Article
Chemistry, Analytical
Yumi Kwon, Seonjeong Lee, Narae Park, Shinyeong Ju, Sungho Shin, Seongjin Yoo, Hankyul Lee, Cheolju Lee
Summary: Phosphorylation is a key component of cellular signaling cascades, controlling important cellular functions. However, phosphoproteomic analysis is typically limited by the amount of sample required for phosphopeptide enrichment. In this study, a new strategy was developed to increase phosphoproteomic signals from a small amount of sample without phosphoenrichment.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Wenyang Zhang, Cheuk-Kuen Lai, Wenjie Huang, Wenyan Li, Shaowen Wu, Qian Kong, Alan C. Hopkinson, Alisdair R. Fernie, K. W. Michael Siu, Shijuan Yan
Summary: This study proposes an eco-friendly strategy for phosphoproteome profiling by developing a reusable phos-trap column and establishing an automated online analytical platform. The platform demonstrates excellent performance in the initial development assessment and is successfully applied to phosphosite analysis in HeLa cells and maize seedlings.
Article
Biochemical Research Methods
Fanni Bugyi, Gabor Toth, Kinga Bernadett Kovacs, Laszlo Drahos, Lilla Turiak
Summary: Efficient phosphoproteomic analysis of small amounts of biological samples requires careful enrichment and purification steps. This study evaluated the performance of various self-packed and commercial centrifugal SPE cartridges/spin tips, and identified several methods that provided excellent results in terms of sample purification, reducing sample loss, and increasing the detection and recovery of phosphopeptides.
JOURNAL OF CHROMATOGRAPHY A
(2022)
Review
Biochemistry & Molecular Biology
Michele Sorgenfrei, Lea M. Hurlimann, Melissa M. Remy, Peter M. Keller, Markus A. Seeger
Summary: This article summarizes various biomolecules used for capturing live bacteria, including immune proteins, antibodies, aptamers, phage proteins, and antimicrobial peptides. The article also discusses the potential use of nanobodies targeting conserved surface-accessible proteins as promising biomolecules for pathogen capture.
TRENDS IN BIOCHEMICAL SCIENCES
(2022)
Article
Materials Science, Biomaterials
Dandan Jiang, Siyu Wu, Yangyang Li, Ruixue Qi, Jinghai Liu
Summary: In this study, magnetic polyoxometalate-based metal-organic frameworks were designed and used for phosphopeptide enrichment. The material exhibited strong affinity and selectivity for phosphopeptides, and coupled with mass spectrometry detection, achieved high sensitivity and reusability, showing great potential for practical application in phosphopeptide detection.
ACS BIOMATERIALS SCIENCE & ENGINEERING
(2023)
Editorial Material
Cell Biology
Wendy N. Erber
Summary: This paper reflects on the author's experience working with David Y. Mason in the Leukaemia Research Laboratories at the University of Oxford in the early 1980s. The laboratory focused on developing immunoenzymatic staining methods for leukemia diagnosis.
Article
Environmental Sciences
Kerrin Toner, Stephen R. Midway
Summary: Most earth's systems and organisms contain microplastics with lethal and sublethal effects. Studies show a knowledge gap in past patterns of microplastic ingestion in fish. Research suggests that stream fish in the southeastern U.S. likely did not ingest large amounts of microplastics during the 20th century.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Medicine, General & Internal
Alba Folgueiras-Gonzalez, Robin van den Braak, Martin Deijs, Lia van der Hoek, Ad de Groof
Summary: The study investigated the application of fast and simple high-throughput virus enrichment methods on tissue homogenates. It was found that sonication in high EDTA concentrations along with organic extraction with Vertrel(TM) XF combined with core bead chromatography enrichment can significantly increase the proportion of viral reads in processed samples.
Article
Chemistry, Analytical
Hongtao Tian, Zhizhen Lai, Mo Zhang, Shuai Liu, Renjun Zhang, Jiang Zhou, Zhili Li
Summary: A novel solid-phase-supported probe FSP-PITC was developed in this study, which enables direct coupling and detection of amino metabolites by immobilizing phenyl isothiocyanate on magnetic beads. This probe simplifies the processing steps, enhances capacity, and allows accurate qualitative and quantitative analysis, facilitating rapid detection and discovery of metabolites.
ANALYTICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Betzaida Cuevas-Cordoba, Cristobal Fresno, Joshua Haase-Hernandez, Martin Barbosa-Amezcua, Minerva Mata-Rocha, Marcela Munoz-Torrico, Miguel A. Salazar-Lezama, Jose A. Martinez-Orozco, Luis A. Narvaez-Diaz, Jorge Salas-Hernandez, Vanessa Gonzalez-Covarrubias, Xavier Soberon
Summary: NGS is used to study genetic variation in Mycobacterium tuberculosis, but it's challenging to distinguish target organism reads from other microorganisms in clinical samples. A bioinformatic pipeline was developed to filter out non-M. tuberculosis reads and increase the reliability of genetic variant reports. This pipeline successfully reduced off-target sequences and improved the accuracy of variant calling.
Article
Biochemical Research Methods
Yumi Komori, Tomoya Niinae, Koshi Imami, Jun Yanagibayashi, Kenichi Yasunaga, Shinya Imamura, Masami Tomita, Yasushi Ishihama
Summary: We developed a bioinertized nanoflow LC/MS/MS system for sensitive analysis of phosphopeptides. Metal ion depletion from the mobile phase and prevention of indirect contact with metal components significantly improved the recovery of phosphopeptides. By inserting an online metal ion removal device, the identified phosphopeptides showed an average increase in peak areas of 9.9-fold overall and 77-fold for multiply phosphorylated peptides.
MOLECULAR & CELLULAR PROTEOMICS
(2023)
Article
Multidisciplinary Sciences
Mike Marquet, Janine Zoellkau, Jana Pastuschek, Adrian Viehweger, Ekkehard Schleussner, Oliwia Makarewicz, Mathias W. Pletz, Ralf Ehricht, Christian Brandt
Summary: Metagenomic sequencing is valuable for clinical research, and Nanopore's adaptive sampling method can increase sequencing depth, taxonomic profiling sensitivity, and consistency of microbial composition.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Analytical
Siyuan Jing, Yu Huang, Yinjuan Chen, Xueqing He, Zhong Chen, Xingyu Lu, Minghuo Wu, Thomas C. Wanger
Summary: This study developed a simple and effective method using density gradient ultracentrifugation (DGU) to extract and separate various types of nano-/microplastics (NMPs) from environmental samples. By changing the density of the density gradient medium, different sizes of NMPs could be extracted and separated from soil samples. The effectiveness and compatibility of DGU were confirmed through the correct identification of NMPs using various analytical methods.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Bertrand Jern Han Wong, Weijia Kong, Hui Peng, Wilson Wen Bin Goh
Summary: Proteomic studies aim to characterize the protein composition of complex biological samples. To address the challenge of low proteome coverage and interpretability, researchers developed PROSE, a fast and scalable pipeline that scores proteins based on gene co-expression network matrices. PROSE shows high accuracy in missing protein prediction and can capture key phenotypic features in proteomics datasets.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Chemistry, Analytical
Shuai Liu, Zhizhen Lai, Mo Zhang, Hongtao Tian, Jiang Zhou, Zhili Li
Summary: A simple and efficient enrichment strategy based on Amino-functionalized Polymer-Magnetic MicroParticles (NH2-PMMPs) with coral-like porous structures was developed to detect 320 anionic metabolites, including 102 polar phosphate metabolites. Previously unknown polar phosphate metabolites were identified in serum samples using this enrichment method, demonstrating its advantages for mass spectrometric analysis. The high sensitivity of the method enabled the detection of 36 polar anion metabolites from 10 cell equivalent samples.
ANALYTICA CHIMICA ACTA
(2023)
Article
Medicine, Research & Experimental
Agnes Langer, Lara Lucke-Paulig, Lucia Gassner, Rejko Krueger, Daniel Weiss, Alireza Gharabaghi, Heidemarie Zach, Walter Maetzler, Markus A. Hobert
Summary: This study compared the effects of deep brain stimulation and dopaminergic medication on gait parameters in patients with advanced Parkinson disease. The results showed that dopaminergic medication had larger additional effects on gait parameters under both single-tasking and dual-tasking conditions, while deep brain stimulation only improved specific gait parameters.
