Article
Biochemistry & Molecular Biology
Md Arifur Rahman, Ardeshir Amirkhani, Farhana Parvin, Durdana Chowdhury, Mark P. Molloy, Anand Kumar Deva, Karen Vickery, Honghua Hu
Summary: This study aimed to investigate the differences in protein components between dry surface biofilms (DSBs) and hydrated biofilms. Using high-throughput mass spectrometry, the study found that proteins associated with peptidoglycan biosynthesis pathway were upregulated in 12-day DSBs, while proteins associated with energy metabolism were upregulated in 12-day hydrated biofilms. However, the levels of gene expression did not fully correspond with the protein levels.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Ho Le Han, Reneelyn E. Danganan, Zhun Li, Na-Ri Shin, Reuel M. Bennett, Gina R. Dedeles, Song-Gun Kim
Summary: A novel extremely halophilic archaeon, strain RHB-C-T, was isolated from a saturated brine pond in Bolinao, Pangasinan, Philippines. It belongs to the genus Halorubrum and is proposed as a new species Halorubrum salinarum sp. nov.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Environmental Sciences
M. J. Romeu, D. Dominguez-Perez, D. Almeida, J. Morais, M. J. Araujo, H. Osorio, A. Campos, V. Vasconcelos, F. J. Mergulhao
Summary: Cyanobacterial molecular biology can identify pathways affecting biofouling organisms adhesion and settlement, providing novel antifouling strategies. Proteomic analyses offer insights into cyanobacteria adaption to different environments. Qualitative studies in some strains show limited knowledge on protein expression. Conducting quantitative proteomic analysis on biofilm cells from a filamentous strain reveals potential protein differences between biofilms formed on different surfaces under varying hydrodynamic conditions.
ENVIRONMENTAL RESEARCH
(2021)
Article
Microbiology
Peng Li, Chaminda J. Seneviratne, Qingxian Luan, Lijian Jin
Summary: Candida albicans biofilms exhibit significantly increased antifungal resistance, with a higher survival rate and complex cellular pathways in response to caspofungin treatment. Key proteins involved in cell wall integrity, stress response, and metabolic activities play a crucial role in the antifungal resistance of C. albicans biofilms.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Parsifal F. Islas-Morales, Anny Cardenas, Maria J. Mosqueira, Luis Felipe Jimenez-Garcia, Christian R. Voolstra
Summary: Nucleoli are subcellular compartments responsible for transcription and maturation of pre-ribosomal RNAs. This study provides evidence for the presence of nucleolus-like subcellular domains in TACK crenarchaeon Saccharolobus solfataricus, suggesting that these domains are not exclusive to eukaryotes.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Marine & Freshwater Biology
Ruonan Jia, Shaojun Huang, Wanying Zhai, Shouwen Jiang, Wenhao Li, Faxiang Wang, Qianghua Xu
Summary: Using mass spectrometry technology, this study found significant differences in the head kidney proteome of Antarctic icefish compared to red-blooded fish. The expression of proteins involved in erythropoiesis and heme biogenesis was downregulated, while those associated with lymphocytes and megakaryocytes were upregulated, suggesting a shift in hematopoiesis in the icefish head kidney. These findings provide valuable data for studying immunity and hematopoiesis in different species.
Article
Biochemistry & Molecular Biology
Ying-Chao Ma, Wan-Ping Su, Zhong-Shi Sun, Zu-Xin Zhang, Peng-Yu Li, Bo Zhang, Li-Ying Sui
Summary: This study explored the factors affecting the extraction efficiency of C50 carotenoids through single-factor and orthogonal experiments. The results showed that C50 carotenoids could be effectively extracted by suspending and homogenizing cell pellets in methanol, incubating in the dark at 30 degrees C, and drying over vacuum rotary evaporation. The main component of carotenoids extracted from Halorubrum sp. HRM-150 was bacterioruberin, which exhibited high antioxidant capacity.
PROCESS BIOCHEMISTRY
(2023)
Article
Microbiology
Chi Young Hwang, Eui-Sang Cho, Won Jong Rhee, Eunjung Kim, Myung-Ji Seo
Summary: In this study, a novel haloarchaeal species capable of producing C-50 carotenoid was isolated from seawater near Yeongheung Island. The derived bacterioruberin showed antioxidant activity, suggesting its potential applications in health and nutrition.
