151
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Transcriptome Profiling in Human Diseases: New Advances and Perspectives. Int J Mol Sci 2017; 18:ijms18081652. [PMID: 28758927 PMCID: PMC5578042 DOI: 10.3390/ijms18081652] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 07/21/2017] [Accepted: 07/27/2017] [Indexed: 12/14/2022] Open
Abstract
In the last decades, transcriptome profiling has been one of the most utilized approaches to investigate human diseases at the molecular level. Through expression studies, many molecular biomarkers and therapeutic targets have been found for several human pathologies. This number is continuously increasing thanks to total RNA sequencing. Indeed, this new technology has completely revolutionized transcriptome analysis allowing the quantification of gene expression levels and allele-specific expression in a single experiment, as well as to identify novel genes, splice isoforms, fusion transcripts, and to investigate the world of non-coding RNA at an unprecedented level. RNA sequencing has also been employed in important projects, like ENCODE (Encyclopedia of the regulatory elements) and TCGA (The Cancer Genome Atlas), to provide a snapshot of the transcriptome of dozens of cell lines and thousands of primary tumor specimens. Moreover, these studies have also paved the way to the development of data integration approaches in order to facilitate management and analysis of data and to identify novel disease markers and molecular targets to use in the clinics. In this scenario, several ongoing clinical trials utilize transcriptome profiling through RNA sequencing strategies as an important instrument in the diagnosis of numerous human pathologies.
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152
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Chovancova P, Merk V, Marx A, Leist M, Kranaster R. Reverse-transcription quantitative PCR directly from cells without RNA extraction and without isothermal reverse-transcription: a 'zero-step' RT-qPCR protocol. Biol Methods Protoc 2017; 2:bpx008. [PMID: 32002469 PMCID: PMC6977950 DOI: 10.1093/biomethods/bpx008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/05/2017] [Accepted: 04/25/2017] [Indexed: 02/06/2023] Open
Abstract
We describe an ultra-rapid and sensitive method to quantify gene expression levels in
cultured cells. The procedure is based on reverse-transcription quantitative PCR (RT-qPCR)
directly from cells, without RNA extraction and without an isothermal
reverse-transcription step. Human neurons (Lund human mesencephalic cells) were lysed at
different stages of differentiation, and the lysates were used directly as template for
the combined RT-qPCR reaction. We detected a down-regulation of a proliferation marker and
an up-regulation of neuronal dopaminergic genes expression. We were able to detect the
reference gene target from as few as a single cell, demonstrating the application of the
method for efficient amplification from small cell numbers. The data were fully in line
with those obtained by the standard two-step RT-qPCR from the extracted total RNA. Our
‘zero-step’ RT-qPCR method proved to be simple and reliable with a total time from cell
lysis to the end of the qPCR as short as 1.5 h. It is therefore particularly suitable for
RT-qPCRs where large numbers of samples must be handled, or where data are required within
short time.
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Affiliation(s)
- Petra Chovancova
- In vitro Toxicology and Biomedicine, University of Konstanz, D-78457 Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Verena Merk
- myPOLS Biotec GmbH, D-78457 Konstanz, Germany
| | - Andreas Marx
- myPOLS Biotec GmbH, D-78457 Konstanz, Germany.,Department of Chemistry, University of Konstanz, D-78457 Konstanz, Germany
| | - Marcel Leist
- In vitro Toxicology and Biomedicine, University of Konstanz, D-78457 Konstanz, Germany
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153
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Kiseleva YY, Ptitsyn KG, Tikhonova OV, Radko SP, Kurbatov LK, Vakhrushev IV, Zgoda VG, Ponomarenko EA, Lisitsa AV, Archakov AI. [PCR analysis of the absolute number of copies of human chromosome 18 transcripts in liver and HepG2 cells]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2017; 63:147-153. [PMID: 28414286 DOI: 10.18097/pbmc20176302147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Using reverse transcription in conjunction with the quantitative real-time PCR or digital droplet PCR, the transcriptome profiling of human chromosome 18 has been carried out in liver hepatocytes and hepatoblastoma cells (HepG2 cell line) in terms of the absolute number of each transcript per cell. The transcript abundance varies within the range of 0.006 to 9635 and 0.011 to 4819 copies per cell for HepG2 cell line and hepatocytes, respectively. The expression profiles for genes of chromosome 18 in hepatocytes and HepG2 cells were found to significantly correlate: the Spearman's correlation coefficient was equal to 0.81. The distribution of frequency of transcripts over their abundance was bimodal for HepG2 cells and unimodal for liver hepatocytes. Bioinformatic analysis of the differential gene expression has revealed that genes of chromosome 18, overexpressed in HepG2 cells compared to hepatocytes, are associated with cell division and cell adhesion processes. It is assumed that the enhanced expression of those genes in HepG2 cells is related to the proliferation activity of cultured cells. The differences in transcriptome profiles have to be taken into account when modelling liver hepatocytes with cultured HepG2 cells.
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Affiliation(s)
- Y Y Kiseleva
- Institute of Biomedical Chemistry, Moscow, Russia
| | - K G Ptitsyn
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - S P Radko
- Institute of Biomedical Chemistry, Moscow, Russia
| | - L K Kurbatov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - V G Zgoda
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - A V Lisitsa
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A I Archakov
- Institute of Biomedical Chemistry, Moscow, Russia
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154
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Anauate AC, Leal MF, Wisnieski F, Santos LC, Gigek CO, Chen ES, Geraldis JC, Calcagno DQ, Assumpção PP, Demachki S, Arasaki CH, Lourenço LG, Artigiani R, Burbano RR, Smith MAC. Identification of suitable reference genes for miRNA expression normalization in gastric cancer. Gene 2017; 621:59-68. [PMID: 28411081 DOI: 10.1016/j.gene.2017.04.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 03/28/2017] [Accepted: 04/10/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Ana Carolina Anauate
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Mariana Ferreira Leal
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, São Paulo, Brazil; Departamento de Ortopedia e Traumatologia, Universidade Federal de São Paulo, São Paulo, Brazil; Núcleo de Pesquisas em Oncologia, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brazil
| | - Fernanda Wisnieski
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Leonardo Caires Santos
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Carolina Oliveira Gigek
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, São Paulo, Brazil; Disciplina de Gastroenterologia Cirúrgica, Departamento de Cirurgia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Elizabeth Suchi Chen
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Jaqueline Cruz Geraldis
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Danielle Queiroz Calcagno
- Núcleo de Pesquisas em Oncologia, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brazil
| | - Paulo Pimentel Assumpção
- Núcleo de Pesquisas em Oncologia, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brazil
| | - Samia Demachki
- Núcleo de Pesquisas em Oncologia, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brazil
| | - Carlos Haruo Arasaki
- Disciplina de Gastroenterologia Cirúrgica, Departamento de Cirurgia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Laércio Gomes Lourenço
- Disciplina de Gastroenterologia Cirúrgica, Departamento de Cirurgia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Ricardo Artigiani
- Departamento de Patologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Rommel Rodríguez Burbano
- Núcleo de Pesquisas em Oncologia, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brazil; Laboratório de Citogenética Humana, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil; Laboratório de Biologia Molecular, Hospital Ophir Loyola, Belém, Brazil
| | - Marília Arruda Cardoso Smith
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, São Paulo, Brazil.
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155
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Bustin SA, Huggett JF. Reproducibility of biomedical research - The importance of editorial vigilance. BIOMOLECULAR DETECTION AND QUANTIFICATION 2017; 11:1-3. [PMID: 28331813 PMCID: PMC5348116 DOI: 10.1016/j.bdq.2017.01.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Many journal editors are a failing to implement their own authors' instructions, resulting in the publication of many articles that do not meet basic standards of transparency, employ unsuitable data analysis methods and report overly optimistic conclusions. This problem is particularly acute where quantitative measurements are made and results in the publication of papers that lack scientific rigor and contributes to the concerns with regard to the reproducibility of biomedical research. This hampers research areas such as biomarker identification, as reproducing all but the most striking changes is challenging and translation to patient care rare.
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Affiliation(s)
- Stephen A Bustin
- Faculty of Medical Science , Anglia Ruskin University, Chelmsford, CM1 1SQ, United Kingdom
| | - Jim F Huggett
- Analytical Microbiology, School of Bioscience and Medicine, Faculty of Health and Medical Science, University of Surrey, Guildford, GU2 7XH, United Kingdom
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156
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Marino AMF, Percipalle M, Giunta RP, Salvaggio A, Caracappa G, Alfonzetti T, Aparo A, Reale S. Development and validation of a real-time PCR assay for the detection of Toxoplasma gondii DNA in animal and meat samples. J Vet Diagn Invest 2017; 29:203-207. [PMID: 28176611 DOI: 10.1177/1040638716682808] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We report a rapid and reliable method for the detection of Toxoplasma gondii in meat and animal tissues based on real-time polymerase chain reaction (PCR). Samples were collected from cattle, small ruminants, horses, and pigs raised or imported into Sicily, Italy. All DNA preparations were assayed by real-time PCR tests targeted to a 98-bp long fragment in the AF 529-bp repeat element and to the B1 gene using specific primers. Diagnostic sensitivity (100%), diagnostic specificity (100%), limit of detection (0.01 pg), efficiency (92-109%), and precision (mean coefficient of variation = 0.60%), repeatability (100%), reproducibility (100%), and robustness were evaluated using 240 DNA extracted samples (120 positives and 120 negative as per the OIE nested PCR method) from different matrices. Positive results were confirmed by the repetition of both real-time and nested PCR assays. Our study demonstrates the viability of a reliable, rapid, and specific real-time PCR on a large scale to monitor contamination with Toxoplasma cysts in meat and animal specimens. This validated method can be used for postmortem detection in domestic and wild animals and for food safety purposes.