Article
Clinical Neurology
Eva-Juliane Vollstedt, Susen Schaake, Katja Lohmann, Shalini Padmanabhan, Alexis Brice, Suzanne Lesage, Christelle Tesson, Marie Vidailhet, Isabel Wurster, Faycel Hentati, Anat Mirelman, Nir Giladi, Karen Marder, Cheryl Waters, Stanley Fahn, Meike Kasten, Norbert Bruggemann, Max Borsche, Tatiana Foroud, Eduardo Tolosa, Alicia Garrido, Grazia Annesi, Monica Gagliardi, Maria Bozi, Leonidas Stefanis, Joaquim J. Ferreira, Leonor Correia Guedes, Micol Avenali, Simona Petrucci, Lorraine Clark, Ekaterina Y. Fedotova, Natalya Y. Abramycheva, Victoria Alvarez, Manuel Menendez-Gonzalez, Silvia Jesus Maestre, Pilar Gomez-Garre, Pablo Mir, Andrea Carmine Belin, Caroline Ran, Chin-Hsien Lin, Ming-Che Kuo, David Crosiers, Zbigniew K. Wszolek, Owen A. Ross, Joseph Jankovic, Kenya Nishioka, Manabu Funayama, Jordi Clarimon, Caroline H. Williams-Gray, Marta Camacho, Mario Cornejo-Olivas, Luis Torres-Ramirez, Yih-Ru Wu, Guey-Jen Lee-Chen, Ana Morgadinho, Teeratorn Pulkes, Pichet Termsarasab, Daniela Berg, Gregor Kuhlenbaumer, Andrea A. Kuhn, Friederike Borngraeber, Giuseppe de Michele, Anna De Rosa, Alexander Zimprich, Andreas Puschmann, George D. Mellick, Jolanta Dorszewska, Jonathan Carr, Rosangela Ferese, Stefano Gambardella, Bruce Chase, Katerina Markopoulou, Wataru Satake, Tatsushi Toda, Malco Rossi, Marcelo Merello, Timothy Lynch, Diana A. Olszewska, Shen-Yang Lim, Azlina Ahmad-Annuar, Ai Huey Tan, Bashayer Al-Mubarak, Hasmet Hanagasi, Dariusz Koziorowski, Sibel Ertan, Gencer Genc, Patricia de Carvalho Aguiar, Melinda Barkhuizen, Marcia M. G. Pimentel, Rachel Saunders-Pullman, Bart van de Warrenburg, Susan Bressman, Mathias Toft, Silke Appel-Cresswell, Anthony E. Lang, Matej Skorvanek, Agnita J. W. Boon, Rejko Kruger, Esther M. Sammler, Vitor Tumas, Bao-Rong Zhang, Gaetan Garraux, Sun Ju Chung, Yun Joong Kim, Juliane Winkelmann, Carolyn M. Sue, Eng-King Tan, Joana Damasio, Peter Klivenyi, Vladimir S. Kostic, David Arkadir, Mika Martikainen, Vanderci Borges, Jens Michael Hertz, Laura Brighina, Mariana Spitz, Oksana Suchowersky, Olaf Riess, Parimal Das, Brit Mollenhauer, Emilia M. Gatto, Maria Skaalum Petersen, Nobutaka Hattori, Ruey-Meei Wu, Sergey N. Illarioshkin, Enza Maria Valente, Jan O. Aasly, Anna Aasly, Roy N. Alcalay, Avner Thaler, Matthew J. Farrer, Kathrin Brockmann, Jean-Christophe Corvol, Christine Klein
Summary: Through a worldwide online survey, we established an international cohort of individuals with PD-linked variants, providing harmonized and quality-controlled clinical and genetic data for each participant and promoting collaboration among researchers in the field of monogenic PD.
