Article
Infectious Diseases
Francesca De Falco, Federica Corrado, Anna Cutarelli, Leonardo Leonardi, Sante Roperto
Summary: This study compared the levels of BPV DNA in bovine samples using ddPCR and qPCR, finding that ddPCR was more sensitive and accurate than qPCR, allowing the detection of more BPV genotypes.
TRANSBOUNDARY AND EMERGING DISEASES
(2021)
Article
Chemistry, Multidisciplinary
Rokshana Parvin, Lexiang Zhang, Yan Zu, Fangfu Ye
Summary: Exosomal microRNAs have great potential as noninvasive biomarkers, and a duplex photothermal digital PCR strategy combined with a lipid nanoparticle-based exosome capture approach was proposed in this study. Microfluidically-generated molybdenum disulfide-nanocomposite-doped gelatin microcarriers were used for PCR thermocycling triggered by near-infrared, allowing for efficient profiling of microRNAs expression. The method showed promising results for liver cancer diagnostics.
Article
Engineering, Chemical
Franziska Schlenker, Elena Kipf, Nadine Borst, Nils Paust, Roland Zengerle, Felix von Stetten, Peter Juelg, Tobias Hutzenlaub
Summary: Centrifugal microfluidics is used to implement a four-plex digital droplet polymerase chain reaction with stable droplet generation and fluorescence imaging, including an automated process for four-color imaging. The platform demonstrates successful quantification of cancer-associated point mutations in a diagnostic DNA background, showing high sensitivity and linear performance across all targets on the LabDisk.
Article
Gastroenterology & Hepatology
Xiao Li, Yan-Li Lin, Jia-Kang Shao, Xiao-Jie Wu, Xiang Li, He Yao, Fa-Liang Shi, Long-Song Li, Wen-Gang Zhang, Zheng-Yao Chang, Ning-Li Chai, You-Liang Wang, En-Qiang Linghu
Summary: This study found that the expression levels of plasma exosomal circRNA are significantly increased in gastric cancer patients and can distinguish between early and advanced gastric cancer patients. Therefore, plasma exosomal circRNA may be a potential biomarker for the diagnosis of gastric cancer in both the early and late stages.
WORLD JOURNAL OF GASTROENTEROLOGY
(2023)
Article
Chemistry, Analytical
Liao Chen, Vivek Yadav, Chenguang Zhang, Xiaoye Huo, Ceming Wang, Satyajyoti Senapati, Hsueh-Chia Chang
Summary: The droplet digital PCR (ddPCR) platform reported in this study utilizes a unique flattened pipette tip design to achieve rapid, stable, and highly sensitive quantification of low virus RNA load without the need for bulky lab-bound equipment. The technology allows for fast generation of thousands of monodispersed droplets, which can be easily counted or imaged for accurate quantification of target copies. This platform shows promising potential for rapid virus detection and epidemic control, offering a convenient solution for point-of-care (POC) applications.
ANALYTICAL CHEMISTRY
(2021)
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
Oncology
Jin-Yi Han, Keun Soo Ahn, Tae-Seok Kim, Yong Hoon Kim, Kwang Bum Cho, Dong Woo Shin, Won-Ki Baek, Seong-Il Suh, Byeong-Churl Jang, Koo Jeong Kang
Summary: Utilization of cell free DNA from bile fluid shows promising potential for diagnosing and monitoring patients with biliary tract cancers, with mutational variants reliably detected and showing a strong positive correlation with tissue samples, suggesting bile as an effective biopsy fluid for ctDNA analysis.
Article
Multidisciplinary Sciences
Mustafa Fatih Abasiyanik, Blake Flood, Jing Lin, Sefika Ozcan, Sherin J. Rouhani, Athalia Pyzer, Jonathan Trujillo, Chaojie Zhen, Ping Wu, Stephen Jumic, Andrew Wang, Thomas F. Gajewski, Peng Wang, Madeline Hartley, Bekim Ameti, Rachael Niemiec, Marian Fernando, Vasudha Mishra, Peter Savage, Bulent Aydogan, Cindy Bethel, Scott Matushek, Kathleen G. Beavis, Nishant Agrawal, Jeremy Segal, Savas Tay, Evgeny Izumchenko
Summary: Saliva has significant advantages as a test medium for detecting SARS-CoV-2 infection, with a developed testing pipeline showing high effectiveness in detecting infected cases in both outpatient and inpatient settings. The saliva-based testing has the potential for higher sensitivity in detecting low-abundance viral loads, making it a reliable alternative to traditional testing methods.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Jianshi Jin, Reiko Yamamoto, Tadashi Takeuchi, Guangwei Cui, Eiji Miyauchi, Nozomi Hojo, Koichi Ikuta, Hiroshi Ohno, Katsuyuki Shiroguchi
Summary: The study develops a method called Barcoding Bacteria for Identification and Quantification (BarBIQ) that allows for the classification and quantification of individual bacterial cells in the microbiota. It is found that BarBIQ reveals location-dependent differences in the microbiota, which cannot be shown by conventional 16S rRNA gene-amplicon sequencing methods.
