1
|
Panicker VP, Narayanan A, Sreedharan Nair AK, Krishnan A, Ajay N, Kumar V. Standardization of quantitative PCR (qPCR) method to detect the level of parasitaemia in Babesia gibsoni infected dogs. J Microbiol Methods 2024; 224:107009. [PMID: 39098402 DOI: 10.1016/j.mimet.2024.107009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 07/31/2024] [Accepted: 07/31/2024] [Indexed: 08/06/2024]
Abstract
The present investigation aimed to quantitatively assess the level of parasitemia in dogs using qPCR.The dogs selected for this study were infected with the haemoprotozoan parasite Babesia gibsoni. In the study, dogs diagnosed with babesiosis were divided into two groups (n = 12) and subjected to distinct treatment strategies. The first group received clindamycin-metronidazole-doxycycline (CMD) therapy, while the second group was treated with a combination of buparvaquone-azithromycin (BPV-AZM). The level of parasitemia in the infected dogs was determined using an absolute quantification-based qPCR method. This assessment was conducted both prior to initiating the treatment and on the 10th day following the commencement of the treatment protocols. On the tenth day after the initiation of treatment, the CMD group exhibited a lower level of parasitemia in comparison to the BPV-AZM group. In the CMD treated groups, the mean parasitemia decreased from 4.9E + 06 to 3.4E + 06, indicating a reduction in parasitic load. Conversely, in the BPV-AZM treatment groups, the mean parasitemia increased from 1.62E + 06 to 2.87E + 06, suggesting an increase in parasitic load. On the 10th day, the CMD-treated group demonstrated a statistically significant decline in the level of parasitemia, with a P-value of ≤0.001. This indicates a strong and significant reduction in parasitic load following the CMD treatment. Therefore, the absolute quantification-based qPCR method could effectively assess the initial treatment response by measuring the level of parasitemia.
Collapse
Affiliation(s)
- Varuna Purushothama Panicker
- Department of Veterinary Biochemistry, College of Veterinary and Animal Sciences, Kerala Veterinary and Animal Sciences University, Pookode, Wayanad, India.
| | - Athira Narayanan
- University Veterinary Hospital & Teaching Veterinary Clinical Complex, Kerala Veterinary and Animal Sciences University, Pookode, Wayanad, India
| | - Ajith Kumar Sreedharan Nair
- University Veterinary Hospital & Teaching Veterinary Clinical Complex, Kerala Veterinary and Animal Sciences University, Pookode, Wayanad, India
| | - Anjaly Krishnan
- Project Scientist B, IHCI, NIE-ICMR, Chennai, Tamil Nadu 600077, India
| | - Nimna Ajay
- Department of Veterinary Biochemistry, College of Veterinary and Animal Sciences, Kerala Veterinary and Animal Sciences University, Pookode, Wayanad, India
| | - Vinod Kumar
- Department of Veterinary Epidemiology and Preventive Medicine, College of Veterinary and Animal Sciences, Kerala Veterinary and Animal Sciences University, Pookode, Wayanad, India
| |
Collapse
|
2
|
Enabulele EE, Le Clec'h W, Roberts EK, Thompson CW, McDonough MM, Ferguson AW, Bradley RD, Anderson TJC, Platt RN. Prospecting for Zoonotic Pathogens by Using Targeted DNA Enrichment. Emerg Infect Dis 2023; 29:1566-1579. [PMID: 37486179 PMCID: PMC10370864 DOI: 10.3201/eid2908.221818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023] Open
Abstract
More than 60 zoonoses are linked to small mammals, including some of the most devastating pathogens in human history. Millions of museum-archived tissues are available to understand natural history of those pathogens. Our goal was to maximize the value of museum collections for pathogen-based research by using targeted sequence capture. We generated a probe panel that includes 39,916 80-bp RNA probes targeting 32 pathogen groups, including bacteria, helminths, fungi, and protozoans. Laboratory-generated, mock-control samples showed that we are capable of enriching targeted loci from pathogen DNA 2,882‒6,746-fold. We identified bacterial species in museum-archived samples, including Bartonella, a known human zoonosis. These results showed that probe-based enrichment of pathogens is a highly customizable and efficient method for identifying pathogens from museum-archived tissues.
