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.
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
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
Biotechnology & Applied Microbiology
Chunlei Jiao, Claas Reckstadt, Fabian Koenig, Christina Homberger, Jiaqi Yu, Joerg Vogel, Alexander J. Westermann, Cynthia M. Sharma, Chase L. Beisel
Summary: We developed a method called TIGER (transcribed RNAs inferred by genetically encoded records) to capture the transcriptional history of individual bacterial cells. This method utilizes reprogrammed tracrRNAs (Rptrs) to convert selected cellular transcripts into stored DNA edits, allowing for future sequencing and analysis. TIGER can record and quantify heterologous and endogenous transcripts, distinguish single-nucleotide differences, and read out single-cell phenomena, providing insights into complex cellular responses.
NATURE BIOTECHNOLOGY
(2023)
Article
Ophthalmology
Jeremy J. Hoffman, John K. G. Dart, Surjo K. De, Nicole Carnt, Georgia Cleary, Scott Hau
Summary: This study evaluated the sensitivity and specificity of PCR, IVCM, and culture in diagnosing MK, finding IVCM to be the most sensitive technique for AK and FK diagnosis, while culture remains the gold standard for BK. With FK and AK becoming common in the UK, ophthalmology units need to have access to all these techniques to optimize their management of MK.
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
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.
Article
Environmental Sciences
Sina V. Moghadam, Arash Jafarzadeh, Akanksha Matta, Samer Dessouky, Jeffrey Hutchinson, Vikram Kapoor
Summary: This study examined the performance of a detention basin in mitigating nitrogen pollution using quantitative PCR to measure the abundance of N-cycling genes in the soil media. Results showed a net export of nitrogen from the basin, with no significant differences in in- and outflow concentrations. The abundance of different genes varied with season and soil sampling depth, and Actinobacteria and Proteobacteria were the dominant phyla based on 16S rRNA gene sequencing.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2023)
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
Chemistry, Analytical
Chao Ling, Yanbin Chang, Xingyue Wang, Xiaoying Cao, Qianrong Tu, Bo Liu, Shifeng Huang
Summary: Current single-base mutation detection approaches are time-consuming, labor-intensive, and costly. Two methods based on CRISPR/Cas12a have been established for detecting single-base mutations with 100% differentiation, where fluorescence signals can be detected for variants but not for wild strains. Both methods have their own advantages, and they are expected to be applied in clinical diagnosis in the near future.
ANALYTICA CHIMICA ACTA
(2023)
Article
Chemistry, Multidisciplinary
Sudheendran Mavila, Heidi R. Culver, Alex J. Anderson, Tania R. Prieto, Christopher N. Bowman
Summary: An athermal approach using self-immolative thioester linked nucleic acids (TENA) for mRNA enrichment from total RNA has shown comparable performance to a commercial kit. The method is compatible with downstream applications such as RT-qPCR for gene expression analysis.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Plant Sciences
Adam C. Faller, Dhivya Shanmughanandhan, Subramanyam Ragupathy, Yanjun Zhang, Zhengfei Lu, Peter Chang, Gary Swanson, Steven G. Newmaster
Summary: Traditional botanical protein sources like peas and soybeans face new challenges in authentication as powdered supplements. The use of qPCR provides an efficient and economical method for identifying the botanical source of protein products and quantifying relative proportions.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Hematology
Katherine M. Dominy, Simone Claudiani, Matthew O'Hare, Richard Szydlo, Gareth Gerrard, Pierre Foskett, Letizia Foroni, Dragana Milojkovic, Jane F. Apperley, Jamshid Khorashad
Summary: The introduction of tyrosine kinase inhibitor treatment has greatly improved the clinical outcome of chronic myeloid leukaemia patients. However, the different transcripts may have an impact on qPCR results, but our study showed that it does not affect patient management or outcome.
