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Karin BR, Arellano S, Wang L, Walzer K, Pomerantz A, Vasquez JM, Chatla K, Sudmant PH, Bach BH, Smith LL, McGuire JA. Highly-multiplexed and efficient long-amplicon PacBio and Nanopore sequencing of hundreds of full mitochondrial genomes. BMC Genomics 2023; 24:229. [PMID: 37131128 PMCID: PMC10155392 DOI: 10.1186/s12864-023-09277-6] [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: 08/03/2022] [Accepted: 03/24/2023] [Indexed: 05/04/2023] Open
Abstract
BACKGROUND Mitochondrial genome sequences have become critical to the study of biodiversity. Genome skimming and other short-read based methods are the most common approaches, but they are not well-suited to scale up to multiplexing hundreds of samples. Here, we report on a new approach to sequence hundreds to thousands of complete mitochondrial genomes in parallel using long-amplicon sequencing. We amplified the mitochondrial genome of 677 specimens in two partially overlapping amplicons and implemented an asymmetric PCR-based indexing approach to multiplex 1,159 long amplicons together on a single PacBio SMRT Sequel II cell. We also tested this method on Oxford Nanopore Technologies (ONT) MinION R9.4 to assess if this method could be applied to other long-read technologies. We implemented several optimizations that make this method significantly more efficient than alternative mitochondrial genome sequencing methods. RESULTS With the PacBio sequencing data we recovered at least one of the two fragments for 96% of samples (~ 80-90%) with mean coverage ~ 1,500x. The ONT data recovered less than 50% of input fragments likely due to low throughput and the design of the Barcoded Universal Primers which were optimized for PacBio sequencing. We compared a single mitochondrial gene alignment to half and full mitochondrial genomes and found, as expected, increased tree support with longer alignments, though whole mitochondrial genomes were not significantly better than half mitochondrial genomes. CONCLUSIONS This method can effectively capture thousands of long amplicons in a single run and be used to build more robust phylogenies quickly and effectively. We provide several recommendations for future users depending on the evolutionary scale of their system. A natural extension of this method is to collect multi-locus datasets consisting of mitochondrial genomes and several long nuclear loci at once.
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Affiliation(s)
- Benjamin R Karin
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA.
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA.
| | - Selene Arellano
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA
| | - Laura Wang
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA
| | - Kayla Walzer
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA
| | - Aaron Pomerantz
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA
| | - Juan Manuel Vasquez
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA
| | - Kamalakar Chatla
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA
| | - Peter H Sudmant
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Bryan H Bach
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Lydia L Smith
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
| | - Jimmy A McGuire
- Department of Integrative Biology, Valley Life Sciences Building, University of California, Berkeley, CA, 94708, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
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Calvo R, Guiloff R, Calvo-Mena R, Arellano S, Caro P. [Proximal tibiofibular joint dislocation diagnosis and treatment]. Acta Ortop Mex 2021; 35:560-566. [PMID: 35793258] [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: 06/15/2023]
Abstract
INTRODUCTION Proximal tibiofibular joint dislocations (PTFJD) are uncommon and underdiagnosed injuries. Urgent reduction is mandatory to avoid chronic disfunction. The scarcely available literature does not present a unified management guideline. An acute PTFJD case report with spontaneous reduction and a review of the literature is presented, aiming to assist the diagnosis and management of this pathology. CASE REPORT A 22-years old male presented to the emergency department with high intensity right knee pain after falling in a four-wheel motorcycle. The physical exam revealed a prominent painful mass on the lateral aspect of his knee and proximal leg. His range of motion and knee stability were unremarkable. X-rays were informed negative for musculoskeletal injuries. According to a sustained suspicion of PTFJD, the study was continued with a magnetic resonance imaging (MRI), which suggested PTFJD. During the following 24 hours, the patient referred he was entirely asymptomatic after feeling a loud "clank". He has been followed for three months with MRI, and remains asymptomatic with full functions. CONCLUSION PTFJD diagnosis requires appropriate images. Urgent close reduction is mandatory; if unsuccessful, open reduction, primary repair and internal fixation are indicated. The prognosis of spontaneous reduction remains uncertain and requires a serial clinical evaluation. In the case of recurrence, the appropriate surgical management is indicated according to the elapsed time from the injury.
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Affiliation(s)
- R Calvo
- Facultad de Medicina Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | - R Guiloff
- Facultad de Medicina Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | - R Calvo-Mena
- Facultad de Medicina Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | - S Arellano
- Facultad de Medicina Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | - P Caro
- Facultad de Medicina Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
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Liu EJ, Aiuppa A, Alan A, Arellano S, Bitetto M, Bobrowski N, Carn S, Clarke R, Corrales E, de Moor JM, Diaz JA, Edmonds M, Fischer TP, Freer J, Fricke GM, Galle B, Gerdes G, Giudice G, Gutmann A, Hayer C, Itikarai I, Jones J, Mason E, McCormick Kilbride BT, Mulina K, Nowicki S, Rahilly K, Richardson T, Rüdiger J, Schipper CI, Watson IM, Wood K. Aerial strategies advance volcanic gas measurements at inaccessible, strongly degassing volcanoes. Sci Adv 2020; 6:6/44/eabb9103. [PMID: 33127674 PMCID: PMC7608812 DOI: 10.1126/sciadv.abb9103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
Volcanic emissions are a critical pathway in Earth's carbon cycle. Here, we show that aerial measurements of volcanic gases using unoccupied aerial systems (UAS) transform our ability to measure and monitor plumes remotely and to constrain global volatile fluxes from volcanoes. Combining multi-scale measurements from ground-based remote sensing, long-range aerial sampling, and satellites, we present comprehensive gas fluxes-3760 ± [600, 310] tons day-1 CO2 and 5150 ± [730, 340] tons day-1 SO2-for a strong yet previously uncharacterized volcanic emitter: Manam, Papua New Guinea. The CO2/ST ratio of 1.07 ± 0.06 suggests a modest slab sediment contribution to the sub-arc mantle. We find that aerial strategies reduce uncertainties associated with ground-based remote sensing of SO2 flux and enable near-real-time measurements of plume chemistry and carbon isotope composition. Our data emphasize the need to account for time averaging of temporal variability in volcanic gas emissions in global flux estimates.
