Article
Biotechnology & Applied Microbiology
Alexander Barquero, Simone Marini, Christina Boucher, Jaime Ruiz, Mattia Prosperi
Summary: This study developed a mobile application called KARGAMobile for real-time, portable analysis of antibiotic resistance genes in nanopore sequencing. The app utilizes compressed reference databases and different data structures to save memory usage, and features a user-friendly graphical interface and visual report generation.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Benjamin R. R. Karin, Selene Arellano, Laura Wang, Kayla Walzer, Aaron Pomerantz, Juan Manuel Vasquez, Kamalakar Chatla, Peter H. H. Sudmant, Bryan H. H. Bach, Lydia L. L. Smith, Jimmy A. A. McGuire
Summary: A new method for sequencing hundreds to thousands of complete mitochondrial genomes in parallel using long-amplicon sequencing is reported. This method is more efficient than other mitochondrial genome sequencing methods. It can be used to quickly and effectively build more robust phylogenies and provides recommendations for future users.
Article
Medicine, Research & Experimental
Ymke van Der Pol, Normastuti Adhini Tantyo, Nils Evander, Anouk E. Hentschel, Birgit M. M. Wever, Jip Ramaker, Sanne Bootsma, Marieke F. Fransen, Kristiaan J. Lenos, Louis Vermeulen, Famke L. Schneiders, Idris Bahce, Jakko A. Nieuwenhuijzen, Renske D. M. Steenbergen, D. Michiel Pegtel, Norbert Moldovan, Florent Mouliere
Summary: This study demonstrates the use of Oxford Nanopore Technologies (ONT) sequencing to obtain genomic and fragmentomic data from liquid biopsies. The results show that copy number aberrations and cfDNA fragmentation patterns can be determined in less than 24 hours. Furthermore, ONT sequencing allows analysis of previously understudied cfDNA populations.
EMBO MOLECULAR MEDICINE
(2023)
Review
Microbiology
Pin Chen, Zepeng Sun, Jiawei Wang, Xinlong Liu, Yun Bai, Jiang Chen, Anna Liu, Feng Qiao, Yang Chen, Chenyan Yuan, Jingjie Sha, Jinghui Zhang, Li-Qun Xu, Jian Li
Summary: Sequencing technology is widely used in molecular biology research and is crucial for the development and applications of molecular biology. It has undergone three generations of development since 1977, and is applied in various fields such as disease diagnosis, drug target discovery, and species protection. Nanopore sequencing technology has emerged as an advanced portable sequencing technology with the advantages of small size, portability, and direct reading using physical methods.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemical Research Methods
Aimeric Bruno, Jean-Marc Aury, Stefan Engelen
Summary: BoardION is an interactive web application designed for analyzing the efficiency of ONT sequencing runs, allowing users to optimize data quality and compare multiple flowcells. It enables users to remotely monitor experiments and assess library preparation protocols or sample quality in real time.
BMC BIOINFORMATICS
(2021)
Article
Genetics & Heredity
Sarah Stahl-Rommel, Miten Jain, Hang N. Nguyen, Richard R. Arnold, Serena M. Aunon-Chancellor, Gretta Marie Sharp, Christian L. Castro, Kristen K. John, Sissel Juul, Daniel J. Turner, David Stoddart, Benedict Paten, Mark Akeson, Aaron S. Burton, Sarah L. Castro-Wallace
Summary: A culture-independent swab-to-sequencer method for real-time microbial profiling on the ISS has been developed, validated, and implemented successfully. Extensive ground-based assessments and analog testing during NEEMO missions confirmed the accuracy of the method. Four independent experiments on the ISS showed consistent results with historical culture-based data, demonstrating the potential of this simplified method for future space missions.
Article
Chemistry, Multidisciplinary
Jinyue Zhang, Yu Wang, Yuqin Wang, Panke Zhang, Hong-Yuan Chen, Shuo Huang
Summary: DNA lesions induced by alkylating agents can be directly distinguished by observing the enzymatic stalling kinetics, which is not interfered with by the sequence context.
Article
Multidisciplinary Sciences
Balazs Kakuk, Dora Tombacz, Zsolt Balazs, Norbert Moldovan, Zsolt Csabai, Gabor Torma, Klara Megyeri, Michael Snyder, Zsolt Boldogkoi
Summary: Long-read sequencing (LRS) is a powerful new approach that offers significant advantages over traditional short-read sequencing. In this study, two third-generation LRS platforms were used to analyze the human cytomegalovirus transcriptome, revealing numerous novel transcript variants and a highly complex meshwork of transcriptional read-throughs and overlaps.
