Article
Biochemical Research Methods
Lizhuo Ai, Aleksandra Binek, Simion Kreimer, Matthew Ayres, Aleksandr Stotland, Jennifer E. Van Eyk
Summary: Heart tissue sample preparation for mass spectrometry analysis can be improved by using high-field asymmetric ion mobility spectrometry coupled to mass spectrometry, which reduces manual sample handling and shortens processing time. This method provides unique protein identification and quantification similar to the commonly used IN-Seq method in a shorter timeframe.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Delphine Vincent, AnhDuyen Bui, Doris Ram, Vilnis Ezernieks, Frank Bedon, Joe Panozzo, Pankaj Maharjan, Simone Rochfort, Hans Daetwyler, Matthew Hayden
Summary: This study optimized a LC-MS shotgun quantitative proteomics method to screen wheat genotypes for breeding lines with better performance. A large number of wheat proteins were identified using this method, and data mining tools were used to explore the flour proteome.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Alexander L. Rusanov, Peter M. Kozhin, Olga Tikhonova, Victor G. Zgoda, Dmitry S. Loginov, Adela Chlastakova, Martin Selinger, Jan Sterba, Libor Grubhoffer, Nataliya G. Luzgina
Summary: The study compared the proteomic profiles of immortalized cell lines and primary cells, finding significant differences in the abundances of various proteins associated with phagocytosis. This suggests that validation of results using PMJ2-R cells as a model for peritoneal macrophages should be carefully conducted.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Analytical
Yangyang Bian, Florian P. Bayer, Yun-Chien Chang, Chen Meng, Stefanie Hoefer, Nan Deng, Runsheng Zheng, Oleksandr Boychenko, Bernhard Kuster
Summary: Microflow liquid chromatography tandem mass spectrometry (mu LC-MS/MS) has been shown to be a robust and high-throughput method for analyzing proteomes, capable of measuring thousands of proteins from various samples. The system demonstrated the potential for in-depth and high-throughput clinical applications through analyzing a large number of samples over a period of two years.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Marianna Naki, Olga Gourdomichali, Katerina Zonke, Fedon-Giasin Kattan, Manousos Makridakis, Georgia Kontostathi, Antonia Vlahou, Epaminondas Doxakis
Summary: The study identified the proteins in the vicinity of DDIT4 in unstressed and acute stress conditions using APEX2 biotin-labeling enzyme fused with DDIT4 and mass spectrometry. The results showed that DDIT4 had more interaction partners during acute stress compared to unstressed conditions, but the molecular function and classification of the proteins were essentially the same in both conditions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Xintong Sui, Qiong Wu, Xiaozhen Cui, Xi Wang, Luobin Zhang, Nan Deng, Yangyang Bian, Ruilian Xu, Ruijun Tian
Summary: Capillary- and micro-flow liquid chromatography-tandem mass spectrometry (capLC-MS/MS and mu LC-MS/MS) offer an alternative to nano-flow LC-MS/MS with high robustness and throughput. In this study, the capLC-MS/MS and mu LC-MS/MS systems were compared in terms of sensitivity, analysis throughput, separation efficiency, and robustness. The results showed that capLC-MS/MS was more sensitive, while mu LC-MS/MS had higher analysis throughput and separation efficiency. Both systems demonstrated good reproducibility in long-term performance testing.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Entomology
Yulica Santos-Ortega, Nabil Killiny
Summary: Controlling the vector Diaphorina citri is crucial for managing the devastating citrus disease, Huanglongbing. Targeting egg hatching of D. citri through RNA interference may effectively reduce vector population and disease transmission. Analyzing the chorion proteome of D. citri provides potential targets for better control of psyllid populations.
Article
Biochemical Research Methods
Ashley Di Meo, Dorsa Sohaei, Ihor Batruch, Pantelis Alexandrou, Ioannis Prassas, Eleftherios P. Diamandis
Summary: The analysis utilized LC-MS/MS technology to profile the normal human proteome from 117 samples across 46 normal tissues and organs, quantifying 10,438 unique proteins. By combining data from biological fluid proteomics of healthy individuals, tandem mass spectra corresponding to 13,028 unique human protein-coding genes were generated, serving as an important complementary resource for future biomarker discovery.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Neil A. McCracken, Sarah A. Peck Justice, Aruna B. Wijeratne, Amber L. Mosley
Summary: The study introduces a user-friendly analysis of the melt shift calculation workflow and quantitatively assesses the impact of key steps in the analysis workflow on the final output list of stabilized and destabilized proteins. It also presents a more optimized analysis workflow, illustrating the importance of selected calculation steps on the final list of reported proteins of interest in a study. The development of the R based program Inflect offers a valuable resource for the research community to analyze data from TPP and CETSA experiments.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Multidisciplinary Sciences
Tattym E. Shaiken, Sandra L. Grimm, Mohamad Siam, Amanda Williams, Abdol-Hossein Rezaeian, Daniel Kraushaar, Emily Ricco, Matthew J. Robertson, Cristian Coarfa, Antrix Jain, Anna Malovannaya, Fabio Stossi, Antone R. Opekun, Alyssa P. Price, Julien Dubrulle
Summary: Despite the unclear structural organization within the cytoplasm, recent models propose the existence of viscous fluid and solid elastic phases called cytosol and cytomatrix. The cytomatrix contains structural proteins, ribosomes, and metabolome enzymes, and it exhibits unique biosynthetic pathways. The cytosol and cytomatrix form an interconnected network that affects protein translation and promotes cellular flexibility, potentially contributing to the survival of malignant cells.