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Affiliation(s)
- E J Liu
- University College London, London WC1E6BS, UK.
- University of Cambridge, Cambridge CB23EQ, UK
| | - A Aiuppa
- Università di Palermo, 90123 Palermo, Italy
| | - A Alan
- GasLAB, Universidad de Costa Rica, San José, Costa Rica
| | - S Arellano
- Chalmers University of Technology, Göteborg, Sweden
| | - M Bitetto
- Università di Palermo, 90123 Palermo, Italy
| | - N Bobrowski
- Heidelberg University, Heidelberg, Germany
- Max Planck Institute for Chemistry, Mainz, Germany
| | - S Carn
- Michigan Technological University, Houghton, MI 49931, USA
| | - R Clarke
- University of Bristol, Bristol, BS8 1TR, UK
| | - E Corrales
- GasLAB, Universidad de Costa Rica, San José, Costa Rica
| | - J M de Moor
- Universidad Nacional, Heredia, 40101-3000 Costa Rica
| | - J A Diaz
- GasLAB, Universidad de Costa Rica, San José, Costa Rica
| | - M Edmonds
- University of Cambridge, Cambridge CB23EQ, UK
| | - T P Fischer
- University of New Mexico, Albuquerque, NM 87131, USA
| | - J Freer
- University of Bristol, Bristol, BS8 1TR, UK
- University of Saskatchewan, Centre for Hydrology, Canmore, Alberta T1W 3G1, Canada
| | - G M Fricke
- University of New Mexico, Albuquerque, NM 87131, USA
| | - B Galle
- Chalmers University of Technology, Göteborg, Sweden
| | - G Gerdes
- Chalmers University of Technology, Göteborg, Sweden
| | - G Giudice
- INGV, Osservatorio Etneo, Sezione di Catania, 95125 Catania, Italy
| | - A Gutmann
- Johannes Gutenberg-Universität, Mainz 55128, Germany
| | - C Hayer
- University of Manchester, Manchester, M13 9PL, UK
| | - I Itikarai
- Rabaul Volcanological Observatory, Rabaul, Papua New Guinea
| | - J Jones
- University of New Mexico, Albuquerque, NM 87131, USA
| | - E Mason
- University of Cambridge, Cambridge CB23EQ, UK
| | | | - K Mulina
- Rabaul Volcanological Observatory, Rabaul, Papua New Guinea
| | - S Nowicki
- University of New Mexico, Albuquerque, NM 87131, USA
| | - K Rahilly
- University of New Mexico, Albuquerque, NM 87131, USA
| | | | - J Rüdiger
- Johannes Gutenberg-Universität, Mainz 55128, Germany
| | - C I Schipper
- Victoria University of Wellington, Wellington 6012, New Zealand
| | - I M Watson
- University of Bristol, Bristol, BS8 1TR, UK
| | - K Wood
- University of Bristol, Bristol, BS8 1TR, UK
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Vargas-Domínguez A, Arellano S, Alonso P, Viramontes Madrid JL. [Sensitivity, specificity, and predictive values of fine-needle biopsy in thyroid cancer]. GAC MED MEX 1994; 130:55-8. [PMID: 7851696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
One-hundred and eleven patients were studied with the objective of exploring the diagnostic usefulness of the fine needle aspiration (FNA) biopsy in cases with cancer of the thyroid gland. The mean age of the total sample was 42.4 years, with 89 percent females. A thyroid gland FNA was done in all cases as well as a surgical intervention for the establishment of a definitive diagnosis (i.e., gold standard). The cytologic diagnosis was done by the same expert pathologist in all cases. The diagnostic accuracy was obtained using a 2 x 2 table. Sensitivity was found to be 72 percent and specificity 91 percent, with 85.5 percent of diagnostic accuracy. Taking into account a 30 percent prevalence in our sample, predictive values were found to be 81 percent for positive and 87 percent for negative. It is concluded that FNA is better than the gold standard in the following points: it is easy to do, it has lower risk, and it has lower discomfort and financial cost. FNA showed a better utility to identify the absence of cancer. This is a procedure which is recommended for use in hospitals similar to the General Hospital of Mexico S.S. as part of the presurgical diagnosis in cases with clinical suspicion of thyroid gland malignancy.
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Sánchez-Borges M, de Orozco A, Arellano S, de Gallego V, Avila-Millián E, Suárez-Chacón R. Preventive role of atopy in lung cancer. Clin Immunol Immunopathol 1986; 41:314-9. [PMID: 3780049 DOI: 10.1016/0090-1229(86)90002-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Incidence of atopic disease, serum and sputum IgE, and sputum IgA levels were studied in lung cancer patients, and compared with those in lung benign disease patients and normal controls. A significantly lower prevalence of personal atopic history was observed in the cancer group in comparison with the other two experimental groups. Patients with lung cancer showed significantly higher serum IgE levels than benign-disease and normal control individuals. At the same time, patients with epidermoid lung carcinoma had significantly increased levels of serum IgE and sputum IgA than those with lung adenocarcinoma.
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