Pub Date : 2021-11-25eCollection Date: 2022-01-03DOI: 10.15698/mic2022.01.767
Mathieu Durand, Philippe Thibault, Simon Lévesque, Ariane Brault, Alex Carignan, Louis Valiquette, Philippe Martin, Simon Labbé
The early diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is required to identify and isolate contagious patients to prevent further transmission of SARS-CoV-2. In this study, we present a multitarget real-time TaqMan reverse transcription PCR (rRT-PCR) assay for the quantitative detection of SARS-CoV-2 and some of its circulating variants harboring mutations that give the virus a selective advantage. Seven different primer-probe sets that included probes containing locked nucleic acid (LNA) nucleotides were designed to amplify specific wild-type and mutant sequences in Orf1ab, Envelope (E), Spike (S), and Nucleocapsid (N) genes. Furthermore, a newly developed primer-probe set targeted human β2-microglobulin (B2M) as a highly sensitive internal control for RT efficacy. All singleplex and fourplex assays detected ≤ 14 copies/reaction of quantified synthetic RNA transcripts, with a linear amplification range of nine logarithmic orders. Primer-probe sets for detection of SARS-CoV-2 exhibited no false-positive amplifications with other common respiratory pathogens, including human coronaviruses NL63, 229E, OC43, and HKU-1. Fourplex assays were evaluated using 160 clinical samples positive for SARS-CoV-2. Results showed that SARS-CoV-2 viral RNA was detected in all samples, including viral strains harboring mutations in the Spike coding sequence that became dominant in the pandemic. Given the emergence of SARS-CoV-2 variants and their rapid spread in some populations, fourplex rRT-PCR assay containing four primer-probe sets represents a reliable approach to allow quicker detection of circulating relevant variants in a single reaction.
{"title":"Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its first variants in fourplex real-time quantitative reverse transcription-PCR assays.","authors":"Mathieu Durand, Philippe Thibault, Simon Lévesque, Ariane Brault, Alex Carignan, Louis Valiquette, Philippe Martin, Simon Labbé","doi":"10.15698/mic2022.01.767","DOIUrl":"https://doi.org/10.15698/mic2022.01.767","url":null,"abstract":"<p><p>The early diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is required to identify and isolate contagious patients to prevent further transmission of SARS-CoV-2. In this study, we present a multitarget real-time TaqMan reverse transcription PCR (rRT-PCR) assay for the quantitative detection of SARS-CoV-2 and some of its circulating variants harboring mutations that give the virus a selective advantage. Seven different primer-probe sets that included probes containing locked nucleic acid (LNA) nucleotides were designed to amplify specific wild-type and mutant sequences in Orf1ab, Envelope (E), Spike (S), and Nucleocapsid (N) genes. Furthermore, a newly developed primer-probe set targeted human β<sub>2</sub>-microglobulin (B2M) as a highly sensitive internal control for RT efficacy. All singleplex and fourplex assays detected ≤ 14 copies/reaction of quantified synthetic RNA transcripts, with a linear amplification range of nine logarithmic orders. Primer-probe sets for detection of SARS-CoV-2 exhibited no false-positive amplifications with other common respiratory pathogens, including human coronaviruses NL63, 229E, OC43, and HKU-1. Fourplex assays were evaluated using 160 clinical samples positive for SARS-CoV-2. Results showed that SARS-CoV-2 viral RNA was detected in all samples, including viral strains harboring mutations in the Spike coding sequence that became dominant in the pandemic. Given the emergence of SARS-CoV-2 variants and their rapid spread in some populations, fourplex rRT-PCR assay containing four primer-probe sets represents a reliable approach to allow quicker detection of circulating relevant variants in a single reaction.</p>","PeriodicalId":18397,"journal":{"name":"Microbial Cell","volume":null,"pages":null},"PeriodicalIF":4.6,"publicationDate":"2021-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8717086/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39963973","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-10-27eCollection Date: 2021-12-06DOI: 10.15698/mic2021.12.766
Cinzia Klemm, Henry Wood, Grace Heredge Thomas, Guðjón Ólafsson, Mara Teixeira Torres, Peter H Thorpe