Article
Oncology
Sungchan Gwark, Hee-Sung Ahn, Jeonghun Yeom, Jiyoung Yu, Yumi Oh, Jae Ho Jeong, Jin-Hee Ahn, Kyung Hae Jung, Sung-Bae Kim, Hee Jin Lee, Gyungyub Gong, Sae Byul Lee, Il Yong Chung, Hee Jeong Kim, Beom Seok Ko, Jong Won Lee, Byung Ho Son, Sei Hyun Ahn, Kyunggon Kim, Jisun Kim
Summary: Proteomic analysis of plasma proteins in breast cancer patients undergoing neoadjuvant chemotherapy identified potential biomarkers such as MBL2 and P4HB that were significantly associated with survival outcomes and could differentiate between low- and high-risk groups. Further investigation is needed to understand the role of these markers in predicting prognosis and their therapeutic potential for preventing recurrence.
Article
Parasitology
Ricardo Perez-Sanchez, Angel Carnero-Moran, M. Luz Valero, Ana Oleaga
Summary: Using a proteomics informed by transcriptomics (PIT) approach, the researchers successfully obtained and characterized the proteome of the saliva of Ornithodoros erraticus adult ticks. They identified novel salivary proteins and functions, and found significant differences between sexes in the saliva proteome of O. erraticus ticks. These findings improve our understanding of feeding physiology in O. erraticus ticks and will contribute to the development of vaccines for controlling O. erraticus infestations and the diseases it transmits.
PARASITES & VECTORS
(2022)
Article
Veterinary Sciences
Sataporn Phochantachinda, Boonrat Chantong, Onrapak Reamtong, Duangthip Chatchaisak
Summary: This study identified 87 proteins specific to Canis spp. in plasma samples from ageing and adult dogs, with a subset of proteins involved in inflammation-mediated acute phase response and apolipoprotein metabolism pathways in CCDS. However, plasma A beta(42) was not a reliable diagnostic biomarker for CCDS, and further research in a larger cohort is needed to understand the correlation between protein expression and the pathogenesis of the disease.
BMC VETERINARY RESEARCH
(2021)
Article
Biochemical Research Methods
Witold M. M. Winnik, William Padgett, Emily M. M. Pitzer, David W. W. Herr
Summary: This study applied label-free quantitation (LFQ) to analyze the proteome of rat brain cortex during early postnatal period. By comparing the datasets of published mouse and rat cortex proteomics, similarities and differences were identified. Importantly, significant similarities were found between rat cortex and mouse cortex, although mice had lower abundance of synaptic proteins.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Chemistry, Applied
William Leonard, Pangzhen Zhang, Danyang Ying, Shuai Nie, Evan Tindal, Zhongxiang Fang
Summary: This study investigated the protein fractions from hempseed and its derivatives, showing that extrusion enhanced the amino acid content and improved the functional properties of hempseed protein. Structural and thermal changes in hempseed protein were confirmed, leading to improved solubility, binding capacity, emulsification properties, and digestibility.