MOVEMENT DISORDERS
(2023)
Article
Clinical Neurology
Pierre-Emmanuel Sugier, Elise A. Lucotte, Cloe Domenighetti, Matthew H. Law, Mark M. Iles, Kevin Brown, Christopher Amos, James D. McKay, Rayjean J. Hung, Mojgan Karimi, Delphine Bacq-Daian, Anne Boland-Auge, Robert Olaso, Jean-francois Deleuze, Fabienne Lesueur, Evgenia Ostroumova, Ausrele Kesminiene, Florent de Vathaire, Pascal Guenel, Ashwin Ashok Kumar Sreelatha, Claudia Schulte, Sandeep Grover, Patrick May, Dheeraj R. Bobbili, Milena Radivojkov-Blagojevic, Peter Lichtner, Andrew B. Singleton, Dena G. Hernandez, Connor Edsall, George D. Mellick, Alexander Zimprich, Walter Pirker, Ekaterina Rogaeva, Anthony E. Lang, Sulev Koks, Pille Taba, Suzanne Lesage, Alexis Brice, Jean-Christophe Corvol, Marie-Christine Chartier-Harlin, Eugenie Mutez, Kathrin Brockmann, Angela B. Deutschlaender, Georges M. Hadjigeorgiou, Efthimios Dardiotis, Leonidas Stefanis, Athina Maria Simitsi, Enza Maria Valente, Simona Petrucci, Letizia Straniero, Anna Zecchinelli, Gianni Pezzoli, Laura Brighina, Carlo Ferrarese, Grazia Annesi, Andrea Quattrone, Monica Gagliardi, Hirotaka Matsuo, Akiyoshi Nakayama, Nobutaka Hattori, Kenya Nishioka, Sun Ju Chung, Yun Joong Kim, Pierre Kolber, Bart P. C. van de Warrenburg, Bastiaan R. Bloem, Jan Aasly, Mathias Toft, Lasse Pihlstrom, Leonor Correia Guedes, Joaquim J. Ferreira, Soraya Bardien, Jonathan Carr, Eduardo Tolosa, Mario Ezquerra, Pau Pastor, Monica Diez-Fairen, Karin Wirdefeldt, Nancy Pedersen, Caroline Ran, Andrea C. Belin, Andreas Puschmann, Emil Ygland Roedstroem, Carl E. Clarke, Karen E. Morrison, Manuela Tan, Dimitri Krainc, Lena F. Burbulla, Matt J. Farrer, Rejko Kruger, Thomas Gasser, Manu Sharma, Therese Truong, Alexis Elbaz
Summary: By using genome-wide association studies, this study found that Parkinson's disease (PD) is genetically correlated with melanoma and prostate cancer, while it is inversely correlated with ovarian cancer. These findings suggest that pleiotropic genes contribute to the association between PD and specific cancers.
MOVEMENT DISORDERS
(2023)
Article
Biochemistry & Molecular Biology
Ayami Okuzumi, Taku Hatano, Gen Matsumoto, Shuko Nojiri, Shin-ichi Ueno, Yoko Imamichi-Tatano, Haruka Kimura, Soichiro Kakuta, Akihide Kondo, Takeshi Fukuhara, Yuanzhe Li, Manabu Funayama, Shinji Saiki, Daisuke Taniguchi, Taiji Tsunemi, Deborah McIntyre, Jean-Jacques Gerardy, Michel Mittelbronn, Rejko Kruger, Yasuo Uchiyama, Nobuyuki Nukina, Nobutaka Hattori
Summary: A modified assay system (IP/RT-QuIC) has been developed to detect pathogenic alpha-synuclein seeds in the serum of individuals with synucleinopathies. The system showed high diagnostic performance for differentiating Parkinson's disease and multiple system atrophy from controls.
Article
Cell & Tissue Engineering
Axel Chemla, Giuseppe Arena, Claudia Saraiva, Clara Berenguer-Escuder, Dajana Grossmann, Anne Grunewald, Christine Klein, Philip Seibler, Jens C. Schwamborn, Rejko Kruger
Summary: In this study, two Parkinson's disease patients' primary skin fibroblasts carrying distinct heterozygous mutations in the RHOT1 gene encoding Miro1 were reprogrammed into induced pluripotent stem cells (iPSCs) using episomal reprogramming. Isogenic gene-corrected lines were generated using CRISPR/Cas9 technology. Both isogenic pairs were comprehensively characterized and quality assured to study the Miro1-related molecular mechanisms underlying neurodegeneration in iPSC-derived neuronal models.
STEM CELL RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Svitlana Rozanova, Julian Uszkoreit, Karin Schork, Bettina Serschnitzki, Martin Eisenacher, Lars Toenges, Katalin Barkovits-Boeddinghaus, Katrin Marcus
Summary: Proteomic studies using mass spectrometry (MS)-based quantification are important for discovering new biomarkers, but the accuracy of the outcomes can be affected by various analytical conditions. Therefore, it is crucial to assess the quality of the acquired data, including raw data, identification, and quantification levels. This study demonstrates the assessment of four independent datasets from cerebrospinal fluid, highlighting the impact of sample processing-based differences on the quality of quantitative data. Additionally, a free and open source quality control tool called MaCProQC is provided for systematic and rapid data comparison.
