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Young D, Joshi A, Huang L, Munk B, Wurzbacher C, Youssef NH, Elshahed MS, Moon CD, Ochsenreither K, Griffith GW, Callaghan TM, Sczyrba A, Lebuhn M, Flad V. Simultaneous Metabarcoding and Quantification of Neocallimastigomycetes from Environmental Samples: Insights into Community Composition and Novel Lineages. Microorganisms 2022; 10:1749. [PMID: 36144352 PMCID: PMC9504928 DOI: 10.3390/microorganisms10091749] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/16/2022] [Accepted: 08/24/2022] [Indexed: 11/30/2022] Open
Abstract
Anaerobic fungi from the herbivore digestive tract (Neocallimastigomycetes) are primary lignocellulose modifiers and hold promise for biotechnological applications. Their molecular detection is currently difficult due to the non-specificity of published primer pairs, which impairs evolutionary and ecological research with environmental samples. We developed and validated a Neocallimastigomycetes-specific PCR primer pair targeting the D2 region of the ribosomal large subunit suitable for screening, quantifying, and sequencing. We evaluated this primer pair in silico on sequences from all known genera, in vitro with pure cultures covering 16 of the 20 known genera, and on environmental samples with highly diverse microbiomes. The amplified region allowed phylogenetic differentiation of all known genera and most species. The amplicon is about 350 bp long, suitable for short-read high-throughput sequencing as well as qPCR assays. Sequencing of herbivore fecal samples verified the specificity of the primer pair and recovered highly diverse and so far unknown anaerobic gut fungal taxa. As the chosen barcoding region can be easily aligned and is taxonomically informative, the sequences can be used for classification and phylogenetic inferences. Several new Neocallimastigomycetes clades were obtained, some of which represent putative novel lineages such as a clade from feces of the rodent Dolichotis patagonum (mara).
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Affiliation(s)
- Diana Young
- Micro and Molecular Biology, Central Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture, 85354 Freising, Germany
| | - Akshay Joshi
- Biocatalysis, Environment and Process Technology Unit, Life Science and Facility Management, ZHAW, 8820 Wadenswil, Switzerland
- Department of Microbiology, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Liren Huang
- Center for Biotechnology (CeBiTec), University of Bielefeld, 33615 Bielefeld, Germany
| | - Bernhard Munk
- Chair of Urban Water Systems Engineering, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Christian Wurzbacher
- Chair of Urban Water Systems Engineering, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Noha H. Youssef
- Department of Microbiology and Molecular Genetics (OSU), Oklahoma State University, Stillwater, OK 74074, USA
| | - Mostafa S. Elshahed
- Department of Microbiology and Molecular Genetics (OSU), Oklahoma State University, Stillwater, OK 74074, USA
| | - Christina D. Moon
- AgResearch, Grasslands Research Centre, Palmerston North 4442, New Zealand
| | - Katrin Ochsenreither
- Process Engineering in Life Sciences 2: Technical Biology (KIT), Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Gareth W. Griffith
- Department of Life Sciences (DoLS), Aberystwyth University, Aberystwyth SY23 3DD, Wales, UK
| | | | - Alexander Sczyrba
- Center for Biotechnology (CeBiTec), University of Bielefeld, 33615 Bielefeld, Germany
| | - Michael Lebuhn
- Micro and Molecular Biology, Central Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture, 85354 Freising, Germany
| | - Veronika Flad
- Micro and Molecular Biology, Central Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture, 85354 Freising, Germany
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Keller A, Krivec N, Markouli C, Spits C. Measuring Early Germ-Layer Specification Bias in Human Pluripotent Stem Cells. Methods Mol Biol 2022; 2429:57-72. [PMID: 35507155 DOI: 10.1007/978-1-0716-1979-7_5] [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: 06/14/2023]
Abstract
Human pluripotent stem cells have a wide variety of potential applications, ranging from clinical translation to in vitro disease modeling. However, there is significant variation in the potential of individual cell lines to differentiate towards each of the three germ layers as a result of (epi)genetic background, culture conditions, and other factors. We describe here in detail a methodology to evaluate this bias using short directed differentiation towards neuroectoderm, mesendoderm, and definitive endoderm in combination with quantification by RT-qPCR and immunofluorescent stains.
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Affiliation(s)
- Alexander Keller
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, Jette, Belgium
| | - Nuša Krivec
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, Jette, Belgium
| | - Christina Markouli
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, Jette, Belgium
| | - Claudia Spits
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, Jette, Belgium.
