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Sepúlveda VE, Goldman WE, Matute DR. Genotypic diversity, virulence, and molecular genetic tools in Histoplasma. Microbiol Mol Biol Rev 2024; 88:e0007623. [PMID: 38819148 DOI: 10.1128/mmbr.00076-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024] Open
Abstract
SUMMARYHistoplasmosis is arguably the most common fungal respiratory infection worldwide, with hundreds of thousands of new infections occurring annually in the United States alone. The infection can progress in the lung or disseminate to visceral organs and can be difficult to treat with antifungal drugs. Histoplasma, the causative agent of the disease, is a pathogenic fungus that causes life-threatening lung infections and is globally distributed. The fungus has the ability to germinate from conidia into either hyphal (mold) or yeast form, depending on the environmental temperature. This transition also regulates virulence. Histoplasma and histoplasmosis have been classified as being of emergent importance, and in 2022, the World Health Organization included Histoplasma as 1 of the 19 most concerning human fungal pathogens. In this review, we synthesize the current understanding of the ecological niche, evolutionary history, and virulence strategies of Histoplasma. We also describe general patterns of the symptomatology and epidemiology of histoplasmosis. We underscore areas where research is sorely needed and highlight research avenues that have been productive.
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Affiliation(s)
- Victoria E Sepúlveda
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - William E Goldman
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Daniel R Matute
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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2
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Genetic Diversity of Human Fungal Pathogens. CURRENT CLINICAL MICROBIOLOGY REPORTS 2023. [DOI: 10.1007/s40588-023-00188-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
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3
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Zhou M, Abid M, Yin H, Wu H, Teklue T, Qiu HJ, Sun Y. Establishment of an Efficient and Flexible Genetic Manipulation Platform Based on a Fosmid Library for Rapid Generation of Recombinant Pseudorabies Virus. Front Microbiol 2018; 9:2132. [PMID: 30233561 PMCID: PMC6133995 DOI: 10.3389/fmicb.2018.02132] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/20/2018] [Indexed: 12/15/2022] Open
Abstract
Conventional genetic engineering of pseudorabies virus (PRV) is essentially based on homologous recombination or bacterial artificial chromosome. However, these techniques require multiple plaque purification, which is labor-intensive and time-consuming. The aim of the present study was to develop an efficient, direct, and flexible genetic manipulation platform for PRV. To this end, the PRV genomic DNA was extracted from purified PRV virions and sheared into approximately 30–45-kb DNA fragments. After end-blunting and phosphorylation, the DNA fragments were separated by pulsed-field gel electrophoresis, the recovered DNA fragments were inserted into the cloning-ready fosmids. The fosmids were then transformed into Escherichia coli and selected clones were end-sequenced for full-length genome assembly. Overlapping fosmid combinations that cover the complete genome of PRV were directly transfected into Vero cells and PRV was rescued. The morphology and one-step growth curve of the rescued virus were indistinguishable from those of the parent virus. Based on this system, a recombinant PRV expressing enhanced green fluorescent protein fused with the VP26 gene was generated within 2 weeks, and this recombinant virus can be used to observe the capsid transport in axons. The new genetic manipulation platform developed in the present study is an efficient, flexible, and stable method for the study of the PRV life cycle and development of novel vaccines.
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Affiliation(s)
- Mo Zhou
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Muhammad Abid
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hang Yin
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hongxia Wu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Teshale Teklue
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hua-Ji Qiu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yuan Sun
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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Li J, Gu F, Wu R, Yang J, Zhang KQ. Phylogenomic evolutionary surveys of subtilase superfamily genes in fungi. Sci Rep 2017; 7:45456. [PMID: 28358043 PMCID: PMC5371821 DOI: 10.1038/srep45456] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 02/28/2017] [Indexed: 01/10/2023] Open
Abstract
Subtilases belong to a superfamily of serine proteases which are ubiquitous in fungi and are suspected to have developed distinct functional properties to help fungi adapt to different ecological niches. In this study, we conducted a large-scale phylogenomic survey of subtilase protease genes in 83 whole genome sequenced fungal species in order to identify the evolutionary patterns and subsequent functional divergences of different subtilase families among the main lineages of the fungal kingdom. Our comparative genomic analyses of the subtilase superfamily indicated that extensive gene duplications, losses and functional diversifications have occurred in fungi, and that the four families of subtilase enzymes in fungi, including proteinase K-like, Pyrolisin, kexin and S53, have distinct evolutionary histories which may have facilitated the adaptation of fungi to a broad array of life strategies. Our study provides new insights into the evolution of the subtilase superfamily in fungi and expands our understanding of the evolution of fungi with different lifestyles.