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Affiliation(s)
- Anna Maria Fausta Marino
- National Reference Centre for Toxoplasmosis, Istituto Zooprofilattico Sperimentale della Sicilia, Catania, Italy (Marino, Giunta, Salvaggio, Percipalle, Caracappa, Alfonzetti, Aparo).,Molecular Biology Department, Istituto Zooprofilattico Sperimentale della Sicilia, Palermo, Italy (Reale)
| | - Maurizio Percipalle
- National Reference Centre for Toxoplasmosis, Istituto Zooprofilattico Sperimentale della Sicilia, Catania, Italy (Marino, Giunta, Salvaggio, Percipalle, Caracappa, Alfonzetti, Aparo).,Molecular Biology Department, Istituto Zooprofilattico Sperimentale della Sicilia, Palermo, Italy (Reale)
| | - Renato Paolo Giunta
- National Reference Centre for Toxoplasmosis, Istituto Zooprofilattico Sperimentale della Sicilia, Catania, Italy (Marino, Giunta, Salvaggio, Percipalle, Caracappa, Alfonzetti, Aparo).,Molecular Biology Department, Istituto Zooprofilattico Sperimentale della Sicilia, Palermo, Italy (Reale)
| | - Antonio Salvaggio
- National Reference Centre for Toxoplasmosis, Istituto Zooprofilattico Sperimentale della Sicilia, Catania, Italy (Marino, Giunta, Salvaggio, Percipalle, Caracappa, Alfonzetti, Aparo).,Molecular Biology Department, Istituto Zooprofilattico Sperimentale della Sicilia, Palermo, Italy (Reale)
| | - Giulia Caracappa
- National Reference Centre for Toxoplasmosis, Istituto Zooprofilattico Sperimentale della Sicilia, Catania, Italy (Marino, Giunta, Salvaggio, Percipalle, Caracappa, Alfonzetti, Aparo).,Molecular Biology Department, Istituto Zooprofilattico Sperimentale della Sicilia, Palermo, Italy (Reale)
| | - Tiziana Alfonzetti
- National Reference Centre for Toxoplasmosis, Istituto Zooprofilattico Sperimentale della Sicilia, Catania, Italy (Marino, Giunta, Salvaggio, Percipalle, Caracappa, Alfonzetti, Aparo).,Molecular Biology Department, Istituto Zooprofilattico Sperimentale della Sicilia, Palermo, Italy (Reale)
| | - Alessandra Aparo
- National Reference Centre for Toxoplasmosis, Istituto Zooprofilattico Sperimentale della Sicilia, Catania, Italy (Marino, Giunta, Salvaggio, Percipalle, Caracappa, Alfonzetti, Aparo).,Molecular Biology Department, Istituto Zooprofilattico Sperimentale della Sicilia, Palermo, Italy (Reale)
| | - Stefano Reale
- National Reference Centre for Toxoplasmosis, Istituto Zooprofilattico Sperimentale della Sicilia, Catania, Italy (Marino, Giunta, Salvaggio, Percipalle, Caracappa, Alfonzetti, Aparo).,Molecular Biology Department, Istituto Zooprofilattico Sperimentale della Sicilia, Palermo, Italy (Reale)
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157
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Fuchs-Telka S, Fister S, Mester PJ, Wagner M, Rossmanith P. Hydrophobic ionic liquids for quantitative bacterial cell lysis with subsequent DNA quantification. Anal Bioanal Chem 2017; 409:1503-1511. [PMID: 28004172 PMCID: PMC5333376 DOI: 10.1007/s00216-016-0112-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 11/17/2016] [Accepted: 11/22/2016] [Indexed: 11/29/2022]
Abstract
DNA is one of the most frequently analyzed molecules in the life sciences. In this article we describe a simple and fast protocol for quantitative DNA isolation from bacteria based on hydrophobic ionic liquid supported cell lysis at elevated temperatures (120-150 °C) for subsequent PCR-based analysis. From a set of five hydrophobic ionic liquids, 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide was identified as the most suitable for quantitative cell lysis and DNA extraction because of limited quantitative PCR inhibition by the aqueous eluate as well as no detectable DNA uptake. The newly developed method was able to efficiently lyse Gram-negative bacterial cells, whereas Gram-positive cells were protected by their thick cell wall. The performance of the final protocol resulted in quantitative DNA extraction efficiencies for Gram-negative bacteria similar to those obtained with a commercial kit, whereas the number of handling steps, and especially the time required, was dramatically reduced. Graphical Abstract After careful evaluation of five hydrophobic ionic liquids, 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide ([BMPyr + ][Ntf 2- ]) was identified as the most suitable ionic liquid for quantitative cell lysis and DNA extraction. When used for Gram-negative bacteria, the protocol presented is simple and very fast and achieves DNA extraction efficiencies similar to those obtained with a commercial kit. ddH 2 O double-distilled water, qPCR quantitative PCR.
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Affiliation(s)
- Sabine Fuchs-Telka
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria
| | - Susanne Fister
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria
| | - Patrick-Julian Mester
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria
| | - Martin Wagner
- Institute for Milk Hygiene, Milk Technology, and Food Science, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria
| | - Peter Rossmanith
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria.
- Institute for Milk Hygiene, Milk Technology, and Food Science, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria.
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158
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Infectious Bursal Disease Virus Activates c-Src To Promote α4β1 Integrin-Dependent Viral Entry by Modulating the Downstream Akt-RhoA GTPase-Actin Rearrangement Cascade. J Virol 2017; 91:JVI.01891-16. [PMID: 27881656 DOI: 10.1128/jvi.01891-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 11/21/2016] [Indexed: 12/21/2022] Open
Abstract
While the entry of infectious bursal disease virus (IBDV) is initiated by the binding of the virus to the two major receptors integrin and HSP90, the signaling events after receptor binding and how they contribute to virus entry remain elusive. We show here that IBDV activates c-Src by inducing the phosphorylation of the Y416 residue in c-Src both in DF-1 chicken fibroblasts and in vivo in the bursa of Fabricius from specific-pathogen-free (SPF) chickens. Importantly, inactivated IBDV fails to stimulate c-Src Y416 phosphorylation, and a very virulent IBDV strain induces a much higher level of c-Src Y416 phosphorylation than does an attenuated strain. Inhibition of c-Src activation by an Src kinase inhibitor or expression of a c-Src dominant negative mutant results in a significant decrease in the internalization of IBDV but has little effect on virus adhesion. Furthermore, short hairpin RNA (shRNA) downregulation of integrin, either the α4 or β1 subunit, but not HSP90 remarkably attenuates IBDV-induced c-Src Y416 phosphorylation, resulting in a decrease in IBDV internalization but not virus adhesion. Moreover, interestingly, inhibition of either c-Src downstream of the phosphatidylinositol 3-kinase (PI3K)/Akt-RhoA signaling cascade or actin rearrangement leads to a significant decrease in IBDV internalization irrespective of the IBDV-induced high levels of c-Src phosphorylation. Cumulatively, our results suggest a novel feed-forward model whereby IBDV activates c-Src for benefiting its cell entry via an integrin-mediated pathway by the activation of downstream PI3K/Akt-RhoA signaling and cytoskeleton actin rearrangement. IMPORTANCE While IBDV-caused immunosuppression is highly related to viral invasion, the molecular basis of the cellular entry of IBDV remains elusive. In this study, we demonstrate that IBDV activates c-Src by inducing the phosphorylation of the Y416 residue in c-Src to promote virus internalization but not virus adhesion. The ability to induce the level of c-Src Y416 phosphorylation correlates with the pathogenicity of an IBDV strain. IBDV-induced c-Src Y416 activation is α4β1 integrin but not HSP90 dependent and involves the activation of the downstream PI3K/Akt-RhoA GTPase-actin rearrangement cascade. Thus, our findings provide new insights into the IBDV infection process and the potential for c-Src as a candidate target for the development of IBDV therapeutic drugs.
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159
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Abstract
Quantitative real-time polymerase chain reaction is a technique for simultaneous amplification and product quantification of a target DNA as the process takes place in real time in a "closed-tube" system. Although this technique can provide an absolute quantification of the initial template copy number, quantification relative to a control sample or second sequence is typically adequate. The quantification process employs melting curve analysis and/or fluorescent detection systems and can provide amplification and genotyping in a relatively short time. Here we describe the properties and uses of various fluorescent detection systems used for quantification.
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Affiliation(s)
- Charanjeet Singh
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sinchita Roy-Chowdhuri
- Department of Pathology, Cytopathology and Molecular Pathology, MD Anderson Cancer Center, The University ofTexas, Houston, TX, USA.
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160
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Sun Y, Xu L, Zhang F, Song Z, Hu Y, Ji Y, Shen J, Li B, Lu H, Yang H. A promising magnetic SERS immunosensor for sensitive detection of avian influenza virus. Biosens Bioelectron 2016; 89:906-912. [PMID: 27818055 DOI: 10.1016/j.bios.2016.09.100] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 09/12/2016] [Accepted: 09/27/2016] [Indexed: 10/20/2022]
Abstract
Avian influenza viruses infect a great number of global populations every year and can lead to severe epidemics with high morbidity and mortality. Facile, rapid and sensitive detection of viruses is very crucial to control the viral spread at its early stage. In this work, we developed a novel magnetic immunosensor based on surface enhanced Raman scattering (SERS) spectroscopy to detect intact but inactivated influenza virus H3N2 (A/Shanghai/4084T/2012) by constructing a sandwich complex consisting of SERS tags, target influenza viruses and highly SERS-active magnetic supporting substrates. The procedure of sample pretreatment could be significantly simplified since the magnetic supporting substrates allowed the enrichment and separation of viruses from a complex matrix. With a portable Raman spectrometer, the immunosensor could detect H3N2 down to 102TCID50/mL (TCID50 refers to tissue culture infection dose at 50% end point), with a good linear relationship from 102 to 5×103 TCID50/mL. Considering its time efficiency, portability and sensitivity, the proposed SERS-based magnetic immunoassay is very promising for a point-of-care (POC) test in clinical and diagnostic praxis.
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Affiliation(s)
- Yang Sun
- Department of Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China; Institute of Arthritis Research, Guanghua Integrative Medicine Hospital, Shanghai 200052, China; Shanghai TargetDrug Ltd., Shanghai 201202, China
| | - Li Xu
- The Education Ministry Key Lab of Resource Chemistry, Shanghai Key Laboratory of Rare Earth Functional Materials, Shanghai Municipal Education Committee Key Laboratory of Molecular Imaging Probes and Sensors and Department of Chemistry, Shanghai Normal University, Shanghai 200234, China
| | - Fengdi Zhang
- Department of Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Zhigang Song
- Department of Pathogen Diagnosis and Biosafety, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Yunwen Hu
- Department of Pathogen Diagnosis and Biosafety, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Yongjia Ji
- Department of Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Jiayin Shen
- Department of Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Ben Li
- Shanghai TargetDrug Ltd., Shanghai 201202, China
| | - Hongzhou Lu
- Department of Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China.
| | - Haifeng Yang
- The Education Ministry Key Lab of Resource Chemistry, Shanghai Key Laboratory of Rare Earth Functional Materials, Shanghai Municipal Education Committee Key Laboratory of Molecular Imaging Probes and Sensors and Department of Chemistry, Shanghai Normal University, Shanghai 200234, China.
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161
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Velizheva NP, Rechsteiner MP, Wong CE, Zhong Q, Rössle M, Bode B, Moch H, Soltermann A, Wild PJ, Tischler V. Cytology smears as excellent starting material for next-generation sequencing-based molecular testing of patients with adenocarcinoma of the lung. Cancer Cytopathol 2016; 125:30-40. [DOI: 10.1002/cncy.21771] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 07/08/2016] [Accepted: 07/27/2016] [Indexed: 11/10/2022]
Affiliation(s)
| | | | - Christine E. Wong
- Institute of Surgical Pathology; University Hospital Zurich; Zurich Switzerland
| | - Qing Zhong
- Institute of Surgical Pathology; University Hospital Zurich; Zurich Switzerland
| | - Matthias Rössle
- Cantonal Hospital Graubunden, Institute of Pathology; Chur Switzerland
| | - Beata Bode
- Institute of Surgical Pathology; University Hospital Zurich; Zurich Switzerland
| | - Holger Moch
- Institute of Surgical Pathology; University Hospital Zurich; Zurich Switzerland
| | - Alex Soltermann
- Institute of Surgical Pathology; University Hospital Zurich; Zurich Switzerland
| | - Peter J. Wild
- Institute of Surgical Pathology; University Hospital Zurich; Zurich Switzerland
| | - Verena Tischler
- Institute of Surgical Pathology; University Hospital Zurich; Zurich Switzerland
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162
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Zhang Y, Li Q, Guo L, Huang Q, Shi J, Yang Y, Liu D, Fan C. Ion-Mediated Polymerase Chain Reactions Performed with an Electronically Driven Microfluidic Device. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606137] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Yi Zhang
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility; CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Qian Li
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility; CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Linjie Guo
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility; CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Qing Huang
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility; CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Jiye Shi
- Kellogg College; University of Oxford; Oxford OX2 6PN UK
- UCB Pharma; 208 Bath Road Slough SL1 3WE UK
| | - Yang Yang
- National Center for NanoScience and Technology (NCNST); Beijing 100190 China
| | - Dongsheng Liu
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education; Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility; CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
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163
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Zhang Y, Li Q, Guo L, Huang Q, Shi J, Yang Y, Liu D, Fan C. Ion-Mediated Polymerase Chain Reactions Performed with an Electronically Driven Microfluidic Device. Angew Chem Int Ed Engl 2016; 55:12450-4. [DOI: 10.1002/anie.201606137] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 07/19/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Yi Zhang
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility; CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Qian Li
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility; CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Linjie Guo
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility; CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Qing Huang
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility; CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Jiye Shi
- Kellogg College; University of Oxford; Oxford OX2 6PN UK
- UCB Pharma; 208 Bath Road Slough SL1 3WE UK
| | - Yang Yang
- National Center for NanoScience and Technology (NCNST); Beijing 100190 China
| | - Dongsheng Liu
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education; Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility; CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
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164
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Sun H. A multi-layer microchip for high-throughput single-cell gene expression profiling. Anal Biochem 2016; 508:1-8. [DOI: 10.1016/j.ab.2016.05.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 05/21/2016] [Accepted: 05/23/2016] [Indexed: 10/21/2022]
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165
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Oh EH, Jung S, Kim WJ, Kim KP, Kim SK. Microparticle-based RT-qPCR for highly selective rare mutation detection. Biosens Bioelectron 2016; 87:229-235. [PMID: 27566396 DOI: 10.1016/j.bios.2016.08.057] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/12/2016] [Accepted: 08/17/2016] [Indexed: 01/08/2023]
Abstract
The quantitative reverse transcription polymerase chain reaction (RT-qPCR) has become one of the most widely used methods in the detection of disease-specific RNAs. The RT-qPCR involves two separate steps, RT and qPCR. In this study, we suggest a new RT-qPCR protocol with the particles of primer-immobilized networks (PINs), performing capture, RT and amplification of a target RNA in one particle. The production of undesired cDNAs was dramatically suppressed by the specific capture of the target RNA within the particle. Afterward, RT and amplification processes are performed without loss of cDNAs as exchanging the reaction solution. The biomarker gene of chronic myeloid leukemia, Bcr-Abl fusion transcript, is detected in the sensitivity of single mutant leukemic cell mixed in 104 normal cell using this protocol with the excellent restraint of non-specific signal. This protocol that whole processes are performed in the particle in a row is preferred for the highly specific detection of target RNAs in complex sample.
