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Bomberg M, Miettinen H. Anionic nanocellulose as competing agent in microbial DNA extraction from mine process samples. J Microbiol Methods 2023; 215:106850. [PMID: 37907119 DOI: 10.1016/j.mimet.2023.106850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 09/04/2023] [Accepted: 10/25/2023] [Indexed: 11/02/2023]
Abstract
Microorganisms in flotation and minerals processing may significantly affect the grade and yield of metal concentrates. However, studying the phenomena requires working techniques to detach microorganisms and their DNA from mineral particles to which they strongly adhere. We developed a new method utilizing the competitive properties of anionic nanocellulose to block sorption of DNA to and detach microbial cells from mineral particles from ore processing. In general, up to one ng DNA mL-1 sample was obtained with the custom anionic nanocellulose method (CM) compared to DNA amounts below the Qubit assay's detection limit for extractions with a commercial kit (KIT). Similarly, 0.5-4 orders of magnitude more bacterial 16S and fungal 5.8S rRNA gene copies were detected by qPCR from CM treated samples compared to KIT extractions. A clear difference in the detected microbial community structure between CM and KIT extracted samples was also observed. Commercial kits optimized for mineral soils are easy to use and time efficient but may miss a considerable part of the microbial communities. A competing agent such as anionic nanocellulose may decrease the interaction between microorganisms or their DNA and minerals and provide a comprehensive view into the microbial communities in mineral processing environments.
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Affiliation(s)
- Malin Bomberg
- VTT Technical Research Centre of Finland, P.O. Box 1000, 02044 VTT, Finland.
| | - Hanna Miettinen
- VTT Technical Research Centre of Finland, P.O. Box 1000, 02044 VTT, Finland
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2
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Sasi R, Suchithra TV. Wastewater microbial diversity versus molecular analysis at a glance: a mini-review. Braz J Microbiol 2023; 54:3033-3039. [PMID: 37723328 PMCID: PMC10689596 DOI: 10.1007/s42770-023-01130-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 09/10/2023] [Indexed: 09/20/2023] Open
Abstract
Microorganisms play a vital role in biological wastewater treatment by converting organic and toxic materials into harmless substances. Understanding microbial communities' structure, taxonomy, phylogeny, and metabolic activities is essential to improve these processes. Molecular microbial ecology employs molecular techniques to study community profiles and phylogenetic information since culture-dependent approaches have limitations in providing a comprehensive understanding of microbial diversity in a system. Genomic advancements such as DNA hybridization, microarray analysis, sequencing, and reverse sample genome probing have enabled the detailed characterization of microbial communities in wastewater treatment facilities. This mini-review summarizes the current state of knowledge on the diversity of microorganisms in wastewater treatment plants, emphasizing critical microbial processes such as nitrogen and phosphorus removal.
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Affiliation(s)
- R Sasi
- School of Biotechnology, National Institute of Technology Calicut, Kozhikode, Kerala, India, 673601
| | - T V Suchithra
- School of Biotechnology, National Institute of Technology Calicut, Kozhikode, Kerala, India, 673601.
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Li S, Jiang H, Guo W, Zhang W, Zhang Q. From Soil to River: Revealing the Mechanisms Underlying the High Riverine Nitrate Levels in a Forest Dominated Catchment. Water Res 2023; 241:120155. [PMID: 37270954 DOI: 10.1016/j.watres.2023.120155] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/04/2023] [Accepted: 05/30/2023] [Indexed: 06/06/2023]
Abstract
Elevated riverine nitrate (NO3-) levels have led to increased eutrophication and other ecological implications. While high riverine NO3- levels were generally ascribed to anthropogenic activities, high NO3- levels in some pristine or minimally disturbed rivers were reported. The drivers of these unexpectedly high NO3- levels remain unclear. This study combined natural abundance isotopes, 15N-labeling techniques, and molecular techniques to reveal the processes driving the high NO3- levels in a sparsely populated forest river. The natural abundance isotopes revealed that the NO3- was mainly from soil sources and that NO3- removal processes were insignificant. The 15N-labeling experiments also quantitatively showed that the biological NO3- removal processes, i.e., denitrification, dissimilatory NO3- reduction to ammonium (DNRA), and anaerobic ammonia oxidation (anammox), in the soils and sediments were weak relative to nitrification in summer. While nitrification was minor in winter, the NO3- removal was insignificant relative to the large NO3- stock in the catchment. Stepwise multiple regression analyses and structural equation models revealed that in summer, nitrification in the soils was regulated by the amoA-AOB gene abundances and NH4+-N contents. Low temperature constrained nitrification in winter. Denitrification was largely controlled by moisture content in both seasons, and anammox and DNRA could be explained by the competition with nitrification and denitrification on their substrate (nitrite-NO2-). We also revealed the strong hydrological control on the transport of soil NO3- to the river. This study effectively revealed the mechanisms underlying the high NO3- levels in a nearly pristine river, which has implications for the understanding of riverine NO3- levels worldwide.
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Affiliation(s)
- Shen Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Hao Jiang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430074, PR China.
| | - Wenjing Guo
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China
| | - Wenshi Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China
| | - Quanfa Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430074, PR China
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Huang P, Hameed R, Abbas M, Balooch S, Alharthi B, Du Y, Abbas A, Younas A, Du D. Integrated omic techniques and their genomic features for invasive weeds. Funct Integr Genomics 2023; 23:44. [PMID: 36680630 DOI: 10.1007/s10142-023-00971-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/01/2023] [Accepted: 01/11/2023] [Indexed: 01/22/2023]
Abstract
Many emerging invasive weeds display rapid adaptation against different stressful environments compared to their natives. Rapid adaptation and dispersal habits helped invasive populations have strong diversity within the population compared to their natives. Advances in molecular marker techniques may lead to an in-depth understanding of the genetic diversity of invasive weeds. The use of molecular techniques is rapidly growing, and their implications in invasive weed studies are considered powerful tools for genome purposes. Here, we review different approach used multi-omics by invasive weed studies to understand the functional structural and genomic changes in these species under different environmental fluctuations, particularly, to check the accessibility of advance-sequencing techniques used by researchers in genome sequence projects. In this review-based study, we also examine the importance and efficiency of different molecular techniques in identifying and characterizing different genes, associated markers, proteins, metabolites, and key metabolic pathways in invasive and native weeds. Use of these techniques could help weed scientists to further reduce the knowledge gaps in understanding invasive weeds traits. Although these techniques can provide robust insights about the molecular functioning, employing a single omics platform can rarely elucidate the gene-level regulation and the associated real-time expression of weedy traits due to the complex and overlapping nature of biological interactions. We conclude that different multi-omic techniques will provide long-term benefits in launching new genome projects to enhance the understanding of invasive weeds' invasion process.
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Affiliation(s)
- Ping Huang
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Rashida Hameed
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Manzer Abbas
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, 644000, Sichuan Province, People's Republic of China
| | - Sidra Balooch
- Institute of Botany, Bahauddin Zakariya University, Multan, Punjab, Pakistan
| | - Badr Alharthi
- Department of Biology, University College of Al Khurmah, Taif University, PO. Box 11099, Taif, 21944, Saudi Arabia
| | - Yizhou Du
- Faculty of Engineering, School of Computer Science, University of Sydney, Sydney, New South Wales, Australia
| | - Adeel Abbas
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China.
| | - Afifa Younas
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Daolin Du
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China.
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Peper ST. Molecular Surveillance of West Nile Virus in Mosquitoes and Sentinel Chickens. Methods Mol Biol 2023; 2585:157-169. [PMID: 36331773 DOI: 10.1007/978-1-0716-2760-0_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Arboviral surveillance is a critical step in any effective mosquito control program. Surveillance aids in the early detection of pathogen transmission as well as establishes a baseline of transmission activity. Two of the most practical forms of arboviral surveillance is through the use of testing mosquito pools for the presence of pathogen and screening sentinel chickens for pathogen exposure. This chapter describes the process for each of these methods for West Nile virus.
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Affiliation(s)
- Steven T Peper
- Anastasia Mosquito Control District, St. Augustine, FL, USA.
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Ribeiro VM, Júnior DMG, Ottino J, Valle GR, de Miranda Estevam LGT, de Carvalho OV, Paz GF. Report of the presence of Leishmania infantum in the milk of a naturally infected female dog in Brazil. Vet Parasitol Reg Stud Reports 2022; 36:100795. [PMID: 36436888 DOI: 10.1016/j.vprsr.2022.100795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 09/22/2022] [Accepted: 10/05/2022] [Indexed: 11/07/2022]
Abstract
Dogs are the most important reservoir of Leishmania infantum, the causal agent of visceral leishmaniasis in Brazil. Although lymphoid tissue is the most important biological tissue where amastigotes can be found, this paper describes the presence of L. infantum DNA in the milk of a lactating naturally infected female dog. This finding suggests the need for further studies to elucidate whether breastfeeding can be a route of infection.
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Affiliation(s)
| | | | - Jennifer Ottino
- Santo Agostinho Hospital Veterinário, Brazil; Instituto de Ciências Biológicas da Universidade Federal de Minas Gerais, Brazil
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Kerry RG, Montalbo FJP, Das R, Patra S, Mahapatra GP, Maurya GK, Nayak V, Jena AB, Ukhurebor KE, Jena RC, Gouda S, Majhi S, Rout JR. An overview of remote monitoring methods in biodiversity conservation. Environ Sci Pollut Res Int 2022; 29:80179-80221. [PMID: 36197618 PMCID: PMC9534007 DOI: 10.1007/s11356-022-23242-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Conservation of biodiversity is critical for the coexistence of humans and the sustenance of other living organisms within the ecosystem. Identification and prioritization of specific regions to be conserved are impossible without proper information about the sites. Advanced monitoring agencies like the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) had accredited that the sum total of species that are now threatened with extinction is higher than ever before in the past and are progressing toward extinct at an alarming rate. Besides this, the conceptualized global responses to these crises are still inadequate and entail drastic changes. Therefore, more sophisticated monitoring and conservation techniques are required which can simultaneously cover a larger surface area within a stipulated time frame and gather a large pool of data. Hence, this study is an overview of remote monitoring methods in biodiversity conservation via a survey of evidence-based reviews and related studies, wherein the description of the application of some technology for biodiversity conservation and monitoring is highlighted. Finally, the paper also describes various transformative smart technologies like artificial intelligence (AI) and/or machine learning algorithms for enhanced working efficiency of currently available techniques that will aid remote monitoring methods in biodiversity conservation.