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Affiliation(s)
- Juan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P.R. China
| | - Fei Gu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P.R. China
| | - Runian Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P.R. China
| | - JinKui Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P.R. China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P.R. China
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5
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Draft Genome Sequence of Acetobacter aceti Strain 1023, a Vinegar Factory Isolate. GENOME ANNOUNCEMENTS 2014; 2:2/3/e00550-14. [PMID: 24903876 PMCID: PMC4047455 DOI: 10.1128/genomea.00550-14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The genome sequence of Acetobacter aceti 1023, an acetic acid bacterium adapted to traditional vinegar fermentation, comprises 3.0 Mb (chromosome plus plasmids). A. aceti 1023 is closely related to the cocoa fermenter Acetobacter pasteurianus 386B but possesses many additional insertion sequence elements.
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Murphy C, Powlowski J, Wu M, Butler G, Tsang A. Curation of characterized glycoside hydrolases of fungal origin. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2011; 2011:bar020. [PMID: 21622642 PMCID: PMC3263737 DOI: 10.1093/database/bar020] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Fungi produce a wide range of extracellular enzymes to break down plant cell walls, which are composed mainly of cellulose, lignin and hemicellulose. Among them are the glycoside hydrolases (GH), the largest and most diverse family of enzymes active on these substrates. To facilitate research and development of enzymes for the conversion of cell-wall polysaccharides into fermentable sugars, we have manually curated a comprehensive set of characterized fungal glycoside hydrolases. Characterized glycoside hydrolases were retrieved from protein and enzyme databases, as well as literature repositories. A total of 453 characterized glycoside hydrolases have been cataloged. They come from 131 different fungal species, most of which belong to the phylum Ascomycota. These enzymes represent 46 different GH activities and cover 44 of the 115 CAZy GH families. In addition to enzyme source and enzyme family, available biochemical properties such as temperature and pH optima, specific activity, kinetic parameters and substrate specificities were recorded. To simplify comparative studies, enzyme and species abbreviations have been standardized, Gene Ontology terms assigned and reference to supporting evidence provided. The annotated genes have been organized in a searchable, online database called mycoCLAP (Characterized Lignocellulose-Active Proteins of fungal origin). It is anticipated that this manually curated collection of biochemically characterized fungal proteins will be used to enhance functional annotation of novel GH genes. Database URL: http://mycoCLAP.fungalgenomics.ca/.
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Affiliation(s)
- Caitlin Murphy
- Centre for Structural and Functional Genomics, Concordia University, Montreal QC H4B 1R6, Canada
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Yadav V, Kumar M, Deep DK, Kumar H, Sharma R, Tripathi T, Tuteja N, Saxena AK, Johri AK. WITHDRAWN: A phosphate transporter from the root endophytic fungus Piriformospora indica plays a role in phosphate transport to the host plant. J Biol Chem 2010; 285:26532-44. [PMID: 20479005 PMCID: PMC2924090 DOI: 10.1074/jbc.m110.111021] [Citation(s) in RCA: 233] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 05/12/2010] [Indexed: 11/06/2022] Open
Abstract
Because pure cultures and a stable transformation system are not available for arbuscular mycorrhizal fungi, the role of their phosphate transporters for the symbiotic interaction with the plant up till now could not be studied. Here we report the cloning and the functional analysis of a gene encoding a phosphate transporter (PiPT) from the root endophytic fungus Piriformospora indica, which can be grown axenically. The PiPT polypeptide belongs to the major facilitator superfamily. Homology modeling reveals that PiPT exhibits twelve transmembrane helices divided into two halves connected by a large hydrophilic loop in the middle. The function of the protein encoded by PiPT was confirmed by complementation of a yeast phosphate transporter mutant. The kinetic analysis of PiPT (K(m) 25 mum) reveals that it belongs to the high affinity phosphate transporter family (Pht1). Expression of PiPT was localized to the external hyphae of P. indica colonized with maize plant root, which suggests that external hyphae are the initial site of phosphate uptake from the soil. To understand the physiological role of PiPT, knockdown transformants of the gene were prepared using electroporation and RNA interference. Knockdown transformants transported a significantly lower amount of phosphate to the host plant than wild-type P. indica. Higher amounts of phosphate were found in plants colonized with wild-type P. indica than that of non-colonized and plants colonized with knockdown PiPT P. indica. These observations suggest that PiPT is actively involved in the phosphate transportation and, in turn, P. indica helps improve the nutritional status of the host plant.