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Affiliation(s)
- Eun Hae Oh
- Center for BioMicrosystems, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Seungwon Jung
- Center for BioMicrosystems, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Won Jin Kim
- Department of Applied Chemistry, The Institute of Natural Science, College of Applied Science, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Kwang Pyo Kim
- Department of Applied Chemistry, The Institute of Natural Science, College of Applied Science, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Sang Kyung Kim
- Center for BioMicrosystems, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Department of Biomedical Engineering, Korea University of Science and Technology, Daejeon 34113, Republic of Korea.
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166
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Goldberg CS, Turner CR, Deiner K, Klymus KE, Thomsen PF, Murphy MA, Spear SF, McKee A, Oyler‐McCance SJ, Cornman RS, Laramie MB, Mahon AR, Lance RF, Pilliod DS, Strickler KM, Waits LP, Fremier AK, Takahara T, Herder JE, Taberlet P. Critical considerations for the application of environmental
DNA
methods to detect aquatic species. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12595] [Citation(s) in RCA: 497] [Impact Index Per Article: 62.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Caren S. Goldberg
- School of the Environment Washington State University 100 Dairy Rd. Pullman WA 99164 USA
| | - Cameron R. Turner
- Department of Biological Sciences University of Notre Dame Notre Dame IN 46556 USA
| | - Kristy Deiner
- Department of Biological Sciences University of Notre Dame Notre Dame IN 46556 USA
| | - Katy E. Klymus
- Lake Erie Center University of Toledo 6200 Bayshore Rd. Oregon OH 43616 USA
| | - Philip Francis Thomsen
- Centre for GeoGenetics Natural History Museum of Denmark University of Copenhagen Øster Voldgade 5‐7 DK‐1350 Copenhagen Denmark
| | - Melanie A. Murphy
- Department of Ecosystem Science andManagement Program in Ecology University of Wyoming Department 3354 1000 E University Ave Laramie WY 82071 USA
| | | | - Anna McKee
- U.S. Geological Survey South Atlantic Water Science Center 1770 Corporate Drive Suite 500 Norcross GA 30093 USA
| | - Sara J. Oyler‐McCance
- U.S. Geological Survey Fort Collins Science Center 2150 Centre Ave, Building C Fort Collins CO 80526 USA
| | - Robert Scott Cornman
- U.S. Geological Survey Fort Collins Science Center 2150 Centre Ave, Building C Fort Collins CO 80526 USA
| | - Matthew B. Laramie
- U.S. Geological Survey Forest and Rangeland Ecosystem Science Center Boise ID 83706 USA
| | - Andrew R. Mahon
- Department of Biology Institute for Great Lakes Research Central Michigan University Mount Pleasant MI 48859 USA
| | - Richard F. Lance
- Environmental Laboratory US Army Engineer Research & Development Center Vicksburg MS 39180 USA
| | - David S. Pilliod
- U.S. Geological Survey Forest and Rangeland Ecosystem Science Center Boise ID 83706 USA
| | - Katherine M. Strickler
- School of the Environment Washington State University 100 Dairy Rd. Pullman WA 99164 USA
| | - Lisette P. Waits
- Fish and Wildlife Sciences University of Idaho Moscow ID 83844‐1136 USA
| | - Alexander K. Fremier
- School of the Environment Washington State University 100 Dairy Rd. Pullman WA 99164 USA
| | - Teruhiko Takahara
- Faculty of Life and Environmental Science Shimane University 1060 Nishikawatsu Matsue Shimane 690‐8504 Japan
| | - Jelger E. Herder
- Reptile, Amphibian and Fish Conservation Netherlands (RAVON) P.O. Box 1413 6501 BK Nijmegen The Netherlands
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine Université Grenoble Alpes F‐38000 Grenoble France
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167
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Fujita H, Kataoka Y, Tobita S, Kuwahara M, Sugimoto N. Novel One-Tube-One-Step Real-Time Methodology for Rapid Transcriptomic Biomarker Detection: Signal Amplification by Ternary Initiation Complexes. Anal Chem 2016; 88:7137-44. [PMID: 27347743 DOI: 10.1021/acs.analchem.6b01192] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We have developed a novel RNA detection method, termed signal amplification by ternary initiation complexes (SATIC), in which an analyte sample is simply mixed with the relevant reagents and allowed to stand for a short time under isothermal conditions (37 °C). The advantage of the technique is that there is no requirement for (i) heat annealing, (ii) thermal cycling during the reaction, (iii) a reverse transcription step, or (iv) enzymatic or mechanical fragmentation of the target RNA. SATIC involves the formation of a ternary initiation complex between the target RNA, a circular DNA template, and a DNA primer, followed by rolling circle amplification (RCA) to generate multiple copies of G-quadruplex (G4) on a long DNA strand like beads on a string. The G4s can be specifically fluorescence-stained with N(3)-hydroxyethyl thioflavin T (ThT-HE), which emits weakly with single- and double-stranded RNA/DNA but strongly with parallel G4s. An improved dual SATIC system, which involves the formation of two different ternary initiation complexes in the RCA process, exhibited a wide quantitative detection range of 1-5000 pM. Furthermore, this enabled visual observation-based RNA detection, which is more rapid and convenient than conventional isothermal methods, such as reverse transcription-loop-mediated isothermal amplification, signal mediated amplification of RNA technology, and RNA-primed rolling circle amplification. Thus, SATIC methodology may serve as an on-site and real-time measurement technique for transcriptomic biomarkers for various diseases.
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Affiliation(s)
- Hiroto Fujita
- Graduate School of Science and Technology, Gunma University , 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Yuka Kataoka
- Graduate School of Science and Technology, Gunma University , 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Seiji Tobita
- Graduate School of Science and Technology, Gunma University , 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Masayasu Kuwahara
- Graduate School of Science and Technology, Gunma University , 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
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168
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Cnops L, van Griensven J, Honko AN, Bausch DG, Sprecher A, Hill CE, Colebunders R, Johnson JC, Griffiths A, Palacios GF, Kraft CS, Kobinger G, Hewlett A, Norwood DA, Sabeti P, Jahrling PB, Formenty P, Kuhn JH, Ariën KK. Essentials of filoviral load quantification. THE LANCET. INFECTIOUS DISEASES 2016; 16:e134-e138. [PMID: 27296694 DOI: 10.1016/s1473-3099(16)30063-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 04/07/2016] [Accepted: 04/20/2016] [Indexed: 11/29/2022]
Abstract
Quantitative measurement of viral load is an important parameter in the management of filovirus disease outbreaks because viral load correlates with severity of disease, survival, and infectivity. During the ongoing Ebola virus disease outbreak in parts of Western Africa, most assays used in the detection of Ebola virus disease by more than 44 diagnostic laboratories yielded qualitative results. Regulatory hurdles involved in validating quantitative assays and the urgent need for a rapid Ebola virus disease diagnosis precluded development of validated quantitative assays during the outbreak. Because of sparse quantitative data obtained from these outbreaks, opportunities for study of correlations between patient outcome, changes in viral load during the course of an outbreak, disease course in asymptomatic individuals, and the potential for virus transmission between infected patients and contacts have been limited. We strongly urge the continued development of quantitative viral load assays to carefully evaluate these parameters in future outbreaks of filovirus disease.
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Affiliation(s)
- Lieselotte Cnops
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Johan van Griensven
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Anna N Honko
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | | | - Armand Sprecher
- Médecins Sans Frontières-Operational Center of Brussels, Brussels, Belgium
| | - Charles E Hill
- Molecular Diagnostics Laboratory, Emory University Hospital, Atlanta, GA, USA
| | - Robert Colebunders
- International Health Unit, Global Health Institute, Faculty of Medicine and Health Sciences, Antwerp University, Antwerp, Belgium
| | - Joshua C Johnson
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Anthony Griffiths
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Gustavo F Palacios
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Colleen S Kraft
- Pathology and Laboratory Medicine, Emory University Medical School, Atlanta, GA, USA
| | - Gary Kobinger
- National Microbiology Laboratory, Public Health Agency of Canada, University of Manitoba, Winnipeg, MB, Canada
| | | | - David A Norwood
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Pardis Sabeti
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Peter B Jahrling
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | | | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Kevin K Ariën
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.
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169
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Egatz-Gomez A, Wang C, Klacsmann F, Pan Z, Marczak S, Wang Y, Sun G, Senapati S, Chang HC. Future microfluidic and nanofluidic modular platforms for nucleic acid liquid biopsy in precision medicine. BIOMICROFLUIDICS 2016; 10:032902. [PMID: 27190565 PMCID: PMC4859827 DOI: 10.1063/1.4948525] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 04/20/2016] [Indexed: 05/05/2023]
Abstract
Nucleic acid biomarkers have enormous potential in non-invasive diagnostics and disease management. In medical research and in the near future in the clinics, there is a great demand for accurate miRNA, mRNA, and ctDNA identification and profiling. They may lead to screening of early stage cancer that is not detectable by tissue biopsy or imaging. Moreover, because their cost is low and they are non-invasive, they can become a regular screening test during annual checkups or allow a dynamic treatment program that adjusts its drug and dosage frequently. We briefly review a few existing viral and endogenous RNA assays that have been approved by the Federal Drug Administration. These tests are based on the main nucleic acid detection technologies, namely, quantitative reverse transcription polymerase chain reaction (PCR), microarrays, and next-generation sequencing. Several of the challenges that these three technologies still face regarding the quantitative measurement of a panel of nucleic acids are outlined. Finally, we review a cluster of microfluidic technologies from our group with potential for point-of-care nucleic acid quantification without nucleic acid amplification, designed to overcome specific limitations of current technologies. We suggest that integration of these technologies in a modular design can offer a low-cost, robust, and yet sensitive/selective platform for a variety of precision medicine applications.
