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You X, Yao Y, Gao J, Liao Y. Corynebacterium bovis infection after autologous fat grafting in breast augmentation: a case report. Front Cell Infect Microbiol 2023; 13:1265872. [PMID: 38145043 PMCID: PMC10739324 DOI: 10.3389/fcimb.2023.1265872] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/17/2023] [Indexed: 12/26/2023] Open
Abstract
In this report, we present a case study of a rare human bacterium, Corynebacterium bovis, which caused an infection in a patient who had undergone autologous fat-based breast augmentation using cryopreserved fat. This infection occurred during a secondary fat grafting procedure. To identify the bacteria causing the infection, we used high-throughput DNA sequencing technology since this bacterium is seldomly reported in human infections. The patient was successfully treated with intravenous imipenem. We also discuss potential factors that may have contributed to this unusual bacterial infection and propose that DNA sequencing can be a useful tool in cases where standard culture techniques fail to identify the causative agent. Additionally, we highlight the importance of further research on the cryopreservation of fat. In summary, this case highlights the possibility of rare bacterial infections occurring after fat grafting procedures and emphasizes the importance of identifying the causative agent through advanced techniques such as DNA sequencing. Further research is needed to improve our understanding of the risks associated with cryopreservation of fat and to identify ways to prevent these types of infections in the future.
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Affiliation(s)
| | | | | | - YunJun Liao
- Department of Plastic and Cosmetic Surgery, Nanfang Hospital, Southern Medical University, Guang Zhou, Guang Dong, China
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2
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Spena S, Cairo A, Gianniello F, Pappalardo E, Mortarino M, Garagiola I, Martinelli I, Peyvandi F. Genetic Variants Identified by Whole Exome Sequencing in a Large Italian Family with High Plasma Levels of Factor VIII and Von Willebrand Factor. Int J Mol Sci 2023; 24:14167. [PMID: 37762470 PMCID: PMC10532311 DOI: 10.3390/ijms241814167] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
High plasma levels of factor VIII (FVIII) and von Willebrand factor (VWF) have been indicated as independent risk factors for venous thromboembolism. However, the genetic factors responsible for their increase remain poorly known. In a large Italian family with high FVIII/VWF levels and thrombotic episodes, whole exome sequencing (WES) was performed on 12 family members to identify variants/genes involved in FVIII/VWF increase. Twenty variants spread over a 8300 Kb region on chromosome 5 were identified in 12 genes, including the low frequency rs13158382, located upstream of the MIR143/145 genes, which might affect miR-143/145 transcription or processing. The expression of miR-143/145 and VWF mRNA were evaluated in the peripheral blood mononuclear cells of six family members. Members with the variant (n = 3) showed lower levels of both miRNAs and higher levels of VWF mRNA compared to members without the variant (n = 3). An analysis of genetic and expression data from a larger cohort of individuals from the 1000 Genomes and GEUVADIS project confirmed a statistically significant reduction (p-value = 0.023) in miR-143 in heterozygous (n = 35) compared to homozygous wild-type individuals (n = 386). This family-based study identified a new genetic variant potentially involved in VWF increase by affecting miR-143/145 expression.
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Affiliation(s)
- Silvia Spena
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, 20122 Milan, Italy; (S.S.); (A.C.); (F.G.); (M.M.); (I.G.); (I.M.)
| | - Andrea Cairo
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, 20122 Milan, Italy; (S.S.); (A.C.); (F.G.); (M.M.); (I.G.); (I.M.)
| | - Francesca Gianniello
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, 20122 Milan, Italy; (S.S.); (A.C.); (F.G.); (M.M.); (I.G.); (I.M.)
| | - Emanuela Pappalardo
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, 20122 Milan, Italy;
| | - Mimosa Mortarino
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, 20122 Milan, Italy; (S.S.); (A.C.); (F.G.); (M.M.); (I.G.); (I.M.)
| | - Isabella Garagiola
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, 20122 Milan, Italy; (S.S.); (A.C.); (F.G.); (M.M.); (I.G.); (I.M.)
| | - Ida Martinelli
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, 20122 Milan, Italy; (S.S.); (A.C.); (F.G.); (M.M.); (I.G.); (I.M.)
| | - Flora Peyvandi
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, 20122 Milan, Italy; (S.S.); (A.C.); (F.G.); (M.M.); (I.G.); (I.M.)
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, 20122 Milan, Italy;
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3
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Neidhöfer C, Sib E, Benhsain AH, Mutschnik-Raab C, Schwabe A, Wollkopf A, Wetzig N, Sieber MA, Thiele R, Döhla M, Engelhart S, Mutters NT, Parčina M. Examining Different Analysis Protocols Targeting Hospital Sanitary Facility Microbiomes. Microorganisms 2023; 11:microorganisms11010185. [PMID: 36677477 PMCID: PMC9867353 DOI: 10.3390/microorganisms11010185] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/02/2023] [Accepted: 01/07/2023] [Indexed: 01/15/2023] Open
Abstract
Indoor spaces exhibit microbial compositions that are distinctly dissimilar from one another and from outdoor spaces. Unique in this regard, and a topic that has only recently come into focus, is the microbiome of hospitals. While the benefits of knowing exactly which microorganisms propagate how and where in hospitals are undoubtedly beneficial for preventing hospital-acquired infections, there are, to date, no standardized procedures on how to best study the hospital microbiome. Our study aimed to investigate the microbiome of hospital sanitary facilities, outlining the extent to which hospital microbiome analyses differ according to sample-preparation protocol. For this purpose, fifty samples were collected from two separate hospitals-from three wards and one hospital laboratory-using two different storage media from which DNA was extracted using two different extraction kits and sequenced with two different primer pairs (V1-V2 and V3-V4). There were no observable differences between the sample-preservation media, small differences in detected taxa between the DNA extraction kits (mainly concerning Propionibacteriaceae), and large differences in detected taxa between the two primer pairs V1-V2 and V3-V4. This analysis also showed that microbial occurrences and compositions can vary greatly from toilets to sinks to showers and across wards and hospitals. In surgical wards, patient toilets appeared to be characterized by lower species richness and diversity than staff toilets. Which sampling sites are the best for which assessments should be analyzed in more depth. The fact that the sample processing methods we investigated (apart from the choice of primers) seem to have changed the results only slightly suggests that comparing hospital microbiome studies is a realistic option. The observed differences in species richness and diversity between patient and staff toilets should be further investigated, as these, if confirmed, could be a result of excreted antimicrobials.
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Affiliation(s)
- Claudio Neidhöfer
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
- Correspondence:
| | - Esther Sib
- Institute for Hygiene and Public Health, University of Bonn, 53127 Bonn, Germany
| | - Al-Harith Benhsain
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | | | - Anna Schwabe
- Institute for Hygiene and Public Health, University of Bonn, 53127 Bonn, Germany
| | - Alexander Wollkopf
- Institute for Hygiene and Public Health, University of Bonn, 53127 Bonn, Germany
| | - Nina Wetzig
- Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, 53757 Sankt Augustin, Germany
| | - Martin A. Sieber
- Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, 53757 Sankt Augustin, Germany
| | - Ralf Thiele
- Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, 53757 Sankt Augustin, Germany
| | - Manuel Döhla
- Institute for Hygiene and Public Health, University of Bonn, 53127 Bonn, Germany
- Department of Microbiology and Hospital Hygiene, Bundeswehr Central Hospital Koblenz, 56072 Koblenz, Germany
| | - Steffen Engelhart
- Institute for Hygiene and Public Health, University of Bonn, 53127 Bonn, Germany
| | - Nico T. Mutters
- Institute for Hygiene and Public Health, University of Bonn, 53127 Bonn, Germany
| | - Marijo Parčina
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
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Benítez-Guerrero T, Vélez-Ixta JM, Juárez-Castelán CJ, Corona-Cervantes K, Piña-Escobedo A, Martínez-Corona H, De Sales-Millán A, Cruz-Narváez Y, Gómez-Cruz CY, Ramírez-Lozada T, Acosta-Altamirano G, Sierra-Martínez M, Zárate-Segura PB, García-Mena J. Gut Microbiota Associated with Gestational Health Conditions in a Sample of Mexican Women. Nutrients 2022; 14. [PMID: 36432504 DOI: 10.3390/nu14224818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
Gestational diabetes (GD), pre-gestational diabetes (PD), and pre-eclampsia (PE) are morbidities affecting gestational health which have been associated with dysbiosis of the mother's gut microbiota. This study aimed to assess the extent of change in the gut microbiota diversity, short-chain fatty acids (SCFA) production, and fecal metabolites profile in a sample of Mexican women affected by these disorders. Fecal samples were collected from women with GD, PD, or PE in the third trimester of pregnancy, along with clinical and biochemical data. Gut microbiota was characterized by high-throughput DNA sequencing of V3-16S rRNA gene libraries; SCFA and metabolites were measured by High-Pressure Liquid Chromatography (HPLC) and (Fourier Transform Ion Cyclotron Mass Spectrometry (FT-ICR MS), respectively, in extracts prepared from feces. Although the results for fecal microbiota did not show statistically significant differences in alfa diversity for GD, PD, and PE concerning controls, there was a difference in beta diversity for GD versus CO, and a high abundance of Proteobacteria, followed by Firmicutes and Bacteroidota among gestational health conditions. DESeq2 analysis revealed bacterial genera associated with each health condition; the Spearman's correlation analyses showed selected anthropometric, biochemical, dietary, and SCFA metadata associated with specific bacterial abundances, and although the HPLC did not show relevant differences in SCFA content among the studied groups, FT-ICR MS disclosed the presence of interesting metabolites of complex phenolic, valeric, arachidic, and caprylic acid nature. The major conclusion of our work is that GD, PD, and PE are associated with fecal bacterial microbiota profiles, with distinct predictive metagenomes.
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Juárez-Castelán CJ, Vélez-Ixta JM, Corona-Cervantes K, Piña-Escobedo A, Cruz-Narváez Y, Hinojosa-Velasco A, Landero-Montes-de-Oca ME, Davila-Gonzalez E, González-Del-Olmo E, Bastida-Gonzalez F, Zárate-Segura PB, García-Mena J. The Entero-Mammary Pathway and Perinatal Transmission of Gut Microbiota and SARS-CoV-2. Int J Mol Sci 2022; 23. [PMID: 36142219 DOI: 10.3390/ijms231810306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 08/09/2022] [Revised: 09/02/2022] [Accepted: 09/04/2022] [Indexed: 02/08/2023] Open
Abstract
COVID-19 is a severe respiratory disease threatening pregnant women, which increases the possibility of adverse pregnancy outcomes. Several recent studies have demonstrated the ability of SARS-CoV-2 to infect the mother enterocytes, disturbing the gut microbiota diversity. The aim of this study was to characterize the entero-mammary microbiota of women in the presence of the virus during delivery. Fifty mother−neonate pairs were included in a transversal descriptive work. The presence of SARS-CoV-2 RNA was detected in nasopharyngeal, mother rectal swabs (MRS) and neonate rectal swabs (NRS) collected from the pairs, and human colostrum (HC) samples collected from mothers. The microbiota diversity was characterized by high-throughput DNA sequencing of V3-16S rRNA gene libraries prepared from HC, MRS, and NRS. Data were analyzed with QIIME2 and R. Our results indicate that several bacterial taxa are highly abundant in MRS positive for SARS-CoV-2 RNA. These bacteria mostly belong to the Firmicutes phylum; for instance, the families Bifidobacteriaceae, Oscillospiraceae, and Microbacteriaceae have been previously associated with anti-inflammatory effects, which could explain the capability of women to overcome the infection. All samples, both positive and negative for SARS-CoV-2, featured a high abundance of the Firmicutes phylum. Further data analysis showed that nearly 20% of the bacterial diversity found in HC was also identified in MRS. Spearman correlation analysis highlighted that some genera of the Proteobacteria and Actinobacteria phyla were negatively correlated with MRS and NRS (p < 0.005). This study provides new insights into the gut microbiota of pregnant women and their potential association with a better outcome during SARS-CoV-2 infection.
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Bello-Medina PC, Corona-Cervantes K, Zavala Torres NG, González A, Pérez-Morales M, González-Franco DA, Gómez A, García-Mena J, Díaz-Cintra S, Pacheco-López G. Chronic-Antibiotics Induced Gut Microbiota Dysbiosis Rescues Memory Impairment and Reduces β-Amyloid Aggregation in a Preclinical Alzheimer's Disease Model. Int J Mol Sci 2022; 23:8209. [PMID: 35897785 PMCID: PMC9331718 DOI: 10.3390/ijms23158209] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/08/2022] [Accepted: 07/12/2022] [Indexed: 02/03/2023] Open
Abstract
Alzheimer's disease (AD) is a multifactorial pathology characterized by β-amyloid (Aβ) deposits, Tau hyperphosphorylation, neuroinflammatory response, and cognitive deficit. Changes in the bacterial gut microbiota (BGM) have been reported as a possible etiological factor of AD. We assessed in offspring (F1) 3xTg, the effect of BGM dysbiosisdysbiosis in mothers (F0) at gestation and F1 from lactation up to the age of 5 months on Aβ and Tau levels in the hippocampus, as well as on spatial memory at the early symptomatic stage of AD. We found that BGM dysbiosisdysbiosis with antibiotics (Abx) treatment in F0 was vertically transferred to their F1 3xTg mice, as observed on postnatal day (PD) 30 and 150. On PD150, we observed a delay in spatial memory impairment and Aβ deposits, but not in Tau and pTau protein in the hippocampus at the early symptomatic stage of AD. These effects are correlated with relative abundance of bacteria and alpha diversity, and are specific to bacterial consortia. Our results suggest that this specific BGM could reduce neuroinflammatory responses related to cerebral amyloidosis and cognitive deficit and activate metabolic pathways associated with the biosynthesis of triggering or protective molecules for AD.
