1
|
Bershteyn M, Bröer S, Parekh M, Maury Y, Havlicek S, Kriks S, Fuentealba L, Lee S, Zhou R, Subramanyam G, Sezan M, Sevilla ES, Blankenberger W, Spatazza J, Zhou L, Nethercott H, Traver D, Hampel P, Kim H, Watson M, Salter N, Nesterova A, Au W, Kriegstein A, Alvarez-Buylla A, Rubenstein J, Banik G, Bulfone A, Priest C, Nicholas CR. Human pallial MGE-type GABAergic interneuron cell therapy for chronic focal epilepsy. Cell Stem Cell 2023; 30:1331-1350.e11. [PMID: 37802038 PMCID: PMC10993865 DOI: 10.1016/j.stem.2023.08.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 03/17/2023] [Accepted: 08/25/2023] [Indexed: 10/08/2023]
Abstract
Mesial temporal lobe epilepsy (MTLE) is the most common focal epilepsy. One-third of patients have drug-refractory seizures and are left with suboptimal therapeutic options such as brain tissue-destructive surgery. Here, we report the development and characterization of a cell therapy alternative for drug-resistant MTLE, which is derived from a human embryonic stem cell line and comprises cryopreserved, post-mitotic, medial ganglionic eminence (MGE) pallial-type GABAergic interneurons. Single-dose intrahippocampal delivery of the interneurons in a mouse model of chronic MTLE resulted in consistent mesiotemporal seizure suppression, with most animals becoming seizure-free and surviving longer. The grafted interneurons dispersed locally, functionally integrated, persisted long term, and significantly reduced dentate granule cell dispersion, a pathological hallmark of MTLE. These disease-modifying effects were dose-dependent, with a broad therapeutic range. No adverse effects were observed. These findings support an ongoing phase 1/2 clinical trial (NCT05135091) for drug-resistant MTLE.
Collapse
Affiliation(s)
| | - Sonja Bröer
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | - Mansi Parekh
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | - Yves Maury
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | - Steven Havlicek
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | - Sonja Kriks
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | - Luis Fuentealba
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | - Seonok Lee
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | - Robin Zhou
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | | | - Meliz Sezan
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | | | | | - Julien Spatazza
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | - Li Zhou
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - David Traver
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | - Philip Hampel
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | - Hannah Kim
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | - Michael Watson
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | - Naomi Salter
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | | | - Wai Au
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | - Arnold Kriegstein
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Arturo Alvarez-Buylla
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - John Rubenstein
- Department of Psychiatry, Weill Institute for Neurosciences, Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Gautam Banik
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA
| | | | | | - Cory R Nicholas
- Neurona Therapeutics Inc., South San Francisco, CA 94080, USA.
| |
Collapse
|
2
|
Morales G, Abelson B, Reasoner S, Miller J, Earl AM, Hadjifrangiskou M, Schmitz J. The Role of Mobile Genetic Elements in Virulence Factor Carriage from Symptomatic and Asymptomatic Cases of Escherichia coli Bacteriuria. Microbiol Spectr 2023; 11:e0471022. [PMID: 37195213 PMCID: PMC10269530 DOI: 10.1128/spectrum.04710-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 05/01/2023] [Indexed: 05/18/2023] Open
Abstract
Uropathogenic Escherichia coli (UPEC) is extremely diverse genotypically and phenotypically. Individual strains can variably carry diverse virulence factors, making it challenging to define a molecular signature for this pathotype. For many bacterial pathogens, mobile genetic elements (MGEs) constitute a major mechanism of virulence factor acquisition. For urinary E. coli, the total distribution of MGEs and their role in the acquisition of virulence factors is not well defined, including in the context of symptomatic infection versus asymptomatic bacteriuria (ASB). In this work, we characterized 151 isolates of E. coli, derived from patients with either urinary tract infection (UTI) or ASB. For both sets of E. coli, we catalogued the presence of plasmids, prophage, and transposons. We analyzed MGE sequences for the presence of virulence factors and antimicrobial resistance genes. These MGEs were associated with only ~4% of total virulence associated genes, while plasmids contributed to ~15% of antimicrobial resistance genes under consideration. Our analyses suggests that, across strains of E. coli, MGEs are not a prominent driver of urinary tract pathogenesis and symptomatic infection. IMPORTANCE Escherichia coli is the most common etiological agent of urinary tract infections (UTIs), with UTI-associated strains designated "uropathogenic" E. coli or UPEC. Across urinary strains of E. coli, the global landscape of MGEs and its relationship to virulence factor carriage and clinical symptomatology require greater clarity. Here, we demonstrate that many of the putative virulence factors of UPEC are not associated with acquisition due to MGEs. The current work enhances our understanding of the strain-to-strain variability and pathogenic potential of urine-associated E. coli and points toward more subtle genomic differences distinguishing ASB from UTI isolates.
Collapse
Affiliation(s)
- Grace Morales
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, USA
| | - Benjamin Abelson
- Department of Urology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Seth Reasoner
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, USA
| | - Jordan Miller
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, USA
| | - Ashlee M. Earl
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Maria Hadjifrangiskou
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, USA
- Department of Urology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University, Nashville, Tennessee, USA
| | - Jonathan Schmitz
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, USA
- Department of Urology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University, Nashville, Tennessee, USA
| |
Collapse
|
3
|
Riley AB, Grillo MA, Epstein B, Tiffin P, Heath KD. Discordant population structure among rhizobium divided genomes and their legume hosts. Mol Ecol 2023; 32:2646-2659. [PMID: 36161739 DOI: 10.1111/mec.16704] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 11/29/2022]
Abstract
Symbiosis often occurs between partners with distinct life history characteristics and dispersal mechanisms. Many bacterial symbionts have genomes comprising multiple replicons with distinct rates of evolution and horizontal transmission. Such differences might drive differences in population structure between hosts and symbionts and among the elements of the divided genomes of bacterial symbionts. These differences might, in turn, shape the evolution of symbiotic interactions and bacterial evolution. Here we use whole genome resequencing of a hierarchically structured sample of 191 strains of Sinorhizobium meliloti collected from 21 locations in southern Europe to characterize population structures of this bacterial symbiont, which forms a root nodule symbiosis with the host plant Medicago truncatula. S. meliloti genomes showed high local (within-site) variation and little isolation by distance. This was particularly true for the two symbiosis elements, pSymA and pSymB, which have population structures that are similar to each other, but distinct from both the bacterial chromosome and the host plant. Given limited recombination on the chromosome, compared to the symbiosis elements, distinct population structures may result from differences in effective gene flow. Alternatively, positive or purifying selection, with little recombination, may explain distinct geographical patterns at the chromosome. Discordant population structure between hosts and symbionts indicates that geographically and genetically distinct host populations in different parts of the range might interact with genetically similar symbionts, potentially minimizing local specialization.
Collapse
Affiliation(s)
- Alex B Riley
- Department of Plant Biology, University of Illinois, Urbana, Illinois, USA
| | - Michael A Grillo
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Brendan Epstein
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Katy D Heath
- Department of Plant Biology, University of Illinois, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA
| |
Collapse
|
4
|
Silva-de-Jesus AC, Ferrari RG, Panzenhagen P, Conte-Junior CA. Staphylococcus aureus biofilm: the role in disseminating antimicrobial resistance over the meat chain. Microbiology (Reading) 2022; 168. [PMID: 36201337 DOI: 10.1099/mic.0.001245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Staphylococcus aureus is responsible for severe skin and respiratory infections and food poisoning, resulting in hospitalizations and high morbidity worldwide. Staphylococci have extensive virulence mechanisms and antimicrobial resistance that pose a global challenge to contain the spread of infectious outbreaks. Antimicrobials are used as growth promoters, and for prevention and treatment of infections in animals that provide us with food. The improvement of animal health is undeniable, but the selection of multidrug-resistant strains that can spread resistance genes among microorganisms is undesirable. The administration of sublethal doses of antimicrobials in farm animals causes stress to Staphylococci inducing the formation of a complex extracellular polymeric structure called biofilm. Such a structure may favor the persistence of infection by disseminating antimicrobial-resistant strains that can be consumed in contaminated food of animal origin. In ruminant mastitis and hospitals, the potential of the biofilm structure in the persistence of infections, especially those caused by S. aureus, has already been demonstrated, as well as its role as a source of resistant genes. In the meat production chain, the potential for persistent contamination by biofilm structure is evidently a worrying health risk . This review brings together studies demonstrating that biofilm production facilitates the exchange of mobile genetic elements and random mutations in S. aureus strains within the structure. This contributes to the emergence of more resistant clonal complexes and, with biofilm support, persists in the meat production chain.
