Review
Biochemistry & Molecular Biology
Ruben Agregan, Noemi Echegaray, Maria Lopez-Pedrouso, Radwan Kharabsheh, Daniel Franco, Jose M. Lorenzo
Summary: Proteomics has made significant advances in the field of medicine and has applications in other scientific areas, such as the study of milk. Milk proteomics can help characterize milk samples and products in detail, with significant applications in industry for quality control and improvement.
Article
Chemistry, Analytical
Julien Slagboom, Chiel Kaal, Arif Arrahman, Freek J. Vonk, Govert W. Somsen, Juan J. Calvete, Wolfgang Wuster, Jeroen Kool
Summary: Snakebite envenoming is a global issue, and characterizing snake venom can help in developing efficient antivenoms. Various analytical methods such as venomics have been used to analyze the composition and properties of snake venom toxins. The study involves sample preparation, separation, detection, and quantitation techniques.
MICROCHEMICAL JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Agata Piasecka, Andrea Baier
Summary: This study investigated the impact of three trophic modes on the growth parameters and biochemical composition of Chlorella species. The results showed that mixotrophic cultivation using an agro-industrial by-product stimulated the growth of all species, yielding high amounts of protein-rich biomass. The study also provided insights into the proteome of Chlorella cells cultured under molasses supplementation conditions.
Article
Chemistry, Analytical
Yue Sun, Yu Liang, Chao Wang, Baofeng Zhao, Zhen Liang, Xiaodan Zhang, Yukui Zhang, Lihua Zhang
Summary: Comprehensive characterization of membrane proteins at the level of proteoforms in complex biological samples by top-down mass spectrometry (MS) is of vital importance in revealing their precise functions. However, severe peak broadening in the separation of hydrophobic membrane proteins, caused by resistance to mass transfer and strong adsorption on separation materials, leads to MS spectra overlap and signal suppression, which makes against the in-depth research on membrane proteoforms.
ANALYTICAL CHEMISTRY
(2023)
Review
Chemistry, Analytical
Ketki Bagwe, Noah Gould, Kendall R. Johnson, Alexander R. Ivanov
Summary: Tissues and cell populations exhibit high levels of heterogeneity at the cellular level, making it important to analyze smaller sample sizes to capture subtle differences between cells. Capillary electrophoresis coupled with mass spectrometry (CE-MS) is a powerful technique for proteomics and metabolomics analysis at the single-cell level, and this review focuses on its applications and recent advances in sample preparation, separation, MS acquisition, and data analysis.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Stefania Bergamini, Elisa Bellei, Luigi Generali, Aldo Tomasi, Carlo Bertoldi
Summary: This study evaluated proteomic changes induced by CHX and CHX+ADS in supragingival dental sites susceptible to discoloration effects. The results showed that long-term use of CHX led to changes in the TSCM proteome, but these changes were reduced when using CHX+ADS. The ADS limited TSCM formation and the antiseptic effect of CHX reduced its impact on bacterial cell permeability, while Maillard's reaction produced molecules that could facilitate bacterial adhesion.
Article
Biochemical Research Methods
Shakila H. Peli Thanthri, Thomas H. Linz
Summary: This report presents a microfluidic thermal gel transient isotachophoresis (TG-tITP) method for rapid and high-resolution separation of native proteins. By utilizing the viscosity response of thermal gels and temperature gradients, this method achieves a wide mass range separation with 15,000-fold less protein loading and five-fold faster analysis times.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Daniil G. Ivanov, Yang Yang, Jake W. Pawlowski, Ian J. Carrick, Igor A. Kaltashov
Summary: Intact-mass measurements are important for protein characterization, but currently limited to systems with low structural diversity. Limited charge reduction combined with XP-RC/MS provides meaningful information and detailed glycosylation patterns.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Khiry L. Patterson, Albert B. Arul, Min Ji Choi, Nekesa C. Ol, Marsalas D. Whitaker, Angel C. Bodrick, Julia B. Libby, Shania Hansen, Logan Dumitrescu, Katherine A. . Gifford, Angela L. Jefferson, Timothy J. Hohman, Rena A. S. Robinson
Summary: Proteomics research has been transformed by the combination of high-throughput LC-MS/MS instruments and automated sample preparation workflows. However, large-scale experiments require thoughtful QC protocols to ensure reproducibility and quantitative accuracy.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Review
Chemistry, Analytical
Yuanyuan Wu, Wenmei Zhang, Yaoyao Zhao, Xiayan Wang, Guangsheng Guo