JOURNAL OF MICROBIOLOGY
(2022)
Article
Environmental Sciences
Simon Mills, Anna Christine Trego, John Ward, Juan Castilla-Archilla, Johannes Hertel, Ines Thiele, Piet N. L. Lens, Umer Zeeshan Ijaz, Gavin Collins
Summary: This study utilized laboratory-scale bioreactors to investigate the formation, maturation, disintegration, and re-formation of new granules. The findings highlighted distinct morphological features of granule sizes and biofilm development stages, which are important for maximizing bioreactor performance.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2021)
Article
Plant Sciences
Yaqiong Wu, Zhengjin Huang, Chunhong Zhang, Chong Shi, Lianfei Lyu, Weilin Li, Wenlong Wu
Summary: This study found that 50% shading can improve the growth index of blueberry and enrich the flavonoid biosynthesis. Additionally, the analysis of the interaction network of differentially expressed proteins revealed key regulatory factors.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Microbiology
Changsu Lee, Hye Seon Song, Se Hee Lee, Joon Yong Kim, Jin-Kyu Rhee, Seong Woon Roh
Summary: In this study, three facultatively oligotrophic haloarchaea were isolated from solar salt and their complete genomes were sequenced, revealing the presence of carbohydrate-active enzyme genes and stress-tolerance protein genes that may have industrial applications. The genome data generated will facilitate further research on halophilic strains and their potential industrial uses.
ARCHIVES OF MICROBIOLOGY
(2021)
Article
Chemistry, Applied
Jinqiu Wang, Xuefei Wen, Yayu Zhang, Pingping Zou, Lei Cheng, Renyou Gan, Xiang Li, Dayu Liu, Fang Geng
Summary: The study systematically investigated the differences in Dictyophora indusiata fruiting bodies between peach-shaped and mature stages postharvest, revealing changes in protein and metabolite expression and highlighting key metabolic pathways and biological changes during maturation.
Article
Multidisciplinary Sciences
Karolina Kwasek, Young Min Choi, Hanping Wang, Kichoon Lee, John Mark Reddish, Macdonald Wick
Summary: This study compared the skeletal muscle proteomic profiles and expression levels of myogenic regulatory factors between fast- and slow-growing yellow perch, identifying different expression patterns in relation to muscle growth dynamics. Fast-growing perch exhibited greater body weight, muscle fiber hypertrophy, mosaic hyperplasia, and higher expression of metabolic enzymes and myogenic regulatory factors compared to slow-growing fish.
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Applied
Mingyi Yang, Qianwei Lin, Zisheng Luo, Zhaojun Ban, Xihong Li, Russel J. Reiter, Shuang Zhang, Lei Wang, Ze Liang, Ming Qi, Li Li
Summary: The protein abundance and metabolic profile in watercored apple were characterized using a combined proteomic and metabolomic approach. The results showed that carbohydrate metabolism, including sucrose and sugar alcohol accumulation, was prioritized enriched in watercored apple. The involvement of calcium signaling in watercore development was implied by the overlap of differently abundant proteins involved in calcium ion binding, starch, and sucrose metabolism. Sucrose synthase protein, involved in calcium ion binding and sugar metabolism, was identified as a potential basis for apple watercore development.
Article
Engineering, Biomedical
Xiaoxia Kang, Xiaoxiao Yang, Conglin Guo, Yuechen Li, Haiwei Ji, Yuling Qin, Li Wu
Summary: Biofilms pose challenges in terms of bacterial characteristics and treatment, thus requiring the development of novel materials and strategies. This review provides a comprehensive summary of effective strategies and methodologies applicable across industries, including the process of biofilms formation, intervention strategies, treatment strategies, and antibacterial substances.
MATERIALS TODAY BIO
(2023)
Article
Biotechnology & Applied Microbiology
Sin Yin Wong, James C. Charlesworth, Nicole Benaud, Brendan P. Burns, Belinda C. Ferrari
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2020)
Letter
Biochemistry & Molecular Biology
Anne Poljak, Perminder Sachdev
MOLECULAR PSYCHIATRY
(2021)
Article
Microbiology
Yan Liao, Solenne Ithurbide, Christian Evenhuis, Jan Lowe, Iain G. Duggin
Summary: In some archaea, FtsZ1 and FtsZ2 have distinct functions in assembling and constricting the division ring, playing key roles in the mechanism of archaeal cell division.