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Affiliation(s)
- Ana Egatz-Gomez
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Ceming Wang
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Flora Klacsmann
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Zehao Pan
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Steve Marczak
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Yunshan Wang
- Electrical and Computer Engineering, University of Utah , Salt Lake City, Utah 84112, USA
| | - Gongchen Sun
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Satyajyoti Senapati
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Hsueh-Chia Chang
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
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170
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Luchi N, Capretti P, Pazzagli M, Pinzani P. Powerful qPCR assays for the early detection of latent invaders: interdisciplinary approaches in clinical cancer research and plant pathology. Appl Microbiol Biotechnol 2016; 100:5189-204. [PMID: 27112348 DOI: 10.1007/s00253-016-7541-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/07/2016] [Accepted: 04/10/2016] [Indexed: 12/29/2022]
Abstract
Latent invaders represent the first step of disease before symptoms occur in the host. Based on recent findings, tumors are considered to be ecosystems in which cancer cells act as invasive species that interact with the native host cell species. Analogously, in plants latent fungal pathogens coevolve within symptomless host tissues. For these reasons, similar detection approaches can be used for an early diagnosis of the invasion process in both plants and humans to prevent or reduce the spread of the disease. Molecular tools based on the evaluation of nucleic acids have been developed for the specific, rapid, and early detection of human diseases. During the last decades, these techniques to assess and quantify the proliferation of latent invaders in host cells have been transferred from the medical field to different areas of scientific research, such as plant pathology. An improvement in molecular biology protocols (especially referring to qPCR assays) specifically designed and optimized for detection in host plants is therefore advisable. This work is a cross-disciplinary review discussing the use of a methodological approach that is employed within both medical and plant sciences. It provides an overview of the principal qPCR tools for the detection of latent invaders, focusing on comparisons between clinical cancer research and plant pathology, and recent advances in the early detection of latent invaders to improve prevention and control strategies.
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Affiliation(s)
- Nicola Luchi
- National Research Council (IPSP-CNR), Institute for Sustainable Plant Protection, Via Madonna del Piano 10, 50019, Sesto Fiorentino Firenze, Italy
| | - Paolo Capretti
- National Research Council (IPSP-CNR), Institute for Sustainable Plant Protection, Via Madonna del Piano 10, 50019, Sesto Fiorentino Firenze, Italy
- Department of Agri-Food Productions and Environmental Sciences (DiSPAA), University of Florence, Piazzale delle Cascine 28, Florence, Italy
| | - Mario Pazzagli
- Department of Clinical, Experimental and Biomedical Sciences, University of Florence, Viale Pieraccini, 6, 50139, Firenze, Italy
| | - Pamela Pinzani
- Department of Clinical, Experimental and Biomedical Sciences, University of Florence, Viale Pieraccini, 6, 50139, Firenze, Italy.
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171
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Henrich N, Holmes B, Isaac-Renton J, Prystajecky N. Exploring readiness for the adoption of new molecular water quality tests: Insights from interviews with policy makers, laboratory managers and watershed managers. ENVIRONMENT INTERNATIONAL 2016; 89-90:12-20. [PMID: 26826358 DOI: 10.1016/j.envint.2016.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 01/06/2016] [Accepted: 01/08/2016] [Indexed: 06/05/2023]
Abstract
Adoption of molecular-based water quality tests has been limited despite their advantage over traditional culture-based tests. A better understanding of the factors affecting adoption of these tests is needed for effective implementation. The Consolidated Framework for Implementation Research (CFIR) was used to analyze interviews with policy makers, watershed managers and laboratory managers in British Columbia (BC), Canada about their perceptions of molecular water tests currently under development in order to assess readiness for adoption and identify factors that may impact implementation. Many of the CFIR constructs were addressed by study participants, thus confirming their validity in the water-testing context. Other constructs were not mentioned, which suggests that awareness about these constructs need to be increased to ensure that they are incorporated into implementation strategies. In general, there was much enthusiasm for the new tests, which were seen to provide valuable information that could enable improved management of watersheds and treatment of source water. However, prior to adopting the tests, stakeholders would require evidence supporting the tests' validity and reliability, would need to assess the complexity of introducing the tests into laboratories and water sampling processes, and would require support interpreting the test results. Even if all the aforementioned issues are satisfactorily addressed, the tests may not be adopted unless regulations and policies were changed to allow the use of these test results to inform decision making. The results support that implementation of new technologies, such as these water quality tests, need to address potential barriers that could hinder uptake despite the advantages of the new product.
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Affiliation(s)
- Natalie Henrich
- Center for Health Evaluation and Outcome Sciences, St. Paul's Hospital, 588-1081 Burrard Street, Vancouver, British Columbia V6Z 1Y6, Canada.
| | - Bev Holmes
- Michael Smith Foundation for Health Research, 200-1285 West Broadway, Vancouver, British Columbia V6H 3X8, Canada.
| | - Judith Isaac-Renton
- British Columbia Public Health Microbiology Reference Laboratory, Provincial Health Services Authority, 655 West 12th Avenue, Vancouver, British Columbia V5Z 4R4, Canada.
| | - Natalie Prystajecky
- British Columbia Public Health Microbiology Reference Laboratory, Provincial Health Services Authority, 655 West 12th Avenue, Vancouver, British Columbia V5Z 4R4, Canada.
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172
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Zhai S, Xu H, Jiang X, Sun S, Qin L, Wei D, Hu L. Expression Depression of CD300LG-γ in Human Pulmonary Carcinoma. Monoclon Antib Immunodiagn Immunother 2016; 35:94-9. [PMID: 26977771 DOI: 10.1089/mab.2015.0043] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Songhui Zhai
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - He Xu
- Department of Immunology, College of Preclinical and Forensic Medicine, Sichuan University, Chengdu, China
| | - Xiaomei Jiang
- Department of Immunology, College of Preclinical and Forensic Medicine, Sichuan University, Chengdu, China
| | - Sheng Sun
- Insitute of Forensic Science, Chongqing Public Security Bureau, Chongqing, China
| | - Lang Qin
- The Reproductive Centre, Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Dapeng Wei
- Department of Immunology, College of Preclinical and Forensic Medicine, Sichuan University, Chengdu, China
| | - Lijuan Hu
- Department of Immunology, College of Preclinical and Forensic Medicine, Sichuan University, Chengdu, China
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173
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Wang WT, Sun YM, Huang W, He B, Zhao YN, Chen YQ. Genome-wide Long Non-coding RNA Analysis Identified Circulating LncRNAs as Novel Non-invasive Diagnostic Biomarkers for Gynecological Disease. Sci Rep 2016; 6:23343. [PMID: 26987697 PMCID: PMC4796908 DOI: 10.1038/srep23343] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 03/02/2016] [Indexed: 12/11/2022] Open
Abstract
Increasing evidence indicates that long non-coding RNAs (lncRNAs) play important roles in human diseases. This study aimed to investigate the tissue and serum lncRNAs that are differentially expressed between patients with endometriosis, a gynecological disease, to evaluate the potential of these lncRNAs as non-invasive markers for the disease. The differentially expressed lncRNAs as competing endogenous RNAs (ceRNAs) were also analyzed to predict their functions in disease development. Genome-wide profiling of lncRNA expression patterns revealed that many lncRNAs were abnormally expressed between sera and tissuesof the patient samples. A set of aberrant differentially expressed lncRNAs were further validated in a validation cohort of 110 serum and 24 tissue samples. Functional analysis predicted that differentially expressed lncRNAs may participate in disease development through crosstalk between the ceRNAs of miRNAs and may be involved in a range of cellular pathways including steroid or hormone responses. We also found a unique set of lncRNAs that were associated with disease severity and progression, and their diagnostic values were also investigated. Our study demonstrated that lncRNAs could potentially serve as non-invasive biomarkers for the diagnosis of endometriosis and as important regulators in the progression of this disease.
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Affiliation(s)
- Wen-Tao Wang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou 510275, China
| | - Yu-Meng Sun
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou 510275, China
| | - Wei Huang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou 510275, China
| | - Bo He
- Dept of Obst &Gyn, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Ya-Nan Zhao
- Dept of Obst &Gyn, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Yue-Qin Chen
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou 510275, China
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174
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Leal MF, Arliani GG, Astur DC, Franciozi CE, Debieux P, Andreoli CV, Smith MC, Pochini ADC, Ejnisman B, Cohen M. Comprehensive selection of reference genes for expression studies in meniscus injury using quantitative real-time PCR. Gene 2016; 584:60-68. [PMID: 26968891 DOI: 10.1016/j.gene.2016.03.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 02/11/2016] [Accepted: 03/04/2016] [Indexed: 11/29/2022]
Abstract
The meniscus plays critical roles in the knee function. Meniscal tears can lead to knee osteoarthritis. Gene expression analysis may be a useful tool for understanding meniscus tears, and reverse-transcription quantitative polymerase chain reaction (RT-qPCR) has become an effective method for such studies. However, this technique requires the use of suitable reference genes for data normalization. We evaluated the suitability of six reference genes (18S, ACTB, B2M, GAPDH, HPRT1 and TBP) using meniscus samples of (1) 19 patients with isolated meniscal tears, (2) 20 patients with meniscal tears and combined anterior cruciate ligament injury (ACL), and (3) 11 controls without meniscal tears. The stability of the candidate reference genes was determined using the NormFinder, geNorm, BestKeeper DataAssist and RefFinder software packages and comparative ΔCt method. Overall, HPRT1 was the best single reference gene. However, GenEx software demonstrated that two or more reference genes should be used for gene expression normalization, which was confirmed when we evaluated TGFβR1 expression using several reference gene combinations. HPRT1+TBP was the most frequently identified pair from the analysis of samples of (1) meniscal tear samples of patients with a concomitant ACL tears, (2) all meniscal tears, and (3) all samples. HPRT1+GAPDH was the most frequently identified pair from the analysis of samples of isolated meniscal tear samples and controls. In the analysis involving only controls, GAPDH+18S was the most frequently identified pair. In the analysis of only isolated meniscal tear samples and in the analysis of meniscal tear samples of patients with concomitant ACL tears and controls, both HPRT1+TBP and HPRT1+GAPDH were identified as suitable pairs. If the gene expression study aims to compare non-injured meniscus, isolated meniscal tears and meniscal tears of patients with ACL tears as three independent groups, the trio of HPRT1+TBP+GAPDH is the most suitable combination of reference genes.
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Affiliation(s)
- Mariana Ferreira Leal
- Departamento de Ortopedia e Traumatologia, Universidade Federal de São Paulo, 04038-032, São Paulo, SP, Brazil; Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, 04023-001, São Paulo, SP, Brazil.
| | - Gustavo Gonçalves Arliani
- Departamento de Ortopedia e Traumatologia, Universidade Federal de São Paulo, 04038-032, São Paulo, SP, Brazil
| | - Diego Costa Astur
- Departamento de Ortopedia e Traumatologia, Universidade Federal de São Paulo, 04038-032, São Paulo, SP, Brazil
| | - Carlos Eduardo Franciozi
- Departamento de Ortopedia e Traumatologia, Universidade Federal de São Paulo, 04038-032, São Paulo, SP, Brazil
| | - Pedro Debieux
- Departamento de Ortopedia e Traumatologia, Universidade Federal de São Paulo, 04038-032, São Paulo, SP, Brazil
| | - Carlos Vicente Andreoli
- Departamento de Ortopedia e Traumatologia, Universidade Federal de São Paulo, 04038-032, São Paulo, SP, Brazil
| | - Marília Cardoso Smith
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, 04023-001, São Paulo, SP, Brazil
| | - Alberto de Castro Pochini
- Departamento de Ortopedia e Traumatologia, Universidade Federal de São Paulo, 04038-032, São Paulo, SP, Brazil
| | - Benno Ejnisman
- Departamento de Ortopedia e Traumatologia, Universidade Federal de São Paulo, 04038-032, São Paulo, SP, Brazil
| | - Moises Cohen
- Departamento de Ortopedia e Traumatologia, Universidade Federal de São Paulo, 04038-032, São Paulo, SP, Brazil
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175
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Yang J, Yang Q, Yu S, Zhang X. Evaluation and validation of suitable reference genes for reverse transcription-quantitative polymerase chain reaction studies in cholangiocarcinoma patients and cell lines. Oncol Lett 2016; 11:2673-2681. [PMID: 27073537 DOI: 10.3892/ol.2016.4232] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Accepted: 01/29/2016] [Indexed: 01/12/2023] Open
Abstract
Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) has become a frequently used method in gene expression studies. The relative quantification method is an important and common method for the evaluation of RT-qPCR data. One of the key requirements of this method is to identify an applicable internal reference gene. However, to the best of our knowledge, no suitable reference genes have been identified for the genetic analysis of cholangiocarcinoma (CCA) in humans and cell lines. In the present study, screening was conducted using 12 common reference genes, which were selected in order to provide an experimental basis for the study of the gene expression in CCA patients and cell lines. Tumor samples and adjacent non-neoplastic tissues from 20 patients with CCA were obtained for the present study. The stability and applicability of the 12 reference gene candidates were validated using GeNorm, NormFinder and BestKeeper software. Based on a comparison of the results, the following reference genes are recommended for various tissue groups: Total sample group, ribosomal protein L29; CCA tissue group, TATA-box binding protein; CCA cell line and tissue group, actin-β; CCA cell line group, 18S ribosomal RNA; CCA tissue and adjacent non-neoplastic tissue group, 5'-aminolevulinate synthase 1; and adjacent non-neoplastic tissue group, hypoxanthine phosphoribosyltransferase 1. The results of the search also clearly reveal that a systematic study regarding the selection of suitable reference genes for studying the target gene profiling in CCA tissues and cell lines has not been previously published. The present study may provide useful information for future studies that examine the gene expression of CCA for choosing suitable reference genes.
