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Wang JC, Chen HH, Hsu TW, Hung KH, Huang CC. A taxonomic revision of the genus Angelica (Apiaceae) in Taiwan with a new species A. aliensis. BOTANICAL STUDIES 2024; 65:3. [PMID: 38252347 PMCID: PMC10803708 DOI: 10.1186/s40529-023-00407-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/13/2023] [Indexed: 01/23/2024]
Abstract
BACKGROUND Angelica L. sensu lato is a taxonomically complex genus, and many studies have utilized morphological and molecular features to resolve its classification issues. In Taiwan, there are six taxa within Angelica, and their taxonomic treatments have been a subject of controversy. In this study, we conducted a comprehensive analysis incorporating morphological and molecular (cpDNA and nrDNA) characteristics to revise the taxonomic treatments of Angelica in Taiwan. RESULTS As a result of our research, we have revised the classification between A. dahurica var. formosana and A. pubescens and merged two varieties of A. morrisonicola into a single taxon. A new taxon, A. aliensis, has been identified and found to share a close relationship with A. tarokoensis. Based on the morphological and molecular characteristics data, it has been determined that the former three taxa should be grouped into the Eurasian Angelica clade, while the remaining four taxa should belong to the littoral Angelica clade. Furthermore, Angelica species in Taiwan distributed at higher altitudes displayed higher genetic diversity, implying that the central mountain range of Taiwan serves as a significant reservoir of plant biodiversity. Genetic drift, such as bottlenecks, has been identified as a potential factor leading to the fixation or reduction of genetic diversity of populations in most Angelica species. We provide key to taxa, synopsis, phenology, and distribution for each taxon of Taiwan. CONCLUSIONS Our comprehensive analysis of morphological and molecular features has shed light on the taxonomic complexities within Angelica in Taiwan, resolving taxonomic issues and providing valuable insights into the phylogenetic relationships of Angelica in Taiwan.
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Affiliation(s)
- Jenn-Che Wang
- Department of Life Science, National Taiwan Normal University, Taipei, 106, Taiwan
| | - Hung-Hsin Chen
- Department of Life Science, National Taiwan Normal University, Taipei, 106, Taiwan
| | - Tsai-Wen Hsu
- Wild Plants Division, Taiwan Biodiversity Research Institute, Nantou, 552, Taiwan
| | - Kuo-Hsiang Hung
- Graduate Institute of Bioresources, Pingtung University of Science and Technology, Pingtung, 912, Taiwan.
- Forestry and Biodiversity Research Center, National Pingtung University of Science and Technology, Pingtung, 912, Taiwan.
| | - Chi-Chun Huang
- Wild Plants Division, Taiwan Biodiversity Research Institute, Nantou, 552, Taiwan.
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2
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Al-Shuhaib MBS, Hashim HO. Mastering DNA chromatogram analysis in Sanger sequencing for reliable clinical analysis. J Genet Eng Biotechnol 2023; 21:115. [PMID: 37955813 PMCID: PMC10643650 DOI: 10.1186/s43141-023-00587-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/06/2023] [Indexed: 11/14/2023]
Abstract
BACKGROUND Sanger dideoxy sequencing is vital in clinical analysis due to its accuracy, ability to analyze genetic markers like SNPs and STRs, capability to generate reliable DNA profiles, and its role in resolving complex clinical cases. The precision and robustness of Sanger sequencing contribute significantly to the scientific basis of clinical investigations. Though the reading of chromatograms seems to be a routine step, many errors conducted in PCR may lead to consequent limitations in the readings of AGCT peaks. These errors are possibly associated with improper DNA amplification and its subsequent interpretation of DNA sequencing files, such as noisy peaks, artifacts, and confusion between double-peak technical errors, heterozygosity, and double infection potentials. Thus, it is not feasible to read nucleic acid sequences without giving serious attention to these technical problems. To ensure the accuracy of DNA sequencing outcomes, it is also imperative to detect and rectify technical challenges that may lead to misinterpretation of the DNA sequence, resulting in errors and incongruities in subsequent analyses. SHORT CONCLUSION This overview sheds light on prominent technical concerns that can emerge prior to and during the interpretation of DNA chromatograms in Sanger sequencing, along with offering strategies to address them effectively. The significance of identifying and tackling these technical limitations during the chromatogram analysis is underscored in this review. Recognizing these concerns can aid in enhancing the quality of downstream analyses for Sanger sequencing results, which holds notable improvement in accuracy, reliability, and ability to provide crucial genetic information in clinical analysis.
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Affiliation(s)
- Mohammed Baqur S Al-Shuhaib
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim 8, Babil, 51001, Iraq.
| | - Hayder O Hashim
- Department of Clinical Laboratory Sciences, College of Pharmacy, University of Babylon, Babil, 51001, Iraq
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3
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Fagre AC, Islam A, Reeves WK, Kading RC, Plowright RK, Gurley ES, McKee CD. Bartonella Infection in Fruit Bats and Bat Flies, Bangladesh. MICROBIAL ECOLOGY 2023; 86:2910-2922. [PMID: 37656196 DOI: 10.1007/s00248-023-02293-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/27/2023] [Indexed: 09/02/2023]
Abstract
Bats harbor diverse intracellular Bartonella bacteria, but there is limited understanding of the factors that influence transmission over time. Investigation of Bartonella dynamics in bats could reveal general factors that control transmission of multiple bat-borne pathogens, including viruses. We used molecular methods to detect Bartonella DNA in paired bat (Pteropus medius) blood and bat flies in the family Nycteribiidae collected from a roost in Faridpur, Bangladesh between September 2020 and January 2021. We detected high prevalence of Bartonella DNA in bat blood (35/55, 64%) and bat flies (59/60, 98%), with sequences grouping into three phylogenetic clades. Prevalence in bat blood increased over the study period (33% to 90%), reflecting an influx of juvenile bats in the population and an increase in the prevalence of bat flies. Discordance between infection status and the clade/genotype of detected Bartonella was also observed in pairs of bats and their flies, providing evidence that bat flies take blood meals from multiple bat hosts. This evidence of bat fly transfer between hosts and the changes in Bartonella prevalence during a period of increasing nycteribiid density support the role of bat flies as vectors of bartonellae. The study provides novel information on comparative prevalence and genetic diversity of Bartonella in pteropodid bats and their ectoparasites, as well as demographic factors that affect Bartonella transmission and potentially other bat-borne pathogens.
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Affiliation(s)
- Anna C Fagre
- Department of Microbiology, Immunology, and Pathology, Center for Vector-Borne Infectious Diseases, Colorado State University, Fort Collins, CO, USA
| | | | - Will K Reeves
- C.P. Gillette Museum of Arthropod Diversity, Fort Collins, CO, USA
| | - Rebekah C Kading
- Department of Microbiology, Immunology, and Pathology, Center for Vector-Borne Infectious Diseases, Colorado State University, Fort Collins, CO, USA
| | - Raina K Plowright
- Department of Public and Ecosystem Health, Cornell University, Ithaca, NY, USA
| | - Emily S Gurley
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Clifton D McKee
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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4
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Chen SY, Huang CC, Cheng YT, Wang CC, Li CY, Lai IL, Hung KH. Effect of geographic isolation on genetic variation and population structure of Euphrasia nankotaizanensis, a threatened endemic alpine herb in Taiwan. Heliyon 2023; 9:e14228. [PMID: 36938387 PMCID: PMC10018478 DOI: 10.1016/j.heliyon.2023.e14228] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/21/2023] [Accepted: 02/27/2023] [Indexed: 03/07/2023] Open
Abstract
Euphrasia nankotaizanensis (Orobanchaceae) is a rare alpine herb that is endemic to Taiwan. Only four small populations remain in Xue, Nanhu, and Cilai Mountains of Taiwan. The distribution of alpine herbs is severely threatened by climate change, which influences genetic variation and population structure. In this study, we investigated the effects of the natural isolation of alpine habitats on the genetic diversity and geographic structure of populations of E. nankotaizanensis using chloroplast (cp) and nuclear DNA (nrDNA) markers. We found lower levels of genetic diversity in E. nankotaizanensis than in other alpine plants and little to no genetic variation within populations, which could be mainly attributed to the small population size and genetic drift. Only one nrDNA haplotype was present in each population. The lack of monophyly of the four populations in cpDNA probably resulted from lineage sorting or occasional long-distance seed dispersal. Phylogeographic analysis suggested that Nanhu Mountain was probably a refugium over the glacial maxima, agreeing with the potential refugia in central Taiwan. The STRUCTURE and AMOVA analyses revealed significant genetic differentiation in nrDNA among the mountains, which resulted from geographical isolation among these mountains. Estimates of the effective population size (Ne) and demography reflected lower Ne values and a recent population decline, probably implying a greater extinction risk for E. nankotaizanensis. We observed genetic depletion and considerable genetic differentiation among mountain populations, which should be considered in future conservation efforts for this species. In addition, this study provides important insights into the long-term potential of alpine herbs in Taiwan, which are useful for a better prediction of their responses to future climate change.
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Affiliation(s)
- Syuan-Yu Chen
- Graduate Institute of Bioresources, Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Chi-Chun Huang
- Taiwan Endemic Species Research Institute, Nantou, Taiwan
| | - Yu-Tzu Cheng
- Department of Forestry, Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Chih-Chiang Wang
- Department of Forestry, Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Chiuan-Yu Li
- Taiwan Endemic Species Research Institute, Nantou, Taiwan
| | - I-Ling Lai
- Graduate Institute of Bioresources, Pingtung University of Science and Technology, Pingtung, Taiwan
- Biodiversity Research Center, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Kuo-Hsiang Hung
- Graduate Institute of Bioresources, Pingtung University of Science and Technology, Pingtung, Taiwan
- Biodiversity Research Center, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Corresponding author. Graduate Institute of Bioresources, Pingtung University of Science and Technology, Pingtung, Taiwan.
