop-mediated isothermal amplification (LAMP), line probe assay (LPA), whole genome sequencing (WGS) and other non-invasive methods of lateral flow urine lipoarabinomannan assay (LF-LAM) and eNose assays are developed. Sputum smear microscopy, Xpert MTB/RIF, and LED-Fluorescence microscopy (LED-FM) are the preferred methods to use in peripheral laboratories. The non-invasive methods of tuberculosis diagnosis are more beneficial in patients from whom collecting sputum sample is difficult particularly in children and HIV co-infected patients. Molecular methods can simultaneously identify the pathogen, M. tuberculosis, and mutations in drug-resistance genes. Even though, many advanced methods are currently available, accurate and affordable diagnostic method for tuberculosis is still challenging. Here, we review and highlight the uses and challenges of currently available conventional and advanced diagnostic methods of tuberculosis screening and diagnosis.
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Alhamid, Galyah, and Huseyin Tombuloglu. "Perspective Chapter: Recent Progressions on the Colorimetric Diagnosis of SARS-CoV-2 by Loop-Mediated Isothermal Amplification (LAMP) Assay." In Infectious Diseases. IntechOpen, 2022. http://dx.doi.org/10.5772/intechopen.105911.

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A simple, fast, and accurate diagnosis of SARS-CoV-2 is of great importance for the patient’s isolation, treatment, and the control of the COVID-19 pandemic. Although RT-qPCR is accepted as the gold standard, studies to improve fast, simple, and more reliable diagnostic methods are continuing. Colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a method that allows visual detection of SARS-CoV-2 without needing expensive fluorescence readers. However, the performance of the assay depends on some factors, such as selection of a target gene (i.e., N, RdRp, S, E, M), primer design, the dye used for visual observation—neutral red, calcein, cresol red, or phenol red—and the reaction conditions such as the buffer pH, reaction temperature, and enzyme concentration. In the last 2 years, plenty of research has been conducted to obtain the best performance. In this chapter, the recent progressions on colorimetric RT-LAMP assay for the diagnosis of SARS-CoV-2 are comprehensively elucidated.
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Alexis S.P. Tubalinal, Gabriel, Leonard Paulo G. Lucero, Jim Andreus V. Mangahas, Marvin A. Villanueva, and Claro N. Mingala. "Application of Noble Metals in the Advances in Animal Disease Diagnostics." In Noble Metals and Intermetallic Compounds - Recent Advanced Studies and Applications [Working Title]. IntechOpen, 2021. http://dx.doi.org/10.5772/intechopen.99162.

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The advent of molecular biology and biotechnology has given ease and comfort for the screening and detection of different animal diseases caused by bacterial, viral, and fungal pathogens. Furthermore, detection of antibiotics and its residues has advanced in recent years. However, most of the process of animal disease diagnostics is still confined in the laboratory. The next step to conduct surveillance and prevent the spread of animal infectious diseases is to detect these diseases in the field. Through the discovery and continuous development in the field of nanobiotechnology, it was found that incorporation of noble metal nanoparticles to biotechnology tools such as the loop-mediated isothermal amplification (LAMP), lateral flow assays (LFAs) and dipsticks provided a promising start to conduct point-of-care diagnostics. Moreover, the modification and application of nanoparticle noble metals has increased the stability, effectiveness, sensitivity and overall efficacy of these diagnostic tools. Thus, recent advances in disease diagnostics used these noble metals such as gold, silver and platinum.
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Conference papers on the topic "LAMP assay"

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Benslimane, Fatiha M., Ola Al-Jamal, Sonia Boughattas, Asmaa A. Al Than, and Hadi M. Yassine. "Evaluation of Reverse Transcription-Loop-Mediated Isothermal Amplification (RTLAMP) for detecting SARS-Cov-2 in Clinical, Environmental and Animal Samples." In Qatar University Annual Research Forum & Exhibition. Qatar University Press, 2020. http://dx.doi.org/10.29117/quarfe.2020.0288.

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Background: First described 20 years ago by Notomi et al. (1999), the loop-mediated isothermal amplification (LAMP) assay is robust, rapid and straightforward, yet retains high sensitivity and specificity. These features have seen the LAMP assay and the inclusion of a reverse transcriptase (RT-LAMP) implemented for a broad range of molecular diagnostic applications extending from infectious diseases, including detection of the original SARS-CoV-1 virus. The advantages of RTLAMP include using different reagents than RT-qPCR, the potential for direct processing of samples without the need for prior RNA extraction and an extremely rapid turn-around time. Several groups have now described different RT-LAMP assays for detection of SARS-CoV-2 RNA. Therefore, the aim of this study is to assess the feasibility, sensitivity and effectiveness of LAMP technique in detecting SARS-CoV-2 in different type of samples. Method: New England Biolabs (NEB) LAMP master mixes were used. Six set of primers specific to SARS-CoV-2 were obtained from IDT. The reaction mix consisting of LAMP master mix, primer working solution and a sample was incubated at 65⁰C and results were collected after 30 mins. Results: In just 30 mins, we were able to detect the virus without any prior sample processing. Our primers were able to detect up to 100 copies of the viruses, which is comparable to the RT-PCR that we currently use in our lab. The primers were tested against all other coronavirus and they have shown 100% specificity to the novel SARS-CoV-2 virus. Both the florescent and calorimetric master mixes were able to detect the virus in all tested samples: clinical, animal and environmental. Conclusion: LAMP is a fast reliable technique that could be used as a quick screening method for the detection of SARS-CoV-2 in different settings and using different collection medium.
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Ali, Waqas Rafique, Ambreen Zahra, Hamza Rasheed, Aqsa Ahmad, Sultan Habibullah Khan, Amen Shamim, Sabin Aslam, and Muhammad Imran Arshad. "Detection of SARS-CoV-2 by RT-LAMP assay in Human COVID-19 patients." In 2022 19th International Bhurban Conference on Applied Sciences and Technology (IBCAST). IEEE, 2022. http://dx.doi.org/10.1109/ibcast54850.2022.9990339.