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Affiliation(s)
- Rout George Kerry
- Department of Biotechnology, Utkal University, Vani Vihar, Bhubaneswar, Odisha 751004 India
| | | | - Rajeswari Das
- Department of Soil Science and Agricultural Chemistry, School of Agriculture, GIET University, Gunupur, Rayagada, Odisha 765022 India
| | - Sushmita Patra
- Indian Council of Agricultural Research-Directorate of Foot and Mouth Disease-International Centre for Foot and Mouth Disease, Arugul, Bhubaneswar, Odisha 752050 India
| | | | - Ganesh Kumar Maurya
- Zoology Section, Mahila MahaVidyalya, Banaras Hindu University, Varanasi, 221005 India
| | - Vinayak Nayak
- Indian Council of Agricultural Research-Directorate of Foot and Mouth Disease-International Centre for Foot and Mouth Disease, Arugul, Bhubaneswar, Odisha 752050 India
| | - Atala Bihari Jena
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | | | - Ram Chandra Jena
- Department of Pharmaceutical Sciences, Utkal University, Vani Vihar, Bhubaneswar, Odisha 751004 India
| | - Sushanto Gouda
- Department of Zoology, Mizoram University, Aizawl, 796009 India
| | - Sanatan Majhi
- Department of Biotechnology, Utkal University, Vani Vihar, Bhubaneswar, Odisha 751004 India
| | - Jyoti Ranjan Rout
- School of Biological Sciences, AIPH University, Bhubaneswar, Odisha 752101 India
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8
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Gomes JA, Wachholz GE, Boquett JA, Vianna FSL, Schuler-Faccini L, Fraga LR. Molecular Mechanisms of ZIKV-Induced Teratogenesis: A Systematic Review of Studies in Animal Models. Mol Neurobiol 2022; 60:68-83. [PMID: 36215025 PMCID: PMC9549063 DOI: 10.1007/s12035-022-03046-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 09/21/2022] [Indexed: 12/09/2022]
Abstract
Zika virus (ZIKV) is a teratogen that causes congenital anomalies, being linked to microcephaly in children exposed during pregnancy. Animal studies have been conducted to investigate the molecular mechanisms related to ZIKV teratogenesis. Although animal models can mimic the effects of ZIKV in human embryo development, few in vivo studies have addressed molecular changes following ZIKV infection in embryos. Moreover, few literature reviews have been conducted with these studies. The aim of this systematic review is to evaluate the molecular mechanisms of ZIKV teratogenesis determined from studies in animal models. PubMed/MEDLINE, EMBASE, Web of Science, and Scopus as well as grey literature were searched for studies that evaluated molecular alterations related to ZIKV teratogenesis which occurred during embryonic development. Nine studies were included: six with mice, one with mice and guinea pigs, one with pigs and one with chickens. In general, studies presented an unclear or high risk of bias for methodological criteria. Most of studies reported embryos exposed to ZIKV presenting microcephaly, reduced cortex thickness, and growth restriction. Different techniques were used to evaluated molecular changes in the animals following ZIKV infection: RNA sequencing, RT-qPCR, and in situ hybridization. It was found that common pathways are changed in most studies, being pathways related to immune response upregulated and those involved to neurodevelopment downregulated.
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Affiliation(s)
- Julia A Gomes
- Teratology Information Service, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, 90035-903, Brazil
- Laboratory of Genomic Medicine, Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, 90035-903, Brazil
| | - Gabriela E Wachholz
- Angiogenesis Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Juliano A Boquett
- Postgraduate Program in Genetics and Molecular Biology, Department of Genetics, Biosciences Institute, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
- Postgraduate Program in Child and Adolescent Health, Faculty of Medicine, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
| | - Fernanda S L Vianna
- Teratology Information Service, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, 90035-903, Brazil
- Laboratory of Genomic Medicine, Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, 90035-903, Brazil
- Postgraduate Program in Genetics and Molecular Biology, Department of Genetics, Biosciences Institute, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
- Postgraduate Program in Medicine: Medical Sciences, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, 90035-003, Brazil
| | - Lavínia Schuler-Faccini
- Teratology Information Service, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, 90035-903, Brazil
- Postgraduate Program in Genetics and Molecular Biology, Department of Genetics, Biosciences Institute, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
- Postgraduate Program in Medicine: Medical Sciences, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, 90035-003, Brazil
| | - Lucas R Fraga
- Teratology Information Service, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, 90035-903, Brazil.
- Laboratory of Genomic Medicine, Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, 90035-903, Brazil.
- Postgraduate Program in Medicine: Medical Sciences, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, 90035-003, Brazil.
- Department of Morphological Sciences, Institute of Health Sciences, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, 90050-170, Brazil.
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Munrós J, Vergara A, Bataller E, García-Lorenzo B, Álvarez-Martínez MJ, Bosch J. Performance of a rapid molecular test to detect Chlamydia trachomatis and Neisseria gonorrhoeae in women with pelvic inflammatory disease. Enferm Infecc Microbiol Clin (Engl Ed) 2022; 40:377-380. [PMID: 35906032 DOI: 10.1016/j.eimce.2021.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/17/2021] [Indexed: 06/15/2023]
Abstract
OBJECTIVE The aim of this study was to investigate the prevalence of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) in women with pelvic inflammatory disease (PID) and the usefulness and cost-effectiveness of a rapid molecular test for the diagnosis and clinical management of PID. METHODS This observational study included 75 patients with mild-to-moderate PID (n=33), severe PID (n=29) and non-specific lower abdominal pain (NSAP) (n=13). CT/NG infections were analyzed using a standard and a rapid test. A cost analysis was carried out. RESULTS Samples of 19 patients (25.3%) were CT/NG positive. Concordance between rapid and standard tests was 100%. No significant differences were observed in the incidence of CT/NG in mild-to-moderate compared to severe PID. Costs differed according only to disease severity. CONCLUSIONS Rapid molecular tests could help with the diagnosis of PID in sexually active women in clinical settings in which a standard technique is not available.
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Affiliation(s)
- Jordina Munrós
- Department of Gynecology, Institut Clínic of Gynecology, Obstetrics and Neonatology, Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain; Institut de Salut Global Barcelona - ISGlobal, Barcelona, Spain
| | - Andrea Vergara
- Institut de Salut Global Barcelona - ISGlobal, Barcelona, Spain; Department of Microbiology, Biomedical Diagnostic Center (CDB), Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain.
| | - Eduardo Bataller
- Department of Gynecology, Institut Clínic of Gynecology, Obstetrics and Neonatology, Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
| | - Borja García-Lorenzo
- Assessment of Innovations and New Technologies Unit, Hospital Clinic of Barcelona, University of Barcelona, Barcelona, Spain
| | - Miriam José Álvarez-Martínez
- Institut de Salut Global Barcelona - ISGlobal, Barcelona, Spain; Department of Microbiology, Biomedical Diagnostic Center (CDB), Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
| | - Jordi Bosch
- Institut de Salut Global Barcelona - ISGlobal, Barcelona, Spain; Department of Microbiology, Biomedical Diagnostic Center (CDB), Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
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Sharma P, Singh SP, Iqbal HMN, Tong YW. Omics approaches in bioremediation of environmental contaminants: An integrated approach for environmental safety and sustainability. Environ Res 2022; 211:113102. [PMID: 35300964 DOI: 10.1016/j.envres.2022.113102] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/28/2022] [Accepted: 03/07/2022] [Indexed: 02/05/2023]
Abstract
Non-degradable pollutants have emerged as a result of industrialization, population growth, and lifestyle changes, endangering human health and the environment. Bioremediation is the process of clearing hazardous contaminants with the help of microorganisms, and cost-effective approach. The low-cost and environmentally acceptable approach to removing environmental pollutants from ecosystems is microbial bioremediation. However, to execute these different bioremediation approaches successfully, this is imperative to have a complete understanding of the variables impacting the development, metabolism, dynamics, and native microbial communities' activity in polluted areas. The emergence of new technologies like next-generation sequencing, protein and metabolic profiling, and advanced bioinformatic tools have provided critical insights into microbial communities and underlying mechanisms in environmental contaminant bioremediation. These omics approaches are meta-genomics, meta-transcriptomics, meta-proteomics, and metabolomics. Moreover, the advancements in these technologies have greatly aided in determining the effectiveness and implementing microbiological bioremediation approaches. At Environmental Protection Agency (EPA)-The government placed special emphasis on exploring how molecular and "omic" technologies may be used to determine the nature, behavior, and functions of the intrinsic microbial communities present at pollution containment systems. Several omics techniques are unquestionably more informative and valuable in elucidating the mechanism of the process and identifying the essential player's involved enzymes and their regulatory elements. This review provides an overview and description of the omics platforms that have been described in recent reports on omics approaches in bioremediation and that demonstrate the effectiveness of integrated omics approaches and their novel future use.
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Affiliation(s)
- Pooja Sharma
- Environmental Research Institute, National University of Singapore, 1 Create Way, 138602, Singapore; Energy and Environmental Sustainability for Megacities (E2S2) Phase II, Campus for Research Excellence and Technological Enterprise (CREATE), 1 CREATE Way, Singapore, 138602, Singapore.
| | - Surendra Pratap Singh
- Plant Molecular Biology Laboratory, Department of Botany, Dayanand Anglo-Vedic (PG) College, Chhatrapati Shahu Ji Maharaj University, Kanpur-208001, India.
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, 64849, Mexico.
| | - Yen Wah Tong
- Environmental Research Institute, National University of Singapore, 1 Create Way, 138602, Singapore; Energy and Environmental Sustainability for Megacities (E2S2) Phase II, Campus for Research Excellence and Technological Enterprise (CREATE), 1 CREATE Way, Singapore, 138602, Singapore; Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive, 117585, Singapore.
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11
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Stamelou E, Giantsis IA, Papageorgiou KV, Petridou E, Davidson I, Polizopοulou ZS, Papa A, Kritas SK. First report of canine Astrovirus and Sapovirus in Greece, hosting both asymptomatic and gastroenteritis symptomatic dogs. Virol J 2022; 19:58. [PMID: 35361253 PMCID: PMC8969266 DOI: 10.1186/s12985-022-01787-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/28/2022] [Indexed: 01/13/2023] Open
Abstract
Background Astrovirus, Norovirus and Sapovirus are widely distributed viruses in humans and animals worldwide. They have frequently been associated with disease, mainly of gastroenteric nature. In dogs, these viruses have been detected both in symptomatic and asymptomatic animals, mainly of young age. Methods In the present epidemiologic study, we investigated the presence of canine Astrovirus (CAstV), canine Norovirus (canine NoV) and canine Sapovirus (Canine SaV) in saliva and stools of 201 domestic dogs originating from throughout Greece, based on two different molecular methods, i.e. conventional and SYBR-Green Real-time RT-PCR. The samples derived from young and adult asymptomatic and symptomatic animals. CAstV was detected in 15/201 (7.5%) and 29/201 (15%) of the examined dogs using conventional RT-PCR and SYBR-Green Real time RT-PCR, respectively. Results The prevalence of the virus was higher at healthy dogs, with a slight discrepancy of the two methods on the aspect of age (67% young dogs with the method of conventional RT-PCR, versus 52% adult positive dogs with the method of SYBR-Green Real-time RT-PCR). Canine SaV was detected in 52/201 (23%) of the dogs (mainly young and asymptomatic), with the method of SYBR-Green Real-time RT-PCR only, while canine NoV was not detected in any sample with either of the two methods applied. Sequencing of the CAstV positive samples resulted in the acquisition of one CAstV sequence. Phylogenetic analysis confirmed the results, clustering the CAstV sequence with homologous canine hosting sequences from other countries. Conclusions CAstV and Canine SaV were proved to circulate in Greek dogs. SYBR-Green Real time RT-PCR showed greater sensitivity in the detection of these viruses. Additionally, we were able to specify the CAstV strain that circulates in Greece, through phylogenetic analysis. To our knowledge, this is the first epidemiological study of CAstV and canine SaV in dogs in Greece, as well as the first time detected in dogs from Greece.