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Homaei Shandiz F, Fani A, Shakeri S, Sheikhi M, Ramezani Farkhani A, Shajiei A, Ayatollahi H. Fluorescent in Situ Hybridization and Real-Time Quantitative Polymerase Chain Reaction to Evaluate HER-2/neu Status in Breast Cancer. Iran J Pathol 2017; 12:67-73. [PMID: 29760755 PMCID: PMC5938726] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 04/06/2016] [Indexed: 11/17/2022]
Abstract
BACKGROUND Breast cancer remains the most common and second lethal cancer in females. HER-2/neu is one of the most important amplified oncogene in breast cancer. The amplification of HER-2 is correlated with decreased survival, metastasis, and early recurrence. The amplification of HER-2/neu gene and synthesis of the protein are reported in 10%-34% of breast cancer cases associated with tumor size, advanced tumor stage, high-grade tumor, young age at diagnosis, absence of steroid hormone receptor, and lymph node involvement. METHODS Fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC) methods are options to evaluate HER-2 expression. The current study aimed at identifying the correlation between FISH and real-time polymerase chain reaction (PCR) in measuring HER-2 expression. RESULTS The study investigated the performance of the real-time PCR as measured against FISH method in IHC +2 borderline cases. In a total of 120 IHC 2+ samples, 58.3% were negative and 41.6% positive for HER-2 gene, confirmed by FISH as a gold standard method. The real-time PCR ratio was <1.8 for a majority (82.8%) of the tumor samples with unamplified HER-2 gene by FISH as a gold standard assay. CONCLUSION Despite the fact that real-time PCR is a promising method to evaluate HER-2 over expression and a supplementary array to FISH, according to the results of the present study it cannot be utilized instead of gold standard techniques; therefore, additional studies should be carried out to appraise the value of this method to evaluate HER-2 over expression.
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Affiliation(s)
- Fatemeh Homaei Shandiz
- Dept. of Radiation Oncology, Mashhad University of Medical Sciences, Cancer Research Center
| | - Azar Fani
- Dept. of Radiation Oncology, Mashhad University of Medical Sciences, Cancer Research Center
| | - Sepideh Shakeri
- Cancer Molecular pathology Research center, Ghaem Hospital, Mashhad university of Medical sciences, Mashhad, Iran
| | - Maryam Sheikhi
- Cancer Molecular pathology Research center, Ghaem Hospital, Mashhad university of Medical sciences, Mashhad, Iran
| | | | - Arezoo Shajiei
- Cancer Molecular pathology Research center, Ghaem Hospital, Mashhad university of Medical sciences, Mashhad, Iran
| | - Hossein Ayatollahi
- Cancer Molecular pathology Research center, Ghaem Hospital, Mashhad university of Medical sciences, Mashhad, Iran
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Monini M, Vignolo E, Ianiro G, Ostanello F, Ruggeri FM, Di Bartolo I. Detection of Torque Teno Sus Virus in Pork Bile and Liver Sausages. Food Environ Virol 2016; 8:283-288. [PMID: 27294982 DOI: 10.1007/s12560-016-9249-1] [Citation(s) in RCA: 4] [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: 04/12/2016] [Accepted: 06/06/2016] [Indexed: 06/06/2023]
Abstract
Torque teno viruses (TTV) are small DNA viruses widespread among humans and pigs. The clinical significance of TTV infections in either humans or pigs is uncertain. In fact, TTV viremia is highly prevalent in patients with different pathologies, but it can also be frequently observed in healthy subjects. Virus infection in pigs is considered a putative cofactor in several diseases; despite being detected frequently in healthy animals, its role still remains unknown. The present study aimed to investigate the presence of Torque teno sus virus (TTSuV) in 62 bile samples collected from pigs at slaughterhouse and in 36 fresh pork liver sausages bought at point of sale. Quantitative Real-Time PCR, confirmed that 19.4 and 58.3 % of bile and sausage samples tested positive for TTSuV, respectively. The mean viral load was established as 5.6 × 104 GE/µl for bile and 7.16 × 103 GE/g for sausages. TTSuV nucleotide sequence analysis confirmed a wide heterogeneity among the circulating TTSuV strains, which included both TTSuV1 and TTSuV2.
