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Akbuğa-Schön T, Suzuki TA, Jakob D, Vu DL, Waters JL, Ley RE. The keystone gut species Christensenella minuta boosts gut microbial biomass and voluntary physical activity in mice. mBio 2024; 15:e0283623. [PMID: 38132571 PMCID: PMC10865807 DOI: 10.1128/mbio.02836-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 12/23/2023] Open
Abstract
The gut bacteria of the family Christensenellaceae are consistently associated with metabolic health, but their role in promoting host health is not fully understood. Here, we explored the effect of Christensenella minuta amendment on voluntary physical activity and the gut microbiome. We inoculated male and female germ-free mice with an obese human donor microbiota together with live or heat-killed C. minuta for 28 days and measured physical activity in respirometry cages. Compared to heat-killed, the live-C. minuta treatment resulted in reduced feed efficiency and higher levels of physical activity, with significantly greater distance traveled for males and higher levels of small movements and resting metabolic rate in females. Sex-specific effects of C. minuta treatment may be in part attributable to different housing conditions for males and females. Amendment with live C. minuta boosted gut microbial biomass in both sexes, immobilizing dietary carbon in the microbiome, and mice with high levels of C. minuta lose more energy in stool. Live C. minuta also reduced within and between-host gut microbial diversity. Overall, our results showed that C. minuta acts as a keystone species: despite low relative abundance, it has a large impact on its ecosystem, from the microbiome to host energy homeostasis.IMPORTANCEThe composition of the human gut microbiome is associated with human health. Within the human gut microbiome, the relative abundance of the bacterial family Christensenellaceae has been shown to correlate with metabolic health and a lean body type. The mechanisms underpinning this effect remain unclear. Here, we show that live C. minuta influences host physical activity and metabolic energy expenditure, accompanied by changes in murine metabolism and the gut microbial community in a sex-dependent manner in comparison to heat-killed C. minuta. Importantly, live C. minuta boosts the biomass of the microbiome in the gut, and a higher level of C. minuta is associated with greater loss of energy in stool. These observations indicate that modulation of activity levels and changes to the microbiome are ways in which the Christensenellaceae can influence host energy homeostasis and health.
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Affiliation(s)
- Tanja Akbuğa-Schön
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Taichi A. Suzuki
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Dennis Jakob
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Mass Spectrometry Facility, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Dai Long Vu
- Mass Spectrometry Facility, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Jillian L. Waters
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Ruth E. Ley
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
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Minegishi M, Kuchimaru T, Nishikawa K, Isagawa T, Iwano S, Iida K, Hara H, Miura S, Sato M, Watanabe S, Shiomi A, Mabuchi Y, Hamana H, Kishi H, Sato T, Sawaki D, Sato S, Hanazono Y, Suzuki A, Kohro T, Kadonosono T, Shimogori T, Miyawaki A, Takeda N, Shintaku H, Kizaka-Kondoh S, Nishimura S. Secretory GFP reconstitution labeling of neighboring cells interrogates cell-cell interactions in metastatic niches. Nat Commun 2023; 14:8031. [PMID: 38052804 DOI: 10.1038/s41467-023-43855-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/17/2023] [Indexed: 12/07/2023] Open
Abstract
Cancer cells inevitably interact with neighboring host tissue-resident cells during the process of metastatic colonization, establishing a metastatic niche to fuel their survival, growth, and invasion. However, the underlying mechanisms in the metastatic niche are yet to be fully elucidated owing to the lack of methodologies for comprehensively studying the mechanisms of cell-cell interactions in the niche. Here, we improve a split green fluorescent protein (GFP)-based genetically encoded system to develop secretory glycosylphosphatidylinositol-anchored reconstitution-activated proteins to highlight intercellular connections (sGRAPHIC) for efficient fluorescent labeling of tissue-resident cells that neighbor on and putatively interact with cancer cells in deep tissues. The sGRAPHIC system enables the isolation of metastatic niche-associated tissue-resident cells for their characterization using a single-cell RNA sequencing platform. We use this sGRAPHIC-leveraged transcriptomic platform to uncover gene expression patterns in metastatic niche-associated hepatocytes in a murine model of liver metastasis. Among the marker genes of metastatic niche-associated hepatocytes, we identify Lgals3, encoding galectin-3, as a potential pro-metastatic factor that accelerates metastatic growth and invasion.
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Affiliation(s)
- Misa Minegishi
- School of Life Science and Technology, Tokyo Institute of Technology, Kanagawa, Japan
- RIKEN Cluster for Pioneering Research, Saitama, Japan
| | - Takahiro Kuchimaru
- RIKEN Cluster for Pioneering Research, Saitama, Japan.
- Graduate School of Medicine, Jichi Medical University, Tochigi, Japan.
- Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan.