Article
Biotechnology & Applied Microbiology
Timothy J. Williams, Michelle A. Allen, Yan Liao, Mark J. Raftery, Ricardo Cavicchioli
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2019)
Editorial Material
Microbiology
Kenneth Timmis, Ricardo Cavicchioli, Jose Luis Garcia, Balbina Nogales, Max Chavarria, Lisa Stein, Terry J. McGenity, Nicole Webster, Brajesh K. Singh, Jo Handelsman, Victor de Lorenzo, Carla Pruzzo, James Timmis, Juan Luis Ramos Martin, Willy Verstraete, Mike Jetten, Antoine Danchin, Wei Huang, Jack Gilbert, Rup Lal, Helena Santos, Sang Yup Lee, Angela Sessitsch, Paola Bonfante, Lone Gram, Raymond T. P. Lin, Eliora Ron, Z. Ceren Karahan, Jan Roelof van der Meer, Seza Artunkal, Dieter Jahn, Lucy Harper
ENVIRONMENTAL MICROBIOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Andrea Strazzulli, Beatrice Cobucci-Ponzano, Roberta Iacono, Rosa Giglio, Luisa Maurelli, Nicola Curci, Corinna Schiano-di-Cola, Annalisa Santangelo, Patrizia Contursi, Vincent Lombard, Bernard Henrissat, Federico M. Lauro, Carlos M. G. A. Fontes, Marco Moracci
Article
Microbiology
Pratibha Panwar, Michelle A. Allen, Timothy J. Williams, Alyce M. Hancock, Sarah Brazendale, James Bevington, Simon Roux, David Paez-Espino, Stephen Nayfach, Maureen Berg, Frederik Schulz, I-Min A. Chen, Marcel Huntemann, Nicole Shapiro, Nikos C. Kyrpides, Tanja Woyke, Emiley A. Eloe-Fadrosh, Ricardo Cavicchioli
Review
Environmental Sciences
Aurore Trottet, Christaline George, Guillaume Drillet, Federico M. Lauro
Summary: The increasing global population has led to heightened urbanization of coastal areas, posing challenges for sustainable food production and security. Aquaculture has emerged as a viable option to ensure food security, but it also comes with environmental impacts and challenges. Effective planning and collaboration are key in addressing the development of aquaculture in urban areas like Singapore.
CRITICAL REVIEWS IN ENVIRONMENTAL SCIENCE AND TECHNOLOGY
(2022)
Article
Ecology
Molly A. Moynihan, Nathalie F. Goodkin, Kyle M. Morgan, Phyllis Y. Y. Kho, Adriana Lopes dos Santos, Federico M. Lauro, David M. Baker, Patrick Martin
Summary: Despite low N-2 fixation rates, coral-associated diazotrophs supply a significant portion of the holobiont's nitrogen demand, particularly in the endolithic community. The activity of diazotrophs is mainly controlled by oxygen, with endolithic microbes playing a major role in coral nitrogen cycling.
Article
Multidisciplinary Sciences
Simon Roux, Blair G. Paul, Sarah C. Bagby, Stephen Nayfach, Michelle A. Allen, Graeme Attwood, Ricardo Cavicchioli, Ludmila Chistoserdova, Robert J. Gruninger, Steven J. Hallam, Maria E. Hernandez, Matthias Hess, Wen-Tso Liu, Tim A. McAllister, Michelle A. O'Malley, Xuefeng Peng, Virginia Rich, Scott R. Saleska, Emiley A. Eloe-Fadrosh
Summary: Researchers have analyzed over 30,000 DGRs from public metagenomes, establishing six major DGR lineages, three of which are primarily encoded by phages, and demonstrating that DGRs are responsible for a significant proportion of amino acid changes in some organisms. These results highlight the constraints under which DGRs evolve, and reveal the distinct roles that these elements play in natural communities.
NATURE COMMUNICATIONS
(2021)
Article
Microbiology
Timothy J. Williams, Michelle A. Allen, Natalia Ivanova, Marcel Huntemann, Sabrina Haque, Alyce M. Hancock, Sarah Brazendale, Ricardo Cavicchioli
Summary: Organic Lake in Antarctica is a cold, hypersaline system that harbors metabolically diverse microorganisms. A new bacterium from the Verrucomicrobia phylum, Candidatus Organicella extenuata, was discovered in the lake, showing genetic similarities to a known endosymbiont of a freshwater ciliate. This discovery highlights the potential for identifying novel endosymbionts by exploring unusual genetic coding parameters.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Liang Shen, Yongqin Liu, Michelle A. Allen, Baiqing Xu, Ninglian Wang, Timothy J. Williams, Feng Wang, Yuguang Zhou, Qing Liu, Ricardo Cavicchioli
Summary: The study revealed a new bacterial clade, Group C, with superior ability to grow at -1 degrees C and distinct genomic traits in comparison to non-polar or alpine Group A. Metagenomic analysis showed an over-representation of Group C in Canadian permafrost communities and an under-representation of Group A in polar and alpine samples, indicating niche adaptation and environmental temperature responses. The findings suggest the potential value of defining genomic markers for specific taxa in monitoring cold environments and understanding environmental changes.