Collapse
|
3
|
Roe CC, Urbanz J, Auten C, Verocai GG, Upshaw-Bia K, Holiday O, Hepp C, Sahl JW. LupiQuant: A real-time PCR based assay for determining host-to-parasite DNA ratios of Onchocerca lupi and host Canis lupus from onchocercosis samples. PLoS One 2022; 17:e0276916. [PMID: 36409718 PMCID: PMC9678315 DOI: 10.1371/journal.pone.0276916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/15/2022] [Indexed: 11/22/2022] Open
Abstract
Onchocerca lupi is a filarial nematode that causes ocular onchocercosis in canines globally including North America and areas of Europe, North Africa, and the Middle East. Reported incidence of this parasite in canines has continued to steadily escalate since the early 21st century and was more recently documented in humans. Whole genome sequencing (WGS) of this parasite can provide insight into gene content, provide novel surveillance targets, and elucidate the origin and range expansion. However, past attempts of whole genome sequencing of other Onchocerca species reported a substantial portion of their data unusable due to the variable over-abundance of host DNA in samples. Here, we have developed a method to determine the host-to-parasite DNA ratio using a quantitative PCR (qPCR) approach that relies on two standard plasmids each of which contains a single copy gene specific to the parasite genus Onchocerca (major body wall myosin gene, myosin) or a single copy gene specific to the canine host (polycystin-1 precursor, pkd1). These plasmid standards were used to determine the copy number of the myosin and pkd1 genes within a sample to calculate the ratio of parasite and host DNA. Furthermore, whole genome sequence (WGS) data for three O. lupi isolates were consistent with our host-to-parasite DNA ratio results. Our study demonstrates, despite unified DNA extraction methods, variable quantities of host DNA within any one sample which will likely affect downstream WGS applications. Our quantification assay of host-to-parasite genome copy number provides a robust and accurate method of assessing canine host DNA load in an O. lupi specimen that will allow informed sample selection for WGS. This study has also provided the first whole genome draft sequence for this species. This approach is also useful for future focused WGS studies of other parasites.
Collapse
Affiliation(s)
- Chandler C. Roe
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States of America
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States of America
- * E-mail:
| | - Jennifer Urbanz
- Eye Care for Animals, Scottsdale, AZ, United States of America
| | - Candace Auten
- Eye Care for Animals, Albuquerque, NM, United States of America
| | - Guilherme G. Verocai
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, United States of America
| | - Kelly Upshaw-Bia
- Navajo Nation Veterinary Management Program, Window Rock, NM, United States of America
| | - Olivia Holiday
- Navajo Nation Veterinary Management Program, Window Rock, NM, United States of America
| | - Crystal Hepp
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States of America
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States of America
- Pathogen and Microbiome Division, Translational Genomics Research Institute, Flagstaff, AZ, United States of America
| | - Jason W. Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States of America
| |
Collapse
|
4
|
Araveti PB, Vijay M, Kar PP, Varunan S, Srivastava A. MMV560185 from pathogen box induces extrinsic pathway of apoptosis in Theileria annulata infected bovine leucocytes. Int J Parasitol Drugs Drug Resist 2022; 18:20-31. [PMID: 35032948 PMCID: PMC8761611 DOI: 10.1016/j.ijpddr.2021.12.003] [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: 07/09/2021] [Revised: 12/22/2021] [Accepted: 12/30/2021] [Indexed: 11/22/2022]
Abstract
Tropical theileriosis is a lymphoproliferative disease caused by the intracellular schizonts of Theileria annulata, an apicomplexan parasite. It causes severe infection in cattle and the untreated cattle would possibly die within 3–4 weeks of infection. The chemotherapy for this disease is largely dependent on the use of hydroxynaphthoquinone, namely buparvaquone. There have been reports recently of the development of resistance against this drug in T. annulata. Hence, identification of new drug molecule(s) or repurposing of existing drug molecule(s) against T. annulata is quite important. Here, we present the screening of 400 compounds included in the open-access Pathogen box from Medicine for Malaria Venture (MMV) to discover the novel compounds with potential inhibitory activity against T. annulata infected bovine leucocytes. We identified two compounds, MMV000062 and MMV560185, with IC50 values of 2.97 μM and 3.07 μM, respectively. MMV000062 and MMV560185 were found non-toxic to BoMac cells with CC50 values 34 μM and > 100 μM, respectively. The therapeutic indices of these compounds, MMV000062 and MMV560185, were calculated as more than 33 and 11, respectively. Further, it was observed that the parasite-infected cells under long-term culture were unable to recover with these compounds. We further deciphered that MMV560185 kills the infected cell by activation of TNFR-1 mediated extrinsic pathway of the apoptosis. The phenotypic characteristics of apoptosis were confirmed by Transmission Electron Microscopy. Our results suggest that it may be possible to develop MMV560185 further for chemotherapeutics of tropical theilerosis.