- Data Science Center, Jichi Medical University, Tochigi, Japan.
| | | | - Takayuki Isagawa
- Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
- Data Science Center, Jichi Medical University, Tochigi, Japan
| | - Satoshi Iwano
- RIKEN Center for Brain Science, Saitama, Japan
- Institute for Tenure Track Promotion, University of Miyazaki, Miyazaki, Japan
| | - Kei Iida
- Faculty of Science and Engineering, Kindai University, Osaka, Japan
| | - Hiromasa Hara
- Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Shizuka Miura
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Marika Sato
- MediGear International Corporation, Kanagawa, Japan
| | | | | | - Yo Mabuchi
- Graduate School of Medicine, Juntendo University, Tokyo, Japan
- School of Medicine, Fujita Health University, Aichi, Japan
| | - Hiroshi Hamana
- Department of Immunology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
| | - Hiroyuki Kishi
- Department of Immunology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
| | - Tatsuyuki Sato
- Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Daigo Sawaki
- Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
- Clinical Pharmacology, Jichi Medical University, Tochigi, Japan
| | - Shigeru Sato
- Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Yutaka Hanazono
- Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Atsushi Suzuki
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Takahide Kohro
- Data Science Center, Jichi Medical University, Tochigi, Japan
| | - Tetsuya Kadonosono
- School of Life Science and Technology, Tokyo Institute of Technology, Kanagawa, Japan
| | | | | | - Norihiko Takeda
- Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | | | - Shinae Kizaka-Kondoh
- School of Life Science and Technology, Tokyo Institute of Technology, Kanagawa, Japan
| | - Satoshi Nishimura
- Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
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3
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de la Cuesta-Zuluaga J, Huus KE, Youngblut ND, Escobar JS, Ley RE. Obesity is the main driver of altered gut microbiome functions in the metabolically unhealthy. Gut Microbes 2023; 15:2246634. [PMID: 37680093 PMCID: PMC10486298 DOI: 10.1080/19490976.2023.2246634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 09/09/2023] Open
Abstract
Obesity (OB) and cardiometabolic disease are major public health issues linked to changes in the gut microbiome. OB and poor cardiometabolic health status (CHS) are often comorbid, which hinders efforts to identify components of the microbiome uniquely linked to either one. Here, we used a deeply phenotyped cohort of 408 adults from Colombia, including subjects with OB, unhealthy CHS, or both, to validate previously reported features of gut microbiome function and diversity independently correlated with OB or CHS using fecal metagenomes. OB was defined by body mass index, waist circumference, and body fat; CHS as healthy or unhealthy according to blood biochemistry and anthropometric data. We found that OB, more so than metabolic status, drove associations with gut microbiome structure and functions. The microbiome of obese individuals with and without co-existing unhealthy CHS was characterized by reduced metagenomic diversity, reduced fermentative potential and elevated capacity to respond to oxidative stress and produce bacterial antigens. Disease-linked features were correlated with increased host blood pressure and inflammatory markers, and were mainly contributed by members of the family Enterobacteriaceae. Our results link OB with a microbiome able to tolerate an inflammatory and oxygenated gut state, and suggest that OB is the main driver of microbiome functional differences when poor CHS is a comorbidity.
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Affiliation(s)
| | - Kelsey E. Huus
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Nicholas D. Youngblut
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Juan S. Escobar
- Vidarium–Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa, Medellin, Colombia
| | - Ruth E. Ley
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
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Mineeva O, Danciu D, Schölkopf B, Ley RE, Rätsch G, Youngblut ND. ResMiCo: Increasing the quality of metagenome-assembled genomes with deep learning. PLoS Comput Biol 2023; 19:e1011001. [PMID: 37126495 PMCID: PMC10174551 DOI: 10.1371/journal.pcbi.1011001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 05/11/2023] [Accepted: 03/06/2023] [Indexed: 05/02/2023] Open
Abstract
The number of published metagenome assemblies is rapidly growing due to advances in sequencing technologies. However, sequencing errors, variable coverage, repetitive genomic regions, and other factors can produce misassemblies, which are challenging to detect for taxonomically novel genomic data. Assembly errors can affect all downstream analyses of the assemblies. Accuracy for the state of the art in reference-free misassembly prediction does not exceed an AUPRC of 0.57, and it is not clear how well these models generalize to real-world data. Here, we present the Residual neural network for Misassembled Contig identification (ResMiCo), a deep learning approach for reference-free identification of misassembled contigs. To develop ResMiCo, we first generated a training dataset of unprecedented size and complexity that can be used for further benchmarking and developments in the field. Through rigorous validation, we show that ResMiCo is substantially more accurate than the state of the art, and the model is robust to novel taxonomic diversity and varying assembly methods. ResMiCo estimated 7% misassembled contigs per metagenome across multiple real-world datasets. We demonstrate how ResMiCo can be used to optimize metagenome assembly hyperparameters to improve accuracy, instead of optimizing solely for contiguity. The accuracy, robustness, and ease-of-use of ResMiCo make the tool suitable for general quality control of metagenome assemblies and assembly methodology optimization.
