Review
Environmental Sciences
Mohammad Y. Ashfaq, Dana A. Da'na, Mohammad A. Al-Ghouti
Summary: Bacteria play diverse roles in the environment, with MALDI-TOF MS technology gaining attention for routine bacterial identification. This technique has been applied in various environmental studies, showing benefits in rapid and cost-effective bacteria identification.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2022)
Article
Biochemistry & Molecular Biology
Xia Wang, Guanqi Wu, Shuo Han, Jingjing Yang, Xiangwei He, Haifang Li
Summary: Plant endophytic bacteria play important roles in plant growth and stress resistance. This study identified and classified endophytic bacteria in Populus based on MALDI-TOF MS data and 16S rRNA gene sequencing, and verified the classification capacity of protein mass fingerprints. The results provide a valuable reference for differentiating and identifying endophytic bacteria.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Microbiology
Praveen Rahi, Estelle Muhle, Cyril Scandola, Gerald Touak, Dominique Clermont
Summary: This study utilized a polyphasic taxonomy approach to accurately classify six strains within the Enterobacter cloacae complex (ECC). The 16S rRNA gene-based phylogeny failed to group all ECC species into a monophyletic cluster, while genome sequence-based phylogenetic approaches successfully grouped all species. A new species named Enterobacter pasteurii sp. nov. was proposed based on comprehensive genotypic and phenotypic characterizations.
MICROBIOLOGY SPECTRUM
(2023)
Article
Chemistry, Analytical
Jiaojiao Sun, Haimei Shi, Yuyan Xue, Wenmin Cheng, Menghuan Yu, Chuanfan Ding, Fuxing Xu, Shaoning Yu
Summary: The accuracy of bacterial identification based on MALDI-TOF MS can be affected by functional proteins, releasing bacteria from functional material can increase accuracy.
Article
Biotechnology & Applied Microbiology
Alexandr Nemec, Lenka Radolfova-Krizova, Martina Maixnerova, Matej Nemec, Petra Spanelova, Renata Safrankova, Ondrej Sedo, Bruno S. Lopes, Paul G. Higgins
Summary: This study identified a novel group of 26 Acinetobacter strains (T24) forming a distinct clade within the genus based on core genome phylogenetic analysis. The strains exhibited differences in carbon source assimilation tests and led to the proposal of two new species, Acinetobacter terrae and Acinetobacter terrestris, associated with terrestrial ecosystems.
SYSTEMATIC AND APPLIED MICROBIOLOGY
(2021)
Article
Microbiology
Adriana Calderaro, Mirko Buttrini, Benedetta Farina, Sara Montecchini, Monica Martinelli, Federica Crocamo, Maria Cristina Arcangeletti, Carlo Chezzi, Flora De Conto
Summary: Colistin resistance is a major threat to global public health, and this study evaluated a MALDI-TOF mass spectrometry peak-based assay to distinguish colistin resistant and susceptible E. coli strains. A classifying algorithm model was developed, with SNN and GA algorithms showing the best performances in recognizing strains.
Review
Biochemistry & Molecular Biology
Daria Janiszewska, Malgorzata Szultka-Mlynska, Pawel Pomastowski, Boguslaw Buszewski
Summary: The quick and accurate identification of microorganisms and the study of antibiotic resistance are crucial in various fields. MALDI-TOF MS is a rapidly growing identification method that allows for a broad spectrum of data, providing insights into the characteristics of microorganisms and their resistance mechanisms.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Infectious Diseases
Eugene Sheck, Andrey Romanov, Valeria Shapovalova, Elvira Shaidullina, Alexey Martinovich, Natali Ivanchik, Anna Mikotina, Elena Skleenova, Vladimir Oloviannikov, Ilya Azizov, Vera Vityazeva, Alyona Lavrinenko, Roman Kozlov, Mikhail Edelstein
Summary: This study assessed the prevalence, species distribution, antimicrobial resistance patterns, and carbapenemase gene content of clinical Acinetobacter non-baumannii (Anb) isolates. It also evaluated the performance of MALDI-TOF MS systems for the species-level identification of Anb isolates. The findings revealed the presence of 14 Anb species, with A. pittii being the most abundant, and the first-time identification of two environmental species in clinical samples.