BRITISH JOURNAL OF HAEMATOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Jose Miguel Mancheno, Estibaliz Atondo, Julen Tomas-Cortazar, Jose Luis Lavin, Laura Plaza-Vinuesa, Itziar Martin-Ruiz, Diego Barriales, Ainhoa Palacios, Claudio Daniel Navo, Leticia Sampedro, Ainize Pena-Cearra, Miguel Angel Pascual-Itoiz, Janire Castelo, Ana Carreras-Gonzalez, Donatello Castellana, Aize Pellon, Susana Delgado, Patricia Ruas-Madiedo, Blanca delas Rivas, Leticia Abecia, Rosario Munoz, Gonzalo Jimenez-Oses, Juan Anguita, Hector Rodriguez
Summary: The occurrence and development of colorectal cancer is associated with the presence of Fusobacterium nucleatum, dietary components, and reduction of acetylated derivatives of spermidine. The study found that a new tannase orthologue of F. nucleatum (TanBF(nn)) has structural differences affecting the active site and substrate accessibility. Spermidine and its derivatives inhibit the hydrolytic activity of TanBF(nn) and increase the toxicity of gallotannins to F. nucleatum.
MICROBIAL BIOTECHNOLOGY
(2022)
Article
Green & Sustainable Science & Technology
Guillermo Pardo, Agustin del Prado, Javier Fernandez-Alvarez, David R. Yanez-Ruiz, Alejandro Belanche
Summary: The implementation of Precision Livestock Farming (PLF) can reduce the environmental impact of livestock production. This study analyzed the environmental impact of intensive dairy goat production and explored the influence of adopting a smart-farming PLF platform on environmental performance. Results showed significant reductions in greenhouse gas emissions and similar trends in other impact categories after the PLF-platform implementation.
JOURNAL OF CLEANER PRODUCTION
(2022)
Article
Gastroenterology & Hepatology
Maria Juarez-Fernandez, Naroa Goikoetxea-Usandizaga, David Porras, Maria Victoria Garcia-Mediavilla, Miren Bravo, Marina Serrano-Macia, Jorge Simon, Teresa C. Delgado, Sofia Lachiondo-Ortega, Susana Martinez-Florez, Oscar Lorenzo, Mercedes Rincon, Marta Varela-Rey, Leticia Abecia, Hector Rodriguez, Juan Anguita, Esther Nistal, Maria Luz Martinez-Chantar, Sonia Sanchez-Campos
Summary: This study provides evidence for the relevance of the interaction between mitochondria and microbiota in NASH and identifies targeting this interaction as a valuable therapeutic approach.
Article
Agriculture, Dairy & Animal Science
Laura Sarri, Joaquim Balcells, Ahmad Reza Seradj, Ramona N. Pena, Gustavo A. Ramirez, Marc Tor, Gabriel de la Fuente
Summary: Fat metabolism is an important process in meat production companies, which affects the quality of meat. The source and incorporation rate of fat differ in different growth phases. The liver plays a critical role in fat metabolism during the fattening phase. Leaner pigs rely more on dietary fatty acids for fat deposition compared to fatter pigs. The activity of stearoyl-CoA desaturase is higher in the fattening phase.
Article
Green & Sustainable Science & Technology
Alejandro Belanche, Alexander N. Hristov, Henk J. van Lingen, Stuart E. Denman, Ermias Kebreab, Angela Schwarm, Michael Kreuzer, Mutian Niu, Maguy Eugene, Vincent Niderkorn, Cecile Martin, Harry Archimede, Mark McGee, Christopher K. Reynolds, Les A. Crompton, Ali Reza Bayat, Zhongtang Yu, Andre Bannink, Jan Dijkstra, Alex Chaves, Harry Clark, Stefan Muetzel, Vibeke Lind, Jon M. Moorby, John A. Rooke, Aurelie Aubry, Walter Antezana, Min Wang, Roger Hegarty, V Hutton Oddy, Julian Hill, Philip E. Vercoe, Jean Victor Savian, Adibe Luiz Abdalla, Yosra A. Soltan, Alda Lucia Gomes Monteiro, Juan Carlos Ku-Vera, Gustavo Jaurena, Carlos A. Gomez-Bravo, Olga L. Mayorga, Guilhermo F. S. Congio, David R. Yanez-Ruiz
Summary: This study developed empirical models to predict enteric methane emissions from sheep using a global database. The models showed that including variables such as body weight and organic matter digestibility improved prediction accuracy. Age-specific equations were also found to enhance prediction performance. The study concluded that predicting sheep methane production requires considering variables such as dry matter intake, body weight, and rumen propionate proportion, and appropriate universal equations can be used across different diets and climatic conditions.
