1
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Neely BA, Palmblad M. Rewinding the Molecular Clock: Looking at Pioneering Molecular Phylogenetics Experiments in the Light of Proteomics. J Proteome Res 2021; 20:4640-4645. [PMID: 34523928 PMCID: PMC8491155 DOI: 10.1021/acs.jproteome.1c00528] [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] [Indexed: 01/21/2023]
Abstract
![]()
Science is full of
overlooked and undervalued research waiting
to be rediscovered. Proteomics is no exception. In this perspective,
we follow the ripples from a 1960 study of Zuckerkandl, Jones, and
Pauling comparing tryptic peptides across animal species. This pioneering
work directly led to the molecular clock hypothesis and the ensuing
explosion in molecular phylogenetics. In the decades following, proteins
continued to provide essential clues on evolutionary history. While
technology has continued to improve, contemporary proteomics has strayed
from this larger biological context, rarely comparing species or asking
how protein structure, function, and interactions have evolved. Here
we recombine proteomics with molecular phylogenetics, highlighting
the value of framing proteomic results in a larger biological context
and how almost forgotten research, though technologically surpassed,
can still generate new ideas and illuminate our work from a different
perspective. Though it is infeasible to read all research published
on a large topic, looking up older papers can be surprisingly rewarding
when rediscovering a “gem” at the end of a long citation
chain, aided by digital collections and perpetually helpful librarians.
Proper literature study reduces unnecessary repetition and allows
research to be more insightful and impactful by truly standing on
the shoulders of giants. All data was uploaded to MassIVE (https://massive.ucsd.edu/)
as dataset MSV000087993.
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Affiliation(s)
- Benjamin A Neely
- National Institute of Standards and Technology, Charleston, South Carolina 29412, United States
| | - Magnus Palmblad
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
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2
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Modernizing the Toolkit for Arthropod Bloodmeal Identification. INSECTS 2021; 12:insects12010037. [PMID: 33418885 PMCID: PMC7825046 DOI: 10.3390/insects12010037] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/30/2020] [Accepted: 12/31/2020] [Indexed: 11/24/2022]
Abstract
Simple Summary The ability to identify the source of vertebrate blood in mosquitoes, ticks, and other blood-feeding arthropod vectors greatly enhances our knowledge of how vector-borne pathogens are spread. The source of the bloodmeal is identified by analyzing the remnants of blood remaining in the arthropod at the time of capture, though this is often fraught with challenges. This review provides a roadmap and guide for those considering modern techniques for arthropod bloodmeal identification with a focus on progress made in the field over the past decade. We highlight genome regions that can be used to identify the vertebrate source of arthropod bloodmeals as well as technological advances made in other fields that have introduced innovative new ways to identify vertebrate meal source based on unique properties of the DNA sequence, protein signatures, or residual molecules present in the blood. Additionally, engineering progress in miniaturization has led to a number of field-deployable technologies that bring the laboratory directly to the arthropods at the site of collection. Although many of these advancements have helped to address the technical challenges of the past, the challenge of successfully analyzing degraded DNA in bloodmeals remains to be solved. Abstract Understanding vertebrate–vector interactions is vitally important for understanding the transmission dynamics of arthropod-vectored pathogens and depends on the ability to accurately identify the vertebrate source of blood-engorged arthropods in field collections using molecular methods. A decade ago, molecular techniques being applied to arthropod blood meal identification were thoroughly reviewed, but there have been significant advancements in the techniques and technologies available since that time. This review highlights the available diagnostic markers in mitochondrial and nuclear DNA and discusses their benefits and shortcomings for use in molecular identification assays. Advances in real-time PCR, high resolution melting analysis, digital PCR, next generation sequencing, microsphere assays, mass spectrometry, and stable isotope analysis each offer novel approaches and advantages to bloodmeal analysis that have gained traction in the field. New, field-forward technologies and platforms have also come into use that offer promising solutions for point-of-care and remote field deployment for rapid bloodmeal source identification. Some of the lessons learned over the last decade, particularly in the fields of DNA barcoding and sequence analysis, are discussed. Though many advancements have been made, technical challenges remain concerning the prevention of sample degradation both by the arthropod before the sample has been obtained and during storage. This review provides a roadmap and guide for those considering modern techniques for arthropod bloodmeal identification and reviews how advances in molecular technology over the past decade have been applied in this unique biomedical context.