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Affiliation(s)
- Olga Mineeva
- Department of Computer Science, ETH Zürich, Zürich, Switzerland
- Department of Empirical Inference, Max Planck Institute for Intelligent Systems, Tübingen, Germany
- Swiss Institute for Bioinformatics, Lausanne, Switzerland
| | - Daniel Danciu
- Department of Computer Science, ETH Zürich, Zürich, Switzerland
| | - Bernhard Schölkopf
- Department of Computer Science, ETH Zürich, Zürich, Switzerland
- Department of Empirical Inference, Max Planck Institute for Intelligent Systems, Tübingen, Germany
- ETH AI center, ETH Zürich, Zürich, Switzerland
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Gunnar Rätsch
- Department of Computer Science, ETH Zürich, Zürich, Switzerland
- Swiss Institute for Bioinformatics, Lausanne, Switzerland
- ETH AI center, ETH Zürich, Zürich, Switzerland
- Department of Biology, ETH Zürich, Zürich, Switzerland
- Medical Informatics Unit, Zürich University Hospital, Zürich, Switzerland
| | - Nicholas D Youngblut
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
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Rather MA, Agarwal D, Bhat TA, Khan IA, Zafar I, Kumar S, Amin A, Sundaray JK, Qadri T. Bioinformatics approaches and big data analytics opportunities in improving fisheries and aquaculture. Int J Biol Macromol 2023; 233:123549. [PMID: 36740117 DOI: 10.1016/j.ijbiomac.2023.123549] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023]
Abstract
Aquaculture has witnessed an excellent growth rate during the last two decades and offers huge potential to provide nutritional as well as livelihood security. Genomic research has contributed significantly toward the development of beneficial technologies for aquaculture. The existing high throughput technologies like next-generation technologies generate oceanic data which requires extensive analysis using appropriate tools. Bioinformatics is a rapidly evolving science that involves integrating gene based information and computational technology to produce new knowledge for the benefit of aquaculture. Bioinformatics provides new opportunities as well as challenges for information and data processing in new generation aquaculture. Rapid technical advancements have opened up a world of possibilities for using current genomics to improve aquaculture performance. Understanding the genes that govern economically relevant characteristics, necessitates a significant amount of additional research. The various dimensions of data sources includes next-generation DNA sequencing, protein sequencing, RNA sequencing gene expression profiles, metabolic pathways, molecular markers, and so on. Appropriate bioinformatics tools are developed to mine the biologically relevant and commercially useful results. The purpose of this scoping review is to present various arms of diverse bioinformatics tools with special emphasis on practical translation to the aquaculture industry.
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Affiliation(s)
- Mohd Ashraf Rather
- Division of Fish Genetics and Biotechnology, Faculty of Fisheries Ganderbal, Sher-e- Kashmir University of Agricultural Science and Technology, Kashmir, India.
| | - Deepak Agarwal
- Institute of Fisheries Post Graduation Studies OMR Campus, Vaniyanchavadi, Chennai, India
| | | | - Irfan Ahamd Khan
- Division of Fish Genetics and Biotechnology, Faculty of Fisheries Ganderbal, Sher-e- Kashmir University of Agricultural Science and Technology, Kashmir, India
| | - Imran Zafar
- Department of Bioinformatics and Computational Biology, Virtual University Punjab, Pakistan
| | - Sujit Kumar
- Department of Bioinformatics and Computational Biology, Virtual University Punjab, Pakistan
| | - Adnan Amin
- Postgraduate Institute of Fisheries Education and Research Kamdhenu University, Gandhinagar-India University of Kurasthra, India; Department of Aquatic Environmental Management, Faculty of Fisheries Rangil- Ganderbel -SKUAST-K, India
| | - Jitendra Kumar Sundaray
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha 751002, India
| | - Tahiya Qadri
- Division of Food Science and Technology, SKUAST-K, Shalimar, India
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6
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Piñeiro C, Pichel JC. BigSeqKit: a parallel Big Data toolkit to process FASTA and FASTQ files at scale. Gigascience 2022; 12:giad062. [PMID: 37522758 PMCID: PMC10388699 DOI: 10.1093/gigascience/giad062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/25/2023] [Accepted: 07/10/2023] [Indexed: 08/01/2023] Open
Abstract
BACKGROUND High-throughput sequencing technologies have led to an unprecedented explosion in the amounts of sequencing data available, which are typically stored using FASTA and FASTQ files. We can find in the literature several tools to process and manipulate those type of files with the aim of transforming sequence data into biological knowledge. However, none of them are well fitted for processing efficiently very large files, likely in the order of terabytes in the following years, since they are based on sequential processing. Only some routines of the well-known seqkit tool are partly parallelized. In any case, its scalability is limited to use few threads on a single computing node. RESULTS Our approach, BigSeqKit, takes advantage of a high-performance computing-Big Data framework to parallelize and optimize the commands included in seqkit with the aim of speeding up the manipulation of FASTA/FASTQ files. In this way, in most cases, it is from tens to hundreds of times faster than several state-of-the-art tools. At the same time, our toolkit is easy to use and install on any kind of hardware platform (local server or cluster), and its routines can be used as a bioinformatics library or from the command line. CONCLUSIONS BigSeqKit is a very complete and ultra-fast toolkit to process and manipulate large FASTA and FASTQ files. It is publicly available at https://github.com/citiususc/BigSeqKit.