JOURNAL OF CLEANER PRODUCTION
(2023)
Article
Agriculture, Dairy & Animal Science
R. Huang, P. Romero, A. Belanche, E. M. Ungerfeld, D. Yanez-Ruiz, D. P. Morgavi, M. Popova
Summary: Some antimethanogenic feed additives for ruminants can lead to the accumulation of rumen dihydrogen (H2), which may affect optimal fermentation. However, combining an H2 acceptor with a methanogenesis inhibitor can decrease rumen H2 build-up and improve beneficial metabolite production for the host ruminant.
Article
Agriculture, Dairy & Animal Science
P. Romero, R. Huang, E. Jimenez, J. M. Palma-Hidalgo, E. M. Ungerfeld, M. Popova, D. P. Morgavi, A. Belanche, D. R. Yanez-Ruiz
Summary: Most mitigation strategies to reduce enteric methane production in the rumen result in an excess of rumen dihydrogen that is not utilized efficiently. This study investigated the potential of phenolic compounds to act as hydrogen acceptors, thereby improving rumen fermentation and reducing methane production. The results showed that Asparagopsis taxiformis effectively inhibited methane production, increased hydrogen accumulation, and improved rumen fermentation in goats.
Article
Gastroenterology & Hepatology
Naroa Goikoetxea-Usandizaga, Miren Bravo, Leire Egia-Mendikute, Leticia Abecia, Marina Serrano-Macia, Rocio G. Urdinguio, Marc Clos-Garcia, Ruben Rodriguez-Agudo, Raquel Araujo-Legido, Lucia Lopez-Bermudo, Teresa C. Delgado, Sofia Lachiondo-Ortega, Irene Gonzalez-Recio, Claudia Gil-Pitarch, Ainize Pena-Cearra, Jorge Simon, Raquel Benede-Ubieto, Silvia Arino, Jose M. Herranz, Mikel Azkargorta, Julio Salazar-Bermeo, Nuria Marti, Marta Varela-Rey, Juan M. Falcon-Perez, Oscar Lorenzo, Ruben Nogueiras, Felix Elortza, Yulia A. Nevzorova, Francisco J. Cubero, Domingo Saura, Luis Alfonso Martinez-Cruz, Guadalupe Sabio, Asis Palazon, Pau Sancho-Bru, Natalia Elguezabal, Mario F. Fraga, Matias A. Avila, Ramon Bataller, Jose J. G. Marin, Franz Martin, Maria Luz Martinez-Chantar
Summary: Alcohol-associated liver disease (ALD), accounting for 70% of liver-related deaths in Europe, has no effective approved therapies. However, targeting methylation-controlled J protein (MCJ) may help in recovering mitochondrial fitness without collateral oxidative damage. Liver-specific MCJ silencing can prevent major ALD hallmarks, such as mitochondrial dysfunction, steatosis, inflammation, and oxidative stress, improving lipid metabolism and liver injury.
Article
Agriculture, Dairy & Animal Science
Pablo G. Toral, Leticia Abecia, Gonzalo Hervas, David R. Yanez-Ruiz, Pilar Frutos
Summary: This study used metabolomics to investigate the differences between high-feed efficient and low-feed efficient lactating ewes, finding that amino acid metabolism plays a significant role in feed efficiency.