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the highly infectious coronavirus disease COVID-19. Extensive research has been performed in recent months to better understand how SARS-CoV-2 infects and manipulates its host to identify potential drug targets and support patient recovery from COVID-19. However, the function of many SARS-CoV-2 proteins remains uncharacterised. Here we used the Synthetic Physical Interactions (SPI) method to recruit SARS-CoV-2 proteins to most of the budding yeast proteome to identify conserved pathways which are affected by SARS-CoV-2 proteins. The set of yeast proteins that result in growth defects when associated with the viral proteins have homologous functions that overlap those identified in studies performed in mammalian cells. Specifically, we were able to show that recruiting the SARS-CoV-2 NSP1 protein to HOPS, a vesicle-docking complex, is sufficient to perturb membrane trafficking in yeast consistent with the hijacking of the endoplasmic-reticulum-Golgi intermediate compartment trafficking pathway during viral infection of mammalian cells. These data demonstrate that the yeast SPI method is a rapid way to identify potential functions of ectopic viral proteins.
{"title":"Forced association of SARS-CoV-2 proteins with the yeast proteome perturb vesicle trafficking.","authors":"Cinzia Klemm, Henry Wood, Grace Heredge Thomas, Guðjón Ólafsson, Mara Teixeira Torres, Peter H Thorpe","doi":"10.15698/mic2021.12.766","DOIUrl":"10.15698/mic2021.12.766","url":null,"abstract":"<p><p>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the highly infectious coronavirus disease COVID-19. Extensive research has been performed in recent months to better understand how SARS-CoV-2 infects and manipulates its host to identify potential drug targets and support patient recovery from COVID-19. However, the function of many SARS-CoV-2 proteins remains uncharacterised. Here we used the Synthetic Physical Interactions (SPI) method to recruit SARS-CoV-2 proteins to most of the budding yeast proteome to identify conserved pathways which are affected by SARS-CoV-2 proteins. The set of yeast proteins that result in growth defects when associated with the viral proteins have homologous functions that overlap those identified in studies performed in mammalian cells. Specifically, we were able to show that recruiting the SARS-CoV-2 NSP1 protein to HOPS, a vesicle-docking complex, is sufficient to perturb membrane trafficking in yeast consistent with the hijacking of the endoplasmic-reticulum-Golgi intermediate compartment trafficking pathway during viral infection of mammalian cells. These data demonstrate that the yeast SPI method is a rapid way to identify potential functions of ectopic viral proteins.</p>","PeriodicalId":18397,"journal":{"name":"Microbial Cell","volume":null,"pages":null},"PeriodicalIF":4.6,"publicationDate":"2021-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8642885/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9106606","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-10-06eCollection Date: 2021-11-01DOI: 10.15698/mic2021.11.764
Giovana Parreira de Aquino, Marco Antonio Mendes Gomes, Roberto Köpke Salinas, Maria Fernanda Laranjeira-Silva
Trypanosomiases and leishmaniases are neglected tropical diseases that have been spreading to previously non-affected areas in recent years. Identification of new chemotherapeutics is needed as there are no vaccines and the currently available treatment options are highly toxic and often ineffective. The causative agents for these diseases are the protozoan parasites of the Trypanosomatidae family, and they alternate between invertebrate and vertebrate hosts during their life cycles. Hence, these parasites must be able to adapt to different environments and compete with their hosts for several essential compounds, such as amino acids, vitamins, ions, carbohydrates, and lipids. Among these nutrients, lipids and fatty acids (FAs) are essential for parasite survival. Trypanosomatids require massive amounts of FAs, and they can either synthesize FAs de novo or scavenge them from the host. Moreover, FAs are the major energy source during specific life cycle stages of T. brucei, T. cruzi, and Leishmania. Therefore, considering the distinctive features of FAs metabolism in trypanosomatids, these pathways could be exploited for the development of novel antiparasitic drugs. In this review, we highlight specific aspects of lipid and FA metabolism in the protozoan parasites T. brucei, T. cruzi, and Leishmania spp., as well as the pathways that have been explored for the development of new chemotherapies.