Summary: Research on single-cell proteomics is crucial for understanding the growth, development, and diseases in organisms. However, the complexity and limited quantity of proteins in single cells have hindered the progress in this field. Mass spectrometry-based single-cell proteomics, particularly electrospray ionization mass spectrometry (ESI-MS), has rapidly advanced due to its minimal sample requirements, high sensitivity, and structural information without antibody labeling. Nevertheless, the variations in pretreatment methods, separation techniques, and MS instruments greatly affect the throughput and coverage of single-cell proteomic technologies. This review categorizes recent publications based on different methods for single-cell protein sample separation, highlights the performance of these methods in terms of detection coverage and throughput, and discusses the applications and future prospects of ESI-MS-based single-cell proteomics.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Shivam Yadav, Martin Centola, Mathilda Glaesmann, Denys Pogoryelov, Roman Ladig, Mike Heilemann, L. C. Rai, Ozkan Yildiz, Enrico Schleiff
Summary: This study reveals the role of a cyanobacterial cyclophilin in stress responses and assembly of photosynthetic complexes, and presents its unique structural features.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Masataka Nakagawa, Yui Tomioka, Chiaki Sakuma, Yasunori Kurosawa, Takashi Shibata, Tsutomu Arakawa, Teruo Akuta
Summary: A new protocol for conducting two-dimensional (2D) electrophoresis was developed by combining agarose native gel electrophoresis with sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis (PAGE) or flat SDS agarose gel electrophoresis. The technique utilizes His/MES buffer during the first-dimensional agarose native gel electrophoresis to visualize basic and acidic proteins in their native states or complex structures. The gel strip from the first-dimensional agarose gel electrophoresis is soaked in SDS and placed on top of vertical SDS-PAGE gels or flat SDS-MetaPhor high-resolution agarose gels for the second-dimensional separation.
Article
Biochemical Research Methods
Jianmei Tao, Shuailong Jia, Meiqin Wang, Zhuobin Huang, Bo Wang, Wenwen Zhang, Yinyu Wei, Wenzhuo Li, Hongliang Jiang, Zhifeng Du
Summary: A comprehensive method combining protein separation and ion mobility mass spectrometry was used to identify the binding proteins of cisplatin in blood, with 39 proteins found to be platinated and involved in complement and coagulation cascade pathways. The study provided a new approach for systematically identifying metal drug binding proteins in blood and gaining insights into the toxicity of platinum anticancer drugs.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Rijul Bhimwal, Richard R. Rustandi, Anne Payne, Mohamed Dawod
Summary: This review highlights the noteworthy advancements in capillary gel electrophoresis for protein separation and analysis from 2015 to 2021. It provides an overview of the technique's historical perspective, principles, challenges, and limitations, and discusses the advancements made to overcome these issues and expand our understanding of the method. The review also presents applications of capillary gel electrophoresis and future directions for the technique.
JOURNAL OF CHROMATOGRAPHY A
(2022)
Article
Multidisciplinary Sciences
John P. McGee, Pei Su, Kenneth R. Durbin, Michael A. R. Hollas, Nicholas W. Bateman, G. Larry Maxwell, Thomas P. Conrads, Ryan T. Fellers, Rafael D. Melani, Jeannie M. Camarillo, Jared O. Kafader, Neil L. Kelleher
Summary: This study introduces a semi-automated single-ion mass spectrometry workflow for top-down tandem mass spectrometry analysis directly from tissue microenvironments. The results demonstrate that this method can identify multiple proteoforms in tumor samples within a short period of time, and effectively identify proteoform signatures in tumor and stromal regions.
NATURE COMMUNICATIONS
(2023)
Article
Environmental Sciences
Jowenna X. F. Sim, Casey L. Doolette, Sotirios Vasileiadis, Barbara Drigo, Ethan R. Wyrsch, Steven P. Djordjevic, Erica Donner, Dimitrios G. Karpouzas, Enzo Lombi
Summary: The study investigated the effects of 20 commercial pesticides on nitrogen microbial cycling in three different agricultural soils in southern Australia, showing that the effects of pesticides on N microbial cycling are dose-independent and soil-specific. Some pesticides, such as fungicides and herbicides, significantly reduced PN and NAG activities in alkaline loam soil with low organic carbon content. The most prominent effects were observed on the dominant ammonia-oxidizing archaea in the nitrifier community, particularly in soil samples treated with fungicides.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Multidisciplinary Sciences
Cameron J. Reid, Max L. Cummins, Stefan Borjesson, Michael S. M. Brouwer, Henrik Hasman, Anette M. Hammerum, Louise Roer, Stefanie Hess, Thomas Berendonk, Kristina Nesporova, Marisa Haenni, Jean-Yves Madec, Astrid Bethe, Geovana B. Michael, Anne-Kathrin Schink, Stefan Schwarz, Monika Dolejska, Steven P. Djordjevic
