Article
Multidisciplinary Sciences
Kristine Korzow Richter, Maria C. Codlin, Melina Seabrook, Christina Warinner
Summary: Collagen peptide mass fingerprinting by MALDI-TOF-MS, also known as ZooMS, is a rapidly growing analytical technique in the fields of archaeology, ecology, and cultural heritage. It enables rapid taxonomic identification of large bone assemblages and cultural heritage objects. However, there are limitations that need to be addressed for future advancements.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Nutrition & Dietetics
Pierpaolo Scarano, Rosa Guida, Daniela Zuzolo, Maria Tartaglia, Antonello Prigioniero, Alessia Postiglione, Gabriella Pinto, Anna Illiano, Angela Amoresano, Rosario Schicchi, Anna Geraci, Rosaria Sciarrillo, Carmine Guarino
Summary: This study focused on the extraction, quantification, and characterization of bioactive compounds from Arbutus unedo L. fruits in different ripening states. Results showed that ultrasound-assisted extraction performed better than maceration extraction, and ethanol-water mixture extracts had a positive effect on the content of total phenolic compounds. The chemical profile of the extracts depended on the degree of fruit ripeness. The findings suggest that A. unedo fruits may have significant applications in the food and nutraceutical industry.
FRONTIERS IN NUTRITION
(2022)
Article
Chemistry, Applied
Weili Li, Sen Mei, Huanzhen Zhou, Muhammad Salman Farid, Tao Hu, Tao Wu
Summary: This study used metabolomics and feature-based molecular network (FBMN) analysis to investigate the non-volatile metabolite fingerprints of Pixian douban (PXDB) during its two-year maturation process. The study identified 45 key metabolites involved in flavor formation across 10 major metabolic pathways.
Article
Agriculture, Dairy & Animal Science
H. Ozturk, N. Akin
Summary: The study analyzed the peptide profiles of traditionally produced Tulum cheeses in Turkey using liquid chromatography-tandem mass spectrometry over 180 days of ripening, identifying a total of 203 peptides. Most of the identified peptides were derived from beta-CN, with increasing numbers of alpha(S1)- and beta-CN-derived peptides as ripening days increased. Various bioactive peptides were found, including antihypertensive, antimicrobial, and antioxidant peptides, among others.
JOURNAL OF DAIRY SCIENCE
(2021)
Article
Anthropology
Roshan Paladugu, Kristine Korzow Richter, Maria Joao Valente, Sonia Gabriel, Cleia Detry, Christina Warinner, Cristina Barrocas Dias
Summary: A novel peptide marker has been discovered to reliably distinguish between horse and donkey skeletal remains. This method has the potential to enhance our understanding of the relative importance of these two species in past human societies and facilitate the collection of morphological data for studying equids in Iberia and throughout Eurasia and Africa.
JOURNAL OF ARCHAEOLOGICAL SCIENCE
(2023)
Article
Agriculture, Multidisciplinary
Wenhua Yang, Jianli Zhou, Qiuya Gu, Jean Damascene Harindintwali, Xiaobin Yu, Xiaobo Liu
Summary: Three ginsenoside hydrolases, BG07 (glucoamylase), BG19 (g-glucosidase), and BG23 (g-glucosidase), were identified from Aspergillus tubingensis JE0609 by transcriptome analysis and peptide mass fingerprinting. Among them, BG23 showed high enzymatic activity when expressed in Komagataella phaffii. The enzymatic property studies revealed that BG23 is an acidic and mesophilic enzyme. Furthermore, a one-pot combinatorial enzyme-catalyzed strategy based on BG23 and BGA35 (g-galactosidase from Aspergillus oryzae) achieved a high yield of CK.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Cell Biology
Matiss Ozols, Alexander Eckersley, Kieran T. Mellody, Venkatesh Mallikarjun, Stacey Warwood, Ronan O'Cualain, David Knight, Rachel E. B. Watson, Christopher E. M. Griffiths, Joe Swift, Michael J. Sherratt
Summary: Peptide location fingerprinting is a proteomic analysis technique that can identify structural modification-associated differences in complex biological samples, such as photoaged and intrinsically aged skin proteomes. This technique has the potential for discovering new biomarker candidates in various pathways, and has been demonstrated to be effective in identifying biomarkers in ageing tendon using published MS data sets.