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Affiliation(s)
- Efthymia Stamelou
- School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Ioannis A Giantsis
- Department of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, 53100, Florina, Greece.
| | - Konstantinos V Papageorgiou
- School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Evanthia Petridou
- School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Irit Davidson
- Kimron Veterinary Institute, 50250, Bet Dagan, Israel
| | - Zoe S Polizopοulou
- School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Anna Papa
- Laboratory of Microbiology, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Spyridon K Kritas
- School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
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Albloshi AMK, Alqumber MAA. Infective endocarditis: Role of molecular techniques in early diagnosis. Saudi J Biol Sci 2021; 28:6844-6852. [PMID: 34866984 PMCID: PMC8626217 DOI: 10.1016/j.sjbs.2021.07.060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/12/2021] [Accepted: 07/21/2021] [Indexed: 11/17/2022] Open
Abstract
Infective endocarditis (IE), a heart valve infection primarily caused by bacteria such as streptococci or staphylococci, causes significant morbidity and mortality. Despite the long-term use of broad-spectrum antimicrobials, the infection is often difficult to manage. The latest diagnostic modalities for IE are discussed in this study. Blood culture use in pathogen identification can lead to loss of precious time as well as generation of false negative reports. The first steps in diagnosis are blood cultures and echocardiography, but molecular techniques can be extremely useful and may be used for an accurate and early diagnosis.
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Affiliation(s)
| | - Mohammed A A Alqumber
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Albaha University, Saudi Arabia
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Sharma P, Sirohi R, Tong YW, Kim SH, Pandey A. Metal and metal(loids) removal efficiency using genetically engineered microbes: Applications and challenges. J Hazard Mater 2021; 416:125855. [PMID: 34492804 DOI: 10.1016/j.jhazmat.2021.125855] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/30/2021] [Accepted: 04/06/2021] [Indexed: 06/13/2023]
Abstract
The environment is being polluted in different many with metal and metalloid pollution, mostly due to anthropogenic activity, which is directly affecting human and environmental health. Metals and metalloids are highly toxic at low concentrations and contribute primarily to the survival equilibrium of activities in the environment. However, because of non-degradable, they persist in nature and these metal and metalloids bioaccumulate in the food chain. Genetically engineered microorganisms (GEMs) mediated techniques for the removal of metals and metalloids are considered an environmentally safe and economically feasible strategy. Various forms of GEMs, including fungi, algae, and bacteria have been produced by recombinant DNA and RNA technologies, which have been used to eliminate metal and metalloids compounds from the polluted areas. Besides, GEMs have the potentiality to produce enzymes and other metabolites that are capable of tolerating metals stress and detoxify the pollutants. Thus, the aim of this review is to discuss the use of GEMs as advanced tools to produce metabolites, signaling molecules, proteins through genetic expression during metal and metalloids interaction, which help in the breakdown of persistent pollutants in the environment.
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Affiliation(s)
- Pooja Sharma
- Centre for Energy and Environmental Sustainability, Lucknow 226029, Uttar Pradesh, India
| | - Ranjna Sirohi
- Department of Chemical & Biological Engineering, Korea University, Seoul 136713, Republic of Korea
| | - Yen Wah Tong
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore
| | - Sang Hyoun Kim
- Department of Chemical and Environmental Engineering, Yonsei University, Seoul, Republic of Korea
| | - Ashok Pandey
- Centre for Energy and Environmental Sustainability, Lucknow 226029, Uttar Pradesh, India; Centre for Innovation and Translational Research, CSIR-Indian Institute of Toxicology Research, Lucknow 226001, Uttar Pradesh, India.
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Ardura A, Martinez JL, Zaiko A, Garcia-Vazquez E. Poorer diversity but tougher species in old ballast water: Biosecurity challenges explored from visual and molecular techniques. Mar Pollut Bull 2021; 168:112465. [PMID: 33991987 DOI: 10.1016/j.marpolbul.2021.112465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 04/30/2021] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
Millions of tons of water cross the oceans inside ships' ballast tanks every day. Planktonic species hitch-hike with water and some may pose risks to ecosystems and economies if get released and establish outside their native range. We monitored ballast water in different trans-equatorial travels, visually and using molecular techniques, and found significant increases of potential nuisance taxa over travel duration, despite evident diversity depletion. Thus, less diverse but more resistant and potentially more harmful communities persist in ballast water over long voyages. If we consider the enormous volume transported every day, the persistence of resistant species in ballast water would be threating the global marine biodiversity. This should be taken into account when modeling and assessing the bioinvasion risks associated with the ballast water and transfer considered in the future research.
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Affiliation(s)
- Alba Ardura
- Department of Functional Biology, University of Oviedo, C/ Julian Claveria s/n, 33006 Oviedo, Spain.
| | - Jose L Martinez
- Scientific-technical Services, University of Oviedo, Oviedo, Asturias, Spain
| | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street East, 7010 Nelson, New Zealand; Marine Research Institute, Klaipeda University, H. Manto 84, LT-92294 Klaipeda, Lithuania
| | - Eva Garcia-Vazquez
- Department of Functional Biology, University of Oviedo, C/ Julian Claveria s/n, 33006 Oviedo, Spain
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15
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Munrós J, Vergara A, Bataller E, García-Lorenzo B, Álvarez-Martínez MJ, Bosch J. Performance of a rapid molecular test to detect Chlamydia trachomatis and Neisseria gonorrhoeae in women with pelvic inflammatory disease. Enferm Infecc Microbiol Clin 2021; 40:S0213-005X(21)00090-2. [PMID: 34024673 DOI: 10.1016/j.eimc.2021.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 11/03/2022]
Abstract
OBJECTIVE The aim of this study was to investigate the prevalence of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) in women with pelvic inflammatory disease (PID) and the usefulness and cost-effectiveness of a rapid molecular test for the diagnosis and clinical management of PID. METHODS This observational study included 75 patients with mild-to-moderate PID (n=33), severe PID (n=29) and non-specific lower abdominal pain (NSAP) (n=13). CT/NG infections were analyzed using a standard and a rapid test. A cost analysis was carried out. RESULTS Samples of 19 patients (25.3%) were CT/NG positive. Concordance between rapid and standard tests was 100%. No significant differences were observed in the incidence of CT/NG in mild-to-moderate compared to severe PID. Costs differed according only to disease severity. CONCLUSIONS Rapid molecular tests could help with the diagnosis of PID in sexually active women in clinical settings in which a standard technique is not available.
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Affiliation(s)
- Jordina Munrós
- Department of Gynecology, Institut Clínic of Gynecology, Obstetrics and Neonatology, Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain; Institut de Salut Global Barcelona - ISGlobal, Barcelona, Spain
| | - Andrea Vergara
- Institut de Salut Global Barcelona - ISGlobal, Barcelona, Spain; Department of Microbiology, Biomedical Diagnostic Center (CDB), Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain.
| | - Eduardo Bataller
- Department of Gynecology, Institut Clínic of Gynecology, Obstetrics and Neonatology, Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
| | - Borja García-Lorenzo
- Assessment of Innovations and New Technologies Unit, Hospital Clinic of Barcelona, University of Barcelona, Barcelona, Spain
| | - Miriam José Álvarez-Martínez
- Institut de Salut Global Barcelona - ISGlobal, Barcelona, Spain; Department of Microbiology, Biomedical Diagnostic Center (CDB), Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
| | - Jordi Bosch
- Institut de Salut Global Barcelona - ISGlobal, Barcelona, Spain; Department of Microbiology, Biomedical Diagnostic Center (CDB), Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
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Pasalari H, Gholami M, Rezaee A, Esrafili A, Farzadkia M. Perspectives on microbial community in anaerobic digestion with emphasis on environmental parameters: A systematic review. Chemosphere 2021; 270:128618. [PMID: 33121817 DOI: 10.1016/j.chemosphere.2020.128618] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/09/2020] [Accepted: 10/11/2020] [Indexed: 05/07/2023]
Abstract
This paper review is aiming to comprehensively identify and appraise the current available knowledge on microbial composition and microbial dynamics in anaerobic digestion with focus on the interconnections between operational parameters and microbial community. We systematically searched Scopus, Web of Science, pubmed and Embase (up to August 2019) with relative keywords to identify English-language studies published in peer-reviewed journals. The data and information on anaerobic reactor configurations, operational parameters such as pretreatment methods, temperature, trace elements, ammonia, organic loading rate, and feedstock composition and their association with the microbial community and microbial dynamics were extracted from eligible articles. Of 306 potential articles, 112 studies met the present review objectives and inclusion criteria. The results indicated that both aceticlastic and hydrogenotrophic methanogenesis are dominant in anaerobic digesters and their relative composition is depending on environmental conditions. However, hydrogenotrophic methanogens are more often observed in extreme conditions due to their higher robustness compared to aceticlastic methangoens. Firmicutes and Bacteroidetes phyla are most common fermentative bacteria of the acidogenic phase. These bacteria secrete lytic enzymes to degrade organic matters and are able to survive in extreme conditions and environments due to their spores. In addition, among archaea Methanosaeta, Methanobacterium, and Methanosarcinaceae are found at high relative abundance in anaerobic digesters operated with different operational parameters. Overall, understanding the shifts in microbial composition and diversity as results of operational parameters variation in anaerobic digestion process would improve the stability and process performance.
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Affiliation(s)
- Hasan Pasalari
- Research Center for Environmental Health Technology, Iran University of Medical Sciences, Tehran, Iran; Department of Environmental Health Engineering, School of Public Health, Iran University of Medical Sciences, Tehran, IR, Iran
| | - Mitra Gholami
- Research Center for Environmental Health Technology, Iran University of Medical Sciences, Tehran, Iran; Department of Environmental Health Engineering, School of Public Health, Iran University of Medical Sciences, Tehran, IR, Iran
| | - Abbas Rezaee
- Department of Environmental Health Engineering, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ali Esrafili
- Research Center for Environmental Health Technology, Iran University of Medical Sciences, Tehran, Iran; Department of Environmental Health Engineering, School of Public Health, Iran University of Medical Sciences, Tehran, IR, Iran
| | - Mahdi Farzadkia
- Research Center for Environmental Health Technology, Iran University of Medical Sciences, Tehran, Iran; Department of Environmental Health Engineering, School of Public Health, Iran University of Medical Sciences, Tehran, IR, Iran.