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Affiliation(s)
- Vikas Yadav
- From the School of Life Sciences, Jawaharlal Nehru University, New Meharuli Road, New Delhi 110067 and
| | - Manoj Kumar
- From the School of Life Sciences, Jawaharlal Nehru University, New Meharuli Road, New Delhi 110067 and
| | - Deepak Kumar Deep
- From the School of Life Sciences, Jawaharlal Nehru University, New Meharuli Road, New Delhi 110067 and
| | - Hemant Kumar
- From the School of Life Sciences, Jawaharlal Nehru University, New Meharuli Road, New Delhi 110067 and
| | - Ruby Sharma
- From the School of Life Sciences, Jawaharlal Nehru University, New Meharuli Road, New Delhi 110067 and
| | - Takshashila Tripathi
- From the School of Life Sciences, Jawaharlal Nehru University, New Meharuli Road, New Delhi 110067 and
| | - Narendra Tuteja
- the International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Ajay Kumar Saxena
- From the School of Life Sciences, Jawaharlal Nehru University, New Meharuli Road, New Delhi 110067 and
| | - Atul Kumar Johri
- From the School of Life Sciences, Jawaharlal Nehru University, New Meharuli Road, New Delhi 110067 and
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8
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Wang X, Zhang Q, Sun X, Chen Y, Zhai T, Zhuang W, Qi J, Wang Z. Fosmid library construction and initial analysis of end sequences in female half-smooth tongue sole (Cynoglossus semilaevis). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2009; 11:236-242. [PMID: 18763017 DOI: 10.1007/s10126-008-9137-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Accepted: 07/27/2008] [Indexed: 05/26/2023]
Abstract
Half-smooth tongue sole (Cynoglossus semilaevis: Pleuronectiformes) is a commercially important cultured marine flatfish in China and forms an important fishery resource, but the research of its genome is underdeveloped. In this study, we constructed a female C. semilaevis fosmid library and analyzed the fosmid end sequences to provide a preliminary assessment of the genome. The library consists of 49,920 clones with an average insert size of about 39 kb, amounting to 3.23 genome equivalents. Fosmid stability assays indicate that female C. semilaevis DNA was stable during propagation in the fosmid system. Library screening with eight microsatellite markers yielded between two and five positive clones, and none of those tested was absent from the library. End-sequencing of both 5' and 3' ends of 1,152 individual clones generated 2,247 sequences after trimming, with an average sequence length of 855 bp. BLASTN searches of the nr and EST databases of GenBank and BLASTX searches of the nr database resulted in 259 (11.53%) and 287 (12.77%) significant hits (E < e (-5)), respectively. Repetitive sequences analysis resulted in 5.23% of base pairs masked using both the Fugu and Danio databases, repetitive elements were composed of retroelements, DNA transposons, satellites, simple repeats, and low-complexity sequences. The fosmid library, in conjunction with the fosmid end sequences, will serve as a useful resource for large-scale genome sequencing, physical mapping, and positional cloning, and provide a better understanding of female C. semilaevis genome.
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Affiliation(s)
- Xubo Wang
- Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, People's Republic of China
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9
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A scaffold analysis tool using mate-pair information in genome sequencing. J Biomed Biotechnol 2008; 2008:675741. [PMID: 18414585 PMCID: PMC2291285 DOI: 10.1155/2008/675741] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2007] [Accepted: 12/24/2007] [Indexed: 11/27/2022] Open
Abstract
We have developed a Windows-based program, ConPath,
as a scaffold analyzer. ConPath constructs scaffolds by ordering and orienting separate sequence contigs by exploiting the mate-pair information between
contig-pairs. Our algorithm builds directed graphs from link information and traverses them to find the longest acyclic graphs. Using end read pairs of fixed-sized mate-pair libraries,
ConPath determines relative orientations of all contigs,
estimates the gap size of each adjacent contig pair, and reports wrong assembly
information by validating orientations and gap sizes.