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Affiliation(s)
- Paola C. Bello-Medina
- Departamento de Neurobiología del Desarrollo y Neurofisiología, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Querétaro 76230, Mexico;
- Biological and Health Sciences Division, Campus Lerma, Metropolitan Autonomus University (UAM), Lerma 52005, Mexico; (A.G.); (M.P.-M.); (D.A.G.-F.); (A.G.); (G.P.-L.)
| | - Karina Corona-Cervantes
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Zacatenco, Mexico City 07360, Mexico; (K.C.-C.); (N.G.Z.T.)
| | - Norma Gabriela Zavala Torres
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Zacatenco, Mexico City 07360, Mexico; (K.C.-C.); (N.G.Z.T.)
| | - Antonio González
- Biological and Health Sciences Division, Campus Lerma, Metropolitan Autonomus University (UAM), Lerma 52005, Mexico; (A.G.); (M.P.-M.); (D.A.G.-F.); (A.G.); (G.P.-L.)
| | - Marcel Pérez-Morales
- Biological and Health Sciences Division, Campus Lerma, Metropolitan Autonomus University (UAM), Lerma 52005, Mexico; (A.G.); (M.P.-M.); (D.A.G.-F.); (A.G.); (G.P.-L.)
| | - Diego A. González-Franco
- Biological and Health Sciences Division, Campus Lerma, Metropolitan Autonomus University (UAM), Lerma 52005, Mexico; (A.G.); (M.P.-M.); (D.A.G.-F.); (A.G.); (G.P.-L.)
| | - Astrid Gómez
- Biological and Health Sciences Division, Campus Lerma, Metropolitan Autonomus University (UAM), Lerma 52005, Mexico; (A.G.); (M.P.-M.); (D.A.G.-F.); (A.G.); (G.P.-L.)
| | - Jaime García-Mena
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Zacatenco, Mexico City 07360, Mexico; (K.C.-C.); (N.G.Z.T.)
| | - Sofía Díaz-Cintra
- Departamento de Neurobiología del Desarrollo y Neurofisiología, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Querétaro 76230, Mexico;
| | - Gustavo Pacheco-López
- Biological and Health Sciences Division, Campus Lerma, Metropolitan Autonomus University (UAM), Lerma 52005, Mexico; (A.G.); (M.P.-M.); (D.A.G.-F.); (A.G.); (G.P.-L.)
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7
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Spena S, Cairo A, Pappalardo E, Gorski MM, Garagiola I, Hassan S, Gualtierotti R, Peyvandi F. Genetic variants at the chromosomal region 2q21.3 underlying inhibitor development in patients with severe haemophilia A. Haemophilia 2022; 28:270-277. [PMID: 35182444 PMCID: PMC9306754 DOI: 10.1111/hae.14503] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 01/19/2022] [Accepted: 01/23/2022] [Indexed: 11/29/2022]
Abstract
Introduction Inhibitor development affects about 30% of patients with severe haemophilia A (HA) and results from different environmental and genetic risk factors. Previously, we identified the missense variant rs3754689 in the LCT gene linked with this predisposition. Since rs3754689 variant is benign and is located in a conserved haplotype region, we hypothesized that the association signal captured by this variant is located in coinherited, neighbouring genes. Aim To identify novel genetic risk factors associated with inhibitor development in coding regions of R3HDM1, UBXN4, CXCR4, MCM6, DARS and miR128‐1 genes. Methods Targeted sequencing was performed in 246 severe HA patients (72 with and 174 without inhibitor): 181 previously and 65 newly enrolled. Results Forty‐one common and 152 rare variants passed the quality control. Logistic regression analysis of common variants identified rs3754689 and four additional variants (.011 < P < .047; FDR ranging .2‐.38). Logistic regression analysis performed only in the 220 Italian patients showed similar results (.004 < P < .05; FDR ranging .12‐.22). Three of these variants (rs3213892 and rs3816155 in the LCT intron 13 and rs961360 in the R3HDM1 intron10‐exon11 junction) may affect the expression of UBXN4 and R3HDM1, respectively. Rare variants did not show association with inhibitor development. Identified variants were not replicated in the multi‐ethnic SIPPET cohort of 230 severe HA patients. Conclusion Due to the limited sample size that may be responsible of the high FDR values, we could not confirm with certainty the analysed association. Further evaluation of the expression levels of analysed genes will confirm or not their role in inhibitor development.
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Affiliation(s)
- Silvia Spena
- Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, and Luigi Villa Foundation, Milan, Italy
| | - Andrea Cairo
- Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, and Luigi Villa Foundation, Milan, Italy
| | - Emanuela Pappalardo
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Marcin M Gorski
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Isabella Garagiola
- Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, and Luigi Villa Foundation, Milan, Italy
| | - Shermarke Hassan
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy.,Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Roberta Gualtierotti
- Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, and Luigi Villa Foundation, Milan, Italy.,Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Flora Peyvandi
- Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, and Luigi Villa Foundation, Milan, Italy.,Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
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Yao D, Xu L, Wu M, Wang X, Wang K, Li Z, Zhang D. Microbial Community Succession and Metabolite Changes During Fermentation of BS Sufu, the Fermented Black Soybean Curd by Rhizopus microsporus, Rhizopus oryzae, and Actinomucor elegans. Front Microbiol 2021; 12:665826. [PMID: 34248874 PMCID: PMC8267895 DOI: 10.3389/fmicb.2021.665826] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 02/09/2021] [Accepted: 05/17/2021] [Indexed: 11/25/2022] Open
Abstract
BS Sufu is a fermented food that is made by mixed black soybeans and soybeans. Microbial communities and metabolites play an important role for the final product. We characterized microbial diversity of BS Sufu during fermentation by high-throughput DNA sequencing. Meanwhile, volatile compounds were investigated by solid-phase microextraction (SPME) coupled with gas chromatography–mass spectrometry (GC-MS). The results showed that bacterial diversity was higher than that of fungi in BS Sufu. We found the existence of bacterial and fungal core communities, including Enterococcus, Enterobacter, Rhizopus, and Monascus. Network analysis indicated that bacterial and fungal communities maintain positive and negative interactions, which are important to shape the resident microbial communities in Sufu. In addition, 17 free amino acids (FAAs) were detected at the post-fermentation stage, and umami amino acid mainly contributed to taste of BS Sufu. Furtherly, a total of 79 volatile constituents in BS Sufu, including nine alcohols, 31 esters, and four aldehydes, form synergistically the unique odor of Sufu. Additionally, the correlations between microbiota and metabolites were analyzed. Our results suggested that these microbial taxa and metabolites contribute to the taste and flavor of BS Sufu. This study provided information for analysis of BS Sufu at different fermentation periods in terms of the microbial diversity and metabolites, and this information was important to understand the properties of mixed soybeans Sufu.
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Affiliation(s)
- Di Yao
- College of Food Science and Engineering, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Lei Xu
- College of Food Science and Engineering, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Mengna Wu
- College of Food Science and Engineering, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Xiaoyu Wang
- College of Food Science and Engineering, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Kun Wang
- College of Food Science and Engineering, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Zhijiang Li
- College of Food Science and Engineering, Heilongjiang Bayi Agricultural University, Daqing, China.,Heilongjiang Engineering Research Center for Coarse Cereals Processing and Quality Safety, Daqing, China.,Key Laboratory of Agro-Products Processing and Quality Safety of Heilongjiang Province, Daqing, China
| | - Dongjie Zhang
- College of Food Science and Engineering, Heilongjiang Bayi Agricultural University, Daqing, China.,Heilongjiang Engineering Research Center for Coarse Cereals Processing and Quality Safety, Daqing, China.,Key Laboratory of Agro-Products Processing and Quality Safety of Heilongjiang Province, Daqing, China.,National Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing, China
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9
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Cuervo-Zanatta D, Garcia-Mena J, Perez-Cruz C. Gut Microbiota Alterations and Cognitive Impairment Are Sexually Dissociated in a Transgenic Mice Model of Alzheimer's Disease. J Alzheimers Dis 2021; 82:S195-S214. [PMID: 33492296 DOI: 10.3233/jad-201367] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [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: 12/16/2022]
Abstract
BACKGROUND Normal aging is accompanied by cognitive deficiencies, affecting women and men equally. Aging is the main risk factor for Alzheimer's disease (AD), with women having a higher risk. The higher prevalence of AD in women is associated with the abrupt hormonal decline seen after menopause. However, other factors may be involved in this sex-related cognitive decline. Alterations in gut microbiota (GM) and its bioproducts have been reported in AD subjects and transgenic (Tg) mice, having a direct impact on brain amyloid-β pathology in male (M), but not in female (F) mice. OBJECTIVE The aim of this work was to determine GM composition and cognitive dysfunction in M and F wildtype (WT) and Tg mice, in a sex/genotype segregation design. METHODS Anxiety, short term working-memory, spatial learning, and long-term spatial memory were evaluated in 6-month-old WT and Tg male mice. Fecal short chain fatty acids were determined by chromatography, and DNA sequencing and bioinformatic analyses were used to determine GM differences. RESULTS We observed sex-dependent differences in cognitive skills in WT mice, favoring F mice. However, the cognitive advantage of females was lost in Tg mice. GM composition showed few sex-related differences in WT mice. Contrary, Tg-M mice presented a more severe dysbiosis than Tg-F mice. A decreased abundance of Ruminococcaceae was associated with cognitive deficits in Tg-F mice, while butyrate levels were positively associated with better working- and object recognition-memory in WT-F mice. CONCLUSION This report describes a sex-dependent association between GM alterations and cognitive impairment in a mice model of AD.
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Affiliation(s)
- Daniel Cuervo-Zanatta
- Pharmacology Department, Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Laboratory of Neuroplasticity and Neurodegeneration, Mexico City, Mexico.,Genetics and Molecular Biology Department, Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Laboratory of reference and support for the characterization of genomes, transcriptomes and microbiomes, Mexico City, Mexico
| | - Jaime Garcia-Mena
- Genetics and Molecular Biology Department, Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Laboratory of reference and support for the characterization of genomes, transcriptomes and microbiomes, Mexico City, Mexico
| | - Claudia Perez-Cruz
- Pharmacology Department, Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Laboratory of Neuroplasticity and Neurodegeneration, Mexico City, Mexico
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10
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Kakui K, Kano Y. First Complete Mitochondrial Genome of a Tanaidacean Crustacean ( Arctotanais alascensis). Zoolog Sci 2021; 38:267-272. [PMID: 34057352 DOI: 10.2108/zs200167] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 12/04/2020] [Accepted: 01/03/2021] [Indexed: 11/17/2022]
Abstract
We present a complete mitochondrial genomic sequence for the tanaidacean Arctotanais alascensis (Richardson, 1899); this is the first complete mitogenome reported from the order Tanaidacea. The mitogenome is 13,988 bp long and contains 13 protein coding and two ribosomal RNA genes (as is typical for animal mitogenomes), and 21 of 22 transfer RNAs; we did not detect an isoleucine transfer RNA (trnI) gene. The gene order differed markedly from the hypothetical ground pattern for Pancrustacea; only four clusters (trnM + nad2; trnC + trnY + cox1 + trnL2 + cox2; trnD + atp8 + atp6 + cox3; trnH + nad4 + nad4l) ancestrally present were retained. In a malacostracan phylogenetic tree reconstructed from mitogenome data, basal relationships were marginally supported or incongruent with the traditional morphology-based classification and the latest phylogenetic reconstructions from large transcriptomic datasets. Relationships involving more recent divergences were better supported in our tree, suggesting that complete mitogenome sequences are more suitable for phylogenetic analyses within malacostracan orders, presumably including Tanaidacea.
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Affiliation(s)
- Keiichi Kakui
- Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan,
| | - Yasunori Kano
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa 277-8564, Japan
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11
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Bello-Medina PC, Hernández-Quiroz F, Pérez-Morales M, González-Franco DA, Cruz-Pauseno G, García-Mena J, Díaz-Cintra S, Pacheco-López G. Spatial Memory and Gut Microbiota Alterations Are Already Present in Early Adulthood in a Pre-clinical Transgenic Model of Alzheimer's Disease. Front Neurosci 2021; 15:595583. [PMID: 33994914 PMCID: PMC8116633 DOI: 10.3389/fnins.2021.595583] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [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: 08/17/2020] [Accepted: 03/19/2021] [Indexed: 12/14/2022] Open
Abstract
The irreversible and progressive neurodegenerative Alzheimer’s disease (AD) is characterized by cognitive decline, extracellular β-amyloid peptide accumulation, and tau neurofibrillary tangles in the cortex and hippocampus. The triple-transgenic (3xTg) mouse model of AD presents memory impairment in several behavioral paradigms and histopathological alterations from 6 to 16 months old. Additionally, it seems that dysbiotic gut microbiota is present in both mouse models and patients of AD at the cognitive symptomatic stage. The present study aimed to assess spatial learning, memory retention, and gut microbiota alterations in an early adult stage of the 3xTg-AD mice as well as to explore its sexual dimorphism. We evaluated motor activity, novel-object localization training, and retention test as well as collected fecal samples to characterize relative abundance, alpha- and beta-diversity, and linear discriminant analysis (LDA) effect size (LEfSe) analysis in gut microbiota in both female and male 3xTg-AD mice, and controls [non-transgenic mice (NoTg)], at 3 and 5 months old. We found spatial memory deficits in female and male 3xTg-AD but no alteration neither during training nor in motor activity. Importantly, already at 3 months old, we observed decreased relative abundances of Actinobacteria and TM7 in 3xTg-AD compared to NoTg mice, while the beta diversity of gut microbiota was different in female and male 3xTg-AD mice in comparison to NoTg. Our results suggest that gut microbiota modifications in 3xTg-AD mice anticipate and thus could be causally related to cognitive decline already at the early adult age of AD. We propose that microbiota alterations may be used as an early and non-invasive diagnostic biomarker of AD.
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Affiliation(s)
- Paola C Bello-Medina
- División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana (UAM), Unidad Lerma, Lerma, Mexico
| | - Fernando Hernández-Quiroz
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados (CINVESTAV) del Instituto Politécnico Nacional (IPN), Unidad Zacatenco, Ciudad de México, Mexico
| | - Marcel Pérez-Morales
- División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana (UAM), Unidad Lerma, Lerma, Mexico
| | - Diego A González-Franco
- División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana (UAM), Unidad Lerma, Lerma, Mexico
| | - Guadalupe Cruz-Pauseno
- Doctorado en Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana (UAM), Unidad Lerma, Lerma, Mexico
| | - Jaime García-Mena
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados (CINVESTAV) del Instituto Politécnico Nacional (IPN), Unidad Zacatenco, Ciudad de México, Mexico
| | - Sofía Díaz-Cintra
- Departamento de Neurobiología del Desarrollo y Neurofisiología, Instituto de Neurobiología, Universidad Nacional Autónoma de México (UNAM), Querétaro, Mexico
| | - Gustavo Pacheco-López
- División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana (UAM), Unidad Lerma, Lerma, Mexico
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12
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Abdullah, Li C, Zhao M, Wang X, Li X, Xing J. Hypogonadotropic hypogonadism associated with another small supernumerary marker chromosome (sSMC) derived from chromosome 22, a case report. Transl Androl Urol 2021; 10:1797-1802. [PMID: 33968667 PMCID: PMC8100857 DOI: 10.21037/tau-20-1087] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The idiopathic hypogonadotropic hypogonadism (IHH) is portrayed as missing or fragmented pubescence, cryptorchidism, small penis, and infertility. Clinically it is characterized by the low level of sex steroids and gonadotropins, normal radiographic findings of the hypothalamic-pituitary areas, and normal baseline and reserve testing of the rest of the hypothalamic-pituitary axes. Delay puberty and infertility result from an abnormal pattern of episodic GnRH secretion. Mutation in a wide range of genes can clarify ~40% of the reasons for IHH, with the majority remaining hereditarily uncharacterized. New and innovative molecular tools enhance our understanding of the molecular controls underlying pubertal development. In this report, we aim to present a 26-year-old male of IHH associated with a small supernumerary marker chromosome (sSMC) that originated from chromosome 22. The G-banding analysis revealed a karyotype of 47,XY,+mar. High-throughput DNA sequencing identified an 8.54 Mb duplication of 22q11.1-q11.23 encompassing all the region of 22q11 duplication syndrome. Pedigree analysis showed that his mother has carried a balanced reciprocal translocation between Chromosomes 22 and X[t(X;22)]. To the best of our knowledge, this is the second confirmed case of IHH with an sSMC deriving from chromosome 22. Based on our study, the duplicated chromosome fragment 22q11.1-q11.23 might be the reason for the phenotype of our case. Meanwhile, High-throughput DNA sequencing combined with cytogenetic analysis can provide a more accurate clinical diagnosis for patients carrying sSMCs.