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Affiliation(s)
- César Piñeiro
- CiTIUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Juan C Pichel
- CiTIUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
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Draft Genome Sequences of Four Methicillin-Resistant Staphylococcus aureus Strains (M080_2017, M106_2017, M181_2017, and M191_2017), Isolated from a Malaysian Teaching Hospital. Microbiol Resour Announc 2022; 11:e0086722. [DOI: 10.1128/mra.00867-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Draft genome sequences were obtained for four methicillin-resistant
Staphylococcus aureus
(MRSA) strains isolated from various wards of the Hospital Canselor Tuanku Muhriz (HCTM), Kuala Lumpur, Malaysia, in 2017. Using different bioinformatics tools, we annotated the draft genomes and identified multiple antimicrobial resistance genes.
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8
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Carvajal-Agudelo JD, Ramírez-Chaves HE, Ossa-López PA, Rivera-Páez FA. Bacteria related to tick-borne pathogen assemblages in Ornithodoros cf. hasei (Acari: Argasidae) and blood of the wild mammal hosts in the Orinoquia region, Colombia. EXPERIMENTAL & APPLIED ACAROLOGY 2022; 87:253-271. [PMID: 35829939 PMCID: PMC9424158 DOI: 10.1007/s10493-022-00724-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 06/16/2022] [Indexed: 05/19/2023]
Abstract
Interest in research on soft ticks has increased in recent decades, leading to valuable insight into their role as disease vectors. The use of metagenomics-based analyses have helped to elucidate ecological factors involved in pathogen, vector, and host dynamics. To understand the main bacterial assemblages present in Ornithodoros cf. hasei and its mammalian hosts, 84 ticks and 13 blood samples from bat hosts (Chiroptera) were selected, and the 16S rRNA gene V4 region was sequenced in five pools (each one related to each host-tick pairing). Bacterial taxonomic assignment analyses were performed by comparing operational taxonomic units (OTUs) shared between ticks and their host blood. This analysis showed the presence of Proteobacteria (38.8%), Enterobacteriaceae (25%), Firmicutes (12.3%), and Actinobacteria (10.9%) within blood samples, and Rickettsiaceae (39%), Firmicutes (25%), Actinobacteria (13.1%), and Proteobacteria (9%) within ticks. Species related to potentially pathogenic genera were detected in ticks, such as Borrelia sp., Bartonella tamiae, Ehrlichia sp. and Rickettsia-like endosymbiont, and the presence of these organisms was found in all analyzed bat species (Cynomops planirostris, Molossus pretiosus, Noctilio albiventris), and O. cf. hasei. About 41-48.6% of bacterial OTUs (genera and species) were shared between ticks and the blood of bat hosts. Targeted metagenomic screening techniques allowed the detection of tick-associated pathogens for O. cf. hasei and small mammals for the first time, enabling future research on many of these pathogens.
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Affiliation(s)
- Juan D Carvajal-Agudelo
- Grupo de Investigación en Genética, Biodiversidad y Manejo de Ecosistemas (GEBIOME), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Calle 65 N° 26-10, 170004, Manizales, Caldas, Colombia
| | - Héctor E Ramírez-Chaves
- Grupo de Investigación en Genética, Biodiversidad y Manejo de Ecosistemas (GEBIOME), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Calle 65 N° 26-10, 170004, Manizales, Caldas, Colombia
- Centro de Museos, Museo de Historia Natural, Universidad de Caldas, Calle 65 N° 26-10, 170004, Manizales, Caldas, Colombia
| | - Paula A Ossa-López
- Grupo de Investigación en Genética, Biodiversidad y Manejo de Ecosistemas (GEBIOME), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Calle 65 N° 26-10, 170004, Manizales, Caldas, Colombia
- Doctorado en Ciencias, Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Calle 65 No. 26-10, 170004, Manizales, Caldas, Colombia
| | - Fredy A Rivera-Páez
- Grupo de Investigación en Genética, Biodiversidad y Manejo de Ecosistemas (GEBIOME), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Calle 65 N° 26-10, 170004, Manizales, Caldas, Colombia.
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Malik TN, Cartailler JP, Emeson RB. Quantitative Analysis of Adenosine-to-Inosine RNA Editing. Methods Mol Biol 2021; 2181:97-111. [PMID: 32729077 DOI: 10.1007/978-1-0716-0787-9_7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The conversion of adenosine to inosine (A to I) by RNA editing represents a common posttranscriptional mechanism for diversification of both the transcriptome and proteome, and is a part of the cellular response for innate immune tolerance. Due to its preferential base-pairing with cytosine (C), inosine (I) is recognized as guanosine (G) by reverse transcriptase, as well as the cellular splicing and translation machinery. A-to-I editing events appear as A-G discrepancies between genomic DNA and cDNA sequences. Molecular analyses of RNA editing have leveraged these nucleoside differences to quantify RNA editing in ensemble populations of RNA transcripts and within individual cDNAs using high-throughput sequencing or Sanger sequencing-derived analysis of electropherogram peak heights. Here, we briefly review and compare these methods of RNA editing quantification, as well as provide experimental protocols by which such analyses may be achieved.