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Multidisciplinary
Mirko Palla, Sukanya Punthambaker, Benjamin Stranges, Frederic Vigneault, Jeff Nivala, Daniel Wiegand, Aruna Ayer, Timothy Craig, Dmitriy Gremyachinskiy, Helen Franklin, Shaw Sun, James Pollard, Andrew Trans, Cleoma Arnold, Charles Schwab, Colin Mcgaw, Preethi Sarvabhowman, Dhruti Dalal, Eileen Thai, Evan Amato, Ilya Lederman, Meng Taing, Sara Kelley, Adam Qwan, Carl W. Fuller, Stefan Roever, George M. Church
Summary: The use of single-molecule DNA sequencing platform allows for rapid screening of polymerase variants, enabling the identification of enzymes with different features. This approach is valuable for applications requiring polymerases with altered physical properties.
Article
Microbiology
Luca Marcolungo, Alessandro Passera, Simone Maestri, Elena Segala, Massimiliano Alfano, Francesca Gaffuri, Giovanni Marturano, Paola Casati, Piero Attilio Bianco, Massimo Delledonne
Summary: Rapid and sensitive diagnostic assays for plant pathogens are essential for crop disease management. This study established and evaluated a novel nanopore sequencing-based diagnostic assay, which can detect and characterize quarantine pathogens simultaneously, achieving detection and typing within 13 minutes.
Review
Genetics & Heredity
Laura K. White, Jay R. Hesselberth
Summary: This review provides an introduction to nanopore sequencing and its use in direct detection of nucleic acid modifications. Nanopore sequencing, as a third generation sequencing technology, offers advantages in high throughput and direct detection of nucleic acid modifications. Numerous endogenous and synthetic nucleic acid modifications have been studied using nanopore sequencing. Advances in sequencing chemistry and analysis methods are expected to improve the identification and quantification of these epigenetic marks.
FRONTIERS IN GENETICS
(2022)
Article
Instruments & Instrumentation
Brian S. Sheetz, Jason R. Dwyer
Summary: We developed a flow cell apparatus and method for real-time measurements of nanopore conductance in response to pH changes. By time-resolving the measurements of interfacial kinetics, we were able to probe nanopore surface coating presence and properties more thoroughly than before. This work is important for the study of nanopore surface chemistry.
REVIEW OF SCIENTIFIC INSTRUMENTS
(2023)
Article
Biochemistry & Molecular Biology
Hector Rodriguez-Perez, Laura Ciuffreda, Carlos Flores
Summary: NanoRTax is a Nextflow pipeline for nanopore 16S rRNA gene amplicon data that features state-of-the-art taxonomic classification tools and real-time capability. This tool demonstrates the potential for shortening turnaround times in critical care settings and provides a tool for research on early-response strategies for sepsis.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Ecology
Lisa Prudnikow, Birgit Pannicke, Roebbe Wuenschiers
Summary: The possibility of identifying plants based on the taxonomic information from their pollen grains has various applications in biology. In the past, pollen origin was analyzed using microscopy and chemical treatment, which is time-consuming and requires expert knowledge. Now, DNA analysis provides advantages and challenges compared to traditional methods. This article presents a practical guide for genetic pollen analysis using nanopore sequencing, with a focus on pollen collected by pollinating insects.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2023)
Article
Chemistry, Multidisciplinary
Shanyu Zhang, Zhenyuan Cao, Pingping Fan, Yuqin Wang, Wendong Jia, Liying Wang, Kefan Wang, Yao Liu, Xiaoyu Du, Chengzhen Hu, Panke Zhang, Hong-Yuan Chen, Shuo Huang
Summary: Saccharides play critical roles in cellular activities, and the identification of their complex and similar structures presents a technical challenge. Researchers have developed a nanopore sensing strategy that can identify saccharides based on minor structural differences. They also trained a machine learning algorithm for automatic event classification and achieved a high accuracy score.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biology
Renato E. Naranjo, Elena Naydenova, Carolina Proano-Bolanos, Karla Vizuete, Alexis Debut, Marbel Torres Arias, Luis A. Coloma
Summary: This study successfully applied assisted reproduction technologies to breed harlequin frogs in the laboratory. The methods used included hormonal stimulation of gametogenesis, sperm cryopreservation, and in vitro fertilization. While the in vitro fertilization attempts were mostly successful, only around 10% of the embryos were viable.