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Affiliation(s)
- Abdullah
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Cui Li
- Centre for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Minggang Zhao
- Centre for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiang Wang
- Centre for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xu Li
- Centre for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Junping Xing
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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13
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Saadani M, Hönig L, Bien S, Koehler M, Rutten G, Wubet T, Braun U, Bruelheide H. Local Tree Diversity Suppresses Foliar Fungal Infestation and Decreases Morphological But Not Molecular Richness in a Young Subtropical Forest. J Fungi (Basel) 2021; 7:173. [PMID: 33673628 PMCID: PMC7997179 DOI: 10.3390/jof7030173] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 01/31/2021] [Revised: 02/19/2021] [Accepted: 02/23/2021] [Indexed: 12/25/2022] Open
Abstract
Leaf fungal pathogens alter their host species' performance and, thus, changes in fungal species composition can translate into effects at the tree community scale. Conversely, the functional diversity of tree species in a host tree's local neighbourhood can affect the host's foliar fungal infestation. Therefore, understanding the factors that affect fungal infestations is important to advance our understanding of biodiversity-ecosystem functioning (BEF) relationships. Here we make use of the largest BEF tree experiment worldwide, the BEF-China experiment, where we selected tree host species with different neighbour species. Identifying fungal taxa by microscopy and by high-throughput DNA sequencing techniques based on the internal transcribed spacer (ITS) rDNA region, we analysed the fungal richness and infestation rates of our target trees as a function of local species richness. Based on the visual microscopic assessment, we found that a higher tree diversity reduced fungal richness and host-specific fungal infestation in the host's local neighbourhood, while molecular fungal richness was unaffected. This diversity effect was mainly explained by the decrease in host proportion. Thus, the dilution of host species in the local neighbourhood was the primary mechanism in reducing the fungal disease severity. Overall, our study suggests that diverse forests will suffer less from foliar fungal diseases compared to those with lower diversity.
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Affiliation(s)
- Mariem Saadani
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle, Germany; (L.H.); (S.B.); (M.K.); (G.R.); (U.B.); (H.B.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, 04103 Leipzig, Germany;
| | - Lydia Hönig
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle, Germany; (L.H.); (S.B.); (M.K.); (G.R.); (U.B.); (H.B.)
| | - Steffen Bien
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle, Germany; (L.H.); (S.B.); (M.K.); (G.R.); (U.B.); (H.B.)
- Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806 Görlitz, Germany
| | - Michael Koehler
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle, Germany; (L.H.); (S.B.); (M.K.); (G.R.); (U.B.); (H.B.)
| | - Gemma Rutten
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle, Germany; (L.H.); (S.B.); (M.K.); (G.R.); (U.B.); (H.B.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, 04103 Leipzig, Germany;
| | - Tesfaye Wubet
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, 04103 Leipzig, Germany;
- Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, D-06120 Halle, Germany
| | - Uwe Braun
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle, Germany; (L.H.); (S.B.); (M.K.); (G.R.); (U.B.); (H.B.)
| | - Helge Bruelheide
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle, Germany; (L.H.); (S.B.); (M.K.); (G.R.); (U.B.); (H.B.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, 04103 Leipzig, Germany;
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14
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Yan MM, Zhang HH, Huang TL, Zong RR, Liu KW, Miao YT, Yang SY, Huang X, Wang N. [Mechanism of Algal Community Dynamics Driven by the Seasonal Water Bacterial Community in a Stratified Drinking Water Reservoir]. Huan Jing Ke Xue 2021; 42:221-233. [PMID: 33372474 DOI: 10.13227/j.hjkx.202006234] [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] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Phytoplankton and bacteria are crucial components of aquatic food webs, playing critical roles in the structure and function of freshwater ecosystems. However, there are few studies on how the algal and bacterial communities interact and respond to changing environmental conditions in the water reservoirs. Thus, the ecological interaction relationship between the temporal succession of the phytoplankton community and the bacterial community was investigated using 16S rDNA high-throughput sequencing and a co-occurrence network in the Lijiahe Reservoir. The results showed that Bacillariophyta and Chlorophyta were also dominant taxa in the phytoplankton community. In August, Cyanobacteria replaced Bacillariophyta as the second-most dominant taxa, with an average relative abundance of 30.13%. DNA sequencing showed that Proteobacteria, Actinobacteria, and Bacteroidetes dominated throughout the year. Proteobacteria reached a maximum relative abundance of 71.68% in July. Acidobacteria and Deinococcus-Thermus, which were rare taxa, reached maximum relative abundances of 10.20% and 5.56%, respectively. The co-occurrence network showed that the association between algae and bacteria was mainly positive, indicating that the interaction between them may be dominated by mutualism. As a keystone taxa, Methylotenera was significantly and positively related to Chlorella. Scenedesmus was also a keystone taxa and was significantly and negatively correlated with various bacteria, such as Methylobacter, Solitalea, and Rhodoferax. An RDA analysis showed that the succession of algal and bacterial communities was significantly regulated by water temperature, pH, and conductivity, and the environmental factors explained 93.1% and 90% of the variation in the algal community and bacterial community, respectively. The results will provide a scientific basis for exploring the micro-ecological driving mechanism of the interaction between algae and bacteria in deep drinking water reservoir ecosystems.
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Affiliation(s)
- Miao-Miao Yan
- Key Laboratory of Northwest Water Resource, Environment and Ecology, Ministry of Education, Shaanxi Key Laboratory of Environmental Engineering, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Hai-Han Zhang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, Ministry of Education, Shaanxi Key Laboratory of Environmental Engineering, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Ting-Lin Huang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, Ministry of Education, Shaanxi Key Laboratory of Environmental Engineering, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Rong-Rong Zong
- Key Laboratory of Northwest Water Resource, Environment and Ecology, Ministry of Education, Shaanxi Key Laboratory of Environmental Engineering, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Kai-Wen Liu
- Key Laboratory of Northwest Water Resource, Environment and Ecology, Ministry of Education, Shaanxi Key Laboratory of Environmental Engineering, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Yu-Tian Miao
- Key Laboratory of Northwest Water Resource, Environment and Ecology, Ministry of Education, Shaanxi Key Laboratory of Environmental Engineering, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Shang-Ye Yang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, Ministry of Education, Shaanxi Key Laboratory of Environmental Engineering, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Xin Huang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, Ministry of Education, Shaanxi Key Laboratory of Environmental Engineering, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Na Wang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, Ministry of Education, Shaanxi Key Laboratory of Environmental Engineering, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
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15
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Chambard M, Plasson C, Derambure C, Coutant S, Tournier I, Lefranc B, Leprince J, Kiefer-Meyer MC, Driouich A, Follet-Gueye ML, Boulogne I. New Insights into Plant Extracellular DNA. A Study in Soybean Root Extracellular Trap. Cells 2021; 10:E69. [PMID: 33466245 PMCID: PMC7824799 DOI: 10.3390/cells10010069] [Citation(s) in RCA: 9] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 12/13/2022] Open
Abstract
exDNA is found in various organisms, including plants. However, plant exDNA has thus far received little attention related to its origin and role in the RET (root extracellular trap). In this study, we performed the first high-throughput genomic sequencing of plant exDNA from a Fabaceae with worldwide interest: soybean (Glycine max (L.) Merr.). The origin of this exDNA was first investigated in control condition, and the results show high-coverage on organelles (mitochondria/plastid) DNA relative to nuclear DNA, as well as a mix of coding and non-coding sequences. In the second part of this study, we investigated if exDNA release was modified during an elicitation with PEP-13 (a peptide elicitor from oomycete genus Phytophthora). Our results show that treatment of roots with PEP-13 does not affect the composition of exDNA.
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Affiliation(s)
- Marie Chambard
- Normandie University, UNIROUEN, UFR des Sciences et Techniques, Glyco-MEV EA4358, SFR NORVEGE FED 4277, 76821 Mont-Saint-Aignan, France; (C.P.); (M.-C.K.-M.); (A.D.); (M.-L.F.-G.); (I.B.)
- Fédération de Recherche Normandie-Végétal, FED 4277, 76821 Mont-Saint-Aignan, France
| | - Carole Plasson
- Normandie University, UNIROUEN, UFR des Sciences et Techniques, Glyco-MEV EA4358, SFR NORVEGE FED 4277, 76821 Mont-Saint-Aignan, France; (C.P.); (M.-C.K.-M.); (A.D.); (M.-L.F.-G.); (I.B.)
- Fédération de Recherche Normandie-Végétal, FED 4277, 76821 Mont-Saint-Aignan, France
| | - Céline Derambure
- Normandy Center for Genomic and Personalized Medicine, 76000 Rouen, France; (C.D.); (S.C.); (I.T.)
| | - Sophie Coutant
- Normandy Center for Genomic and Personalized Medicine, 76000 Rouen, France; (C.D.); (S.C.); (I.T.)
| | - Isabelle Tournier
- Normandy Center for Genomic and Personalized Medicine, 76000 Rouen, France; (C.D.); (S.C.); (I.T.)
| | - Benjamin Lefranc
- Plateforme de Recherche en Imagerie Cellulaire de Normandie (PRIMACEN), Normandie Université UNIROUEN, INSERM U1239, 76000 Rouen, France; (B.L.); (J.L.)
| | - Jérôme Leprince
- Plateforme de Recherche en Imagerie Cellulaire de Normandie (PRIMACEN), Normandie Université UNIROUEN, INSERM U1239, 76000 Rouen, France; (B.L.); (J.L.)
| | - Marie-Christine Kiefer-Meyer
- Normandie University, UNIROUEN, UFR des Sciences et Techniques, Glyco-MEV EA4358, SFR NORVEGE FED 4277, 76821 Mont-Saint-Aignan, France; (C.P.); (M.-C.K.-M.); (A.D.); (M.-L.F.-G.); (I.B.)
- Fédération de Recherche Normandie-Végétal, FED 4277, 76821 Mont-Saint-Aignan, France
| | - Azeddine Driouich
- Normandie University, UNIROUEN, UFR des Sciences et Techniques, Glyco-MEV EA4358, SFR NORVEGE FED 4277, 76821 Mont-Saint-Aignan, France; (C.P.); (M.-C.K.-M.); (A.D.); (M.-L.F.-G.); (I.B.)
- Fédération de Recherche Normandie-Végétal, FED 4277, 76821 Mont-Saint-Aignan, France
| | - Marie-Laure Follet-Gueye
- Normandie University, UNIROUEN, UFR des Sciences et Techniques, Glyco-MEV EA4358, SFR NORVEGE FED 4277, 76821 Mont-Saint-Aignan, France; (C.P.); (M.-C.K.-M.); (A.D.); (M.-L.F.-G.); (I.B.)
- Fédération de Recherche Normandie-Végétal, FED 4277, 76821 Mont-Saint-Aignan, France
| | - Isabelle Boulogne
- Normandie University, UNIROUEN, UFR des Sciences et Techniques, Glyco-MEV EA4358, SFR NORVEGE FED 4277, 76821 Mont-Saint-Aignan, France; (C.P.); (M.-C.K.-M.); (A.D.); (M.-L.F.-G.); (I.B.)
- Fédération de Recherche Normandie-Végétal, FED 4277, 76821 Mont-Saint-Aignan, France
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16
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Brys R, Haegeman A, Halfmaerten D, Neyrinck S, Staelens A, Auwerx J, Ruttink T. Monitoring of spatiotemporal occupancy patterns of fish and amphibian species in a lentic aquatic system using environmental DNA. Mol Ecol 2020; 30:3097-3110. [PMID: 33222312 PMCID: PMC8359355 DOI: 10.1111/mec.15742] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 09/29/2020] [Accepted: 11/02/2020] [Indexed: 12/21/2022]
Abstract
To effectively monitor, manage and protect aquatic species and understand their interactions, knowledge of their spatiotemporal distribution is needed. In this study, we used a fine-scale spatiotemporal water sampling design, followed by environmental DNA (eDNA) 12S metabarcoding, to investigate occupancy patterns of a natural community of fish and amphibian species in a lentic system. In the same system, we experimentally estimated the spatial and temporal dispersion of eDNA by placing a community of different fish and amphibian species in cages at one side of the pond, creating a controlled point of eDNA emission. Analyses of this cage community revealed a sharp spatial decline in detection rates and relative eDNA quantities at a distance of 5-10 m from the source, depending on the species and its abundance. In addition, none of the caged species could be detected 1 week after removal from the system. This indicates high eDNA decay rates and limited spatial eDNA dispersal, facilitating high local resolution for monitoring spatial occupancy patterns of aquatic species. Remarkably, for seven of the nine cage species, the presence of a single individual could be detected by pooling water of subsamples taken across the whole water body, illustrating the high sensitivity of the eDNA sampling and detection method applied. Finally, our work demonstrated that a fine-scale sampling design in combination with eDNA metabarcoding can cover total biodiversity very precisely and allows the construction of consistent spatiotemporal patterns of relative abundance and local distribution of free-living fish and amphibian species in a lentic ecosystem.
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Affiliation(s)
- Rein Brys
- Research Institute for Nature and Forest, Geraardsbergen, Belgium
| | - Annelies Haegeman
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
| | | | - Sabrina Neyrinck
- Research Institute for Nature and Forest, Geraardsbergen, Belgium
| | - Ariane Staelens
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
| | - Johan Auwerx
- Research Institute for Nature and Forest, Linkebeek, Belgium
| | - Tom Ruttink
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
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17
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Affiliation(s)
- Palak Shah
- Cardiovascular Genomics Center, Heart Failure and Transplantation (P.S.), Inova Heart and Vascular Institute, Falls Church, VA
| | | | - Kristin E Mullins
- Department of Pathology, University of Maryland School of Medicine, Baltimore (K.E.M.)