Collapse
Affiliation(s)
- Ana Carolina Silva-de-Jesus
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, 21941-598, Brazil.,Chemistry Institute, Food Science Program, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rafaela Gomes Ferrari
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, 21941-598, Brazil.,Chemistry Institute, Food Science Program, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Department of Zootechnics, Agrarian Sciences Center, Federal University of Paraiba, Paraíba, Brazil
| | - Pedro Panzenhagen
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, 21941-598, Brazil.,Chemistry Institute, Food Science Program, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Molecular & Analytical Laboratory Center, Faculty of Veterinary, Department of Food Technology, Universidade Federal Fluminense, Niterói, Brazil
| | - Carlos Adam Conte-Junior
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, 21941-598, Brazil.,Chemistry Institute, Food Science Program, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, 21941-909, Brazil.,Graduate Program in Food Science (PPGCAL), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, 21941-909, Brazil.,Graduate Program in Veterinary Hygiene (PPGHV), Faculty of Veterinary Medicine, Fluminense Federal University (UFF), Vital Brazil Filho, Niterói, RJ, 24220-000, Brazil.,Graduate Program in Sanitary Surveillance (PPGVS), National Institute of Health Quality Control (INCQS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, 21040-900, Brazil.,Graduate Program in Chemistry (PGQu), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, 21941-909, Brazil
| |
Collapse
|
5
|
Wu R, Cao Z, Jiang Y, Chen W, Sun Y, Li Q, Mi J, Deng L, Liao X, Feng Y, Lan T, Ma J. Early life dynamics of ARG and MGE associated with intestinal virome in neonatal piglets. Vet Microbiol 2022; 274:109575. [PMID: 36191572 DOI: 10.1016/j.vetmic.2022.109575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/08/2022] [Accepted: 09/11/2022] [Indexed: 10/31/2022]
Abstract
The pre- and post-weaning stages for piglets are critical periods for the maturation of intestinal functions and contamination with antibiotic resistant bacterial pathogens will threaten their intestinal health. The presence of bacteriophage can also alter bacterial populations in the intestine but whether transmission of antibiotic resistance genes (ARG) is affected by phage during maturation of the neonatal piglet intestine is not known. We therefore identified the intestinal virome along with ARGs and mobile genetic elements (MGE) from piglet fecal samples collected from 3 to 28 days representing the different growth stages. We found wide fluctuations for the intestinal virome of weaning piglets and most virus - related antibiotic resistance was derived from temperate phage suggesting a reservoir of multidrug resistance was present in the neonatal porcine gut. Our results provide a comprehensive understanding of ARGs associated with the intestinal virome that therefore represents a potential risk for horizontal ARG transfer to pathogenic bacteria.
Collapse
Affiliation(s)
- Ruiting Wu
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou 510642, Guangdong, China
| | - Ze Cao
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou 510642, Guangdong, China
| | - Yiming Jiang
- Institute of Virology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Institute of Virology, Technical University of Munich, Munich, Germany
| | - Wei Chen
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou 510642, Guangdong, China
| | - Yuan Sun
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou 510642, Guangdong, China
| | - Qianniu Li
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou 510642, Guangdong, China
| | - Jiandui Mi
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou 510642, Guangdong, China
| | - Li Deng
- Institute of Virology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Institute of Virology, Technical University of Munich, Munich, Germany
| | - Xindi Liao
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou 510642, Guangdong, China
| | - Yaoyu Feng
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, China
| | - Tian Lan
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou 510642, Guangdong, China
| | - Jingyun Ma
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou 510642, Guangdong, China.
| |
Collapse
|
6
|
Abstract
Originally, viruses were defined as miniscule infectious agents that passed through filters that retain even the smallest cells. Subsequently, viruses were considered obligate intracellular parasites whose reproduction depends on their cellular hosts for energy supply and molecular building blocks. However, these features are insufficient to unambiguously define viruses as they are broadly understood today. We outline possible approaches to define viruses and explore the boundaries of the virosphere within the virtual space of replicators and the relationships between viruses and other types of replicators. Regardless of how, exactly, viruses are defined, viruses clearly have evolved on many occasions from nonviral replicators, such as plasmids, by recruiting host proteins to become virion components. Conversely, other types of replicators have repeatedly evolved from viruses. Thus, the virosphere is a dynamic entity with extensive evolutionary traffic across its boundaries. We argue that the virosphere proper, here termed orthovirosphere, consists of a distinct variety of replicators that encode structural proteins encasing the replicators' genomes, thereby providing protection and facilitating transmission among hosts. Numerous and diverse replicators, such as virus-derived but capsidless RNA and DNA elements, or defective viruses occupy the zone surrounding the orthovirosphere in the virtual replicator space. We define this zone as the perivirosphere. Although intense debates on the nature of certain replicators that adorn the internal and external boundaries of the virosphere will likely continue, we present an operational definition of virus that recently has been accepted by the International Committee on Taxonomy of Viruses.
Collapse
Affiliation(s)
- Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Valerian V. Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, France
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA
| |
Collapse
|
7
|
Iannelli F, Santoro F, Fox V, Pozzi G. A Mating Procedure for Genetic Transfer of Integrative and Conjugative Elements (ICEs) of Streptococci and Enterococci. Methods Protoc 2021; 4:59. [PMID: 34564305 DOI: 10.3390/mps4030059] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/21/2021] [Accepted: 08/26/2021] [Indexed: 11/21/2022] Open
Abstract
DNA sequencing of whole bacterial genomes has revealed that the entire set of mobile genes (mobilome) represents as much as 25% of the bacterial genome. Despite the huge availability of sequence data, the functional analysis of the mobile genetic elements (MGEs) is rarely reported. Therefore, established laboratory protocols are needed to investigate the biology of this important part of the bacterial genome. Conjugation is a mechanism of horizontal gene transfer which allows the exchange of MGEs among strains of the same or different bacterial species. In streptococci and enterococci, integrative and conjugative elements (ICEs) represent a large part of the mobilome. Here, we describe an efficient and easy-to-perform plate mating protocol for in vitro conjugative transfer of ICEs in streptococci (Streptococcus pneumoniae, Streptococcus agalactiae, Streptococcus gordonii, Streptococcus pyogenes), Enterococcus faecalis, and Bacillus subtilis. Conjugative transfer is carried out on solid media and selection of transconjugants is performed with a multilayer plating. This protocol allows the transfer of large genetic elements with a size up to 81 kb, and a transfer frequency up to 6.7 × 10−3 transconjugants/donor cells.
Collapse
|
8
|
Zhang H, Wang H, Ma Z, Liu Y, Wu Z, Xu H, Qiao M. Characterization of Proteus vulgaris Strain P3M, a Foodborne Multidrug-Resistant Bacterium Isolated from Penaeus vannamei in China. Microb Drug Resist 2021; 27:1360-1370. [PMID: 33877915 DOI: 10.1089/mdr.2020.0502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Proteus vulgaris is an important foodborne opportunistic pathogen, both environmentally and clinically. The use of appropriate antibiotics has significant therapeutic effects, but has led to the emergence and spread of drug-resistant strains. In this study, a P. vulgaris strain, designated "P3M," was isolated from Penaeus vannamei in Tianjin, China. The whole genome of P3M was sequenced, generating detailed information, including the key genes involved in important metabolic pathways and their physiological functions. A total of 218 antibiotic resistance genes (ARGs) were predicted in the genome. The determination of various minimum inhibitory concentrations indicated that P3M is a multidrug-resistant (MDR) bacterium, with significant resistance to 16 antibiotics in seven categories. Determination of fractional inhibitory concentration index showed that the combination of ciprofloxacin plus tetracycline exhibited synergistic antimicrobial activity. Bioinformatics and phylogenetic analyses detected the presence of two two-component systems that mediate multidrug resistance and several mobile genetic elements involved in the horizontal transfer of ARGs in P3M. P. vulgaris strains represent a serious challenge to clinicians and infection control teams for its ubiquity worldwide and close relevance with human life. To the best of our knowledge, we report the first isolation and characterization of an important foodborne MDR P. vulgaris strain, and this study will provide necessary theoretical basis for the selection and clinical use of the appropriate antibiotics.
Collapse
Affiliation(s)
- Hongyang Zhang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Hesuiyuan Wang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Zhongqiang Ma
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Yujie Liu
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Zhenzhou Wu
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Haijin Xu
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Mingqiang Qiao
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| |
Collapse
|
9
|
Kayali O, Icgen B. intI1 Type Mobile Genetic Elements Co-selected Antibiotic-Resistant Genes in Untreated Hospital Wastewaters. Bull Environ Contam Toxicol 2021; 106:399-405. [PMID: 33471190 DOI: 10.1007/s00128-020-03098-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 12/25/2020] [Indexed: 06/12/2023]
Abstract
Dissemination of antibiotic-resistant genes (ARGs) from hospital wastewaters (HWWs) is facilitated by the horizontal gene transfer (HGT) and involves association of ARGs with mobile genetic elements (MGEs). In our previous study, HWWs were found to have relatively high copy numbers of ARGs aadA, tetA, cmlA, sul1, and qnrS. In this study, therefore, the same HWWs were also monitored for 3 MGEs class 1 integron (intI1), insertion sequence common region 1 (ISCR1) and conjugative transposon Tn916/Tn1545 by using quantitative polymerase chain reaction. The gene intI1 with 7.4 × 102 average copy number/mL was found to be the most prevalent MGE and was up to two orders of magnitude higher than ISCR1 (5.5 × 100 average copy number/mL, p < 0.05) and Tn916/Tn1545 (2.3 × 100 average copy number/mL, p < 0.05) in all HWWs tested. Positive correlation between intI1 and the aadA, tetA, cmlA and sul1 genes indicated that the MGEs harbouring class1 integron most likely played major role in co-selecting all these ARGs together.
Collapse
Affiliation(s)
- Osman Kayali
- Department of Biotechnology, Middle East Technical University, 06800, Ankara, Turkey
| | - Bulent Icgen
- Department of Biotechnology, Middle East Technical University, 06800, Ankara, Turkey.
- Department of Environmental Engineering, Middle East Technical University, 06800, Ankara, Turkey.
| |
Collapse
|
10
|
Lukacsovich D, Winterer J, Que L, Luo W, Lukacsovich T, Földy C. Single-Cell RNA-Seq Reveals Developmental Origins and Ontogenetic Stability of Neurexin Alternative Splicing Profiles. Cell Rep 2020; 27:3752-3759.e4. [PMID: 31242409 DOI: 10.1016/j.celrep.2019.05.090] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 02/08/2019] [Accepted: 05/22/2019] [Indexed: 12/12/2022] Open
Abstract
Neurexins are key synaptic organizers that are expressed in thousands of alternatively spliced isoforms. Because transsynaptic neurexin interactions with different postsynaptic molecules are largely isoform dependent, a cell type-level census of different neurexin isoforms could predict molecular interactions relating to synapse identity and function. Using single-cell transcriptomics to study the origin of neurexin diversity in multiple murine mature and embryonic cell types, we have discovered shared neurexin expression patterns in developmentally related cells. By comparing neurexin profiles in immature embryonic neurons, we show that neurexin profiles are specified during early development and remain unchanged throughout neuronal maturation. Thus, our findings reveal ontogenetic stability and provide a cell type-level census of neurexin isoform expression in the cortex.