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Affiliation(s)
- Turnee N Malik
- Training Program in Neuroscience, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jean-Philippe Cartailler
- Department of Molecular Physiology & Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Ronald B Emeson
- Training Program in Neuroscience, Vanderbilt University School of Medicine, Nashville, TN, USA. .,Department of Molecular Physiology & Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA. .,Departments of Pharmacology, Biochemistry and Psychiatry & Behavioral Sciences, Vanderbilt University School of Medicine, Nashville, TN, USA.
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10
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Du L, Liu Q, Fan Z, Tang J, Zhang X, Price M, Yue B, Zhao K. Pyfastx: a robust Python package for fast random access to sequences from plain and gzipped FASTA/Q files. Brief Bioinform 2020; 22:6042388. [PMID: 33341884 DOI: 10.1093/bib/bbaa368] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 10/30/2020] [Accepted: 11/17/2020] [Indexed: 11/14/2022] Open
Abstract
FASTA and FASTQ are the most widely used biological data formats that have become the de facto standard to exchange sequence data between bioinformatics tools. With the avalanche of next-generation sequencing data, the amount of sequence data being deposited and accessed in FASTA/Q formats is increasing dramatically. However, the existing tools have very low efficiency at random retrieval of subsequences due to the requirement of loading the entire index into memory. In addition, most existing tools have no capability to build index for large FASTA/Q files because of the limited memory. Furthermore, the tools do not provide support to randomly accessing sequences from FASTA/Q files compressed by gzip, which is extensively adopted by most public databases to compress data for saving storage. In this study, we developed pyfastx as a versatile Python package with commonly used command-line tools to overcome the above limitations. Compared to other tools, pyfastx yielded the highest performance in terms of building index and random access to sequences, particularly when dealing with large FASTA/Q files with hundreds of millions of sequences. A key advantage of pyfastx over other tools is that it offers an efficient way to randomly extract subsequences directly from gzip compressed FASTA/Q files without needing to uncompress beforehand. Pyfastx can easily be installed from PyPI (https://pypi.org/project/pyfastx) and the source code is freely available at https://github.com/lmdu/pyfastx.
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Affiliation(s)
- Lianming Du
- Institute for Advanced Study, Chengdu University, Chengdu, China
| | - Qin Liu
- College of Life Sciences and Food Engineering, Yibin University, Yibin, China
| | - Zhenxin Fan
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
| | - Jie Tang
- Institute for Advanced Study, Chengdu University, Chengdu, China
| | - Xiuyue Zhang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
| | - Megan Price
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
| | - Bisong Yue
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
| | - Kelei Zhao
- Institute for Advanced Study, Chengdu University, Chengdu, China
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11
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TREML4 receptor regulates inflammation and innate immune cell death during polymicrobial sepsis. Nat Immunol 2020; 21:1585-1596. [DOI: 10.1038/s41590-020-0789-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 08/21/2020] [Indexed: 12/20/2022]
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12
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Xiao H, Ye X, Xu H, Mei Y, Yang Y, Chen X, Yang Y, Liu T, Yu Y, Yang W, Lu Z, Li F. The genetic adaptations of fall armyworm Spodoptera frugiperda facilitated its rapid global dispersal and invasion. Mol Ecol Resour 2020; 20:1050-1068. [PMID: 32359007 DOI: 10.1111/1755-0998.13182] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 12/31/2022]
Abstract
The fall armyworm (Spodoptera frugiperda) is a lepidopteran insect pest that causes huge economic losses. This notorious insect pest has rapidly spread over the world in the past few years. However, the mechanisms of rapid dispersal are not well understood. Here, we report a chromosome-level assembled genome of the fall armyworm, named the ZJ-version, using PacBio and Hi-C technology. The sequenced individual was a female collected from the Zhejiang province of China and had high heterozygosity. The assembled genome size of ZJ-version was 486 Mb, containing 361 contigs with an N50 of 1.13 Mb. Hi-C scaffolding further assembled the genome into 31 chromosomes and a portion of W chromosome, representing 97.4% of all contigs and resulted in a chromosome-level genome with scaffold N50 of 16.3 Mb. The sex chromosomes were identified by genome resequencing of a single male pupa and a single female pupa. About 28% of the genome was annotated as repeat sequences, and 22,623 protein-coding genes were identified. Comparative genomics revealed the expansion of the detoxification-associated gene families, chemoreception-associated gene families, nutrition metabolism and transport system gene families in the fall armyworm. Transcriptomic and phylogenetic analyses focused on these gene families revealed the potential roles of the genes in polyphagia and invasion of fall armyworm. The high-quality of the fall armyworm genome provides an important genomic resource for further explorations of the mechanisms of polyphagia and insecticide resistance, as well as for pest management of fall armyworm.