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17
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Abstract
Taxonomy is the science that explores, describes, names, and classifies all organisms. In this introductory chapter, we highlight the major historical steps in the elaboration of this science, which provides baseline data for all fields of biology and plays a vital role for society but is also an independent, complex, and sound hypothesis-driven scientific discipline.In a first part, we underline that plant taxonomy is one of the earliest scientific disciplines that emerged thousands of years ago, even before the important contributions of the Greeks and Romans (e.g., Theophrastus, Pliny the Elder, and Dioscorides). In the fifteenth-sixteenth centuries, plant taxonomy benefited from the Great Navigations, the invention of the printing press, the creation of botanic gardens, and the use of the drying technique to preserve plant specimens. In parallel with the growing body of morpho-anatomical data, subsequent major steps in the history of plant taxonomy include the emergence of the concept of natural classification , the adoption of the binomial naming system (with the major role of Linnaeus) and other universal rules for the naming of plants, the formulation of the principle of subordination of characters, and the advent of the evolutionary thought. More recently, the cladistic theory (initiated by Hennig) and the rapid advances in DNA technologies allowed to infer phylogenies and to propose true natural, genealogy-based classifications.In a second part, we put the emphasis on the challenges that plant taxonomy faces nowadays. The still very incomplete taxonomic knowledge of the worldwide flora (the so-called taxonomic impediment) is seriously hampering conservation efforts that are especially crucial as biodiversity has entered its sixth extinction crisis. It appears mainly due to insufficient funding, lack of taxonomic expertise, and lack of communication and coordination. We then review recent initiatives to overcome these limitations and to anticipate how taxonomy should and could evolve. In particular, the use of molecular data has been era-splitting for taxonomy and may allow an accelerated pace of species discovery. We examine both strengths and limitations of such techniques in comparison to morphology-based investigations, we give broad recommendations on the use of molecular tools for plant taxonomy, and we highlight the need for an integrative taxonomy based on evidence from multiple sources.
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Affiliation(s)
- Germinal Rouhan
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, Sorbonne Université, Ecole Pratique des Hautes Etudes, Université des Antilles, CNRS, Paris, France.
| | - Myriam Gaudeul
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, Sorbonne Université, Ecole Pratique des Hautes Etudes, Université des Antilles, CNRS, Paris, France
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Gouda S, Kerry RG, Das A, Chauhan NS. Wildlife forensics: A boon for species identification and conservation implications. Forensic Sci Int 2020; 317:110530. [PMID: 33096398 DOI: 10.1016/j.forsciint.2020.110530] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 09/03/2020] [Accepted: 09/26/2020] [Indexed: 01/05/2023]
Abstract
Wildlife trade and fraudulence in food, artefacts and cosmetic industries had raised serious concern in protection of the wild faunal diversity. Lack of proper tools and molecular based techniques for identification of wild species are some of the major constrains faced by the judiciary and law enforcement agencies while framing charges against poachers and illicit agitator. The emergence of wildlife forensics serves as a boon in solving long pending cases of wildlife crimes. Wildlife forensics have proven to be fast, accurate and reliable criminal investigation processes with comprehensive coverage and easy accessibility. It has also helped resolving taxonomic disputes, determining spatiotemporal genetic divergence, evolutionary history, origins and even endemism. Collaboration among inter-disciplinary fields has even led to engineered signature markers and phylogenetics for several species. Development in fields of genetics, molecular and evolutionary biology and other omics techniques have further contributed in accurate identification of species. Wildlife forensics, with the support of proper international mega database units for population reference, will be fundamental in wildlife investigations through its unlimited information sharing ability. The efficient conservation of species will, however, require a collaborative approach consisting of national policy makers, local stakeholders and implementation agencies in addition to experts from the scientific communities.
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Hortelano I, Moreno Y, Moreno-Mesonero L, Ferrús MA. Deep-amplicon sequencing (DAS) analysis to determine the presence of pathogenic Helicobacter species in wastewater reused for irrigation. Environ Pollut 2020; 264:114768. [PMID: 32434114 DOI: 10.1016/j.envpol.2020.114768] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/06/2020] [Accepted: 05/06/2020] [Indexed: 06/11/2023]
Abstract
Wastewater has become one of the most important and least expensive water for the agriculture sector, as well as an alternative to the overexploitation of water resources. However, inappropriate treatment before its reuse can result in a negative impact on the environment, such as the presence of pathogens. This poses an increased risk for environmental safety, which can subsequently lead to an increased risk for human health. Among all the emerging wastewater pathogens, bacteria of the genus Helicobacter are some of the most disturbing ones, since they are directly related to gastric illness and hepatobiliary and gastric cancer. Therefore, the aim of this study was to determine the presence of potentially pathogenic Helicobacter spp. in treated wastewater intended for irrigation. We used a next generation sequencing approach, based on Illumina sequencing in combination with culture and other molecular techniques (qPCR, FISH and DVC-FISH), to analyze 16 wastewater samples, with and without an enrichment step. By culture, one of the direct samples was positive for H. pylori. FISH and DVC-FISH techniques allowed for detecting viable Helicobacter spp., including H. pylori, in seven out of eight samples of wastewater from the tertiary effluents, while qPCR analysis yielded only three positive results. When wastewater microbiome was analyzed, Helicobacter genus was detected in 7 samples. The different molecular techniques used in the present study provided evidence, for the first time, of the presence of species belonging to the genus Helicobacter such as H. pylori, H. hepaticus, H. pullorum and H. suis in wastewater samples, even after disinfection treatment.
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Affiliation(s)
- Irene Hortelano
- Research Institute of Water and Environmental Engineering (IIAMA), Universitat Politècnica de València, 46022, Valencia, Spain
| | - Yolanda Moreno
- Research Institute of Water and Environmental Engineering (IIAMA), Universitat Politècnica de València, 46022, Valencia, Spain.
| | - Laura Moreno-Mesonero
- Research Institute of Water and Environmental Engineering (IIAMA), Universitat Politècnica de València, 46022, Valencia, Spain
| | - María Antonia Ferrús
- Biotechnology Department, Universitat Politècnica de València, 46022, Valencia, Spain
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Kumar G, Mathimani T, Sivaramakrishnan R, Shanmugam S, Bhatia SK, Pugazhendhi A. Application of molecular techniques in biohydrogen production as a clean fuel. Sci Total Environ 2020; 722:137795. [PMID: 32208247 DOI: 10.1016/j.scitotenv.2020.137795] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 03/06/2020] [Accepted: 03/06/2020] [Indexed: 06/10/2023]
Abstract
Considering the future energy demand and pollution to the environment, biohydrogen, a biofuel, produced from biological sources have garnered increased attention. The present review emphasis the various techniques and methods employed to enumerate the microbial community and enhancement of hydrogen production by dark fermentation. Notably, molecular techniques such as terminal restriction fragment length polymorphism (T-RFLP), quantitative real-time PCR (q-PCR), fluorescent in-situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE), ribosomal intergenic spacer analysis (RISA), and next generation sequencing (NGS) have been extensively discussed on identifying the microbial population in hydrogen production. Further, challenges and merits of the molecular techniques have been elaborated.
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Affiliation(s)
- Gopalakrishnan Kumar
- School of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea; Department of Chemistry, Bioscience and Environmental Engineering, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | - Thangavel Mathimani
- Department of Energy and Environment, National Institute of Technology, Tiruchirappalli - 620015, Tamil Nadu, India
| | - Ramachandran Sivaramakrishnan
- Laboratory of Cyanobacterial Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sabarathinam Shanmugam
- Key Laboratory of Low-grade Energy Utilization Technologies and Systems, Chongqing University, Ministry of Education, Chongqing 400044 China; Institute of Engineering Thermophysics, Chongqing University, Chongqing 400044, China
| | - Shashi Kant Bhatia
- Department of Biological Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Arivalagan Pugazhendhi
- Innovative Green Product Synthesis and Renewable Environment Development Research Group, Faculty of Environment and Labour Safety, Ton Duc Thang University, Ho Chi Minh City, Vietnam.
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Candan O, Candan ED. Bacterial diversity of the green turtle (Chelonia mydas) nest environment. Sci Total Environ 2020; 720:137717. [PMID: 32325608 DOI: 10.1016/j.scitotenv.2020.137717] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 01/12/2020] [Accepted: 03/02/2020] [Indexed: 06/11/2023]
Abstract
The green turtle is an endangered species that is highly sensitive to environmental pollution that can adversely affect the healthy development of eggs. Moreover, the presence of some bacteria in nests can be regarded as an indicator of the pollution level in nesting areas. In our study, nest sand and egg contents were collected from Sugözü Beaches (Turkey), in the Mediterranean. Phenotypic and genotypic identification of bacteria were carried out by using conventional phenotypic methods, 16S rRNA gene sequencing respectively. The extended-spectrum beta-lactamase presence and carbapenem resistance of bacteria isolated from egg contents were determined. This is the first report of carbapenem resistance in the eggs. All strains were evaluated in three different categories including growth promoters in agriculture and aquaculture, pathogens that are found in human and animal, and biomonitoring aquatic pollution. According to our analysis, 67 bacterial species were identified from samples. This study is the first record of Alcaligenes, Zobellella, Lysinibacillus, Sphingobacterium, Achromobacter, Acinetobacter, Alcanivorax, Ochrobactrum, Microbacterium, Rhodococcus, and Stenotrophomonas isolated from sea turtles. Pathogens detected in the bacterial flora can threaten both sea turtles and field workers. These data can contribute to the development of new conservation strategies on the treatment of sea turtles, nest protection, and pollution detection on nesting beaches.