Article
Microbiology
Eloise J. Busby, Ronan M. M. Doyle, Clara Leboreiro Babe, Kathryn A. A. Harris, Damien Mack, Gema Mendez-Cervantes, Denise M. M. O'Sullivan, Vicky Pang, Zahra Sadouki, Priya Solanki, Jim F. F. Huggett, Timothy D. D. McHugh, Emmanuel Q. Q. Wey
Summary: Managing the transmission of antimicrobial resistance requires reliable methods for tracking outbreaks. MALDI-TOF MS was compared with orthogonal approaches for strain typing, including WGS and FTIR, for Acinetobacter baumannii isolates associated with a healthcare-associated infection event. Reliable molecular typing methods can help to trace transmission routes and manage outbreaks.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Alexandr Nemec, Lenka Radolfova-Krizova, Martina Maixnerova, Violetta Shestivska, Petra Spanelova, Paul G. Higgins
Summary: This study investigated a taxonomically novel group within the genus Acinetobacter, finding that five strains exhibited unique characteristics in terms of genome sequences, strain features, and molecular mass spectra compared to known Acinetobacter species. As a result, these five strains represent a new environmental species, proposed to be named Acinetobacter silvestris sp. nov.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Microbiology
Hazan Zengin Canalp, Banu Bayraktar
Summary: This study investigated the accuracy and feasibility of a rapid identification method for blood pathogens and found that the RID method significantly reduced the turnaround time compared to the SIRID method, making it a valuable tool for patient management.
MICROBIOLOGY SPECTRUM
(2021)
Review
Microbiology
Fernando Sanchez-Juanes, Noelia Calvo Sanchez, Moncef Belhassen Garcia, Carmen Vieira Lista, Raul Manzano Roman, Rufino Alamo Sanz, Antonio Muro Alvarez, Juan Luis Munoz Bellido
Summary: Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a simple, fast, and specific method used for bacterial identification, and has also been shown to be useful for identifying certain parasites and arthropod vectors. Fast, simple, and reliable methods for identifying arthropod vectors are crucial for controlling diseases transmitted by these vectors.
Review
Spectroscopy
Natalija Topic Popovic, Snjezana P. Kazazic, Krunoslav Bojanic, Ivancica Strunjak-Perovic, Rozelindra Coz-Rakovac
Summary: MALDI-TOF MS is an excellent tool for bacterial identification with high throughput, sensitivity, and specificity. Lack of standardized protocol and impact of various factors on its performance require specific optimizations based on bacterial representatives and strain requirements.
MASS SPECTROMETRY REVIEWS
(2021)
Article
Biochemistry & Molecular Biology
Michal Zloch, Ewelina Maslak, Wojciech Kupczyk, Marek Jackowski, Pawel Pomastowski, Boguslaw Buszewski
Summary: This study evaluated the use of different culture media in reflecting the microbial compositions of diabetic foot infections in Poland. The results showed significant differences in species coverage and efficiency between the investigated media. Selecting the appropriate media set can significantly improve the accuracy of reflecting the microbial compositions of diabetic foot infections.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Microbiology
Alexandr Nemec, Lenka Radolfova-Krizova, Martina Maixnerova, Matej Nemec, Violetta Shestivska, Petra Spanelova, Martina Kyselkova, Gottfried Wilharm, Paul G. Higgins
Summary: We studied a novel taxon of the genus Acinetobacter and identified its distinct characteristics through genome analysis and mass spectrometry. These novel strains have unique biological features that differentiate them from known Acinetobacter species. The taxon is widely distributed in various ecological and geographical environments.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Engineering, Environmental
Alper James G. Alcaraz, David Potesil, Kamil Mikulasek, Derek Green, Bradley Park, Connor Burbridge, Kerstin Bluhm, Othman Soufan, Taylor Lane, Marek Pipal, Markus Brinkmann, Jianguo Xia, Zbynek Zdrahal, David Schneider, Doug Crump, Niladri Basu, Natacha Hogan, Markus Hecker
Summary: This study aimed to develop a comprehensive early life stage toxicity pathway model for fish exposed to estrogenic chemicals, rooted in mechanistic toxicology. The integration of omics data improved the interpretation of perturbations in early life stage fish, showing promise as a replacement for standard adult live animal tests. The study provided evidence of conservation of toxicity pathways across levels of biological organization.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Dominik Hrebik, Tibor Fuzik, Maria Gondova, Lenka Smerdova, Athanassios Adamopoulos, Ondrej Sedo, Zbynek Zdrahal, Pavel Plevka
Summary: This study elucidated the structure of the rhinovirus 14 complex with ICAM-1, showing how this complex is crucial for virus activation and genome release. The binding of ICAM-1 induces conformational changes in the capsid of rhinovirus 14, priming it for activation and genome release under acidic pH conditions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Oncology
Marian Babincak, Rastislav Jendzelovsky, Jan Kosuth, Martin Majernik, Jana Vargova, Kamil Mikulasek, Zbynek Zdrahal, Peter Fedorocko
Summary: Hypoxic conditions in tumors often lead to poor prognosis in cancer patients. Skyrin (SKR), a plant metabolite, has shown significant efficacy against cancer cells, while sparing healthy cells, and can reverse TRAIL resistance in hypoxic conditions. This suggests SKR could be a potential anticancer drug, especially as an adjuvant to TRAIL treatment in hypoxic and therapy-resistant tumors.