Article
Food Science & Technology
Katrien Dierickx, Samantha Presslee, Virginia L. Harvey
Summary: This research presents an alternative proteomic technique for reliable species identification of fish specimens. The study demonstrates the efficacy of collagen peptide mass fingerprinting in identifying different tissue types of fish samples, highlighting its importance in detecting mislabelling fraud in the food chain.
Article
Anthropology
Samantha Brown, Maxim Kozlikin, Michael Shunkov, Anatoly Derevianko, Thomas Higham, Katerina Douka, Kristine Korzow Richter
Summary: The use of glutamine deamidation to measure decay in archaeological bones has been controversial, with growing evidence suggesting no reliable link between deamidation and chronological age. A study on fossils from Denisova Cave shows high intra and inter layer variability, cautioning against linking deamidation with decay or age.
JOURNAL OF ARCHAEOLOGICAL SCIENCE
(2021)
Article
Agriculture, Dairy & Animal Science
Michele Faccia, Giuseppe Natrella, Giuseppe Gambacorta, Antonio Trani
Summary: The study evaluated the effect of ripening cheese in a traditional cellar without artificial temperature control on the chemical, microbiological, and sensory characteristics of Protected Geographical Indication Canestrato di Moliterno cheese. The nonconventional ripening environment resulted in differences in microbial counts, accelerated maturation, and unique sensory features in the cheese products. The study also found significant qualitative differences in free fatty acid profiles and sensory characteristics between cheese ripened in the natural cellar and controlled maturation room.
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Alexander Eckersley, Matiss Ozols, Peikai Chen, Vivian Tam, Judith A. Hoyland, Andrew Trafford, Danny Chan, Michael J. Sherratt
Summary: By using the Peptide Location Fingerprinting technique, this study identified age-related structural differences in proteins within the intervertebral disc, specifically in degeneration-prone and -resistant regions. These differences were found to potentially lead to damage accumulation and impaired maintenance. Additionally, some proteins exhibited localized ageing effects in the lateral region.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Humanities, Multidisciplinary
Daniel P. Kirby, Marie Svoboda, Joy Mazurek, Lin Rosa Spaabaek, John Southon
Summary: This paper investigates a discrete coating found on a group of Egyptian panel paintings, including six mummy portraits and one funerary panel, dating from the first to third century CE. The coating has been observed on the surface and recesses of the paint layers, and analysis confirmed its composition as deamidated hen egg. The C-14 dating indicates that the coating is not a modern addition. The function of this coating, possibly used for aesthetic or symbolic purposes, remains unknown.
Article
Anthropology
Michael Buckley, Virginia L. Harvey, David Petiffer, Hannah Russ, Wim Wouters, Wim Van Neer
Summary: This study explores the potential of collagen peptide mass fingerprinting (ZooMS) for identifying fish remains from the Medieval Newport shipwreck. Through the inclusion of over 50 reference taxa, the archaeologists identified nine distinct taxonomic groups, dominated by ling. However, the inability to identify all taxonomic groups accurately highlights the need for a larger reference collection or collagen sequences.
ARCHAEOLOGICAL AND ANTHROPOLOGICAL SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Muhammad Hamza, Ashaq Ali, Suliman Khan, Saeed Ahmed, Zarlish Attique, Saad Ur Rehman, Ayesha Khan, Hussain Ali, Muhammad Rizwan, Anum Munir, Arshad Mehmood Khan, Faiza Siddique, Azhar Mehmood, Faisal Nouroz, Sajid Khan
Summary: The study aims to identify viral peptides of SARS-CoV-2 using peptide mass fingerprinting (PMF) to predict novel structure and find inhibitors. Docking analysis showed 15 peptides as potential selective inhibitors for SARS-CoV-2.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Chemistry, Applied
Tomoya Yoshinari, Aoi Sekine, Naoki Kobayashi, Yuzo Nishizaki, Naoki Sugimoto, Yukiko Hara-Kudo, Maiko Watanabe
Summary: This study used SDS-PAGE and MALDI-TOF MS to analyze the sources of 36 enzyme preparations (EPs), and found that 30 EPs had consistent sources with the manufacturer's information, 5 EPs showed high sequence similarity to closely-related species, and 6 enzymes could not be identified. This approach can rapidly determine the biological origin of enzymes and contribute to ensuring the safety of EPs.