Collapse
Affiliation(s)
- David Lukacsovich
- Laboratory of Neural Connectivity, Brain Research Institute, Faculties of Medicine and Natural Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Jochen Winterer
- Laboratory of Neural Connectivity, Brain Research Institute, Faculties of Medicine and Natural Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Lin Que
- Laboratory of Neural Connectivity, Brain Research Institute, Faculties of Medicine and Natural Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Wenshu Luo
- Laboratory of Neural Connectivity, Brain Research Institute, Faculties of Medicine and Natural Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Tamas Lukacsovich
- Laboratory of Neural Connectivity, Brain Research Institute, Faculties of Medicine and Natural Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Csaba Földy
- Laboratory of Neural Connectivity, Brain Research Institute, Faculties of Medicine and Natural Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
| |
Collapse
|
11
|
Mancia Leon WR, Spatazza J, Rakela B, Chatterjee A, Pande V, Maniatis T, Hasenstaub AR, Stryker MP, Alvarez-Buylla A. Clustered gamma-protocadherins regulate cortical interneuron programmed cell death. eLife 2020; 9:e55374. [PMID: 32633719 PMCID: PMC7373431 DOI: 10.7554/elife.55374] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 07/06/2020] [Indexed: 01/19/2023] Open
Abstract
Cortical function critically depends on inhibitory/excitatory balance. Cortical inhibitory interneurons (cINs) are born in the ventral forebrain and migrate into cortex, where their numbers are adjusted by programmed cell death. Here, we show that loss of clustered gamma protocadherins (Pcdhg), but not of genes in the alpha or beta clusters, increased dramatically cIN BAX-dependent cell death in mice. Surprisingly, electrophysiological and morphological properties of Pcdhg-deficient and wild-type cINs during the period of cIN cell death were indistinguishable. Co-transplantation of wild-type with Pcdhg-deficient interneuron precursors further reduced mutant cIN survival, but the proportion of mutant and wild-type cells undergoing cell death was not affected by their density. Transplantation also allowed us to test for the contribution of Pcdhg isoforms to the regulation of cIN cell death. We conclude that Pcdhg, specifically Pcdhgc3, Pcdhgc4, and Pcdhgc5, play a critical role in regulating cIN survival during the endogenous period of programmed cIN death.
Collapse
Affiliation(s)
- Walter R Mancia Leon
- Department of Neurological Surgery and The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San FranciscoSan FranciscoUnited States
| | - Julien Spatazza
- Department of Neurological Surgery and The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San FranciscoSan FranciscoUnited States
| | - Benjamin Rakela
- Department of Physiology and Center for Integrative Neuroscience, University of California, San FranciscoSan FranciscoUnited States
| | - Ankita Chatterjee
- Department of Neurological Surgery and The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San FranciscoSan FranciscoUnited States
| | - Viraj Pande
- Department of Neurological Surgery and The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San FranciscoSan FranciscoUnited States
| | - Tom Maniatis
- Department of Biochemistry and Molecular Biophysics, Columbia UniversityNew YorkUnited States
| | - Andrea R Hasenstaub
- Department of Otolaryngology-Head and Neck Surgery, University of California, San FranciscoSan FranciscoUnited States
- Kavli Institute for Fundamental Neuroscience, University of California, San FranciscoSan FranciscoUnited States
| | - Michael P Stryker
- Department of Physiology and Center for Integrative Neuroscience, University of California, San FranciscoSan FranciscoUnited States
- Kavli Institute for Fundamental Neuroscience, University of California, San FranciscoSan FranciscoUnited States
| | - Arturo Alvarez-Buylla
- Department of Neurological Surgery and The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San FranciscoSan FranciscoUnited States
- Kavli Institute for Fundamental Neuroscience, University of California, San FranciscoSan FranciscoUnited States
| |
Collapse
|
12
|
Pai ELL, Chen J, Fazel Darbandi S, Cho FS, Chen J, Lindtner S, Chu JS, Paz JT, Vogt D, Paredes MF, Rubenstein JLR. Maf and Mafb control mouse pallial interneuron fate and maturation through neuropsychiatric disease gene regulation. eLife 2020; 9:e54903. [PMID: 32452758 PMCID: PMC7282818 DOI: 10.7554/elife.54903] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 05/22/2020] [Indexed: 12/31/2022] Open
Abstract
Maf (c-Maf) and Mafb transcription factors (TFs) have compensatory roles in repressing somatostatin (SST+) interneuron (IN) production in medial ganglionic eminence (MGE) secondary progenitors in mice. Maf and Mafb conditional deletion (cDKO) decreases the survival of MGE-derived cortical interneurons (CINs) and changes their physiological properties. Herein, we show that (1) Mef2c and Snap25 are positively regulated by Maf and Mafb to drive IN morphological maturation; (2) Maf and Mafb promote Mef2c expression which specifies parvalbumin (PV+) INs; (3) Elmo1, Igfbp4 and Mef2c are candidate markers of immature PV+ hippocampal INs (HIN). Furthermore, Maf/Mafb neonatal cDKOs have decreased CINs and increased HINs, that express Pnoc, an HIN specific marker. Our findings not only elucidate key gene targets of Maf and Mafb that control IN development, but also identify for the first time TFs that differentially regulate CIN vs. HIN production.
Collapse
Affiliation(s)
- Emily Ling-Lin Pai
- Department of Psychiatry, University of California San FranciscoSan FranciscoUnited States
- Neuroscience Graduate Program, University of California San FranciscoSan FranciscoUnited States
| | - Jin Chen
- Department of Cellular and Molecular Pharmacology, University of California San FranciscoSan FranciscoUnited States
- Howard Hughes Medical Institute, University of California San FranciscoSan FranciscoUnited States
| | - Siavash Fazel Darbandi
- Department of Psychiatry, University of California San FranciscoSan FranciscoUnited States
| | - Frances S Cho
- Neuroscience Graduate Program, University of California San FranciscoSan FranciscoUnited States
- Department of Neurology, University of California San FranciscoSan FranciscoUnited States
- Gladstone Institute of Neurological Disease, Gladstone InstitutesSan FranciscoUnited States
| | - Jiapei Chen
- Gladstone Institute of Neurological Disease, Gladstone InstitutesSan FranciscoUnited States
- Biomedical Sciences Graduate Program, University of California San FranciscoSan FranciscoUnited States
| | - Susan Lindtner
- Department of Psychiatry, University of California San FranciscoSan FranciscoUnited States
| | - Julia S Chu
- Department of Neurology, University of California San FranciscoSan FranciscoUnited States
| | - Jeanne T Paz
- Neuroscience Graduate Program, University of California San FranciscoSan FranciscoUnited States
- Department of Neurology, University of California San FranciscoSan FranciscoUnited States
- Gladstone Institute of Neurological Disease, Gladstone InstitutesSan FranciscoUnited States
- The Kavli Institute for Fundamental Neuroscience, University of California San FranciscoSan FranciscoUnited States
| | - Daniel Vogt
- Department of Pediatrics and Human Development, Michigan State UniversityGrand RapidsUnited States
| | - Mercedes F Paredes
- Neuroscience Graduate Program, University of California San FranciscoSan FranciscoUnited States
- Department of Neurology, University of California San FranciscoSan FranciscoUnited States
- The Kavli Institute for Fundamental Neuroscience, University of California San FranciscoSan FranciscoUnited States
| | - John LR Rubenstein
- Department of Psychiatry, University of California San FranciscoSan FranciscoUnited States
- The Kavli Institute for Fundamental Neuroscience, University of California San FranciscoSan FranciscoUnited States
| |
Collapse
|
13
|
Angara K, Pai ELL, Bilinovich SM, Stafford AM, Nguyen JT, Li KX, Paul A, Rubenstein JL, Vogt D. Nf1 deletion results in depletion of the Lhx6 transcription factor and a specific loss of parvalbumin + cortical interneurons. Proc Natl Acad Sci U S A 2020; 117:6189-6195. [PMID: 32123116 PMCID: PMC7084085 DOI: 10.1073/pnas.1915458117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Neurofibromatosis 1 (NF1) is caused by mutations in the NF1 gene, which encodes the protein, neurofibromin, an inhibitor of Ras activity. Cortical GABAergic interneurons (CINs) are implicated in NF1 pathology, but the cellular and molecular changes to CINs are unknown. We deleted mouse Nf1 from the medial ganglionic eminence, which gives rise to both oligodendrocytes and CINs that express somatostatin and parvalbumin. Nf1 loss led to a persistence of immature oligodendrocytes that prevented later-generated oligodendrocytes from occupying the cortex. Moreover, molecular and cellular properties of parvalbumin (PV)-positive CINs were altered by the loss of Nf1, without changes in somatostatin (SST)-positive CINs. We discovered that loss of Nf1 results in a dose-dependent decrease in Lhx6 expression, the transcription factor necessary to establish SST+ and PV+ CINs, which was rescued by the MEK inhibitor SL327, revealing a mechanism whereby a neurofibromin/Ras/MEK pathway regulates a critical CIN developmental milestone.