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Affiliation(s)
- Onur Candan
- Ordu University, Faculty of Arts and Sciences, Department of Molecular Biology and Genetics, 52200 Ordu, Turkey.
| | - Esra Deniz Candan
- Giresun University, Vocational School of Health Services, Department of Medical Services and Techniques, 28100 Giresun, Turkey
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Unwin VT, Ahmed R, Noviyanti R, Puspitasari AM, Utami RAS, Trianty L, Lukito T, Syafruddin D, Poespoprodjo JR, Santana-Morales MA, Ter Kuile FO, Adams ER. Use of a highly-sensitive rapid diagnostic test to screen for malaria in pregnancy in Indonesia. Malar J 2020; 19:28. [PMID: 31948448 DOI: 10.1186/s12936-020-3110-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 01/08/2020] [Indexed: 11/30/2022] Open
Abstract
Background The sensitivity of rapid diagnostic tests (RDTs) for malaria is inadequate for detecting low-density, often asymptomatic infections, such as those that can occur when screening pregnant women for malaria. The performance of the Alere™ Ultra-sensitive Malaria Ag Plasmodium falciparum RDT (uRDT) was assessed retrospectively in pregnant women in Indonesia. Methods The diagnostic performance of the uRDT and the CareStart™ Malaria HRP2/pLDH VOM (Plasmodium vivax, Plasmodium ovale and Plasmodium malariae) Combo RDT (csRDT) were assessed using 270 stored red blood cell pellets and plasma samples from asymptomatic pregnant women. These included 112 P. falciparum negative and 158 P. falciparum positive samples detected by a composite test (qPCR, LAMP, nPCR) as reference standard. Diagnostic indicators: sensitivity, specificity, negative predictive value (NPV), positive predictive value (PPV), diagnostic odds ratio (DOR) and the level of agreement (kappa) were calculated for comparison. Results Compared with the reference test, the uRDT had a sensitivity of 19.6% (95% CI 13.9–26.8) and specificity of 98.2% (93.1–99.7%). The csRDT was 22.8% (16.7–30.3) sensitive and 95.5% (89.4–98.3) specific for P. falciparum infections. Performance of the uRDT was non-significantly different to the csRDT (p = 0.169). RDT outcome was stratified by qPCR cycling threshold (Ct), and performance of the RDTs was found to be comparable across parasite loads. Conclusion The uRDT performed similarly to the currently used csRDTs in detecting P. falciparum infections in asymptomatic pregnant women. In these settings, molecular diagnostics are currently the most sensitive for malaria.
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Taei M, Chadeganipour M, Mohammadi R. An alarming rise of non-albicans Candida species and uncommon yeasts in the clinical samples; a combination of various molecular techniques for identification of etiologic agents. BMC Res Notes 2019; 12:779. [PMID: 31783903 PMCID: PMC6883655 DOI: 10.1186/s13104-019-4811-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 11/14/2019] [Indexed: 01/26/2023] Open
Abstract
OBJECTIVE Yeasts are unicellular microorganisms may cause systemic infection in immunocompromised patients. The aim of this study was to identify yeast strains isolated from clinical specimens using molecular techniques. RESULTS A total of 202 yeast strains isolated from 341 clinical samples between February 2017 and May 2019. All clinical isolates were identified using phenotypic and molecular tests including PCR-RFLP, duplex-PCR, multiplex-PCR, and PCR-sequencing. The most yeast fungal isolates were obtained from urine (66.8%), nail (9.4%), skin lesion (7.9%), bronchoalveolar lavage (5.9%), and blood (3.9%). One hundred and twenty-one Candida species were identified as non-albicans versus 76 Candida albicans. Trichosporon asahii, and Pichia terricola were uncommon non-Candida yeasts isolated from urine samples. For the first time, we isolated P. terricola as etiological agent of urinary tract infection in a pregnant female. Since Candida species show different levels of resistance to antifungal agents, precise identification of clinical isolates is critical for better treatment of infection.
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Affiliation(s)
- Monireh Taei
- Department of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mostafa Chadeganipour
- Department of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Rasoul Mohammadi
- Department of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran. .,Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran.
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Andrés C, Piñana M, Vila J, Esperalba J, Trejo-Zahínos J, Codina MG, Martín MC, Fuentes F, Rubio S, Pumarola T, Antón A. The high genetic similarity between rhinoviruses and enteroviruses remains as a pitfall for molecular diagnostic tools: A three-year overview. Infect Genet Evol 2019; 75:103996. [PMID: 31401308 DOI: 10.1016/j.meegid.2019.103996] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 07/29/2019] [Accepted: 08/06/2019] [Indexed: 12/22/2022]
Abstract
BACKGROUND Enteroviruses (EVs) and rhinoviruses (RVs) belong to the Enterovirus genus within the Picornaviridae family, and show genetic similarities. These viruses are related to mild diseases, but EVs infections can sometimes lead to more severe complications. Current diagnostic molecular techniques should discriminate between the four EV and the three RV species that infect humans. The aim was to revise the EV and RV PCR-confirmed specimens by sequencing for genetic characterisation. MATERIAL AND METHODS Respiratory tract specimens were collected from patients with suspicion of respiratory infection. Respiratory viruses' laboratory-confirmation was performed by commercial multiplex real-time RT-PCR assays. Genetic characterisation of all EV and in a selection of RV was performed based on the phylogenetic analyses of partial VP1 and VP4/2 sequences, respectively. RESULTS From 19,957 tested specimens, 309 (1.5%) were EV-positive, 2546 (12%) were RV-positive, and 233 (1%) were EV/RV co-detections. The phylogenetic analyses revealed that: among single EV detections, 177/309 (57%) were characterised as EV, 2/309 (1%) as RV, and 130/309 (42%) could not be typed; among single 1771 RV detections (Ct < 35), 1651/1771 (93%) were characterised as RV, 3/1771 (0.3%) as EV and 117/1771 (6.7%) could not be typed. Among EV/RV co-detections, 62/233 (27%) were characterised as EV, 130/233 (56%) as RV and 41/233 (18%) could not be typed. CONCLUSIONS A diagnostic method well considered for routine laboratory-confirmation of respiratory viruses should discriminate EV and RV targets. RVs are usually associated with mild respiratory disease, but the potential relatedness of EVs to neurological complications makes their monitoring mandatory. Therefore, an accurate detection and differentiation should be required in commercial diagnostic solutions.
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Chauhan V, Thakur S, Sood RK, Thakur K. Limitations of CBNAAT for diagnosis of mycobacterium tuberculosis in gastric aspirate and pleural fluid. Indian J Tuberc 2019; 66:308-309. [PMID: 31151501 DOI: 10.1016/j.ijtb.2019.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 01/04/2017] [Accepted: 01/08/2019] [Indexed: 06/09/2023]
Affiliation(s)
- Vivek Chauhan
- Dr. RPGMC Kangra at Tanda, District Kangra, Himachal Pradesh, India.
| | - Suman Thakur
- Dr. RPGMC Kangra at Tanda, District Kangra, Himachal Pradesh, India
| | | | - Kamlesh Thakur
- Dr. RPGMC Kangra at Tanda, District Kangra, Himachal Pradesh, India
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Abstract
Approximately 93 years ago at the zoological laboratories of Harvard University, Keeler, a medical geneticist, discovered a retina from a male albino mouse that was completely devoid of visual cells (rods). This rodless mouse was to be the first ever reported murine model of retinal degeneration. Over the years, naturally occurring retinal degeneration mouse mutants have been identified in several common laboratory inbred lines including FVB/NJ (Pde6brd1) and C57BL/6N (Crb1rd8). It is therefore imperative that vision researchers employing other genetically induced retinal degeneration models and experimental models such as laser-induced choroidal neovascularization (CNV) or bright white-light exposure screen for such naturally occurring mutations to prevent costly misinterpretations. In this regard, we describe herein simple molecular-based techniques for screening the presence of some commonly encountered rd mutations (Pde6brd1, Crb1rd8, Pde6brd10, and Rpe65rd12).
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Truchado P, Gil MI, Moreno-Candel M, Allende A. Impact of weather conditions, leaf age and irrigation water disinfection on the major epiphytic bacterial genera of baby spinach grown in an open field. Food Microbiol 2019; 78:46-52. [PMID: 30497607 DOI: 10.1016/j.fm.2018.09.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/27/2018] [Accepted: 09/24/2018] [Indexed: 12/21/2022]
Abstract
The effects of factors such as weather conditions, leaf age and irrigation water disinfection on the main bacterial genera (total bacterial, Enterobacteriaceae and Pseudomonas) of baby spinach were studied. Culture-dependent and independent quantification techniques were compared. Cultivation was carried out over two consecutive trials in commercial open field divided in two plots: 1) baby spinach irrigated with untreated surface water and 2) baby spinach irrigated with chlorine dioxide (ClO2) treated water. In all the cases, higher concentrations of bacteria were detected using molecular quantification in comparison with culture dependent techniques. Based on the obtained results, wind speed, solar radiation and relative humidity seem to have an impact on the levels of total bacterial, Enterobacteriaceae and Pseudomonas during cultivation of baby spinach. However, further studies would be needed to confirm this tendency. Water disinfection treatments (ClO2), when applied to irrigation water, impacted differently the bacterial genera evaluated in the present study. Thus, although no significant effects were observed in total bacterial enumerations of baby spinach irrigated with ClO2 treated water; significant reductions were detected in Enterobacteriaceae (19%) and Pseudomonas spp. (14%) levels. These results were also confirmed using specific culture-dependent methods. On the other hand, leaf age did not influence the levels of the main bacterial genera of baby spinach. Considering that, a large proportion of foodborne and pathogenic bacteria associated to fresh produce belong to the Enterobacteriaceae family and Pseudomonas genera, reductions in these bacterial groups could be beneficial. However, these groups are very diverse, making difficult to link the measurement of Enterobacteriaceae and Pseudomonas levels with the presence/abundance of potential pathogenic and spoilage microorganisms.
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Hantel A, Stock W, Kosuri S. Molecular Minimal Residual Disease Testing in Acute Myeloid Leukemia: A Review for the Practicing Clinician. Clin Lymphoma Myeloma Leuk 2018; 18:636-47. [PMID: 30006258 DOI: 10.1016/j.clml.2018.06.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/12/2018] [Accepted: 06/19/2018] [Indexed: 11/21/2022]
Abstract
Minimal residual disease (MRD) testing in acute myeloid leukemia is increasingly being used to assess treatment response and stratify the risk of relapse for individual patients. Molecular methods for MRD testing began with PCR-based assays for individual recurrent mutations. To date, there is robust evidence for testing NPM1, CBFB-MYH11, and RUNX1/RUNXT1 mutations using this approach, though the best timing and threshold level for each mutation varies. More recent approaches have been with PCR-based multigene panels, occasionally combined with flow cytometric techniques, and next-generation sequencing techniques. This review outlines the various techniques used in molecular approaches to MRD, the evidence behind individual mutation testing, and the novel approaches for evaluating multigene MRD so that clinicians can understand and incorporate these evaluations into their practice.