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Affiliation(s)
- Huamei Xiao
- Key Laboratory of Crop Growth and Development Regulation of Jiangxi Province, College of Life Sciences and Resource Environment, Yichun University, Yichun, China.,State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xinhai Ye
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Hongxing Xu
- Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yang Mei
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yi Yang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xi Chen
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yajun Yang
- Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Tao Liu
- Annoroad Gene Technology (Beijing) Co Ltd, Beijing, China
| | - Yongyi Yu
- Annoroad Gene Technology (Beijing) Co Ltd, Beijing, China
| | - Weifei Yang
- Annoroad Gene Technology (Beijing) Co Ltd, Beijing, China
| | - Zhongxian Lu
- Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Fei Li
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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13
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Syntrophy via Interspecies H 2 Transfer between Christensenella and Methanobrevibacter Underlies Their Global Cooccurrence in the Human Gut. mBio 2020; 11:mBio.03235-19. [PMID: 32019803 PMCID: PMC7002349 DOI: 10.1128/mbio.03235-19] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Across human populations, 16S rRNA gene-based surveys of gut microbiomes have revealed that the bacterial family Christensenellaceae and the archaeal family Methanobacteriaceae cooccur and are enriched in individuals with a lean, compared to an obese, body mass index (BMI). Whether these association patterns reflect interactions between metabolic partners, as well as whether these associations play a role in the lean host phenotype with which they associate, remains to be ascertained. Here, we validated previously reported cooccurrence patterns of the two families and their association with a lean BMI with a meta-analysis of 1,821 metagenomes derived from 10 independent studies. Furthermore, we report positive associations at the genus and species levels between Christensenella spp. and Methanobrevibacter smithii, the most abundant methanogen of the human gut. By coculturing three Christensenella spp. with M. smithii, we show that Christensenella spp. efficiently support the metabolism of M. smithii via H2 production far better than Bacteroides thetaiotaomicron does. Christensenella minuta forms flocs colonized by M. smithii even when H2 is in excess. In culture with C. minuta, H2 consumption by M. smithii shifts the metabolic output of C. minuta's fermentation toward acetate rather than butyrate. Together, these results indicate that the widespread cooccurrence of these microorganisms is underpinned by both physical and metabolic interactions. Their combined metabolic activity may provide insights into their association with a lean host BMI.IMPORTANCE The human gut microbiome is made of trillions of microbial cells, most of which are Bacteria, with a subset of Archaea The bacterial family Christensenellaceae and the archaeal family Methanobacteriaceae are widespread in human guts. They correlate with each other and with a lean body type. Whether species of these two families interact and how they affect the body type are unanswered questions. Here, we show that species within these families correlate with each other across people. We also demonstrate that particular species of these two families grow together in dense flocs, wherein the bacteria provide hydrogen gas to the archaea, which then make methane. When the archaea are present, the ratio of bacterial products (which are nutrients for humans) is changed. These observations indicate that when these species grow together, their products have the potential to affect the physiology of their human host.
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14
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Huang Z, Titus T, Postlethwait JH, Meng F. Eye Degeneration and Loss of otx5b Expression in the Cavefish Sinocyclocheilus tileihornes. J Mol Evol 2019; 87:199-208. [PMID: 31332479 PMCID: PMC6711879 DOI: 10.1007/s00239-019-09901-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 07/13/2019] [Indexed: 12/17/2022]
Abstract
Cave animals possess remarkable phenotypes associated with existence in their dark environments. The Chinese cavefish Sinocyclocheilus tileihornes shows substantial eye degeneration, a trait shared by most cave species. The extent to which independent evolution of troglomorphic traits uses convergent molecular genetic mechanisms is as yet unknown. We performed transcriptome-wide gene expression profiling in S. tileihornes eyes and compared results with those from the closely related surface species S. angustiporus and an independently derived congeneric cavefish, S. anophthalmus. In total, 52.85 million 100 bp long paired-end clean reads were generated for S. tileihornes, and we identified differentially expressed genes between the three possible pairs of species. Functional analysis of genes differentially expressed between S. tileihornes and S. angustiporus revealed that phototransduction (KEGG id: dre04744) was the most significantly enriched pathway, indicating the obvious differences in response to captured photons between the cavefish S. tileihornes and the surface species S. angustiporus. Analysis of key genes regulating eye development showed complete absence of otx5b (orthodenticle homolog 5) expression in S. tileihornes eyes, probably related to degradation of rods, but normal expression of crx (cone-rod homeobox). The enriched pathways and Otx5 are involved in phototransduction, photoreceptor formation, and regulation of photoreceptor-related gene expression. Unlike the S. tileihornes reported here, S. anophthalmus has reduced crx and otx5 expression. These results show that different species of cavefish within the same genus that independently evolved troglodyte characteristics can have different genetic mechanisms of eye degeneration.