Summary: This study presents a pan-genomic analysis of Escherichia coli ST58 isolates from animal and human sources. The analysis reveals a major sub-lineage of ST58 that is characterized by the presence of ColV plasmids carrying virulence genes, and a distinct accessory genome including genes typical of the Yersiniabactin High Pathogenicity Island. This sub-lineage has a broad host range, with poultry and swine being the predominant sources.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Joel S. Bloch, Alan John, Runyu Mao, Somnath Mukherjee, Jeremy Boilevin, Rossitza N. Irobalieva, Tamis Darbre, Nichollas E. Scott, Jean-Louis Reymond, Anthony A. Kossiakoff, Ethan D. Goddard-Borger, Kaspar P. Locher
Summary: C-linked glycosylation is essential for the trafficking, folding, and function of secretory and transmembrane proteins involved in cellular communication processes. Cryogenic-electron microscopy structures of Caenorhabditis elegans CMT reveal how the CMT recognizes the glycosylation sequon and triggers conformational activation of the donor substrate, enabling C-glycosylation of proteins. These findings have implications for understanding human diseases and potential therapeutic targeting of specific CMT paralogs.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Microbiology
Oliver McNeilly, Riti Mann, Max Laurence Cummins, Steven P. Djordjevic, Mehrad Hamidian, Cindy Gunawan
Summary: Several recent studies have found that bacteria are developing resistance to broad-spectrum antimicrobial silver nanoparticles (nanosilver; NAg). This is concerning because NAg is a crucial alternative antimicrobial agent. The present study focuses on the development of resistance to NAg in the globally prevalent bacterial pathogen Acinetobacter baumannii. The findings highlight the risks of long-term NAg use on a priority pathogen and emphasize the need for strategies to overcome bacterial NAg adaptation and preserve the efficacy of this potent antimicrobial agent in the era of antimicrobial resistance.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biochemistry & Molecular Biology
Alan John, Stefanie M. Bader, Niccolay Madiedo Soler, Kharizta Wiradiputri, Swapnil Tichkule, Sean T. Smyth, Stuart A. Ralph, Aaron R. Jex, Nichollas E. Scott, Christopher J. Tonkin, Ethan D. Goddard-Borger
Summary: Cryptosporidium parvum is a common cause of diarrheal disease worldwide and developing vaccines to prevent or limit infection is important. The study investigates the architecture, conservation, and glycosylation of the CpTSP protein family in C. parvum. The results show that these proteins are modified with C-, O-, and N-linked glycans and are found on the cell surface and in secretory pathway-like structures. The study also reveals the presence of CpTSP1 in sporozoites and meronts, shedding new light on potential vaccine targets for cryptosporidiosis.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Jessica M. Lewis, Nichollas E. Scott
Summary: CRISPRi was used to investigate the effects of silencing O-linked glycosylation in four species of Burkholderia. The results showed that inducible silencing of PglL did not abolish glycosylation completely and did not lead to phenotypic changes or alterations in proteome associated with glycosylation null strains. In addition, high levels of rhamnose induction of CRISPRi had extensive impacts on the Burkholderia proteomes, making it difficult to determine the specific effects driven by CRISPRi guides without appropriate controls.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Genetics & Heredity
Paarthiphan Elankumuran, Glenn F. Browning, Marc S. Marenda, Amanda Kidsley, Marwan Osman, Marisa Haenni, James R. Johnson, Darren J. Trott, Cameron J. Reid, Steven P. Djordjevic
Summary: ST372 is the major Escherichia coli sequence type in dogs globally and is sporadically responsible for extraintestinal infections in humans. However, it is unclear whether ST372 strains from dogs and humans represent shared or distinct populations. In this study, the authors conducted bioinformatics analyses on 407 ST372 E. coli whole-genome sequences to characterize their epidemiological features, population structure, and associated accessory genomes. The results confirm that dogs are the dominant host of ST372, with distinct clusters within the population structure exhibiting different O:H types. Evidence of transmission between dogs and humans within different clusters was also found.
MICROBIAL GENOMICS
(2023)
Article
Microbiology
Max L. Cummins, Dmitriy Li, Aeman Ahmad, Rhys Bushell, Amir H. Noormohammadi, Dinidu S. Wijesurendra, Andrew Stent, Marc S. Marenda, Steven P. Djordjevic
Summary: Bacterial chondronecrosis with osteomyelitis (BCO) is a problem in the poultry industry, but its pathogenesis is not well-studied. This study analyzed 205 APEC(BCO) genome sequences and found that APEC(BCO) and APEC(colibac) are similar in phylogeny and genotype. APEC(BCO) frequently carry ColV-like plasmids with similar VAGs as APEC(colibac). The study provides insights for the management and treatment of lameness in poultry.