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Affiliation(s)
- Jinghui Yang
- Department of Hepatopancreatobiliary Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Qiwei Yang
- Central Laboratory, Second Hospital of Jilin University, Changchun, Jilin 130041, P.R. China
| | - Shan Yu
- Department of Neurology, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Xuewen Zhang
- Department of Hepatopancreatobiliary Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
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176
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ANDERGASSEN ULRICH, KÖLBL ALEXANDRAC, MAHNER SVEN, JESCHKE UDO. Real-time RT-PCR systems for CTC detection from blood samples of breast cancer and gynaecological tumour patients (Review). Oncol Rep 2016; 35:1905-15. [DOI: 10.3892/or.2016.4608] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 11/15/2015] [Indexed: 11/06/2022] Open
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177
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Abstract
Tissue engineering focuses on three primary components: stem cells, biomaterials, and growth factors. Together, the combination of these components is used to regrow and repair damaged tissues that normally do not regenerate easily on their own. Much attention has been focused on the use of embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), due to their broad differentiation potential. However, ESCs and iPSCs require very detailed protocols to differentiate into target tissues, which are not always successful. Furthermore, procurement of ESCs is considered ethically controversial in some regions and procurement of iPSCs requires laborious transformation of adult tissues and characterization. However, mesenchymal stem cells are an adult stem cell population that are not ethically controversial and are readily available for procurement. Furthermore, mesenchymal stem cells exhibit the ability to differentiate into a variety of cell types arising from the mesoderm. In particular, human Wharton's jelly cells (hWJCs) are mesenchymal-type stem cells found in umbilical cords that possess remarkable differentiation potential. hWJCs are a highly desirable stem cell population due to their abundance in supply, high proliferation rates, and ability to differentiate into multiple cell types arising from all three germ layers. hWJCs are used to generate several neurological phenotypes arising from the ectoderm and are considered for engineering mechanosensory hair cells found in the auditory complex. Here, we report the methods for isolating hWJCs from human umbilical cords and non-virally transfected for use in cochlear tissue engineering studies.
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178
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Ma YJ, Sun XH, Xu XY, Zhao Y, Pan YJ, Hwang CA, Wu VCH. Investigation of Reference Genes in Vibrio parahaemolyticus for Gene Expression Analysis Using Quantitative RT-PCR. PLoS One 2015; 10:e0144362. [PMID: 26659406 PMCID: PMC4676679 DOI: 10.1371/journal.pone.0144362] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Accepted: 11/17/2015] [Indexed: 01/14/2023] Open
Abstract
Vibrio parahaemolyticus is a significant human pathogen capable of causing foodborne gastroenteritis associated with the consumption of contaminated raw or undercooked seafood. Quantitative RT-PCR (qRT-PCR) is a useful tool for studying gene expression in V. parahaemolyticus to characterize its virulence factors and understand the effect of environmental conditions on its pathogenicity. However, there is not a stable gene in V. parahaemolyticus that has been identified for use as a reference gene for qRT-PCR. This study evaluated the stability of 6 reference genes (16S rRNA, recA, rpoS, pvsA, pvuA, and gapdh) in 5 V. parahaemolyticus strains (O3:K6-clinical strain-tdh+, ATCC33846-tdh+, ATCC33847-tdh+, ATCC17802-trh+, and F13-environmental strain-tdh+) cultured at 4 different temperatures (15, 25, 37 and 42°C). Stability values were calculated using GeNorm, NormFinder, BestKeeper, and Delta CT algorithms. The results indicated that recA was the most stably expressed gene in the V. parahaemolyticus strains cultured at different temperatures. This study examined multiple V. parahaemolyticus strains and growth temperatures, hence the finding provided stronger evidence that recA can be used as a reference gene for gene expression studies in V. parahaemolyticus.
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Affiliation(s)
- Yue-jiao Ma
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, People's Republic of China
- Shanghai Engineering Research Center of Aquatic Product Processing & Preservation, Shanghai 201306, China
| | - Xiao-hong Sun
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, People's Republic of China
- Shanghai Engineering Research Center of Aquatic Product Processing & Preservation, Shanghai 201306, China
- * E-mail: (VCHW); (XS)
| | - Xiao-yan Xu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, People's Republic of China
| | - Yong Zhao
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, People's Republic of China
- Shanghai Engineering Research Center of Aquatic Product Processing & Preservation, Shanghai 201306, China
| | - Ying-jie Pan
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, People's Republic of China
- Shanghai Engineering Research Center of Aquatic Product Processing & Preservation, Shanghai 201306, China
| | - Cheng-An Hwang
- Residue Chemistry and Predictive Microbiology Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, 19038, United States of America
| | - Vivian C. H. Wu
- The Pathogenic Microbiology Laboratory, School of Food and Agriculture, University of Maine, Orono, ME, 04469–5735, United States of America
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Albany, CA, 94710, United States of America
- * E-mail: (VCHW); (XS)
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179
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Use of Quantitative Real Time Polymerase Chain Reaction to Assess Gene Transcripts Associated With Antibody-Mediated Rejection of Kidney Transplants. Transplantation 2015; 99:1981-8. [PMID: 25675206 DOI: 10.1097/tp.0000000000000621] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
INTRODUCTION Microarray studies have shown elevated transcript levels of endothelial and natural killer (NK) cell-associated genes during antibody-mediated rejection (AMR) of the renal allograft. This study aimed to assess the use of quantitative real-time polymerase chain reaction as an alternative to microarray analysis on a subset of these elevated genes. METHODS Thirty-nine renal transplant biopsies from patients with de novo donor-specific antibodies and eighteen 1-year surveillance biopsies with no histological evidence of rejection were analyzed for expression of 11 genes previously identified as elevated in AMR. RESULTS Expression levels of natural killer markers were correlated to microcirculation inflammation and graft outcomes to a greater extent than endothelial markers. Creating a predictive model reduced the number of gene transcripts to be assessed to 2, SH2D1b and MYBL1, resulting in 66.7% sensitivity and 89.7% specificity for graft loss. DISCUSSION This work demonstrates that elevated gene expression levels, proposed to be associated with AMR, can be detected by established quantitative real-time polymerase chain reaction technology, making transition to the clinical setting feasible. Transcript analysis provides additional diagnostic information to the classification schema for AMR diagnosis but it remains to be determined whether significant numbers of centres will validate transcript analysis in their laboratories and put such analysis into clinical use.
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180
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Kabir MS, Clements MO, Atkins M, Kimmitt PT. Application of RT-Bst to enhance detection of pathogenic viruses of the respiratory tract. Br J Biomed Sci 2015; 72:128-34. [PMID: 26510269 DOI: 10.1080/09674845.2015.11666809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Inefficiency of RT-PCR can be associated with the suboptimal process of reverse transcription as only 40-80% of RNA is converted to cDNA. We employed a novel method, RT-Bst, to enrich the concentration of cDNA for subsequent multiplex PCR detection of selected RNA viruses. The RT-Bst method amplifies cDNA through reverse transcription of viral RNA using reverse transcriptase and amplification of cDNA using Bst DNA polymerase. Viral RNA was extracted from 25 nasopharyngeal samples for detection of influenza A, B and C; parainfluenza 1-4; human coronaviruses 229E and OC43; respiratory syncytial virus (RSV) and rhinovirus. Both multiplex one-step RT-PCR and RT-Bst PCR were used to compare their performances for detection of virus sequences. These findings were compared with routine laboratory detection. When using RT-Bst PCR, 28% of samples yielded a viral pathogen compared to 20% with RT-PCR and 12% using routine diagnostic tests. RT-Bst PCR was shown to have particular utility in the detection of RSV RNA as this was present in 20% of the samples studied compared to 8% when using RT-PCR. For one patient, RT-Bst PCR was able to detect RSV five days earlier than conventional hospital diagnostic testing. RT-Bst and RT-Bst PCR can be used as alternative approaches to reverse transcription and one-step RT-PCR, respectively, for sequence-independent amplification of RNA virus sequences and a larger scale analysis of this new diagnostic approach is warranted.
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181
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Xue-tao X, Kai-yi L, Jia-ying Z. Portable and sensitive quantitative detection of DNA using personal glucose meters and exonuclease III-assisted signal amplification. Analyst 2015; 139:4982-6. [PMID: 25105176 DOI: 10.1039/c4an00905c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A portable and sensitive quantitative DNA detection method using personal glucose meters (PGMs) and Exonuclease III-assisted signal amplification was developed. In the presence of target DNA, a target recycling process that can release target and linker DNA was obtained. The released linker DNA was used to link capture DNA on magnetic beads and the DNA invertase. After the washing away of unbound target DNA and subsequent DNA-invertase conjugation, the bound DNA-invertase can be used to catalyze the hydrolysis of sucrose into glucose with millions of turnovers, which transforms the concentration of target DNA into the level of glucose monitored by PGMs. There was a linear relationship between the signal of PGM and the concentration of target DNA in the range of 0.5 pM to 100 pM. A correlation coefficient of 0.989 was obtained, and the relative standard deviation (RSD) was 4.1% for a concentration of 50 pM target DNA (n = 9). In addition, the method exhibits excellent sequence selectivity, being able to differentiate a single mismatch in the target DNA. What is more, there was almost no effect from biological complexes on detection performance, which suggests our method can be successfully applied to DNA detection in real biological samples.
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Affiliation(s)
- Xu Xue-tao
- HKUST Fok Ying Tung Graduate School, GuangZhou, GuangDong 511458, P. R. China.