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3
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Pal U, Kitsou C, Drecktrah D, Yaş ÖB, Fikrig E. Interactions Between Ticks and Lyme Disease Spirochetes. Curr Issues Mol Biol 2020; 42:113-144. [PMID: 33289683 PMCID: PMC8045411 DOI: 10.21775/cimb.042.113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Borrelia burgdorferi sensu lato causes Lyme borreliosis in a variety of animals and humans. These atypical bacterial pathogens are maintained in a complex enzootic life cycle that primarily involves a vertebrate host and Ixodes spp. ticks. In the Northeastern United States, I. scapularis is the main vector, while wild rodents serve as the mammalian reservoir host. As B. burgdorferi is transmitted only by I. scapularis and closely related ticks, the spirochete-tick interactions are thought to be highly specific. Various borrelial and arthropod proteins that directly or indirectly contribute to the natural cycle of B. burgdorferi infection have been identified. Discrete molecular interactions between spirochetes and tick components also have been discovered, which often play critical roles in pathogen persistence and transmission by the arthropod vector. This review will focus on the past discoveries and future challenges that are relevant to our understanding of the molecular interactions between B. burgdorferi and Ixodes ticks. This information will not only impact scientific advancements in the research of tick- transmitted infections but will also contribute to the development of novel preventive measures that interfere with the B. burgdorferi life cycle.
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Affiliation(s)
- Utpal Pal
- Department of Veterinary Medicine, University of Maryland, 8075 Greenmead Drive, College Park, MD 20742, USA
- Virginia-Maryland College of Veterinary Medicine, 8075 Greenmead Drive, College Park, MD 20742, USA
| | - Chrysoula Kitsou
- Department of Veterinary Medicine, University of Maryland, 8075 Greenmead Drive, College Park, MD 20742, USA
| | - Dan Drecktrah
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Özlem Büyüktanir Yaş
- Department of Microbiology and Clinical Microbiology, Faculty of Medicine, Istinye University, Zeytinburnu, İstanbul, 34010, Turkey
| | - Erol Fikrig
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
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4
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Hlavackova K, Dvorak V, Chaskopoulou A, Volf P, Halada P. A novel MALDI-TOF MS-based method for blood meal identification in insect vectors: A proof of concept study on phlebotomine sand flies. PLoS Negl Trop Dis 2019; 13:e0007669. [PMID: 31498786 PMCID: PMC6733444 DOI: 10.1371/journal.pntd.0007669] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/29/2019] [Indexed: 12/24/2022] Open
Abstract
Background Identification of blood sources of hematophagous arthropods is crucial for understanding the transmission cycles of vector-borne diseases. Many different approaches towards host determination were proposed, including precipitin test, ELISA, DNA- and mass spectrometry-based methods; yet all face certain complications and limitations, mostly related to blood degradation. This study presents a novel method for blood meal identification, peptide mass mapping (PMM) analysis of host-specific hemoglobin peptides using MALDI-TOF mass spectrometry. Methodology/Principal findings To identify blood meal source, proteins from abdomens of engorged sand fly females were extracted, cleaved by trypsin and peptide fragments of host hemoglobin were sequenced using MALDI-TOF MS. The method provided correct host identification of 100% experimentally fed sand flies until 36h post blood meal (PBM) and for 80% samples even 48h PBM. In females fed on two hosts, both blood meal sources were correctly assigned for 60% of specimens until 36h PBM. In a validation study on field-collected females, the method yielded unambiguous host determination for 96% of specimens. The suitability of PMM-based MALDI-TOF MS was proven experimentally also on lab-reared Culex mosquitoes. Conclusions/Significance PMM-based MALDI-TOF MS analysis targeting host specific hemoglobin peptides represents a sensitive and cost-effective method with a fast and simple preparation protocol. As demonstrated here on phlebotomine sand flies and mosquitoes, it allows reliable and rapid blood source determination even 48h PBM with minimal material input and provides more robust and specific results than other currently used methods. This approach was also successfully tested on field-caught engorged females and proved to be a promising useful tool for large-scale screening of host preferences studies. Unlike other methods including MALDI-TOF protein profiling, it allows correct identification of mixed blood meals as was demonstrated on both experimentally fed and field-collected sand flies. Leishmaniases belong among the most important and yet neglected vector-borne diseases, transmitted mostly by bite of female phlebotomine sand flies. To understand role of different reservoir hosts in the transmission cycles, it is important to determine blood meal sources of bloodfeeding females. Most of currently used methods face challenges due to tiny volumes of engorged blood, in case of mammals also enucleated, as well as quick progress of blood digestion which leads to rapid DNA and protein degradation. New approach towards blood source determination presented in this study is based on MALDI-TOF mass spectrometry that identifies unique peptide sequences of host hemoglobins, showing high precision and sensitivity together with a longer time period for successful host determination when compared to nowadays standardly used DNA sequencing. It was tested and verified on engorged phlebotomine sand flies from both laboratory colonies and natural endemic areas and also on Culex mosquitoes and shall be universal to hematophagous insects. Beside blood meal identification, it allows also the use of both morphological and molecular methods (DNA- or protein-based) for the species identification of the analysed specimen.