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5
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Seidlova V, Straková P, Kejíková R, Nemcova M, Bartonička T, Salát J, Dufková L, Šikutová S, Mendel J, McKee C, Zukal J, Pikula J, Rudolf I. Detection of Leptospira species in bat cadavers, Czech and Slovak Republics. Emerg Microbes Infect 2022; 11:2211-2213. [PMID: 36039905 PMCID: PMC9518262 DOI: 10.1080/22221751.2022.2117095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Kidney samples from 300 bat cadavers from the Czech and Slovak Republics were tested for Leptospira DNA using PCR and sequencing of three genes (lipL32, flab, and 16S ribosomal RNA). Overall detection rate was 4.7% and two bat species (Myotis myotis and Nyctalus noctula) were PCR-positive for at least one gene. Detected Leptospira sequences were similar to L. interrogans and L. borgpetersenii, and included a potentially novel species related to L. weilii.
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Affiliation(s)
- Veronika Seidlova
- Institute of Vertebrate Biology, Czech Academy of Sciences v.v.i., Květná 8, 603 65 Brno, Czech Republic.,Department of Ecology and Diseases of Zoo Animals, Game, Fish and Bees, University of Veterinary Sciences Brno, Palackého tř. 1946/1, 612 42 Brno, Czech Republic
| | - Petra Straková
- Veterinary Research Institute, Department of Infectious Diseases and Preventive Medicine, Hudcova 70, 62100 Brno, Czech Republic
| | - Romana Kejíková
- Institute of Vertebrate Biology, Czech Academy of Sciences v.v.i., Květná 8, 603 65 Brno, Czech Republic
| | - Monika Nemcova
- Department of Ecology and Diseases of Zoo Animals, Game, Fish and Bees, University of Veterinary Sciences Brno, Palackého tř. 1946/1, 612 42 Brno, Czech Republic
| | - Tomáš Bartonička
- Department of Botany and Zoology, Masaryk University, Kotlářská 267/2, 611 37 Brno, Czech Republic
| | - Jiří Salát
- Veterinary Research Institute, Department of Infectious Diseases and Preventive Medicine, Hudcova 70, 62100 Brno, Czech Republic
| | - Lucie Dufková
- Veterinary Research Institute, Department of Infectious Diseases and Preventive Medicine, Hudcova 70, 62100 Brno, Czech Republic
| | - Silvie Šikutová
- Institute of Vertebrate Biology, Czech Academy of Sciences v.v.i., Květná 8, 603 65 Brno, Czech Republic
| | - Jan Mendel
- Institute of Vertebrate Biology, Czech Academy of Sciences v.v.i., Květná 8, 603 65 Brno, Czech Republic
| | - Clifton McKee
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St., Baltimore, MD 21205, USA
| | - Jan Zukal
- Institute of Vertebrate Biology, Czech Academy of Sciences v.v.i., Květná 8, 603 65 Brno, Czech Republic
| | - Jiri Pikula
- Department of Ecology and Diseases of Zoo Animals, Game, Fish and Bees, University of Veterinary Sciences Brno, Palackého tř. 1946/1, 612 42 Brno, Czech Republic
| | - Ivo Rudolf
- Institute of Vertebrate Biology, Czech Academy of Sciences v.v.i., Květná 8, 603 65 Brno, Czech Republic
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6
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Hennig SL, McNabb BR, Trott JF, Van Eenennaam AL, Murray JD. LincRNA#1 knockout alone does not affect polled phenotype in cattle heterozygous for the celtic POLLED allele. Sci Rep 2022; 12:7627. [PMID: 35538091 PMCID: PMC9090918 DOI: 10.1038/s41598-022-11669-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 04/25/2022] [Indexed: 11/09/2022] Open
Abstract
A long intergenic non-coding RNA (lincRNA#1) is overexpressed in the horn bud region of polled (hornless) bovine fetuses, suggesting a potential role in horn bud suppression. Genome editing was used to test whether the absence of this sequence was associated with the horned phenotype. Two gRNAs with high mutation efficiencies targeting the 5' and the 3' regions flanking the lincRNA#1 sequence were co-injected with Cas9 as ribonucleoprotein complexes into bovine zygotes (n = 121) 6 h post insemination. Of the resulting blastocysts (n = 31), 84% had the expected 3.7 kb deletion; of these embryos with the 3.7 kb deletions, 88% were biallelic knockouts. Thirty-nine presumptive edited 7-day blastocysts were transferred to 13 synchronized recipient cows resulting in ten pregnancies, five with embryos heterozygous for the dominant PC POLLED allele at the POLLED locus, and five with the recessive pp genotype. Eight (80%) of the resulting fetuses were biallelic lincRNA#1 knockouts, with the remaining two being mosaic. RT-qPCR analysis was used to confirm the absence of lincRNA#1 expression in knockout fetuses. Phenotypic and histological analysis of the genotypically (PCp) POLLED, lincRNA#1 knockout fetuses revealed similar morphology to non-edited, control polled fetuses, indicating the absence of lincRNA#1 alone does not result in a horned phenotype.
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Affiliation(s)
- Sadie L Hennig
- Department of Animal Science, University of California-Davis, Davis, CA, USA
| | - Bret R McNabb
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
| | - Josephine F Trott
- Department of Animal Science, University of California-Davis, Davis, CA, USA
| | | | - James D Murray
- Department of Animal Science, University of California-Davis, Davis, CA, USA. .,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA.
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7
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Conant D, Hsiau T, Rossi N, Oki J, Maures T, Waite K, Yang J, Joshi S, Kelso R, Holden K, Enzmann BL, Stoner R. Inference of CRISPR Edits from Sanger Trace Data. CRISPR J 2022; 5:123-130. [PMID: 35119294 DOI: 10.1089/crispr.2021.0113] [Citation(s) in RCA: 202] [Impact Index Per Article: 101.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Efficient and precise genome editing requires a fast, quantitative, and inexpensive assay to assess genotype following editing. Here, we present ICE (Inference of CRISPR Edits), which enables robust analysis of CRISPR edits using Sanger data. ICE proposes potential outcomes for editing with guide RNAs, and then determines which are supported by the data via regression. The ICE algorithm is robust and reproducible, and it can be used to analyze CRISPR experiments within days after transfection. We also confirm that ICE produces accurate estimates of editing outcomes across a variety of benchmarks, and within the context of other existing Sanger analysis tools. The ICE tool is free to use and open source, and offers several improvements over current analysis tools, such as batch analysis and support for a variety of editing conditions. It is available online at ice.synthego.com, and the source code is available at github.com/synthego-open/ice.
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Affiliation(s)
| | - Tim Hsiau
- Synthego, Redwood City, California, USA
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8
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A Survey of Tick Infestation and Tick-Borne Piroplasm Infection of Cattle in Oudalan and Séno Provinces, Northern Burkina Faso. Pathogens 2021; 11:pathogens11010031. [PMID: 35055979 PMCID: PMC8777743 DOI: 10.3390/pathogens11010031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/19/2021] [Accepted: 12/24/2021] [Indexed: 12/01/2022] Open
Abstract
In this study, cattle farms located in Oudalan and Séno, two provinces in the Sahel region, northern Burkina Faso, were surveyed. Cattle owners were interviewed, cattle were examined for tick infestation, and ticks as well as blood samples were collected during the dry season (October). Blood DNA samples were tested for Babesia and Theileria infections using nested PCRs and sequencing. A total of 22 herds, 174 Zebu cattle were investigated at 6 different sites. Overall, 76 cattle (43.7 %) from 18 farms (81.8%) were found infested with ticks. Cattle in Séno, adult cattle (>5 years) and those owned by the Fulani ethnic group were significantly (p < 0.05) more likely to be tick-infested. A total of 144 adult ticks belonging to five species namely: Hyalomma impeltatum, Hyalomma impressum, Hyalomma rufipes, Rhipicephalus evertsi evertsi, and Rhipicephalus guilhoni were collected from the animals. Piroplasms were detected in the blood DNA of 23 (13.2%) cattle. The cattle in Séno and adult cattle were significantly more likely to be piroplasm-positive. Five pathogens diversely distributed were identified. Theileria mutans (12/174), Babesia bigemina (5/174), Theileria annulata (3/174), and Theileria velifera (3/174) were detected for the first time in northern Burkina Faso, whereas Babesia occultans (1/174) was found for the first time in cattle in West Africa. The analysis of the sequences, including B. bigemina RAP-1a, T. annulata Tams1 genes, and the 18S rRNA genes of all the five protozoa, revealed identities ranging from 98.4 to 100% with previously published sequences. Phylogenetic analysis based on the 18S rRNA gene sequences located north Burkina Faso piroplasms in the same clade as isolates from Africa and other regions of the world. Notably, T. mutans sequences were distributed in two clades: the T. mutans Intona strain clade and the Theileria sp. (strain MSD)/ Theileria sp. B15a clade, suggesting the presence of at least two strains in the area. These findings indicate that the control of ticks and tick-borne diseases should be taken into account in strategies to improve animal health in the Sahel region.
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9
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Establishment and genetic characterization of cell lines derived from proliferating nasal polyps and sinonasal inverted papillomas. Sci Rep 2021; 11:17100. [PMID: 34429452 PMCID: PMC8384845 DOI: 10.1038/s41598-021-96444-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 08/10/2021] [Indexed: 11/25/2022] Open
Abstract
To better understand the pathogenesis of nasal polyps (NPs) and sinonasal inverted papillomas (SIPs), we aimed to establish cell lines from fresh tissues of NPs and SIPs and characterize them. Primary cell cultures were obtained from two NP tissues (NP2 and NP3) and one SIP tissue (IP4). All the cells were polygonal in shape, expressed cytokeratin 14, and had normal diploid chromosome status. HPV58 DNA was detected in NP3. To obtain immortal primary cells, NP2 and IP4 cells were transduced with a combination of mutant CDK4, cyclinD1 and TERT. These cells were thereafter named NP2/K4DT and IP4/K4DT, respectively. HPV58-positive NP3 cells were transduced with TERT alone, the resulting cells named NP3/T. Phenotypic and genotypic identity of original tissues and derived cells was investigated. All the cell cultures with transgenes were confirmed to be derived from their parental cells and primary tumor tissues by analysis of short tandem repeats (STR) and maintained in vitro growth, genetic profiles and gene expression characteristics of the primary cells. These virtually immortalized cells, as well as the primary cells, have potential as in vitro models for studying the pathogenesis of NPs and SIPs and for preclinical study to develop new therapeutic agents.