FOOD ADDITIVES AND CONTAMINANTS PART A-CHEMISTRY ANALYSIS CONTROL EXPOSURE & RISK ASSESSMENT
(2023)
Article
Multidisciplinary Sciences
Eunkyoung Lee, Steffen Vanneste, Jessica Perez-Sancho, Francisco Benitez-Fuente, Matthew Strelau, Alberto P. Macho, Miguel A. Botella, Jiri Friml, Abel Rosado
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Review
Plant Sciences
Mario Fenech, Iraida Amaya, Victoriano Valpuesta, Miguel A. Botella
FRONTIERS IN PLANT SCIENCE
(2019)
Article
Biochemistry & Molecular Biology
Lourdes Rubio, Jordi Diaz-Garcia, Vitor Amorim-Silva, Alberto P. Macho, Miguel A. Botella, Jose A. Fernandez
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2019)
Article
Biotechnology & Applied Microbiology
Jose G. Vallarino, Catharina Merchante, Jose F. Sanchez-Sevilla, Maria Angels de Luis Balaguer, Delphine M. Pott, Maria T. Ariza, Ana Casanal, David Pose, Amalia Vioque, Iraida Amaya, Lothar Willmitzer, Roberto Solano, Rosangela Sozzani, Alisdair R. Fernie, Miguel A. Botella, James J. Giovannoni, Victoriano Valpuesta, Sonia Osorio
PLANT BIOTECHNOLOGY JOURNAL
(2020)
Article
Agriculture, Multidisciplinary
Begona Orozco-Navarrete, Zuzanna Kaczmarska, Florine Dupeux, Maria Garrido-Arandia, Delphine Pott, Araceli Diaz Perales, Ana Casanal, Jose A. Marquez, Victoriano Valpuesta, Catharina Merchante
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2020)
Article
Plant Sciences
EunKyoung Lee, Brenda Vila Nova Santana, Elizabeth Samuels, Francisco Benitez-Fuente, Erica Corsi, Miguel A. Botella, Jessica Perez-Sancho, Steffen Vanneste, Jiri Friml, Alberto Macho, Aristea Alves Azevedo, Abel Rosado
JOURNAL OF EXPERIMENTAL BOTANY
(2020)
Article
Genetics & Heredity
Maria Belen Cuadrado-Pedetti, Ines Rauschert, Maria Martha Sainz, Vitor Amorim-Silva, Miguel Angel Botella, Omar Borsani, Mariana Sotelo-Silveira
Summary: Mutations in the Arabidopsis TTL1 gene led to reduced tolerance to osmotic stress, affecting root growth rate by inhibiting cell elongation and reducing cortical cell numbers. The study suggests that TTL1 may play a role in controlling cell expansion orientation during root growth, crucial for adapting to osmotic stress.
Article
Plant Sciences
Jose F. Sanchez-Sevilla, Miguel A. Botella, Victoriano Valpuesta, Victoria Sanchez-Vera
Summary: Autophagy is a catabolic and recycling pathway essential for maintaining cellular homeostasis in plants. In cultivated strawberry fruits, autophagy occurs in two waves, characterized by differential expression of ATG genes and ATG8 lipidation. This process plays a significant role in fruit ripening, affecting growth and development.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biology
Juan L. Benavente, Dritan Siliqi, Lourdes Infantes, Laura Lagartera, Alberto Mills, Federico Gago, Noemi Ruiz-Lopez, Miguel A. Botella, Maria J. Sanchez-Barrena, Armando Albert
Summary: Extended synaptotagmins play a central role in non-vesicular lipid transfer between the ER and plasma membrane, acting as molecular tethers and lipid transfer proteins. They integrate different molecular signals in response to stress by binding to lipids through a Ca2+-dependent site and a site for phosphorylated forms of phosphatidylinositol, while their highly flexible hinge points facilitate lipid extraction, protein loading, and transfer between the plasma membrane and ER.
