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
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
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
Chemistry, Applied
Yunhe Hong, Nicholas Birse, Brian Quinn, Yicong Li, Wenyang Jia, Saskia van Ruth, Christopher T. Elliott
Summary: In this study, the difference between wild and farmed salmon production was successfully characterized using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-ToF MS) combined with chemometric analysis. The established method involved multivariate analysis techniques, such as principal component analysis (PCA), partial least squares-discriminant analysis (PLS-DA), and orthogonal partial least squares-discriminant analysis (OPLS-DA), to identify distinctive features in wild and farmed salmon products. The proposed method achieved 100% classification accuracy in discriminating farmed and wild salmon, as well as distinguishing different species of wild salmon. The results suggest that this method could be used as a reference for detecting salmon fraud related to production type and expand the application of MALDI-ToF technology in food authenticity testing.
Article
Microbiology
Arnaud Jabet, Anne-Cecile Normand, Alicia Moreno-Sabater, Jacques Guillot, Veronica Risco-Castillo, Sophie Brun, Magalie Demar, Romain Blaizot, Cecile Nabet, Ann Packeu, Renaud Piarroux
Summary: The objective of the study was to reduce recurrent errors between phylogenetically close species by adding new reference spectra. Diversifying the references and adding spectra from various culture media and culture durations improved identification performance, although confusion remained between certain closely related species.
Article
Food Science & Technology
Minghui Yan, Liwen Luo, Dandan Li, Zhenmin Liu, Ran Wei, Jia Yi, Liang Qiao, Chunping You
Summary: We developed an efficient strategy to assess the risk of biofilm formation by psychrotrophic Pseudomonas in raw milk using MALDI-TOF MS. By collecting molecular mass fingerprints of whole cells and combining multivariate statistical analysis with machine learning, we established a classification model for the biofilm-forming ability of psychrotrophs. The results showed that different biofilm-forming capabilities of Pseudomonas can be well distinguished by the MALDI-TOF MS molecular mass fingerprints. The established classification model demonstrated 100% accuracy in identifying biofilm-forming risk.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2023)
Article
Microbiology
Camila Morschbacher Wilhelm, Maiara dos Santos Carneiro, Everton Inamine, Afonso Luis Barth
Summary: This study aimed to evaluate an adaptation of the MBT-ASTRA technique for faster antimicrobial susceptibility testing. The adapted method showed high categorical agreement with the standard method, indicating its potential for rapid AST results.
MICROBIOLOGY SPECTRUM
(2023)
Article
Infectious Diseases
T. Garrigos, C. Neuwirth, A. Chapuis, J. Bador, L. Amoureux
Summary: The study aimed to establish a MALDI-TOF/MS Bruker database including 18 Achromobacter species and evaluate its suitability in laboratory settings. The new database accurately identified 99.4% of isolates, significantly outperforming the Bruker default database at 50.9%. This highlights the potential of using MALDI-TOF/MS with a local database for rapid and accurate identification.
CLINICAL MICROBIOLOGY AND INFECTION
(2021)
Retraction
Chemistry, Multidisciplinary
Feng Ding, Yuna Qian, Zaian Deng, Jitai Zhang, Yongchao Zhou, Lan Yang, Fangyan Wang, Juping Wang, Zhihua Zhou, Jianliang Shen
Summary: The study on size-selected silver nanoparticles for MALDI-TOF mass spectrometry of amyloid-beta peptides by Feng Ding et al. was retracted from Nanoscale journal in 2018.
Article
Infectious Diseases
Ana Candela, Manuel J. Arroyo, Maria Sanchez-Cueto, Mercedes Marin, Emilia Cercenado, Gema Mendez, Patricia Munoz, Luis Mancera, David Rodriguez-Temporal, Belen Rodriguez-Sanchez
Summary: The study evaluated matrix-assisted laser desorption ionization-iime of flight mass spectrometry (MALDI-TOF MS) and Fourier-transform infrared spectroscopy (FTIR-S) as diagnostic alternatives for the detection of Pseudomonas aeruginosa sequence type (ST) 175 isolates involved in a hospital outbreak. The results showed that the combination of these two technologies, along with machine learning tools, can effectively monitor high-risk clones and isolates in nosocomial outbreaks.