{"title":"Lipid and fatty acid metabolism in trypanosomatids.","authors":"Giovana Parreira de Aquino, Marco Antonio Mendes Gomes, Roberto Köpke Salinas, Maria Fernanda Laranjeira-Silva","doi":"10.15698/mic2021.11.764","DOIUrl":"https://doi.org/10.15698/mic2021.11.764","url":null,"abstract":"<p><p>Trypanosomiases and leishmaniases are neglected tropical diseases that have been spreading to previously non-affected areas in recent years. Identification of new chemotherapeutics is needed as there are no vaccines and the currently available treatment options are highly toxic and often ineffective. The causative agents for these diseases are the protozoan parasites of the Trypanosomatidae family, and they alternate between invertebrate and vertebrate hosts during their life cycles. Hence, these parasites must be able to adapt to different environments and compete with their hosts for several essential compounds, such as amino acids, vitamins, ions, carbohydrates, and lipids. Among these nutrients, lipids and fatty acids (FAs) are essential for parasite survival. Trypanosomatids require massive amounts of FAs, and they can either synthesize FAs <i>de novo</i> or scavenge them from the host. Moreover, FAs are the major energy source during specific life cycle stages of <i>T. brucei, T. cruzi</i>, and <i>Leishmania</i>. Therefore, considering the distinctive features of FAs metabolism in trypanosomatids, these pathways could be exploited for the development of novel antiparasitic drugs. In this review, we highlight specific aspects of lipid and FA metabolism in the protozoan parasites <i>T. brucei, T. cruzi,</i> and <i>Leishmania</i> spp., as well as the pathways that have been explored for the development of new chemotherapies.</p>","PeriodicalId":18397,"journal":{"name":"Microbial Cell","volume":null,"pages":null},"PeriodicalIF":4.6,"publicationDate":"2021-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8561143/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39736490","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-09-21eCollection Date: 2021-11-01DOI: 10.15698/mic2021.11.763
Lars Kaduhr, Cindy Brachmann, Keerthiraju Ethiraju Ravichandran, James D West, Sebastian Glatt, Raffael Schaffrath
Ubiquitin related modifier 1 (Urm1) is a unique eukaryotic member of the ubiquitin-fold (UbF) protein family and conserved from yeast to humans. Urm1 is dual-functional, acting both as a sulfur carrier for thiolation of tRNA anticodons and as a protein modifier in a lysine-directed Ub-like conjugation also known as urmylation. Although Urm1 conjugation coincides with oxidative stress and targets proteins like 2-Cys peroxiredoxins from yeast (Ahp1) and fly (Prx5), it was unclear how urmylation proceeds molecularly and whether it is affected by the activity of these antioxidant enzymes. An in-depth study of Ahp1 urmylation in yeast from our laboratory (Brachmann et al., 2020) uncovered that promiscuous lysine target sites and specific redox requirements determine the Urm1 acceptor activity of the peroxiredoxin. The results clearly show that the dimer interface and the 2-Cys based redox-active centers of Ahp1 are affecting the Urm1 conjugation reaction. Together with in vivo assays demonstrating that high organic peroxide concentrations can prevent Ahp1 from being urmylated, Brachmann et al. provide insights into a potential link between Urm1 utilization and oxidant defense of cells. Here, we highlight these major findings and discuss wider implications with regards to an emerging link between Urm1 conjugation and redox biology. Moreover, from these studies we propose to redefine our perspective on Urm1 and the molecular nature of urmylation, a post-translational conjugation that may not be that ubiquitin-like after all.