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10
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Yanta CA, Bessonov K, Robinson G, Troell K, Guy RA. CryptoGenotyper: A new bioinformatics tool for rapid Cryptosporidium identification. Food Waterborne Parasitol 2021; 23:e00115. [PMID: 33748443 PMCID: PMC7966988 DOI: 10.1016/j.fawpar.2021.e00115] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/09/2021] [Accepted: 02/15/2021] [Indexed: 01/09/2023] Open
Abstract
Cryptosporidium is a protozoan parasite that is transmitted to both humans and animals through zoonotic or anthroponotic means. When a host is infected with this parasite, it causes a gastrointestinal disease known as cryptosporidiosis. To understand the transmission dynamics of Cryptosporidium, the small subunit (SSU or 18S) rRNA and gp60 genes are commonly studied through PCR analysis and conventional Sanger sequencing. However, analyzing sequence chromatograms manually is both time consuming and prone to human error, especially in the presence of poorly resolved, heterozygous peaks and the absence of a validated database. For this study, we developed a Cryptosporidium genotyping tool, called CryptoGenotyper, which has the capability to read raw Sanger sequencing data for the two common Cryptosporidium gene targets (SSU rRNA and gp60) and classify the sequence data into standard nomenclature. The CryptoGenotyper has the capacity to perform quality control and properly classify sequences using a high quality, manually curated reference database, saving users' time and removing bias during data analysis. The incorporated heterozygous base calling algorithms for the SSU rRNA gene target resolves double peaks, therefore recovering data previously classified as inconclusive. The CryptoGenotyper successfully genotyped 99.3% (428/431) and 95.1% (154/162) of SSU rRNA chromatograms containing single and mixed sequences, respectively, and correctly subtyped 95.6% (947/991) of gp60 chromatograms without manual intervention. This new, user-friendly tool can provide both fast and reproducible analyses of Sanger sequencing data for the two most common Cryptosporidium gene targets.
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Affiliation(s)
- Christine A Yanta
- National Microbiology Laboratory, Public Health Agency of Canada, 110 Stone Road West, Guelph, ON N1G 3W4, Canada
| | - Kyrylo Bessonov
- National Microbiology Laboratory, Public Health Agency of Canada, 110 Stone Road West, Guelph, ON N1G 3W4, Canada
| | - Guy Robinson
- Cryptosporidium Reference Unit, Public Health Wales, Microbiology and Health Protection, Singleton Hospital, Swansea SA2 8QA, UK.,Swansea University Medical School, Singleton Park, Swansea SA2 8PP, UK
| | - Karin Troell
- National Veterinary Institute, 751 89 Uppsala, Sweden.,Department of Medical Biochemistry and Microbiology, Uppsala University, Sweden
| | - Rebecca A Guy
- National Microbiology Laboratory, Public Health Agency of Canada, 110 Stone Road West, Guelph, ON N1G 3W4, Canada
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11
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Kim DH, Lee J, Suh Y, Lee K. Necessity for Validation of Effectiveness of Selected Guide RNA In Silico for Application of CRISPR/Cas9. Mol Biotechnol 2021; 63:140-149. [PMID: 33386580 DOI: 10.1007/s12033-020-00290-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2020] [Indexed: 12/26/2022]
Abstract
Selection of guide RNA (gRNA) is important to increase the efficiency of gene editing in the CRISPR/Cas9 system. Due to the variation in actual efficiency of insertion/deletion (indel) mutation among selected gRNAs in silico, reliable methods for validation of efficiency of gRNA need to be developed. Three gRNAs with high on-target scores (72.0 for target 1, 65.4 for target 2, and 62.9 for target 3) were designed to target the quail retinol binding protein 7 (qRbp7) gene, and indel efficiencies were predicted by the Sanger sequencing and Inference of CRISPR Edits (ICE) analysis of sorted cell populations receiving the CRISPR/Cas9 vector. Unlike the order of on-target scores among 3 gRNAs, predicted rates of indel mutations were highest in gRNA2, intermediate in gRNA1, and lowest in gRNA3. This was confirmed by actual indel mutation rates, 51.8% in gRNA2, 31% in gRNA1, and 12.9% in gRNA3, which were calculated by sequencing individual allele cloned into a vector. These data showed a rapid and reliable method for estimation of the efficiency of selected gRNAs, providing a critical necessary step for successful gene editing for further applications.
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Affiliation(s)
- Dong-Hwan Kim
- Department of Animal Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Joonbum Lee
- Department of Animal Sciences, The Ohio State University, Columbus, OH, 43210, USA
- Interdisciplinary Ph.D. Program in Nutrition, The Ohio State University, Columbus, OH, 43210, USA
| | - Yeunsu Suh
- Department of Animal Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Kichoon Lee
- Department of Animal Sciences, The Ohio State University, Columbus, OH, 43210, USA.
- Interdisciplinary Ph.D. Program in Nutrition, The Ohio State University, Columbus, OH, 43210, USA.
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12
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Flipse J, Duim B, Wallinga JA, de Wijkerslooth LRH, van der Graaf-van Bloois L, Timmerman AJ, Zomer AL, Veldman KT, Wagenaar JA, Bloembergen P. A Case of Persistent Diarrhea in a Man with the Molecular Detection of Various Campylobacter species and the First Isolation of candidatus Campylobacter infans. Pathogens 2020; 9:E1003. [PMID: 33265947 PMCID: PMC7761484 DOI: 10.3390/pathogens9121003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/10/2020] [Accepted: 11/10/2020] [Indexed: 11/18/2022] Open
Abstract
A man with a well-controlled HIV infection, previously diagnosed with lymphogranuloma venereum and treated for Hodgkin's lymphoma, was suffering from chronic diarrhea. He travelled to Indonesia in the month prior to the start of complaints. Over a 15-month period, sequences related to Campylobactertroglodytis/upsaliensis, C. pinnepediorum/mucosalis/concisus and C. hominis were detected by 16S rRNA qPCR-based assays in various stool samples and in a colon biopsy. Culture revealed the first isolation of "candidatus Campylobacter infans", a species identified recently by molecular methods only. The patient was treated with azithromycin, ciprofloxacin and tetracycline. To identify potential continuous exposure of the patient to Campylobacter, stool samples of the partner and the cat of the patient were analyzed and C. pinnepediorum/mucosalis/concisus and C. helveticus, respectively, were detected. The diversity in detected species in this immunocompromised patient with a lack of repeatedly consistent findings resulted in the conclusion that not any of the Campylobacter species was the primary cause of the clinical condition. This study shows the challenges in detection and interpretation of diagnostic results regarding Campylobacter.
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Affiliation(s)
- Jacky Flipse
- Laboratory of Medical Microbiology and Infectious Diseases, Isala Clinics, 8025 AB Zwolle, The Netherlands; (J.A.W.); (P.B.)
| | - Birgitta Duim
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands; (L.v.d.G.-v.B.); (A.J.T.); (A.L.Z.); (J.A.W.)
- WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, 3584 CL Utrecht, The Netherlands
| | - Janny A. Wallinga
- Laboratory of Medical Microbiology and Infectious Diseases, Isala Clinics, 8025 AB Zwolle, The Netherlands; (J.A.W.); (P.B.)
| | | | - Linda van der Graaf-van Bloois
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands; (L.v.d.G.-v.B.); (A.J.T.); (A.L.Z.); (J.A.W.)
- WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, 3584 CL Utrecht, The Netherlands
| | - Arjen J. Timmerman
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands; (L.v.d.G.-v.B.); (A.J.T.); (A.L.Z.); (J.A.W.)
- WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, 3584 CL Utrecht, The Netherlands
| | - Aldert L. Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands; (L.v.d.G.-v.B.); (A.J.T.); (A.L.Z.); (J.A.W.)
- WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, 3584 CL Utrecht, The Netherlands
| | - Kees T. Veldman
- Wageningen Bioveterinary Research, 8221 RA Lelystad, The Netherlands;
| | - Jaap A. Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands; (L.v.d.G.-v.B.); (A.J.T.); (A.L.Z.); (J.A.W.)
- WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, 3584 CL Utrecht, The Netherlands
- Wageningen Bioveterinary Research, 8221 RA Lelystad, The Netherlands;
| | - Peter Bloembergen
- Laboratory of Medical Microbiology and Infectious Diseases, Isala Clinics, 8025 AB Zwolle, The Netherlands; (J.A.W.); (P.B.)
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Henrich B, Hammerlage S, Scharf S, Haberhausen D, Fürnkranz U, Köhrer K, Peitzmann L, Fiori PL, Spergser J, Pfeffer K, Dilthey AT. Characterisation of mobile genetic elements in Mycoplasma hominis with the description of ICEHo-II, a variant mycoplasma integrative and conjugative element. Mob DNA 2020; 11:30. [PMID: 33292499 PMCID: PMC7648426 DOI: 10.1186/s13100-020-00225-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 10/22/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Mobile genetic elements are found in genomes throughout the microbial world, mediating genome plasticity and important prokaryotic phenotypes. Even the cell wall-less mycoplasmas, which are known to harbour a minimal set of genes, seem to accumulate mobile genetic elements. In Mycoplasma hominis, a facultative pathogen of the human urogenital tract and an inherently very heterogeneous species, four different MGE-classes had been detected until now: insertion sequence ISMhom-1, prophage MHoV-1, a tetracycline resistance mediating transposon, and ICEHo, a species-specific variant of a mycoplasma integrative and conjugative element encoding a T4SS secretion system (termed MICE). RESULTS To characterize the prevalence of these MGEs, genomes of 23 M. hominis isolates were assembled using whole genome sequencing and bioinformatically analysed for the presence of mobile genetic elements. In addition to the previously described MGEs, a new ICEHo variant was found, which we designate ICEHo-II. Of 15 ICEHo-II genes, five are common MICE genes; eight are unique to ICEHo-II; and two represent a duplication of a gene also present in ICEHo-I. In 150 M. hominis isolates and based on a screening PCR, prevalence of ICEHo-I was 40.7%; of ICEHo-II, 28.7%; and of both elements, 15.3%. Activity of ICEHo-I and -II was demonstrated by detection of circularized extrachromosomal forms of the elements through PCR and subsequent Sanger sequencing. CONCLUSIONS Nanopore sequencing enabled the identification of mobile genetic elements and of ICEHo-II, a novel MICE element of M. hominis, whose phenotypic impact and potential impact on pathogenicity can now be elucidated.