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YANG, Zexiao, Yilin LUO, Zhengqun MENG, Xueping YAO, Han ZHANG, Yin WANG, Xiaoxue XIANG, Lijun ZHOU, Yadong LIU, and Yan LI. "Preliminary Study on The RT-LAMP Assay for Rabbit Hemorrhagic Disease Virus Type 2 Detection." In International Conference on Biological Engineering and Pharmacy 2016 (BEP 2016). Paris, France: Atlantis Press, 2017. http://dx.doi.org/10.2991/bep-16.2017.27.

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Kinahan, David J., Lourdes A. N. Julius, Cor Schoen, Tanja Dreo, and Jens Ducree. "Automated DNA purification and multiplexed lamp assay preparation on a centrifugal microfluidic “Lab-on-a-Disc” platform." In 2018 IEEE Micro Electro Mechanical Systems (MEMS). IEEE, 2018. http://dx.doi.org/10.1109/memsys.2018.8346761.

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Singleton, J., D. Guelig, J. Buser, R. Burton, O. Edeh, K. Hawkins, B. Weigl, and P. LaBarre. "Advancing electricity-free molecular diagnostics at the point-of-care: Optimizing the NINA platform for a malaria LAMP assay." In 2014 IEEE Global Humanitarian Technology Conference (GHTC). IEEE, 2014. http://dx.doi.org/10.1109/ghtc.2014.6970363.

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Wu, Xi, Cole Reynolds, Euiwon Bae, Brianna Dowden, Yoo Hyun Kim, Bartek Rajwa, and J. Paul Robinson. "Rapid molecular point-of-detection (POD) of mycotoxins-producing fungi in agricultural products using loop-mediated isothermal amplification (LAMP) assay." In Sensing for Agriculture and Food Quality and Safety XIV, edited by Moon S. Kim and Byoung-Kwan Cho. SPIE, 2022. http://dx.doi.org/10.1117/12.2623298.

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Teramoto, Shinji, Yu Mikami, Emiko Toyota, and Yutsuki Nakajima. "Clinical Significance Of The Newly Developed Lamp Assay For Rapid Detection Of M. Tuberculosis Of Sputum Samples Collected From The Patients Suspected Of Pulmonary Tuberculosis." In American Thoracic Society 2011 International Conference, May 13-18, 2011 • Denver Colorado. American Thoracic Society, 2011. http://dx.doi.org/10.1164/ajrccm-conference.2011.183.1_meetingabstracts.a1205.

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Halim, Aprilliani Prissilla, Nastiti Wijayanti, Lisna Hidayati, and Tri Rini Nuringtyas. "Antioxidant Activity Evaluation of Agarwood Aquilaria malaccensis Lamk. Leaves Extract Using DPPH, FRAP and ABTS Assays." In 7th International Conference on Biological Science (ICBS 2021). Paris, France: Atlantis Press, 2022. http://dx.doi.org/10.2991/absr.k.220406.004.

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Galeano Zea, July A., Cesar Bedoya, Cardona Andrés, Fabián Cortés-Mancera, Patrick Sandoz, and Artur Zarzycki. "Modified position-referenced microscopy for the analysis of low-magnification biological events: a case of study in the wound healing assay with a human hepatoma cell line." In Latin America Optics and Photonics Conference. Washington, D.C.: OSA, 2016. http://dx.doi.org/10.1364/laop.2016.ltu4a.52.

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Dos Santos, L. F., J. C. Martins, K. O. Lima, L. F. T. Gomes, M. T. de Melo, A. C. Tedesco, L. D. Carlos, R. A. S. Ferreira, and R. R. Gonçalves. "In vitro assays and nanothermometry studies of infrared-to- visible upconversion of nanocrystalline Er3+,Yb3+ co-doped Y2O3 nanoparticles for theranostic applications." In Latin America Optics and Photonics Conference. Washington, D.C.: Optica Publishing Group, 2022. http://dx.doi.org/10.1364/laop.2022.tu4a.34.