Article
Infectious Diseases
Yohannes E. Messele, Darren J. Trott, Mauida F. Hasoon, Tania Veltman, Joe P. McMeniman, Stephen P. Kidd, Steven P. Djordjevic, Kiro R. Petrovski, Wai Y. Low
Summary: The genetic characteristics and phylogenetic relationships among Escherichia coli isolates from cattle, pigs, poultry, and humans were analyzed using whole genome sequencing data. Most cattle and pig isolates belonged to phylogroups A and B1, while avian and human isolates belonged to B2 and D. Some cattle isolates carried extended-spectrum and AmpC beta-lactamase genes. The results indicate that cattle isolates from feedlots pose a reduced risk of being a source of clinically important antimicrobial-resistant E. coli.
Article
Biochemical Research Methods
Ashleigh L. Dale, Lok Man, Stuart J. Cordwell
Summary: Lysine acetylation is a reversible post-translational modification that plays a dynamic role in bile resistance and bacterial protein function. The study identified a large number of acetylated lysines in the gastrointestinal pathogen Campylobacter jejuni, with potential implications for its interaction with fibronectin.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Multidisciplinary Sciences
Mariana G. Sartorio, Evan J. Pardue, Nichollas E. Scott, Mario F. Feldman
Summary: Extracellular vesicles are produced in all three domains of life, and their biogenesis has common ancient origins in eukaryotes and archaea. Bacterial vesicles were discovered several decades ago, but there is skepticism about their biological relevance due to the lack of established biogenesis mechanisms. However, a study on Bacteroides thetaiotaomicron (Bt) showed that OMV production in bacteria is a highly regulated process, with OMVs playing key physiological roles through adaptation of their cargo for utilization of different polysaccharides.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Microbiology
Tamara Alhamami, Piklu Roy Chowdhury, Henrietta Venter, Tania Veltman, Alec Truswell, Sam Abraham, Sylvia A. Sapula, Mandi Carr, Steven P. Djordjevic, Darren J. Trott
Summary: Pasteurella multocida isolates from Australian feedlot cattle with bovine respiratory disease exhibited significant genetic diversity, with different capsular serogroups, lipopolysaccharide genotypes, and sequence types. Additionally, antibiotic resistance was predominantly observed in certain sequence types. The study provides insights into the genomic diversity and antimicrobial resistance associations of P. multocida in Australia.
VETERINARY MICROBIOLOGY
(2023)
Article
Microbiology
Mauida F. Hasoon, Veronica M. Jarocki, Majed H. Mohammed, Steven P. Djordjevic, Hiu Ying Esther Yip, Mandi Carr, Aliakbar Khabiri, Ania Ahani Azari, Reza Amanollahi, Raziallah Jafari Jozani, Brodhi Carracher, Joanne Mollinger, Ania T. Deutscher, Farhid Hemmatzadeh, Darren J. Trott
Summary: Antimicrobial susceptibility of Australian Mycoplasma bovis isolates has not been reported. This study examined minimal inhibitory concentrations (MICs) of 12 antimicrobials against Australian M. bovis isolates and used whole genome sequencing to identify point mutations in target genes associated with high macrolide MICs. Most samples from bovine respiratory disease cases tested positive for M. bovis. The majority of isolates had low MICs for several antimicrobials, but a small proportion exhibited high MICs for macrolides and lincosamides. Whole genome sequencing revealed mutations in the 23S rRNA gene associated with macrolide resistance. Monitoring for emerging macrolide resistance in Australian M. bovis isolates is needed.
VETERINARY MICROBIOLOGY
(2023)
Article
Microbiology
Piklu Roy Chowdhury, Priyanka Hastak, Matthew Demaere, Ethan Wyrsch, Dmitriy Li, Paarthiphan Elankumaran, Monika Dolejska, Glenn F. Browning, Mark S. Marenda, Thomas Gottlieb, Elaine Cheong, John Merlino, Garry S. A. Myers, Steven P. Djordjevic
Summary: This study performed a comprehensive analysis of 925 genomes of extraintestinal pathogenic Escherichia coli (ExPEC) ST38, revealing two clades and several clusters associated with specific blaCTX-M alleles. The study also identified various virulence genes carried by poorly characterized plasmids. Multiple potential inter-host and host-environment transmission events were also identified.
Article
Genetics & Heredity
Dmitriy Li, Paarthiphan Elankumaran, Timothy Kudinha, Amanda K. Kidsley, Darren J. Trott, Veronica Maria Jarocki, Steven Philip Djordjevic
Summary: Extraintestinal pathogenic Escherichia coli (ExPEC) are the most frequent cause of urinary tract infections (UTIs) globally. Whole genome sequencing (WGS) of E. coli isolates from a regional hospital in Australia in 2006 revealed several common sequence types and identified specific virulence plasmids. In addition, closely related isolates from the same patient associated with different pathologies and evidence of strain-sharing events involving isolates sourced from companion and wild animals were identified.
MICROBIAL GENOMICS
(2023)