泛素相关修饰因子1 (Ubiquitin related modifier 1, Urm1)是泛素折叠蛋白(ubitin -fold, UbF)家族中一个独特的真核成员,从酵母到人类都是保守的。Urm1具有双重功能,既可以作为tRNA反密码子硫基化的硫载体,也可以作为赖氨酸导向的ub样偶联(也称为urmyation)的蛋白质修饰剂。尽管Urm1结合与氧化应激相吻合,并针对酵母(Ahp1)和苍蝇(Prx5)中的2-Cys过氧化物还毒素等蛋白,但目前尚不清楚Urm1化是如何在分子上进行的,以及它是否受到这些抗氧化酶活性的影响。我们实验室(Brachmann et al., 2020)对酵母中Ahp1酶解的深入研究发现,混杂的赖氨酸靶点和特定的氧化还原需求决定了过氧化物还原素的Urm1受体活性。结果清楚地表明,二聚体界面和Ahp1的2-Cys氧化还原活性中心影响着Urm1的偶联反应。Brachmann等人对Urm1利用与细胞氧化防御之间的潜在联系进行了深入研究,并通过体内实验证明高有机过氧化物浓度可以阻止Ahp1被urmyylation。在这里,我们强调了这些主要发现,并讨论了关于Urm1偶联和氧化还原生物学之间的新兴联系的更广泛的影响。此外,从这些研究中,我们建议重新定义我们对Urm1和urmy化的分子性质的看法,urmy化是一种翻译后的偶联,可能根本不像泛素那样。
{"title":"Urm1, not quite a ubiquitin-like modifier?","authors":"Lars Kaduhr, Cindy Brachmann, Keerthiraju Ethiraju Ravichandran, James D West, Sebastian Glatt, Raffael Schaffrath","doi":"10.15698/mic2021.11.763","DOIUrl":"https://doi.org/10.15698/mic2021.11.763","url":null,"abstract":"<p><p>Ubiquitin related modifier 1 (Urm1) is a unique eukaryotic member of the ubiquitin-fold (UbF) protein family and conserved from yeast to humans. Urm1 is dual-functional, acting both as a sulfur carrier for thiolation of tRNA anticodons and as a protein modifier in a lysine-directed Ub-like conjugation also known as urmylation. Although Urm1 conjugation coincides with oxidative stress and targets proteins like 2-Cys peroxiredoxins from yeast (Ahp1) and fly (Prx5), it was unclear how urmylation proceeds molecularly and whether it is affected by the activity of these antioxidant enzymes. An in-depth study of Ahp1 urmylation in yeast from our laboratory (Brachmann <i>et al.</i>, 2020) uncovered that promiscuous lysine target sites and specific redox requirements determine the Urm1 acceptor activity of the peroxiredoxin. The results clearly show that the dimer interface and the 2-Cys based redox-active centers of Ahp1 are affecting the Urm1 conjugation reaction. Together with <i>in vivo</i> assays demonstrating that high organic peroxide concentrations can prevent Ahp1 from being urmylated, Brachmann <i>et al.</i> provide insights into a potential link between Urm1 utilization and oxidant defense of cells. Here, we highlight these major findings and discuss wider implications with regards to an emerging link between Urm1 conjugation and redox biology. Moreover, from these studies we propose to redefine our perspective on Urm1 and the molecular nature of urmylation, a post-translational conjugation that may not be that ubiquitin-like after all.</p>","PeriodicalId":18397,"journal":{"name":"Microbial Cell","volume":null,"pages":null},"PeriodicalIF":4.6,"publicationDate":"2021-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8561144/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39895086","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-08-09eCollection Date: 2021-10-04DOI: 10.15698/mic2021.10.761
Jorge González-Bacerio, Maikel Izquierdo, Mirtha Elisa Aguado, Ana C Varela, Maikel González-Matos, Maday Alonso Del Rivero
Several microbial metalo-aminopeptidases are emerging as novel targets for the treatment of human infectious diseases. Some of them are well validated as targets and some are not; some are essential enzymes and others are important for virulence and pathogenesis. For another group, it is not clear if their enzymatic activity is involved in the critical functions that they mediate. But one aspect has been established: they display relevant roles in bacteria and protozoa that could be targeted for therapeutic purposes. This work aims to describe these biological functions for several microbial metalo-aminopeptidases.