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18
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Anderson AC, Rothballer M, Altenburger MJ, Woelber JP, Karygianni L, Vach K, Hellwig E, Al-Ahmad A. Long-Term Fluctuation of Oral Biofilm Microbiota following Different Dietary Phases. Appl Environ Microbiol 2020; 86:e01421-20. [PMID: 32801176 DOI: 10.1128/AEM.01421-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/05/2020] [Indexed: 02/06/2023] Open
Abstract
Caries development is associated with shifts in the oral biofilm microbiota and primarily linked to frequent simple carbohydrate consumption. Different nutritional ingredients can either promote or prevent caries development. To investigate the effects of selected ingredients on the oral biofilm microbiota in situ, 11 study participants underwent 3-month-long dietary phases with intake of a regular diet (PI), additional frequent sucrose (PII), milk and yoghurt (PIII), and a diet rich in dietary fiber (PIV) and then returned to their regular diet (PV). Oral biofilm was sampled and analyzed applying 16S rRNA Illumina MiSeq sequencing. Additionally, the effect on the enamel was analyzed by measuring enamel surface roughness with laser scanning microscopy. The beta-diversity results showed that the microbiota in all the following phases differed significantly from PI and that the microbial community in PII was significantly different from all other phases. The abundance of the genus Streptococcus fluctuated over the course of the five phases, with a significant increase in PII (P = 0.01), decreasing in PIII and PIV (PIII and PIV versus PII: P < 0.00001) and increasing again toward PV. Other taxa showed various fluctuations of their abundances, with PV returning approximately to the levels of PI. In conclusion, while elevated sucrose consumption favored caries-promoting non-mutans streptococci, frequent milk and yoghurt intake caused a significant decrease in the abundance of these microbial taxa and in addition reduced enamel surface roughness. These results indicate that modulations of the oral biofilm microbiota can be attained even in adults through dietary changes and corresponding recommendations can be made for the prevention of caries development.IMPORTANCE Caries affects a large proportion of the population worldwide, resulting in high treatment costs. Its etiology can be ascribed to shifts of the microbiota in dental biofilms primarily driven by dietary factors. It is unclear how diet affects the microbial community of plaque biofilm in situ and whether it can be modulated to help prevent caries development. To address these issues, we analyzed changes of the in situ plaque microbiota following 3-month-long dietary changes involving elevated sucrose, dairy, and dietary fiber consumption over a period of 15 months. Applying high-throughput sequencing, we found non-mutans streptococci, a taxonomic group involved in the beginning stages toward microbial dysbiosis, in decreased abundance with elevated dairy and dietary fiber intake. Through analysis of the enamel surface roughness, these effects were confirmed. Therefore, correspondent dietary measures can be recommended for children as well as adults for caries prevention.
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Yan MM, Chen SN, Huang TL, Jia JY, Liu KW, Miao YT, Zong RR. [Water Quality and Bacterial Population Driving Mechanism of Algae Vertical Succession in Stratified Reservoir]. Huan Jing Ke Xue 2020; 41:3285-3296. [PMID: 32608902 DOI: 10.13227/j.hjkx.202001131] [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] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Phytoplankton and bacteria are important components of the aquatic food web, and play a critical role in substance circulation and energy exchange in freshwater ecosystems. The succession of algae is closely related to the metabolism and structural succession of bacterial populations in the water column. Thus, in this study, the vertical succession characteristics of phytoplankton and bacteria community structure and their coupling with water quality were investigated during an algal bloom in the Lijiahe Reservoir using high-throughput DNA sequencing and Biolog technologies. The results showed that the Lijiahe Reservoir was in the thermal stratification stage in August, and the pH, dissolved oxygen, and NH4+-N of the water column gradually decreased with depth (P<0.001). Algal cell concentration and chlorophyll a exhibited a simultaneous trend (P<0.001), and the maximum values in the surface layer were 3363.33×104 cells·L-1 and 7.03 μg·L-1, respectively. The algal community structure was dominated by Microcystis at water depths of 0 m and 3 m, and at 6 m water depth, Cyclotella replaced Microcystis as the most dominant algae, with a relative abundance of 57.28%. Biolog analysis indicated that the outbreak of Microcystis had a significant impact on bacterial metabolic activity and its relative abundance, but the diversity of bacterial population metabolic activity varied less. A total of 1420 operational taxonomic units were found by high-throughput sequencing, belonging to 10 bacterial phyla. Of these, Actinobacteria and Proteobacteria dominated in all water layers, and their relative abundances were more than 50%. The relative abundance of Chlorobi and Planctomycetes varied significantly with water depth, reaching their maxima at a depth of 6 m with values of 10.29% and 6.78%, respectively, which were both negatively correlated with algal density (P<0.05). Firmicutes and Gemmatimonadetes were positively correlated with algal density (P<0.05). A heat map fingerprint showed that the vertical distribution of the bacterial community structure of the Lijiahe Reservoir varied significantly, and with the increase in water depth, the bacterial community was more uniformly distributed and tended to diversify. Redundancy analysis (RDA) showed that the vertical distribution of the bacterial and algal community structure was regulated by different water qualities, and the difference was significant. This study investigated the coupling mechanism of algal and bacterial communities during the algal bloom in the Lijiahe Reservoir, and the results provided a scientific basis for the investigation of the molecular microecological driving mechanism of water-source algal blooms.
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Affiliation(s)
- Miao-Miao Yan
- Key Laboratory of Northwest Water Resource, Environment and Ecology, Ministry of Education, Shaanxi Key Laboratory of Environmental Engineering, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Sheng-Nan Chen
- Key Laboratory of Northwest Water Resource, Environment and Ecology, Ministry of Education, Shaanxi Key Laboratory of Environmental Engineering, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Ting-Lin Huang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, Ministry of Education, Shaanxi Key Laboratory of Environmental Engineering, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Jing-Yu Jia
- Key Laboratory of Northwest Water Resource, Environment and Ecology, Ministry of Education, Shaanxi Key Laboratory of Environmental Engineering, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Kai-Wen Liu
- Key Laboratory of Northwest Water Resource, Environment and Ecology, Ministry of Education, Shaanxi Key Laboratory of Environmental Engineering, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Yu-Tian Miao
- Key Laboratory of Northwest Water Resource, Environment and Ecology, Ministry of Education, Shaanxi Key Laboratory of Environmental Engineering, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Rong-Rong Zong
- Key Laboratory of Northwest Water Resource, Environment and Ecology, Ministry of Education, Shaanxi Key Laboratory of Environmental Engineering, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
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20
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Israeli O, Makdasi E, Cohen-Gihon I, Zvi A, Lazar S, Shifman O, Levy H, Gur D, Laskar O, Beth-Din A. A rapid high-throughput sequencing-based approach for the identification of unknown bacterial pathogens in whole blood. Future Sci OA 2020; 6:FSO476. [PMID: 32670604 PMCID: PMC7351085 DOI: 10.2144/fsoa-2020-0013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 01/06/2020] [Accepted: 03/09/2020] [Indexed: 01/26/2023] Open
Abstract
High-throughput DNA sequencing (HTS) of pathogens in whole blood samples is hampered by the high host/pathogen nucleic acids ratio. We describe a novel and rapid bacterial enrichment procedure whose implementation is exemplified in simulated bacteremic human blood samples. The procedure involves depletion of the host DNA, rapid HTS and bioinformatic analyses. Following this procedure, Y. pestis, F. tularensis and B. anthracis spiked-in samples displayed an improved host/pathogen DNA ratio of 2.5-5.9 orders of magnitude, in samples with bacteria spiked-in at 103-105 CFU/ml. The procedure described in this study enables rapid and detailed metagenomic profiling of pathogens within 8-9 h, circumventing the challenges imposed by the high background present in the bacteremic blood and by the unknown nature of the sample.
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Affiliation(s)
- Ofir Israeli
- Department of Biochemistry & Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Efi Makdasi
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Inbar Cohen-Gihon
- Department of Biochemistry & Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Anat Zvi
- Department of Biochemistry & Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Shirley Lazar
- Department of Biochemistry & Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ohad Shifman
- Department of Biochemistry & Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Haim Levy
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - David Gur
- Department of Biochemistry & Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Orly Laskar
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Adi Beth-Din
- Department of Biochemistry & Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
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Hanghøj K, Renaud G, Albrechtsen A, Orlando L. DamMet: ancient methylome mapping accounting for errors, true variants, and post-mortem DNA damage. Gigascience 2019; 8:5475519. [PMID: 31004132 PMCID: PMC6474913 DOI: 10.1093/gigascience/giz025] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 10/29/2018] [Revised: 02/07/2019] [Accepted: 02/27/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Recent computational advances in ancient DNA research have opened access to the detection of ancient DNA methylation footprints at the genome-wide scale. The most commonly used approach infers the methylation state of a given genomic region on the basis of the amount of nucleotide mis-incorporations observed at CpG dinucleotide sites. However, this approach overlooks a number of confounding factors, including the presence of sequencing errors and true variants. The scale and distribution of the inferred methylation measurements are also variable across samples, precluding direct comparisons. FINDINGS Here, we present DamMet, an open-source software program retrieving maximum likelihood estimates of regional CpG methylation levels from ancient DNA sequencing data. It builds on a novel statistical model of post-mortem DNA damage for dinucleotides, accounting for sequencing errors, genotypes, and differential post-mortem cytosine deamination rates at both methylated and unmethylated sites. To validate DamMet, we extended gargammel, a sequence simulator for ancient DNA data, by introducing methylation-dependent features of post-mortem DNA decay. This new simulator provides direct validation of DamMet predictions. Additionally, the methylation levels inferred by DamMet were found to be correlated to those inferred by epiPALEOMIX and both on par and directly comparable to those measured from whole-genome bisulphite sequencing experiments of fresh tissues. CONCLUSIONS DamMet provides genuine estimates for local DNA methylation levels in ancient individual genomes. The returned estimates are directly cross-sample comparable, and the software is available as an open-source C++ program hosted at https://gitlab.com/KHanghoj/DamMet along with a manual and tutorial.
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Affiliation(s)
- Kristian Hanghøj
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, Øster Voldgade 5-7, 1350K Copenhagen, Denmark.,Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse III, Paul Sabatier (UPS), 31000 Toulouse, France
| | - Gabriel Renaud
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Anders Albrechtsen
- Computational and RNA Biology, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark, Øster voldgade 5-7, 1350k
| | - Ludovic Orlando
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, Øster Voldgade 5-7, 1350K Copenhagen, Denmark.,Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse III, Paul Sabatier (UPS), 31000 Toulouse, France
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22
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Fernández-Martínez MÁ, dos Santos Severino R, Moreno-Paz M, Gallardo-Carreño I, Blanco Y, Warren-Rhodes K, García-Villadangos M, Ruiz-Bermejo M, Barberán A, Wettergreen D, Cabrol N, Parro V. Prokaryotic Community Structure and Metabolisms in Shallow Subsurface of Atacama Desert Playas and Alluvial Fans After Heavy Rains: Repairing and Preparing for Next Dry Period. Front Microbiol 2019; 10:1641. [PMID: 31396176 PMCID: PMC6668633 DOI: 10.3389/fmicb.2019.01641] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 04/02/2019] [Accepted: 07/02/2019] [Indexed: 11/13/2022] Open
Abstract
The Atacama Desert, the oldest and driest desert on Earth, displays significant rains only once per decade. To investigate how microbial communities take advantage of these sporadic wet events, we carried out a geomicrobiological study a few days after a heavy rain event in 2015. Different physicochemical and microbial community analyses were conducted on samples collected from playas and an alluvial fan from surface, 10, 20, 50, and 80 cm depth. Gravimetric moisture content peaks were measured in 10 and 20 cm depth samples (from 1.65 to 4.1% w/w maximum values) while, in general, main anions such as chloride, nitrate, and sulfate concentrations increased with depth, with maximum values of 13-1,125; 168-10,109; and 9,904-30,952 ppm, respectively. Small organic anions such as formate and acetate had maximum concentrations from 2.61 to 3.44 ppm and 6.73 to 28.75 ppm, respectively. Microbial diversity inferred from DNA analysis showed Actinobacteria and Alphaproteobacteria as the most abundant and widespread bacterial taxa among the samples, followed by Chloroflexi and Firmicutes at specific sites. Archaea were mainly dominated by Nitrososphaerales, Methanobacteria, with the detection of other groups such as Halobacteria. Metaproteomics showed a high and even distribution of proteins involved in primary metabolic processes such as energy production and biosynthetic pathways, and a limited but remarkable presence of proteins related to resistance to environmental stressors such as radiation, oxidation, or desiccation. The results indicated that extra humidity in the system allows the microbial community to repair, and prepare for the upcoming hyperarid period. Additionally, it supplies biomarkers to the medium whose preservation potential could be high under strong desiccation conditions and relevant for planetary exploration.
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Affiliation(s)
| | | | | | | | | | - Kimberley Warren-Rhodes
- Carl Sagan Center, SETI Institute, Mountain View, CA, United States
- NASA Ames Research Center, Moffett Field, Mountain View, CA, United States
| | | | | | - Albert Barberán
- Department of Soil, Water, and Environmental Science, University of Arizona, Tucson, AZ, United States
| | - David Wettergreen
- Carnegie Mellon University, Robotics Institute, Pittsburgh, PA, United States
| | - Nathalie Cabrol
- Carl Sagan Center, SETI Institute, Mountain View, CA, United States
- NASA Ames Research Center, Moffett Field, Mountain View, CA, United States
| | - Víctor Parro
- Centro de Astrobiología (CAB, CSIC-INTA), Madrid, Spain
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23
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Mills N, Bensman EM, Poehlman WL, Ligon WB, Feltus FA. Moving Just Enough Deep Sequencing Data to Get the Job Done. Bioinform Biol Insights 2019; 13:1177932219856359. [PMID: 31236009 PMCID: PMC6572328 DOI: 10.1177/1177932219856359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 04/23/2019] [Accepted: 05/21/2019] [Indexed: 11/20/2022] Open
Abstract
Motivation: As the size of high-throughput DNA sequence datasets continues to grow, the cost of transferring and storing the datasets may prevent their processing in all but the largest data centers or commercial cloud providers. To lower this cost, it should be possible to process only a subset of the original data while still preserving the biological information of interest. Results: Using 4 high-throughput DNA sequence datasets of differing sequencing depth from 2 species as use cases, we demonstrate the effect of processing partial datasets on the number of detected RNA transcripts using an RNA-Seq workflow. We used transcript detection to decide on a cutoff point. We then physically transferred the minimal partial dataset and compared with the transfer of the full dataset, which showed a reduction of approximately 25% in the total transfer time. These results suggest that as sequencing datasets get larger, one way to speed up analysis is to simply transfer the minimal amount of data that still sufficiently detects biological signal. Availability: All results were generated using public datasets from NCBI and publicly available open source software.