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Affiliation(s)
- Birgit Henrich
- Institute of Med. Microbiology and Hospital Hygiene of the Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany.
| | - Stephanie Hammerlage
- Institute of Med. Microbiology and Hospital Hygiene of the Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany
| | - Sebastian Scharf
- Institute of Med. Microbiology and Hospital Hygiene of the Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany.,Department of Haematology, Oncology and Clinical Immunology, Medical Faculty, University of Duesseldorf, Duesseldorf, Germany
| | - Diana Haberhausen
- Institute of Med. Microbiology and Hospital Hygiene of the Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany
| | - Ursula Fürnkranz
- Institute for Specific Prophylaxis and Tropical Medicine, Centre for Pathophysiology, Immunology and Infectiology, Medical University of Vienna, Vienna, Austria
| | - Karl Köhrer
- Biological and Medical Research Centre (BMFZ) of the Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany
| | - Lena Peitzmann
- Biological and Medical Research Centre (BMFZ) of the Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany
| | - Pier Luigi Fiori
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Joachim Spergser
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Klaus Pfeffer
- Institute of Med. Microbiology and Hospital Hygiene of the Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany
| | - Alexander T Dilthey
- Institute of Med. Microbiology and Hospital Hygiene of the Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany.,Institute of Medical Statistics and Computational Biology, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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14
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New insights into the coexistence of Contracaecum rudolphii A and Contracaecum rudolphii B (Nematoda: Anisakidae) in Phalacrocorax carbo sinensis from Sardinia: genetic variability and phylogenetic analysis. Parasitology 2020; 147:1538-1551. [PMID: 32741423 DOI: 10.1017/s0031182020001341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Contracaecum sp. nematodes are important parasites of fish eating birds that can cause animal health problems. In the present study, specimens of Contracaecum rudolphii sensu lato, from the great cormorant Phalacrocorax carbo sinensis from Sardinia, were characterized based on morphological and molecular data. The morphological analysis allowed to identify all the fourth stage larvae (n = 1918) as Contracaecum sp., and adults, male (n = 5845) and female (n = 8312), as C. rudolphii sensu lato. Population genetics and phylogenetic relationships were inferred based on mitochondrial and nuclear markers. Multiple sequence alignment of the ribosomal internal transcribed spacer showed the coexistence of C. rudolphii A (n = 157), C. rudolphii B (n = 22) and a rare heterozygote of these species. Moreover, mitochondrial markers, namely NADH dehydrogenase subunits I (nad1), cytochrome c oxidase subunit (cox1 and cox2) and small subunit of rRNA (rrnS), showed that the studied C. rudolphii A populations had undergone bottleneck, or founder effect event, subsequent to a rapid population growth and expansion. The observed heterozygote is with a mitochondrial pattern of C. rudolphii B. Although, both Contracaecum species showed high genetic diversity, no genetic structure between localities was detected. Phylogenetic reconstructions supported the paraphyly of the avian Contracaecum species including C. ogmorhini (parasite of otariids).
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da Silva R, Pedraza-Marrón CDR, Sampaio I, Betancur-R R, Gomes G, Schneider H. New insights about species delimitation in red snappers (Lutjanus purpureus and L. campechanus) using multilocus data. Mol Phylogenet Evol 2020; 147:106780. [PMID: 32135307 DOI: 10.1016/j.ympev.2020.106780] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 01/29/2020] [Accepted: 02/26/2020] [Indexed: 01/08/2023]
Abstract
Lutjanus campechanus and Lutjanus purpureus are two commercially important lutjanid fishes (snappers) with non-sympatric distribution throughout Western Atlantic. Even though both taxa have traditionally been regarded as valid species, their taxonomic status remains under debate. In the present study, we used phylogeographic approaches and molecular methods of species delimitation to elucidate the taxonomic issues between both species, based on 1478 base pairs from four genomic regions. We found haplotypes shared between the two species, particularly in relation to nuclear DNA (nuDNA) sequences. The molecular delimitation of species supported the discrimination of L. purpureus and L. campechanus as distinct evolutionary units. Nonetheless, a unidirectional gene flow was found from L. campechanus towards L. purpureus. Therefore, it seems plausible to infer that L. campechanus and L. purpureus are two evolutionary units in which the apparent sharing of haplotypes should be driven by introgression.
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Affiliation(s)
- Raimundo da Silva
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança, Pará, Brazil
| | | | - Iracilda Sampaio
- Laboratório de Genética e Biologia Molecular, Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança, Pará, Brazil
| | | | - Grazielle Gomes
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança, Pará, Brazil; Laboratório de Genética e Biologia Molecular, Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança, Pará, Brazil.
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von Oheimb KCM, von Oheimb PV, Hirano T, Do TV, Ablett J, Luong HV, Pham SV, Naggs F. Cryptic diversity of limestone karst inhabiting land snails (Cyclophorus spp.) in northern Vietnam, their evolutionary history and the description of four new species. PLoS One 2019; 14:e0222163. [PMID: 31644567 PMCID: PMC6808330 DOI: 10.1371/journal.pone.0222163] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 08/21/2019] [Indexed: 11/18/2022] Open
Abstract
Limestone karsts can form terrestrial habitat islands for calcium-dependent organisms. In Vietnam, many karst habitats are threatened, while their rich biodiversity is still far from being thoroughly explored. Given that conservation of karst biota strongly relies on correct species identification, the presence of undetected cryptic species can pose severe problems. The present study focuses on cryptic diversity among karst-inhabiting land snails of the genus Cyclophorus in northern Vietnam, where specimens with a similar shell morphology have been reported from various regions. In order to examine the diversity and evolutionary history of this “widespread morphotype”, we generated a Bayesian phylogeny based on DNA sequence data. Automatic Barcode Gap Discovery (ABGD) and the Bayesian implementation of the Poisson tree processes model (bPTP) contributed to species delimitation and analyses of shell shape and size aided the morphological characterisation of individual species. We found that the examined specimens of the widespread morphotype did not form a single monophyletic group in the phylogeny but clustered into several different clades. We delimited nine different species that develop the widespread morphotype and described four of them as new. Processes of convergent evolution were probably involved in the origin of the delimited species, while their generally allopatric distribution could result from interspecific competition. Our findings indicate ongoing processes of speciation and a potential case of morphological character displacement. The high degree of morphological overlap found among the species underlines the importance of DNA sequence data for species delimitation and description in the genus Cyclophorus. Given the findings of the present study and the high potential that as yet undiscovered cryptic taxa have also evolved in other groups of karst-inhabiting organisms, we argue for a systematic and efficient detection and description of Vietnam’s karst biodiversity to provide a solid basis for future conservation planning.
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Affiliation(s)
- Katharina C. M. von Oheimb
- Life Sciences Department, The Natural History Museum, London, England, United Kingdom
- Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
- * E-mail:
| | - Parm Viktor von Oheimb
- Life Sciences Department, The Natural History Museum, London, England, United Kingdom
- Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Takahiro Hirano
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Tu Van Do
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Ha Noi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Ha Noi, Vietnam
| | - Jonathan Ablett
- Life Sciences Department, The Natural History Museum, London, England, United Kingdom
| | - Hao Van Luong
- Centre for Rescue and Conservation of Organisms, Hoang Lien National Park, Sa Pa, Vietnam
| | - Sang Van Pham
- Department of Specimen Preparation and Exhibitive Design, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, Ha Noi, Vietnam
| | - Fred Naggs
- Life Sciences Department, The Natural History Museum, London, England, United Kingdom
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17
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Portugal MEG, Raboni SM, Nogueira MB, Vidal LRR, Dingueleski AH, Kluk E, Bonfim C, Ribeiro LL, Torres-Pereira CC. High frequency of multiple HPV types detection in Fanconi anemia patients oral swabs. Transpl Infect Dis 2018; 21:e13030. [PMID: 30449057 DOI: 10.1111/tid.13030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/16/2018] [Accepted: 11/06/2018] [Indexed: 01/24/2023]
Abstract
BACKGROUND Fanconi anemia (FA) is a rare genetic disease usually characterized by bone marrow failure and congenital malformations. The risk of development of malignancies in the oral cavity of FA patients, such as squamous cell carcinoma (SCC), increases significantly after a hematopoietic stem cells transplant (HSCT), and may also be linked with the presence of human papillomavirus (HPV) infections in the oral cavity. We investigated the prevalence and the HPV genotypes in oral mucosa of Brazilian FA patients. METHODS AND RESULTS Oral swabs of 49 FA patients were collected. The median age of patients was 20 years (range 5-44) and 57% were over 18 years. Oral lesions were present in 20% of all patients, being 90% leukoplakia. HPV DNA was detected in 28% (14/49) of patients, and one of them also reported genital HPV lesions. Sixty-seven percent of all patients had undergone HSCT, including 12 patients (86%) of those with HPV results. Multiple HPV types were detected in 78% and 71% of HPV samples by Sanger sequencing and reverse hybridization methods, respectively. The most prevalent HPV types detected were 6, 11, 18, and 68. CONCLUSIONS HPV prevalence in the oral mucosa of the assessed FA patients was higher than reported in the general population. Additional studies with collection of sequential samples are needed to know the natural history of the presence of multiple HPV types in these individuals and its association with the development of tumors, to evaluate the implementation of preventive measures, such as vaccination, and to guide early treatment.