{"title":"Using microbial metalo-aminopeptidases as targets in human infectious diseases.","authors":"Jorge González-Bacerio, Maikel Izquierdo, Mirtha Elisa Aguado, Ana C Varela, Maikel González-Matos, Maday Alonso Del Rivero","doi":"10.15698/mic2021.10.761","DOIUrl":"https://doi.org/10.15698/mic2021.10.761","url":null,"abstract":"<p><p>Several microbial metalo-aminopeptidases are emerging as novel targets for the treatment of human infectious diseases. Some of them are well validated as targets and some are not; some are essential enzymes and others are important for virulence and pathogenesis. For another group, it is not clear if their enzymatic activity is involved in the critical functions that they mediate. But one aspect has been established: they display relevant roles in bacteria and protozoa that could be targeted for therapeutic purposes. This work aims to describe these biological functions for several microbial metalo-aminopeptidases.</p>","PeriodicalId":18397,"journal":{"name":"Microbial Cell","volume":null,"pages":null},"PeriodicalIF":4.6,"publicationDate":"2021-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8485470/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39556417","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-08-05eCollection Date: 2021-09-06DOI: 10.15698/mic2021.09.758
Miguel A Chiurillo, Noelia Lander
Trypanosomes are early divergent protists with distinctive features among eukaryotic cells. Together with Trypanosoma brucei and Leishmania spp., Trypanosoma cruzi has been one of the most studied members of the group. This protozoan parasite is the causative agent of Chagas disease, a leading cause of heart disease in the Americas, for which there is no vaccine or satisfactory treatment available. Understanding T. cruzi biology is crucial to identify alternative targets for antiparasitic interventions. Genetic manipulation of T. cruzi has been historically challenging. However, the emergence of CRISPR/Cas9 technology has significantly improved the ability to generate genetically modified T. cruzi cell lines. Still, the system alone is not sufficient to answer all biologically relevant questions. In general, current genetic methods have limitations that should be overcome to advance in the study of this peculiar parasite. In this brief historic overview, we highlight the strengths and weaknesses of the molecular strategies that have been developed to genetically modify T. cruzi, emphasizing the future directions of the field.
{"title":"The long and winding road of reverse genetics in <i>Trypanosoma cruzi</i>.","authors":"Miguel A Chiurillo, Noelia Lander","doi":"10.15698/mic2021.09.758","DOIUrl":"https://doi.org/10.15698/mic2021.09.758","url":null,"abstract":"<p><p>Trypanosomes are early divergent protists with distinctive features among eukaryotic cells. Together with <i>Trypanosoma brucei</i> and <i>Leishmania</i> spp., <i>Trypanosoma cruzi</i> has been one of the most studied members of the group. This protozoan parasite is the causative agent of Chagas disease, a leading cause of heart disease in the Americas, for which there is no vaccine or satisfactory treatment available. Understanding <i>T. cruzi</i> biology is crucial to identify alternative targets for antiparasitic interventions. Genetic manipulation of <i>T. cruzi</i> has been historically challenging. However, the emergence of CRISPR/Cas9 technology has significantly improved the ability to generate genetically modified <i>T. cruzi</i> cell lines. Still, the system alone is not sufficient to answer all biologically relevant questions. In general, current genetic methods have limitations that should be overcome to advance in the study of this peculiar parasite. In this brief historic overview, we highlight the strengths and weaknesses of the molecular strategies that have been developed to genetically modify <i>T. cruzi</i>, emphasizing the future directions of the field.</p>","PeriodicalId":18397,"journal":{"name":"Microbial Cell","volume":null,"pages":null},"PeriodicalIF":4.6,"publicationDate":"2021-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8404153/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39420471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-08-04eCollection Date: 2021-09-06DOI: 10.15698/mic2021.09.759
Wanqiu Huang, Danni Wang, Yu-Feng Yao
Infections are highly orchestrated and dynamic processes, which involve both pathogen and host. Transcriptional profiling at the single-cell level enables the analysis of cell diversity, heterogeneity of the immune response, and detailed molecular mechanisms underlying infectious diseases caused by bacteria, viruses, fungi, and parasites. Herein, we highlight recent remarkable advances in single-cell RNA sequencing (scRNA-seq) technologies and their applications in the investigation of host-pathogen interactions, current challenges and potential prospects for disease treatment are discussed as well. We propose that with the aid of scRNA-seq, the mechanism of infectious diseases will be further revealed thus inspiring the development of novel interventions and therapies.