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Curtis KA, Morrison D, Rudolph DL, Shankar A, Bloomfield LSP, Switzer WM, Owen SM. A multiplexed RT-LAMP assay for detection of group M HIV-1 in plasma or whole blood. J Virol Methods 2018; 255:91-97. [PMID: 29474813 DOI: 10.1016/j.jviromet.2018.02.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 02/15/2018] [Accepted: 02/19/2018] [Indexed: 12/24/2022]
Abstract
Isothermal nucleic acid amplification techniques, such as reverse-transcription loop-mediated isothermal amplification (RT-LAMP), exhibit characteristics that are suitable for the development of a rapid, low-cost NAT that can be used at the POC. For demonstration of utility for global use, studies are needed to validate the performance of RT-LAMP for the detection of divergent subtypes. In this study, we designed and evaluated multiplexed HIV-1 integrase RT-LAMP primers to detect subtypes within group M, along with an RNase P positive internal processing and amplification control. Using a panel of 26 viral isolates representing the major circulating subtypes, we demonstrated detection of all isolates of subtypes A1, C, D, F1, F2, G, CRF01_AE, CRF02_AG, and two unique recombinant forms (URFs). A whole blood panel created with one representative isolate of each subtype was successfully amplified with the group M HIV-1 integrase and RNase P internal control primers. The group M HIV-1 RT-LAMP assay was further evaluated on 61 plasma specimens obtained from persons from Cameroon and Uganda. The sequence-conserved group M HIV-1 RT-LAMP primers, coupled to a low-cost amplification device, may improve diagnosis of acute infection at the POC and provide timely confirmation of HIV status.
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Affiliation(s)
- Kelly A Curtis
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Daphne Morrison
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Donna L Rudolph
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Anupama Shankar
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Laura S P Bloomfield
- Stanford University School of Medicine, Stanford, CA, USA; Emmett Interdisciplinary Program in Environment and Resources, Stanford, CA, USA
| | - William M Switzer
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - S Michele Owen
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Ghazaei C. Pathogenic Leptospira: Advances in understanding the molecular pathogenesis and virulence. Open Vet J 2018; 8:13-24. [PMID: 29445617 PMCID: PMC5806663 DOI: 10.4314/ovj.v8i1.4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Accepted: 01/08/2018] [Indexed: 12/16/2022] Open
Abstract
Leptospirosis is a common zoonotic disease has emerged as a major public health problem, with developing countries bearing disproportionate burdens. Although the diverse range of clinical manifestations of the leptospirosis in humans is widely documented, the mechanisms through which the pathogen causes disease remain undetermined. In addition, leptospirosis is a much-neglected life-threatening disease although it is one of the most important zoonoses occurring in a diverse range of epidemiological distribution. Recent advances in molecular profiling of pathogenic species of the genus Leptospira have improved our understanding of the evolutionary factors that determine virulence and mechanisms that the bacteria employ to survive. However, a major impediment to the formulation of intervention strategies has been the limited understanding of the disease determinants. Consequently, the association of the biological mechanisms to the pathogenesis of Leptospira, as well as the functions of numerous essential virulence factors still remain implicit. This review examines recent advances in genetic screening technologies, the underlying microbiological processes, the virulence factors and associated molecular mechanisms driving pathogenesis of Leptospira species.
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Affiliation(s)
- Ciamak Ghazaei
- Department of Microbiology, University of Mohaghegh Ardabili, P.O. Box 179, Ardabil, Iran
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Dwivedi S, Purohit P, Misra R, Pareek P, Goel A, Khattri S, Pant KK, Misra S, Sharma P. Diseases and Molecular Diagnostics: A Step Closer to Precision Medicine. Indian J Clin Biochem 2017; 32:374-398. [PMID: 29062170 PMCID: PMC5634985 DOI: 10.1007/s12291-017-0688-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The current advent of molecular technologies together with a multidisciplinary interplay of several fields led to the development of genomics, which concentrates on the detection of pathogenic events at the genome level. The structural and functional genomics approaches have now pinpointed the technical challenge in the exploration of disease-related genes and the recognition of their structural alterations or elucidation of gene function. Various promising technologies and diagnostic applications of structural genomics are currently preparing a large database of disease-genes, genetic alterations etc., by mutation scanning and DNA chip technology. Further the functional genomics also exploring the expression genetics (hybridization-, PCR- and sequence-based technologies), two-hybrid technology, next generation sequencing with Bioinformatics and computational biology. Advances in microarray “chip” technology as microarrays have allowed the parallel analysis of gene expression patterns of thousands of genes simultaneously. Sequence information collected from the genomes of many individuals is leading to the rapid discovery of single nucleotide polymorphisms or SNPs. Further advances of genetic engineering have also revolutionized immunoassay biotechnology via engineering of antibody-encoding genes and the phage display technology. The Biotechnology plays an important role in the development of diagnostic assays in response to an outbreak or critical disease response need. However, there is also need to pinpoint various obstacles and issues related to the commercialization and widespread dispersal of genetic knowledge derived from the exploitation of the biotechnology industry and the development and marketing of diagnostic services. Implementation of genetic criteria for patient selection and individual assessment of the risks and benefits of treatment emerges as a major challenge to the pharmaceutical industry. Thus this field is revolutionizing current era and further it may open new vistas in the field of disease management.
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Affiliation(s)
- Shailendra Dwivedi
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, 342005 India
| | - Purvi Purohit
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, 342005 India
| | - Radhieka Misra
- Era's Lucknow Medical College and Hospital, Lucknow, 226003 India
| | - Puneet Pareek
- Department of Radio-Therapy, All India Institute of Medical Sciences, Jodhpur, 342005 India
| | - Apul Goel
- Department of Urology, King George Medical University, Lucknow, 226003 India
| | - Sanjay Khattri
- Department of Pharmacology and Therapeutics, King George Medical University, Lucknow, 226003 India
| | - Kamlesh Kumar Pant
- Department of Pharmacology and Therapeutics, King George Medical University, Lucknow, 226003 India
| | - Sanjeev Misra
- Department of Surgical Oncology, All India Institute of Medical Sciences, Jodhpur, 342005 India
| | - Praveen Sharma
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, 342005 India
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32
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Schmitt FC, Vielh P. Expectations and Projections for the Future of Nongynecolgical Cytology 10 Years Ago: Did They Materialize and How Did We Do? Acta Cytol 2017; 61:373-407. [PMID: 28693027 DOI: 10.1159/000477713] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 05/23/2017] [Indexed: 01/15/2023]
Abstract
In 2007, an article entitled "How Technology Is Reshaping the Practice of Nongynecologic Cytology: Frontiers of Cytology Symposium" [Bibbo: Acta Cytol 2007;51:123-152] was published. The moderator and editor was Marluce Bibbo, previous Editor-in-Chief of Acta Cytologica, and 17 participants from countries throughout the world were asked to answer how new technologies were being applied in their respective laboratories and whether future advances and challenges can be predicted. Ten years later, two previous participants in this Golden Anniversary Cytology Symposium were asked by Kari Syrjänen, current Editor-in-Chief of Acta Cytologica, to make a reappraisal of the 2007 predictions.
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Affiliation(s)
- Fernando C Schmitt
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
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33
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Saratale RG, Saratale GD, Pugazhendhi A, Zhen G, Kumar G, Kadier A, Sivagurunathan P. Microbiome involved in microbial electrochemical systems (MESs): A review. Chemosphere 2017; 177:176-188. [PMID: 28288426 DOI: 10.1016/j.chemosphere.2017.02.143] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 02/22/2017] [Accepted: 02/27/2017] [Indexed: 06/06/2023]
Abstract
Microbial electrochemical systems (MESs) are an attracting technology for the disposal of wastewater treatment and simultaneous energy production. In MESs, at the anode microorganisms through the catalytic activity generates electrons that can be converted into electricity or other valuable chemical compounds. Microorganisms those having ability to donate and accept electrons to and from anode and cathode electrodes, respectively are recognized as 'exoelectrogens'. In the MESs, it renders an important function for its performance. In the present mini-review, we have discussed the role of microbiome including pure culture, enriched culture and mixed culture in different BESs application. The effects of operational and biological factors on microbiome development have been discussed. Further discussion about the molecular techniques for the evaluation of microbial community analysis is addressed. In addition different electrochemical techniques for extracellular electron transfer (EET) mechanism of electroactive biofilms have been discussed. This review highlights the importance of microbiome in the development of MESs, effective operational factors for exo-electrogens activities as well their key challenges and future technological aspects are also briefly discussed.
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Affiliation(s)
- Rijuta Ganesh Saratale
- Research Institute of Biotechnology and Medical Converged Science, Dongguk University- Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, 10326, Republic of Korea
| | - Ganesh Dattatraya Saratale
- Department of Food Science and Biotechnology, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, 10326, Republic of Korea
| | - Arivalagan Pugazhendhi
- Department of Environmental Engineering, Daegu University, Jillyang, Gyeongsan, Gyeongbuk, Republic of Korea
| | - Guangyin Zhen
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Dongchuan Rd. 500, Shanghai 200241, China
| | - Gopalakrishnan Kumar
- Department of Environmental Engineering, Daegu University, Jillyang, Gyeongsan, Gyeongbuk, Republic of Korea
| | - Abudukeremu Kadier
- Department of Chemical and Process Engineering, Faculty of Engineering and Built Environment, National University of Malaysia (UKM), 43600 UKM Bangi, Selangor, Malaysia
| | - Periyasamy Sivagurunathan
- Green Energy Technology Research Group, Ton Duc Thang University, Ho Chi Minh City, Viet Nam; Faculty of Environment and Labour Safety, Ton Duc Thang University, Ho Chi Minh City, Viet Nam.
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Abstract
Constructed wetlands (CWs) constitute an interesting alternative option to conventional systems for wastewater treatment. This technology is based on the utilization of the concerted activity of microorganisms for the removal of contaminants. Consequently, knowledge on the microbial assemblages dwelling CWs and the different environmental factors which can alter their activities is crucial for understanding their performance. In the last decades, the use of molecular techniques to characterize these communities and more recently, application of -omics tools, have broaden our view of microbial diversity and function in wastewater microbiology. In this manuscript, a review of the current knowledge on microbial diversity in CWs is offered, placing particular emphasis on the different molecular studies carried out in this field. The effect of environmental conditions, such as plant species, hydraulic design, water depth, organic carbon, temperature and substrate type on prokaryotic communities has been carefully revised, and the different studies highlight the importance of these factors in carbon, nitrogen and sulfur cycles. Overall, the novel -omics open a new horizon to study the diversity and ecophysiology of microbial assemblages and their interactions in CWs, particularly for those microorganisms belonging to the rare biosphere not detectable with conventional molecular techniques.
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Affiliation(s)
- Olga Sánchez
- Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
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35
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Monobe MM, da Silva RC, Araujo Junior JP, Takahira RK. Microfilaruria by Dirofilaria immitis in a dog: a rare clinical pathological finding. J Parasit Dis 2017; 41:805-8. [PMID: 28848282 DOI: 10.1007/s12639-017-0892-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 01/27/2017] [Indexed: 10/20/2022] Open
Abstract
A 6-year-old Labrador with history of hyperpnea, respiratory distress, ascites and paraparesis, presented Dirofilaria immitis microfilariae in the blood smear, cytology of the abdominal fluid and urine. The positive samples were confirmed by multiplex-PCR (COI gene) and sequencing, and presented 98% homology to D. immitis (GenBank accession nos. KC107805.1, EU159111.1, EU163945.1, DQ358815.1, and AJ537512-1). Based on the presented results and the physiopathology of the heartworm disease, molecular techniques may be helpful and accurate in the diagnosis of the disease in vertebrates, and microfilaruria, even uncommon, should be considered on a renal failure evaluation.