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Affiliation(s)
- Nicholas Mills
- Holcombe Department of Electrical and Computer Engineering, Clemson University, Clemson, SC, USA
| | | | - William L Poehlman
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA
| | - Walter B Ligon
- Holcombe Department of Electrical and Computer Engineering, Clemson University, Clemson, SC, USA
| | - F Alex Feltus
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA
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24
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Li S, Wang X, Li Y, Lai H, Liu Y, Jin L. Non-invasive analysis of tumor mutation profiles and druggable mutations by sequencing of cell free DNA of Chinese metastatic breast cancer patients. Thorac Cancer 2019. [PMID: 30793491 DOI: 10.1111/1759‐7714.13002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Metastatic breast cancer (MBC) remains an incurable disease worldwide. Tumor gene mutations have evolved and led to drug resistance in the treatment course of MBC. However, data on the mutation profiles and druggable genomic alterations of MBC remain limited, particularly among Chinese patients. Our study aimed to depict the mutation profiles and identify druggable mutations in circulating tumor DNA (ctDNA) in Chinese MBC patients. METHODS Targeted deep sequencing of a 1021-gene panel was performed on 17 blood samples and 5 available tissue samples from 17 Chinese MBC patients. RESULTS We identified 60 somatic mutations in 17 blood samples (sensitivity 100%). Somatic mutations were identified in the blood samples of all patients, and 41.18% (7/17) of patients harbored at least one druggable mutation. A high ctDNA level in plasma is associated with shorter progression-free survival. CONCLUSION Targeted deep sequencing of cell free DNA is a highly sensitive, noninvasive method to depict tumor mutation profiles, identify druggable mutations in MBC, and predict patient outcome. Our study shed light on the utility of ctDNA as noninvasive "liquid biopsy" in the management of MBC.
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Affiliation(s)
- Shunying Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China.,Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Xiaobao Wang
- Department of Otorhinolaryngology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Yuquan Li
- Division of Cardiac Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, China
| | - Hongna Lai
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China.,Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Yujie Liu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China.,Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Liang Jin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China.,Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
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25
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Li S, Wang X, Li Y, Lai H, Liu Y, Jin L. Non-invasive analysis of tumor mutation profiles and druggable mutations by sequencing of cell free DNA of Chinese metastatic breast cancer patients. Thorac Cancer 2019; 10:807-814. [PMID: 30793491 PMCID: PMC6449225 DOI: 10.1111/1759-7714.13002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 12/17/2018] [Revised: 01/11/2019] [Accepted: 01/13/2019] [Indexed: 11/27/2022] Open
Abstract
Background Metastatic breast cancer (MBC) remains an incurable disease worldwide. Tumor gene mutations have evolved and led to drug resistance in the treatment course of MBC. However, data on the mutation profiles and druggable genomic alterations of MBC remain limited, particularly among Chinese patients. Our study aimed to depict the mutation profiles and identify druggable mutations in circulating tumor DNA (ctDNA) in Chinese MBC patients. Methods Targeted deep sequencing of a 1021‐gene panel was performed on 17 blood samples and 5 available tissue samples from 17 Chinese MBC patients. Results We identified 60 somatic mutations in 17 blood samples (sensitivity 100%). Somatic mutations were identified in the blood samples of all patients, and 41.18% (7/17) of patients harbored at least one druggable mutation. A high ctDNA level in plasma is associated with shorter progression‐free survival. Conclusion Targeted deep sequencing of cell free DNA is a highly sensitive, noninvasive method to depict tumor mutation profiles, identify druggable mutations in MBC, and predict patient outcome. Our study shed light on the utility of ctDNA as noninvasive “liquid biopsy” in the management of MBC.
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Affiliation(s)
- Shunying Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China.,Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Xiaobao Wang
- Department of Otorhinolaryngology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Yuquan Li
- Division of Cardiac Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, China
| | - Hongna Lai
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China.,Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Yujie Liu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China.,Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Liang Jin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China.,Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
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26
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Chávez-Carbajal A, Nirmalkar K, Pérez-Lizaur A, Hernández-Quiroz F, Ramírez-Del-Alto S, García-Mena J, Hernández-Guerrero C. Gut Microbiota and Predicted Metabolic Pathways in a Sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome. Int J Mol Sci 2019; 20:ijms20020438. [PMID: 30669548 PMCID: PMC6358992 DOI: 10.3390/ijms20020438] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [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: 12/21/2018] [Revised: 01/17/2019] [Accepted: 01/17/2019] [Indexed: 02/06/2023] Open
Abstract
Obesity is an excessive fat accumulation that could lead to complications like metabolic syndrome. There are reports on gut microbiota and metabolic syndrome in relation to dietary, host genetics, and other environmental factors; however, it is necessary to explore the role of the gut microbiota metabolic pathways in populations like Mexicans, where the prevalence of obesity and metabolic syndrome is high. This study identify alterations of the gut microbiota in a sample of healthy Mexican women (CO), women with obesity (OB), and women with obesity plus metabolic syndrome (OMS). We studied 67 women, characterizing their anthropometric and biochemical parameters along with their gut bacterial diversity by high-throughput DNA sequencing. Our results indicate that in OB or OMS women, Firmicutes was the most abundant bacterial phylum. We observed significant changes in abundances of bacteria belonging to the Ruminococcaceae, Lachnospiraceae, and Erysipelotrichaceae families and significant enrichment of gut bacteria from 16 different taxa that might explain the observed metabolic alterations between the groups. Finally, the predicted functional metagenome of the gut microbiota found in each category shows differences in metabolic pathways related to lipid metabolism. We demonstrate that Mexican women have a particular bacterial gut microbiota characteristic of each phenotype. There are bacteria that potentially explain the observed metabolic differences between the groups, and gut bacteria in OMS and OB conditions carry more genes of metabolic pathways implicated in lipid metabolism.
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Affiliation(s)
- Alejandra Chávez-Carbajal
- Departamento de Genética y Biología Molecular, Cinvestav-IPN, Av IPN 2508, Ciudad de México 07360, Mexico.
| | - Khemlal Nirmalkar
- Departamento de Genética y Biología Molecular, Cinvestav-IPN, Av IPN 2508, Ciudad de México 07360, Mexico.
| | - Ana Pérez-Lizaur
- Departamento de Salud, Universidad Iberoamericana, Ciudad de México, Paseo de la Reforma 880, Ciudad de México 01219, Mexico.
| | - Fernando Hernández-Quiroz
- Departamento de Genética y Biología Molecular, Cinvestav-IPN, Av IPN 2508, Ciudad de México 07360, Mexico.
| | - Silvia Ramírez-Del-Alto
- Departamento de Salud, Universidad Iberoamericana, Ciudad de México, Paseo de la Reforma 880, Ciudad de México 01219, Mexico.
| | - Jaime García-Mena
- Departamento de Genética y Biología Molecular, Cinvestav-IPN, Av IPN 2508, Ciudad de México 07360, Mexico.
| | - César Hernández-Guerrero
- Departamento de Salud, Universidad Iberoamericana, Ciudad de México, Paseo de la Reforma 880, Ciudad de México 01219, Mexico.
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27
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Clarke LJ, Suter L, King R, Bissett A, Deagle BE. Antarctic Krill Are Reservoirs for Distinct Southern Ocean Microbial Communities. Front Microbiol 2019; 9:3226. [PMID: 30697197 PMCID: PMC6340936 DOI: 10.3389/fmicb.2018.03226] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 09/20/2018] [Accepted: 12/11/2018] [Indexed: 11/13/2022] Open
Abstract
Host-associated bacterial communities have received limited attention in polar habitats, but are likely to represent distinct nutrient-rich niches compared to the surrounding environment. Antarctic krill (Euphausia superba) are a super-abundant species with a circumpolar distribution, and the krill microbiome may make a substantial contribution to marine bacterial diversity in the Southern Ocean. We used high-throughput sequencing of the bacterial 16S ribosomal RNA gene to characterize bacterial diversity in seawater and krill tissue samples from four locations south of the Kerguelen Plateau, one of the most productive regions in the Indian Sector of the Southern Ocean. Krill-associated bacterial communities were distinct from those of the surrounding seawater, with different communities inhabiting the moults, digestive tract and faecal pellets, including several phyla not detected in the surrounding seawater. Digestive tissues from many individuals contained a potential gut symbiont (order: Mycoplasmoidales) shown to improve survival on a low quality diet in other crustaceans. Antarctic krill swarms thus influence Southern Ocean microbial communities not only through top-down grazing of eukaryotic cells and release of nutrients into the water column, but also by transporting distinct microbial assemblages horizontally via migration and vertically via sinking faecal pellets and moulted exuviae. Changes to Antarctic krill demographics or distribution through fishing pressure or climate-induced range shifts will also influence the composition and dispersal of Southern Ocean microbial communities.
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Affiliation(s)
- Laurence J Clarke
- Antarctic Climate and Ecosystems Cooperative Research Centre, University of Tasmania, Hobart, TAS, Australia
| | - Léonie Suter
- Australian Antarctic Division, Kingston, TAS, Australia
| | - Robert King
- Australian Antarctic Division, Kingston, TAS, Australia
| | - Andrew Bissett
- Commonwealth Scientific and Industrial Research Organisation, Hobart, TAS, Australia
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Christoff AP, Sereia AF, Hernandes C, de Oliveira LF. Uncovering the hidden microbiota in hospital and built environments: New approaches and solutions. Exp Biol Med (Maywood) 2019; 244:534-542. [PMID: 30616384 DOI: 10.1177/1535370218821857] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 11/15/2022] Open
Abstract
IMPACT STATEMENT Research concerning the microbiome of indoor environments like hospitals, houses or buildings could have several implications for human health. Today, there is an ongoing shift in the paradigm of microbial analysis, from single isolated bacterial samples to entire microbiome profiles using high-throughput DNA sequencing methods. The use of sequencing methods in several studies has revealed an unprecedented microbial diversity in indoor environments, leading to a larger comprehension of the entire microbiome context. Here, we present a review of these microbiome studies using high-throughput DNA sequencing, including some new approaches and ideas that can be broadly applied in microbial tracking and epidemiological surveillance of indoor environments.
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Affiliation(s)
- Ana P Christoff
- 1 Neoprospecta Microbiome Technologies, CEP 88057-260, SC - Brasil
| | - Aline Fr Sereia
- 1 Neoprospecta Microbiome Technologies, CEP 88057-260, SC - Brasil
| | - Camila Hernandes
- 2 Hospital Israelita Albert Einstein, São Paulo, CEP 05651-901, SP - Brasil
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29
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Abstract
Viruses represent one of the major environmental agents that cause human illness and disease. However, the ability to diagnose viral infections is limited by detection capability and scope. Here we describe several emerging technologies that provide rapid and/or high-quality viral diagnostic information. Two technologies, novel CRISPR-based diagnostics and a portable DNA sequencing instrument, are uniquely suited to increase the number of viral agents analyzed, even in point of care settings. We also discuss a phage-based method for generating comprehensive viral profiles of previous exposure/infection and a fluid-phase immunoassay that yields highly quantitative viral antibody analyses. Future applications of these approaches will accelerate on-site clinical diagnosis of viral infections and provide insights into the role viruses play in complex diseases.
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Affiliation(s)
- Peter D Burbelo
- Dental Clinical Research Core, National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD, USA
| | - Michael J Iadarola
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Adrija Chaturvedi
- Dental Clinical Research Core, National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD, USA
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30
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Favalli N, Bassi G, Scheuermann J, Neri D. DNA-encoded chemical libraries - achievements and remaining challenges. FEBS Lett 2018; 592:2168-2180. [PMID: 29683493 PMCID: PMC6126621 DOI: 10.1002/1873-3468.13068] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 04/11/2018] [Accepted: 04/13/2018] [Indexed: 11/10/2022]
Abstract
DNA-encoded chemical libraries (DECLs) are collections of compounds, individually coupled to DNA tags serving as amplifiable identification barcodes. Since individual compounds can be identified by the associated DNA tag, they can be stored as a mixture, allowing the synthesis and screening of combinatorial libraries of unprecedented size, facilitated by the implementation of split-and-pool synthetic procedures or other experimental methodologies. In this review, we briefly present relevant concepts and technologies, which are required for the implementation and interpretation of screening procedures with DNA-encoded chemical libraries. Moreover, we illustrate some success stories, detailing how novel ligands were discovered from encoded libraries. Finally, we critically review what can realistically be achieved with the technology at the present time, highlighting challenges and opportunities for the future.
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Affiliation(s)
- Nicholas Favalli
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich (Switzerland)
| | - Gabriele Bassi
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich (Switzerland)
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich (Switzerland)
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich (Switzerland)
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31
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Weerakkody R, Ross D, Parry DA, Ziganshin B, Vandrovcova J, Gampawar P, Abdullah A, Biggs J, Dumfarth J, Ibrahim Y, Bicknell C, Field M, Elefteriades J, Cheshire N, Aitman TJ. Targeted genetic analysis in a large cohort of familial and sporadic cases of aneurysm or dissection of the thoracic aorta. Genet Med 2018. [PMID: 29543232 PMCID: PMC6004315 DOI: 10.1038/gim.2018.27] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [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] [Indexed: 01/16/2023] Open
Abstract
Purpose Thoracic aortic aneurysm/aortic dissection (TAAD) is a disorder with highly variable age of onset and phenotype. We sought to determine the prevalence of pathogenic variants in TAAD-associated genes in a mixed cohort of sporadic and familial TAAD patients and identify relevant genotype-phenotype relationships. Methods We used a targeted PCR and next generation sequencing-based panel for genetic analysis of 15 TAAD associated genes in 1025 unrelated TAAD cases. Results We identified 49 pathogenic or likely pathogenic (P/LP) variants in 47 cases (4.9% of those successfully sequenced). Almost half of the variants were in non-syndromic cases with no known family history of aortic disease. Twenty-five variants were within FBN1 and two patients were found to harbour two P/LP variants. Presence of a related syndrome, younger age at presentation, family history of aortic disease and involvement of the ascending aorta increased the risk of carrying a P/LP variant. Conclusions Given the poor prognosis of TAAD that is undiagnosed prior to acute rupture or dissection, genetic analysis of both familial and sporadic cases of TAAD will lead to new diagnoses, more informed management and possibly reduced mortality through earlier, preclinical diagnosis in genetically determined cases and their family members.
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Affiliation(s)
- Ruwan Weerakkody
- Department of Medicine, Institute of Clinical Sciences, Imperial College London, London, UK.,Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.,Department of Surgery and Cancer, Imperial College London, London, UK
| | - David Ross
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - David A Parry
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Bulat Ziganshin
- Aortic Institute at Yale-New Haven Hospital, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jana Vandrovcova
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London, UK
| | - Piyush Gampawar
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Abdulshakur Abdullah
- Department of Medicine, Institute of Clinical Sciences, Imperial College London, London, UK
| | - Jennifer Biggs
- Department of Medicine, Institute of Clinical Sciences, Imperial College London, London, UK
| | - Julia Dumfarth
- Aortic Institute at Yale-New Haven Hospital, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Yousef Ibrahim
- Department of Surgery and Cancer, Imperial College London, London, UK
| | | | - Colin Bicknell
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Mark Field
- Department of Cardiac Surgery, Liverpool Heart and Chest Hospital, Liverpool, UK
| | - John Elefteriades
- Aortic Institute at Yale-New Haven Hospital, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Nick Cheshire
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Timothy J Aitman
- Department of Medicine, Institute of Clinical Sciences, Imperial College London, London, UK. .,Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK. .,Aortic Institute at Yale-New Haven Hospital, Yale University School of Medicine, New Haven, Connecticut, USA.