Collapse
|
5
|
Evaluation of a high-throughput, cost-effective Illumina library preparation kit. Sci Rep 2021; 11:15925. [PMID: 34354114 PMCID: PMC8342411 DOI: 10.1038/s41598-021-94911-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 07/19/2021] [Indexed: 11/08/2022] Open
Abstract
Library preparation for high-throughput sequencing applications is a critical step in producing representative, unbiased sequencing data. The iGenomX Riptide High Throughput Rapid Library Prep Kit purports to provide high-quality sequencing data with lower costs compared to other Illumina library kits. To test these claims, we compared sequence data quality of Riptide libraries to libraries constructed with KAPA Hyper and NEBNext Ultra. Across several single-source genome samples, mapping performance and de novo assembly of Riptide libraries were similar to conventional libraries prepared with the same DNA. Poor performance of some libraries resulted in low sequencing depth. In particular, degraded DNA samples may be challenging to sequence with Riptide. There was little cross-well plate contamination with the overwhelming majority of reads belong to the proper source genomes. The sequencing of metagenome samples using different Riptide primer sets resulted in variable taxonomic assignment of reads. Increased adoption of the Riptide kit will decrease library preparation costs. However, this method might not be suitable for degraded DNA.
Collapse
|
6
|
Enoka VIL, Kikuvi GM, Ndung'u PW. Effect of garlic and onion extract chitosan nanoparticles on selected intestinal bacterial flora in indigenous rainbow rooster chicken in Kenya. AIMS MOLECULAR SCIENCE 2021. [DOI: 10.3934/molsci.2021008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
|
7
|
Zhao B, Xiong C, Li J, Zhang D, Shi Y, Sun W, Duan X. Species Quantification in Complex Herbal Formulas-Vector Control Quantitative Analysis as a New Method. Front Pharmacol 2020; 11:488193. [PMID: 33324200 PMCID: PMC7725679 DOI: 10.3389/fphar.2020.488193] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/16/2020] [Indexed: 11/17/2022] Open
Abstract
Product mislabeling and/or species fraud in Traditional Chinese Medicine (TCM) not only decrease TCM quality, but also pose a potential health issue to the end user. Up to now, methods to control TCM quality have been developed to detect specific metabolites or identify the original species. However, species quantification in complex herbal formulas is rarely concerned. Here, we reported a simple Vector Control Quantitative Analysis (VCQA) method for flexible and accurate multiplex species quantification in traditional Chinese herbal formulas. We developed PCR-based strategy to quickly generate the integrated DNA fragments from multiple targeted species, which can be assembled into the quantitative vector in one round of cloning by Golden Gate ligation and Gateway recombination technique. With this method, we recruited the nuclear ribosomal DNA Internal Transcribed Spacer (ITS) region for the quantification of Ligusticum sinense “Chuanxiong,” Angelica dahurica (Hoffm.) Benth. & Hook.f. ex Franch. & Sav., Notopterygium incisum K. C. Ting ex H. T. Chang, Asarum sieboldii Miq., Saposhnikovia divaricata (Turcz.) Schischk., Nepeta cataria L., Mentha canadensis L., and Glycyrrhiza uralensis Fisch. ex DC. in ChuanXiong ChaTiao Wan, a classic Chinese herbal formula with very long historical background. We found that, firstly, VCQA method could eliminate the factors affecting such as the variations in DNA extracts when in combination with the use of universal and species-specific primers. Secondly, this method detected the limit of quantification of A. sieboldii Miq. in formula products down to 1%. Thirdly, the stability of quality of ChuanXiong ChaTiao Wan formula varies significantly among different manufacturers. In conclusion, VCQA method has the potential power and can be used as an alternative method for species quantification of complex TCM formulas.