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Affiliation(s)
- Kristyna Hlavackova
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Vit Dvorak
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | | | - Petr Volf
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Petr Halada
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
- * E-mail:
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5
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Heylen D, Schmidt O, Dautel H, Gern L, Kampen H, Newton J, Gray J. Host identification in unfed ticks from stable isotope compositions (δ 13 C and δ 15 N). MEDICAL AND VETERINARY ENTOMOLOGY 2019; 33:360-366. [PMID: 30883848 DOI: 10.1111/mve.12372] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/21/2019] [Accepted: 02/08/2019] [Indexed: 06/09/2023]
Abstract
Determination of the ratios of natural stable isotopes (13 C/12 C and 15 N/14 N) in unfed Ixodes ricinus nymphs and adults, which, in their previous stage, fed on captive wild rodents (Apodemus sylvaticus and Myodes glareolus), wild birds (Parus major and Cyanistes caeruleus) or domestic ruminants (Ovis aries and Bos taurus), demonstrated that it is possible to identify each host category with confidence. First, the tick-blood spacing, which is the difference between values obtained from ticks and the blood of hosts that they had fed on in the previous stage, was consistent (152 spacings investigated from 15 host individuals in total). Second, potential confounding factors (tick age and sex) did not affect the discriminatory power of the isotope patterns, nor did different rearing conditions (room temperature vs. 4 °C) or the duration of development (maximum of 430 days). The findings that the tick-blood isotope spacings, across a diverse range of hosts, were similar and predictable, and that confounders had little or no effect on this, strongly support the usage of the isotope approach. Because each of the host categories has a different role in the population dynamics of I. ricinus and in tick-borne pathogen ecology, the method described here has great potential for the clarification of tick and tick-borne pathogen ecology in the field.
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Affiliation(s)
- D Heylen
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, U.S.A
- Interuniversity Institute for Biostatistics and statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium
- Department of Biology, University of Antwerp, Wilrijk, Belgium
| | - O Schmidt
- UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, Ireland
| | - H Dautel
- IS Insect Services GmbH, Berlin, Germany
| | - L Gern
- Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - H Kampen
- Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - J Newton
- Scottish Universities Environmental Research Centre, East Kilbride, U.K
| | - J Gray
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin, Ireland
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6
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Chen F, Ma X, Chen C, Li K, Chen S, Wen H, Gong P. A Validated Chiral-RP-UPLC-MS/MS Method for the Enantiomeric Detection of Rivaroxaban In vitro. CURR PHARM ANAL 2019. [DOI: 10.2174/1573412914666180409145403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Rivaroxaban is the first oral, selective direct FXa inhibitor with rapid onset of
action and its biological toxicity may be related to the enantiomer.
</P><P>
Objective: The aim of the current study was to develop and validate a precise, accurate, and specific
direct Chiral-RP-UPLC-MS/MS method for the enantiomeric separation and detection of rivaroxaban
and its enantiomer.
Methods:
The present study screened various conditions of chromatographic and mass spectra, including
chromatographic column model, flow velocity, phase ratio, column temperature, and collision energy,
parent/daughter ion pairs, etc. Try to match the chromatographic and mass spectrometric conditions.