Article
Microbiology
Pauliina Rajala, Dong-Qiang Cheng, Scott A. Rice, Federico M. Lauro
Summary: The study found that metal corrosion in deep-sea environments is driven by both biotic and abiotic processes, with microbially induced corrosion playing a key role, which differs significantly from the microbial communities in the surrounding sediment, dominated by sulfur-cycling bacteria.
Article
Microbiology
Pratibha Panwar, Michelle A. Allen, Timothy J. Williams, Sabrina Haque, Sarah Brazendale, Alyce M. Hancock, David Paez-Espino, Ricardo Cavicchioli
Summary: The formation of Antarctic microbial communities is influenced by various factors, with sunlight hours and the population structure of green sulfur bacteria playing important roles. Studies show that a specific population of green sulfur bacteria provides essential ecosystem services in Antarctica.
Article
Microbiology
Timothy J. Williams, Michelle A. Allen, Pratibha Panwar, Ricardo Cavicchioli
Summary: Uncultivated microbial clades, known as microbial dark matter, are believed to have important yet uncharacterized functions in nutrient cycling. Using metagenomes from an Antarctic lake, researchers generated 12 metagenome-assembled genomes (MAGs) for four dark matter phyla, revealing their potential roles in hydrogen and sulfide production, nitrate reduction, sulfate reduction, and carbon dioxide fixation. These microbial clades contribute to sulfur cycling, degradation of complex organic matter, ammonification, and chemolithoautotrophic carbon dioxide fixation in diverse global environments.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Microbiology
Khandaker Rayhan Mahbub, Caroline Chenard, Steven Batinovic, Steve Petrovski, Federico M. Lauro, Md Hafizur Rahman, Mallavarapu Megharaj, Ashley E. Franks, Maurizio Labbate
Summary: This study compared the genomes of three metal-resistant bacteria isolated from mercury-contaminated soil. Diverse and novel mobile genetic elements (MGEs) were found, with evidence of lateral gene transfer (LGT) events shaping the genomic structure and heavy metal resistance. The strains Sphingobium sp SA2 and Sphingopyxis sp SE2 were resistant to multiple metals, while Pseudoxanthomonas sp SE1 showed resistance to mercury only. Whole genome sequencing revealed that the Sphingobium and Sphingopyxis strains contained multiple chromosomes and plasmids, while the Pseudoxanthomonas strain had one circular chromosome. Metal resistance genes were associated with various MGEs, including genomic islands (GIs), integrative conjugative elements (ICEs), transposons, insertion sequences (IS), recombinase in trio (RIT) elements, and group II introns. The study highlights the importance of LGT in the evolution of metal resistance in bacteria.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Ecology
Winona Wijaya, Zahirah Suhaimi, Cherlyn Xin'Er Chua, Rohan Shawn Sunil, Sandra Kolundzija, Ahmad Muzakkir Bin Rohaizat, Norzarifah Binti Md. Azmi, Nur Hazlin Hazrin-Chong, Federico M. Lauro
Summary: The study investigates the factors influencing the microbial populations in the Johor Strait, which is characterized by low water turnover rates and nutrient build-up. By conducting a temporally-intensive sampling and analysis, the study reveals that microbial community succession is influenced by pulse disturbances from freshwater input and tidal currents, as well as top-down controls from marine viruses and predatory bacteria. The occurrence of harmful algal blooms is likely to happen when there are simultaneous gaps in both top-down and bottom-up controls.
ISME COMMUNICATIONS
(2023)
Article
Biotechnology & Applied Microbiology
Stephen Nayfach, Simon Roux, Rekha Seshadri, Daniel Udwary, Neha Varghese, Frederik Schulz, Dongying Wu, David Paez-Espino, I-Min Chen, Marcel Huntemann, Krishna Palaniappan, Joshua Ladau, Supratim Mukherjee, T. B. K. Reddy, Torben Nielsen, Edward Kirton, Jose P. Faria, Janaka N. Edirisinghe, Christopher S. Henry, Sean P. Jungbluth, Dylan Chivian, Paramvir Dehal, Elisha M. Wood-Charlson, Adam P. Arkin, Susannah G. Tringe, Axel Visel, Tanja Woyke, Nigel J. Mouncey, Natalia N. Ivanova, Nikos C. Kyrpides, Emiley A. Eloe-Fadrosh
Summary: Reconstructing bacterial and archaeal genomes from shotgun metagenomes has led to the creation of a comprehensive catalog representing a significant expansion of the known phylogenetic diversity of bacteria and archaea. This resource is available for streamlined comparative analyses, interactive exploration, metabolic modeling, and bulk download, demonstrating the utility of genome-centric approaches for understanding genomic properties of uncultivated microorganisms.
NATURE BIOTECHNOLOGY
(2021)