Collapse
Affiliation(s)
- Bo Zhao
- College of Pharmacy, Guilin Medical University, Guilin, China.,Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Chao Xiong
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.,School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Jingjian Li
- College of Pharmacy, Guilin Medical University, Guilin, China
| | - Deng Zhang
- Guangxi Institute of Botany, The Chinese Academy of Sciences, Guilin, China
| | - Yancai Shi
- Guangxi Institute of Botany, The Chinese Academy of Sciences, Guilin, China
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiaoqun Duan
- College of Pharmacy, Guilin Medical University, Guilin, China
| |
Collapse
|
8
|
Capture-based enrichment of Theileria parva DNA enables full genome assembly of first buffalo-derived strain and reveals exceptional intra-specific genetic diversity. PLoS Negl Trop Dis 2020; 14:e0008781. [PMID: 33119590 PMCID: PMC7654785 DOI: 10.1371/journal.pntd.0008781] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 11/10/2020] [Accepted: 09/08/2020] [Indexed: 12/19/2022] Open
Abstract
Theileria parva is an economically important, intracellular, tick-transmitted parasite of cattle. A live vaccine against the parasite is effective against challenge from cattle-transmissible T. parva but not against genotypes originating from the African Cape buffalo, a major wildlife reservoir, prompting the need to characterize genome-wide variation within and between cattle- and buffalo-associated T. parva populations. Here, we describe a capture-based target enrichment approach that enables, for the first time, de novo assembly of nearly complete T. parva genomes derived from infected host cell lines. This approach has exceptionally high specificity and sensitivity and is successful for both cattle- and buffalo-derived T. parva parasites. De novo genome assemblies generated for cattle genotypes differ from the reference by ~54K single nucleotide polymorphisms (SNPs) throughout the 8.31 Mb genome, an average of 6.5 SNPs/kb. We report the first buffalo-derived T. parva genome, which is ~20 kb larger than the genome from the reference, cattle-derived, Muguga strain, and contains 25 new potential genes. The average non-synonymous nucleotide diversity (πN) per gene, between buffalo-derived T. parva and the Muguga strain, was 1.3%. This remarkably high level of genetic divergence is supported by an average Wright’s fixation index (FST), genome-wide, of 0.44, reflecting a degree of genetic differentiation between cattle- and buffalo-derived T. parva parasites more commonly seen between, rather than within, species. These findings present clear implications for vaccine development, further demonstrated by the ability to assemble nearly all known antigens in the buffalo-derived strain, which will be critical in design of next generation vaccines. The DNA capture approach used provides a clear advantage in specificity over alternative T. parva DNA enrichment methods used previously, such as those that utilize schizont purification, is less labor intensive, and enables in-depth comparative genomics in this apicomplexan parasite. An estimated 50 million cattle in sub-Saharan Africa are at risk of the deadly livestock disease East coast fever (ECF), caused by the parasite Theileria parva, which imposes tremendous economic hardship on smallholder farmers. An existing ECF vaccine protects against strains circulating among cattle, but not against T. parva derived from African Cape buffalo, its main wildlife carrier. Understanding this difference in protective efficacy requires characterization of the genetic diversity in T. parva strains associated with each mammalian host, a goal that has been hindered by the proliferation of T. parva in nucleated host cells, with much larger genomes. Here we adapted a sequence capture approach to target the whole parasite genome, enabling enrichment of parasite DNA over that of the host. Choices in protocol development resulted in nearly 100% parasite genome specificity and sensitivity, making this approach the most successful yet to generate T. parva genome sequence data in a high-throughput manner. The analyses uncovered a degree of genetic differentiation between cattle- and buffalo-derived genotypes that is akin to levels more commonly seen between species. This approach, which will enable an in-depth T. parva population genomics study from cattle and buffalo in the endemic regions, can easily be adapted to other intracellular pathogens.