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32
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Punetha J, Kesari A, Uapinyoying P, Giri M, Clarke NF, Waddell LB, North KN, Ghaoui R, O'Grady GL, Oates EC, Sandaradura SA, Bönnemann CG, Donkervoort S, Plotz PH, Smith EC, Tesi-Rocha C, Bertorini TE, Tarnopolsky MA, Reitter B, Hausmanowa-Petrusewicz I, Hoffman EP. Targeted Re-Sequencing Emulsion PCR Panel for Myopathies: Results in 94 Cases. J Neuromuscul Dis 2018; 3:209-225. [PMID: 27854218 DOI: 10.3233/jnd-160151] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 12/11/2022]
Abstract
BACKGROUND Molecular diagnostics in the genetic myopathies often requires testing of the largest and most complex transcript units in the human genome (DMD, TTN, NEB). Iteratively targeting single genes for sequencing has traditionally entailed high costs and long turnaround times. Exome sequencing has begun to supplant single targeted genes, but there are concerns regarding coverage and needed depth of the very large and complex genes that frequently cause myopathies. OBJECTIVE To evaluate efficiency of next-generation sequencing technologies to provide molecular diagnostics for patients with previously undiagnosed myopathies. METHODS We tested a targeted re-sequencing approach, using a 45 gene emulsion PCR myopathy panel, with subsequent sequencing on the Illumina platform in 94 undiagnosed patients. We compared the targeted re-sequencing approach to exome sequencing for 10 of these patients studied. RESULTS We detected likely pathogenic mutations in 33 out of 94 patients with a molecular diagnostic rate of approximately 35%. The remaining patients showed variants of unknown significance (35/94 patients) or no mutations detected in the 45 genes tested (26/94 patients). Mutation detection rates for targeted re-sequencing vs. whole exome were similar in both methods; however exome sequencing showed better distribution of reads and fewer exon dropouts. CONCLUSIONS Given that costs of highly parallel re-sequencing and whole exome sequencing are similar, and that exome sequencing now takes considerably less laboratory processing time than targeted re-sequencing, we recommend exome sequencing as the standard approach for molecular diagnostics of myopathies.
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Affiliation(s)
- Jaya Punetha
- Research Center for Genetic Medicine, Children's National Medical Center, Washington DC, USA.,Department of Integrative Systems Biology, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Akanchha Kesari
- Research Center for Genetic Medicine, Children's National Medical Center, Washington DC, USA
| | - Prech Uapinyoying
- Research Center for Genetic Medicine, Children's National Medical Center, Washington DC, USA.,Department of Integrative Systems Biology, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Mamta Giri
- Research Center for Genetic Medicine, Children's National Medical Center, Washington DC, USA
| | - Nigel F Clarke
- INMR, The Children's Hospital at Westmead & Discipline of Paediatrics and Child Health, University of Sydney, Sydney, Australia
| | - Leigh B Waddell
- INMR, The Children's Hospital at Westmead & Discipline of Paediatrics and Child Health, University of Sydney, Sydney, Australia
| | - Kathryn N North
- INMR, The Children's Hospital at Westmead & Discipline of Paediatrics and Child Health, University of Sydney, Sydney, Australia.,Murdoch Childrens Research Institute, Melbourne, Australia; Department of Paediatrics, Faculty of Medicine, University of Melbourne, Melbourne, Australia
| | - Roula Ghaoui
- INMR, The Children's Hospital at Westmead & Discipline of Paediatrics and Child Health, University of Sydney, Sydney, Australia
| | - Gina L O'Grady
- INMR, The Children's Hospital at Westmead & Discipline of Paediatrics and Child Health, University of Sydney, Sydney, Australia
| | - Emily C Oates
- INMR, The Children's Hospital at Westmead & Discipline of Paediatrics and Child Health, University of Sydney, Sydney, Australia
| | - Sarah A Sandaradura
- INMR, The Children's Hospital at Westmead & Discipline of Paediatrics and Child Health, University of Sydney, Sydney, Australia
| | - Carsten G Bönnemann
- National Institute of Neurological Disorders and Stroke/NIH, Porter Neuroscience Research Center, Bethesda, MD, USA
| | - Sandra Donkervoort
- National Institute of Neurological Disorders and Stroke/NIH, Porter Neuroscience Research Center, Bethesda, MD, USA
| | - Paul H Plotz
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Edward C Smith
- Department of Pediatrics, Division of Pediatric Neurology, Duke University Medical Center, Durham, NC, USA
| | - Carolina Tesi-Rocha
- Research Center for Genetic Medicine, Children's National Medical Center, Washington DC, USA
| | - Tulio E Bertorini
- Department of Neurology, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Mark A Tarnopolsky
- Departments of Pediatrics and Medicine, McMaster University, Neuromuscular Disease Clinic, Health Sciences Centre, ON, Canada
| | - Bernd Reitter
- Children's Hospital, Johannes Gutenberg University, Mainz, Germany
| | | | - Eric P Hoffman
- Research Center for Genetic Medicine, Children's National Medical Center, Washington DC, USA.,Department of Integrative Systems Biology, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
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Matsumura Y, Pitout JDD, Gomi R, Matsuda T, Noguchi T, Yamamoto M, Peirano G, DeVinney R, Bradford PA, Motyl MR, Tanaka M, Nagao M, Takakura S, Ichiyama S. Global Escherichia coli Sequence Type 131 Clade with bla CTX-M-27 Gene. Emerg Infect Dis 2018; 22:1900-1907. [PMID: 27767006 PMCID: PMC5088012 DOI: 10.3201/eid2211.160519] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The Escherichia coli sequence type (ST) 131 C2/H30Rx clade with the blaCTX-M-15 gene had been most responsible for the global dissemination of extended-spectrum β-lactamase (ESBL)-producing E. coli. ST131 C1/H30R with blaCTX-M-27 emerged among ESBL-producing E. coli in Japan during the late 2000s. To investigate the possible expansion of a single clade, we performed whole-genome sequencing for 43 Japan and 10 global ST131 isolates with blaCTX-M-27 (n = 16), blaCTX-M-14 (n = 16), blaCTX-M-15 (n = 13), and others (n = 8). We also included 8 ST131 genomes available in public databases. Core genome-based analysis of 61 isolates showed that ST131 with blaCTX-M-27 from 5 countries formed a distinct cluster within the C1/H30R clade, named C1-M27 clade. Accessory genome analysis identified a unique prophage-like region, supporting C1-M27 as a distinct clade. Our findings indicate that the increase of ESBL-producing E. coli in Japan is due mainly to emergence of the C1-M27 clade.
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Choi SH, Jung SH, Chung YJ. Validation of Customized Cancer Panel for Detecting Somatic Mutations and Copy Number Alterations. Genomics Inform 2018; 15:136-141. [PMID: 29307139 PMCID: PMC5769856 DOI: 10.5808/gi.2017.15.4.136] [Citation(s) in RCA: 3] [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: 11/23/2017] [Revised: 11/28/2017] [Accepted: 11/28/2017] [Indexed: 12/15/2022] Open
Abstract
Accurate detection of genomic alterations, especially druggable hotspot mutations in tumors, has become an essential part of precision medicine. With targeted sequencing, we can obtain deeper coverage of reads and handle data more easily with a relatively lower cost and less time than whole-exome or whole-genome sequencing. Recently, we designed a customized gene panel for targeted sequencing of major solid cancers. In this study, we aimed to validate its performance. The cancer panel targets 95 cancer-related genes. In terms of the limit of detection, more than 86% of target mutations with a mutant allele frequency (MAF) <1% can be identified, and any mutation with >3% MAF can be detected. When we applied this system for the analysis of Acrometrix Oncology Hotspot Control DNA, which contains more than 500 COSMIC mutations across 53 genes, 99% of the expected mutations were robustly detected. We also confirmed the high reproducibility of the detection of mutations in multiple independent analyses. When we explored copy number alterations (CNAs), the expected CNAs were successfully detected, and this result was confirmed by target-specific genomic quantitative polymerase chain reaction. Taken together, these results support the reliability and accuracy of our cancer panel in detecting mutations. This panel could be useful for key mutation profiling research in solid tumors and clinical translation.
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Affiliation(s)
- Su-Hye Choi
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea.,Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea.,Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Seung-Hyun Jung
- Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea.,Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Yeun-Jun Chung
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea.,Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea.,Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
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35
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Kieran TJ, Gottdenker NL, Varian CP, Saldaña A, Means N, Owens D, Calzada JE, Glenn TC. Blood Meal Source Characterization Using Illumina Sequencing in the Chagas Disease Vector Rhodnius pallescens (Hemiptera: Reduviidae) in Panamá. J Med Entomol 2017; 54:1786-1789. [PMID: 29029145 DOI: 10.1093/jme/tjx170] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [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: 04/14/2017] [Indexed: 06/07/2023]
Abstract
Accurate blood meal identification is critical to understand hematophagous vector-host relationships. This study describes a customizable Next-Generation Sequencing (NGS) approach to identify blood meals from Rhodnius pallescens (Hemiptera: Reduviidae) triatomines using multiple barcoded primers and existing software to pick operational taxonomic units and match sequences for blood meal identification. We precisely identified all positive control samples using this method and further examined 74 wild-caught R. pallescens samples. With this novel blood meal identification method, we detected 13 vertebrate species in the blood meals, as well as single and multiple blood meals in individual bugs. Our results demonstrate the reliability and descriptive uses of our method.
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Affiliation(s)
- Troy J Kieran
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA
| | - Nicole L Gottdenker
- Department of Veterinary Pathology, College of Veterinary Medicine, The University of Georgia, Athens, GA
| | - Christina P Varian
- Department of Veterinary Pathology, College of Veterinary Medicine, The University of Georgia, Athens, GA
| | - Azael Saldaña
- Department of Parasitology, Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama City, Panamá
| | - Nicolas Means
- University of Oklahoma Health Sciences Center, University of Oklahoma, Oklahoma City, OK
| | - Darlisha Owens
- Department of Biology, Grambling State University, Grambling, LA
| | - Jose E Calzada
- Department of Parasitology, Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama City, Panamá
| | - Travis C Glenn
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA
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36
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Moura A, Tourdjman M, Leclercq A, Hamelin E, Laurent E, Fredriksen N, Van Cauteren D, Bracq-Dieye H, Thouvenot P, Vales G, Tessaud-Rita N, Maury MM, Alexandru A, Criscuolo A, Quevillon E, Donguy MP, Enouf V, de Valk H, Brisse S, Lecuit M. Real-Time Whole-Genome Sequencing for Surveillance of Listeria monocytogenes, France. Emerg Infect Dis 2017. [PMID: 28643628 PMCID: PMC5572858 DOI: 10.3201/eid2309.170336] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
During 2015–2016, we evaluated the performance of whole-genome sequencing (WGS) as a routine typing tool. Its added value for microbiological and epidemiologic surveillance of listeriosis was compared with that for pulsed-field gel electrophoresis (PFGE), the current standard method. A total of 2,743 Listeria monocytogenes isolates collected as part of routine surveillance were characterized in parallel by PFGE and core genome multilocus sequence typing (cgMLST) extracted from WGS. We investigated PFGE and cgMLST clusters containing human isolates. Discrimination of isolates was significantly higher by cgMLST than by PFGE (p<0.001). cgMLST discriminated unrelated isolates that shared identical PFGE profiles and phylogenetically closely related isolates with distinct PFGE profiles. This procedure also refined epidemiologic investigations to include only phylogenetically closely related isolates, improved source identification, and facilitated epidemiologic investigations, enabling identification of more outbreaks at earlier stages. WGS-based typing should replace PFGE as the primary typing method for L. monocytogenes.
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37
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Der Sarkissian C, Pichereau V, Dupont C, Ilsøe PC, Perrigault M, Butler P, Chauvaud L, Eiríksson J, Scourse J, Paillard C, Orlando L. Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past. Mol Ecol Resour 2017; 17:835-853. [PMID: 28394451 DOI: 10.1111/1755-0998.12679] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [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: 12/17/2016] [Revised: 03/24/2017] [Accepted: 04/03/2017] [Indexed: 02/05/2023]
Abstract
Marine mollusc shells enclose a wealth of information on coastal organisms and their environment. Their life history traits as well as (palaeo-) environmental conditions, including temperature, food availability, salinity and pollution, can be traced through the analysis of their shell (micro-) structure and biogeochemical composition. Adding to this list, the DNA entrapped in shell carbonate biominerals potentially offers a novel and complementary proxy both for reconstructing palaeoenvironments and tracking mollusc evolutionary trajectories. Here, we assess this potential by applying DNA extraction, high-throughput shotgun DNA sequencing and metagenomic analyses to marine mollusc shells spanning the last ~7,000 years. We report successful DNA extraction from shells, including a variety of ancient specimens, and find that DNA recovery is highly dependent on their biomineral structure, carbonate layer preservation and disease state. We demonstrate positive taxonomic identification of mollusc species using a combination of mitochondrial DNA genomes, barcodes, genome-scale data and metagenomic approaches. We also find shell biominerals to contain a diversity of microbial DNA from the marine environment. Finally, we reconstruct genomic sequences of organisms closely related to the Vibrio tapetis bacteria from Manila clam shells previously diagnosed with Brown Ring Disease. Our results reveal marine mollusc shells as novel genetic archives of the past, which opens new perspectives in ancient DNA research, with the potential to reconstruct the evolutionary history of molluscs, microbial communities and pathogens in the face of environmental changes. Other future applications include conservation of endangered mollusc species and aquaculture management.