LIFE SCIENCE ALLIANCE
(2021)
Article
Biochemistry & Molecular Biology
Mariem Bradai, Vitor Amorim-Silva, Nibras Belgaroui, Alicia Esteban del Valle, Marie-Edith Chaboute, Anne-Catherine Schmit, Rosa Lozano-Duran, Miguel Angel Botella, Moez Hanin, Chantal Ebel
Summary: PP1 participates in regulating the BR signaling pathway by activating BES1 and controlling its phosphorylation status. Overexpression of PP1 leads to enhanced primary root growth and down-regulation of BR-regulated genes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Byung-Ho Kang, Charles T. Anderson, Shin-ichi Arimura, Emmanuelle Bayer, Magdalena Bezanilla, Miguel A. Botella, Federica Brandizzi, Tessa M. Burch-Smith, Kent D. Chapman, Kai Duenser, Yangnan Gu, Yvon Jaillais, Helmut Kirchhoff, Marisa S. Otegui, Abel Rosado, Yu Tang, Juergen Kleine-Vehn, Pengwei Wang, Bethany Karlin Zolman
Summary: The article summarizes a modern view of plant cell structures and unresolved mysteries, discussing the complexities of internal structures and the shapes revealed by new microscopy techniques. Future research will continue to focus on the combination of imaging modalities with functional studies.
Article
Multidisciplinary Sciences
Christopher Kesten, Alvaro Garcia-Moreno, Vitor Amorim-Silva, Alexandra Menna, Araceli G. Castillo, Francisco Percio, Laia Armengot, Noemi Ruiz-Lopez, Yvon Jaillais, Clara Sanchez-Rodriguez, Miguel A. Botella
Summary: This study identifies TTL proteins as new members of the cellulose synthase complex (CSC), which play a crucial role in adjusting cellulose synthesis and maintaining plant growth under stressful conditions.
Article
Biochemistry & Molecular Biology
Noemi Ruiz-Lopez, Jessica Perez-Sancho, Alicia Esteban del Valle, Richard P. Haslam, Steffen Vanneste, Rafael Catala, Carlos Perea-Resa, Daniel Van Damme, Selene Garcia-Hernandez, Armando Albert, Jose Vallarino, Jinxing Lin, Jiri Friml, Alberto P. Macho, Julio Salinas, Abel Rosado, Johnathan A. Napier, Vitor Amorim-Silva, Miguel A. Botella
Summary: Endoplasmic reticulum-plasma membrane contact sites (ER-PM CS) are essential for maintaining plasma membrane integrity under abiotic stresses in plant cells. The proteins SYT1 and SYT3 function as ER-PM tethers to preserve plasma membrane integrity. Cold stress can lead to increased accumulation of diacylglycerol at the plasma membrane, and SYT1 preferentially binds diacylglycerol in vivo.
Article
Biochemistry & Molecular Biology
Carmen Martin-Pizarro, Jose G. Vallarino, Sonia Osorio, Victoriano Meco, Maria Urrutia, Jeremy Pillet, Ana Casanal, Catharina Merchante, Iraida Amaya, Lothar Willmitzer, Alisdair R. Fernie, James J. Giovannoni, Miguel A. Botella, Victoriano Valpuesta, David Pose
Summary: This study identified and characterized the ripening inducing factor FaRIF in strawberry, which plays a crucial role in controlling key ripening-related processes such as fruit softening, pigment and sugar accumulation. Functional analyses through stable transgenic lines showed that FaRIF is a key regulator of strawberry fruit ripening from early developmental stages, controlling various metabolic pathways and the balance of aerobic/anaerobic metabolism. This research suggests that FaRIF is a potential target for genetic modifications to enhance the quality of strawberry fruits.