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Affiliation(s)
- Zushi Huang
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tom Titus
- Institute of Neuroscience, University of Oregon, Eugene, OR, 97403, USA
| | | | - Fanwei Meng
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
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15
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Camargo AP, de Souza RSC, de Britto Costa P, Gerhardt IR, Dante RA, Teodoro GS, Abrahão A, Lambers H, Carazzolle MF, Huntemann M, Clum A, Foster B, Foster B, Roux S, Palaniappan K, Varghese N, Mukherjee S, Reddy TBK, Daum C, Copeland A, Chen IMA, Ivanova NN, Kyrpides NC, Pennacchio C, Eloe-Fadrosh EA, Arruda P, Oliveira RS. Microbiomes of Velloziaceae from phosphorus-impoverished soils of the campos rupestres, a biodiversity hotspot. Sci Data 2019; 6:140. [PMID: 31366912 PMCID: PMC6668480 DOI: 10.1038/s41597-019-0141-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/25/2019] [Indexed: 12/22/2022] Open
Abstract
The rocky, seasonally-dry and nutrient-impoverished soils of the Brazilian campos rupestres impose severe growth-limiting conditions on plants. Species of a dominant plant family, Velloziaceae, are highly specialized to low-nutrient conditions and seasonal water availability of this environment, where phosphorus (P) is the key limiting nutrient. Despite plant-microbe associations playing critical roles in stressful ecosystems, the contribution of these interactions in the campos rupestres remains poorly studied. Here we present the first microbiome data of Velloziaceae spp. thriving in contrasting substrates of campos rupestres. We assessed the microbiomes of Vellozia epidendroides, which occupies shallow patches of soil, and Barbacenia macrantha, growing on exposed rocks. The prokaryotic and fungal profiles were assessed by rRNA barcode sequencing of epiphytic and endophytic compartments of roots, stems, leaves and surrounding soil/rocks. We also generated root and substrate (rock/soil)-associated metagenomes of each plant species. We foresee that these data will contribute to decipher how the microbiome contributes to plant functioning in the campos rupestres, and to unravel new strategies for improved crop productivity in stressful environments.
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Affiliation(s)
- Antonio Pedro Camargo
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), 13083-875, Campinas, SP, Brazil
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), 13083-875, Campinas, SP, Brazil
- Genomics for Climate Change Research Center, Universidade Estadual de Campinas (UNICAMP), 13083-875, Campinas, SP, Brazil
| | - Rafael Soares Correa de Souza
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), 13083-875, Campinas, SP, Brazil.
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), 13083-875, Campinas, SP, Brazil.
- Genomics for Climate Change Research Center, Universidade Estadual de Campinas (UNICAMP), 13083-875, Campinas, SP, Brazil.
| | - Patrícia de Britto Costa
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), 13083-862, Campinas, SP, Brazil
- School of Biological Sciences, University of Western Australia (UWA), Perth, WA, 6009, Australia
| | - Isabel Rodrigues Gerhardt
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), 13083-875, Campinas, SP, Brazil
- Genomics for Climate Change Research Center, Universidade Estadual de Campinas (UNICAMP), 13083-875, Campinas, SP, Brazil
- Embrapa Informática Agropecuária, 13083-886, Campinas, SP, Brazil
| | - Ricardo Augusto Dante
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), 13083-875, Campinas, SP, Brazil
- Genomics for Climate Change Research Center, Universidade Estadual de Campinas (UNICAMP), 13083-875, Campinas, SP, Brazil
- Embrapa Informática Agropecuária, 13083-886, Campinas, SP, Brazil
| | - Grazielle Sales Teodoro
- Instituto de Ciências Biológicas, Universidade Federal do Para (UFPA), 66075-750, Belem, PA, Brazil
| | - Anna Abrahão
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), 13083-862, Campinas, SP, Brazil
- School of Biological Sciences, University of Western Australia (UWA), Perth, WA, 6009, Australia
| | - Hans Lambers
- School of Biological Sciences, University of Western Australia (UWA), Perth, WA, 6009, Australia
| | - Marcelo Falsarella Carazzolle
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), 13083-875, Campinas, SP, Brazil
| | - Marcel Huntemann
- Department of Energy Joint Genome Institute, Walnut Creek, California, 94598, USA
| | - Alicia Clum
- Department of Energy Joint Genome Institute, Walnut Creek, California, 94598, USA
| | - Brian Foster
- Department of Energy Joint Genome Institute, Walnut Creek, California, 94598, USA
| | - Bryce Foster
- Department of Energy Joint Genome Institute, Walnut Creek, California, 94598, USA
| | - Simon Roux
- Department of Energy Joint Genome Institute, Walnut Creek, California, 94598, USA
| | | | - Neha Varghese
- Department of Energy Joint Genome Institute, Walnut Creek, California, 94598, USA
| | - Supratim Mukherjee
- Department of Energy Joint Genome Institute, Walnut Creek, California, 94598, USA
| | - T B K Reddy
- Department of Energy Joint Genome Institute, Walnut Creek, California, 94598, USA
| | - Chris Daum
- Department of Energy Joint Genome Institute, Walnut Creek, California, 94598, USA
| | - Alex Copeland
- Department of Energy Joint Genome Institute, Walnut Creek, California, 94598, USA
| | - I-Min A Chen
- Department of Energy Joint Genome Institute, Walnut Creek, California, 94598, USA
| | - Natalia N Ivanova
- Department of Energy Joint Genome Institute, Walnut Creek, California, 94598, USA
| | - Nikos C Kyrpides
- Department of Energy Joint Genome Institute, Walnut Creek, California, 94598, USA
| | - Christa Pennacchio
- Department of Energy Joint Genome Institute, Walnut Creek, California, 94598, USA
| | | | - Paulo Arruda
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), 13083-875, Campinas, SP, Brazil
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), 13083-875, Campinas, SP, Brazil
- Genomics for Climate Change Research Center, Universidade Estadual de Campinas (UNICAMP), 13083-875, Campinas, SP, Brazil
| | - Rafael Silva Oliveira
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), 13083-862, Campinas, SP, Brazil.