Collapse
Affiliation(s)
- Kartik Angara
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503
| | - Emily Ling-Lin Pai
- Department of Psychiatry, University of California, San Francisco, CA 94158
- Neuroscience Program, University of California, San Francisco, CA 94158
- Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, CA 94158
| | - Stephanie M Bilinovich
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503
| | - April M Stafford
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503
| | - Julie T Nguyen
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503
| | - Katie X Li
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503
| | - Anirban Paul
- Department of Neural and Behavioral Sciences, PennState University, Hershey, PA 17033
| | - John L Rubenstein
- Department of Psychiatry, University of California, San Francisco, CA 94158
- Neuroscience Program, University of California, San Francisco, CA 94158
- Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, CA 94158
| | - Daniel Vogt
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503;
- Neuroscience Program, Michigan State University, Grand Rapids, MI 49503
| |
Collapse
|
14
|
Pai ELL, Vogt D, Clemente-Perez A, McKinsey GL, Cho FS, Hu JS, Wimer M, Paul A, Fazel Darbandi S, Pla R, Nowakowski TJ, Goodrich LV, Paz JT, Rubenstein JLR. Mafb and c-Maf Have Prenatal Compensatory and Postnatal Antagonistic Roles in Cortical Interneuron Fate and Function. Cell Rep 2020; 26:1157-1173.e5. [PMID: 30699346 PMCID: PMC6602795 DOI: 10.1016/j.celrep.2019.01.031] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 11/17/2018] [Accepted: 01/08/2019] [Indexed: 10/27/2022] Open
Abstract
Mafb and c-Maf transcription factor (TF) expression is enriched in medial ganglionic eminence (MGE) lineages, beginning in late-secondary progenitors and continuing into mature parvalbumin (PV+) and somatostatin (SST+) interneurons. However, the functions of Maf TFs in MGE development remain to be elucidated. Herein, Mafb and c-Maf were conditionally deleted, alone and together, in the MGE and its lineages. Analyses of Maf mutant mice revealed redundant functions of Mafb and c-Maf in secondary MGE progenitors, where they repress the generation of SST+ cortical and hippocampal interneurons. By contrast, Mafb and c-Maf have distinct roles in postnatal cortical interneuron (CIN) morphological maturation, synaptogenesis, and cortical circuit integration. Thus, Mafb and c-Maf have redundant and opposing functions at different steps in CIN development.
Collapse
Affiliation(s)
- Emily Ling-Lin Pai
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Daniel Vogt
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, USA
| | - Alexandra Clemente-Perez
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA; Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA
| | - Gabriel L McKinsey
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Frances S Cho
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA; Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA
| | - Jia Sheng Hu
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Matt Wimer
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA; Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA
| | - Anirban Paul
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Siavash Fazel Darbandi
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ramon Pla
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Tomasz J Nowakowski
- Department of Anatomy, Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lisa V Goodrich
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Jeanne T Paz
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA; Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA
| | - John L R Rubenstein
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA.
| |
Collapse
|
15
|
Browne PD, Kot W, Jørgensen TS, Hansen LH. The Mobilome: Metagenomic Analysis of Circular Plasmids, Viruses, and Other Extrachromosomal Elements. Methods Mol Biol 2020; 2075:253-264. [PMID: 31584168 DOI: 10.1007/978-1-4939-9877-7_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Isolation, sequencing, and analysis of circular genetic elements bring new insights to mobile genetic elements related to microbial ecology. One method used to study circular plasmids, viruses, and other elements is called the mobilome method. The mobilome method presented here is an unamplified mobilome approach allowing fast isolation of circular DNA elements from a variety of samples followed by directly building unamplified Illumina-compatible sequencing libraries using enzymatic tagging and fragmentation. Several methods for bioinformatic analysis of mobilome data are also suggested.
Collapse
Affiliation(s)
- Patrick Denis Browne
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Witold Kot
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Tue Sparholt Jørgensen
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
- DTU BIOSUSTAIN, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Lars Hestbjerg Hansen
- Department of Environmental Science, Aarhus University, Roskilde, Denmark.
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark.
| |
Collapse
|
16
|
Ortiz-Severín J, Travisany D, Maass A, Chávez FP, Cambiazo V. Piscirickettsia salmonis Cryptic Plasmids: Source of Mobile DNA and Virulence Factors. Pathogens 2019; 8:E269. [PMID: 31795181 DOI: 10.3390/pathogens8040269] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/18/2019] [Accepted: 11/22/2019] [Indexed: 11/16/2022] Open
Abstract
Four large cryptic plasmids were identified in the salmon pathogen Piscirickettsia salmonis reference strain LF-89. These plasmids appeared highly novel, with less than 7% nucleotidic identity to the nr plasmid database. Plasmid copy number analysis revealed that they are harbored in chromosome equivalent ratios. In addition to plasmid-related genes (plasmidial autonomous replication, partitioning, maintenance, and mobilization genes), mobile genetic elements such as transposases, integrases, and prophage sequences were also identified in P. salmonis plasmids. However, bacterial lysis was not observed upon the induction of prophages. A total of twelve putative virulence factors (VFs) were identified, in addition to two global transcriptional regulators, the widely conserved CsrA protein and the regulator Crp/Fnr. Eleven of the putative VFs were overexpressed during infection in two salmon-derived cellular infection models, supporting their role as VFs. The ubiquity of these plasmids was also confirmed by sequence similarity in the genomes of other P. salmonis strains. The ontology of P. salmonis plasmids suggests a role in bacterial fitness and adaptation to the environment as they encode proteins related to mobilization, nutrient transport and utilization, and bacterial virulence. Further functional characterization of P. salmonis plasmids may improve our knowledge regarding virulence and mobile elements in this intracellular pathogen.
Collapse
|
17
|
Duan ZRS, Che A, Chu P, Modol L, Bollmann Y, Babij R, Fetcho RN, Otsuka T, Fuccillo MV, Liston C, Pisapia DJ, Cossart R, De Marco García NV. GABAergic Restriction of Network Dynamics Regulates Interneuron Survival in the Developing Cortex. Neuron 2019; 105:75-92.e5. [PMID: 31780329 DOI: 10.1016/j.neuron.2019.10.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 07/23/2019] [Accepted: 10/01/2019] [Indexed: 12/15/2022]
Abstract
During neonatal development, sensory cortices generate spontaneous activity patterns shaped by both sensory experience and intrinsic influences. How these patterns contribute to the assembly of neuronal circuits is not clearly understood. Using longitudinal in vivo calcium imaging in un-anesthetized mouse pups, we show that spatially segregated functional assemblies composed of interneurons and pyramidal cells are prominent in the somatosensory cortex by postnatal day (P) 7. Both reduction of GABA release and synaptic inputs onto pyramidal cells erode the emergence of functional topography, leading to increased network synchrony. This aberrant pattern effectively blocks interneuron apoptosis, causing increased survival of parvalbumin and somatostatin interneurons. Furthermore, the effect of GABA on apoptosis is mediated by inputs from medial ganglionic eminence (MGE)-derived but not caudal ganglionic eminence (CGE)-derived interneurons. These findings indicate that immature MGE interneurons are fundamental for shaping GABA-driven activity patterns that balance the number of interneurons integrating into maturing cortical networks.
Collapse
Affiliation(s)
- Zhe Ran S Duan
- Center for Neurogenetics, Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA; Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10021, USA
| | - Alicia Che
- Center for Neurogenetics, Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Philip Chu
- Center for Neurogenetics, Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Laura Modol
- Aix Marseille University, INSERM, INMED, Turing Center for Living Systems, Marseille, France
| | - Yannick Bollmann
- Aix Marseille University, INSERM, INMED, Turing Center for Living Systems, Marseille, France
| | - Rachel Babij
- Center for Neurogenetics, Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA; Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10021, USA
| | - Robert N Fetcho
- Center for Neurogenetics, Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA; Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10021, USA
| | - Takumi Otsuka
- Center for Neurogenetics, Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Marc V Fuccillo
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Conor Liston
- Center for Neurogenetics, Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - David J Pisapia
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Rosa Cossart
- Aix Marseille University, INSERM, INMED, Turing Center for Living Systems, Marseille, France
| | - Natalia V De Marco García
- Center for Neurogenetics, Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA.
| |
Collapse
|
18
|
Pallares-Vega R, Blaak H, van der Plaats R, de Roda Husman AM, Hernandez Leal L, van Loosdrecht MCM, Weissbrodt DG, Schmitt H. Determinants of presence and removal of antibiotic resistance genes during WWTP treatment: A cross-sectional study. Water Res 2019; 161:319-328. [PMID: 31203037 DOI: 10.1016/j.watres.2019.05.100] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 05/28/2019] [Accepted: 05/29/2019] [Indexed: 05/21/2023]
Abstract
Wastewater treatment plants (WWTPs), linking human fecal residues and the environment, are considered as hotspots for the spread of antimicrobial resistance (AMR). In order to evaluate the role of WWTPs and underlying operational parameters for the removal of AMR, the presence and removal efficiency of a selected set of 6 antimicrobial resistance genes (ARGs) and 2 mobile genetic elements (MGEs) was evaluated by means of qPCR in influent and effluent samples from 62 Dutch WWTPs. The role of possible factors impacting the concentrations of ARGs and MGEs in the influent and their removal was identified through statistical analysis. ARGs and the class I integron-integrase gene (intI1) were, on average, removed to a similar extent (1.76 log reduction) or better (+0.30-1.90 logs) than the total bacteria (measured as 16S rRNA gene). In contrast, broad-host-range plasmids (IncP-1) had a significantly increased (p < 0.001) relative abundance after treatment. The presence of healthcare institutions in the area served did only slightly increase the concentrations of ARGs or MGEs in influent. From the extended panel of operational parameters, rainfall, increasing the hydraulic load of the plant, most significantly (p < 0.05) affected the treatment efficiency by decreasing it on average -0.38 logs per time the flow exceeded the average daily flow. Our results suggest that overall, WWTP treatments do not favor the proliferation of the assessed resistance genes but might increase the relative abundance of broad-host-range plasmids of the IncP-1 type.