{"title":"Understanding the pathogenesis of infectious diseases by single-cell RNA sequencing.","authors":"Wanqiu Huang, Danni Wang, Yu-Feng Yao","doi":"10.15698/mic2021.09.759","DOIUrl":"https://doi.org/10.15698/mic2021.09.759","url":null,"abstract":"<p><p>Infections are highly orchestrated and dynamic processes, which involve both pathogen and host. Transcriptional profiling at the single-cell level enables the analysis of cell diversity, heterogeneity of the immune response, and detailed molecular mechanisms underlying infectious diseases caused by bacteria, viruses, fungi, and parasites. Herein, we highlight recent remarkable advances in single-cell RNA sequencing (scRNA-seq) technologies and their applications in the investigation of host-pathogen interactions, current challenges and potential prospects for disease treatment are discussed as well. We propose that with the aid of scRNA-seq, the mechanism of infectious diseases will be further revealed thus inspiring the development of novel interventions and therapies.</p>","PeriodicalId":18397,"journal":{"name":"Microbial Cell","volume":null,"pages":null},"PeriodicalIF":4.6,"publicationDate":"2021-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8404151/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39420390","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
This work presents a study on the airborne bacteria recorded in three Andalusian show caves, subjected to different managements. The main differences within the caves were the absence of lighting and phototrophic biofilms in Cueva de Ardales, the periodic maintenance and low occurrence of phototrophic biofilms in Gruta de las Maravillas, and the abundance of phototrophic biofilms in speleothems and walls in Cueva del Tesoro. These factors conditioned the diversity of bacteria in the caves and therefore there are large differences among the CFU m-3, determined using a suction impact collector, equipment widely used in aerobiological studies. The study of the bacterial diversity, inside and outside the caves, indicates that the air is mostly populated by bacteria thriving in the subterranean environment. In addition, the diversity seems to be related with the presence of abundant phototrophic biofilms, but not with the number of visitors received by each cave.
这项研究介绍了在三个安达卢西亚表演洞穴中记录到的空气传播细菌,这些洞穴受到不同的管理。洞穴内的主要差异在于阿达莱斯岩洞(Cueva de Ardales)没有照明和光养生物膜,马拉维拉斯岩洞(Gruta de las Maravillas)定期维护且光养生物膜较少,而特索罗岩洞(Cueva del Tesoro)的洞穴和洞壁上有大量光养生物膜。这些因素决定了洞穴中细菌的多样性,因此,使用空气生物学研究中广泛使用的设备--抽吸冲击收集器测定的每立方米 CFU 数量之间存在很大差异。对洞穴内外细菌多样性的研究表明,空气中的细菌大多在地下环境中繁衍生息。此外,多样性似乎与是否存在丰富的光养生物膜有关,但与每个洞穴接待的游客数量无关。
{"title":"Airborne bacteria in show caves from Southern Spain.","authors":"Irene Dominguez-Moñino, Valme Jurado, Miguel Angel Rogerio-Candelera, Bernardo Hermosin, Cesareo Saiz-Jimenez","doi":"10.15698/mic2021.10.762","DOIUrl":"10.15698/mic2021.10.762","url":null,"abstract":"<p><p>This work presents a study on the airborne bacteria recorded in three Andalusian show caves, subjected to different managements. The main differences within the caves were the absence of lighting and phototrophic biofilms in <i>Cueva de Ardales</i>, the periodic maintenance and low occurrence of phototrophic biofilms in <i>Gruta de las Maravillas</i>, and the abundance of phototrophic biofilms in speleothems and walls in <i>Cueva del Tesoro</i>. These factors conditioned the diversity of bacteria in the caves and therefore there are large differences among the CFU m<sup>-3</sup>, determined using a suction impact collector, equipment widely used in aerobiological studies. The study of the bacterial diversity, inside and outside the caves, indicates that the air is mostly populated by bacteria thriving in the subterranean environment. In addition, the diversity seems to be related with the presence of abundant phototrophic biofilms, but not with the number of visitors received by each cave.</p>","PeriodicalId":18397,"journal":{"name":"Microbial Cell","volume":null,"pages":null},"PeriodicalIF":4.6,"publicationDate":"2021-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8485469/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39556418","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-07-02eCollection Date: 2021-08-02DOI: 10.15698/mic2021.08.756