Results:
Good Rs (Rs>2.5) was achieved on a Chiralpak IC column (4.6 × 250 mm, 5µm) using
H2O:acetonitrile (10:90) as mobile phase at 25 oC column temperature. The rate of flow was set at 0.4
ml/min and enantiomers were detected by triple-quadruple tandem mass spectrometry using positive
electrospray ionization (ESI) with MRM transitions of m/z 436.07>144.95. The cone voltage and collision
energy were kept at 48 V and 28 eV, respectively. The limit of detection and quantification of (S)-
rivaroxaban were 0.39 and 1.30 ng/ml, respectively. This method was validated and found to be selective,
precise, accurate, linear and robust for the quantitative determination of chiral impurities. It is also
a good application for the blood samples analysis in vitro.
Conclusion:
Chiral-RP-UPLC-MS/MS method has entirely detected (S)-rivaroxaban and its (R)- enantiomer
in very low concentration and complex matrix directly, especially for blood samples.
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Affiliation(s)
- Fuxin Chen
- Department of Chemistry and Chemical Engineering, Xi'an University of Science & Technology, Xi'an 710054, China
| | - Xiaoxian Ma
- Department of Chemistry and Chemical Engineering, Xi'an University of Science & Technology, Xi'an 710054, China
| | - Chuangqian Chen
- Department of Chemistry and Chemical Engineering, Xi'an University of Science & Technology, Xi'an 710054, China
| | - Kanshe Li
- Department of Chemistry and Chemical Engineering, Xi'an University of Science & Technology, Xi'an 710054, China
| | - Suying Chen
- Department of Chemistry and Chemical Engineering, Xi'an University of Science & Technology, Xi'an 710054, China
| | - He Wen
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an 710021, China
| | - Pin Gong
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an 710021, China
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7
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Zhu Y, Zhang R, Zhang B, Zhao T, Wang P, Liang G, Cheng G. Blood meal acquisition enhances arbovirus replication in mosquitoes through activation of the GABAergic system. Nat Commun 2017; 8:1262. [PMID: 29093445 PMCID: PMC5665997 DOI: 10.1038/s41467-017-01244-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 08/30/2017] [Indexed: 11/13/2022] Open
Abstract
Mosquitoes are hematophagous insects that carry-on and transmit many human viruses. However, little information is available regarding the common mechanisms underlying the infection of mosquitoes by these viruses. In this study, we reveal that the hematophagous nature of mosquitoes contributes to arboviral infection after a blood meal, which suppresses antiviral innate immunity by activating the GABAergic pathway. dsRNA-mediated interruption of the GABA signaling and blockage of the GABAA receptor by the specific inhibitors both significantly impaired arbovirus replication. Consistently, inoculation of GABA enhanced arboviral infection, indicating that GABA signaling facilitates the arboviral infection of mosquitoes. The ingestion of blood by mosquitoes resulted in robust GABA production from glutamic acid derived from blood protein digestion. The oral introduction of glutamic acid increased virus acquisition by mosquitoes via activation of the GABAergic system. Our study reveals that blood meals enhance arbovirus replication in mosquitoes through activation of the GABAergic system. Transmission of many human viruses depends on replication in their mosquito vectors. Here, Zhu et al. show that glutamic acid digested from the blood meal activates GABA signaling, resulting in suppression of antiviral innate immunity and increased virus replication in mosquitoes.
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Affiliation(s)
- Yibin Zhu
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China.,Institute of pathogenic organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, 518055, China.,School of Life Science, Tsinghua University, Beijing, 100084, China
| | - Rudian Zhang
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China.,School of Life Science, Tsinghua University, Beijing, 100084, China
| | - Bei Zhang
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Tongyan Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Penghua Wang
- Department of Microbiology and Immunology, School of Medicine, New York Medical College, Valhalla, NY, 10595, USA
| | - Guodong Liang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Viral Disease Control and Prevention, Beijing, 102206, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310000, China
| | - Gong Cheng
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China. .,Institute of pathogenic organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, 518055, China.
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8
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Shao W, Lam H. Tandem mass spectral libraries of peptides and their roles in proteomics research. MASS SPECTROMETRY REVIEWS 2017; 36:634-648. [PMID: 27403644 DOI: 10.1002/mas.21512] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 05/21/2016] [Indexed: 05/15/2023]
Abstract
Proteomics is a rapidly maturing field aimed at the high-throughput identification and quantification of all proteins in a biological system. The cornerstone of proteomic technology is tandem mass spectrometry of peptides resulting from the digestion of protein mixtures. The fragmentation pattern of each peptide ion is captured in its tandem mass spectrum, which enables its identification and acts as a fingerprint for the peptide. Spectral libraries are simply searchable collections of these fingerprints, which have taken on an increasingly prominent role in proteomic data analysis. This review describes the historical development of spectral libraries in proteomics, details the computational procedures behind library building and searching, surveys the current applications of spectral libraries, and discusses the outstanding challenges. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:634-648, 2017.