Article
Biochemistry & Molecular Biology
Stefan Prost, Ana Paula Machado, Julia Zumbroich, Lisa Preier, Sarita Mahtani-Williams, Rene Meissner, Katerina Guschanski, Jaelle C. Brealey, Carlos Rodriguez Fernandes, Paul Vercammen, Luke T. B. Hunter, Alexei V. Abramov, Martin Plasil, Petr Horin, Lena Godsall-Bottriell, Paul Bottriell, Desire Lee Dalton, Antoinette Kotze, Pamela Anna Burger
Summary: Cheetahs, as apex predators, play important roles in ecosystems, but they are facing a precarious conservation status due to habitat loss, human-wildlife conflict, and illegal trafficking. A comprehensive genome-wide analysis of cheetah phylogeography revealed that their genetic differentiation is more complex than previously thought, with distinct genetic characteristics in East African cheetahs compared to Southern African cheetahs. Inbreeding was observed in critically endangered Iranian and Northwestern subspecies, and cheetahs were found to have the lowest genome-wide heterozygosity among big cats. These findings provide valuable information for evidence-based conservation policy decisions and protecting this species in light of ongoing translocations and the threat of illegal trafficking.
Article
Public, Environmental & Occupational Health
Ricardo S. P. Patino, David Salazar-Valenzuela, Alberto A. Robles-Loaiza, Paola Santacruz-Ortega, Jose R. Almeida
Summary: Snakebite accidents in the Napo Province of Ecuador show similar characteristics to other areas in the Amazon region. Bothrops atrox was the most commonly responsible snake species, with more local clinical manifestations than systemic signs. The use of antivenom exceeded the suggested dosage in relation to the severity of the cases, and there was a low incidence of adverse reactions. Antimicrobial therapy was frequently administered.
TRANSACTIONS OF THE ROYAL SOCIETY OF TROPICAL MEDICINE AND HYGIENE
(2023)
Article
Food Science & Technology
Antonio L. Vera-Palacios, Juan D. Sacoto-Torres, Josselin A. Hernandez-Altamirano, Andres Moreno, Maria C. Penuela-Mora, David Salazar-Valenzuela, Noroska G. S. Mogollon, Jose R. Almeida
Summary: Bothrops atrox snakebites are a significant problem in the Amazon basin. Urospatha sagittifolia (Araceae) has potential biomedical value as a natural enzyme inhibitor to neutralize the catalytically active toxins from the venom, reducing their toxic effects. This study evaluated the ability of U. sagittifolia to inhibit the venom enzymes and observed significant reductions in lethality, edema, and hemorrhage.
Article
Biodiversity Conservation
John G. Himes, Alejandro Arteaga, Luis Enrique Vera-Perez, Kevin M. Enge
Summary: This article examines records of Atractus lehmanni and concludes that this species occurs in Colombia instead of Ecuador.
Article
Biodiversity Conservation
M. Magliolo, V. N. Naude, V. C. van der Merwe, S. Prost, P. Orozco-terWengel, P. A. Burger, A. Kotze, J. P. Grobler, D. L. Dalton
Summary: In South Africa, the cheetah population is divided into free-roamers, managed metapopulation, and captive facilities. To preserve overall genetic variation, interventions such as genetic exchanges and supplementation with unrelated individuals are proposed. Simulation results showed that without intervention or with only genetic exchanges, there were significant losses of heterozygosity and an increase in the frequencies of close relatives. However, introducing individuals from captive facilities maintained genetic diversity and relatedness.
ANIMAL CONSERVATION
(2023)
Article
Evolutionary Biology
Paola A. Carrasco, Claudia Koch, Felipe G. Grazziotin, Pablo J. Venegas, Juan C. Chaparro, Gustavo J. Scrocchi, David Salazar-Valenzuela, Gerardo C. Leynaud, Camilo Mattoni
Summary: This study presents a total-evidence phylogeny of New World pitvipers, incorporating both morphological and molecular data. The results reveal a single colonization event of the Americas by pitvipers, leading to the divergence of a Neotropical clade and a North American/Neotropical clade. Morphological character analyses highlight the significance of features related to head scalation, the jaws, and the dorsum of the skull in phylogenetic inference, and detect morphological convergences associated with arboreality.
Article
Zoology
Alejandro Arteaga, Abel Batista
Summary: This study presents a molecular phylogeny of Neotropical snail-eating snakes, including 60 out of 133 recognized species. It describes four new species of Sibon and one new species of Dipsas, based on unique combinations of molecular, meristic, and color pattern characteristics. It also provides evidence for taxonomic revisions and additional cryptic diversity within the studied snake species.
Article
Biology
Andrius Pasukonis, Shirley Jennifer Serrano-Rojas, Marie-Therese Fischer, Matthias-Claudio Loretto, Daniel A. Shaykevich, Bibiana Rojas, Max Ringler, Alexandre B. Roland, Alejandro Marcillo-Lara, Eva Ringler, Camilo Rodriguez, Luis A. Coloma, Lauren A. O'Connell
Summary: This study found that reproductive strategies shape the movement patterns of poison frogs, but may not necessarily be related to navigational performance. Males displayed more explorative behavior, while females outperformed in parental care.