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Affiliation(s)
- Magda Eline Guerrart Portugal
- Postgraduate Program in Internal Medicine and Health Science, Federal University of Paraná, Curitiba, Brazil.,Laboratory of Virology, Federal University of Paraná, Curitiba, Brazil.,Herrero Faculty - Dentistry Graduation Course, Curitiba, Brazil
| | - Sonia Mara Raboni
- Postgraduate Program in Internal Medicine and Health Science, Federal University of Paraná, Curitiba, Brazil.,Laboratory of Virology, Federal University of Paraná, Curitiba, Brazil.,Infectious Diseases Division, Federal University of Paraná, Curitiba, Brazil
| | | | | | | | - Edelaine Kluk
- Herrero Faculty - Dentistry Graduation Course, Curitiba, Brazil
| | - Carmem Bonfim
- Bone Marrow Transplant Division, Federal University of Paraná, Curitiba, Brazil
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18
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Biodiversity and apomixis: Insights from the East-Asian holly ferns in Polystichum section Xiphopolystichum. Mol Phylogenet Evol 2018; 127:345-355. [PMID: 29763663 DOI: 10.1016/j.ympev.2018.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 04/30/2018] [Accepted: 05/03/2018] [Indexed: 11/24/2022]
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19
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Hsia GSP, Musso CM, Alvizi L, Brito LA, Kobayashi GS, Pavanello RCM, Zatz M, Gardham A, Wakeling E, Zechi-Ceide RM, Bertola D, Passos-Bueno MR. Complexity of the 5' Untranslated Region of EIF4A3, a Critical Factor for Craniofacial and Neural Development. Front Genet 2018; 9:149. [PMID: 29922329 PMCID: PMC5996909 DOI: 10.3389/fgene.2018.00149] [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: 02/15/2018] [Accepted: 04/10/2018] [Indexed: 01/09/2023] Open
Abstract
Repeats in coding and non-coding regions have increasingly been associated with many human genetic disorders, such as Richieri-Costa-Pereira syndrome (RCPS). RCPS, mostly characterized by midline cleft mandible, Robin sequence and limb defects, is an autosomal-recessive acrofacial dysostosis mainly reported in Brazilian patients. This disorder is caused by decreased levels of EIF4A3, mostly due to an increased number of repeats at the EIF4A3 5′UTR. EIF4A3 5′UTR alleles are CG-rich and vary in size and organization of three types of motifs. An exclusive allelic pattern was identified among affected individuals, in which the CGCA-motif is the most prevalent, herein referred as “disease-associated CGCA-20nt motif.” The origin of the pathogenic alleles containing the disease-associated motif, as well as the functional effects of the 5′UTR motifs on EIF4A3 expression, to date, are entirely unknown. Here, we characterized 43 different EIF4A3 5′UTR alleles in a cohort of 380 unaffected individuals. We identified eight heterozygous unaffected individuals harboring the disease-associated CGCA-20nt motif and our haplotype analyses indicate that there are more than one haplotype associated with RCPS. The combined analysis of number, motif organization and haplotypic diversity, as well as the observation of two apparently distinct haplotypes associated with the disease-associated CGCA-20nt motif, suggest that the RCPS alleles might have arisen from independent unequal crossing-over events between ancient alleles at least twice. Moreover, we have shown that the number and sequence of motifs in the 5′UTR region is associated with EIF4A3 repression, which is not mediated by CpG methylation. In conclusion, this study has shown that the large number of repeats in EIF4A3 does not represent a dynamic mutation and RCPS can arise in any population harboring alleles with the CGCA-20nt motif. We also provided further evidence that EIF4A3 5′UTR is a regulatory region and the size and sequence type of the repeats at 5′UTR may contribute to clinical variability in RCPS.
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Affiliation(s)
- Gabriella S P Hsia
- Centro de Estudos do Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Camila M Musso
- Centro de Estudos do Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Lucas Alvizi
- Centro de Estudos do Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Luciano A Brito
- Centro de Estudos do Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Gerson S Kobayashi
- Centro de Estudos do Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Rita C M Pavanello
- Centro de Estudos do Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Mayana Zatz
- Centro de Estudos do Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Alice Gardham
- North East Thames Genetics Service, Great Ormond Street Hospital, London, United Kingdom
| | - Emma Wakeling
- North East Thames Genetics Service, Great Ormond Street Hospital, London, United Kingdom
| | - Roseli M Zechi-Ceide
- Hospital de Reabilitação de Anomalias Craniofaciais, Universidade de São Paulo, São Paulo, Brazil
| | - Debora Bertola
- Centro de Estudos do Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.,Instituto da Criança, Hospital das Clínicas da FMUSP, Universidade de São Paulo, São Paulo, Brazil
| | - Maria Rita Passos-Bueno
- Centro de Estudos do Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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20
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Nielsen CF, van Putten SM, Lund IK, Melander MC, Nørregaard KS, Jürgensen HJ, Reckzeh K, Christensen KR, Ingvarsen SZ, Gårdsvoll H, Jensen KE, Hamerlik P, Engelholm LH, Behrendt N. The collagen receptor uPARAP/Endo180 as a novel target for antibody-drug conjugate mediated treatment of mesenchymal and leukemic cancers. Oncotarget 2018; 8:44605-44624. [PMID: 28574834 PMCID: PMC5546505 DOI: 10.18632/oncotarget.17883] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 04/24/2017] [Indexed: 11/29/2022] Open
Abstract
A key task in developing the field of personalized cancer therapy is the identification of novel molecular targets that enable treatment of cancers not susceptible to other means of specific therapy. The collagen receptor uPARAP/Endo180 is overexpressed by malignant cells in several non-epithelial cancers, notably including sarcomas, glioblastomas and subsets of acute myeloid leukemia. In contrast, in healthy adult individuals, expression is restricted to minor subsets of mesenchymal cells. Functionally, uPARAP/Endo180 is a rapidly recycling endocytic receptor that delivers its cargo directly into the endosomal-lysosomal system, thus opening a potential route of entry into receptor-positive cells. This combination of specific expression and endocytic function appears well suited for targeting of uPARAP/Endo180-positive cancers by antibody-drug conjugate (ADC) mediated drug delivery. Therefore, we utilized a specific monoclonal antibody against uPARAP/Endo180, raised through immunization of a uPARAP/Endo180 knock-out mouse, which reacts with both the human and the murine receptor, to construct a uPARAP-directed ADC. This antibody was coupled to the highly toxic dolastatin derivative, monomethyl auristatin E, via a cathepsin-labile valine-citrulline linker. With this ADC, we show strong and receptor-dependent cytotoxicity in vitro in uPARAP/Endo180-positive cancer cell lines of sarcoma, glioblastoma and leukemic origin. Furthermore, we demonstrate the potency of the ADC in vivo in a xenograft mouse model with human uPARAP/Endo180-positive leukemic cells, obtaining a complete cure of all tested mice following intravenous ADC treatment with no sign of adverse effects. Our study identifies uPARAP/Endo180 as a promising target for novel therapy against several highly malignant cancer types.
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Affiliation(s)
- Christoffer Fagernæs Nielsen
- The Finsen Laboratory, Rigshospitalet, Biotech Research and Innovation Center (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Sander Maarten van Putten
- The Finsen Laboratory, Rigshospitalet, Biotech Research and Innovation Center (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Ida Katrine Lund
- The Finsen Laboratory, Rigshospitalet, Biotech Research and Innovation Center (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Maria Carlsén Melander
- The Finsen Laboratory, Rigshospitalet, Biotech Research and Innovation Center (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Kirstine Sandal Nørregaard
- The Finsen Laboratory, Rigshospitalet, Biotech Research and Innovation Center (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Henrik Jessen Jürgensen
- The Finsen Laboratory, Rigshospitalet, Biotech Research and Innovation Center (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark.,Proteases and Tissue Remodeling Section, Oral and Pharyngeal Cancer Branch, NIDCR, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Kristian Reckzeh
- The Finsen Laboratory, Rigshospitalet, Biotech Research and Innovation Center (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Kristine Rothaus Christensen
- Experimental Animal Models Section, Department of Veterinary Disease Biology, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Signe Ziir Ingvarsen
- The Finsen Laboratory, Rigshospitalet, Biotech Research and Innovation Center (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Henrik Gårdsvoll
- The Finsen Laboratory, Rigshospitalet, Biotech Research and Innovation Center (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | | | - Petra Hamerlik
- Danish Cancer Society Research Center, DK-2100 Copenhagen Ø, Denmark
| | - Lars Henning Engelholm
- The Finsen Laboratory, Rigshospitalet, Biotech Research and Innovation Center (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Niels Behrendt
- The Finsen Laboratory, Rigshospitalet, Biotech Research and Innovation Center (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
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von Oheimb PV, von Oheimb KCM, Hirano T, Do TV, Luong HV, Ablett J, Pham SV, Naggs F. Competition matters: Determining the drivers of land snail community assembly among limestone karst areas in northern Vietnam. Ecol Evol 2018; 8:4136-4149. [PMID: 29721286 PMCID: PMC5916308 DOI: 10.1002/ece3.3984] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 12/28/2017] [Accepted: 02/09/2018] [Indexed: 11/11/2022] Open
Abstract
The insular limestone karsts of northern Vietnam harbor a very rich biodiversity. Many taxa are strongly associated with these environments, and individual species communities can differ considerably among karst areas. The exact processes that have shaped the biotic composition of these habitats, however, remain largely unknown. In this study, the role of two major processes for the assembly of snail communities on limestone karsts was investigated, interspecific competition and filtering of taxa due to geographical factors. Communities of operculate land snails of the genus Cyclophorus were studied using the dry and fluid-preserved specimen collections of the Natural History Museum, London. Phylogenetic distances (based on a Bayesian analysis using DNA sequence data) and shell characters (based on 200 semilandmarks) were used as proxies for ecological similarity and were analyzed to reveal patterns of overdispersion (indicating competition) or clustering (indicating filtering) in observed communities compared to random communities. Among the seven studied karst areas, a total of 15 Cyclophorus lineages were found. Unique communities were present in each area. The analyses revealed phylogenetic overdispersion in six and morphological overdispersion in four of seven karst areas. The pattern of frequent phylogenetic overdispersion indicated that competition among lineages is the major process shaping the Cyclophorus communities studied. The Coastal Area, which was phylogenetically overdispersed, showed a clear morphological clustering, which could have been caused by similar ecological adaptations among taxa in this environment. Only the community in the Cuc Phuong Area showed a pattern of phylogenetic clustering, which was partly caused by an absence of a certain, phylogenetically very distinct group in this region. Filtering due to geographical factors could have been involved here. This study shows how museum collections can be used to examine community assembly and contributes to the understanding of the processes that have shaped karst communities in Vietnam.
