Article
Parasitology
Gereon Schares, Majda Globokar Vrhovec, Mareen Tuschy, Maike Joeres, Andrea Baerwald, Bretislav Koudela, Jitender P. Dubey, Pavlo Maksimov, Franz J. Conraths
Summary: The 529-bp repeat of H. hammondi can be used to establish a quantitative real-time PCR assay, with excellent specificity and sensitivity. This assay is a valuable diagnostic tool for epidemiological and cell biological studies on H. hammondi and related parasites.
PARASITES & VECTORS
(2021)
Article
Biochemical Research Methods
Weidu Song, Chuanhao Zhang, Huichao Lin, Taiyi Zhang, Haixia Liu, Xiaowen Huang
Summary: The proposed real-time rotary PCR reaction system (RRP) meets the requirements of low cost, low-power consumption, potential for miniaturization, and portability. Experimental and theoretical results demonstrate its feasibility in the rapid quantitative detection of Pseudomonas aeruginosa and have broad application prospects in bacteria detection and food safety.
Article
Biochemical Research Methods
Shaolei Huang, Yiquan An, Bangchao Xi, Xianglian Gong, Zhongfu Chen, Shan Shao, Shengxiang Ge, Jun Zhang, Dongxu Zhang, Ningshao Xia
Summary: Nucleic acid detection is a method that directly identifies the presence of pathogenic microorganisms and has advantages of high sensitivity, commendable specificity, and a short window period. A real-time PCR system based on multiple temperature zones was proposed to solve the time-consuming problem, enabling fast detection speed and high sensitivity under extreme conditions.
Article
Chemistry, Analytical
Padideh Mohammadyousef, Miltiadis Paliouras, Mark A. Trifiro, Andrew G. Kirk
Summary: In response to the need for rapid infectious pathogen detection, researchers have been working on adapting PCR for POC applications. This paper introduces a compact plasmonic PCR thermocycler for fast DNA amplification using photothermal heating with gold nanorods and a VCSEL. An ultrasensitive real-time amplicon detection strategy is also reported, based on monitoring UV absorption of the PCR sample cycle-by-cycle. This system allows for high detection sensitivity and does not require specific probes or fluorophores.
Article
Chemistry, Analytical
Zheng Lin Tan, Masato Yasuura, Yukichi Horiguchi, Hiroki Ashiba, Takashi Fukuda
Summary: This paper presents a new method called gel capsule-based digital PCR (gc-dPCR), which improves the stability of hydrogel capsules compared to droplets. This method enhances the sensitivity and stability of ddPCR, reduces its cost, and provides a more accurate quantification of low-concentration samples.
Review
Medicine, General & Internal
Edinson Dante Meregildo-Rodriguez, Martha Genara Asmat-Rubio, Gustavo Adolfo Vasquez-Tirado
Summary: Tuberculosis is a global public health emergency. Improved diagnostic methods are urgently needed to address this epidemic. Droplet digital PCR (ddPCR) shows comparable diagnostic performance to qPCR for pulmonary tuberculosis, and better performance for extrapulmonary tuberculosis.
FRONTIERS IN MEDICINE
(2023)
Article
Ophthalmology
Satoko Nakano, Yasuhiro Tomaru, Toshiaki Kubota, Hiroshi Takase, Manabu Mochizuki, Norio Shimizu, Sunao Sugita
Summary: The Direct Strip PCR test offers rapid and accurate detection of infectious pathogens causing uveitis. It shows high concordance with qPCR results, even when used by beginners, indicating its reliability for clinical use. Additionally, it can be used for intraoperative diagnosis, improving the prognosis of infectious diseases.
Article
Optics
Damian Presti, Julian Bergier, Lucas Ripoll, Cristina Borio, Gustavo A. Torchia, Marcos Bilen
Summary: Since the global pandemic of SARS-CoV-2, the need for a low-cost and faster diagnostic tool for evaluating symptomatic patients has emerged. Point-of-care testing and point-of-need testing systems have been developed to provide accurate and rapid diagnostics. In this study, a bio-photonic device using an iso-thermal system was developed for detecting SARS-CoV-2. The device showed comparable sensitivity to the commercially used reference method and was built with simple and low-cost components, making it a high-efficiency and affordable instrument.