Collapse
Affiliation(s)
- Rebeca Pallares-Vega
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, the Netherlands; Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Hetty Blaak
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
| | | | - Ana M de Roda Husman
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
| | - Lucia Hernandez Leal
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, the Netherlands
| | | | - David G Weissbrodt
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Heike Schmitt
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, the Netherlands; Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands; Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands.
| |
Collapse
|
19
|
Flores-Ríos R, Quatrini R, Loyola A. Endogenous and Foreign Nucleoid-Associated Proteins of Bacteria: Occurrence, Interactions and Effects on Mobile Genetic Elements and Host's Biology. Comput Struct Biotechnol J 2019; 17:746-756. [PMID: 31303979 PMCID: PMC6606824 DOI: 10.1016/j.csbj.2019.06.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/05/2019] [Accepted: 06/11/2019] [Indexed: 02/08/2023] Open
Abstract
Mobile Genetic Elements (MGEs) are mosaics of functional gene modules of diverse evolutionary origin and are generally divergent from the hosts´ genetic background. Existing biases in base composition and codon usage of these elements` genes impose transcription and translation limitations that may affect the physical and regulatory integration of MGEs in new hosts. Stable appropriation of the foreign DNA depends on a number of host factors among which are the Nucleoid-Associated Proteins (NAPs). These small, basic, highly abundant proteins bind and bend DNA, altering its topology and folding, thereby affecting all known essential DNA metabolism related processes. Both chromosomally- (endogenous) and MGE- (foreign) encoded NAPs have been shown to exist in bacteria. While the role of host-encoded NAPs in xenogeneic silencing of both episomal (plasmids) and integrative MGEs (pathogenicity islands and prophages) is well acknowledged, less is known about the role of MGE-encoded NAPs in the foreign elements biology or their influence on the host's chromosome expression dynamics. Here we review existing literature on the topic, present examples on the positive and negative effects that endogenous and foreign NAPs exert on global transcriptional gene expression, MGE integrative and excisive recombination dynamics, persistence and transfer to suitable hosts and discuss the nature and relevance of synergistic and antagonizing higher order interactions between diverse types of NAPs.
Collapse
Affiliation(s)
| | - Raquel Quatrini
- Fundación Ciencia y Vida, Avenida Zañartu 1482, Ñuñoa, Santiago, Chile.,Millennium Nucleus in the Biology of Intestinal Microbiota, Santiago, Chile
| | - Alejandra Loyola
- Fundación Ciencia y Vida, Avenida Zañartu 1482, Ñuñoa, Santiago, Chile
| |
Collapse
|
20
|
Decano AG, Ludden C, Feltwell T, Judge K, Parkhill J, Downing T. Complete Assembly of Escherichia coli Sequence Type 131 Genomes Using Long Reads Demonstrates Antibiotic Resistance Gene Variation within Diverse Plasmid and Chromosomal Contexts. mSphere 2019; 4:e00130-19. [PMID: 31068432 PMCID: PMC6506616 DOI: 10.1128/msphere.00130-19] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 04/24/2019] [Indexed: 11/20/2022] Open
Abstract
The incidence of infections caused by extraintestinal Escherichia coli (ExPEC) is rising globally, which is a major public health concern. ExPEC strains that are resistant to antimicrobials have been associated with excess mortality, prolonged hospital stays, and higher health care costs. E. coli sequence type 131 (ST131) is a major ExPEC clonal group worldwide, with variable plasmid composition, and has an array of genes enabling antimicrobial resistance (AMR). ST131 isolates frequently encode the AMR genes blaCTX-M-14, blaCTX-M-15, and blaCTX-M-27, which are often rearranged, amplified, and translocated by mobile genetic elements (MGEs). Short DNA reads do not fully resolve the architecture of repetitive elements on plasmids to allow MGE structures encoding blaCTX-M genes to be fully determined. Here, we performed long-read sequencing to decipher the genome structures of six E. coli ST131 isolates from six patients. Most long-read assemblies generated entire chromosomes and plasmids as single contigs, in contrast to more fragmented assemblies created with short reads alone. The long-read assemblies highlighted diverse accessory genomes with blaCTX-M-15, blaCTX-M-14, and blaCTX-M-27 genes identified in three, one, and one isolates, respectively. One sample had no blaCTX-M gene. Two samples had chromosomal blaCTX-M-14 and blaCTX-M-15 genes, and the latter was at three distinct locations, likely transposed by the adjacent MGEs: ISEcp1, IS903B, and Tn2 This study showed that AMR genes exist in multiple different chromosomal and plasmid contexts, even between closely related isolates within a clonal group such as E. coli ST131.IMPORTANCE Drug-resistant bacteria are a major cause of illness worldwide, and a specific subtype called Escherichia coli ST131 causes a significant number of these infections. ST131 bacteria become resistant to treatments by modifying their DNA and by transferring genes among one another via large packages of genes called plasmids, like a game of pass-the-parcel. Tackling infections more effectively requires a better understanding of what plasmids are being exchanged and their exact contents. To achieve this, we applied new high-resolution DNA sequencing technology to six ST131 samples from infected patients and compared the output to that of an existing approach. A combination of methods shows that drug resistance genes on plasmids are highly mobile because they can jump into ST131's chromosomes. We found that the plasmids are very elastic and undergo extensive rearrangements even in closely related samples. This application of DNA sequencing technologies illustrates at a new level the highly dynamic nature of ST131 genomes.
Collapse
Affiliation(s)
| | - Catherine Ludden
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | - Kim Judge
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Tim Downing
- School of Biotechnology, Dublin City University, Dublin, Ireland
| |
Collapse
|
21
|
Zhang L, Yuan HJ, Cao B, Kong CC, Yuan F, Li J, Ni HY, Wu HY, Chang L, Liu Y, Luo CX. MGE-derived nNOS + interneurons promote fear acquisition in nNOS -/- mice. Biochem Biophys Res Commun 2017; 493:1560-1566. [PMID: 28974418 DOI: 10.1016/j.bbrc.2017.09.158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 09/28/2017] [Indexed: 10/18/2022]
Abstract
Neuronal nitric oxide synthase (nNOS) 1, mainly responsible for NO release in central nervous system (CNS) 2, plays a significant role in multiple physiological functions. However, the function of nNOS+ interneurons in fear learning has not been much explored. Here we focused on the medial ganglionic eminences (MGE) 3-derived nNOS+ interneurons in fear learning. To determine the origin of nNOS+ interneurons, we cultured neurons in vitro from MGE, cortex, lateral ganglionic eminence (LGE) 4, caudal ganglionic eminences (CGE) 5 and preoptic area (POA) 6. The results showed that MGE contained the most abundant precursors of nNOS+ interneurons. Moreover, donor cells from E12.5 embryos demonstrated the highest positive rate of nNOS+ interneurons compared with other embryonic periods (E11.5, E12, E13, E13.5 and E14). Additionally, these cells from E12.5 embryos showed long axonal and abundant dendritic arbors after 10 days culture, indicating the capability to disperse and integrate in host neural circuits after transplantation. To investigate the role of MGE-derived nNOS+ interneurons in fear learning, donor MGE cells were transplanted into dentate gyrus (DG) 7 of nNOS knock-out (nNOS-/-) or wild-type mice. Results showed that the transplantation of MGE cells promoted the acquisition of nNOS-/- but not the wild-type mice, suggesting the importance of nNOS+ neurons in fear acquisition. Moreover, we transplanted MGE cells from nNOS-/- mice or wild-type mice into DG of the nNOS-/- mice and found that only MGE cells from wild-type mice but not the nNOS-/- mice rescued the deficit in acquisition of the nNOS-/- mice, further confirming the positive role of nNOS+ neurons in fear learning.
Collapse
Affiliation(s)
- Lin Zhang
- Department of Pharmacology, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Hong-Jin Yuan
- Department of Pharmacology, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Bo Cao
- Department of Pharmacology, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Cheng-Cheng Kong
- Institution of Stem Cells and Neuroregeneration, Nanjing Medical University, Nanjing 211166, China
| | - Fang Yuan
- Institution of Stem Cells and Neuroregeneration, Nanjing Medical University, Nanjing 211166, China
| | - Jun Li
- Department of Pharmacology, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Huan-Yu Ni
- Department of Pharmacology, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Hai-Yin Wu
- Department of Pharmacology, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China; Laboratory of Cerebrovascular Disease, Nanjing Medical University, Nanjing 211166, China
| | - Lei Chang
- Department of Pharmacology, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China; Laboratory of Cerebrovascular Disease, Nanjing Medical University, Nanjing 211166, China
| | - Yan Liu
- Institution of Stem Cells and Neuroregeneration, Nanjing Medical University, Nanjing 211166, China
| | - Chun-Xia Luo
- Department of Pharmacology, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China; Laboratory of Cerebrovascular Disease, Nanjing Medical University, Nanjing 211166, China; Institution of Stem Cells and Neuroregeneration, Nanjing Medical University, Nanjing 211166, China.
| |
Collapse
|
22
|
Abstract
Cortical interneurons are a diverse group of neurons that project locally and are crucial for regulating information processing and flow throughout the cortex. Recent studies in mice have advanced our understanding of how these neurons are specified, migrate and mature. Here, we evaluate new findings that provide insights into the development of cortical interneurons and that shed light on when their fate is determined, on the influence that regional domains have on their development, and on the role that key transcription factors and other crucial regulatory genes play in these events. We focus on cortical interneurons that are derived from the medial ganglionic eminence, as most studies have examined this interneuron population. We also assess how these data inform our understanding of neuropsychiatric disease and discuss the potential role of cortical interneurons in cell-based therapies.