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Affiliation(s)
| | | | - Takahiro Hirano
- Center for Northeast Asian Studies Tohoku University Sendai Japan
| | - Tu Van Do
- Department of Aquatic Ecology and Water Environment Institute of Ecology and Biological Resources Vietnam Academy of Science and Technology Ha Noi Vietnam
| | - Hao Van Luong
- Centre for Rescue and Conservation of Organisms Hoang Lien National Park Sa Pa Vietnam
| | - Jonathan Ablett
- Life Sciences Department The Natural History Museum London UK
| | - Sang Van Pham
- Department of Specimen Preparation and Exhibitive Design Vietnam National Museum of Nature Vietnam Academy of Science and Technology Ha Noi Vietnam
| | - Fred Naggs
- Life Sciences Department The Natural History Museum London UK
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22
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Veeranagouda Y, Debono-Lagneaux D, Fournet H, Thill G, Didier M. CRISPR-Cas9-Edited Site Sequencing (CRES-Seq): An Efficient and High-Throughput Method for the Selection of CRISPR-Cas9-Edited Clones. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2018; 121:31.14.1-31.14.11. [PMID: 29337372 DOI: 10.1002/cpmb.53] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The emergence of clustered regularly interspaced short palindromic repeats-Cas9 (CRISPR-Cas9) gene editing systems has enabled the creation of specific mutants at low cost, in a short time and with high efficiency, in eukaryotic cells. Since a CRISPR-Cas9 system typically creates an array of mutations in targeted sites, a successful gene editing project requires careful selection of edited clones. This process can be very challenging, especially when working with multiallelic genes and/or polyploid cells (such as cancer and plants cells). Here we described a next-generation sequencing method called CRISPR-Cas9 Edited Site Sequencing (CRES-Seq) for the efficient and high-throughput screening of CRISPR-Cas9-edited clones. CRES-Seq facilitates the precise genotyping up to 96 CRISPR-Cas9-edited sites (CRES) in a single MiniSeq (Illumina) run with an approximate sequencing cost of $6/clone. CRES-Seq is particularly useful when multiple genes are simultaneously targeted by CRISPR-Cas9, and also for screening of clones generated from multiallelic genes/polyploid cells. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Yaligara Veeranagouda
- Molecular Biology and Genomics, Translational Sciences, Sanofi R&D, Chilly-Mazarin, France
| | | | - Hamida Fournet
- Molecular Biology and Genomics, Translational Sciences, Sanofi R&D, Chilly-Mazarin, France
| | - Gilbert Thill
- Molecular Biology and Genomics, Translational Sciences, Sanofi R&D, Chilly-Mazarin, France
| | - Michel Didier
- Molecular Biology and Genomics, Translational Sciences, Sanofi R&D, Chilly-Mazarin, France
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23
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Discrimination of Mixed Infections of Echinococcus Species Based on in Silico Sequence Analysis: A New Way of Reflecting Overlapped Strains in Indigenous Areas. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2017. [DOI: 10.5812/archcid.14168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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24
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Bubien V, Bonnet F, Dupiot-Chiron J, Barouk-Simonet E, Jones N, de Reynies A, MacGrogan G, Sevenet N, Letouzé E, Longy M. Combined tumor genomic profiling and exome sequencing in a breast cancer family implicates ATM in tumorigenesis: A proof of principle study. Genes Chromosomes Cancer 2017; 56:788-799. [PMID: 28691344 DOI: 10.1002/gcc.22482] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 05/11/2017] [Accepted: 07/06/2017] [Indexed: 11/08/2022] Open
Abstract
Familial breast cancers (BCs) account for 10%-20% of all diagnosed BCs, yet only 20% of such tumors arise in the context of a germline mutation in known tumor suppressor genes such as BRCA1 or BRCA2. The vast genetic heterogeneity which characterizes non BRCA1 and non BRCA2 (or BRCAx) families makes grouped studies impossible to perform. Next generation sequencing techniques, however, allow individual families to be studied to identify rare and or private mutations but the high number of genetic variants identified need to be sorted using pathogenicity or recurrence criteria. An additional sorting criterion may be represented by the identification of candidate regions defined by tumor genomic rearrangements. Indeed, comparative genomic hybridization (CGH) using single nucleotide polymorphism (SNP) arrays allows the detection of conserved ancestral haplotypes within recurrent regions of loss of heterozygosity, common to several familial tumors, which can highlight genomic loci harboring a germline mutation in cancer predisposition genes. The combination of both exome sequencing and SNP array-CGH for a series of familial BC revealed a germline ATM mutation associated with a loss of the wild-type allele in two BC from a BRCAx family. The analysis of additional breast tumors from ten BC families in which a germline ATM mutation had been identified revealed a high frequency of wild-type allele loss. This result argues strongly in favor of the involvement of ATM in these tumors as a tumor suppressor gene and confirms that germline ATM mutations are involved in a subset of familial BC.
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Affiliation(s)
- Virginie Bubien
- INSERM U1218, Mammary & Leukemic Oncogenesis group, Université de Bordeaux, Bordeaux, France.,Cancer Genetics Department, Institut Bergonié, Bordeaux, France
| | - Françoise Bonnet
- INSERM U1218, Mammary & Leukemic Oncogenesis group, Université de Bordeaux, Bordeaux, France.,Cancer Genetics Department, Institut Bergonié, Bordeaux, France
| | | | | | - Natalie Jones
- INSERM U1218, Mammary & Leukemic Oncogenesis group, Université de Bordeaux, Bordeaux, France.,Cancer Genetics Department, Institut Bergonié, Bordeaux, France
| | - Aurélien de Reynies
- Programme CIT, Bioinformatics Department, Ligue Nationale contre le Cancer (Cartes d'Identité des Tumeurs), Paris, France
| | - Gaëtan MacGrogan
- INSERM U1218, Mammary & Leukemic Oncogenesis group, Université de Bordeaux, Bordeaux, France.,BioPathology Department, Institut Bergonié, Bordeaux, France
| | - Nicolas Sevenet
- INSERM U1218, Mammary & Leukemic Oncogenesis group, Université de Bordeaux, Bordeaux, France.,Cancer Genetics Department, Institut Bergonié, Bordeaux, France
| | - Eric Letouzé
- Programme CIT, Bioinformatics Department, Ligue Nationale contre le Cancer (Cartes d'Identité des Tumeurs), Paris, France
| | - Michel Longy
- INSERM U1218, Mammary & Leukemic Oncogenesis group, Université de Bordeaux, Bordeaux, France.,Cancer Genetics Department, Institut Bergonié, Bordeaux, France
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25
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Silva RDA, Silva D, Veneza I, Sampaio I, Schneider H, Gomes G. Development of EPIC-PCR Markers for Lutjanus purpureus (Lutjanidae-Perciformes) and their Potential Applicability in Population Analyses. AN ACAD BRAS CIENC 2017; 89:2095-2100. [PMID: 28678957 DOI: 10.1590/0001-3765201720150476] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 05/25/2016] [Indexed: 11/21/2022] Open
Abstract
In the present study, a novel set of eight EPIC primers were developed for Lutjanus purpureus and assayed in five other marine teleosts including three lutjanids, one scianid and one anablepid. Most of the genomic regions used in this study presented genetic diversity indexes equal or greater than the intragenic regions commonly used in population genetics studies. Moreover, six out of eight markers showed cross-amplification with other taxa. Thus, the primers described here may be used to elucidate questions at the intraspecific level for a large number of taxa.
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Affiliation(s)
- Raimundo DA Silva
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal do Pará, Campus Bragança, Alameda Leandro Ribeiro, s/n, Aldeia, 68600-000 Bragança, PA, Brazil
| | - Danillo Silva
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal do Pará, Campus Bragança, Alameda Leandro Ribeiro, s/n, Aldeia, 68600-000 Bragança, PA, Brazil
| | - Ivana Veneza
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal do Pará, Campus Bragança, Alameda Leandro Ribeiro, s/n, Aldeia, 68600-000 Bragança, PA, Brazil
| | - Iracilda Sampaio
- Laboratório de Genética e Biologia Molecular, Instituto de Estudos Costeiros, Universidade Federal do Pará, Campus Bragança, Alameda Leandro Ribeiro, s/n, Aldeia, 68600-000 Bragança, PA, Brazil
| | - Horacio Schneider
- Laboratório de Genética e Biologia Molecular, Instituto de Estudos Costeiros, Universidade Federal do Pará, Campus Bragança, Alameda Leandro Ribeiro, s/n, Aldeia, 68600-000 Bragança, PA, Brazil
| | - Grazielle Gomes
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal do Pará, Campus Bragança, Alameda Leandro Ribeiro, s/n, Aldeia, 68600-000 Bragança, PA, Brazil
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26
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Madeira PM, Chefaoui RM, Cunha RL, Moreira F, Dias S, Calado G, Castilho R. High unexpected genetic diversity of a narrow endemic terrestrial mollusc. PeerJ 2017; 5:e3069. [PMID: 28321363 PMCID: PMC5357342 DOI: 10.7717/peerj.3069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 02/06/2017] [Indexed: 11/20/2022] Open
Abstract
The Iberian Peninsula has an extensive record of species displaying strong genetic structure as a result of their survival in isolated pockets throughout the Pleistocene ice ages. We used mitochondrial and nuclear sequence data to analyze phylogeographic patterns in endemic land snails from a valley of central Portugal (Vale da Couda), putatively assigned to Candidula coudensis, that show an exceptionally narrow distributional range. The genetic survey presented here shows the existence of five main mitochondrial lineages in Vale da Couda that do not cluster together suggesting independent evolutionary histories. Our results also indicate a departure from the expectation that species with restricted distributions have low genetic variability. The putative past and contemporary models of geographic distribution of Vale da Couda lineages are compatible with a scenario of species co-existence in more southern locations during the last glacial maximum (LGM) followed by a post-LGM northern dispersal tracking the species optimal thermal, humidity and soil physical conditions.