NATURE MICROBIOLOGY
(2021)
Article
Microbiology
Yan Liao, Verena Vogel, Sabine Hauber, Juergen Bartel, Omer S. Alkhnbashi, Sandra Maass, Thandi S. Schwarz, Rolf Backofen, Doerte Becher, Iain G. Duggin, Anita Marchfelder
Summary: The transcription factor CdrS plays a central role in coordinating metabolism and cell division in the archaeon Haloferax volcanii. It regulates the expression of genes associated with cell division, protein degradation, and metabolism. Additionally, CdrS has multiple DNA-binding sites and is involved in the regulation of essential cell division genes, suggesting its sophisticated role in coordinating cellular pathways.
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
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
Zhiguang Qiu, Chanyarat Paungfoo-Lonhienne, Jun Ye, Axa Gonzalez Garcia, Ian Petersen, Lawrence Di Bella, Richard Hobbs, Minka Ibanez, Marijke Heenan, Weijin Wang, Steven Reeves, Susanne Schmidt
Summary: The study examines the effects of biofertilizers formulated with organic waste, mineral nitrogen, or plant growth-promoting rhizobacteria on nitrogen efficiency. The results from commercial sugarcane farms indicate that using biofertilizers with a 60% nitrogen rate can improve crop yield and induce changes in soil microbial communities.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Khawar S. Siddiqui, Anne Poljak, Haluk Ertan, Wallace Bridge
Summary: This article introduces a method for determining enzyme activity based on isothermal titration calorimetry, which can solve the problem of most enzymes being unsuitable for spectrophotometric assays. The method is suitable for teaching laboratory classes and provides a flexible and easy-to-use method for studying the functional characteristics of uncharacterized enzymes.
BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION
(2022)
Article
Multidisciplinary Sciences
Kristie Stefanoska, Mehul Gajwani, Amanda R. P. Tan, Holly Ahel, Prita R. Asih, Alexander Volkerling, Anne Poljak, Arne Ittner
Summary: Hyperphosphorylation of neuronal tau protein is a characteristic of neurodegenerative tauopathies such as Alzheimer's disease. This study reveals that tau phosphorylation is regulated by interdependence, where initial site-specific phosphorylation triggers subsequent multi-site phosphorylation. The interdependence of specific tau residues determines the propagation of phosphorylation, and targeting the master sites and p38 tau kinase can effectively reduce hyperphosphorylation.
Article
Biochemistry & Molecular Biology
Emmanuel Prikas, Esmeralda Paric, Prita R. Asih, Kristie Stefanoska, Holly Stefen, Thomas Fath, Anne Poljak, Arne Ittner
Summary: Microtubule-associated protein tau plays a central role in Alzheimer's disease and other tauopathies. This study used proximity-labelling proteomics to examine tau interactions in neurons and mouse brains. The results show that tau interacts with proteins involved in cytoskeletal regulation, synaptic vesicle regulation, and postsynaptic receptor regulation. These interactions are related to Parkinson's disease, Alzheimer's disease, and prion disease. Furthermore, the study demonstrates that tau interacts with N-ethylmaleimide sensitive fusion protein (NSF) and reduces its activity, leading to altered trafficking of AMPA-type glutamate receptors (AMPAR) and enhanced memory formation.
Review
Clinical Neurology
Satoshi Hosoki, Gurpreet K. Hansra, Tharusha Jayasena, Anne Poljak, Karen A. Mather, Vibeke S. Catts, Ruslan Rust, Abhay Sagare, Jason C. Kovacic, Amy Brodtmann, Anders Wallin, Berislav V. Zlokovic, Masafumi Ihara, Perminder S. Sachdev
Summary: This review examines the role of large and small vessel disease in vascular cognitive impairment and dementia (VCID) and considers the underlying pathophysiological processes that lead to vascular brain injury. It discusses the potential of key molecules involved in these processes as molecular biomarkers and the challenges in translating these biomarkers into clinical application.
NATURE REVIEWS NEUROLOGY
(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)