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182
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Pinto PR, Rocco DDFM, Okuda LS, Machado-Lima A, Castilho G, da Silva KS, Gomes DJ, Pinto RDS, Iborra RT, Ferreira GDS, Nakandakare ER, Machado UF, Correa-Giannella MLC, Catanozi S, Passarelli M. Aerobic exercise training enhances the in vivo cholesterol trafficking from macrophages to the liver independently of changes in the expression of genes involved in lipid flux in macrophages and aorta. Lipids Health Dis 2015; 14:109. [PMID: 26377330 PMCID: PMC4572640 DOI: 10.1186/s12944-015-0093-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 08/12/2015] [Indexed: 12/26/2022] Open
Abstract
Background Regular exercise prevents and regresses atherosclerosis by improving lipid metabolism and antioxidant defenses. Exercise ameliorates the reverse cholesterol transport (RCT), an antiatherogenic system that drives cholesterol from arterial macrophages to the liver for excretion into bile and feces. In this study we analyzed the role of aerobic exercise on the in vivo RCT and expression of genes and proteins involved in lipid flux and inflammation in peritoneal macrophages, aortic arch and liver from wild type mice. Methods Twelve-week-old male mice were divided into sedentary and trained groups. Exercise training was performed in a treadmill (15 m/min, 30 min/day, 5 days/week). Plasma lipids were determined by enzymatic methods and lipoprotein profile by fast protein liquid chromatography. After intraperitoneal injection of J774-macrophages the RCT was assessed by measuring the recovery of 3H-cholesterol in plasma, feces and liver. The expression of liver receptors was determined by immunoblot, macrophages and aortic mRNAs by qRT-PCR. 14C-cholesterol efflux mediated by apo A-I and HDL2 and the uptake of 3H-cholesteryl oleoyl ether (3H-COE)-acetylated-LDL were determined in macrophages isolated from sedentary and trained animals 48 h after the last exercise session. Results Body weight, plasma lipids, lipoprotein profile, glucose and blood pressure were not modified by exercise training. A greater amount of 3H-cholesterol was recovered in plasma (24 h and 48 h) and liver (48 h) from trained animals in comparison to sedentary. No difference was found in 3H-cholesterol excreted in feces between trained and sedentary mice. The hepatic expression of scavenger receptor class B type I (SR-BI) and LDL receptor (B-E) was enhanced by exercise. We observed 2.8 and 1.7 fold rise, respectively, in LXR and Cyp7a mRNA in the liver of trained as compared to sedentary mice. Macrophage and aortic expression of genes involved in lipid efflux was not systematically changed by physical exercise. In agreement, 14C-cholestrol efflux and uptake of 3H-COE-acetylated-LDL by macrophages was similar between sedentary and trained animals. Conclusion Aerobic exercise in vivo accelerates the traffic of cholesterol from macrophages to the liver contributing to prevention and regression of atherosclerosis, independently of changes in macrophage and aorta gene expression.
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Affiliation(s)
- Paula Ramos Pinto
- Lipids Laboratory (LIM - 10), University of São Paulo Medical School, Av. Dr. Arnaldo 455, room 3305, Sao Paulo, SP, CEP 01246000, Brazil.
| | - Débora Dias Ferraretto Moura Rocco
- Lipids Laboratory (LIM - 10), University of São Paulo Medical School, Av. Dr. Arnaldo 455, room 3305, Sao Paulo, SP, CEP 01246000, Brazil.
| | - Ligia Shimabukuro Okuda
- Lipids Laboratory (LIM - 10), University of São Paulo Medical School, Av. Dr. Arnaldo 455, room 3305, Sao Paulo, SP, CEP 01246000, Brazil.
| | - Adriana Machado-Lima
- Lipids Laboratory (LIM - 10), University of São Paulo Medical School, Av. Dr. Arnaldo 455, room 3305, Sao Paulo, SP, CEP 01246000, Brazil.
| | - Gabriela Castilho
- Lipids Laboratory (LIM - 10), University of São Paulo Medical School, Av. Dr. Arnaldo 455, room 3305, Sao Paulo, SP, CEP 01246000, Brazil.
| | - Karolline Santana da Silva
- Lipids Laboratory (LIM - 10), University of São Paulo Medical School, Av. Dr. Arnaldo 455, room 3305, Sao Paulo, SP, CEP 01246000, Brazil.
| | - Diego Juvenal Gomes
- Lipids Laboratory (LIM - 10), University of São Paulo Medical School, Av. Dr. Arnaldo 455, room 3305, Sao Paulo, SP, CEP 01246000, Brazil.
| | - Raphael de Souza Pinto
- Lipids Laboratory (LIM - 10), University of São Paulo Medical School, Av. Dr. Arnaldo 455, room 3305, Sao Paulo, SP, CEP 01246000, Brazil.
| | - Rodrigo Tallada Iborra
- Lipids Laboratory (LIM - 10), University of São Paulo Medical School, Av. Dr. Arnaldo 455, room 3305, Sao Paulo, SP, CEP 01246000, Brazil.
| | - Guilherme da Silva Ferreira
- Lipids Laboratory (LIM - 10), University of São Paulo Medical School, Av. Dr. Arnaldo 455, room 3305, Sao Paulo, SP, CEP 01246000, Brazil.
| | - Edna Regina Nakandakare
- Lipids Laboratory (LIM - 10), University of São Paulo Medical School, Av. Dr. Arnaldo 455, room 3305, Sao Paulo, SP, CEP 01246000, Brazil.
| | - Ubiratan Fabres Machado
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of Sao Paulo, São Paulo, Brazil.
| | | | - Sergio Catanozi
- Lipids Laboratory (LIM - 10), University of São Paulo Medical School, Av. Dr. Arnaldo 455, room 3305, Sao Paulo, SP, CEP 01246000, Brazil.
| | - Marisa Passarelli
- Lipids Laboratory (LIM - 10), University of São Paulo Medical School, Av. Dr. Arnaldo 455, room 3305, Sao Paulo, SP, CEP 01246000, Brazil.
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Validation of candidate reference genes for qRT-PCR studies in symbiotic and non-symbiotic Casuarina glauca Sieb. ex Spreng. under salinity conditions. Symbiosis 2015. [DOI: 10.1007/s13199-015-0330-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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184
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Wang P, Jing F, Li G, Wu Z, Cheng Z, Zhang J, Zhang H, Jia C, Jin Q, Mao H, Zhao J. Absolute quantification of lung cancer related microRNA by droplet digital PCR. Biosens Bioelectron 2015; 74:836-42. [PMID: 26232679 DOI: 10.1016/j.bios.2015.07.048] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 07/20/2015] [Accepted: 07/21/2015] [Indexed: 11/16/2022]
Abstract
Digital polymerase chain reaction (digital PCR) enables the absolute quantification of nucleic acids through the counting of single molecules, thus eliminating the need for standard curves or endogenous controls. In this study, we developed a droplet digital PCR (ddPCR) system based on an oil saturated PDMS (OSP) microfluidic chip platform for quantification of lung cancer related microRNA (miRNA). The OSP chip was made with PDMS and was oil saturated to constrain oil swallow and maintain the stability of droplets. Two inlets were designed for oil and sample injection with a syringe pump at the outlet. Highly uniform monodisperse water-in-oil emulsion droplets to be used for subsequent detection and analysis were generated at the cross section of the channel. We compared miRNA quantification by the ddPCR system and quantitative real-time PCR (qPCR) to demonstrate that the ddPCR system was superior to qPCR both in its detection limit and smaller fold changes measurement. This droplet PCR system provides new possibilities for highly sensitive and efficient detection of cancer-related genes.
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Affiliation(s)
- Ping Wang
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Science, Shanghai 200050, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Fengxiang Jing
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Science, Shanghai 200050, China
| | - Gang Li
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Science, Shanghai 200050, China; School of Optoelectronic Engineering, Chongqing University, Chongqing 400044, China
| | - Zhenhua Wu
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Science, Shanghai 200050, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Zule Cheng
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Science, Shanghai 200050, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jishen Zhang
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Science, Shanghai 200050, China
| | - Honglian Zhang
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Science, Shanghai 200050, China
| | - Chunping Jia
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Science, Shanghai 200050, China
| | - Qinghui Jin
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Science, Shanghai 200050, China
| | - Hongju Mao
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Science, Shanghai 200050, China.
| | - Jianlong Zhao
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Science, Shanghai 200050, China.
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185
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Puddu M, Stark WJ, Grass RN. Silica Microcapsules for Long-Term, Robust, and Reliable Room Temperature RNA Preservation. Adv Healthc Mater 2015; 4:1332-8. [PMID: 25899883 DOI: 10.1002/adhm.201500132] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 03/27/2015] [Indexed: 11/08/2022]
Abstract
As a consequence of the latest revolutionary discoveries on its functions, RNA is certainly the hottest topic at the moment, being an exceptional tool in biology as well as in medicine. For the various applications, a proper RNA storage is required to prevent the degradation of this extremely unstable molecule. Here a novel freezing-free RNA storage strategy is presented, based on its encapsulation in silica spheres. The silica microcapsules protect the RNA by providing a water-free environment. In this way RNA can be safely stored for prolonged periods of time at ambient and elevated temperatures, maintaining its original integrity, as proved by gel-electrophoresis, capillary electrophoresis, and real-time reverse transcription-polymerase chain reaction (RT-qPCR). The RNA degradation rate at 65 °C in silica microcapsules is approximately ten times smaller in comparison to dry RNA samples or to samples stored in RNAstable matrix, a commercially available product. Moreover, RNA half-life at 65 °C is nearly identical to that of DNA within the silica microcapsules. Samples intended for use in gene expression are compatible with further analysis (RT-qPCR, Sanger sequencing). The novel storage technology permits to safely handle, store, and transport RNA samples, avoiding the expensive shipments and the problems of space presented by freezing-based strategies.
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Affiliation(s)
- Michela Puddu
- ETH Zurich, Institute for Chemical and Bioengineering; Department of Chemistry and Applied Biosciences; Vladimir-Prelog-Weg 1-5/10 8093 Zürich Switzerland
| | - Wendelin J. Stark
- ETH Zurich, Institute for Chemical and Bioengineering; Department of Chemistry and Applied Biosciences; Vladimir-Prelog-Weg 1-5/10 8093 Zürich Switzerland
| | - Robert N. Grass
- ETH Zurich, Institute for Chemical and Bioengineering; Department of Chemistry and Applied Biosciences; Vladimir-Prelog-Weg 1-5/10 8093 Zürich Switzerland
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186
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Boychuk CR, Gyarmati P, Xu H, Smith BN. Glucose sensing by GABAergic neurons in the mouse nucleus tractus solitarii. J Neurophysiol 2015; 114:999-1007. [PMID: 26084907 DOI: 10.1152/jn.00310.2015] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 06/15/2015] [Indexed: 12/23/2022] Open
Abstract
Changes in blood glucose concentration alter autonomic function in a manner consistent with altered neural activity in brain regions controlling digestive processes, including neurons in the brain stem nucleus tractus solitarii (NTS), which process viscerosensory information. With whole cell or on-cell patch-clamp recordings, responses to elevating glucose concentration from 2.5 to 15 mM were assessed in identified GABAergic NTS neurons in slices from transgenic mice that express EGFP in a subset of GABA neurons. Single-cell real-time RT-PCR was also performed to detect glutamic acid decarboxylase (GAD67) in recorded neurons. In most identified GABA neurons (73%), elevating glucose concentration from 2.5 to 15 mM resulted in either increased (40%) or decreased (33%) neuronal excitability, reflected by altered membrane potential and/or action potential firing. Effects on membrane potential were maintained when action potentials or fast synaptic inputs were blocked, suggesting direct glucose sensing by GABA neurons. Glucose-inhibited GABA neurons were found predominantly in the lateral NTS, whereas glucose-excited cells were mainly in the medial NTS, suggesting regional segregation of responses. Responses were prevented in the presence of glucosamine, a glucokinase (GCK) inhibitor. Depolarizing responses were prevented when KATP channel activity was blocked with tolbutamide. Whereas effects on synaptic input to identified GABAergic neurons were variable in GABA neurons, elevating glucose increased glutamate release subsequent to stimulation of tractus solitarius in unlabeled, unidentified neurons. These results indicate that GABAergic NTS neurons act as GCK-dependent glucose sensors in the vagal complex, providing a means of modulating central autonomic signals when glucose is elevated.