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Affiliation(s)
- Pedro M Madeira
- CCMAR, Centre for Marine Sciences , Campus de Gambelas, Faro , Portugal
| | - Rosa M Chefaoui
- CCMAR, Centre for Marine Sciences , Campus de Gambelas, Faro , Portugal
| | - Regina L Cunha
- CCMAR, Centre for Marine Sciences , Campus de Gambelas, Faro , Portugal
| | - Francisco Moreira
- Departamento de Ciências da Vida, Escola de Psicologia e Ciências da Vida, Universidade Lusófona, Campo Grande, Lisboa, Portugal; REN Biodiversity Chair, CIBIO/InBIO Associate Laboratory, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal; Centro de Ecologia Aplicada Prof. Baeta Neves/InBIO Associate Laboratory, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, Lisboa, Portugal
| | - Susana Dias
- Departamento de Ciências da Vida, Escola de Psicologia e Ciências da Vida, Universidade Lusófona, Campo Grande, Lisboa, Portugal; Centro de Ecologia Aplicada Prof. Baeta Neves/InBIO Associate Laboratory, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, Lisboa, Portugal
| | - Gonçalo Calado
- Departamento de Ciências da Vida, Escola de Psicologia e Ciências da Vida, Universidade Lusófona , Campo Grande, Lisboa , Portugal
| | - Rita Castilho
- CCMAR, Centre for Marine Sciences , Campus de Gambelas, Faro , Portugal
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27
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Lack of Spatial Subdivision for the Snapper Lutjanus purpureus (Lutjanidae - Perciformes) from Southwest Atlantic Based on Multi-Locus Analyses. PLoS One 2016; 11:e0161617. [PMID: 27556738 PMCID: PMC4996478 DOI: 10.1371/journal.pone.0161617] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 08/09/2016] [Indexed: 11/25/2022] Open
Abstract
The Caribbean snapper Lutjanus purpureus is a marine species fish commonly found associated with rocky seabeds and is widely distributed along of Western Atlantic. Data on stock delineation and stock recognition are essential for establishing conservation measures for commercially fished species. However, few studies have investigated the population genetic structure of this economically valuable species, and previous studies (based on only a portion of the mitochondrial DNA) provide an incomplete picture. The present study used a multi-locus approach (12 segments of mitochondrial and nuclear DNA) to elucidate the levels of genetic diversity and genetic connectivity of L. purpureus populations and their demographic history. L. purpureus has high levels of genetic diversity, which probably implies in high effective population sizes values for the species. The data show that this species is genetically homogeneous throughout the geographic region analyzed, most likely as a result of dispersal during larval phase. Regarding demographic history, a historical population growth event occurred, likely due to sea level changes during the Pleistocene.
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28
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Dehairs J, Talebi A, Cherifi Y, Swinnen JV. CRISP-ID: decoding CRISPR mediated indels by Sanger sequencing. Sci Rep 2016; 6:28973. [PMID: 27363488 PMCID: PMC4929496 DOI: 10.1038/srep28973] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 06/07/2016] [Indexed: 01/01/2023] Open
Abstract
The advent of next generation gene editing technologies has revolutionized the fields of genome engineering in allowing the generation of gene knockout models and functional gene analysis. However, the screening of resultant clones remains challenging due to the simultaneous presence of different indels. Here, we present CRISP-ID, a web application which uses a unique algorithm for genotyping up to three alleles from a single Sanger sequencing trace, providing a robust and readily accessible platform to directly identify indels and significantly speed up the characterization of clones.
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Affiliation(s)
- Jonas Dehairs
- Laboratory of Lipid Metabolism and Cancer, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Ali Talebi
- Laboratory of Lipid Metabolism and Cancer, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | | | - Johannes V Swinnen
- Laboratory of Lipid Metabolism and Cancer, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
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29
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McGrath PS, Watson CL, Ingram C, Helmrath MA, Wells JM. The Basic Helix-Loop-Helix Transcription Factor NEUROG3 Is Required for Development of the Human Endocrine Pancreas. Diabetes 2015; 64:2497-505. [PMID: 25650326 PMCID: PMC4477351 DOI: 10.2337/db14-1412] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 01/20/2015] [Indexed: 12/18/2022]
Abstract
Neurogenin3 (NEUROG3) is a basic helix-loop-helix transcription factor required for development of the endocrine pancreas in mice. In contrast, humans with NEUROG3 mutations are born with endocrine pancreas function, calling into question whether NEUROG3 is required for human endocrine pancreas development. To test this directly, we generated human embryonic stem cell (hESC) lines where both alleles of NEUROG3 were disrupted using CRISPR/Cas9-mediated gene targeting. NEUROG3(-/-) hESC lines efficiently formed pancreatic progenitors but lacked detectible NEUROG3 protein and did not form endocrine cells in vitro. Moreover, NEUROG3(-/-) hESC lines were unable to form mature pancreatic endocrine cells after engraftment of PDX1(+)/NKX6.1(+) pancreatic progenitors into mice. In contrast, a 75-90% knockdown of NEUROG3 caused a reduction, but not a loss, of pancreatic endocrine cell development. We conclude that NEUROG3 is essential for endocrine pancreas development in humans and that as little as 10% NEUROG3 is sufficient for formation of pancreatic endocrine cells.
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Affiliation(s)
- Patrick S McGrath
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Carey L Watson
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH Department of General Surgery, University of Cincinnati, Cincinnati, OH
| | - Cameron Ingram
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Michael A Helmrath
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH Department of General Surgery, University of Cincinnati, Cincinnati, OH
| | - James M Wells
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
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30
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Boundenga L, Ollomo B, Rougeron V, Mouele LY, Mve-Ondo B, Delicat-Loembet LM, Moukodoum ND, Okouga AP, Arnathau C, Elguero E, Durand P, Liégeois F, Boué V, Motsch P, Le Flohic G, Ndoungouet A, Paupy C, Ba CT, Renaud F, Prugnolle F. Diversity of malaria parasites in great apes in Gabon. Malar J 2015; 14:111. [PMID: 25889049 PMCID: PMC4364493 DOI: 10.1186/s12936-015-0622-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 02/22/2015] [Indexed: 12/25/2022] Open
Abstract
Background Until 2009, the Laverania subgenus counted only two representatives: Plasmodium falciparum and Plasmodium reichenowi. The recent development of non-invasive methods allowed re-exploration of plasmodial diversity in African apes. Although a large number of great ape populations have now been studied regarding Plasmodium infections in Africa, there are still vast areas of their distribution that remained unexplored. Gabon constitutes an important part of the range of western central African great ape subspecies (Pan troglodytes troglodytes and Gorilla gorilla gorilla), but has not been studied so far. In the present study, the diversity of Plasmodium species circulating in great apes in Gabon was analysed. Methods The analysis of 1,261 faecal samples from 791 chimpanzees and 470 gorillas collected from 24 sites all over Gabon was performed. Plasmodium infections were characterized by amplification and sequencing of a portion of the Plasmodium cytochrome b gene. Results The analysis of the 1,261 samples revealed that at least six Plasmodium species circulate in great apes in Gabon (Plasmodium praefalciparum, Plasmodium gorA (syn Plasmodium adleri), Plasmodium gorB (syn Plasmodium blacklocki) in gorillas and Plasmodium gaboni, P. reichenowi and Plasmodium billcollinsi in chimpanzees). No new phylogenetic lineages were discovered. The average infection rate was 21.3% for gorillas and 15.4% for chimpanzees. A logistic regression showed that the probability of infection was significantly dependent on the freshness of the droppings but not of the host species or of the average pluviometry of the months of collection.
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Affiliation(s)
- Larson Boundenga
- Centre International de Recherche Médicale de Franceville, BP 769, Franceville-Gabon, Gabon. .,Laboratoire d'Écologie et Biologie évolutive, Département de Biologie Animale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop de Dakar, Dakar, BP5005, Sénégal.
| | - Benjamin Ollomo
- Centre International de Recherche Médicale de Franceville, BP 769, Franceville-Gabon, Gabon.
| | - Virginie Rougeron
- Centre International de Recherche Médicale de Franceville, BP 769, Franceville-Gabon, Gabon. .,MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle), UMR CNRS 5290 / IRD 224, Université Montpellier 1, Montpellier, France.
| | - Lauriane Yacka Mouele
- Centre International de Recherche Médicale de Franceville, BP 769, Franceville-Gabon, Gabon.
| | - Bertrand Mve-Ondo
- Centre International de Recherche Médicale de Franceville, BP 769, Franceville-Gabon, Gabon.
| | | | | | - Alain Prince Okouga
- Centre International de Recherche Médicale de Franceville, BP 769, Franceville-Gabon, Gabon.
| | - Céline Arnathau
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle), UMR CNRS 5290 / IRD 224, Université Montpellier 1, Montpellier, France.
| | - Eric Elguero
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle), UMR CNRS 5290 / IRD 224, Université Montpellier 1, Montpellier, France.
| | - Patrick Durand
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle), UMR CNRS 5290 / IRD 224, Université Montpellier 1, Montpellier, France.
| | - Florian Liégeois
- Centre International de Recherche Médicale de Franceville, BP 769, Franceville-Gabon, Gabon. .,TransVIHMI (Recherche Translationnelle sur le VIH et les Maladies Infectieuses), UMI 233, Institut de Recherche pour le Développement (IRD) and Université Montpellier 1, Montpellier, France.
| | - Vanina Boué
- Centre International de Recherche Médicale de Franceville, BP 769, Franceville-Gabon, Gabon.
| | - Peggy Motsch
- Centre International de Recherche Médicale de Franceville, BP 769, Franceville-Gabon, Gabon.
| | - Guillaume Le Flohic
- Centre International de Recherche Médicale de Franceville, BP 769, Franceville-Gabon, Gabon.
| | - Alphonse Ndoungouet
- Centre International de Recherche Médicale de Franceville, BP 769, Franceville-Gabon, Gabon.
| | - Christophe Paupy
- Centre International de Recherche Médicale de Franceville, BP 769, Franceville-Gabon, Gabon. .,MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle), UMR CNRS 5290 / IRD 224, Université Montpellier 1, Montpellier, France.
| | - Cheikh Tidiane Ba
- Laboratoire d'Écologie et Biologie évolutive, Département de Biologie Animale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop de Dakar, Dakar, BP5005, Sénégal.
| | - Francois Renaud
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle), UMR CNRS 5290 / IRD 224, Université Montpellier 1, Montpellier, France.
| | - Franck Prugnolle
- Centre International de Recherche Médicale de Franceville, BP 769, Franceville-Gabon, Gabon. .,MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle), UMR CNRS 5290 / IRD 224, Université Montpellier 1, Montpellier, France.