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Affiliation(s)
- Wenguang Shao
- Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
- Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Henry Lam
- Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
- Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
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9
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Yakob L. How do biting disease vectors behaviourally respond to host availability? Parasit Vectors 2016; 9:468. [PMID: 27562086 PMCID: PMC5000478 DOI: 10.1186/s13071-016-1762-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 08/17/2016] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Ecological theory predicts a diverse range of functional responses of species to resource availability; but in the context of human blood consumption by disease vectors, a simplistic, linear response is ubiquitously assumed. A simple and flexible model formulation is presented that extends the Holling's Types to account for a wider range of qualitatively distinct behaviours, and used to examine the impact of different vector responses to the relative availability of multiple blood-host species. RESULTS Epidemiological models of falciparum malaria, Chagas disease and Lyme disease demonstrate that the standard, often implicit, assumption of a linear functional response can lead to spurious under- or over-estimates in disease transmission potential, across a full range of pathogen life-cycles. It is shown how the functional response in vector biting can augment disease intervention outcomes. Interactions between vector biting behaviour and uneven pathogen transmission probabilities between alternative hosts, as is the case for Chagas disease, can render infection more resilient to control. CONCLUSIONS Both the novel response formula and the nested vector-borne disease structure offer a flexible framework that can be applied to other vector-borne diseases in assessing the role of this newly identified aspect of biting behavioural ecology.
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Affiliation(s)
- Laith Yakob
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
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10
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Nessen MA, van der Zwaan DJ, Grevers S, Dalebout H, Staats M, Kok E, Palmblad M. Authentication of Closely Related Fish and Derived Fish Products Using Tandem Mass Spectrometry and Spectral Library Matching. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:3669-3677. [PMID: 27086584 DOI: 10.1021/acs.jafc.5b05322] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Proteomics methodology has seen increased application in food authentication, including tandem mass spectrometry of targeted species-specific peptides in raw, processed, or mixed food products. We have previously described an alternative principle that uses untargeted data acquisition and spectral library matching, essentially spectral counting, to compare and identify samples without the need for genomic sequence information in food species populations. Here, we present an interlaboratory comparison demonstrating how a method based on this principle performs in a realistic context. We also increasingly challenge the method by using data from different types of mass spectrometers, by trying to distinguish closely related and commercially important flatfish, and by analyzing heavily contaminated samples. The method was found to be robust in different laboratories, and 94-97% of the analyzed samples were correctly identified, including all processed and contaminated samples.
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Affiliation(s)
- Merel A Nessen
- RIKILT Wageningen UR , P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | | | - Sander Grevers
- Center for Proteomics and Metabolomics, Leiden University Medical Center , P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Hans Dalebout
- Center for Proteomics and Metabolomics, Leiden University Medical Center , P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Martijn Staats
- RIKILT Wageningen UR , P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Esther Kok
- RIKILT Wageningen UR , P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Magnus Palmblad
- Center for Proteomics and Metabolomics, Leiden University Medical Center , P.O. Box 9600, 2300 RC Leiden, The Netherlands
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11
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Griss J. Spectral library searching in proteomics. Proteomics 2016; 16:729-40. [PMID: 26616598 DOI: 10.1002/pmic.201500296] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 10/15/2015] [Accepted: 10/29/2015] [Indexed: 12/12/2022]
Abstract
Spectral library searching has become a mature method to identify tandem mass spectra in proteomics data analysis. This review provides a comprehensive overview of available spectral library search engines and highlights their distinct features. Additionally, resources providing spectral libraries are summarized and tools presented that extend experimental spectral libraries by simulating spectra. Finally, spectrum clustering algorithms are discussed that utilize the same spectrum-to-spectrum matching algorithms as spectral library search engines and allow novel methods to analyse proteomics data.