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Faye M, Dacheux L, Weidmann M, Diop SA, Loucoubar C, Bourhy H, Sall AA, Faye O. Development and validation of sensitive real-time RT-PCR assay for broad detection of rabies virus. J Virol Methods 2017; 243:120-30. [PMID: 28174073 DOI: 10.1016/j.jviromet.2016.12.019] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/26/2016] [Accepted: 12/27/2016] [Indexed: 01/17/2023]
Abstract
Rabies virus (RABV) remains one of the most important global zoonotic pathogens. RABV causes rabies, an acute encephalomyelitis associated with a high rate of mortality in humans and animals and affecting different parts of the world, particularly in Asia and Africa. Confirmation of rabies diagnosis relies on laboratory diagnosis, in which molecular techniques such as detection of viral RNA by reverse transcription polymerase chain reaction (RT-PCR) are increasingly being used. In this study, two real-time quantitative RT-PCR assays were developed for large-spectrum detection of RABV, with a focus on African isolates. The primer and probe sets were targeted highly conserved regions of the nucleoprotein (N) and polymerase (L) genes. The results indicated the absence of non-specific amplification and cross-reaction with a range of other viruses belonging to the same taxonomic family, i.e. Rhabdoviridae, as well as negative brain tissues from various host species. Analytical sensitivity ranged between 100 to 10 standard RNA copies detected per reaction for N-gene and L-gene assays, respectively. Effective detection and high sensitivity of these assays on African isolates showed that they can be successfully applied in general research and used in diagnostic process and epizootic surveillance in Africa using a double-check strategy.
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Coiro CJ, Coelho LGG, da Silva RC, Langoni H. Molecular characterization of Leishmania spp. isolated from Brazilian stray dogs from an endemic area for canine visceral leishmaniasis. Vet Parasitol Reg Stud Reports 2016; 7:9-13. [PMID: 31014661 DOI: 10.1016/j.vprsr.2016.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 08/22/2016] [Accepted: 11/28/2016] [Indexed: 10/27/2022]
Abstract
Canine visceral leishmaniasis (CVL) is a worldwide anthropozoonosis caused by an intracellular parasite protozoan, Leishmania spp. In Americas, Leishmania (Leishmania) infantum is the causative agent, transmitted by sandflies, Lutzomyia longipalpis, after blood meal in domestic dogs, the main reservoir. The present study was aimed to determine the occurrence of Leishmania spp. and L. infantum in peripheral blood, and popliteal lymph node and bone marrow aspirate samples of 164 Brazilian stray dogs from an endemic area for CVL using the Polymerase Chain Reaction (PCR). For Leishmania spp., 56 (34.15%; 27.32-41.71%) blood, 102 (62.20%; 54.56-69.26%) lymph node, and 115 (70.12%; 62.71-76.60%) bone marrow samples tested positive, whereas 46 (28.05%; 21.74-35.38%), 94 (57.32%; 49.65-64.64%), and 114 (69.51%; 62.07-76.04%), respectively, resulted positive for L. infantum. Restriction Fragment Length Polymorphism (ITS1-RFLP) and sequencing were used to characterize the positive samples to Leishmania spp., but negative to L. infantum. Twenty (10 blood, 9 lymph node and 1 bone marrow) samples were characterized and matched the L. donovani complex species, with 99-100% similarity to L. donovani complex species (GenBank accession n.KC998879.1, JQ730002.1, GU045591.1, HQ830353.1, HM130608.1). The present study reports a high prevalence of stray dogs infected with leishmania species responsible for VL in the studied area, in which the observed diversity of leishmania species may contributes for further epidemiological studies.
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Affiliation(s)
- Carla Janeiro Coiro
- School of Veterinary Medicine and Animal Science, UNESP Univ Estadual Paulista, Department of Veterinary Hygiene and Public Health, Campus Botucatu, São Paulo, Brazil
| | - Laiza Gabriela Gavioli Coelho
- School of Veterinary Medicine and Animal Science, UNESP Univ Estadual Paulista, Department of Veterinary Hygiene and Public Health, Campus Botucatu, São Paulo, Brazil
| | - Rodrigo Costa da Silva
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Mississippi State, USA
| | - Helio Langoni
- School of Veterinary Medicine and Animal Science, UNESP Univ Estadual Paulista, Department of Veterinary Hygiene and Public Health, Campus Botucatu, São Paulo, Brazil.
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Amor A, Rodriguez E, Saugar JM, Arroyo A, López-Quintana B, Abera B, Yimer M, Yizengaw E, Zewdie D, Ayehubizu Z, Hailu T, Mulu W, Echazú A, Krolewieki AJ, Aparicio P, Herrador Z, Anegagrie M, Benito A. High prevalence of Strongyloides stercoralis in school-aged children in a rural highland of north-western Ethiopia: the role of intensive diagnostic work-up. Parasit Vectors 2016; 9:617. [PMID: 27903301 PMCID: PMC5131444 DOI: 10.1186/s13071-016-1912-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 11/24/2016] [Indexed: 12/11/2022] Open
Abstract
Background Soil-transmitted helminthiases (hookworms, Ascaris lumbricoides and Trichuris trichiura) are extremely prevalent in school-aged children living in poor sanitary conditions. Recent epidemiological data suggest that Strongyloides stercoralis is highly unreported. However, accurate data are essential for conducting interventions aimed at introducing control and elimination programmes. Methods We conducted a cross-sectional survey of 396 randomly selected school-aged children in Amhara region in rural area in north-western Ethiopia, to assess the prevalence of S. stercoralis and other intestinal helminths. We examined stools using three techniques: conventional stool concentration; and two S. stercoralis-specific methods, i.e. the Baermann technique and polymerase chain reaction. The diagnostic accuracy of these three methods was then compared. Results There was an overall prevalence of helminths of 77.5%, with distribution differing according to school setting. Soil-transmitted helminths were recorded in 69.2%. Prevalence of S. stercoralis and hookworm infection was 20.7 and 54.5%, respectively, and co-infection was detected in 16.3% of cases. Schistosoma mansoni had a prevalence of 15.7%. Prevalence of S. stercoralis was shown 3.5% by the conventional method, 12.1% by the Baermann method, and 13.4% by PCR, which thus proved to be the most sensitive. Conclusions Our results suggest that S. stercoralis could be overlooked and neglected in Ethiopia, if studies of soil-transmitted helminths rely on conventional diagnostic techniques alone. A combination of molecular and stool microscopy techniques yields a significantly higher prevalence. In view of the fact that current control policies for triggering drug administration are based on parasite prevalence levels, a comprehensive diagnostic approach should instead be applied to ensure comprehensive control of helminth infections.
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Affiliation(s)
- Aranzazu Amor
- National Center of Tropical Medicine, Institute of Health Carlos III, Madrid, Spain. .,Mundo Sano Foundation, Madrid, Spain.
| | - Esperanza Rodriguez
- Parasitology Service, National Centre for Microbiology, Institute of Health Carlos III, Madrid, Spain
| | - José M Saugar
- Parasitology Service, National Centre for Microbiology, Institute of Health Carlos III, Madrid, Spain
| | - Ana Arroyo
- Service of Microbiology and Parasitology, Hospital La Paz-Carlos III, Madrid, Spain
| | | | - Bayeh Abera
- Department of Microbiology, Immunology and Parasitology, College of Medicine and Health Science, Bahir Dar University, Bahir Dar, Ethiopia
| | - Mulat Yimer
- Department of Microbiology, Immunology and Parasitology, College of Medicine and Health Science, Bahir Dar University, Bahir Dar, Ethiopia
| | - Endalew Yizengaw
- Department of Microbiology, Immunology and Parasitology, College of Medicine and Health Science, Bahir Dar University, Bahir Dar, Ethiopia
| | - Derejew Zewdie
- Department of Microbiology, Immunology and Parasitology, College of Medicine and Health Science, Bahir Dar University, Bahir Dar, Ethiopia
| | - Zimman Ayehubizu
- Department of Microbiology, Immunology and Parasitology, College of Medicine and Health Science, Bahir Dar University, Bahir Dar, Ethiopia
| | - Tadesse Hailu
- Department of Microbiology, Immunology and Parasitology, College of Medicine and Health Science, Bahir Dar University, Bahir Dar, Ethiopia
| | - Wondemagegn Mulu
- Department of Microbiology, Immunology and Parasitology, College of Medicine and Health Science, Bahir Dar University, Bahir Dar, Ethiopia
| | - Adriana Echazú
- Instituto de Investigaciones en Enfermedades Tropicales, Universidad Nacional de Salta, sede regional Orán, San Ramón de la Nueva Orán, Salta, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Alejandro J Krolewieki
- Instituto de Investigaciones en Enfermedades Tropicales, Universidad Nacional de Salta, sede regional Orán, San Ramón de la Nueva Orán, Salta, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Pilar Aparicio
- National School of Health, Institute of health Carlos III, Madrid, Spain
| | - Zaida Herrador
- National Center of Tropical Medicine, Institute of Health Carlos III, Madrid, Spain
| | - Melaku Anegagrie
- National Center of Tropical Medicine, Institute of Health Carlos III, Madrid, Spain.,Mundo Sano Foundation, Madrid, Spain
| | - Agustín Benito
- National Center of Tropical Medicine, Institute of Health Carlos III, Madrid, Spain
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Taşkan E. Performance of mixed algae for treatment of slaughterhouse wastewater and microbial community analysis. Environ Sci Pollut Res Int 2016; 23:20474-20482. [PMID: 27460027 DOI: 10.1007/s11356-016-7241-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 07/12/2016] [Indexed: 06/06/2023]
Abstract
This study investigated organic matter (OM) and nutrient removal efficiency of mixed algal species from slaughterhouse wastewater (SWW) by using photo-bioreactor. For this purpose, different dilution multiples of 10, 4, and 2 were applied to the SWW, and pure wastewater was finally used for algal cultivation. OM and nutrient removal performance in an algal photo-bioreactor were severely affected by the dilution ratio. After 7 days of cultivation, the highest removal percentages of total organic carbon (TOC), total nitrogen (TN), and total phosphorus (TP) were 89.6, 70.2, and 96.2 %, respectively. Furthermore, the changes in eukaryotic algae and cyanobacterial species in the algal photo-bioreactors were investigated using polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) techniques. The results indicated that cyanobacterial species were more efficient than eukaryotic species in removing nutrients from the SWW. This study suggests that mixed algal photo-bioreactors could be used efficiently in the treatment of SWW.