JOURNAL OF THE OPTICAL SOCIETY OF AMERICA A-OPTICS IMAGE SCIENCE AND VISION
(2023)
Article
Biotechnology & Applied Microbiology
Suresh Reddy Banda, Holger Klapproth, Nicolaas Smit, Sonja Bednar, Thomas Brandstetter, Juergen Ruehe
Summary: The sensitivity of a PCR-based biochip assay depends on the efficiency of PCR amplicons in binding to the microarray spots. Asymmetric PCR is often inefficient in generating single-stranded (ss) amplicons. However, a novel variant called Asymmetric Exponential and Linear Amplification (AELA) can overcome these issues and generate large amounts of ss-amplicons. AELA-PCR combines both exponential and linear amplification of the target nucleic acid, resulting in higher biochip sensitivity compared to conventional methods.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Biochemical Research Methods
Byoung-Hoon Kang, Kyung-Won Jang, Eun-Sil Yu, Hyejeong Jeong, Ki-Hun Jeong
Summary: A multi-channel plasmonic real-time reverse-transcription polymerase chain reaction system is used to demonstrate high-throughput and multi-target detection of the SARS-CoV-2 virus with four simultaneous reactions in a single assay within 15 min.
Article
Biochemical Research Methods
Renna L. Nouwairi, Larissa L. Cunha, Rachelle Turiello, Orion Scott, Jeff Hickey, Scott Thomson, Stuart Knowles, Jeff D. Chapman, James P. Landers
Summary: This article describes a field-forward prototype instrument capable of ultra-fast thermal cycling for real-time PCR amplification of DNA and RNA. The instrument can complete 40 cycles of real-time PCR in under 10 minutes, an 84% reduction in time compared to standard assays.
Article
Multidisciplinary Sciences
Jae Jong Kim, Hyoung-Min Park, A. Young Kyoung, In Kyung Park, Si-Kyu Lim, Byoung Chul Park
Summary: Genetic mutations like SNP are common in genetic disorders and cancers, and PCR methods are widely used for SNP detection. The specifically designed PCR platform STexS can efficiently distinguish small amounts of SNP mixed in normal DNA, aiding in targeting potential SNPs or genetically mutated biomarkers in human clinical samples.
SCIENTIFIC REPORTS
(2021)
Article
Computer Science, Information Systems
Sreeja Cherillath Sukumaran, Mohammed Misbahuddin
Summary: Cloud computing technology offers scalable computing technologies, but privacy issues remain a barrier for adoption. DNA computing techniques are widely accepted due to biological complexity and can address data security issues in mobile cloud computing.
JOURNAL OF KING SAUD UNIVERSITY-COMPUTER AND INFORMATION SCIENCES
(2021)
Article
Fisheries
Bradley M. Richardson, Matt J. Griffin, Michael E. Colvin, David J. Wise, Cynthia Ware, Charles C. Mischke, Terrence E. Greenway, Todd S. Byars, Larry A. Hanson, Mark L. Lawrence
Summary: This study examines the impact of an atypical strain of Aeromonas hydrophila in channel catfish aquaculture, providing insights into rapid field sampling methods and the importance of accurate quantitative PCR detection. Results show that the location of swab collection (gill vs. lower intestine) on pond-raised catfish is affected by the pond's condition, with implications for prevalence estimates and outbreak risk assessment. Furthermore, the study highlights the presence of a carrier state of the pathogen in apparently healthy fish, suggesting avenues for future research on disease mechanisms in catfish aquaculture.
Review
Virology
Pratima Harsh, Pratima Tripathi
Summary: Recent epidemics and pandemics caused by different viruses have had devastating effects on the human race, global economy, and mental health. Early diagnosis and understanding of viral infections are crucial for timely management. Scientists have developed various diagnostic techniques, including biosensor-based, immunological-based, and molecular-based approaches, to identify and detect viral infections.