We have utilized ConPath in more than 10 microbial genome projects, including
Mannheimia succiniciproducens and Vibro vulnificus,
where we verified contig assembly and identified several erroneous contigs using the four types of error defined in ConPath. Also, ConPath supports some convenient features and viewers that permit investigation of each contig in detail; these include contig viewer, scaffold viewer, edge information list, mate-pair list, and the printing of complex scaffold structures.
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10
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Croll D, Wille L, Gamper HA, Mathimaran N, Lammers PJ, Corradi N, Sanders IR. Genetic diversity and host plant preferences revealed by simple sequence repeat and mitochondrial markers in a population of the arbuscular mycorrhizal fungus Glomus intraradices. THE NEW PHYTOLOGIST 2008; 178:672-87. [PMID: 18298433 DOI: 10.1111/j.1469-8137.2008.02381.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are important symbionts of plants that improve plant nutrient acquisition and promote plant diversity. Although within-species genetic differences among AMF have been shown to differentially affect plant growth, very little is actually known about the degree of genetic diversity in AMF populations. This is largely because of difficulties in isolation and cultivation of the fungi in a clean system allowing reliable genotyping to be performed. A population of the arbuscular mycorrhizal fungus Glomus intraradices growing in an in vitro cultivation system was studied using newly developed simple sequence repeat (SSR), nuclear gene intron and mitochondrial ribosomal gene intron markers. The markers revealed a strong differentiation at the nuclear and mitochondrial level among isolates. Genotypes were nonrandomly distributed among four plots showing genetic subdivisions in the field. Meanwhile, identical genotypes were found in geographically distant locations. AMF genotypes showed significant preferences to different host plant species (Glycine max, Helianthus annuus and Allium porrum) used before the fungal in vitro culture establishment. Host plants in a field could provide a heterogeneous environment favouring certain genotypes. Such preferences may partly explain within-population patterns of genetic diversity.
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Affiliation(s)
- Daniel Croll
- Department of Ecology & Evolution, Biophore Building, University of Lausanne, CH-1015 Lausanne, Switzerland
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11
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Zhang L, Bao Z, Cheng J, Li H, Huang X, Wang S, Zhang C, Hu J. Fosmid library construction and initial analysis of end sequences in Zhikong scallop (Chlamys farreri). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2007; 9:606-12. [PMID: 17605073 DOI: 10.1007/s10126-007-9014-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2007] [Revised: 03/22/2007] [Accepted: 04/03/2007] [Indexed: 05/16/2023]
Abstract
Zhikong scallop (Chlamys farreri Jones et Preston, 1904) is one of the most commercially important bivalves in China, but research on its genome is underdeveloped. In this study, we constructed the first Zhikong scallop fosmid library, and analyzed the fosmid end sequences to provide a preliminary assessment of the genome. The library consists of 133,851 clones with an average insert size of about 40 kb, amounting to 4.3 genome equivalents. Fosmid stability assays indicate that Zhikong scallop DNA was stable during propagation in the fosmid system. Library screening with two genes and seven microsatellite markers yielded between two and eight positive clones, and none of those tested was absent from the library. End-sequencing of 480 individual clones generated 828 sequences after trimming, with an average sequence length of 624 bp. BLASTN searches of the nr and EST databases of GenBank and BLASTX searches of the nr database resulted in 213 (25.72%) and 44 (5.31%) significant hits (E < e(-5)), respectively. Repetitive sequences analysis resulted in 375 repeats, accounting for 15.84% of total length, which were composed of interspersed repetitive sequences, tandem repeats, and low-complexity sequences. The fosmid library, in conjunction with the fosmid end sequences, will serve as a useful resource for physical mapping and positional cloning, and provide a better understanding of the Zhikong scallop genome.