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Affiliation(s)
- Johannes Griss
- Division of Immunology, Allergy and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Austria.,European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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12
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Song Y, Laskay ÜA, Vilcins IME, Barbour AG, Wysocki VH. Top-down-assisted bottom-up method for homologous protein sequencing: hemoglobin from 33 bird species. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1875-84. [PMID: 26111519 PMCID: PMC6467653 DOI: 10.1007/s13361-015-1185-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 05/08/2015] [Accepted: 05/08/2015] [Indexed: 05/12/2023]
Abstract
Ticks are vectors for disease transmission because they are indiscriminant in their feeding on multiple vertebrate hosts, transmitting pathogens between their hosts. Identifying the hosts on which ticks have fed is important for disease prevention and intervention. We have previously shown that hemoglobin (Hb) remnants from a host on which a tick fed can be used to reveal the host's identity. For the present research, blood was collected from 33 bird species that are common in the U.S. as hosts for ticks but that have unknown Hb sequences. A top-down-assisted bottom-up mass spectrometry approach with a customized searching database, based on variability in known bird hemoglobin sequences, has been devised to facilitate fast and complete sequencing of hemoglobin from birds with unknown sequences. These hemoglobin sequences will be added to a hemoglobin database and used for tick host identification. The general approach has the potential to sequence any set of homologous proteins completely in a rapid manner. Graphical Abstract ᅟ.
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Affiliation(s)
- Yang Song
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721, USA
| | - Ünige A Laskay
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721, USA
| | - Inger-Marie E Vilcins
- Emerging and Acute Infectious Diseases Branch, Department of State Health Services, Austin, TX, 78756, USA
| | - Alan G Barbour
- Microbiology and Molecular Genetics, Medicine, and Ecology and Evolutionary Biology, University of California, Irvine, CA, 92687, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA.
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721, USA.
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13
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Léger E, Liu X, Masseglia S, Noël V, Vourc'h G, Bonnet S, McCoy KD. Reliability of molecular host-identification methods for ticks: an experimental in vitro study with Ixodes ricinus. Parasit Vectors 2015; 8:433. [PMID: 26296344 PMCID: PMC4546307 DOI: 10.1186/s13071-015-1043-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 08/12/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Reliable information on host use by arthropod vectors is required to study pathogen transmission ecology and to predict disease risk. Direct observation of host use is often difficult or impossible and indirect methods are therefore necessary. However, the reliability of currently available methods to identify the last host of blood-feeding arthropods has not been evaluated, and may be particularly problematic for ticks because host blood has been digested at capture. Biases in host detection may lead to erroneous conclusions on both vector ecology and pathogen circulation. METHODS Here, we experimentally tested for biases in host detection using the generalist three-host tick Ixodes ricinus as a model system. We fed ticks using an artificial feeding system and amplified blood meal traces post-moult (i.e., in the succeeding unfed life stage) via both a quantitative real-time polymerase chain reaction assay and a reverse line blotting method. We then experimentally tested for three types of biases in host detection: 1) time post-moult, 2) tick life stage and 3) host type (non-nucleated mammal blood versus nucleated avian blood), and compared these biases between the two molecular methods. RESULTS Our results show that all three factors can influence host detection in ticks but not necessarily in the expected way. Although host detection rates decreased with time post-moult, mammal blood tended to be more readily detected than bird blood. Tick life stage was also an important factor; detection was higher in nymphs than in adults and, in some cases, remnants from both larval and nymphal blood meals could be detected in the adult stage. These biases were similar for the two detection techniques. CONCLUSIONS We show that different factors associated with questing ticks may influence our ability to correctly infer previous host use and that these factors may bias inferences from field-based studies. As these biases may be common to other vector-borne disease systems, their implications for our understanding of vector ecology and disease transmission require more explicit consideration.