Collapse
Affiliation(s)
- Jia Sheng Hu
- Department of Psychiatry, University of California, San Francisco, CA 94158, USA.,Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, CA 94158, USA
| | - Daniel Vogt
- Department of Psychiatry, University of California, San Francisco, CA 94158, USA.,Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, CA 94158, USA
| | - Magnus Sandberg
- Department of Psychiatry, University of California, San Francisco, CA 94158, USA.,Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, CA 94158, USA
| | - John L Rubenstein
- Department of Psychiatry, University of California, San Francisco, CA 94158, USA .,Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, CA 94158, USA
| |
Collapse
|
23
|
Close JL, Yao Z, Levi BP, Miller JA, Bakken TE, Menon V, Ting JT, Wall A, Krostag AR, Thomsen ER, Nelson AM, Mich JK, Hodge RD, Shehata SI, Glass IA, Bort S, Shapovalova NV, Ngo NK, Grimley JS, Phillips JW, Thompson CL, Ramanathan S, Lein E. Single-Cell Profiling of an In Vitro Model of Human Interneuron Development Reveals Temporal Dynamics of Cell Type Production and Maturation. Neuron 2017; 93:1035-1048.e5. [PMID: 28279351 DOI: 10.1016/j.neuron.2017.02.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 11/12/2016] [Accepted: 01/30/2017] [Indexed: 12/31/2022]
Abstract
GABAergic interneurons are essential for neural circuit function, and their loss or dysfunction is implicated in human neuropsychiatric disease. In vitro methods for interneuron generation hold promise for studying human cellular and functional properties and, ultimately, for therapeutic cell replacement. Here we describe a protocol for generating cortical interneurons from hESCs and analyze the properties and maturation time course of cell types using single-cell RNA-seq. We find that the cell types produced mimic in vivo temporal patterns of neuron and glial production, with immature progenitors and neurons observed early and mature cortical neurons and glial cell types produced late. By comparing the transcriptomes of immature interneurons to those of more mature neurons, we identified genes important for human interneuron differentiation. Many of these genes were previously implicated in neurodevelopmental and neuropsychiatric disorders.
Collapse
Affiliation(s)
- Jennie L Close
- Allen Institute for Brain Science, Seattle, WA 98109, USA.
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Boaz P Levi
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Vilas Menon
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Abigail Wall
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Angel M Nelson
- Allen Institute for Cell Science, Seattle, WA 98109, USA
| | - John K Mich
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Ian A Glass
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Susan Bort
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - N Kiet Ngo
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | | | - Sharad Ramanathan
- Molecular and Cellular Biology Department, Harvard University, Cambridge, MA 02138, USA
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| |
Collapse
|
24
|
Jamrozy D, Coll F, Mather AE, Harris SR, Harrison EM, MacGowan A, Karas A, Elston T, Estée Török M, Parkhill J, Peacock SJ. Evolution of mobile genetic element composition in an epidemic methicillin-resistant Staphylococcus aureus: temporal changes correlated with frequent loss and gain events. BMC Genomics 2017; 18:684. [PMID: 28870171 PMCID: PMC5584012 DOI: 10.1186/s12864-017-4065-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 08/15/2017] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Horizontal transfer of mobile genetic elements (MGEs) that carry virulence and antimicrobial resistance genes mediates the evolution of methicillin-resistant Staphylococcus aureus, and the emergence of new MRSA clones. Most MRSA lineages show an association with specific MGEs and the evolution of MGE composition following clonal expansion has not been widely studied. RESULTS We investigated the genomes of 1193 S. aureus bloodstream isolates, 1169 of which were MRSA, collected in the UK and the Republic of Ireland between 2001 and 2010. The majority of isolates belonged to clonal complex (CC)22 (n = 923), which contained diverse MGEs including elements that were found in other MRSA lineages. Several MGEs showed variable distribution across the CC22 phylogeny, including two antimicrobial resistance plasmids (pWBG751-like and SAP078A-like, carrying erythromycin and heavy metal resistance genes, respectively), a pathogenicity island carrying the enterotoxin C gene and two phage types Sa1int and Sa6int. Multiple gains and losses of these five MGEs were identified in the CC22 phylogeny using ancestral state reconstruction. Analysis of the temporal distribution of the five MGEs between 2001 and 2010 revealed an unexpected reduction in prevalence of the two plasmids and the pathogenicity island, and an increase in the two phage types. This occurred across the lineage and was not correlated with changes in the relative prevalence of CC22, or of any sub-lineages within in. CONCLUSIONS Ancestral state reconstruction coupled with temporal trend analysis demonstrated that epidemic MRSA CC22 has an evolving MGE composition, and indicates that this important MRSA lineage has continued to adapt to changing selective pressure since its emergence.
Collapse
Affiliation(s)
- Dorota Jamrozy
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Francesc Coll
- London School of Hygiene and Tropical Medicine, London, WC1E 7HT UK
| | - Alison E. Mather
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES UK
| | - Simon R. Harris
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Ewan M. Harrison
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 0QQ UK
| | - Alasdair MacGowan
- British Society for Antimicrobial Chemotherapy, B1 3NJ, Birmingham, UK
| | - Andreas Karas
- Public Health England, Clinical Microbiology and Public Health Laboratory, Cambridge, CB21 5XA UK
| | - Tony Elston
- Colchester Hospital University NHS Foundation Trust, Colchester, CO4 5JL UK
| | - M. Estée Török
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 0QQ UK
- Public Health England, Clinical Microbiology and Public Health Laboratory, Cambridge, CB21 5XA UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ UK
| | - Julian Parkhill
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Sharon J. Peacock
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
- London School of Hygiene and Tropical Medicine, London, WC1E 7HT UK
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 0QQ UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ UK
| |
Collapse
|
25
|
Xiang Y, Tanaka Y, Patterson B, Kang YJ, Govindaiah G, Roselaar N, Cakir B, Kim KY, Lombroso AP, Hwang SM, Zhong M, Stanley EG, Elefanty AG, Naegele JR, Lee SH, Weissman SM, Park IH. Fusion of Regionally Specified hPSC-Derived Organoids Models Human Brain Development and Interneuron Migration. Cell Stem Cell 2017; 21:383-398.e7. [PMID: 28757360 DOI: 10.1016/j.stem.2017.07.007] [Citation(s) in RCA: 390] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 06/06/2017] [Accepted: 07/11/2017] [Indexed: 01/18/2023]
Abstract
Organoid techniques provide unique platforms to model brain development and neurological disorders. Whereas several methods for recapitulating corticogenesis have been described, a system modeling human medial ganglionic eminence (MGE) development, a critical ventral brain domain producing cortical interneurons and related lineages, has been lacking until recently. Here, we describe the generation of MGE and cortex-specific organoids from human pluripotent stem cells that recapitulate the development of MGE and cortex domains, respectively. Population and single-cell RNA sequencing (RNA-seq) profiling combined with bulk assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) analyses revealed transcriptional and chromatin accessibility dynamics and lineage relationships during MGE and cortical organoid development. Furthermore, MGE and cortical organoids generated physiologically functional neurons and neuronal networks. Finally, fusing region-specific organoids followed by live imaging enabled analysis of human interneuron migration and integration. Together, our study provides a platform for generating domain-specific brain organoids and modeling human interneuron migration and offers deeper insight into molecular dynamics during human brain development.
Collapse
Affiliation(s)
- Yangfei Xiang
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Yoshiaki Tanaka
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Benjamin Patterson
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Young-Jin Kang
- Department of Neurology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Gubbi Govindaiah
- Department of Neurology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Naomi Roselaar
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Bilal Cakir
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Kun-Yong Kim
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Adam P Lombroso
- Department of Biology, Program in Neuroscience and Behavior, Hall-Atwater Laboratory, Wesleyan University, Middletown, CT 06459, USA
| | - Sung-Min Hwang
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Mei Zhong
- Department of Cell Biology, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Edouard G Stanley
- Murdoch Childrens Research Institute, The Royal Children's Hospital, Parkville, VIC 3052, Australia; Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3052, Australia; Department of Anatomy and Developmental Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Andrew G Elefanty
- Murdoch Childrens Research Institute, The Royal Children's Hospital, Parkville, VIC 3052, Australia; Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3052, Australia; Department of Anatomy and Developmental Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Janice R Naegele
- Department of Biology, Program in Neuroscience and Behavior, Hall-Atwater Laboratory, Wesleyan University, Middletown, CT 06459, USA
| | - Sang-Hun Lee
- Department of Neurology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Sherman M Weissman
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - In-Hyun Park
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA.
| |
Collapse
|
26
|
Fandel TM, Trivedi A, Nicholas CR, Zhang H, Chen J, Martinez AF, Noble-Haeusslein LJ, Kriegstein AR. Transplanted Human Stem Cell-Derived Interneuron Precursors Mitigate Mouse Bladder Dysfunction and Central Neuropathic Pain after Spinal Cord Injury. Cell Stem Cell 2016; 19:544-557. [PMID: 27666009 DOI: 10.1016/j.stem.2016.08.020] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 05/24/2016] [Accepted: 08/19/2016] [Indexed: 12/19/2022]
Abstract
Neuropathic pain and bladder dysfunction represent significant quality-of-life issues for many spinal cord injury patients. Loss of GABAergic tone in the injured spinal cord may contribute to the emergence of these symptoms. Previous studies have shown that transplantation of rodent inhibitory interneuron precursors from the medial ganglionic eminence (MGE) enhances GABAergic signaling in the brain and spinal cord. Here we look at whether transplanted MGE-like cells derived from human embryonic stem cells (hESC-MGEs) can mitigate the pathological effects of spinal cord injury. We find that 6 months after transplantation into injured mouse spinal cords, hESC-MGEs differentiate into GABAergic neuron subtypes and receive synaptic inputs, suggesting functional integration into host spinal cord. Moreover, the transplanted animals show improved bladder function and mitigation of pain-related symptoms. Our results therefore suggest that this approach may be a valuable strategy for ameliorating the adverse effects of spinal cord injury.