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Combined QTL and selective sweep mappings with coding SNP annotation and cis-eQTL analysis revealed PARK2 and JAG2 as new candidate genes for adiposity regulation. G3-GENES GENOMES GENETICS 2015; 5:517-29. [PMID: 25653314 PMCID: PMC4390568 DOI: 10.1534/g3.115.016865] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Very few causal genes have been identified by quantitative trait loci (QTL) mapping because of the large size of QTL, and most of them were identified thanks to functional links already known with the targeted phenotype. Here, we propose to combine selection signature detection, coding SNP annotation, and cis-expression QTL analyses to identify potential causal genes underlying QTL identified in divergent line designs. As a model, we chose experimental chicken lines divergently selected for only one trait, the abdominal fat weight, in which several QTL were previously mapped. Using new haplotype-based statistics exploiting the very high SNP density generated through whole-genome resequencing, we found 129 significant selective sweeps. Most of the QTL colocalized with at least one sweep, which markedly narrowed candidate region size. Some of those sweeps contained only one gene, therefore making them strong positional causal candidates with no presupposed function. We then focused on two of these QTL/sweeps. The absence of nonsynonymous SNPs in their coding regions strongly suggests the existence of causal mutations acting in cis on their expression, confirmed by cis-eQTL identification using either allele-specific expression or genetic mapping analyses. Additional expression analyses of those two genes in the chicken and mice contrasted for adiposity reinforces their link with this phenotype. This study shows for the first time the interest of combining selective sweeps mapping, coding SNP annotation and cis-eQTL analyses for identifying causative genes for a complex trait, in the context of divergent lines selected for this specific trait. Moreover, it highlights two genes, JAG2 and PARK2, as new potential negative and positive key regulators of adiposity in chicken and mice.
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Huang R, Yin J, Chen Y, Deng F, Chen J, Gao X, Liu Z, Yu X, Zheng J. The amino acid variation within the binding pocket 7 and 9 of HLA-DRB1 molecules are associated with primary Sjögren's syndrome. J Autoimmun 2015; 57:53-9. [PMID: 25582848 DOI: 10.1016/j.jaut.2014.11.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 11/27/2014] [Indexed: 12/01/2022]
Abstract
Primary Sjögren's syndrome (pSS) is associated with HLA-DRB1 loci, but the association of amino acid variations in the hypervariable region of the HLA-DR β1 chain with pSS is largely unknown. In this study, we aimed to identify the amino acid variations within the hypervariable region of HLA-DRB1 molecule which are associated with the susceptibility to pSS. We sequenced the 2nd exon of the HLA-DRB1 locus in 52 pSS patients and 179 controls. The HLA-DRB1*0803 is the allele that shows the strongest association with pSS in Chinese population (OR = 3.0, P = 2.4 × 10(-4)). Furthermore, amino acid variations within the binding pocket P7 and P9 are associated with the susceptibility to pSS. An interaction between two residues within P7, β47 and β67, is associated with pSS. Structural modeling studies demonstrated that the electrostatics of peptide binding pocket 9 are opposite in pSS-susceptible and -protective HLA-DRB1 alleles. In conclusion, our results suggest that structural heterogeneity of the HLA-DRB1 peptide binding pocket P7 and P9 might play a role in the pathogenesis of pSS.
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Affiliation(s)
- Renliang Huang
- The Medical College of Xiamen University, Xiamen University, 361005 Xiamen, China
| | - Junping Yin
- The Medical College of Xiamen University, Xiamen University, 361005 Xiamen, China
| | - Yan Chen
- The Medical College of Xiamen University, Xiamen University, 361005 Xiamen, China
| | - Fengyuan Deng
- The Medical College of Xiamen University, Xiamen University, 361005 Xiamen, China
| | - Juan Chen
- First Affiliated Hospital of Xiamen University, China
| | - Xing Gao
- Xiamen University Hospital, China
| | - Zuguo Liu
- The Medical College of Xiamen University, Xiamen University, 361005 Xiamen, China
| | - Xinhua Yu
- The Medical College of Xiamen University, Xiamen University, 361005 Xiamen, China; Priority Area Asthma and Allergy, Research Center Borstel, 23845 Borstel, Germany; Airway Research Center North (ARCN), UGMLC, Member of the German Center for Lung Research, Germany
| | - Junfeng Zheng
- The Medical College of Xiamen University, Xiamen University, 361005 Xiamen, China; First Affiliated Hospital of Xiamen University, China.
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Lin CH, Lee YS, Huang YY, Hsieh SH, Chen ZS, Tsai CN. Polymorphisms of GLP-1 receptor gene and response to GLP-1 analogue in patients with poorly controlled type 2 diabetes. J Diabetes Res 2015; 2015:176949. [PMID: 25785276 PMCID: PMC4345081 DOI: 10.1155/2015/176949] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 12/22/2014] [Accepted: 01/05/2015] [Indexed: 02/01/2023] Open
Abstract
AIM The relationship between genetic polymorphisms of the glucagon-like peptide-1 (GLP-1) receptor (GLP1R) gene and unresponsiveness to GLP-1 analogue treatment in patients with poorly controlled type 2 diabetes mellitus (DM) is unclear. METHODS Thirty-six patients with poorly controlled type 2 DM were enrolled and they received six days of continuous subcutaneous insulin infusion for this study. After the normalization of blood glucose in the first 3 days, the patients then received a combination therapy with injections of the GLP-1 analogue, exenatide, for another 3 days. All 13 exons and intron-exon boundaries of the GLP1R gene were amplified to investigate the association. RESULTS The short tandem repeat at 8GA/7GA (rs5875654) had complete linkage disequilibrium (LD, with r2 = 1) with single nucleotide polymorphism (SNP) rs761386. Quantitative trait loci analysis of GLP1R gene variation with clinical response of GLP1 analogue showed the missense rs3765467 and rs761386 significantly associated with changes in the standard deviation of plasma glucose (SDPG(baseline) - SDPG(treatment with GLP-1 analogue)) (P = 0.041 and 0.019, resp.). The reported P values became insignificant after multiple testing adjustments. CONCLUSION The variable response to the GLP-1 analogue was not statistically correlated with polymorphisms of the GLP1R gene in patients with poorly controlled type 2 DM.
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Affiliation(s)
- Chia-Hung Lin
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
- Graduate Institute of Clinical Medical Sciences, Chang Gung University, Taoyuan 333, Taiwan
| | - Yun-Shien Lee
- Department of Biotechnology, Ming Chuan University, Taoyuan 333, Taiwan
- Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
| | - Yu-Yao Huang
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
| | - Sheng-Hwu Hsieh
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
| | - Zih-Syuan Chen
- Graduate Institute of Clinical Medical Sciences, Chang Gung University, Taoyuan 333, Taiwan
| | - Chi-Neu Tsai
- Graduate Institute of Clinical Medical Sciences, Chang Gung University, Taoyuan 333, Taiwan
- *Chi-Neu Tsai:
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Avanesyan A. Plant DNA detection from grasshopper guts: A step-by-step protocol, from tissue preparation to obtaining plant DNA sequences. APPLICATIONS IN PLANT SCIENCES 2014; 2:apps1300082. [PMID: 25202604 PMCID: PMC4103608 DOI: 10.3732/apps.1300082] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Accepted: 12/18/2013] [Indexed: 06/03/2023]
Abstract
PREMISE OF THE STUDY A PCR-based method of identifying ingested plant DNA in gut contents of Melanoplus grasshoppers was developed. Although previous investigations have focused on a variety of insects, there are no protocols available for plant DNA detection developed for grasshoppers, agricultural pests that significantly influence plant community composition. • METHODS AND RESULTS The developed protocol successfully used the noncoding region of the chloroplast trnL (UAA) gene and was tested in several feeding experiments. Plant DNA was obtained at seven time points post-ingestion from whole guts and separate gut sections, and was detectable up to 12 h post-ingestion in nymphs and 22 h post-ingestion in adult grasshoppers. • CONCLUSIONS The proposed protocol is an effective, relatively quick, and low-cost method of detecting plant DNA from the grasshopper gut and its different sections. This has important applications, from exploring plant "movement" during food consumption, to detecting plant-insect interactions.
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Affiliation(s)
- Alina Avanesyan
- Department of Biological Sciences, University of Cincinnati, 614 Rieveschl Hall, Cincinnati, Ohio 45221-0006 USA
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Chen YC, Lee YS, Shih CC, Wu T, Chen CM. Mutations of proline-rich transmembrane protein-2 and paroxysmal kinesigenic dyskinesia in Taiwan. Mov Disord 2013; 28:1459-60. [DOI: 10.1002/mds.25399] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Revised: 12/31/2012] [Accepted: 01/10/2013] [Indexed: 11/06/2022] Open
Affiliation(s)
- Yi-Chun Chen
- Department of Neurology; Chang Gung Memorial Hospital Linkou Medical Center and College of Medicine; Chang Gung University; Taoyuan Taiwan
| | - Yun-Shien Lee
- Department of Biotechnology; Ming Chuan University; Guishan Township Taiwan
- Genomic Medicine Research Core Laboratory; Chang Gung Memorial Hospital; Taoyuan Taiwan
| | - Chen-Chang Shih
- Department of Neurology; Hualien Mennonite Christian Hospital; Hualien Taiwan
| | - Tony Wu
- Department of Neurology; Chang Gung Memorial Hospital Linkou Medical Center and College of Medicine; Chang Gung University; Taoyuan Taiwan
| | - Chiung-Mei Chen
- Department of Neurology; Chang Gung Memorial Hospital Linkou Medical Center and College of Medicine; Chang Gung University; Taoyuan Taiwan
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