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Affiliation(s)
- Marina Monini
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Edoardo Vignolo
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Giovanni Ianiro
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Fabio Ostanello
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano dell'Emilia, BO, Italy
| | - Franco Maria Ruggeri
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Ilaria Di Bartolo
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
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Araujo S, Freitas LO, Goulart LR, Goulart IMB. Molecular Evidence for the Aerial Route of Infection of Mycobacterium leprae and the Role of Asymptomatic Carriers in the Persistence of Leprosy. Clin Infect Dis 2016; 63:1412-1420. [PMID: 27558564 DOI: 10.1093/cid/ciw570] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [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: 02/16/2016] [Accepted: 07/11/2016] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Leprosy persists as a public health problem. The chain of transmission and mechanism of infection are not completely understood. In the current study, we investigated the route of infection and of disease onset, from airway exposure, colonization, and bloodstream dissemination. METHODS Mycobacterium leprae DNA was detected through quantitative polymerase chain reaction in nasal vestibule, nasal turbinate mucosa, and peripheral blood samples, along with anti-phenolic glycolipid I serology and skin tests from the same individual, from 113 leprosy patients and 104 household contacts of patients (HHCs). Bivariate statistics and multiple correspondence analysis were employed. RESULTS The rates of DNA positivity among patients were 66.4% (75 of 113) for nasal swab samples, 71.7% (81 of 113) for nasal turbinate biopsy samples, 19.5% (22 of 113) for blood samples, with seropositivity of 62.8% (71 of 113 samples) and with increasing incidences toward the multibacillary pole of the clinical spectrum. Positivity among HHCs were as follows: 49% (51 of 104) for nasal swab samples, 53.8% (56 of 104) for nasal biopsy samples, 6.7% (7 of 104) for blood samples, and 18.3% (19 of 104 samples) for anti-phenolic glycolipid I serology. During the follow-up of 5-7 years, out of 104 HHCs, 7 developed leprosy (6.7%). Risk for the disease outcome was estimated by comparing results in HHCs who develop leprosy with those not affected. Neither nasal passage nor mucosa positivity was determinant of later disease onset; however, blood presence increased the risk for disease development (relative risk/positive likelihood ratio, 5.54; 95% confidence interval, 1.30-23.62), as did seropositivity (positive likelihood ratio, 3.69 [1.67-8.16]; relative risk, 5.97 [1.45-24.5]). CONCLUSIONS Our findings strongly suggest that the aerosol route of infection and transmission is predominant and that HHCs contribute to the infection risk to themselves and probably to others.
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Affiliation(s)
- Sergio Araujo
- National Reference Center for Sanitary Dermatology and Leprosy, Clinics Hospital.,Postgraduate Program in Health Sciences, School of Medicine
| | | | - Luiz Ricardo Goulart
- National Reference Center for Sanitary Dermatology and Leprosy, Clinics Hospital.,Postgraduate Program in Health Sciences, School of Medicine.,Institute of Biochemistry and Genetics, Federal University of Uberlandia, Minas Gerais, Brazil.,Department of Medical Microbiology and Immunology, University of California, Davis
| | - Isabela Maria Bernardes Goulart
- National Reference Center for Sanitary Dermatology and Leprosy, Clinics Hospital.,Postgraduate Program in Health Sciences, School of Medicine
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Bharuthram A, Paximadis M, Picton ACP, Tiemessen CT. Comparison of a quantitative Real-Time PCR assay and droplet digital PCR for copy number analysis of the CCL4L genes. Infect Genet Evol 2014; 25:28-35. [PMID: 24727646 DOI: 10.1016/j.meegid.2014.03.028] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [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: 12/23/2013] [Revised: 02/25/2014] [Accepted: 03/24/2014] [Indexed: 02/02/2023]
Abstract
The controversy surrounding the findings that copy number variation, of the CCL3 encoding genes, influences HIV-1 infection and disease progression has been in part attributed to the variable results obtained from methods used for copy number evaluation. Like CCL3, the genes encoding the CC chemokine CCL4, also a natural ligand of the CCR5 receptor, are found to occur in population-specific multiple copy number and have been shown to play a protective role against HIV-1. This study evaluated the standard method of quantitative Real-Time PCR (qPCR) and droplet digital PCR (ddPCR) for CCL4L gene copy number determination. The CCL4 encoding genes are CCL4, occurring in two copies per diploid genome (pdg), and the non-allelic CCL4L genes, comprised of CCL4L1 and CCL4L2, which are both found in multiple copies pdg. Copy number of CCL4L, CCL4L1 and CCL4L2 was determined in a cohort of HIV-1-uninfected individuals from the South African Black (n=23) and Caucasian (n=32) population groups using qPCR and ddPCR. A stronger correlation between the number of CCL4L copies and the sum of CCL4L1 and CCL4L2 copies generated by ddPCR (r=0.99, p<0.0001) compared to qPCR (r=0.87, p<0.0001) was observed. Real-Time qPCR exhibited greater inaccuracy at higher copy numbers which is particularly relevant to our cohort of Black individuals who have a higher range of CCL4L copies (3-6) compared to Caucasians (0-4) and a higher population median (4 and 2, respectively). Medians and ranges of CCL4L1 (Black: 2, 0-4, Caucasian: 0, 0-2) and CCL4L2 (Black: 2, 1-5, Caucasian: 2, 0-3) were also higher in the Black population. Droplet digital PCR was shown to be a far superior method to qPCR for assessment of CCL4 gene copy number variation, the accuracy of which is essential for studies of the contribution of variable gene copy number to phenotypic outcomes of host infection and disease course.
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Affiliation(s)
- Avani Bharuthram
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Maria Paximadis
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Anabela C P Picton
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Caroline T Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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