Article
Plant Sciences
Mario Fenech, Vitor Amorim-Silva, Alicia Esteban del Valle, Dominique Arnaud, Noemi Ruiz-Lopez, Araceli G. Castillo, Nicholas Smirnoff, Miguel A. Botella
Summary: The study analyzed the subcellular localization and potential interactions of enzymes involved in L-ascorbate biosynthesis pathway in photosynthetic organisms. It was found that most enzymes showed dual cytosolic/nuclear localization and could interact with each other through coimmunoprecipitation, although direct interactions were not observed in yeast-two hybrid analysis. The research highlighted the crucial role of GDP-L-galactose phosphorylase (GGP) in regulating ascorbate synthesis and its impact on enzyme interactions within the pathway.
Article
Biochemical Research Methods
Tanushree Halder, Elke Stroeher, Hui Liu, Yinglong Chen, Guijun Yan, Kadambot H. M. Siddique
Summary: Improving the root system of wheat is crucial for enhancing grain yield and climate resilience. This study identified proteins associated with root length and root mass in wheat using label-free quantitative proteomics. The findings revealed potential biomarkers that could be used for improving the root system of wheat.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Yinhua Pan, Quanqing Zou, Wu Yin, Zhen Huang, Yingzhu Zhao, Zongming Mo, Lihui Li, Jianrong Yang
Summary: A prognostic model of BC based on LNM-related genes was established in this study, providing guidance for prognosis evaluation and precise treatment of BC. The genes related to lymph node metastasis in BC are largely unknown and need further exploration. Searching for potential lymph node metastasis-related genes of BC will provide meaningful biomarkers for BC treatment. Our model, based on TCGA-BRCA data, effectively predicted patient outcomes and classified BC patients. The identified feature genes might have a predictive function in immunotherapy. The results of this study provide a new reference for the prognosis and treatment of BC patients with lymph node metastasis.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Qiushi Liang, Joon M. Pijnenburg, Erikjan Rijkers, Arnold G. Vulto, Ans T. van der Ploeg, Niek P. van Til, Eva C. Vlaar, Jeroen A. A. Demmers, W. W. M. Pim Pijnappel
Summary: Pompe disease is a lysosomal storage disorder characterized by glycogen accumulation in skeletal muscle, leading to profound pathology. This study showed that lentiviral gene therapy with LV-IGF2.GAAco can nearly completely correct disease-associated proteomic changes, supporting its future clinical development as a new treatment option for Pompe disease.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Chuang Liu, Wenjing Zhang, Qianli Dong, Haipeng Liu
Summary: This study fills the knowledge gap about the matrix proteins involved in the formation of mineralized exoskeletons in decapod crustaceans. By comparing with well-studied molluscan biomineralization proteins, it is proposed that decapod crustaceans evolved novel proteins while sharing some proteins with molluscs. This study provides insights into the evolution and adaptation of crustaceans and molluscs in forming their exoskeletons.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Rania D. Baka, Josipa Kules, Angelo Beletic, Vladimir Farkas, Dina Resetar Maslov, Blanka Beer Ljubic, Ivana Rubic, Vladimir Mrljak, Mark McLaughlin, David Eckersall, Zoe Polizopoulou
Summary: This study analyzed serum samples from dogs with epilepsy and identified potential markers of epilepsy, proteins involved in nerve tissue regeneration, and proteins altered by antiepileptic medication. The findings provide insight into the pathogenesis of epilepsy and the effects of medication on extracellular matrix proteins.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Viviane M. Codognoto, Fabiana F. de Souza, Thais R. Cataldi, Carlos A. Labate, Laiza S. de Camargo, Pedro H. Esteves Trindade, Roberto R. da Rosa Filho, Diego J. B. de Oliveira, Eunice Oba
Summary: This study aimed to compare urine proteomics from non- and pregnant buffaloes to identify potential biomarkers of early pregnancy. A total of 798 proteins were reported in the urine considering all groups, and the differential proteins play essential roles during pregnancy.
JOURNAL OF PROTEOMICS
(2024)