Collapse
|
9
|
Sahoo S, Sahoo N, Biswal S, Mohanty B, Behera B, Pahari A, Bhuyan K. Determining Theileria annulata parasitemia through qPCR in lactating cows of Odisha, - a theileriosis-endemic region of India. Anim Biotechnol 2020; 33:487-492. [PMID: 33026945 DOI: 10.1080/10495398.2020.1806859] [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: 10/23/2022]
Abstract
Study was undertaken in a theileriosis-endemic region of India during May 2018 to April 2019 among milch cows. Blood samples collected from apparently healthy (n = 65) and Theileria-suspect cows (n = 65) were screened against T. annulata and T. orientalis infection by SYBR Green‒based real time PCR using primers designed from the isolates of study area. Cows having single infection with T. annulata with/without clinical signs of inappetence, low milk yield, pale mucous membranes, fever, enlarged prescapular lymph node, soil licking, panting, coughing, salivation and lachrymation were subjected to further investigation where parasitaemia and piroplasms per 1000 erythrocytes ranged from 1.6 × 107 to 1.2 × 108 parasites/mL of blood and 3-24 piroplasms in moderate group (16/65), 4.4 × 108 to 6.9 × 109 parasites/mL of blood and >88 piroplasms in severe group (30/65) and 1.6 × 104 to 5.5 × 106 parasites/mL of blood and 0-1 piroplasms in asymptomatic or carriers (17/65), respectively. Study unfolded significant difference in T. annulata parasitaemia among apparently healthy and ill cows. Phylogenetic analysis of our T. annulata isolates (NCBI accession numbers MN098316, MN098317 and MN098318) exhibited maximum similarity with the isolates detected in other parts of India.
Collapse
Affiliation(s)
- Sonali Sahoo
- Department of Veterinary Epidemiology and Preventive Medicine, Odisha University of Agriculture and Technology, Bhubaneswar, India
| | - Niranjana Sahoo
- Department of Veterinary Epidemiology and Preventive Medicine, Odisha University of Agriculture and Technology, Bhubaneswar, India.,Centre for Wildlife Health, Odisha University of Agriculture and Technology, Bhubaneswar, India
| | - Sangram Biswal
- Department of Veterinary Epidemiology and Preventive Medicine, Odisha University of Agriculture and Technology, Bhubaneswar, India
| | - Bijayendranath Mohanty
- Department of Veterinary Parasitology, Odisha University of Agriculture and Technology, Bhubaneswar, India
| | - Bikash Behera
- Centre for Wildlife Health, Odisha University of Agriculture and Technology, Bhubaneswar, India
| | - Avishek Pahari
- Centre for Wildlife Health, Odisha University of Agriculture and Technology, Bhubaneswar, India
| | - Kashyap Bhuyan
- Department of Veterinary Epidemiology and Preventive Medicine, Odisha University of Agriculture and Technology, Bhubaneswar, India
| |
Collapse
|
10
|
Rchiad Z, Haidar M, Ansari HR, Tajeri S, Mfarrej S, Ben Rached F, Kaushik A, Langsley G, Pain A. Novel tumour suppressor roles for GZMA and RASGRP1 in Theileria annulata-transformed macrophages and human B lymphoma cells. Cell Microbiol 2020; 22:e13255. [PMID: 32830401 PMCID: PMC7685166 DOI: 10.1111/cmi.13255] [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: 06/09/2020] [Revised: 08/03/2020] [Accepted: 08/07/2020] [Indexed: 12/22/2022]
Abstract
Theileria annulata is a tick-transmitted apicomplexan parasite that infects and transforms bovine leukocytes into disseminating tumours that cause a disease called tropical theileriosis. Using comparative transcriptomics we identified genes transcriptionally perturbed during Theileria-induced leukocyte transformation. Dataset comparisons highlighted a small set of genes associated with Theileria-transformed leukocyte dissemination. The roles of Granzyme A (GZMA) and RAS guanyl-releasing protein 1 (RASGRP1) were verified by CRISPR/Cas9-mediated knockdown. Knocking down expression of GZMA and RASGRP1 in attenuated macrophages led to a regain in their dissemination in Rag2/γC mice confirming their role as dissemination suppressors in vivo. We further evaluated the roles of GZMA and RASGRP1 in human B lymphomas by comparing the transcriptome of 934 human cancer cell lines to that of Theileria-transformed bovine host cells. We confirmed dampened dissemination potential of human B lymphomas that overexpress GZMA and RASGRP1. Our results provide evidence that GZMA and RASGRP1 have a novel tumour suppressor function in both T. annulata-infected bovine host leukocytes and in human B lymphomas.