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Affiliation(s)
- Clio Der Sarkissian
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark
| | - Vianney Pichereau
- Lemar UMR6539 CNRS/UBO/IRD/Ifremer, Université de Brest, IUEM, Plouzané, France
| | | | - Peter C Ilsøe
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark
| | - Mickael Perrigault
- Lemar UMR6539 CNRS/UBO/IRD/Ifremer, Université de Brest, IUEM, Plouzané, France
| | - Paul Butler
- CGES, College of Life and Environmental Sciences, University of Exeter, Penryn, Cornwall, UK
| | - Laurent Chauvaud
- Lemar UMR6539 CNRS/UBO/IRD/Ifremer, Université de Brest, IUEM, Plouzané, France
| | - Jón Eiríksson
- Institute of Earth Sciences, University of Iceland, Askja, Reykjavík, Iceland
| | - James Scourse
- CGES, College of Life and Environmental Sciences, University of Exeter, Penryn, Cornwall, UK
| | - Christine Paillard
- Lemar UMR6539 CNRS/UBO/IRD/Ifremer, Université de Brest, IUEM, Plouzané, France
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark
- Université de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, CNRS UMR 5288, Toulouse, France
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Abstract
Hereditary bleeding and platelet disorders (BPDs) are characterized by marked genetic heterogeneity, far greater than previously appreciated. The list of genes involved in the regulation of megakaryopoiesis, platelet formation, platelet function and bleeding has been growing rapidly since the introduction of high-throughput sequencing (HTS) approaches in research. Thanks to the gradual adoption of HTS in diagnostic practice, these discoveries are improving the diagnostic yield for BPD patients, who may or may not present with bleeding problems and often have other clinical symptoms unrelated to the blood system. However, it was previously found that screening for all known etiologies gives a diagnostic yield of over 90% when the phenotype closely matches a known BPD but drops to 10% when the phenotype is indicative of a novel disorder. Thus, further research is needed to identify currently unknown etiologies for BPDs. Novel genes are likely to be found to be implicated in BPDs. New modes of inheritance, including digenic inheritance, are likely to play a role in some cases. Additionally, identifying and interpreting pathogenic variants outside exons is a looming challenge that can only be tackled with an improved understanding of the regulatory landscape of relevant cell types and with the transition from targeted sequencing to whole-genome sequencing in the clinic.
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Affiliation(s)
- K Freson
- Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
| | - E Turro
- Department of Haematology and MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
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39
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Parducci L, Bennett KD, Ficetola GF, Alsos IG, Suyama Y, Wood JR, Pedersen MW. Ancient plant DNA in lake sediments. New Phytol 2017; 214:924-942. [PMID: 28370025 DOI: 10.1111/nph.14470] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [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: 10/01/2016] [Accepted: 12/07/2016] [Indexed: 05/14/2023]
Abstract
Contents 924 I. 925 II. 925 III. 927 IV. 929 V. 930 VI. 930 VII. 931 VIII. 933 IX. 935 X. 936 XI. 938 938 References 938 SUMMARY: Recent advances in sequencing technologies now permit the analyses of plant DNA from fossil samples (ancient plant DNA, plant aDNA), and thus enable the molecular reconstruction of palaeofloras. Hitherto, ancient frozen soils have proved excellent in preserving DNA molecules, and have thus been the most commonly used source of plant aDNA. However, DNA from soil mainly represents taxa growing a few metres from the sampling point. Lakes have larger catchment areas and recent studies have suggested that plant aDNA from lake sediments is a more powerful tool for palaeofloristic reconstruction. Furthermore, lakes can be found globally in nearly all environments, and are therefore not limited to perennially frozen areas. Here, we review the latest approaches and methods for the study of plant aDNA from lake sediments and discuss the progress made up to the present. We argue that aDNA analyses add new and additional perspectives for the study of ancient plant populations and, in time, will provide higher taxonomic resolution and more precise estimation of abundance. Despite this, key questions and challenges remain for such plant aDNA studies. Finally, we provide guidelines on technical issues, including lake selection, and we suggest directions for future research on plant aDNA studies in lake sediments.
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Affiliation(s)
- Laura Parducci
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, 75236, Sweden
| | - Keith D Bennett
- Department of Geography & Sustainable Development, School of Geography & Geosciences, University of St Andrews, St Andrews, Fife, KY16 9AL, UK
- Marine Laboratory, Queen's University Belfast, Portaferry, BT22 1LS, UK
| | - Gentile Francesco Ficetola
- CNRS, Université Grenoble-Alpes, Laboratoire d'Ecologie Alpine (LECA), Grenoble, F-38000, France
- Department of Biosciences, Università degli Studi di Milano, Milan, 20133, Italy
| | - Inger Greve Alsos
- Tromsø Museum, UiT - The Arctic University of Norway, Tromsø, NO-9037, Norway
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi, 989-6711, Japan
| | - Jamie R Wood
- Long-term Ecology Lab, Landcare Research, PO Box 69040, Lincoln Canterbury, 7640, New Zealand
| | - Mikkel Winther Pedersen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, 1350, Denmark
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Zhao F, Xu K. Distribution of Ciliates in Intertidal Sediments across Geographic Distances: A Molecular View. Protist 2017; 168:171-82. [PMID: 28285259 DOI: 10.1016/j.protis.2017.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 12/30/2016] [Accepted: 01/10/2017] [Indexed: 12/22/2022]
Abstract
The estimation of the diversity and geographic distribution of protists in particular ciliates has long been an ongoing debate. We estimated the distribution of ciliates in intertidal sediments with geographic distance ranging from 10cm to 1,000km, using high-throughput DNA sequencing. Higher community similarity, in particular that of rare ciliate taxa, occurred between replicates than between sites. Statistical analyses showed that the community dissimilarities of both abundant and moderately abundant ciliates had correlations with geographic distance at the scales of 50m, 200km and 1000km, indicating a distance-decay relationship. No significant correlation was observed for rare taxa. The analysis of Bray-Curtis similarity showed a higher pairwise community similarity in abundant taxa than in moderately abundant taxa, and that in rare taxa was the lowest. Abundant taxa usually can disperse in a wider range than rare taxa, though their distribution is restricted by distance to some extent. Rare taxa are potentially more sensitive to changing environments, but no distance-decay relationship could be observed. The data indicate contrasting patterns of geographic distribution of the abundant and rare ciliate taxa and a weak distance-decay relationship for relatively abundant taxa at a scale over 50m.
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Choi S, Go JH, Kim EK, Lee H, Lee WM, Cho CS, Han K. Mutational Analysis of Extranodal NK/T-Cell Lymphoma Using Targeted Sequencing with a Comprehensive Cancer Panel. Genomics Inform 2016; 14:78-84. [PMID: 27729836 PMCID: PMC5056900 DOI: 10.5808/gi.2016.14.3.78] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [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: 08/01/2016] [Revised: 08/10/2016] [Accepted: 08/11/2016] [Indexed: 02/06/2023] Open
Abstract
Extranodal natural killer (NK)/T-cell lymphoma, nasal type (NKTCL), is a malignant disorder of cytotoxic lymphocytes of NK or T cells. It is an aggressive neoplasm with a very poor prognosis. Although extranodal NKTCL reportedly has a strong association with Epstein-Barr virus, the molecular pathogenesis of NKTCL has been unexplored. The recent technological advancements in next-generation sequencing (NGS) have made DNA sequencing cost- and time-effective, with more reliable results. Using the Ion Proton Comprehensive Cancer Panel, we sequenced 409 cancer-related genes to identify somatic mutations in five NKTCL tissue samples. The sequencing analysis detected 25 mutations in 21 genes. Among them, KMT2D, a histone modification-related gene, was the most frequently mutated gene (four of the five cases). This result was consistent with recent NGS studies that have suggested KMT2D as a novel driver gene in NKTCL. Mutations were also found in ARID1A, a chromatin remodeling gene, and TP53, which also recurred in recent NGS studies. We also found mutations in 18 novel candidate genes, with molecular functions that were potentially implicated in cancer development. We suggest that these genes may result in multiple oncogenic events and may be used as potential bio-markers of NKTCL in the future.
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Affiliation(s)
- Seungkyu Choi
- Department of Pathology, Dankook University College of Medicine, Cheonan 31116, Korea
| | - Jai Hyang Go
- Department of Pathology, Dankook University College of Medicine, Cheonan 31116, Korea
| | - Eun Kyung Kim
- Department of Pathology, Eulji Medical Center, Eulji University School of Medicine, Seoul 01830, Korea
| | - Hojung Lee
- Department of Pathology, Eulji Medical Center, Eulji University School of Medicine, Seoul 01830, Korea
| | - Won Mi Lee
- Department of Pathology, Eulji Medical Center, Eulji University School of Medicine, Seoul 01830, Korea
| | - Chun-Sung Cho
- Department of Neurosurgery, Dankook University College of Medicine, Cheonan 31116, Korea
| | - Kyudong Han
- Department of Nanobiomedical Science, BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Korea
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Lyu C, Xue F, Liu X, Liu W, Fu R, Sun T, Wu R, Zhang L, Li H, Zhang D, Yang R, Zhang L. Identification of mutations in the F8 and F9 gene in families with haemophilia using targeted high-throughput sequencing. Haemophilia 2016; 22:e427-34. [PMID: 27292088 DOI: 10.1111/hae.12924] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2016] [Indexed: 11/27/2022]
Abstract
INTRODUCTION At present, many methods are available for the genetic diagnosis of haemophilia, including indirect linkage analysis, direct sequencing. However, these methods are time-consuming, labourious, and limited in their application. Therefore, the development of new, more effective techniques is necessary. AIM To detect the F8 and F9 gene mutations in patients with haemophilia and their female relatives in 29 haemophilia A (HA) and 11 haemophilia B (HB) families. METHODS FVIII C and FIX:C were analyzed using one-stage method, and factor VIII and factor IX inhibitors were tested using the Bethesda method. Intron 22 and one inversions were identified using long-distance polymerase chain reaction (PCR) and standard PCR. Non-inversion mutations of the F8 and F9 gene were identified by targeted high-throughput sequencing. All mutations were verified by Sanger sequencing. RESULTS Intron 22 inversion was detected in eight HA families and intron one inversion was detected in one HA family. Apart from the inversion mutations, 20 mutations were identified in HA families, including 17 previously reported and three novel mutations: c.5724G>A (p.Trp1908*), c.6116-1_6120delGAGTGTinsTCC (p.Lys2039Ilefs*13), and c.5220-2A>C. We found a complex rearrangement in HA: intron one inversion concomitant with exon one deletion. In HB, eight recurrent mutations were detected, including six missense mutations and two nonsense mutations. CONCLUSION Targeted high-throughput sequencing is an effective technique to detect the F8 and F9 gene mutations, especially for the discovery of novel mutations. The method is highly accurate, time-saving and shows great advantage in uncovering large deletion mutations and also in distinguishing the wild-type genotype and heterozygous large deletions.
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Affiliation(s)
- C Lyu
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - F Xue
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.
| | - X Liu
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - W Liu
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - R Fu
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - T Sun
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - R Wu
- BGI-Tianjin, Tianjin, China
| | - L Zhang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - H Li
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - D Zhang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - R Yang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.
| | - L Zhang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.
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Pezeshkpoor B, Berkemeier AC, Czogalla KJ, Oldenburg J, El-Maarri O. Evidence of pathogenicity of a mutation in 3' untranslated region causing mild haemophilia A. Haemophilia 2016; 22:598-603. [PMID: 27216882 DOI: 10.1111/hae.12923] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2016] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Despite the high mutation detection rate, in a small group of haemophilia A patients, using current screening methods, no causal mutation in F8 can be detected. In such cases, the causal mutation might be in the non-coding sequences of F8. AIM Rarely, mutations in non-coding sequences reveal a pivotal role. Here, we analysed a mild haemophilia A patient harbouring a mutation in the 3' untranslated region (UTR) of F8 and elucidated the molecular mechanism leading to haemophilia phenotype. METHODS To find the causal mutation, the complete F8 genomic region was analysed by next generation sequencing. The effect of the identified alteration on F8 expression was evaluated in silico and analysed for the splicing effect at mRNA level. Moreover, in vitro studies using a luciferase reporter system were performed to functionally analyse the mutation. RESULTS We identified an alteration in the 3' UTR (c.*56G>T) as the only change in F8 gene. Pedigree analysis showed a segregation pattern for three affected members for the presumptive mutation. Moreover, the variant was predicted in silico to create a new donor splice site, which was also detected at mRNA level, resulting in a 159 bp deletion in 3' UTR of F8. Finally, the variant showed reduced expression of the gene reporter firefly luciferase in cell line expression analysis. CONCLUSION Our results advocate the patient specific c.*56G>T base change in the 3' UTR to be a disease-associated mutation leading to alternative splicing explaining the mild haemophilia A phenotype.
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Affiliation(s)
- B Pezeshkpoor
- Institute of Experimental Haematology and Transfusion Medicine, University of Bonn, Bonn, Germany.,Center for Rare Diseases Bonn (ZSEB), University Clinic Bonn, Bonn, Germany
| | - A-C Berkemeier
- Institute of Experimental Haematology and Transfusion Medicine, University of Bonn, Bonn, Germany.,Center for Rare Diseases Bonn (ZSEB), University Clinic Bonn, Bonn, Germany
| | - K J Czogalla
- Institute of Experimental Haematology and Transfusion Medicine, University of Bonn, Bonn, Germany.,Center for Rare Diseases Bonn (ZSEB), University Clinic Bonn, Bonn, Germany
| | - J Oldenburg
- Institute of Experimental Haematology and Transfusion Medicine, University of Bonn, Bonn, Germany.,Center for Rare Diseases Bonn (ZSEB), University Clinic Bonn, Bonn, Germany
| | - O El-Maarri
- Institute of Experimental Haematology and Transfusion Medicine, University of Bonn, Bonn, Germany.,Department of Natural Sciences, Lebanese American University, Byblos/Beirut, Lebanon
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Looney TJ, Lee JY, Roskin KM, Hoh RA, King J, Glanville J, Liu Y, Pham TD, Dekker CL, Davis MM, Boyd SD. Human B-cell isotype switching origins of IgE. J Allergy Clin Immunol 2015; 137:579-586.e7. [PMID: 26309181 DOI: 10.1016/j.jaci.2015.07.014] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 06/29/2015] [Accepted: 07/01/2015] [Indexed: 01/13/2023]
Abstract
BACKGROUND B cells expressing IgE contribute to immunity against parasites and venoms and are the source of antigen specificity in allergic patients, yet the developmental pathways producing these B cells in human subjects remain a subject of debate. Much of our knowledge of IgE lineage development derives from model studies in mice rather than from human subjects. OBJECTIVE We evaluate models for isotype switching to IgE in human subjects using immunoglobulin heavy chain (IGH) mutational lineage data. METHODS We analyzed IGH repertoires in 9 allergic and 24 healthy adults using high-throughput DNA sequencing of 15,843,270 IGH rearrangements to identify clonal lineages of B cells containing members expressing IgE. Somatic mutations in IGH inherited from common ancestors within the clonal lineage are used to infer the relationships between B cells. RESULTS Data from 613,641 multi-isotype B-cell clonal lineages, of which 592 include an IgE member, are consistent with indirect switching to IgE from IgG- or IgA-expressing lineage members in human subjects. We also find that these inferred isotype switching frequencies are similar in healthy and allergic subjects. CONCLUSIONS We found evidence that secondary isotype switching of mutated IgG1-expressing B cells is the primary source of IgE in human subjects, with lesser contributions from precursors expressing other switched isotypes and rarely IgM or IgD, suggesting that IgE is derived from previously antigen-experienced B cells rather than naive B cells that typically express low-affinity unmutated antibodies. These data provide a basis from which to evaluate allergen-specific human antibody repertoires in healthy and diseased subjects.