NATURE COMMUNICATIONS
(2022)
Article
Agriculture, Multidisciplinary
Lin He, Seong Hwan Kim, Jun Myoung Yu
Summary: Black shoot blight disease caused by Erwinia pyrifoliae has significant negative effects on pear production in Korea, necessitating the development of rapid and accurate detection methods. In this study, a droplet digital polymerase chain reaction (ddPCR) method was developed for the detection and quantification of E. pyrifoliae. The method demonstrated good linearity and repeatability and was validated using samples of artificially inoculated immature pear fruits. This study presents the first application of ddPCR for the detection and quantification of E. pyrifoliae, with potential applications in epidemiology and early prediction of black shoot blight outbreaks.
PLANT PATHOLOGY JOURNAL
(2023)
Article
Infectious Diseases
Anupop Jitmuang, Anapat Nititammaluk, Thitaya Boonsong, Patsharaporn Techasintana Sarasombath, Suree Sompradeekul, Methee Chayakulkeeree
Summary: The study evaluated the performance of ddPCR in diagnosing PCP and found that using different cutoff values in HIV-positive and negative patients resulted in better performance. Most PCP patients, including those with DHPS gene mutations, showed favorable outcomes.
JOURNAL OF INFECTION
(2021)
Article
Hematology
Koji Sasaki, Shinichi Tsujimoto, Mayuko Miyake, Yuri Uchiyama, Junji Ikeda, Masahiro Yoshitomi, Yuko Shimosato, Mayu Tokumasu, Hidemasa Matsuo, Kenichi Yoshida, Kentaro Ohki, Taeko Kaburagi, Genki Yamato, Yusuke Hara, Masanobu Takeuchi, Akitoshi Kinoshita, Daisuke Tomizawa, Takashi Taga, Souichi Adachi, Akio Tawa, Keizo Horibe, Yasuhide Hayashi, Naomichi Matsumoto, Shuichi Ito, Norio Shiba
Summary: In this study, KIT D816V mutation was identified as a risk factor for relapse in pediatric patients with RUNX1-RUNX1T1-positive AML, leading to significantly inferior 5 year event-free survival compared to those without the mutation. The presence of KIT D816V minor clones in patients with CBF-AML was confirmed, highlighting the importance of examining these minor clones for prognostic evaluation.
BRITISH JOURNAL OF HAEMATOLOGY
(2021)
Article
Microbiology
Andrea Mancusi, Yolande T. R. Proroga, Angela Giordano, Santa Girardi, Francescantonio D'Orilia, Renato Pinto, Paolo Sarnelli, Laura Rinaldi, Federico Capuano, Maria Paola Maurelli
Summary: Toxoplasmosis is a parasitic disease transmitted through food, water, and soil. Researchers have validated a highly sensitive DNA detection method for quickly and accurately detecting Toxoplasma gondii in mussels, reducing the risk of human infection.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Oncology
Louise Raunkilde, Torben Frostrup Hansen, Rikke Fredslund Andersen, Birgitte Mayland Havelund, Caroline Brenner Thomsen, Lars Henrik Jensen
Summary: Although imaging is the gold standard in evaluating the treatment effect in metastatic colorectal cancer, this study found that a reduction in methylated circulating tumor DNA (ctDNA) after one treatment cycle is a better marker of progression-free survival than imaging. Methylated ctDNA can be an early indicator of treatment benefit and is a promising endpoint in clinical trials.
Article
Plant Sciences
Li Wang, Qian Tian, Pei Zhou, Wenjun Zhao, Xianchao Sun
Summary: A droplet digital PCR (ddPCR) method was developed to detect Clavibacter michiganensis subsp. michiganensis, the pathogen causing bacterial canker disease in tomatoes. The ddPCR method was highly specific and 100-fold more sensitive than traditional qPCR. This new detection method has significant implications for pathogen quarantine and disease control in tomato plants.