TRANSBOUNDARY AND EMERGING DISEASES
(2023)
Review
Chemistry, Analytical
Judy Gopal, Manikandan Muthu
Summary: Mushrooms have transitioned from a luxury food to a widely accepted nutrient-rich food. Mushroom polysaccharides have become icons of mushroom bioactivity, and the analytical techniques for their analysis have been consolidated and summarized.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Polymer Science
Hans. R. Kricheldorf, Steffen M. Weidner
Summary: Alcohol-initiated ring-opening polymerizations of L-lactide were investigated, with variations in the alcohol nature, LA/initiator ratio, LA/SnOct2 ratio, and time. Neat SnOct2 exhibited catalytic activity in THF and some aromatic solvents, while its activity was strongly reduced in solvents like 1,3-dioxolane, dimethylformamide (DMF), and N-methyl pyrrolidone (NMP). The formation of cyclization was observed at 115°C in toluene but not at 70°C, which was attributed to the reduced mobility of the initially formed linear chains in toluene.
EUROPEAN POLYMER JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Zeljko Debeljak, Ann-Christin Niehoff, Ana Bandjak, Dario Mandic, Bojana Bosnjak, Marija Heffer, Stefan Mrdenovic, Ivana Markovic, Milorad Zjalic, Vatroslav Seric
Summary: This study aimed to develop and evaluate matrix-assisted laser desorption ionization time-of-flight mass spectrometry imaging of blood smears. Different blood plasma removal, matrix deposition, and instrumental settings were evaluated, and the study sets the foundations for future application of this technique in clinical diagnostics and research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Eliza Matuszewska, Szymon Plewa, Dagmara Pietkiewicz, Kacper Kossakowski, Joanna Matysiak, Grzegorz Rosinski, Jan Matysiak
Summary: Bee pollen is a valuable medicinal and nutritional product, but its consumption may cause adverse effects due to its unknown composition. This study identified bioactive proteins, including potential allergens, in bee pollen collected in Poland. Standardizing bee pollen is crucial due to its content of both beneficial and harmful compounds, and awareness of allergens can prevent health risks associated with consuming these popular superfoods.
Article
Chemistry, Organic
Bernard Fernandez, Jean Armengaud, Gilles Subra, Christine Enjalbal
Summary: This study investigates the feasibility of using high energy charge remote fragmentations to analyze the N-terminus of proteins, and compares it with low energy collision-induced dissociations. The results show that the amino acid composition significantly affects the dissociation pathways of peptide backbones.
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Ashley Scott, Robert C. Power, Victoria Altmann-Wendling, Michel Artzy, Mario A. S. Martin, Stefanie Eisenmann, Richard Hagan, Domingo C. Salazar-Garcia, Yossi Salmon, Dmitry Yegorov, Ianir Milevski, Israel Finkelstein, Philipp W. Stockhammer, Christina Warinner
Summary: By analyzing microremains and proteins preserved in dental calculus from individuals in the Southern Levant during the second millennium BCE, it has been found that people in the Eastern Mediterranean had access to food from distant locations such as South Asia, including soybean, banana, and turmeric, pushing back the earliest evidence of these foods in the Mediterranean by centuries or even millennia. This challenges previous perceptions of the complexity and intensity of Indo-Mediterranean trade during the Bronze Age and the degree of globalization in early Eastern Mediterranean cuisine.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
James A. Fellows Yates, Aida Andrades Valtuena, Ashild J. Vagene, Becky Cribdon, Irina M. Velsko, Maxime Borry, Miriam J. Bravo-Lopez, Antonio Fernandez-Guerra, Eleanor J. Green, Shreya L. Ramachandran, Peter D. Heintzman, Maria A. Spyrou, Alexander Huebner, Abigail S. Gancz, Jessica Hider, Aurora F. Allshouse, Valentina Zaro, Christina Warinner
Summary: AncientMetagenomeDir is a collection of annotated metagenomic sample lists from published studies, providing basic, standardized metadata and accession numbers for interdisciplinary ancient metagenomics research. This collection aims to standardize metadata reporting for future studies in this field.