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Affiliation(s)
- Carie R Boychuk
- Department of Physiology, University of Kentucky College of Medicine, Lexington, Kentucky
| | - Peter Gyarmati
- Department of Physiology, University of Kentucky College of Medicine, Lexington, Kentucky
| | - Hong Xu
- Department of Physiology, University of Kentucky College of Medicine, Lexington, Kentucky
| | - Bret N Smith
- Department of Physiology, University of Kentucky College of Medicine, Lexington, Kentucky
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187
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Ganime A, Leite J, de Abreu Corrêa A, Melgaço F, Carvalho-Costa F, Miagostovich M. Evaluation of the swab sampling method to recover viruses from fomites. J Virol Methods 2015; 217:24-7. [DOI: 10.1016/j.jviromet.2015.02.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 12/15/2014] [Accepted: 02/11/2015] [Indexed: 11/27/2022]
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188
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Aydemir N, McArdle H, Patel S, Whitford W, Evans CW, Travas-Sejdic J, Williams DE. A Label-Free, Sensitive, Real-Time, Semiquantitative Electrochemical Measurement Method for DNA Polymerase Amplification (ePCR). Anal Chem 2015; 87:5189-97. [PMID: 25946200 DOI: 10.1021/acs.analchem.5b00079] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Oligonucleotide hybridization to a complementary sequence that is covalently attached to an electrochemically active conducting polymer (ECP) coating the working electrode of an electrochemical cell causes an increase in reaction impedance for the ferro-ferricyanide redox couple. We demonstrate the use of this effect to measure, in real time, the progress of DNA polymerase chain reaction (PCR) amplification of a minor component of a DNA extract. The forward primer is attached to the ECP. The solution contains other PCR components and the redox couple. Each cycle of amplification gives an easily measurable impedance increase. Target concentration can be estimated by cycle count to reach a threshold impedance. As proof of principle, we demonstrate an electrochemical real-time quantitative PCR (e-PCR) measurement in the total DNA extracted from chicken blood of an 844 base pair region of the mitochondrial Cytochrome c oxidase gene, present at ∼1 ppm of total DNA. We show that the detection and semiquantitation of as few as 2 copies/μL of target can be achieved within less than 10 PCR cycles.
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Affiliation(s)
| | | | - Selina Patel
- ∇School of Biological Sciences, University of Auckland, Auckland 1022, New Zealand
| | - Whitney Whitford
- ∇School of Biological Sciences, University of Auckland, Auckland 1022, New Zealand
| | - Clive W Evans
- ∇School of Biological Sciences, University of Auckland, Auckland 1022, New Zealand
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Generation and Characterization of a Transgenic Mouse Carrying a Functional Human β -Globin Gene with the IVSI-6 Thalassemia Mutation. BIOMED RESEARCH INTERNATIONAL 2015; 2015:687635. [PMID: 26097845 PMCID: PMC4434229 DOI: 10.1155/2015/687635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 12/03/2014] [Accepted: 12/03/2014] [Indexed: 11/17/2022]
Abstract
Mouse models that carry mutations causing thalassemia represent a suitable tool to test in vivo new mutation-specific therapeutic approaches. Transgenic mice carrying the β-globin IVSI-6 mutation (the most frequent in Middle-Eastern regions and recurrent in Italy and Greece) are, at present, not available. We report the production and characterization of a transgenic mouse line (TG-β-IVSI-6) carrying the IVSI-6 thalassemia point mutation within the human β-globin gene. In the TG-β-IVSI-6 mouse (a) the transgenic integration region is located in mouse chromosome 7; (b) the expression of the transgene is tissue specific; (c) as expected, normally spliced human β-globin mRNA is produced, giving rise to β-globin production and formation of a human-mouse tetrameric chimeric hemoglobin muα-globin2/huβ-globin2 and, more importantly, (d) the aberrant β-globin-IVSI-6 RNAs are present in blood cells. The TG-β-IVSI-6 mouse reproduces the molecular features of IVSI-6 β-thalassemia and might be used as an in vivo model to characterize the effects of antisense oligodeoxynucleotides targeting the cryptic sites responsible for the generation of aberrantly spliced β-globin RNA sequences, caused by the IVSI-6 mutation. These experiments are expected to be crucial for the development of a personalized therapy for β-thalassemia.
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190
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Machado-Lima A, Iborra RT, Pinto RS, Castilho G, Sartori CH, Oliveira ER, Okuda LS, Nakandakare ER, Giannella-Neto D, Machado UF, Corrêa-Giannella MLC, Traldi P, Porcu S, Roverso M, Lapolla A, Passarelli M. In Type 2 Diabetes Mellitus Glycated Albumin Alters Macrophage Gene Expression Impairing ABCA1-Mediated Cholesterol Efflux. J Cell Physiol 2015; 230:1250-7. [DOI: 10.1002/jcp.24860] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 10/30/2014] [Indexed: 01/16/2023]
Affiliation(s)
- Adriana Machado-Lima
- Lipids Laboratory (LIM 10); Faculty of Medical Sciences; University of Sao Paulo; Sao Paulo Brazil
| | - Rodrigo T. Iborra
- Lipids Laboratory (LIM 10); Faculty of Medical Sciences; University of Sao Paulo; Sao Paulo Brazil
| | - Raphael S. Pinto
- Lipids Laboratory (LIM 10); Faculty of Medical Sciences; University of Sao Paulo; Sao Paulo Brazil
| | - Gabriela Castilho
- Lipids Laboratory (LIM 10); Faculty of Medical Sciences; University of Sao Paulo; Sao Paulo Brazil
| | - Camila H. Sartori
- Lipids Laboratory (LIM 10); Faculty of Medical Sciences; University of Sao Paulo; Sao Paulo Brazil
| | - Erika R. Oliveira
- Cellular and Molecular Endocrinology Laboratory (LIM 25); Faculty of Medical Sciences; University of Sao Paulo; Sao Paulo Brazil
| | - Ligia S. Okuda
- Lipids Laboratory (LIM 10); Faculty of Medical Sciences; University of Sao Paulo; Sao Paulo Brazil
| | - Edna R. Nakandakare
- Lipids Laboratory (LIM 10); Faculty of Medical Sciences; University of Sao Paulo; Sao Paulo Brazil
| | | | - Ubiratan F. Machado
- Department of Physiology and Biophysics; Institute of Biomedical Sciences; University of São Paulo; Sao Paulo Brazil
| | - Maria Lucia C. Corrêa-Giannella
- Cellular and Molecular Endocrinology Laboratory (LIM 25); Faculty of Medical Sciences; University of Sao Paulo; Sao Paulo Brazil
| | | | - Simona Porcu
- Department of Medicine; University of Padova; Padova Italy
| | - Marco Roverso
- Department of Medicine; University of Padova; Padova Italy
| | | | - Marisa Passarelli
- Lipids Laboratory (LIM 10); Faculty of Medical Sciences; University of Sao Paulo; Sao Paulo Brazil
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191
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Trindade F, Ferreira R, Amado F, Vitorino R. Biofluid proteases profiling in diabetes mellitus. Adv Clin Chem 2015; 69:161-207. [PMID: 25934362 DOI: 10.1016/bs.acc.2014.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The investigation of protease relevance in biologic systems beyond catabolism of proteins and peptides to amino acids has stimulated interest as to their role in the pathogenesis of several disorders including diabetes mellitus (DM). Evaluation of proteases and the assessment of their activity in biofluids are fundamental to elucidate these proteolytic systems in DM and its related complications. In contrast to traditional immunoassay or substrate based approaches that targeted specific proteases and their inhibitors, the field of degradomics has provided a comprehensive approach to study these enzymes. Although the degradome contains over 500 proteases, very few have been associated with DM and its micro- and macrovascular complications. In this paper, we review these proteases and their respective inhibitors with emphasis on DM. It is likely that future research will expand these initial studies and look to develop high throughput automated technologies to identify and characterize biofluid proteases of diagnostic and prognostic value in other pathologies.
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Affiliation(s)
- Fábio Trindade
- QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Rita Ferreira
- QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Francisco Amado
- QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, Aveiro, Portugal; School of Health Sciences, University of Aveiro, Aveiro, Portugal
| | - Rui Vitorino
- QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, Aveiro, Portugal; Institute for Research in Biomedicine, iBiMED, Health Sciences Program, University of Aveiro, Aveiro, Portugal.
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192
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Balasuriya UBR. RNA extraction from equine samples for equine influenza virus. Methods Mol Biol 2015; 1161:379-92. [PMID: 24899447 DOI: 10.1007/978-1-4939-0758-8_33] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The primary goals of this chapter are to discuss common viral RNA isolation and purification methods that are routinely used by various diagnostic laboratories, to highlight the advantages and drawbacks of each method, and to identify the most suitable and reliable method to increase the sensitivity and specificity of RT-PCR assays for the detection of equine influenza virus (EIV) in clinical specimens. Our experiences and review of literature show that magnetic bead-based nucleic extraction methods (manual and automatic) work well for isolation and purification of EIV RNA from nasal swab specimens. Furthermore, most of the information presented in this chapter could be directly applicable to isolation and purification of nucleic acids (both DNA and RNA) from other equine clinical samples.
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Affiliation(s)
- Udeni B R Balasuriya
- Department of Veterinary Science, University of Kentucky, 108 Maxwell H. Gluck Equine Research Center, Lexington, KY, 40546-0099, USA,
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193
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Zhao G, Yao Y, Hao G, Fang D, Yin B, Cao X, Chen W. Gene regulation in Aspergillus oryzae promotes hyphal growth and flavor formation in soy sauce koji. RSC Adv 2015. [DOI: 10.1039/c4ra16819d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Aspergillus oryzae100-8 and the parental strainA. oryzae3.042 are used in soy sauce fermentation in China.
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Affiliation(s)
- Guozhong Zhao
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- China
| | - Yunping Yao
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- China
| | - Guangfei Hao
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- China
| | - Dongsheng Fang
- Yangzhou University Healthy Source Dairy Co. Ltd
- Yangzhou 225004
- P. R. China
| | - Boxing Yin
- Yangzhou University Healthy Source Dairy Co. Ltd
- Yangzhou 225004
- P. R. China
| | - Xiaohong Cao
- Key Laboratory of Food Nutrition and Safety (Tianjin University of Science & Technology)
- Ministry of Education
- Tianjin 300457
- China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- China
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194
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Johnson G, Ferrini A, Dolan SK, Nolan T, Agrawal S, Doyle S, Bustin SA. Biomarkers for invasive aspergillosis: the challenges continue. Biomark Med 2014; 8:429-51. [PMID: 24712434 DOI: 10.2217/bmm.13.129] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The incidence of invasive aspergillosis (IA), an opportunistic infection in immunocompromised individuals, is rising, but its early diagnosis remains challenging and treatment options are limited. Hence there is an urgent need to improve existing diagnostic procedures as well as develop novel approaches. The clinical usefulness of galactomannan and β-d-glucan, widely used assays detecting cell-wall antigens of Aspergillus, is unclear and depends on clinicians' awareness of their practical limitations. This leaves room for new methods that utilise genomic, proteomic and metabolomics approaches as well as novel detection procedures, for example point-of-care lateral-flow devices. Each of these strategies has its own limitations and it is likely that a combination of methods will be required to achieve optimal performance for the diagnosis of IA and subsequent appropriate patient management.
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Affiliation(s)
- Gemma Johnson
- Blizard Institute, Queen Mary University of London, London, UK
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195
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Maloney S, Francis F, Bletchly C, Norton R. Evaluation of a commercially available synthetic RNA lipid enveloped control molecule. J Virol Methods 2014; 211:19-21. [PMID: 25447757 DOI: 10.1016/j.jviromet.2014.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 09/05/2014] [Accepted: 10/03/2014] [Indexed: 11/26/2022]
Abstract
Detection of viral ribonucleic acid with RT PCR is a useful tool for viral detection. One of the drawbacks of this technique is the difficulty in including an internal control molecule to ensure the validity of the extraction and amplification process. In this study the potential usefulness of a novel lipid enveloped commercially available RNA control molecule is investigated. Initial optimisation of the detection assay was performed by amplification of IC (internal control) spiked into PCR water. Thirty-two clinical respiratory samples were spiked with the IC before and after extraction and RT PCR was then performed. Inefficient extraction was simulated. Inhibition of the RT PCR was achieved by serial dilution of heparin sulfate into samples post extraction. No Targets that matched the IC (Internal Control) primers were identified in 32 extracted sputum samples as determined by the absence of non specific amplification curves. The unextracted IC had an increased CT (cycle threshold) value compared to IC that had been extracted. Inefficient extraction was detected by an increased CT. Increasing concentrations of heparin inhibited the PCR in a predictable fashion. The Bioline IC molecule provides a stable RNA IC that has acceptable performance characteristics.