Article
Neurosciences
Odette Fruendt, Anne-Marie Hanff, Annika Moehl, Tobias Mai, Christiane Kirchner, Ali Amouzandeh, Carsten Buhmann, Rejko Kruger, Martin Suedmeyer
Summary: Data on the use of device-aided therapies (DATs) in people with Parkinson's disease (PwP) are scarce. German DAT application rate is rather low, indicating a need for precise identification of symptoms and implementation in future treatment strategies.
Article
Chemistry, Multidisciplinary
Thomas Hix-Janssens, Sudhirkumar Shinde, Rahma Abouhany, Julia Davies, Jessica Neilands, Gunnel Svensaeter, Boerje Sellergren
Summary: Periodontitis is a common oral condition that affects around 7% of adults and has potential links to cardiovascular and Alzheimer's diseases. The lack of accurate clinical methods for identifying at-risk patients leads to both underdiagnosis and overtreatment. Researchers have developed a monitoring approach using high-affinity microcontact imprinted polymer-based receptors and surface plasmon resonance-based biosensor technology to quantify gingipain levels, which are key virulence factors in periodontitis, in biofluids and patient samples.
Article
Biochemical Research Methods
Giuliana Grasso, Eduardo M. Sommella, Fabrizio Merciai, Rahma Abouhany, Sudhirkumar A. Shinde, Pietro Campiglia, Borje Sellergren, Carlo Crescenzi
Summary: In this study, three novel polymeric capture phases were developed for the selective extraction of a biomarker and its analogue drug related to neurodegenerative diseases. The results demonstrated high affinity of the sorbents towards the biomarker and drug. This approach offers a valuable tool for developing efficient analytical procedures.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Robert Hardt, Alireza Dehghani, Carmen Schoor, Markus Goedderz, Nur Cengiz Winter, Shiva Ahmadi, Ramesh Sharma, Karin Schork, Martin Eisenacher, Volkmar Gieselmann, Dominic Winter
Summary: In this study, we used mass spectrometry to investigate the differentiation of pluripotent neural stem cells (NSCs) into oligodendrocytes. We identified Dclk1 as one of the key proteins involved in this process and found that it undergoes a gradual transition between its short and long isoforms during NSC to OPC differentiation. Through interactome analyses, we characterized the interaction partners and substrates of different Dclk1 isoforms. The data from this study are available on ProteomeXchange with identifier PXD040652.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Eveline Santos da Silva, Jean-Yves Servais, Michel Kohnen, Vic Arendt, Therese Staub, Paul CON VINCE Consortium, Judith M. CoVaLux Consortium, Rejko Kruger, Guy Fagherazzi, Paul Wilmes, Judith M. Hubschen, Markus Ollert, Danielle Perez-Bercoff, Carole Seguin-Devaux
Summary: A new variant-adapted surrogate virus neutralization test (sVNT) was established, allowing for the efficient prediction of immune protection against different variants of concern.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Clinical Neurology
Anne-Marie Hanff, Christopher McCrum, Armin Rauschenberger, Gloria A. Aguayo, Maurice P. Zeegers, Anja K. Leist, Rejko Kruger
Summary: This study aimed to validate the algorithm calculating the Functional Mobility Composite Score (FMCS) based on the Parkinson's Disease Questionnaire-39 (PDQ-39). The results showed that the FMCS has good convergent and discriminative validity, making it a reliable measure for assessing functional mobility through patient reports in people with Parkinson's disease.
PARKINSONISM & RELATED DISORDERS
(2023)
Article
Materials Science, Biomaterials
Evgeniia Kislenko, Anil Incel, Kornelia Gawlitza, Boerje Sellergren, Knut Rurack
Summary: Early detection of cancer is crucial for successful treatment. In this study, fluorescent molecularly imprinted polymers (fMIPs) were developed for rapid detection of cancer biomarkers. The polymers were able to differentiate between phosphorylated and non-phosphorylated peptides and capture unprotected peptides in a neutral environment.
JOURNAL OF MATERIALS CHEMISTRY B
(2023)