Collapse
Affiliation(s)
- Zineb Rchiad
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Laboratoire de Biologie Comparative des Apicomplexes, Faculté de Médecine, Université Paris Descartes - Sorbonne Paris Cité, Paris, France.,INSERM U1016, CNRS UMR8104, Cochin Institute, Paris, France.,Centre de Coalition, Innovation, et de prévention des Epidémies au Maroc (CIPEM), Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Malak Haidar
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Laboratoire de Biologie Comparative des Apicomplexes, Faculté de Médecine, Université Paris Descartes - Sorbonne Paris Cité, Paris, France.,INSERM U1016, CNRS UMR8104, Cochin Institute, Paris, France
| | - Hifzur Rahman Ansari
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,King Abdullah International Medical Research Center (KAIMRC), King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Jeddah, Saudi Arabia
| | - Shahin Tajeri
- Laboratoire de Biologie Comparative des Apicomplexes, Faculté de Médecine, Université Paris Descartes - Sorbonne Paris Cité, Paris, France.,INSERM U1016, CNRS UMR8104, Cochin Institute, Paris, France
| | - Sara Mfarrej
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Fathia Ben Rached
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Abhinav Kaushik
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Gordon Langsley
- Laboratoire de Biologie Comparative des Apicomplexes, Faculté de Médecine, Université Paris Descartes - Sorbonne Paris Cité, Paris, France.,INSERM U1016, CNRS UMR8104, Cochin Institute, Paris, France
| | - Arnab Pain
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan
| |
Collapse
|
11
|
Zhang J, Gu H, Dai H, Zhang Z, Miao M. Alternative polyadenylation of the stacyose synthase gene mediates source-sink regulation in cucumber. JOURNAL OF PLANT PHYSIOLOGY 2020; 245:153111. [PMID: 31926460 DOI: 10.1016/j.jplph.2019.153111] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/24/2019] [Accepted: 12/24/2019] [Indexed: 05/24/2023]
Abstract
Alternative polyadenylation (APA) is a pervasive mechanism for gene regulation in eukaryotes. Stachyose is the main assimilate translocated in the cucumber phloem. Stachyose synthase (CsSTS) catalyzes the last step of stachyose biosynthesis in cucumber leaves and plays a key role in the regulation of assimilate partitioning between source and sink. In this study, three CsSTS mRNAs with the same open reading frame and the 5`untranslated region (UTR), but differing in their 3`UTRs, named CsSTS1 (short), CsSTS2 (medium), and CsSTS3 (long), were identified. Southern blot and sequence analysis of the cucumber genome confirmed that these transcripts are regulated through APA from a single gene. No significant difference of in vitro translation efficiency was found among three mRNAs. However, the relative stabilities of three transcripts varied among different tissues and different leaf development stages of cucumber. CsSTS1 expression in cucumber calli was up-regulated by the raffinose (substrate of CsSTS) and down-regulated by stachyose (product of CsSTS), respectively. In cucumber plants, all three isoforms have considerable expression in non-fruit node leaves. However, in fruit-carrying node leaves, the expression of CsSTS2 and CsSTS3 was severely inhibited and only CsSTS1 was highly expressed, indicating fruit setting has a remarkable effect on the relative expression level of three transcripts. This "fruit setting" effect could be observed until at least 36 h after the fruit was removed from the node. Our results suggest that abundant expression of CsSTS1 is beneficial for stachyose loading in source leaves, and APA is a delicate mechanism for CsSTS to regulate cucumber source-sink balance.