Collapse
Affiliation(s)
- Thomas M Fandel
- Department of Neurological Surgery, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA.
| | - Alpa Trivedi
- Department of Neurological Surgery, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Cory R Nicholas
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA; Neurona Therapeutics, 650 Gateway Boulevard, South San Francisco, CA 94080, USA
| | - Haoqian Zhang
- Department of Neurological Surgery, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Jiadong Chen
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Aida F Martinez
- Department of Neurological Surgery, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Linda J Noble-Haeusslein
- Department of Neurological Surgery, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA; Department of Physical Therapy and Rehabilitation Science, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Arnold R Kriegstein
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA.
| |
Collapse
|
27
|
Jones-Dias D, Clemente L, Egas C, Froufe H, Sampaio DA, Vieira L, Fookes M, Thomson NR, Manageiro V, Caniça M. Salmonella Enteritidis Isolate Harboring Multiple Efflux Pumps and Pathogenicity Factors, Shows Absence of O Antigen Polymerase Gene. Front Microbiol 2016; 7:1130. [PMID: 27536269 PMCID: PMC4971094 DOI: 10.3389/fmicb.2016.01130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 07/06/2016] [Indexed: 11/13/2022] Open
Affiliation(s)
- Daniela Jones-Dias
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Health Institute Doutor Ricardo Jorge (INSA)Lisbon, Portugal
- Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, University of PortoPorto, Portugal
| | - Lurdes Clemente
- Microbiology and Mycology Laboratory, Instituto Nacional de Investigação Agrária e VeterináriaLisbon, Portugal
| | - Conceição Egas
- Biocant, Parque Tecnológico de CantanhedeCantanhede, Portugal
| | - Hugo Froufe
- Biocant, Parque Tecnológico de CantanhedeCantanhede, Portugal
| | - Daniel A. Sampaio
- Innovation and Technology Unit, Human Genetics Department, National Health Institute Doutor Ricardo Jorge (INSA)Lisbon, Portugal
| | - Luís Vieira
- Innovation and Technology Unit, Human Genetics Department, National Health Institute Doutor Ricardo Jorge (INSA)Lisbon, Portugal
| | - Maria Fookes
- Wellcome Trust Sanger Institute, Wellcome Trust Genome CampusHinxton, UK
| | | | - Vera Manageiro
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Health Institute Doutor Ricardo Jorge (INSA)Lisbon, Portugal
- Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, University of PortoPorto, Portugal
| | - Manuela Caniça
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Health Institute Doutor Ricardo Jorge (INSA)Lisbon, Portugal
| |
Collapse
|
28
|
Deans AE, Wadghiri YZ, Aristizábal O, Turnbull DH. 3D mapping of neuronal migration in the embryonic mouse brain with magnetic resonance microimaging. Neuroimage 2015; 114:303-10. [PMID: 25869862 DOI: 10.1016/j.neuroimage.2015.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 03/30/2015] [Accepted: 04/03/2015] [Indexed: 10/23/2022] Open
Abstract
A prominent feature of the developing mammalian brain is the widespread migration of neural progenitor (NP) cells during embryogenesis. A striking example is provided by NP cells born in the ventral forebrain of mid-gestation stage mice, which subsequently migrate long distances to their final positions in the cortex and olfactory bulb. Previous studies have used two-dimensional histological methods, making it difficult to analyze three-dimensional (3D) migration patterns. Unlike histology, magnetic resonance microimaging (micro-MRI) is a non-destructive, quantitative and inherently 3D imaging method for analyzing mouse embryos. To allow mapping of migrating NP cells with micro-MRI, cells were labeled in situ in the medial (MGE) and lateral (LGE) ganglionic eminences, using targeted in utero ultrasound-guided injection of micron-sized particles of iron-oxide (MPIO). Ex vivo micro-MRI and histology were then performed 5-6days after injection, demonstrating that the MPIO had magnetically labeled the migrating NP populations, which enabled 3D visualization and automated segmentation of the labeled cells. This approach was used to analyze the distinct patterns of migration from the MGE and LGE, and to construct rostral-caudal migration maps from each progenitor region. Furthermore, abnormal migratory phenotypes were observed in Nkx2.1(-/-) embryos, most notably a significant increase in cortical neurons derived from the Nkx2.1(-/-) LGE. Taken together, these results demonstrate that MPIO labeling and micro-MRI provide an efficient and powerful approach for analyzing 3D cell migration patterns in the normal and mutant mouse embryonic brain.
Collapse
Affiliation(s)
- Abby E Deans
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, 540 First Ave, New York, NY 10016, USA
| | - Youssef Zaim Wadghiri
- Department of Radiology, New York University School of Medicine, 540 First Ave, New York, NY 10016, USA
| | - Orlando Aristizábal
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, 540 First Ave, New York, NY 10016, USA
| | - Daniel H Turnbull
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, 540 First Ave, New York, NY 10016, USA; Department of Radiology, New York University School of Medicine, 540 First Ave, New York, NY 10016, USA; Department of Pathology, New York University School of Medicine, 540 First Ave, New York, NY 10016, USA.
| |
Collapse
|
29
|
Abstract
Mobile genetic elements (MGEs) are pivotal for bacterial evolution and adaptation, allowing shuffling of genes even between distantly related bacterial species. The study of these elements is biologically interesting as the mode of genetic propagation is kaleidoscopic and important, as MGEs are the main vehicles of the increasing bacterial antibiotic resistance that causes thousands of human deaths each year. The study of MGEs has previously focused on plasmids from individual isolates, but the revolution in sequencing technology has allowed the study of mobile genomic elements of entire communities using metagenomic approaches. The problem in using metagenomic sequencing for the study of MGEs is that plasmids and other mobile elements only comprise a small fraction of the total genetic content that are difficult to separate from chromosomal DNA based on sequence alone. The distinction between plasmid and chromosome is important as the mobility and regulation of genes largely depend on their genetic context. Several different approaches have been proposed that specifically enrich plasmid DNA from community samples. Here, we review recent approaches used to study entire plasmid pools from complex environments, and point out possible future developments for and pitfalls of these approaches. Further, we discuss the use of the PacBio long-read sequencing technology for MGE discovery.
Collapse
Affiliation(s)
- Tue S Jørgensen
- Section of Microbiology, Department of Biology, University of Copenhagen Copenhagen, Denmark
| | - Anne S Kiil
- Section of Microbiology, Department of Biology, University of Copenhagen Copenhagen, Denmark
| | - Martin A Hansen
- Section of Microbiology, Department of Biology, University of Copenhagen Copenhagen, Denmark
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen Copenhagen, Denmark
| | - Lars H Hansen
- Section of Microbiology, Department of Biology, University of Copenhagen Copenhagen, Denmark ; Environmental Microbiology and Biotechnology, Department of Environmental Science, Aarhus University Roskilde, Denmark
| |
Collapse
|
30
|
Brown-Jaque M, Calero-Cáceres W, Muniesa M. Transfer of antibiotic-resistance genes via phage-related mobile elements. Plasmid 2015; 79:1-7. [PMID: 25597519 DOI: 10.1016/j.plasmid.2015.01.001] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 01/12/2015] [Accepted: 01/13/2015] [Indexed: 11/29/2022]
Abstract
Antibiotic resistance is a major concern for society because it threatens the effective prevention of infectious diseases. While some bacterial strains display intrinsic resistance, others achieve antibiotic resistance by mutation, by the recombination of foreign DNA into the chromosome or by horizontal gene acquisition. In many cases, these three mechanisms operate together. Several mobile genetic elements (MGEs) have been reported to mobilize different types of resistance genes and despite sharing common features, they are often considered and studied separately. Bacteriophages and phage-related particles have recently been highlighted as MGEs that transfer antibiotic resistance. This review focuses on phages, phage-related elements and on composite MGEs (phages-MGEs) involved in antibiotic resistance mobility. We review common features of these elements, rather than differences, and provide a broad overview of the antibiotic resistance transfer mechanisms observed in nature, which is a necessary first step to controlling them.
Collapse
Affiliation(s)
- Maryury Brown-Jaque
- Department of Microbiology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - William Calero-Cáceres
- Department of Microbiology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Maite Muniesa
- Department of Microbiology, Faculty of Biology, University of Barcelona, Barcelona, Spain.
| |
Collapse
|
31
|
Sebe JY, Looke-Stewart E, Baraban SC. GABAB receptors in maintenance of neocortical circuit function. Exp Neurol 2014; 261:163-70. [PMID: 24873729 PMCID: PMC4324605 DOI: 10.1016/j.expneurol.2014.05.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Revised: 05/04/2014] [Accepted: 05/19/2014] [Indexed: 10/25/2022]
Abstract
Activation of metabotropic GABAB receptors (GABABRs) enhances tonic GABA current and substantially increases the frequency of spontaneous seizures. Despite the and pro-epileptic consequences of GABABR activation, mice lacking functional GABAB receptors (GABAB1R KO mice) exhibit clonic and rare absence seizures. To examine these mutant mice further, we recorded excitatory and inhibitory synaptic inputs and tonic mutant GABA currents from Layer 2 neocortical pyramidal neurons of GABAB1R WT and KO mice (P30-40). Tonic current was increased while the frequency of synaptic inputs was unchanged in KO mice relative to WT littermates. The neocortical laminar distribution of interneuron subtypes derived from the medial ganglionic eminence (MGE) was also not statistically different in KO mice relative to WT while the number of calretinin-positive, caudal GE-derived cells in Layer 1 was reduced. Transplantation of MGE progenitors obtained from KO mice lacking functional GABAB1R did not increase tonic inhibition in the host brain above that of media-injected controls. Taken together, these results suggest a complex role for GABAB receptors in mediating neocortical circuit function.