Article
Cell Biology
Petra Paclikova, Tomasz Witold Radaszkiewicz, David Potesil, Jakub Harnos, Zbynek Zdrahal, Vitezslav Bryja
Summary: This study investigates the role of individual human DVL paralogs in the Wnt pathway, showing that DVL is essential for multiple aspects of Wnt signal transduction. Different DVL paralogs have varying effects on signal strength, with the ratio of individual paralogs being more important than the total amount.
CELLULAR SIGNALLING
(2021)
Article
Environmental Sciences
Alper James G. Alcaraz, Shaina Baraniuk, Kamil Mikulasek, Bradley Park, Taylor Lane, Connor Burbridge, Jessica Ewald, David Potesil, Jianguo Xia, Zbynek Zdrahal, David Schneider, Doug Crump, Niladri Basu, Natacha Hogan, Markus Brinkmann, Markus Hecker
Summary: Current approaches in chemical hazard assessment, which rely on live animal testing, face challenges due to concerns about time, cost, and ethics. This study developed a new approach using a short-term embryo assay to predict the toxicity of fluoxetine and obtained protective points-of-departure.
ENVIRONMENTAL POLLUTION
(2022)
Article
Endocrinology & Metabolism
Pavel Hruska, Jan Kucera, Matej Pekar, Pavol Holeczy, Miloslav Mazur, Marek Buzga, Daniela Kuruczova, Peter Lenart, Jana Fialova Kucerova, David Potesil, Zbynek Zdrahal, Julie Bienertova-Vasku
Summary: The study compared the proteomic profiles of mature adipocytes from different adipose tissue depots, with findings showing that subcutaneous adipocytes are more active in vesicular transport, secretion, and lipid metabolism, while visceral adipocytes have higher protein expression related to mitochondrial energy metabolism and translational or biosynthetic activity.
JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM
(2022)
Article
Cell & Tissue Engineering
Sebastiano Giallongo, Daniela Rehakova, Tommaso Biagini, Oriana Lo Re, Priyanka Raina, Gabriela Lochmanova, Zbynek Zdrahal, Igor Resnick, Pille Pata, Illar Pata, Martin Mistrik, Joao Pedro de Magalhaes, Tommaso Mazza, Irena Koutna, Manlio Vinciguerra
Summary: The study identifies the splicing isoform macroH2A1.1 as a potential regulator of DNA damage repair (DDR) during iPSC reprogramming. MacroH2A1.1 overexpression enhances DDR efficiency through specific activation of the nonhomologous end joining (NHEJ) repair pathway. It also improves iPSC reprogramming, indicating its importance in maintaining genome stability and therapeutic potential.
Article
Chemistry, Analytical
Petra Jezkova, Jana Skrickova, Gejza Wimmer, Jana Zelinkova, Zbynek Zdrahal, Erika Lattova
Summary: In this study, the advantage of phenylhydrazine labeling for the detection and discrimination of sialic acid linkages was demonstrated. The results showed that phenylhydrazine-labeled sialylated oligosaccharides can be easily recognized and produce favorable fragmentation patterns during mass spectrometry experiments. A comparison of two esterification methods showed that methylation exhibited slightly higher linkage specificity. The simplicity and effectiveness of this methodology were confirmed using model compounds and serum samples.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Iosif Kaurov, Jiri Heller, Sebastian Deisenhammer, David Potesil, Zbynek Zdrahal, Hassan Hashimi
Summary: The mitochondrial protein import machinery in trypanosomatids differs greatly from well-studied models such as baker's yeast. A central catalyst of the mitochondrial intermembrane space import and assembly pathway (MIA), Mia40, is missing in trypanosomatids. TbMic20, a thioredoxin-like subunit of the mitochondrial contact site and cristae organizing system (MICOS), was proposed as a potential replacement for Mia40. However, the study shows that TbMic20 is unlikely to be a true replacement for Mia40 and plays an unresolved role in the stability and/or import of MIA substrates in trypanosomatids.