Article
Agronomy
Brian Collins, Ullah Najeeb, Qunying Luo, Daniel K. Y. Tan
Summary: For the first time, the SUFI-2 method was used to calibrate the phenology module of the APSIM-wheat model for spring wheat cultivars in northeast Australia. Results showed that adjusting sowing times can significantly shorten crop cycles and increase grain yields, with photoperiod and vernalisation sensitivities being major contributors to uncertainties in the simulated values.
JOURNAL OF AGRONOMY AND CROP SCIENCE
(2022)
Article
Agronomy
Anowarul Bokshi, Rebecca J. Thistlethwaite, Edward D. Chaplin, Erasmus Kirii, Richard M. Trethowan, Daniel K. Y. Tan
Summary: High temperatures and increasing CO2 concentrations pose a major threat to global wheat production. This research evaluated Australian wheat cultivars for heat tolerance and identified physiological traits associated with adaptation to high temperatures. The findings provide valuable candidates for breeding and selecting wheat cultivars that can better adapt to changing climate conditions.
JOURNAL OF AGRONOMY AND CROP SCIENCE
(2022)
Article
Agronomy
Chinaza B. Onwuchekwa-Henry, Floris Van Ogtrop, Rose Roche, Daniel K. Y. Tan
Summary: This study assessed the effectiveness of Canopeo and GreenSeeker-NDVI tools for in-season estimation of rice yield in Cambodia. The Canopeo index-weather model was found to be a flexible and effective tool for predicting rice yield and managing agricultural resources.
Article
Biochemistry & Molecular Biology
Li Chen, Enhui Shen, Yunlei Zhao, Hongmei Wang, Iain Wilson, Qian-Hao Zhu
Summary: This study utilized publicly available RNA-seq datasets to identify the conservativeness and divergence of lincRNAs in different cotton species and their role in responding to biotic stresses. The study provided new insights into the relationship between the conservativeness and Vd responsiveness of lincRNAs and identified candidate lincRNAs for further functional characterization in disease response.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Genetics & Heredity
Xiaochen Sun, Wenli Wu, Yanfang Yang, Iain Wilson, Fenjuan Shao, Deyou Qiu
Summary: This study provides a comprehensive analysis of m(6)A pathway genes in Poplar 84K, including gene structures, promoter analysis, and expression profiles. The results show tissue-specific expression patterns of m(6)A pathway genes in leaves, xylem, phloem, and roots. Additionally, the transcription factor LBD15 regulates the expression of several m(6)A pathway genes. These findings contribute to the understanding of the functions and epigenetic regulation mechanisms of these genes in Poplar 84K.
Article
Plant Sciences
Qian-Hao Zhu, Shuangxia Jin, Yuman Yuan, Qing Liu, Xianlong Zhang, Iain Wilson
Summary: This study successfully generated a collection of cotton miR482 mutants using CRISPR/Cas9 technology, resulting in lower disease index in response to pathogen infection. The study provides a valuable resource for the cotton community to uncover the role of miR482-NLR module(s) in the interaction between cotton and different pathogens.
Editorial Material
Plant Sciences
Linghe Zeng, Iain Wilson, Fred M. Bourland
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Agronomy
Harris D. D. Ledvinka, Mehdi Toghyani, Daniel K. Y. Tan, Ali Khoddami, Ian D. D. Godwin, Sonia Y. Y. Liu
Summary: Climate change has significant consequences for agriculture, particularly for the poultry industry that relies heavily on feed grains. However, existing literature on the impact of climate factors on grain yield and nutritional composition are inconsistent due to varied research methods and the lack of consideration of interactions between factors. This review investigates the interactive effects of elevated CO2, heat, and drought on four important animal feed grains and provides novel insights into the potential yield improvement and nutrient concentration changes. Alternative crop management practices, plant breeding, feed processing, and enzyme supplementation are also discussed as potential strategies to mitigate the impacts of climate change on animal feed production.