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Affiliation(s)
- Lingling Zhang
- Laboratory of Marine Genetics and Breeding (MGB), Division of Life Science and Technology, Ocean University of China, Qingdao, PR China
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12
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Volik S, Raphael BJ, Huang G, Stratton MR, Bignel G, Murnane J, Brebner JH, Bajsarowicz K, Paris PL, Tao Q, Kowbel D, Lapuk A, Shagin DA, Shagina IA, Gray JW, Cheng JF, de Jong PJ, Pevzner P, Collins C. Decoding the fine-scale structure of a breast cancer genome and transcriptome. Genes Dev 2006; 16:394-404. [PMID: 16461635 PMCID: PMC1415204 DOI: 10.1101/gr.4247306] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2005] [Accepted: 11/30/2005] [Indexed: 11/24/2022]
Abstract
A comprehensive understanding of cancer is predicated upon knowledge of the structure of malignant genomes underlying its many variant forms and the molecular mechanisms giving rise to them. It is well established that solid tumor genomes accumulate a large number of genome rearrangements during tumorigenesis. End Sequence Profiling (ESP) maps and clones genome breakpoints associated with all types of genome rearrangements elucidating the structural organization of tumor genomes. Here we extend the ESP methodology in several directions using the breast cancer cell line MCF-7. First, targeted ESP is applied to multiple amplified loci, revealing a complex process of rearrangement and co-amplification in these regions reminiscent of breakage/fusion/bridge cycles. Second, genome breakpoints identified by ESP are confirmed using a combination of DNA sequencing and PCR. Third, in vitro functional studies assign biological function to a rearranged tumor BAC clone, demonstrating that it encodes anti-apoptotic activity. Finally, ESP is extended to the transcriptome identifying four novel fusion transcripts and providing evidence that expression of fusion genes may be common in tumors. These results demonstrate the distinct advantages of ESP including: (1) the ability to detect all types of rearrangements and copy number changes; (2) straightforward integration of ESP data with the annotated genome sequence; (3) immortalization of the genome; (4) ability to generate tumor-specific reagents for in vitro and in vivo functional studies. Given these properties, ESP could play an important role in a tumor genome project.
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Affiliation(s)
- Stanislav Volik
- Department of Urology, and Cancer Research Institute, University of California San Francisco Comprehensive Cancer Center, San Francisco, California 94115, USA
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Wendl MC. Probabilistic Assessment of Clone Overlaps in DNA Fingerprint Mapping via a Priori Models. J Comput Biol 2005; 12:283-97. [PMID: 15857243 DOI: 10.1089/cmb.2005.12.283] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We construct a combinatorially exact probability distribution for the problem of a priori clone overlap assessment in DNA fingerprint mapping. It is implemented as a general enumeration methodology using Bell's exponential polynomials. Established computational metrics do not consider the conditional nature of the problem. They dramatically overpredict actual match probabilities as a consequence. This elevates the rate of false-negative overlap declarations, which is consistent with previous validation studies. Increased measurement resolution does not significantly improve accuracy. We describe general trends in error behavior for intermediate-size DNA clones and discuss corresponding limits on the ability to assess certain overlaps.
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Affiliation(s)
- Michael C Wendl
- Genome Sequencing Center, Washington University, St. Louis, MO 63108, USA.
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Abstract
Histoplasma capsulatum is a significant respiratory and systemic fungal pathogen. Although many molecular tools have been developed, the fulfillment of Koch's postulates to determine gene function has been hampered by obstacles to homologous gene targeting. Because H. capsulatum displays a considerable array of virulence mechanisms and has a 40-Mb genome that is currently being sequenced, the capability to perform high-throughput molecular manipulations would clearly be beneficial. Recent demonstration and application of experimental RNA interference (RNAi) technology promises a major contribution to advances in this area.
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Affiliation(s)
- Jon P Woods
- Department of Medical Microbiology & Immunology, University of Wisconsin Medical School, 1300 University Avenue, 420 SMI, Madison, Wisconsin 53706-1532 WI, USA.
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15
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2005. [PMCID: PMC2448604 DOI: 10.1002/cfg.419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
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Xu J, Gordon JI. MapLinker: a software tool that aids physical map-linked whole genome shotgun assembly. Bioinformatics 2004; 21:1265-6. [PMID: 15572475 DOI: 10.1093/bioinformatics/bti122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MapLinker is an analysis tool, as well as a browsing interface, that facilitates integration of whole genome sequence assembly with a clone-based physical map. Using the locations of sequence markers on the physical map, MapLinker generates a tentative sequence map of the genome that serves to verify the map and to guide genome-wide finishing.
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Affiliation(s)
- Jian Xu
- Center for Genome Sciences and Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St. Louis, MO 63108, USA.
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