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Affiliation(s)
- Ergin Taşkan
- Faculty of Engineering, Department of Environmental Engineering, Firat University, 23119, Elazig, Turkey.
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Coorevits L, Vanscheeuwijck C, Traen A, Bingé L, Ryckaert I, Padalko E. Evaluation of Copan FLOQSwab for the molecular detection of Chlamydia trachomatis by Abbott RealTime CT PCR. Acta Clin Belg 2015; 70:398-402. [PMID: 26107497 DOI: 10.1179/2295333715y.0000000036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
OBJECTIVES We evaluated Copan FLOQSwabs next to Abbott swabs for the detection of Chlamydia trachomatis (CT) by Abbott RealTime PCR. METHODS We collected 1062 paired swabs from female sex workers. The study was divided in two arms, according to the order of swab collection. RESULTS If the Abbott swab was collected first, 501 couples were concordant and two discordant (Abbott negative and Copan positive). If the Copan swab was collected first, 537 couples were concordant and 10 discordant (eight Abbott negative and Copan positive and two Abbott positive and Copan negative). All discordant samples contained low levels of C. trachomatis. Technical issues lead to retesting of 64 Copan and 21 Abbott swabs. CONCLUSION Our results show that Copan FLOQSwabs can be used interchangeably with Abbott swabs. While appearing to have an advantage in detecting more positive samples, the use of Copan swabs led to a higher retesting rate due to technical errors.
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Affiliation(s)
- L Coorevits
- Department of Laboratory Medicine, Ghent University Hospital , Belgium
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41
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Chettri R, Tamang JP. Bacillus species isolated from tungrymbai and bekang, naturally fermented soybean foods of India. Int J Food Microbiol 2015; 197:72-6. [PMID: 25574846 DOI: 10.1016/j.ijfoodmicro.2014.12.021] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 12/02/2014] [Accepted: 12/19/2014] [Indexed: 10/24/2022]
Abstract
Tungrymbai and bekang are naturally fermented soybean foods commonly consumed in Meghalaya and Mizoram states of India. A total of 39 samples of tungrymbai and 43 samples of bekang were collected from different villages and markets of Meghalaya and Mizoram, respectively and were analysed for microbial load. In both tungrymbai and bekang, the average population of Bacillus spp. was 8.2±0.1 log cfu/g. A total of 428 isolates of Bacillus were isolated from tungrymbai (211) and bekang (217) for detailed identification. On the basis of a combination of phenotypic and molecular characterisation using ARDRA, ITS-PCR and RAPD-PCR techniques, species of Bacillus isolated from tungrymbai were identified as Bacillus licheniformis (25.5%), Bacillus pumilus (19.5%) and Bacillus subtilis (55%), and species of Bacillus from bekang were Bacillus brevis (2%), Bacillus circulans (7.5%), Bacillus coagulans (6.5%), B. licheniformis (16.5%), B. pumilus (9.1%), Bacillus sphaericus (4.6%), B. subtilis (51.8%), and Lysinibacillus fusiformis (2%). The most dominant bacterium in both products was B. subtilis.
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Affiliation(s)
- Rajen Chettri
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Tadong 737102, Sikkim, India
| | - Jyoti Prakash Tamang
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Tadong 737102, Sikkim, India.
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42
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Guillet-Caruba C, Martinez V, Doucet-Populaire F. [The new tools of microbiological diagnosis of tuberculosis]. Rev Med Interne 2014; 35:794-800. [PMID: 25112804 DOI: 10.1016/j.revmed.2014.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 05/06/2014] [Indexed: 10/24/2022]
Abstract
This review focuses on the role of new tools in the "modern" microbiological diagnosis of tuberculosis. Traditional techniques of microscopy and culture remain essential to diagnostic certainty, but some innovations replace daily the older techniques such as the identification of Mycobacterium tuberculosis complex by immunochromatography or mass spectrometry MALDI-TOF type from positive cultures, or susceptibility testing in liquid medium. New tools that use molecular techniques have become important. They all have in common to optimize the fight against tuberculosis by reducing diagnostic delay. They also allow rapid detection of drug resistance. However, the techniques of gene amplification directly from clinical samples are still less sensitive than culture. Bacteriological diagnosis of tuberculosis disease therefore still relies on the complementarities of different phenotypic and molecular techniques.
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Affiliation(s)
- C Guillet-Caruba
- Service de bactériologie-hygiène, hôpital Antoine-Béclère, AP-HP, HUPS, 157, rue de la Porte-de-Trivaux, 92140 Clamart, France
| | - V Martinez
- Service de médecine interne et immunologie clinique, hôpital Antoine-Béclère, AP-HP, HUPS, 157, rue de la Porte-de-Trivaux, 92140 Clamart, France; Inserm U996, labex lhermit, université Paris-Sud, 32, rue des Carnets, 92140 Clamart, France
| | - F Doucet-Populaire
- Service de bactériologie-hygiène, hôpital Antoine-Béclère, AP-HP, HUPS, 157, rue de la Porte-de-Trivaux, 92140 Clamart, France.
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Aguín O, Abuín M, Lozano F, Ferreiroa V, Corral M, Mansilla JP. [Incidence and distribution of the genus Armillaria in vineyards of the five protected designation of origin wines in Galicia (Northwestern Spain)]. Rev Iberoam Micol 2015; 32:13-9. [PMID: 24603128 DOI: 10.1016/j.riam.2013.10.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 10/03/2013] [Accepted: 10/23/2013] [Indexed: 11/22/2022] Open
Abstract
BLACKGROUND The genus Armillaria, specifically Armillaria mellea, is an important phytopathological problem in the wine sector in Galicia (NW Spain), having caused yield reductions in vineyards for the last 15 years. The fungus attacks the root system, resulting in a decrease in vigour, and eventually in the death of the plant. Up to now, there is no chemical or biological method really effective against the pathogen once it has infected the plant. AIMS The main objective of this work was to study the incidence and distribution of the genus Armillaria across the five Galician protected designation of origin (DO) wines (namely Rías Baixas, Ribeiro, Ribeira Sacra, Valdeorras and Monterrei) through the application of molecular techniques. METHODS A total of 624 samples (483 soils and 141 symptomatic vines) were analyzed by nested-PCR/RFLP, PCR-RFLP and phylogeny. RESULTS Armillaria mellea is widely distributed in vineyards of the five DO wines, with the highest incidence in the Ribeiro DO. CONCLUSIONS Preventive control measures against Armillaria mellea must be established in the five DO wines of Galicia, in order to reduce the advance of white root rot.
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Adzitey F, Huda N, Ali GRR. Molecular techniques for detecting and typing of bacteria, advantages and application to foodborne pathogens isolated from ducks. 3 Biotech 2013; 3:97-107. [PMID: 28324565 PMCID: PMC3597138 DOI: 10.1007/s13205-012-0074-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 05/23/2012] [Indexed: 01/18/2023] Open
Abstract
In recent times, several foodborne pathogens have become important and a threat to public health. Surveillance studies have provided data and a better understanding into the existence and spread of foodborne pathogens. The application of molecular techniques for detecting and typing of foodborne pathogens in surveillance studies provide reliable epidemiological data for tracing the source of human infections. A wide range of molecular techniques (including pulsed field gel electrophoresis, multilocus sequence typing, random amplified polymorphism deoxyribonucleic acid, repetitive extragenic palindromic, deoxyribonucleic acid sequencing, multiplex polymerase chain reaction and many more) have been used for detecting, speciating, typing, classifying and/or characterizing foodborne pathogens of great significance to humans. Farm animals including chickens, cattle, sheep, goats and pigs, and others (such as domestic and wild animals) have been reported to be primary reservoirs for foodborne pathogens. The consumption of contaminated poultry meats or products has been considered to be the leading source of human foodborne infections. Ducks like other farm animals are important source of foodborne pathogens and have been implicated in some human foodborne illnesses and deaths. Nonetheless, few studies have been conducted to explore the potential of ducks in causing foodborne outbreaks, diseases and its consequences. This review highlights some common molecular techniques, their advantages and those that have been applied to pathogens isolated from ducks and their related sources.
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Affiliation(s)
- Frederick Adzitey
- Food Technology Division, School of Industrial Technology, Universiti Sains Malaysia, 11800, Pulau Pinang, Malaysia
- Animal Science Department, University for Development Studies, Box TL 1882, Tamale, Ghana
| | - Nurul Huda
- Food Technology Division, School of Industrial Technology, Universiti Sains Malaysia, 11800, Pulau Pinang, Malaysia
| | - Gulam Rusul Rahmat Ali
- Food Technology Division, School of Industrial Technology, Universiti Sains Malaysia, 11800, Pulau Pinang, Malaysia.
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Abstract
In the recent past, the threat of a global bioterrorist attack has increased dramatically. In addition to the already existing microorganisms and techniques, the recent explosion in biotechnology has considerably added to the arsenal of the bioterrorist. Molecular technologies are now available which can be used by committed bioterrorist groups to manipulate and modify microorganisms so as to make them increasingly infectious, virulent or treatment resistant for causing maximum casualties. Infectious diseases which are likely to be used as bioweapons are Anthrax, Botulism, Plague, Smallpox and Brucella. Molecular techniques like immunoassays and nucleic acid amplification are now available to detect bioattacks. This article discusses the threat of bioterrorism. It also evaluates the molecular diagnostic methods and the future of early containment of a bioterrorist attack using molecular techniques.
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Affiliation(s)
- N Moorchung
- Reader (Department of Pathology), AFMC, Pune 411040
| | - A K Sharma
- Consultant (Surgery), Command Hospital (EC), Kolkata
| | - S R Mehta
- DGMS (Army), Dte Gen Medical Services, AG's Branch, Integrated HQ of MOD, 'L' Block, New Delhi
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46
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Sirintrapun SJ, Parwani AV. Molecular Pathology of the Genitourinary Tract: Prostate and Bladder. Surg Pathol Clin 2008; 1:211-36. [PMID: 26837907 DOI: 10.1016/j.path.2008.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The knowledge of cellular mechanisms in tumors of the prostate and bladder has grown exponentially. Molecular technologies have led to the discovery of TMPRSS2 in prostate cancer and the molecular pathways distinguishing low- and high-grade urothelial neoplasms. UroVysion with fluorescence in situ hybridization is already commonplace as an adjunct to cytologic diagnosis of urothelial neoplasms. This trend portends the future in which classification and diagnosis of tumors of the prostate and bladder through morphologic analysis will be supplemented by molecular information correlating with prognosis and targeted therapy. This article outlines tumor molecular pathology of the prostate and bladder encompassing current genomic, epigenomic, and proteonomic findings.
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Affiliation(s)
- S Joseph Sirintrapun
- Pathology Informatics, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Anil V Parwani
- Department of Pathology, University of Pittsburgh Medical Center Shadyside Hospital, Room WG 07, 5230 Centre Avenue, Pittsburgh, PA 15232, USA.
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