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Affiliation(s)
- Timothy J Looney
- Department of Pathology, Transplantation and Infection, Stanford University, Stanford, Calif
| | - Ji-Yeun Lee
- Department of Pathology, Transplantation and Infection, Stanford University, Stanford, Calif
| | - Krishna M Roskin
- Department of Pathology, Transplantation and Infection, Stanford University, Stanford, Calif
| | - Ramona A Hoh
- Department of Pathology, Transplantation and Infection, Stanford University, Stanford, Calif
| | - Jasmine King
- Department of Pathology, Transplantation and Infection, Stanford University, Stanford, Calif; Department of Biology, Transplantation and Infection, Stanford University, Stanford, Calif
| | - Jacob Glanville
- Department of Pathology, Transplantation and Infection, Stanford University, Stanford, Calif; Program in Immunology, Transplantation and Infection, Stanford University, Stanford, Calif
| | - Yi Liu
- Department of Pathology, Transplantation and Infection, Stanford University, Stanford, Calif; Biomedical Informatics Training Program, Transplantation and Infection, Stanford University, Stanford, Calif
| | - Tho D Pham
- Department of Pathology, Transplantation and Infection, Stanford University, Stanford, Calif
| | - Cornelia L Dekker
- Department of Pediatrics, Transplantation and Infection, Stanford University, Stanford, Calif
| | - Mark M Davis
- Department of Microbiology & Immunology, Transplantation and Infection, Stanford University, Stanford, Calif; Howard Hughes Medical Institute, Transplantation and Infection, Stanford University, Stanford, Calif; Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, Calif
| | - Scott D Boyd
- Department of Pathology, Transplantation and Infection, Stanford University, Stanford, Calif.
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Lee HB, Joung JG, Kim J, Lee KM, Ryu HS, Lee HO, Moon HG, Park WY, Noh DY, Han W. The use of FNA samples for whole-exome sequencing and detection of somatic mutations in breast cancer surgical specimens. Cancer Cytopathol 2015; 123:669-77. [PMID: 26265110 DOI: 10.1002/cncy.21599] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [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: 05/23/2015] [Revised: 07/04/2015] [Accepted: 07/07/2015] [Indexed: 01/12/2023]
Abstract
BACKGROUND The availability of suitable biospecimens is critical to the success of advanced genomic analyses. The objective of this study was to assess the sensitivity of fine-needle aspiration (FNA) compared with gross surgical sampling (GSS) from surgical specimens for the detection of somatic mutations in breast cancer using whole-exome sequencing (WES). METHODS DNA was extracted from paired GSS tissues and FNA samples of surgically resected breast cancer from 12 patients and was used for WES. Sanger sequencing was performed to validate selected somatic mutations. Tumor purity was calculated for each sample using sequencing data. RESULTS There was no difference in the total amount of DNA extracted from GSS tissues and FNA samples. WES was successfully performed for all 12 pairs of samples. The median number of somatic mutations identified in individual samples was higher in FNA samples than in GSS tissues (39.5 vs 18.5; P = .036). The somatic mutation profiles from both sampling methods were well correlated for samples that had GSS tissues with high tumor content, as indicated by hematoxylin and eosin staining. Nineteen mutations that were identified exclusively in FNA samples were subjected to Sanger sequencing, and 13 of those mutations (68.4%) were validated. The mean estimated tumor purity was higher in FNA samples than in GSS tissues (55.87% vs 25.76%), and FNA samples were estimated to have a consistently higher proportion of malignant cells. CONCLUSIONS The current results suggest that FNA is feasible for the collection of tumor samples sufficient for WES analysis and that the higher purity obtained using this method may make it more reliable for genomic studies.
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Affiliation(s)
- Han-Byoel Lee
- Department of Surgery, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Je-Gun Joung
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Jisun Kim
- Department of Surgery, Asan Medical Center, Seoul, Republic of Korea
| | - Kyung-Min Lee
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Han Suk Ryu
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hae-Ock Lee
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Hyeong-Gon Moon
- Department of Surgery, Seoul National University College of Medicine, Seoul, Republic of Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea.,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Dong-Young Noh
- Department of Surgery, Seoul National University College of Medicine, Seoul, Republic of Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Wonshik Han
- Department of Surgery, Seoul National University College of Medicine, Seoul, Republic of Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
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Hoh RA, Joshi SA, Liu Y, Wang C, Roskin KM, Lee JY, Pham T, Looney TJ, Jackson KJL, Dixit VP, King J, Lyu SC, Jenks J, Hamilton RG, Nadeau KC, Boyd SD. Single B-cell deconvolution of peanut-specific antibody responses in allergic patients. J Allergy Clin Immunol 2015; 137:157-167. [PMID: 26152318 DOI: 10.1016/j.jaci.2015.05.029] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Revised: 05/09/2015] [Accepted: 05/15/2015] [Indexed: 11/28/2022]
Abstract
BACKGROUND The frequencies, cellular phenotypes, epitope specificity, and clonal diversity of allergen-specific B cells in patients with food allergy are not fully understood but are of major pathogenic and therapeutic significance. OBJECTIVE We sought to characterize peanut allergen-specific B-cell populations and the sequences and binding activities of their antibodies before and during immunotherapy. METHODS B cells binding fluorescently labeled Ara h 1 or Ara h 2 were phenotyped and isolated by means of flow cytometric sorting from 18 patients at baseline and 13 patients during therapy. Fifty-seven mAbs derived from allergen-binding single B cells were evaluated by using ELISA, Western blotting, and peptide epitope mapping. Deep sequencing of the B-cell repertoires identified additional members of the allergen-specific B-cell clones. RESULTS Median allergen-binding B-cell frequencies were 0.0097% (Ara h 1) or 0.029% (Ara h 2) of B cells in baseline blood from allergic patients and approximately 3-fold higher during immunotherapy. Five of 57 allergen-specific cells belonged to clones containing IgE-expressing members. Almost all allergen-specific antibodies were mutated, and binding to both conformational and linear allergen epitopes was detected. Increasing somatic mutation of IgG4 members of a clone was seen in immunotherapy, whereas IgE mutation levels in the clone did not increase. CONCLUSION Most peanut allergen-binding B cells isolated by means of antigen-specific flow sorting express mutated and isotype-switched antibodies. Immunotherapy increases their frequency in the blood, and even narrowly defined allergen epitopes are recognized by numerous distinct B-cell clones in a patient. The results also suggest that oral immunotherapy can stimulate somatic mutation of allergen-specific IgG4.
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Affiliation(s)
- Ramona A Hoh
- Department of Pathology, Stanford University, Stanford, Calif
| | - Shilpa A Joshi
- Department of Pathology, Stanford University, Stanford, Calif
| | - Yi Liu
- Department of Pathology, Stanford University, Stanford, Calif; Biomedical Informatics Training Program, Stanford University, Stanford, Calif
| | - Chen Wang
- Department of Pathology, Stanford University, Stanford, Calif
| | | | - Ji-Yeun Lee
- Department of Pathology, Stanford University, Stanford, Calif
| | - Tho Pham
- Department of Pathology, Stanford University, Stanford, Calif
| | - Tim J Looney
- Department of Pathology, Stanford University, Stanford, Calif
| | | | | | - Jasmine King
- Department of Pathology, Stanford University, Stanford, Calif
| | - Shu-Chen Lyu
- Department of Pediatrics, Stanford University, Stanford, Calif
| | - Jennifer Jenks
- Department of Pediatrics, Stanford University, Stanford, Calif
| | - Robert G Hamilton
- Division of Allergy and Clinical Immunology, School of Medicine, Johns Hopkins University, Baltimore, Md
| | - Kari C Nadeau
- Department of Pediatrics, Stanford University, Stanford, Calif
| | - Scott D Boyd
- Department of Pathology, Stanford University, Stanford, Calif.
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Abstract
Natural enzymes are incredibly proficient catalysts, but engineering them to have new or improved functions is challenging due to the complexity of how an enzyme's sequence relates to its biochemical properties. Here, we present an ultrahigh-throughput method for mapping enzyme sequence-function relationships that combines droplet microfluidic screening with next-generation DNA sequencing. We apply our method to map the activity of millions of glycosidase sequence variants. Microfluidic-based deep mutational scanning provides a comprehensive and unbiased view of the enzyme function landscape. The mapping displays expected patterns of mutational tolerance and a strong correspondence to sequence variation within the enzyme family, but also reveals previously unreported sites that are crucial for glycosidase function. We modified the screening protocol to include a high-temperature incubation step, and the resulting thermotolerance landscape allowed the discovery of mutations that enhance enzyme thermostability. Droplet microfluidics provides a general platform for enzyme screening that, when combined with DNA-sequencing technologies, enables high-throughput mapping of enzyme sequence space.
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Leo VC, Morgan NV, Bem D, Jones ML, Lowe GC, Lordkipanidzé M, Drake S, Simpson MA, Gissen P, Mumford A, Watson SP, Daly ME. Use of next-generation sequencing and candidate gene analysis to identify underlying defects in patients with inherited platelet function disorders. J Thromb Haemost 2015; 13:643-50. [PMID: 25556537 PMCID: PMC4383639 DOI: 10.1111/jth.12836] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 12/14/2014] [Indexed: 12/22/2022]
Abstract
BACKGROUND Inherited platelet function disorders (PFDs) are heterogeneous, and identification of the underlying genetic defects is difficult when based solely on phenotypic and clinical features of the patient. OBJECTIVE To analyze 329 genes regulating platelet function, number, and size in order to identify candidate gene defects in patients with PFDs. PATIENTS/METHODS Targeted analysis of candidate PFD genes was undertaken after next-generation sequencing of exomic DNA from 18 unrelated index cases with PFDs who were recruited into the UK Genotyping and Phenotyping of Platelets (GAPP) study and diagnosed with platelet abnormalities affecting either Gi signaling (n = 12) or secretion (n = 6). The potential pathogenicity of candidate gene defects was assessed using computational predictive algorithms. RESULTS Analysis of the 329 candidate PFD genes identified 63 candidate defects, affecting 40 genes, among index cases with Gi signaling abnormalities, while 53 defects, within 49 genes, were identified among patients with secretion abnormalities. Homozygous gene defects were more commonly associated with secretion abnormalities. Functional annotation analysis identified distinct gene clusters in the two patient subgroups. Thirteen genes with significant annotation enrichment for 'intracellular signaling' harbored 16 of the candidate gene defects identified in nine index cases with Gi signaling abnormalities. Four gene clusters, representing 14 genes, with significantly associated gene ontology annotations were identified among the cases with secretion abnormalities, the most significant association being with 'establishment of protein localization.' CONCLUSION Our findings demonstrate the genetic complexity of PFDs and highlight plausible candidate genes for targeted analysis in patients with platelet secretion and Gi signaling abnormalities.
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Affiliation(s)
- V C Leo
- Department of Cardiovascular Science, University of Sheffield Medical School, University of Sheffield, Sheffield, UK
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Abstract
Recurrent aphthous stomatitis (RAS) is the most common disease affecting oral mucosae. Etiology is unknown, but several factors have been implicated, all of which influence the composition of microbiota residing on oral mucosae, which in turn modulates immunity and thereby affects disease progression. Although no individual pathogens have been conclusively shown to be causative agents of RAS, imbalanced composition of the oral microbiota may play a key role. In this study, we sought to determine composition profiles of bacterial microbiota in the oral mucosa associated with RAS. Using high-throughput 16S rRNA gene sequencing, we characterized the most abundant bacterial populations residing on healthy and ulcerated mucosae in patients with RAS (recruited using highly stringent criteria) and no associated medical conditions; we also compared these to the bacterial microbiota of healthy controls (HCs). Phylum-level diversity comparisons revealed decreased Firmicutes and increased Proteobacteria in ulcerated sites, as compared with healthy sites in RAS patients, and no differences between RAS patients with healthy sites and HCs. Genus-level analysis demonstrated higher abundance of total Bacteroidales in RAS patients with healthy sites over HCs. Porphyromonadaceae comprising species associated with periodontal disease and Veillonellaceae predominated in ulcerated sites over HCs, while no quantitative differences of these families were observed between healthy sites in RAS patients and HCs. Streptococcaceae comprising species associated with oral health predominated in HCs over ulcerated sites but not in HCs over healthy sites in RAS patients. This study demonstrates that mucosal microbiome changes in patients with idiopathic RAS--namely, increased Bacteroidales species in mucosae of RAS patients not affected by active ulceration. While these changes suggest a microbial role in initiation of RAS, this study does not provide data on causality. Within this limitation, the study contributes to the understanding of the potential role of mucosal microbiome changes in oral mucosal disease.
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Affiliation(s)
- K Hijazi
- School of Medicine and Dentistry, Division of Medical and Dental Education, University of Aberdeen, Aberdeen, UK
| | - T Lowe
- Maxillofacial Unit, Aberdeen Royal Infirmary, Aberdeen, UK
| | - C Meharg
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| | - S H Berry
- School of Medicine and Dentistry, Division of Applied Medicine, University of Aberdeen, Aberdeen, UK
| | - J Foley
- School of Medicine and Dentistry, Division of Medical and Dental Education, University of Aberdeen, Aberdeen, UK Edinburgh Dental Institute, Edinburgh, UK
| | - G L Hold
- School of Medicine and Dentistry, Division of Applied Medicine, University of Aberdeen, Aberdeen, UK
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50
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Molshanski-Mor S, Yosef I, Kiro R, Edgar R, Manor M, Gershovits M, Laserson M, Pupko T, Qimron U. Revealing bacterial targets of growth inhibitors encoded by bacteriophage T7. Proc Natl Acad Sci U S A 2014; 111:18715-20. [PMID: 25512533 DOI: 10.1073/pnas.1413271112] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Today's arsenal of antibiotics is ineffective against some emerging strains of antibiotic-resistant pathogens. Novel inhibitors of bacterial growth therefore need to be found. The target of such bacterial-growth inhibitors must be identified, and one way to achieve this is by locating mutations that suppress their inhibitory effect. Here, we identified five growth inhibitors encoded by T7 bacteriophage. High-throughput sequencing of genomic DNA of resistant bacterial mutants evolving against three of these inhibitors revealed unique mutations in three specific genes. We found that a nonessential host gene, ppiB, is required for growth inhibition by one bacteriophage inhibitor and another nonessential gene, pcnB, is required for growth inhibition by a different inhibitor. Notably, we found a previously unidentified growth inhibitor, gene product (Gp) 0.6, that interacts with the essential cytoskeleton protein MreB and inhibits its function. We further identified mutations in two distinct regions in the mreB gene that overcome this inhibition. Bacterial two-hybrid assay and accumulation of Gp0.6 only in MreB-expressing bacteria confirmed interaction of MreB and Gp0.6. Expression of Gp0.6 resulted in lemon-shaped bacteria followed by cell lysis, as previously reported for MreB inhibitors. The described approach may be extended for the identification of new growth inhibitors and their targets across bacterial species and in higher organisms.
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