MOLECULAR AND BIOCHEMICAL PARASITOLOGY
(2022)
Article
Environmental Sciences
Carly Colville, Alper James Alcaraz, Derek Green, Bradley Park, Jianguo Xia, Othman Soufan, Pavel Hruska, David Potesil, Zbynek Zdrahal, Doug Crump, Niladri Basu, Natacha Hogan, Markus Hecker
Summary: This study investigated the mechanistic toxicity of fluoxetine (FLX) in adult fathead minnows using new approach methodologies (NAMs). The results revealed that high concentrations of FLX caused molecular toxicity changes in the liver and brain, leading to lipid-type vacuolation in liver hepatocytes and alterations in serotonin-related signaling processes and reproductive behavior in the brain.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Cell Biology
Zankruti Dave, Olga Vondalova Blanarova, Stepan Cada, Pavlina Janovska, Nikodem Zezula, Martin Behal, Katerina Hanakova, Sri Ranjani Ganji, Pavel Krejci, Kristina Gomoryova, Helena Peschelova, Michal Smida, Zbynek Zdrahal, Sarka Pavlova, Jana Kotaskova, Sarka Pospisilova, Vitezslav Bryja
Summary: In this study, the functional interaction between Lyn and ROR1 was analyzed, and it was found that Lyn could phosphorylate ROR1 and recruit c-CBL. The Lyn-mediated phosphorylation of ROR1 was shown to inhibit the migration and chemotactic properties of CLL cells, as demonstrated by the use of a Lyn inhibitor.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Pathology
Ximena M. Muresan, Eva Slabakova, Jirina Prochazkova, Stanislav Drapela, Radek Fedr, Marketa Pickova, Ondrej Vacek, Rachel Vichova, Tereza Suchankova, Jan Bouchal, Daniela Kurfurstova, Milan Kral, Tereza Hulinova, Radek P. Sykora, Vladimir Student, Vaclav Hejret, Wytske M. van Weerden, Martin Puhr, Vaclav Pustka, David Potesil, Zbynek Zdrahal, Zoran Culig, Karel Soucek
Summary: TLR3 may be involved in the progression and metastasis of prostate cancer by inducing cytokine secretion and regulating cell motility, migration, and tumor invasiveness.
AMERICAN JOURNAL OF PATHOLOGY
(2022)
Article
Cell Biology
Masa Zrimsek, Hana Kucharikova, Kristina Draganic, Pavlina Dobrovolna, Verena Heiss Spornberger, Lisa Winkelmayer, Melanie R. Hassler, Gabriela Lochmanova, Zbynek Zdrahal, Gerda Egger
Summary: Histone deacetylases (HDACs) play important roles in regulating genomic stability, cell cycle, cell death, and differentiation, particularly in tumorigenesis. This study investigated the effects of HDAC inhibition in tumor cells using drug treatment and gene deletion approaches. Changes in protein expression and acetylation were measured, revealing alterations in overall protein abundance and increased acetylation of histones and non-histone proteins, with potential implications for metabolic and DNA damage pathways.
Article
Multidisciplinary Sciences
Milan Hluchy, Pavla Gajduskova, Igor Ruiz de los Mozos, Michal Rajecky, Michael Kluge, Benedict-Tilman Berger, Zuzana Slaba, David Potesil, Elena Weiss, Jernej Ule, Zbynek Zdrahal, Stefan Knapp, Kamil Paruch, Caroline C. Friedel, Dalibor Blazek
Summary: RNA splicing, regulated by the spliceosome, is crucial for gene expression. CDK11 phosphorylates SF3B1 during spliceosome activation, which is important for spliceosome assembly and splicing regulation. Inhibition of CDK11 leads to defective spliceosome activation and disrupts the splicing process.
Article
Plant Sciences
Michal Stroch, Vaclav Karlicky, Petr Ilik, Iva Ilikova, Monika Opatikova, Lukas Nosek, Pavel Pospisil, Marika Svrckova, Marek Rac, Pavel Roudnicky, Zbynek Zdrahal, Vladimir Spunda, Roman Kouril
Summary: The adaptation of higher plants to different light intensities involves reorganization of the photosynthetic apparatus. Spruce has a distinct strategy compared to Arabidopsis in response to light acclimation, where it does not modify its PSII/PSI ratio and PSII antenna size but relies on a stable Chl a/b ratio. The crucial photoprotective mechanism in spruce involves a large PSII antenna with weakly bound LHCIIs and sensitive control of PSI level.
PHOTOSYNTHESIS RESEARCH
(2022)