- School of Biological Sciences, University of Western Australia (UWA), Perth, WA, 6009, Australia.
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16
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Ferris ST, Zakharov PN, Wan X, Calderon B, Artyomov MN, Unanue ER, Carrero JA. The islet-resident macrophage is in an inflammatory state and senses microbial products in blood. J Exp Med 2017. [PMID: 28630088 PMCID: PMC5551574 DOI: 10.1084/jem.20170074] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Ferris et al. show that macrophages in pancreatic islets express a gene signature of activation consistent with barrier macrophages. Macrophages are poised to react to blood inflammatory stimuli. In NOD mice, an additional immune activation signature is observed as early as 3 wk of age. We examined the transcriptional profiles of macrophages that reside in the islets of Langerhans of 3-wk-old non-obese diabetic (NOD), NOD.Rag1−/−, and B6.g7 mice. Islet macrophages expressed an activation signature with high expression of Tnf, Il1b, and MHC-II at both the transcript and protein levels. These features are common with barrier macrophages of the lung and gastrointestinal tract. Moreover, injection of lipopolysaccharide induced rapid inflammatory gene expression, indicating that blood stimulants are accessible to the macrophages and that these macrophages can sense them. In NOD mice, the autoimmune process imparted an increased inflammatory signature, including elevated expression of chemokines and chemokine receptors and an oxidative response. The elevated inflammatory signature indicates that the autoimmune program was active at the time of weaning. Thus, the macrophages of the islets of Langerhans are poised to mount an immune response even at steady state, while the presence of the adaptive immune system elevates their activation state.
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Affiliation(s)
- Stephen T Ferris
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Pavel N Zakharov
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Xiaoxiao Wan
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Boris Calderon
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Emil R Unanue
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Javier A Carrero
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
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17
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Crawford JE, Alves JM, Palmer WJ, Day JP, Sylla M, Ramasamy R, Surendran SN, Black WC, Pain A, Jiggins FM. Population genomics reveals that an anthropophilic population of Aedes aegypti mosquitoes in West Africa recently gave rise to American and Asian populations of this major disease vector. BMC Biol 2017; 15:16. [PMID: 28241828 PMCID: PMC5329927 DOI: 10.1186/s12915-017-0351-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 01/19/2017] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The mosquito Aedes aegypti is the main vector of dengue, Zika, chikungunya and yellow fever viruses. This major disease vector is thought to have arisen when the African subspecies Ae. aegypti formosus evolved from being zoophilic and living in forest habitats into a form that specialises on humans and resides near human population centres. The resulting domestic subspecies, Ae. aegypti aegypti, is found throughout the tropics and largely blood-feeds on humans. RESULTS To understand this transition, we have sequenced the exomes of mosquitoes collected from five populations from around the world. We found that Ae. aegypti specimens from an urban population in Senegal in West Africa were more closely related to populations in Mexico and Sri Lanka than they were to a nearby forest population. We estimate that the populations in Senegal and Mexico split just a few hundred years ago, and we found no evidence of Ae. aegypti aegypti mosquitoes migrating back to Africa from elsewhere in the tropics. The out-of-Africa migration was accompanied by a dramatic reduction in effective population size, resulting in a loss of genetic diversity and rare genetic variants. CONCLUSIONS We conclude that a domestic population of Ae. aegypti in Senegal and domestic populations on other continents are more closely related to each other than to other African populations. This suggests that an ancestral population of Ae. aegypti evolved to become a human specialist in Africa, giving rise to the subspecies Ae. aegypti aegypti. The descendants of this population are still found in West Africa today, and the rest of the world was colonised when mosquitoes from this population migrated out of Africa. This is the first report of an African population of Ae. aegypti aegypti mosquitoes that is closely related to Asian and American populations. As the two subspecies differ in their ability to vector disease, their existence side by side in West Africa may have important implications for disease transmission.
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Affiliation(s)
- Jacob E Crawford
- Department of Integrative Biology, University of California, Berkeley, CA, 94720-3140, USA
- Present Address: Verily Life Sciences, South San Francisco, CA, 94080, USA
| | - Joel M Alves
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
| | - William J Palmer
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Jonathan P Day
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Massamba Sylla
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | | | - Sinnathamby N Surendran
- ID-FISH Technology, Palo Alto, CA, 94303, USA
- Department of Zoology, University of Jaffna, Jaffna, Sri Lanka
| | - William C Black
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Arnab Pain
- Biological and Environmental Sciences and Engineering Division, KAUST, Thuwal, Kingdom of Saudi Arabia
| | - Francis M Jiggins
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.
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