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Luminescent spherical and monodisperse Er3+, Yb3+ co-doped Y2O3 nanoparticles were synthesized by homogenous precipitation followed by annealing. These nanoparticles exhibits high cell viability. On the basis of luminescence nanotermometry, the nanoparticles exhibits features of primary thermometer with high thermal sensitivity.
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Reports on the topic "LAMP assay"

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Gootwine, Elisha, David Thomas, Ruth Braw-Tal, Amir Bor, and P. J. Dziuk. Improvement of Prolificacy of Israeli and U.S. Sheep Breeds through Inclusion of the F Gene of the Booroola Merino-Stage II. United States Department of Agriculture, May 1995. http://dx.doi.org/10.32747/1995.7604931.bard.

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The purposes of this project were: 1) to introduce the FecB gene to the Awassi and Assaf breeds in Israel and the Rambouillet breed in the U.S.A. aiming in the long run to establish Awassi, Assaf and Rambouillet nucclei breeding flocks homozygous for the F gene in which the contribution of the Booroola Merino genetic background will be less than 10%; (In the U.S., Booroola crosses with Suffolk and Targhee were also studied. 2) to evaluate the effect of the FecB gene and different proportions of Booroola Merino genetic background on lamb survival, growth, milk production and wool production in Booroola crosses with the native breeds; 3) to reveal the specific effect of the FecB gene on ovarian development, follicle stimulating hormone (FSH) and inhibin secretion in prepubertal ewe lambs and in adult ewes in order to define physiological criteria for distinguishing carriers of the FecB allele from non-carriers and 4) to identify genetic markers linked to the FecB gene to assist in selection of genotypes within the Booroola crosses. Introgression of the Booroola gene reached the stage of the third backcross in the Awassi, Assaf and the Rambouillet crosses. In all cases the Booroola crosses were superior in prolificacy. However, they were inferior in comparison to the local breeds in production due to Booroola Merino genes other than the FecB. It is expected that the beneficial economic contribution of the Booroola gene will increase along with the upgrading to the local breeds. FSH plasma levels and induced ovulation rate of 5 month old FecB carriers among the crossbreeds. The OarAE101 marker can assist in detecting FecB carriers among Booroola-Awassi crosses. However, this marker is informative only in some of the families.
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Spencer, Thomas E., Elisha Gootwine, Arieh Gertler, and Fuller W. Bazer. Placental lactogen enhances production efficiency in sheep. United States Department of Agriculture, December 2005. http://dx.doi.org/10.32747/2005.7586543.bard.

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The key objectives of this BARD project were to: (1) study long-term effects of immunization of prepubertal ewes against recombinant ovine placental lactogen (roPL) on subsequent birth weights of their lambs and their milk production; (2) optimize the anti-roPL immunization protocol using adjuvant preparations acceptable to producers and regulatory agencies; and (3) determine the physiological mechanism(s) whereby immunization against oPL increases fetal growth and development and mammogenesis. These objectives were based on key findings from a previous BARD project that: (a) immunization of ewes against roPL increased lamb birth weight and ewe milk production during lactation; (b) roPL and recombinant ovine growth hormone (roGH) increased the proliferation and differentiated function of endometrial glands that, in turn, would enhance uterine secretions necessary for fetal and placental growth; and (c) exogenous roPL and roGH stimulated mammogenesis and milk production during lactation. The BARD projects address central problems in sheep production, including reproductive failure due to embryonic/fetal mortality, low birth weight of lambs especially in prolific breeds, and reduced milk yields which affect neonatal survival. The sheep placenta secretes both lactogenic (oPL) and somatogenic (oGH) hormones. The receptors for those hormones are present in the fetus and placenta as well as maternal uterus, and mammary gland. Our research has focused on determining the biological role of these placental hormones in development and differentiation of the uterus during gestation and the mammary gland during pregnancy and lactation. Studies conducted in the current BARD project indicated that the effects of anti-roPL immunization were variable in ewes and that commercially available and widely acceptable adjuvant preparations were not effective to produce high anti-roPL titers in pre-pubertal ewes. In the non-prolific Rambouillet ewe in Texas and in the Awassi and the Assaf in Israel, anti-roPL immunization increased lamb birth weight; however, the magnitude of this effect and the inherent variability precluded our ability to determine the physiological mechanism of how the immunization increases fetal growth. Collectively, our findings suggest that anti-roPL immunization is not currently feasible as an easy and efficacious tool for the producer to increase flock reproductive and production efficiency. The variability in response of individual ewes to anti-roPL immunization likely includes modifying the recombinant hormone and the type of adjuvant used for the immunization. In particular, the oPL may need to be modified to ensure maximum antigenicity in a broad range of breed types. Nonetheless, the investigators continue to collaborate on identifying fundamental mechanisms that can be improved by genetics or management to enhance the efficiency of uteroplacental function and, in turn, fetal growth and development. High prolificacy is a desirable trait in intensive sheep production systems. One of the main limitations of using prolific breeds of sheep is that increased litter size is associated with low birth weights and increased mortality of lambs. Further, low birth weight is associated with an increased propensity for adult diseases and decreased production efficiency. Indeed, our recent studies find that the birth weights of lambs born in large litters can be improved by both genetics and management. Future cooperative research will continue to focus on reproductive efficiency of sheep that have broader implications for improving production efficiency in all types of ruminant livestock.
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