Collapse
Affiliation(s)
- Jinji Zhang
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, 225009, PR China.
| | - Hao Gu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, 225009, PR China.
| | - Haibo Dai
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, 225009, PR China.
| | - Zhiping Zhang
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, 225009, PR China.
| | - Minmin Miao
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, 225009, PR China.
| |
Collapse
|
12
|
Riaz S, Niaz Z, Khan S, Liu Y, Sui Z. Detection, characterization and expression dynamics of histone proteins in the dinoflagellate Alexandrium pacificum during growth regulation. HARMFUL ALGAE 2019; 87:101630. [PMID: 31349883 DOI: 10.1016/j.hal.2019.101630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/29/2019] [Accepted: 06/10/2019] [Indexed: 06/10/2023]
Abstract
Histones are the most abundant proteins associated with eukaryotic nuclear DNA. The exception is dinoflagellates, which have histone protein expression that is mostly reported to be below detectable levels. In this study, we investigated the presence of histone proteins and their functions in the dinoflagellate, Alexandrium pacificum. Histone protein sequences were analyzed, focusing on phylogenetic analysis and histone code. Histone expression was analyzed during the cell cycle and under nutritionally enhanced conditions using quantitative-PCR and western blots. Acid-soluble proteins were subjected to mass spectrometry analysis. To our knowledge, this is the first report of immunological detection of histone proteins (H2B and H4) in any dinoflagellate species. Absolute quantification of histone transcript in activily dividing cells revealed significant transcription in cells. The stable expression of histones during the cell cycle suggested that the histone genes in A. pacificum belonged to a replication-independent class and appeared to have a limited role in DNA packaging. The conservation of numerous post-translationally modified residues of multiple histone variants and differential expression of histones under nutritionally enhanced conditions suggested their functional significance in dinoflagellates. However, we detected histone H2B protein only via mass spectrometry. Histone-like protein was identified as most abundant acid-soluble protein of the cells.
Collapse
Affiliation(s)
- Sadaf Riaz
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China; Department of Microbiology, University of Central Punjab, Lahore, Pakistan
| | - Zeeshan Niaz
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China; Department of Microbiology, Hazara University, Mansehra, Pakistan
| | - Sohrab Khan
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China; Department of Microbiology, Hazara University, Mansehra, Pakistan
| | - Yuan Liu
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China.
| | - Zhenghong Sui
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China.
| |
Collapse
|
13
|
Dandasena D, Bhandari V, Sreenivasamurthy GS, Murthy S, Roy S, Bhanot V, Arora JS, Singh S, Sharma P. A Real-Time PCR based assay for determining parasite to host ratio and parasitaemia in the clinical samples of Bovine Theileriosis. Sci Rep 2018; 8:15441. [PMID: 30337565 PMCID: PMC6194045 DOI: 10.1038/s41598-018-33721-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 09/12/2018] [Indexed: 01/25/2023] Open
Abstract
Theileria annulata is an intracellular parasite that causes active and latent forms of bovine theileriosis. Diagnosis of the disease is primarily based on traditional methods such as microscopy, however, PCR based methods have proven to be superior in the absence of clear disease symptoms. However, diagnosis is difficult in cases of lower parasitaemia by conventional PCR. Hence, a rapid and sensitive method which can detect early infection and low parasite load is required. Therefore, we have developed an absolute quantification based real-time PCR (qPCR) assay. Reference standard curve using recombinant plasmids of a host (hprt) and a parasite gene (tasp) was constructed, and the assay was initially standardised using in vitro T. annulata cell lines. Further, 414 blood samples from suspected theileriosis cases were also evaluated using qPCR. The assay can estimate host to parasite ratios, calculate parasitaemia and treatment effectiveness in the clinical cases of theileriosis. In comparison with the conventional PCR results, 44 additional positive cases were found. Therefore, the assay holds importance in a clinical setting due to its ability to quantify the parasite load in clinical samples. It may be further used in distinguishing active and latent theileriosis infections and detection of drug resistance in the field.