Article
Biology
Simone Rampelli, Silvia Turroni, Carolina Mallol, Cristo Hernandez, Bertila Galvan, Ainara Sistiaga, Elena Biagi, Annalisa Astolfi, Patrizia Brigidi, Stefano Benazzi, Cecil M. Lewis, Christina Warinner, Courtney A. Hofman, Stephanie L. Schnorr, Marco Candela
Summary: By analyzing ancient bacterial profiles from fecal sediments at the El Salt Middle Paleolithic site in Spain, researchers found evidence of a core human gut microbiome that may have been shared by Neanderthals and modern humans before their divergence. This suggests that beneficial gut commensals like Blautia, Dorea, Roseburia, Ruminococcus, Faecalibacterium, and Bifidobacterium have been present in the intestinal microbiome of Homo since the last common ancestor between humans and Neanderthals.
COMMUNICATIONS BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Aida Andrades Valtuena, Gunnar U. Neumann, Maria A. Spyrou, Lyazzat Musralina, Franziska Aron, Arman Beisenov, Andrey B. Belinskiy, Kirsten I. Bos, Alexandra Buzhilova, Matthias Conrad, Leyla B. Djansugurova, Miroslav Dobes, Michal Ernee, Javier Fernandez-Eraso, Bruno Frohlich, Miroslaw Furmanek, Agata Haluszko, Svend Hansen, Eadaoin Harney, Alina N. Hiss, Alexander Hubner, Felix M. Key, Elmira Khussainova, Egor Kitov, Alexandra O. Kitova, Corina Knipper, Denise Kuhnert, Carles Lalueza-Fox, Judith Littleton, Ken Massy, Alissa Mittnik, Jose Antonio Mujika-Alustiza, Inigo Olalde, Luka Papac, Sandra Penske, Jaroslav Peska, Ron Pinhasi, David Reich, Sabine Reinhold, Raphaela Stahl, Harald Stauble, Rezeda I. Tukhbatova, Sergey Vasilyev, Elizaveta Veselovskaya, Christina Warinner, Philipp W. Stockhammer, Wolfgang Haak, Johannes Krause, Alexander Herbig
Summary: A study reveals the dynamic nature of early evolution and ecology of the bacterial pathogen Yersinia pestis, which caused devastating outbreaks throughout human history. The study presents 17 ancient Y. pestis genomes dating back 5,000 to 2,500 years ago, showing correlations between temporal, geographical, and genetic distance and providing clues on its early evolution and potential adaptation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Chi-Chun Liu, David Witonsky, Anna Gosling, Ju Hyeon Lee, Harald Ringbauer, Richard Hagan, Nisha Patel, Raphaela Stahl, John Novembre, Mark Aldenderfer, Christina Warinner, Anna Di Rienzo, Choongwon Jeong
Summary: Present-day Tibetans have genetically and culturally adapted to the high altitude environment of the Tibetan Plateau, with recent research suggesting an early population entering the area within the past 40 thousand years and subsequent groups arriving within the past 10 thousand years. Ancient individuals from high elevation sites in Nepal are most closely related to present-day Tibetans, deriving their ancestry from Late Neolithic populations at the northeastern edge of the Plateau with a minor genetic component from a distinct Paleolithic Eurasian ancestry. Compared to Tibetans, non-Tibetan Tibeto-Burman speakers living at mid-elevations along the Plateau form a distinct genetic cline, and ongoing positive selection of high altitude adaptive alleles is confirmed through a comparison of ancient and present-day highlanders.