Christina S Moesslacher, Johanna M Kohlmayr, Ulrich Stelzl
Yeast is a valuable eukaryotic model organism that has evolved many processes conserved up to humans, yet many protein functions, including certain DNA and protein modifications, are absent. It is this absence of protein function that is fundamental to approaches using yeast as an in vivo test system to investigate human proteins. Functionality of the heterologous expressed proteins is connected to a quantitative, selectable phenotype, enabling the systematic analyses of mechanisms and specificity of DNA modification, post-translational protein modifications as well as the impact of annotated cancer mutations and coding variation on protein activity and interaction. Through continuous improvements of yeast screening systems, this is increasingly carried out on a global scale using deep mutational scanning approaches. Here we discuss the applicability of yeast systems to investigate absent human protein function with a specific focus on the impact of protein variation on protein-protein interaction modulation.
{"title":"Exploring <i>absent</i> protein function in yeast: assaying post translational modification and human genetic variation.","authors":"Christina S Moesslacher, Johanna M Kohlmayr, Ulrich Stelzl","doi":"10.15698/mic2021.08.756","DOIUrl":"10.15698/mic2021.08.756","url":null,"abstract":"<p><p>Yeast is a valuable eukaryotic model organism that has evolved many processes conserved up to humans, yet many protein functions, including certain DNA and protein modifications, are <i>absent</i>. It is this absence of protein function that is fundamental to approaches using yeast as an <i>in vivo</i> test system to investigate human proteins. Functionality of the heterologous expressed proteins is connected to a quantitative, selectable phenotype, enabling the systematic analyses of mechanisms and specificity of DNA modification, post-translational protein modifications as well as the impact of annotated cancer mutations and coding variation on protein activity and interaction. Through continuous improvements of yeast screening systems, this is increasingly carried out on a global scale using deep mutational scanning approaches. Here we discuss the applicability of yeast systems to investigate <i>absent</i> human protein function with a specific focus on the impact of protein variation on protein-protein interaction modulation.</p>","PeriodicalId":18397,"journal":{"name":"Microbial Cell","volume":null,"pages":null},"PeriodicalIF":4.6,"publicationDate":"2021-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8329848/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39313728","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-06-18eCollection Date: 2021-09-06DOI: 10.15698/mic2021.09.760
Nayaret Chamorro, David A Montero, Pablo Gallardo, Mauricio Farfán, Mauricio Contreras, Marjorie De la Fuente, Karen Dubois, Marcela A Hermoso, Rodrigo Quera, Marjorie Pizarro-Guajardo, Daniel Paredes-Sabja, Daniel Ginard, Ramon Rosselló-Móra, Roberto Vidal