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Affiliation(s)
- Samuel Maloney
- The Townsville Hospital, Townsville, Queensland, Australia; Microbiology, Pathology Queensland, Townsville, Queensland 4814, Australia.
| | - Fleur Francis
- Microbiology, Pathology Queensland, Townsville, Queensland 4814, Australia
| | - Cheryl Bletchly
- Molecular Diagnostic Unit, Pathology Queensland, Brisbane, Queensland 4006, Australia
| | - Robert Norton
- The Townsville Hospital, Townsville, Queensland, Australia; Microbiology, Pathology Queensland, Townsville, Queensland 4814, Australia.
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196
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Sun L, Fan Z, Weng X, Ye X, Long J, Fu K, Yan S, Wang B, Zhuo Y, Liu X, Lao K. Rapid detection of Down's syndrome using quantitative real-time PCR (qPCR) targeting segmental duplications on chromosomes 21 and 11. Gene 2014; 552:272-6. [PMID: 25256276 DOI: 10.1016/j.gene.2014.09.044] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 09/09/2014] [Accepted: 09/19/2014] [Indexed: 11/24/2022]
Abstract
OBJECTIVE Development of a qPCR test for the detection of trisomy 21 using segmental duplications. METHODS Segmental duplications in the TTC3 gene on chromosome 21 and the KDM2A gene on chromosome 11 were selected as molecular markers for the diagnostic qPCR assay. A set of consensus primers selected from the conserved regions of these segmental duplications were used to amplify internal diverse sequences that were detected and quantified with different probes labeled with distinct fluorescence. The copy numbers of these two fragments were determined based on the ΔCq values of qPCR. The results of qPCR for prenatal and neonatal screening of Down's syndrome were compared with the conventional karyotype analysis by testing 82 normal individuals and 50 subjects with Down's syndrome. RESULTS The ΔCq values of segmental duplications on chr21 and 11 ranged between 0.33 and 0.75 in normal individuals, and between 0.91 and 1.18 in subjects with Down's syndrome. The ΔCq values of these two segmental duplications clearly discriminated Down's syndrome from normal individuals (P<0.001). Furthermore, the qPCR results were consistent with karyotype analysis. CONCLUSION Our qPCR can be used for rapid prenatal and neonatal screening of Down's syndrome.
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Affiliation(s)
- Lei Sun
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Hospital, Guangxi, China.
| | - Zuqian Fan
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Hospital, Guangxi, China
| | - Xunjin Weng
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Hospital, Guangxi, China
| | - Xuehe Ye
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Hospital, Guangxi, China
| | - Ju Long
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Hospital, Guangxi, China
| | - Kepeng Fu
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Hospital, Guangxi, China
| | - Shanhuo Yan
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Hospital, Guangxi, China
| | - Bo Wang
- Genetics Laboratory, Hubei Maternal and Child Health Hospital, Hubei, China
| | - Yongguang Zhuo
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Hospital, Guangxi, China
| | - Xinxing Liu
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Hospital, Guangxi, China
| | - Kegan Lao
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Hospital, Guangxi, China
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197
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Leal MF, Belangero PS, Cohen C, Figueiredo EA, Loyola LC, Pochini AC, Smith MC, Andreoli CV, Belangero SI, Ejnisman B, Cohen M. Identification of suitable reference genes for gene expression studies of shoulder instability. PLoS One 2014; 9:e105002. [PMID: 25122470 PMCID: PMC4133370 DOI: 10.1371/journal.pone.0105002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 07/15/2014] [Indexed: 11/29/2022] Open
Abstract
Shoulder instability is a common shoulder injury, and patients present with plastic deformation of the glenohumeral capsule. Gene expression analysis may be a useful tool for increasing the general understanding of capsule deformation, and reverse-transcription quantitative polymerase chain reaction (RT-qPCR) has become an effective method for such studies. Although RT-qPCR is highly sensitive and specific, it requires the use of suitable reference genes for data normalization to guarantee meaningful and reproducible results. In the present study, we evaluated the suitability of a set of reference genes using samples from the glenohumeral capsules of individuals with and without shoulder instability. We analyzed the expression of six commonly used reference genes (ACTB, B2M, GAPDH, HPRT1, TBP and TFRC) in the antero-inferior, antero-superior and posterior portions of the glenohumeral capsules of cases and controls. The stability of the candidate reference gene expression was determined using four software packages: NormFinder, geNorm, BestKeeper and DataAssist. Overall, HPRT1 was the best single reference gene, and HPRT1 and B2M composed the best pair of reference genes from different analysis groups, including simultaneous analysis of all tissue samples. GenEx software was used to identify the optimal number of reference genes to be used for normalization and demonstrated that the accumulated standard deviation resulting from the use of 2 reference genes was similar to that resulting from the use of 3 or more reference genes. To identify the optimal combination of reference genes, we evaluated the expression of COL1A1. Although the use of different reference gene combinations yielded variable normalized quantities, the relative quantities within sample groups were similar and confirmed that no obvious differences were observed when using 2, 3 or 4 reference genes. Consequently, the use of 2 stable reference genes for normalization, especially HPRT1 and B2M, is a reliable method for evaluating gene expression by RT-qPCR.
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Affiliation(s)
- Mariana Ferreira Leal
- Departamento de Ortopedia e Traumatologia, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Ferderal de São Paulo, São Paulo, São Paulo, Brazil
- * E-mail:
| | - Paulo Santoro Belangero
- Departamento de Ortopedia e Traumatologia, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Carina Cohen
- Departamento de Ortopedia e Traumatologia, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Eduardo Antônio Figueiredo
- Departamento de Ortopedia e Traumatologia, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Leonor Casilla Loyola
- Departamento de Ortopedia e Traumatologia, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Ferderal de São Paulo, São Paulo, São Paulo, Brazil
| | - Alberto Castro Pochini
- Departamento de Ortopedia e Traumatologia, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Marília Cardoso Smith
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Ferderal de São Paulo, São Paulo, São Paulo, Brazil
| | - Carlos Vicente Andreoli
- Departamento de Ortopedia e Traumatologia, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Sintia Iole Belangero
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Ferderal de São Paulo, São Paulo, São Paulo, Brazil
- Laboratório Interdisciplinar de Neurociência Clínica, Departamento de Psiquiatria, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Benno Ejnisman
- Departamento de Ortopedia e Traumatologia, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Moises Cohen
- Departamento de Ortopedia e Traumatologia, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
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198
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López-Landavery EA, Portillo-López A, Gallardo-Escárate C, Del Río-Portilla MA. Selection of reference genes as internal controls for gene expression in tissues of red abalone Haliotis rufescens (Mollusca, Vetigastropoda; Swainson, 1822). Gene 2014; 549:258-65. [PMID: 25101866 DOI: 10.1016/j.gene.2014.08.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 07/04/2014] [Accepted: 08/01/2014] [Indexed: 01/05/2023]
Abstract
The red abalone Haliotis rufescens is one of the most important species for aquaculture in Baja California, México, and despite this, few gene expression studies have been done in tissues such as gill, head and gonad. For this purpose, reverse transcription and quantitative real time PCR (RT-qPCR) is a powerful tool for gene expression evaluation. For a reliable analysis, however, it is necessary to select and validate housekeeping genes that allow proper transcription quantification. Stability of nine housekeeping genes (ACTB, BGLU, TUBB, CY, GAPDH, HPRTI, RPL5, SDHA and UBC) was evaluated in different tissues of red abalone (gill, head and gonad/digestive gland). Four-fold serial dilutions of cDNA (from 25 ngμL(-1) to 0.39 ngμL(-1)) were used to prepare the standard curve, and it showed gene efficiencies between 0.95 and 0.99, with R(2)=0.99. geNorm and NormFinder analysis showed that RPL5 and CY were the most stable genes considering all tissues, whereas in gill HPRTI and BGLU were most stable. In gonad/digestive gland, RPL5 and TUBB were the most stable genes with geNorm, while SDHA and HPRTI were the best using NormFinder. Similarly, in head the best genes were RPL5 and UBC with geNorm, and GAPDH and CY with NormFinder. The technical variability analysis with RPL5 and abalone gonad/digestive gland tissue indicated a high repeatability with a variation coefficient within groups ≤ 0.56% and between groups ≤ 1.89%. These results will help us for further research in reproduction, thermoregulation and endocrinology in red abalone.
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Affiliation(s)
- Edgar A López-Landavery
- Laboratorio de Genética, Departamento de Acuicultura, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Tijuana-Ensenada N° 3918, Zona Playitas C.P 22860, Ensenada BC, Mexico
| | - Amelia Portillo-López
- Facultad de Ciencias, Universidad Autónoma de Baja California, Km 103 Carretera Tijuana-Ensenada, C.P 22860, Ensenada BC, Mexico
| | - Cristian Gallardo-Escárate
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, P. O. Box 160-C, Concepción, Chile
| | - Miguel A Del Río-Portilla
- Laboratorio de Genética, Departamento de Acuicultura, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Tijuana-Ensenada N° 3918, Zona Playitas C.P 22860, Ensenada BC, Mexico.
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199
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Trindade F, Oppenheim FG, Helmerhorst EJ, Amado F, Gomes PS, Vitorino R. Uncovering the molecular networks in periodontitis. Proteomics Clin Appl 2014; 8:748-61. [PMID: 24828325 DOI: 10.1002/prca.201400028] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 04/16/2014] [Accepted: 05/09/2014] [Indexed: 12/12/2022]
Abstract
Periodontitis is a complex immune-inflammatory disease that results from a preestablished infection in gingiva, mainly due to Gram-negative bacteria that colonize deeper in gingival sulcus and latter periodontal pocket. Host inflammatory and immune responses have both protective and destructive roles. Although cytokines, prostaglandins, and proteases struggle against microbial burden, these molecules promote connective tissue loss and alveolar bone resorption, leading to several histopathological changes, namely destruction of periodontal ligament, deepening of periodontal pocket, and bone loss, which can converge to attain tooth loss. Despite the efforts of genomics, transcriptomics, proteomics/peptidomics, and metabolomics, there is no available biomarker for periodontitis diagnosis, prognosis, and treatment evaluation, which could assist on the established clinical evaluation. Nevertheless, some genes, transcripts, proteins and metabolites have already shown a different expression in healthy subjects and in patients. Though, so far, 'omics approaches only disclosed the host inflammatory response as a consequence of microbial invasion in periodontitis and the diagnosis in periodontitis still relies on clinical parameters, thus a molecular tool for assessing periodontitis lacks in current dental medicine paradigm. Saliva and gingival crevicular fluid have been attracting researchers due to their diagnostic potential, ease, and noninvasive nature of collection. Each one of these fluids has some advantages and disadvantages that are discussed in this review.
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Affiliation(s)
- Fábio Trindade
- QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, Portugal
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200
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Porcine endogenous retroviruses in xenotransplantation--molecular aspects. Viruses 2014; 6:2062-83. [PMID: 24828841 PMCID: PMC4036542 DOI: 10.3390/v6052062] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 04/15/2014] [Accepted: 04/26/2014] [Indexed: 02/06/2023] Open
Abstract
In the context of the shortage of organs and other tissues for use in human transplantation, xenotransplantation procedures with material taken from pigs have come under increased consideration. However, there are unclear consequences of the potential transmission of porcine pathogens to humans. Of particular concern are porcine endogenous retroviruses (PERVs). Three subtypes of PERV have been identified, of which PERV-A and PERV-B have the ability to infect human cells in vitro. The PERV-C subtype does not show this ability but recombinant PERV-A/C forms have demonstrated infectivity in human cells. In view of the risk presented by these observations, the International Xenotransplantation Association recently indicated the existence of four strategies to prevent transmission of PERVs. This article focuses on the molecular aspects of PERV infection in xenotransplantation and reviews the techniques available for the detection of PERV DNA, RNA, reverse transcriptase activity and proteins, and anti-PERV antibodies to enable carrying out these recommendations. These methods could be used to evaluate the risk of PERV transmission in human recipients, enhance the effectiveness and reliability of monitoring procedures, and stimulate discussion on the development of improved, more sensitive methods for the detection of PERVs in the future.
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