JOURNAL OF DAIRY SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
Alejandro Belanche, Marisela Arturo-Schaan, Lara Leboeuf, David Yanez-Ruiz, Ignacio Martin-Garcia
Summary: This study evaluated the effects of dietary supplementation of young ruminants with a blend of plant extracts and yeast cell wall components. The supplementation promoted weight gain and optimized the anatomical and microbiological development of the rumen in young ruminants.
JOURNAL OF DAIRY SCIENCE
(2023)
Article
Biotechnology & Applied Microbiology
Ainize Pena-Cearra, Deguang Song, Janire Castelo, Ainhoa Palacios, Jose Luis Lavin, Mikel Azkargorta, Felix Elortza, Miguel Fuertes, Miguel Angel Pascual-Itoiz, Diego Barriales, Itziar Martin-Ruiz, Asier Fullaondo, Ana M. Aransay, Hector Rodriguez, Noah W. Palm, Juan Anguita, Leticia Abecia
Summary: There is potential association between mitochondrial dysfunction and inflammatory bowel diseases (IBD). The bidirectional interaction between the intestinal microbiota and host mitochondria may affect intestinal inflammation. The study shows that fecal microbiota transplantation (FMT) from MCJ-deficient mice to germ-free mice increases susceptibility to colitis. Furthermore, the study identifies potential microbial signatures associated with complex I deficiency and disease progression.
NPJ BIOFILMS AND MICROBIOMES
(2023)
Article
Gastroenterology & Hepatology
Ainize Pena-Cearra, Janire Castelo, Jose Luis Lavin, Monika Gonzalez-Lopez, Miguel Angel Pascual-Itoiz, Miguel Fuertes, Virginia Gutierrez de Juan, Laura Barcena, Itziar Martin-Ruiz, Aize Pellon, Iratxe Seoane, Diego Barriales, Ainhoa Palacios, Asier Fullaondo, Iago Rodriguez-Lago, Maria L. Martinez-Chantar, Ana M. Aransay, Hector Rodriguez, Juan Anguita, Leticia Abecia
Summary: Anti-TNF therapy is effective in inducing and maintaining remission in intestinal bowel disease. However, a certain percentage of patients do not respond to this therapy. This study suggests that the absence of MCJ, a natural inhibitor of respiratory chain Complex I, leads to changes in gut microbiota, which is a critical determinant of the lack of response in a mouse model of inflammation. The study also highlights the role of macrophage mitochondrial function in the gut ecological niche in affecting the severity of inflammation and the response to current therapies.
Meeting Abstract
Gastroenterology & Hepatology
Maria Juarez-Fernandez, Naroa Goikoetxea, David Porras, Maria-Victoria Garcia-Mediavilla, Hector Rodriguez, Esther Nistal, Susana Martinez-Florez, Mercedes Rincon, Marta Varela-Rey, Javier Gonzalez-Gallego, Leticia Abecia, Juan Anguita, Maria Luz Martinez-Chantar, Sonia Sanchez-Campos
JOURNAL OF HEPATOLOGY
(2022)
Article
Multidisciplinary Sciences
Ainize Pena-Cearra, Miguel Angel Pascual-Itoiz, Jose Luis Lavin, Miguel Fuertes, Itziar Martin-Ruiz, Janire Castelo, Ainhoa Palacios, Diego Barriales, Asier Fullaondo, Ana M. Aransay, Hector Rodriguez, Juan Anguita, Leticia Abecia
Summary: Inflammatory bowel disease (IBD) is a complex and chronic disease. This study found that MCJ deficiency leads to increased TACE activity in chronic inflammation, affecting the metabolic adaptation of colon tissue and potentially associated with reduced microbial members associated with inflammation.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Carolina Simo, Tiziana Fornari, Monica R. Garcia-Risco, Ainize Pena-Cearra, Leticia Abecia, Juan Anguita, Hector Rodriguez, Virginia Garcia-Canas
Summary: In this study, a novel screening strategy was developed to evaluate the effects of food and natural extract on Klebsiella pneumoniae's TMA production. Oregano and red thyme extracts were found to have the potential to inhibit TMA formation.