Review
Neurosciences
Asia Pitkanen, Xavier Ekolle Ndode-Ekane, Niina Lapinlampi, Noora Puhakka
NEUROBIOLOGY OF DISEASE
(2019)
Editorial Material
Clinical Neurology
Cesar Santana-Gomez, Pedro Andrade, Matthew R. Hudson, Tomi Paananen, Robert Ciszek, Gregory Smith, Idrish Ali, Brian K. Rundle, Xavier Ekolle Ndode-Ekane, Pablo M. Casillas-Espinosa, Riikka Immonen, Noora Puhakka, Nigel Jones, Rhys D. Brady, Piero Perucca, Sandy R. Shultz, Asia Pitkanen, Terence J. O'Brien, Richard Staba
Article
Clinical Neurology
Riikka Immonen, Gregory Smith, Rhys D. Brady, David Wright, Leigh Johnston, Neil G. Harris, Eppu Manninen, Raimo Salo, Craig Branch, Dominique Duncan, Ryan Cabeen, Xavier Ekolle Ndode-Ekane, Cesar Santana Gomez, Pablo M. Casillas-Espinosa, Idrish Ali, Sandy R. Shultz, Pedro Andrade, Noora Puhakka, Richard J. Staba, Terence J. O'Brien, Arthur W. Toga, Asla Pitkanen, Olli Grohn
Article
Clinical Neurology
Robert Ciszek, Xavier Ekolle Ndode-Ekane, Cesar Santana Gomez, Pablo M. Casillas-Espinosa, Idrish Ali, Gregory Smith, Noora Puhakka, Niina Lapinlampi, Pedro Andrade, Alaa Kamnaksh, Riikka Immonen, Tomi Paananen, Matthew R. Hudson, Rhys D. Brady, Sandy R. Shultz, Terence J. O'Brien, Richard J. Staba, Jussi Tohka, Asla Pitkanen
Article
Critical Care Medicine
Mehwish Anwer, Leonardo Lara-Valderrabano, Jenni Karttunen, Xavier Ekolle Ndode-Ekane, Noora Puhakka, Asla Pitkanen
JOURNAL OF NEUROTRAUMA
(2020)
Article
Computer Science, Interdisciplinary Applications
Robert Ciszek, Pedro Andrade, Jesse Tapiala, Asla Pitkanen, Xavier Ekolle Ndode-Ekane
Review
Behavioral Sciences
Asla Pitkanen, Tomi Paananen, Jenni Kyyriainen, Shalini Das Gupta, Mette Heiskanen, Niina Vuokila, Ivette Banuelos-Cabrera, Niina Lapinlampi, Natallie Kajevu, Pedro Andrade, Robert Ciszek, Leonardo Lara-Valderrabano, Xavier Ekolle Ndode-Ekane, Noora Puhakka
Summary: A biomarker is a measurable characteristic indicating normal biologic processes, pathogenic processes, or responses to treatment. Reviewing seven biomarker categories revealed minimal overlap in biomarker candidates between TBI, epilepsy, and PTE.
EPILEPSY & BEHAVIOR
(2021)
Article
Clinical Neurology
Niina Lapinlampi, Pedro Andrade, Tomi Paananen, Elina Hamalainen, Xavier Ekolle Ndode-Ekane, Noora Puhakka, Asla Pitkanen
Article
Neurosciences
Jenni Kyyriainen, Jesse Tapiala, Anssi Lipponen, Xavier Ekolle Ndode-Ekane, Asla Pitkanen
NEUROSCIENCE LETTERS
(2020)
Article
Biochemistry & Molecular Biology
Xavier Ekolle Ndode-Ekane, Maria del Mar Puigferrat Perez, Rossella Di Sapia, Niina Lapinlampi, Asia Pitkanen
Summary: Traumatic brain injury disrupts the integrity of thalamic and cortical connections, leading to reorganization in the response to thalamic stimulation. TBI rats show decreased axon terminal density, altered orientation, and anisotropy of terminals in the perilesional cortex. Moreover, optical stimulation of the sensory thalamus induces different EEG responses in TBI rats compared to controls.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Pedro Andrade, Leonardo Lara-Valderrabano, Eppu Manninen, Robert Ciszek, Jesse Tapiala, Xavier Ekolle Ndode-Ekane, Asla Pitkanen
Summary: This study demonstrated that seizure susceptibility increases over weeks-months after traumatic brain injury in rats, and this susceptibility predicts the development of post-traumatic epilepsy or epileptiform activity. The study also found that rats develop chronic sleep disturbance after TBI, and some sleep parameters can serve as novel biomarkers for the development of post-traumatic epileptogenesis.
Article
Biochemistry & Molecular Biology
Xavier Ekolle Ndode-Ekane, Riikka Immonen, Elina Hamalainen, Eppu Manninen, Pedro Andrade, Robert Ciszek, Tomi Paananen, Olli Grohn, Asla Pitkanen
Summary: Adjusting electrode coordinates based on MRI can increase the accuracy of intracerebral electrode placement and improve the interpretation of EEG-recorded signals in rats with TBI-induced brain atrophy.
Article
Clinical Neurology
Xavier Ekolle Ndode-Ekane, Idrish Ali, Cesar Santana-Gomez, Pedro Andrade, Riikka Immonen, Pablo Casillas-Espinosa, Tomi Paananen, Eppu Manninen, Noora Puhakka, Gregory Smith, Rhys D. Brady, Juliana Silva, Emma Braine, Matt Hudson, Glen R. Yamakawa, Nigel C. Jones, Sandy R. Shultz, Neil Harris, David K. Wright, Olli Groehn, Richard Staba, Terence J. O'Brien, Asla Pitkaenen
Summary: The study found that the PTE phenotype induced by lateral FPI is reproducible in a multicenter design, supporting the feasibility of conducting preclinical multicenter trials in PTE to produce clinically translatable data.
Article
Neurosciences
Erwin A. van Vliet, Xavier Ekolle Ndode-Ekane, Lauri J. Lehto, Jan A. Gorter, Pedro Andrade, Eleonora Aronica, Olli Grohn, Asla Pitkanen
NEUROBIOLOGY OF DISEASE
(2020)