Inflammatory bowel diseases (IBDs), which include ulcerative colitis (UC) and Crohn's disease (CD), cause chronic inflammation of the gut, affecting millions of people worldwide. IBDs have been frequently associated with an alteration of the gut microbiota, termed dysbiosis, which is generally characterized by an increase in abundance of Proteobacteria such as Escherichia coli, and a decrease in abundance of Firmicutes such as Faecalibacterium prausnitzii (an indicator of a healthy colonic microbiota). The mechanisms behind the development of IBDs and dysbiosis are incompletely understood. Using samples from colonic biopsies, we studied the mucosa-associated intestinal microbiota in Chilean and Spanish patients with IBD. In agreement with previous studies, microbiome comparison between IBD patients and non-IBD controls indicated that dysbiosis in these patients is characterized by an increase of pro-inflammatory bacteria (mostly Proteobacteria) and a decrease of commensal beneficial bacteria (mostly Firmicutes). Notably, bacteria typically residing on the mucosa of healthy individuals were mostly obligate anaerobes, whereas in the inflamed mucosa an increase of facultative anaerobe and aerobic bacteria was observed. We also identify potential co-occurring and mutually exclusive interactions between bacteria associated with the healthy and inflamed mucosa, which appear to be determined by the oxygen availability and the type of respiration. Finally, we identified a panel of bacterial biomarkers that allow the discrimination between eubiosis from dysbiosis with a high diagnostic performance (96% accurately), which could be used for the development of non-invasive diagnostic methods. Thus, this study is a step forward towards understanding the landscapes and alterations of mucosa-associated intestinal microbiota in patients with IBDs.
{"title":"Landscapes and bacterial signatures of mucosa-associated intestinal microbiota in Chilean and Spanish patients with inflammatory bowel disease.","authors":"Nayaret Chamorro, David A Montero, Pablo Gallardo, Mauricio Farfán, Mauricio Contreras, Marjorie De la Fuente, Karen Dubois, Marcela A Hermoso, Rodrigo Quera, Marjorie Pizarro-Guajardo, Daniel Paredes-Sabja, Daniel Ginard, Ramon Rosselló-Móra, Roberto Vidal","doi":"10.15698/mic2021.09.760","DOIUrl":"10.15698/mic2021.09.760","url":null,"abstract":"<p><p>Inflammatory bowel diseases (IBDs), which include ulcerative colitis (UC) and Crohn's disease (CD), cause chronic inflammation of the gut, affecting millions of people worldwide. IBDs have been frequently associated with an alteration of the gut microbiota, termed dysbiosis, which is generally characterized by an increase in abundance of Proteobacteria such as <i>Escherichia coli</i>, and a decrease in abundance of Firmicutes such as <i>Faecalibacterium prausnitzii</i> (an indicator of a healthy colonic microbiota). The mechanisms behind the development of IBDs and dysbiosis are incompletely understood. Using samples from colonic biopsies, we studied the mucosa-associated intestinal microbiota in Chilean and Spanish patients with IBD. In agreement with previous studies, microbiome comparison between IBD patients and non-IBD controls indicated that dysbiosis in these patients is characterized by an increase of pro-inflammatory bacteria (mostly Proteobacteria) and a decrease of commensal beneficial bacteria (mostly Firmicutes). Notably, bacteria typically residing on the mucosa of healthy individuals were mostly obligate anaerobes, whereas in the inflamed mucosa an increase of facultative anaerobe and aerobic bacteria was observed. We also identify potential co-occurring and mutually exclusive interactions between bacteria associated with the healthy and inflamed mucosa, which appear to be determined by the oxygen availability and the type of respiration. Finally, we identified a panel of bacterial biomarkers that allow the discrimination between eubiosis from dysbiosis with a high diagnostic performance (96% accurately), which could be used for the development of non-invasive diagnostic methods. Thus, this study is a step forward towards understanding the landscapes and alterations of mucosa-associated intestinal microbiota in patients with IBDs.</p>","PeriodicalId":18397,"journal":{"name":"Microbial Cell","volume":null,"pages":null},"PeriodicalIF":4.6,"publicationDate":"2021-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8404152/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39420391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}