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Affiliation(s)
- Elsa Léger
- MIVEGEC (UMR UM2-UM1-CNRS 5290, UR IRD 224), Centre IRD, 911 avenue Agropolis, BP 64501, 34394, Montpellier, Cedex 5, France.
| | - Xiangye Liu
- USC INRA Bartonella-tiques, UMR BIPAR ENVA-ANSES, 94706, Maisons-Alfort, France. .,Laboratory of Infection and Immunity, Xu Zhou Medical College, 221004, Xu Zhou, P.R. China.
| | - Sébastien Masseglia
- Unité Epidémiologie Animale (UR INRA 346), Centre de recherche INRA de Clermont-Ferrand / Theix, 63122, Saint Genès Champanelle, France.
| | - Valérie Noël
- MIVEGEC (UMR UM2-UM1-CNRS 5290, UR IRD 224), Centre IRD, 911 avenue Agropolis, BP 64501, 34394, Montpellier, Cedex 5, France.
| | - Gwenaël Vourc'h
- Unité Epidémiologie Animale (UR INRA 346), Centre de recherche INRA de Clermont-Ferrand / Theix, 63122, Saint Genès Champanelle, France.
| | - Sarah Bonnet
- USC INRA Bartonella-tiques, UMR BIPAR ENVA-ANSES, 94706, Maisons-Alfort, France.
| | - Karen D McCoy
- MIVEGEC (UMR UM2-UM1-CNRS 5290, UR IRD 224), Centre IRD, 911 avenue Agropolis, BP 64501, 34394, Montpellier, Cedex 5, France.
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Hadj-Henni L, De Meulemeester T, Depaquit J, Noël P, Germain A, Helder R, Augot D. Comparison of Vertebrate Cytochrome b and Prepronociceptin for Blood Meal Analyses in Culicoides. Front Vet Sci 2015; 2:15. [PMID: 26664944 PMCID: PMC4672183 DOI: 10.3389/fvets.2015.00015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Accepted: 05/13/2015] [Indexed: 01/09/2023] Open
Abstract
To date, studies on host preferences and blood meal identification have been conducted for Culicoides species using molecular-based methods such as PCR techniques to amplify only a fragment from universal vertebrate mitochondrial genes such as cytochrome c oxidase subunit I or cytochrome b (Cyt b). The vertebrate prepronociceptin gene (PNOC) was also tested in this field. However, the choice of molecular marker to identify blood meal is critical. The objective of our study is to compare the ability of Cyt b and PNOC as molecular markers for blood meal identification depending on the stage of blood meal digestion. In order to determine whether these Cyt b and PNOC could provide a positive result, 565 blood-fed females of Culicoides spp were collected and morphologically identified. The samples were collected between 2012 and 2014, in two localities in France. The collection localities were near either livestock or a forest. To catch the specimens, we used UV CDC miniature light traps. PNOC sequence of donkeys (Equus asinus) was sequenced and submitted because it was missing in GenBank. Our findings emphasize that the PNOC marker is not suitable to separate closely related Equid species such as horses and donkeys. The Cyt b marker was able to identify 204 more samples when compared to PNOC (99.55% of specimens). Cyt b appears to be better able to detect the origin of blood meals from females with digested blood in their abdomens. We conclude that Cyt b is a good marker as it increases the accuracy of blood meal identification of engorged females containing digested blood in their abdomens. The host opportunist behavior of Culicoides, especially that of C. obsoletus and C. scoticus, the main vectors of BTV in Europe was also highlighted.
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Affiliation(s)
- Leila Hadj-Henni
- Université de Reims Champagne-Ardenne, ANSES, SFR Cap Santé, EA4688 - USC «Transmission Vectorielle et Épidémiosurveillance de Maladies Parasitaires (VECPAR)» , Reims , France
| | | | - Jérôme Depaquit
- Université de Reims Champagne-Ardenne, ANSES, SFR Cap Santé, EA4688 - USC «Transmission Vectorielle et Épidémiosurveillance de Maladies Parasitaires (VECPAR)» , Reims , France
| | - Philippe Noël
- Université de Reims Champagne-Ardenne, ANSES, SFR Cap Santé, EA4688 - USC «Transmission Vectorielle et Épidémiosurveillance de Maladies Parasitaires (VECPAR)» , Reims , France
| | - Adeline Germain
- Université de Reims Champagne-Ardenne, ANSES, SFR Cap Santé, EA4688 - USC «Transmission Vectorielle et Épidémiosurveillance de Maladies Parasitaires (VECPAR)» , Reims , France
| | - Remi Helder
- Laboratoire IAE, Université de Reims Champagne-Ardenne, Station URCA-CERFE , Boult-aux-Bois , France
| | - Denis Augot
- Université de Reims Champagne-Ardenne, ANSES, SFR Cap Santé, EA4688 - USC «Transmission Vectorielle et Épidémiosurveillance de Maladies Parasitaires (VECPAR)» , Reims , France
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