Article
Zoology
Andrew R. Gray, Luis A. Coloma
Summary: This passage describes the tadpole of Agalychnis hulli collected from Amazonian Ecuador, highlighting its unique external morphology which suggests a potential evolutionary link with species of Hylomantis. The tadpole is distinguishable from other Agalychnis tadpoles by its distinctive oral disc and row of marginal papillae.
Article
Multidisciplinary Sciences
Amaru Loaiza-Lange, Diana Szekely, Omar Torres-Carvajal, Nicolas Tinoco, David Salazar-Valenzuela, Paul Szekely
Summary: By examining the gastrointestinal contents of Terciopelo pit viper specimens in Ecuador, researchers found 69 identifiable prey items from four major taxonomic groups. The study revealed differences in prey composition based on size and sex, and an ontogenetic shift in diet from diverse prey in juveniles to a specialized diet in adults.
Article
Multidisciplinary Sciences
Joerg Mueller, Oliver Mitesser, H. Martin Schaefer, Sebastian Seibold, Annika Busse, Peter Kriegel, Dominik Rabl, Rudy Gelis, Alejandro Arteaga, Juan Freile, Gabriel Augusto Leite, Tomaz Nascimento de Melo, John G. Lebien, Marconi Campos-Cerqueira, Nico Bluethgen, Constance J. Tremlett, Dennis Boettger, Heike Feldhaar, Nina Grella, Ana Falconi-Lopez, David A. Donoso, Jerome Moriniere, Zuzana Burivalova
Summary: This study used bioacoustics and metabarcoding to measure forest recovery post-agriculture in a global biodiversity hotspot in Ecuador. The results showed that the composition of vocalizing vertebrates identified by experts reflected the restoration gradient, and two automated measures correlated well with restoration. Furthermore, both measures also reflected the composition of non-vocalizing nocturnal insects. This study demonstrates the effectiveness of new technologies in monitoring forest recovery.
NATURE COMMUNICATIONS
(2023)
Proceedings Paper
Green & Sustainable Science & Technology
Monica Paez-Vacas, Martin R. Bustamante, Natasha Baer, Nora H. Oleas, M. Adriana Argoti, F. Sandra Espinoza, Zayda Lozano, Belen Morales-Espin, Maria Mercedes Gavilanez, David A. Donoso, Daniela Franco-Mena, Jorge Brito, C. Miguel Pinto, Laura Salazar, Maria-Jose Endara, Ana Falconi-Lopez, Erick Bravo-Vera, Enmily Sanchez-Lara, Jordi Rivera-Albuja, Liliana Mena, Kevin Munoz-Lara, Daniel Navas, Flor M. Ortiz-Galarza, Tito Pamballo, Domenica Pineda, Jefferson Rivadeneira, Sebastian Segura, Kevin Valencia, Pamela Vasquez-Barba, David Salazar-Valenzuela
Summary: Bioblitz is a global citizen science initiative that aims to survey and identify as many species of fauna and flora as possible within a short period of time, while promoting public engagement. The first Bioblitz held in Quito, Ecuador aimed to survey the local flora and fauna and engage citizens in this activity. Using standard biological diversity assessment methods, multiple species were identified, allowing citizens to learn about the local biodiversity.
CONGRESS ON SUSTAINABILITY, ENERGY AND CITY 2022
(2023)
Article
Archaeology
Anna L. Gosling, Edana Lord, James Boocock, Sophia Cameron-Christie, K. Ann Horsburgh, Olga Kardailsky, Stefan Prost, Stephen Wilcox, David Addison, Adam Thompson, John Kalolo, Andrew C. Clarke, Elizabeth A. Matisoo-Smith
Summary: This study compares the genomic data of the current population and ancient individuals from Tokelau, finding less genetic diversity compared to other Polynesian populations. Rare mitochondrial lineages suggest prehistoric settlement by people from the northwest. Ancient DNA data supports the previous population abandonment and resettlement on Atafu, the northernmost atoll of Tokelau, from a population of Samoan or Samoan-origin. The study also reveals links between Tokelau and other atoll populations in the western Pacific.
JOURNAL OF ISLAND & COASTAL ARCHAEOLOGY
(2023)
Article
Zoology
Alejandro Arteaga, Amanda Quezada, Jose Vieira, Juan M. Guayasamin
Summary: This paper presents a molecular phylogeny of the Atractus genus, identifying three new species of ground snakes and revalidating a previously misidentified snake species. Atractus voucher specimens and sequences stored in GenBank were reidentified, increasing the reported number of Atractus species in Ecuador.