NATURE COMMUNICATIONS
(2022)
Article
Ecology
Ashley Scott, Sabine Reinhold, Taylor Hermes, Alexey A. Kalmykov, Andrey Belinskiy, Alexandra Buzhilova, Natalia Berezina, Anatoliy R. Kantorovich, Vladimir E. Maslov, Farhad Guliyev, Bertille Lyonnet, Parviz Gasimov, Bakhtiyar Jalilov, Jeyhun Eminli, Emil Iskandarov, Emily Hammer, Selin E. Nugent, Richard Hagan, Kerttu Majander, Paivi Onkamo, Kerkko Nordqvist, Natalia Shishlina, Elena Kaverzneva, Arkadiy I. Korolev, Aleksandr A. Khokhlov, Roman V. Smolyaninov, Svetlana V. Sharapova, Rudiger Krause, Marina Karapetian, Eliza Stolarczyk, Johannes Krause, Svend Hansen, Wolfgang Haak, Christina Warinner
Summary: This study investigates the dietary proteins of individuals from the Pontic-Caspian Steppe and neighboring regions, shedding light on the economic foundations and mobility of pastoralist societies from the Neolithic to Greco-Roman periods. The findings reveal that sheep dairying was present during the early forms of pastoralism in the North Caucasus, and there was a shift from cattle to sheep for dairying during the Maykop and early Yamnaya populations. Livestock specialization broke down and dairy herds became more diversified during aridification, potentially driving the increased mobility of the Middle and Late Bronze Age periods. After a hiatus of over 500 years, the North Caucasian steppe was repopulated with Early Iron Age societies that had a mobile dairy economy, including horse milking.
NATURE ECOLOGY & EVOLUTION
(2022)
Review
Chemistry, Multidisciplinary
Christina Warinner, Kristine Korzow Richter, Matthew J. Collins
Summary: Paleoproteomics is a rapidly growing field that uses ancient proteins to explore questions about the past. It has diverse applications in taxonomy, phylogenetics, food analysis, and disease characterization. These studies provide insights into past human activities, environmental changes, and the fossil record, and the future holds promise for further innovation and technological advancements.
Article
Biochemical Research Methods
Evangelos A. Dimopoulos, Alberto Carmagnini, Irina M. Velsko, Christina Warinner, Greger Larson, Laurent A. F. Frantz, Evan K. Irving-Pease
Summary: HAYSTAC is a high-accuracy and scalable taxonomic assignment method for metagenomic data, which can estimate the probability of specific taxa presence. It is specifically designed to handle both ancient and modern DNA data efficiently, and can run high-accuracy hypothesis-driven analyses on incomplete reference databases.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Correction
Biology
Rita M. Austin, Molly Zuckerman, Tanvi P. Honap, Hedwig Lee, Geoff K. Ward, Christina Warinner, Krithivasan Sankaranarayanan, Courtney A. Hofman
COMMUNICATIONS BIOLOGY
(2022)
Article
Biology
Rita M. Austin, Molly Zuckerman, Tanvi P. Honap, Hedwig Lee, Geoff K. Ward, Christina Warinner, Krithivasan Sankaranarayanan, Courtney A. Hofman
Summary: An investigation into the death of a 23-year-old Black male in St. Louis in the 1930s reveals evidence of structural violence and systemic racism. The study finds chronic oral infections and a possible tuberculosis infection in the individual, along with three pre-antibiotic era pathogens that likely contributed to his cause of death. The findings highlight the ongoing inequalities and health disparities faced by marginalized communities.
COMMUNICATIONS BIOLOGY
(2022)
Article
Anthropology
Maria C. Codlin, Katerina Douka, Kristine K. Richter
Summary: Aquatic bird remains provide important evidence for prehispanic lake exploitation in highland Central Mexico. However, little attention has been given to the economic importance of ducks and other lacustrine birds. This study uses the ZooMS technique to identify avian fauna from Teotihuacan, revealing the diverse range of birds exploited by the residents of Tlajinga.
JOURNAL OF ARCHAEOLOGICAL SCIENCE
(2022)
Article
Multidisciplinary Sciences
Juhyeon Lee, Bryan K. Miller, Jamsranjav Bayarsaikhan, Erik Johannesson, Alicia Ventresca Miller, Christina Warinner, Choongwon Jeong
Summary: This study investigates aristocratic and local elite cemeteries at the western frontier of the Xiongnu Empire and finds that genetic diversity within these communities is comparable to the empire as a whole. The study also reveals high diversity within extended families. Lower-status individuals show the highest genetic heterogeneity, implying diverse origins, while higher-status individuals have less genetic diversity, suggesting concentration of elite status and power within specific subsets of the broader Xiongnu population.