Collapse
Affiliation(s)
| | | | - G S Sreenivasamurthy
- Department of Parasitology, College of Veterinary Science, Rajendra Nagar, Hyderabad, India
| | - Shweta Murthy
- National Institute of Animal Biotechnology, Hyderabad, India
| | - Sonti Roy
- National Institute of Animal Biotechnology, Hyderabad, India
| | - Vandna Bhanot
- Disease Investigation Laboratory, LUVAS, Ambala, Haryana, India
| | | | | | - Paresh Sharma
- National Institute of Animal Biotechnology, Hyderabad, India.
| |
Collapse
|
14
|
Li J, Fan F, Wang L, Zhan Q, Wu P, Du J, Yang X, Liu Y. Cloning and expression analysis of cinnamoyl-CoA reductase (CCR) genes in sorghum. PeerJ 2016; 4:e2005. [PMID: 27231650 PMCID: PMC4878380 DOI: 10.7717/peerj.2005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 04/13/2016] [Indexed: 11/20/2022] Open
Abstract
Cinnamoyl-CoA reductase (CCR) is the first enzyme in the monolignol-specific branch of the lignin biosynthetic pathway. In this research, three sorghum CCR genes including SbCCR1, SbCCR2-1 and SbCCR2-2 were cloned and characterized. Analyses of the structure and phylogeny of the three CCR genes showed evolutionary conservation of the functional domains and divergence of function. Transient expression assays in Nicotiana benthamiana leaves demonstrated that the three CCR proteins were localized in the cytoplasm. The expression analysis showed that the three CCR genes were induced by drought. But in 48 h, the expression levels of SbCCR1 and SbCCR2-2 did not differ between CK and the drought treatment; while the expression level of SbCCR2-1 in the drought treatment was higher than in CK. The expression of the SbCCR1 and SbCCR2-1 genes was not induced by sorghum aphid [Melanaphis sacchari (Zehntner)] attack, but SbCCR2-2 was significantly induced by sorghum aphid attack. It is suggested that SbCCR2-2 is involved in the process of pest defense. Absolute quantitative real-time PCR revealed that the three CCR genes were mainly expressed in lignin deposition organs. The gene copy number of SbCCR1 was significantly higher than those of SbCCR2-1 and SbCCR2-2 in the tested tissues, especially in stem. The results provide new insight into the functions of the three CCR genes in sorghum.
Collapse
Affiliation(s)
- Jieqin Li
- College of Agriculture, Anhui Science and Technology University , Fengyang , China
| | - Feifei Fan
- College of Agriculture, Anhui Science and Technology University , Fengyang , China
| | - Lihua Wang
- College of Agriculture, Anhui Science and Technology University , Fengyang , China
| | - Qiuwen Zhan
- College of Agriculture, Anhui Science and Technology University , Fengyang , China
| | - Peijin Wu
- College of Agriculture, Anhui Science and Technology University , Fengyang , China
| | - Junli Du
- College of Agriculture, Anhui Science and Technology University , Fengyang , China
| | - Xiaocui Yang
- College of Agriculture, Anhui Science and Technology University , Fengyang , China
| | - Yanlong Liu
- College of Agriculture, Anhui Science and Technology University , Fengyang , China
| |
Collapse
|