Collapse
Affiliation(s)
- Joy Y Sebe
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Elizabeth Looke-Stewart
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Scott C Baraban
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Graduate Program in Neuroscience, University of California, San Francisco, San Francisco, CA 941432, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA.
| |
Collapse
|
32
|
Xu Q, Chiu HJ, Farr CL, Jaroszewski L, Knuth MW, Miller MD, Lesley SA, Godzik A, Elsliger MA, Deacon AM, Wilson IA. Structures of a bifunctional cell wall hydrolase CwlT containing a novel bacterial lysozyme and an NlpC/P60 DL-endopeptidase. J Mol Biol 2013; 426:169-84. [PMID: 24051416 DOI: 10.1016/j.jmb.2013.09.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 09/07/2013] [Accepted: 09/11/2013] [Indexed: 11/17/2022]
Abstract
Tn916-like conjugative transposons carrying antibiotic resistance genes are found in a diverse range of bacteria. Orf14 within the conjugation module encodes a bifunctional cell wall hydrolase CwlT that consists of an N-terminal bacterial lysozyme domain (N-acetylmuramidase, bLysG) and a C-terminal NlpC/P60 domain (γ-d-glutamyl-l-diamino acid endopeptidase) and is expected to play an important role in the spread of the transposons. We determined the crystal structures of CwlT from two pathogens, Staphylococcus aureus Mu50 (SaCwlT) and Clostridium difficile 630 (CdCwlT). These structures reveal that NlpC/P60 and LysG domains are compact and conserved modules, connected by a short flexible linker. The LysG domain represents a novel family of widely distributed bacterial lysozymes. The overall structure and the active site of bLysG bear significant similarity to other members of the glycoside hydrolase family 23 (GH23), such as the g-type lysozyme (LysG) and Escherichia coli lytic transglycosylase MltE. The active site of bLysG contains a unique structural and sequence signature (DxxQSSES+S) that is important for coordinating a catalytic water. Molecular modeling suggests that the bLysG domain may recognize glycan in a similar manner to MltE. The C-terminal NlpC/P60 domain contains a conserved active site (Cys-His-His-Tyr) that appears to be specific to murein tetrapeptide. Access to the active site is likely regulated by isomerism of a side chain atop the catalytic cysteine, allowing substrate entry or product release (open state), or catalysis (closed state).
Collapse
Affiliation(s)
- Qingping Xu
- Joint Center for Structural Genomics (http://www.jcsg.org); Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Hsiu-Ju Chiu
- Joint Center for Structural Genomics (http://www.jcsg.org); Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Carol L Farr
- Joint Center for Structural Genomics (http://www.jcsg.org); Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Lukasz Jaroszewski
- Joint Center for Structural Genomics (http://www.jcsg.org); Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Program on Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Mark W Knuth
- Joint Center for Structural Genomics (http://www.jcsg.org); Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
| | - Mitchell D Miller
- Joint Center for Structural Genomics (http://www.jcsg.org); Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Scott A Lesley
- Joint Center for Structural Genomics (http://www.jcsg.org); Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
| | - Adam Godzik
- Joint Center for Structural Genomics (http://www.jcsg.org); Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Program on Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Marc-André Elsliger
- Joint Center for Structural Genomics (http://www.jcsg.org); Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ashley M Deacon
- Joint Center for Structural Genomics (http://www.jcsg.org); Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Ian A Wilson
- Joint Center for Structural Genomics (http://www.jcsg.org); Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
| |
Collapse
|
33
|
Abstract
Neurons, astrocytes and oligodendrocytes arise from CNS progenitor cells at defined times and locations during development, with transcription factors serving as key determinants of these different neural cell fates. An emerging theme is that the transcription factors that specify CNS cell fates function in a context-dependent manner, regulated by post-translational modifications and epigenetic alterations that partition the genome (and hence target genes) into active or silent domains. Here we profile the critical roles of the proneural genes, which encode basic-helix-loop-helix (bHLH) transcription factors, in specifying neural cell identities in the developing neocortex. In particular, we focus on the proneural genes Neurogenin 1 (Neurog1), Neurog2 and Achaete scute-like 1 (Ascl1), which are each expressed in a distinct fashion in the progenitor cell pools that give rise to all of the neuronal and glial cell types of the mature neocortex. Notably, while the basic functions of these proneural genes have been elucidated, it is becoming increasingly evident that tight regulatory controls dictate when, where and how they function. Current efforts to better understand how proneural gene function is regulated will not only improve our understanding of neocortical development, but are also critical to the future development of regenerative therapies for the treatment of neuronal degeneration or disease.
Collapse
Affiliation(s)
- G Wilkinson
- Hotchkiss Brain Institute, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | | | | |
Collapse
|
34
|
Luchetti A, Mantovani B. Conserved domains and SINE diversity during animal evolution. Genomics 2013; 102:296-300. [PMID: 23981965 DOI: 10.1016/j.ygeno.2013.08.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 06/25/2013] [Accepted: 08/14/2013] [Indexed: 11/28/2022]
Abstract
Eukaryotic genomes harbour a number of mobile genetic elements (MGEs); moving from one genomic location to another, they are known to impact on the host genome. Short interspersed elements (SINEs) are well-represented, non-autonomous retroelements and they are likely the most diversified MGEs. In some instances, sequence domains conserved across unrelated SINEs have been identified; remarkably, one of these, called Nin, has been conserved since the Radiata-Bilateria splitting. Here we report on two new domains: Inv, derived from Nin, identified in insects and in deuterostomes, and Pln, restricted to polyneopteran insects. The identification of Inv and Pln sequences allowed us to retrieve new SINEs, two in insects and one in a hemichordate. The diverse structural combination of the different domains in different SINE families, during metazoan evolution, offers a clearer view of SINE diversity and their frequent de novo emergence through module exchange, possibly underlying the high evolutionary success of SINEs.
Collapse
Affiliation(s)
- Andrea Luchetti
- Dip. Scienze Biologiche, Geologiche e Ambientali (BiGeA) - Università di Bologna, via Selmi 3, 40126 Bologna, Italy.
| | | |
Collapse
|
35
|
Koyama Y, Hattori T, Shimizu S, Taniguchi M, Yamada K, Takamura H, Kumamoto N, Matsuzaki S, Ito A, Katayama T, Tohyama M. DBZ (DISC1-binding zinc finger protein)-deficient mice display abnormalities in basket cells in the somatosensory cortices. J Chem Neuroanat 2013; 53:1-10. [PMID: 23912123 DOI: 10.1016/j.jchemneu.2013.07.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 07/22/2013] [Accepted: 07/24/2013] [Indexed: 10/26/2022]
Abstract
Disrupted-in-schizophrenia 1 (DISC1)-binding zinc finger protein (DBZ) is a DISC1-interacting molecule and the interaction between DBZ and DISC1 is involved in neurite outgrowth in vitro. DBZ is highly expressed in brain, especially in the cortex. However, the physiological roles of DBZ in vivo have not been clarified. Here, we show that development of basket cells, a morphologically defined class of parvalbumin (PV)-containing interneurons, is disturbed in DBZ knockout (KO) mice. DBZ mRNA was highly expressed in the ventral area of the subventricular zone of the medial ganglionic eminence, where PV-containing cortical interneurons were generated, at embryonic 14.5 days (E14.5). Although the expression level for PV and the number of PV-containing interneurons were not altered in the cortices of DBZ KO mice, basket cells were less branched and had shorter processes in the somatosensory cortices of DBZ KO mice compared with those in the cortices of WT mice. Furthermore, in the somatosensory cortices of DBZ KO mice, the level of mRNAs for the gamma-aminobutyric acid-synthesizing enzymes GAD67 was decreased. These findings show that DBZ is involved in the morphogenesis of basket cells.
Collapse
Affiliation(s)
- Yoshihisa Koyama
- Department of Anatomy and Neuroscience, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Abstract
The genome has traditionally been treated as a Read-Only Memory (ROM) subject to change by copying errors and accidents. In this review, I propose that we need to change that perspective and understand the genome as an intricately formatted Read-Write (RW) data storage system constantly subject to cellular modifications and inscriptions. Cells operate under changing conditions and are continually modifying themselves by genome inscriptions. These inscriptions occur over three distinct time-scales (cell reproduction, multicellular development and evolutionary change) and involve a variety of different processes at each time scale (forming nucleoprotein complexes, epigenetic formatting and changes in DNA sequence structure). Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences.
Collapse
Affiliation(s)
- James A Shapiro
- Dept. of Biochemistry and Molecular Biology, University of Chicago, GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA. http://www.huffingtonpost.com/james-a-shapiro
| |
Collapse
|
37
|
Jaglin XH, Hjerling-Leffler J, Fishell G, Batista-Brito R. The origin of neocortical nitric oxide synthase-expressing inhibitory neurons. Front Neural Circuits 2012; 6:44. [PMID: 22787442 PMCID: PMC3391688 DOI: 10.3389/fncir.2012.00044] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 06/20/2012] [Indexed: 01/08/2023] Open
Abstract
Inhibitory neurons are critical for regulating effective transfer of sensory information and network stability. The precision of inhibitory function likely derives from the existence of a variety of interneuron subtypes. Their specification is largely dependent on the locale of origin of interneuron progenitors. Neocortical and hippocampal inhibitory neurons originate the subpallium, namely in the medial and caudal ganglionic eminences (MGE and CGE), and in the preoptic area (POA). In the hippocampus, neuronal nitric oxide synthase (nNOS)-expressing cells constitute a numerically large GABAergic interneuron population. On the contrary, nNOS-expressing inhibitory neurons constitute the smallest of the known neocortical GABAergic neuronal subtypes. The origins of most neocortical GABAergic neuron subtypes have been thoroughly investigated, however, very little is known about the origin of, or the genetic programs underlying the development of nNOS neurons. Here, we show that the vast majority of neocortical nNOS-expressing neurons arise from the MGE rather than the CGE. Regarding their molecular signature, virtually all neocortical nNOS neurons co-express the neuropeptides somatostatin (SST) and neuropeptide Y (NPY), and about half of them express the calcium-binding protein calretinin (CR). nNOS neurons thus constitute a small cohort of the MGE-derived SST-expressing population of cortical inhibitory neurons. Finally, we show that conditional removal of the transcription factor Sox6 in MGE-derived GABAergic cortical neurons results in an absence of SST and CR expression, as well as reduced expression of nNOS in neocortical nNOS neurons. Based on their respective abundance, origin and molecular signature, our results suggest that neocortical and hippocampal nNOS GABAergic neurons likely subserve different functions and have very different physiological relevance in these two cortical structures.
Collapse
Affiliation(s)
- Xavier H Jaglin
- NYU Neuroscience Institute, New York University Langone Medical Center New York, NY, USA
| | | | | | | |
Collapse
|