Article
Biochemistry & Molecular Biology
Yingying Shao, Detian Mu, Limei Pan, Iain W. Wilson, Yajie Zheng, Lina Zhu, Zhiguo Lu, Lingyun Wan, Jine Fu, Shugen Wei, Lisha Song, Deyou Qiu, Qi Tang
Summary: An optimized protocol for the isolation, purification, and transient gene expression of Uncaria rhynchophylla protoplasts was developed, resulting in a highly efficient protoplast-based transient expression system with a transfection rate of 71%.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Green & Sustainable Science & Technology
Syed Riaz Ahmed, Zeba Ali, Iram Ijaz, Zafran Khan, Nimra Gul, Soha Pervaiz, Hesham F. Alharby, Daniel K. Y. Tan, Muhammad Sayyam Tariq, Maria Ghaffar, Amir Bibi, Khalid Rehman Hakeem
Summary: Climate change has impacted the global food supply chain, causing serious concerns for food security. This study aimed to assess the effects of environmental factors, cutting levels, and spacing on quinoa biomass and quality. The results showed significant interactions between cutting, genotype, and year, as well as cutting, space, and genotype for most morphological traits. Cutting level 3 and spacing level 2 were found to be the most effective in achieving maximum biomass and quality traits.
Article
Agronomy
Jie Zhang, Daniel K. Y. Tan, Hiba Shaghaleh, Tingting Chang, Yousef Alhaj Hamoud
Summary: High temperature significantly affects wheat production. This study evaluated the response and recovery of four wheat cultivars under heat stress and found significant differences in adaptability among the cultivars. Berkut and PBW343 showed stronger adaptability to heat stress.
Article
Biochemistry & Molecular Biology
Detian Mu, Yingying Shao, Jialong He, Lina Zhu, Deyou Qiu, Iain W. Wilson, Yao Zhang, Limei Pan, Yu Zhou, Ying Lu, Qi Tang
Summary: This study reports the stability of reference genes in Uncaria rhynchophylla and their potential role in alkaloid production. The researchers evaluated the expression stability of ten candidate reference genes under stress-related experimental treatments and found that S-adenosylmethionine decarboxylase (SAM) exhibited higher stability. Using SAM as a reference gene, they examined the expression patterns of key alkaloid biosynthetic genes and a transcription factor under stress treatments. The results indicate that the transcription factor WRKY1 may coordinate the expression of tryptophan decarboxylase (TDC), providing a potential method for enhancing alkaloid production in the future through synthetic biology.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Yao Zhang, Detian Mu, Liya Wang, Xujun Wang, Iain W. Wilson, Wenqiang Chen, Jinghan Wang, Zhaoying Liu, Deyou Qiu, Qi Tang
Summary: Reverse transcription quantitative polymerase chain reaction (RT-qPCR) was used to analyze Gelsemium elegans leaf tissue and identify suitable reference genes for data normalization. The optimal stable reference genes varied among the different treatments and at least two reference genes were required for accurate quantification. The expression patterns of 15 genes related to gelsenicine biosynthesis pathway were determined using RT-qPCR and three of these genes showed a strong correlation with the amount of gelsenicine measured. This research is crucial for future molecular analyses of G. elegans, a medically important plant species.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biotechnology & Applied Microbiology
William Crawford, Daniel K. Y. Tan, Floris Van Ogtrop
Summary: This study assessed the research available on Agave planting density and suggested an optimum planting density for the highest dry aboveground productivity using PRISMA. The meta-analysis found that the optimal planting density of Agave is approximately 2,600 plants ha(-1), which provides optimal dry aboveground biomass of 28.8 Mg ha(-1) yr(-1).
FRONTIERS IN CHEMICAL ENGINEERING
(2022)
Review
Horticulture
Viola Devasirvatham, Daniel K. Y. Tan
Summary: Australia's sweet cherry industry is thriving, with increasing production and revenue from both local and export markets. However, challenges such as self-incompatibility and the influence of environmental factors on plant traits need to be addressed. By understanding these traits and employing advanced breeding techniques, such as haplotype breeding, the efficiency and quality of sweet cherry breeding can be improved.