Article
Biochemistry & Molecular Biology
Florian Trigodet, Karen Lolans, Emily Fogarty, Alon Shaiber, Hilary G. Morrison, Luis Barreiro, Bana Jabri, A. Murat Eren
Summary: Long-read sequencing strategies offer comprehensive insights into genetic information organization in genomes and metagenomes by providing extremely long contiguous characterization of individual DNA molecules. However, successful long-read sequencing experiments require high concentrations of highly purified high molecular weight (HMW) DNA. This study compares six HMW DNA extraction strategies using commercially available kits, phenol-chloroform (PC) extraction and agarose encasement followed by agarase digestion with human tongue scrapings. The results suggest that column-based kits with enzyme supplementation may be more appropriate than PC methods for long-read sequencing of metagenomes.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Multidisciplinary Sciences
Ashley Jones, Cynthia Torkel, David Stanley, Jamila Nasim, Justin Borevitz, Benjamin Schwessinger
Summary: Advancements in long-read sequencing technologies have enabled chromosome-scale genome assemblies, but limitations in extracting pure high-molecular weight DNA continue to challenge researchers, especially in plants and fungi. This protocol collection provides an optimized method for high-molecular weight DNA extraction, clean-up, and size selection, which is scalable and cost effective for various species. By following these protocols, long-read sequencing on platforms like PacBio and Oxford Nanopore can achieve high-quality reads exceeding 200 kb with outputs ranging from 15-30 Gbp.
Article
Multidisciplinary Sciences
Sandra Jaudou, Mai-Lan Tran, Fabien Vorimore, Patrick Fach, Sabine Delannoy
Summary: Next generation sequencing is crucial for pathogen characterization, but short-read sequencing has limitations in assembling data. Long-read sequencing, particularly using the MinION device, can overcome these limitations. This study tested three DNA extraction methods and found that salting-out method performed the best in producing high-quality DNA suitable for MinION sequencing.
Article
Genetics & Heredity
Marin Volaric, Damira Veseljak, Brankica Mravinac, Nevenka Mestrovic, Evelin Despot-Slade
Summary: This study optimized the isolation of HMW DNA from the model beetle Tribolium and successfully overcame challenges in HMW handling and library preparation for Nanopore sequencing. Isolation of nuclei and subsequent purification of DNA on an anion-exchange chromatography column resulted in genomic HMW DNA of optimal quality and quantity.
Article
Biochemistry & Molecular Biology
Mozes P. K. Blom
Summary: Modern technologies for characterizing genetic variation at a genome-wide scale offer unprecedented opportunities for studying genetic underpinnings and evolutionary mechanisms that promote and sustain biodiversity. Transitioning from short- to long-read sequencing allows a more comprehensive understanding of genetic diversity over time and space. However, the success of long-read sequencing depends heavily on the integrity of DNA molecules, making the availability of high-quality tissue samples a major concern for projects.
Article
Biotechnology & Applied Microbiology
Ryan R. Wick, Louise M. Judd, Louise T. Cerdeira, Jane Hawkey, Guillaume Meric, Ben Vezina, Kelly L. Wyres, Kathryn E. Holt
Summary: Trycycler is a tool that produces a consensus assembly from multiple input assemblies to reduce errors in long-read sequencing. Post-assembly polishing further improves accuracy. Multiple users converge on similar assemblies that are more accurate than those produced by automated assembly tools.
Article
Biochemical Research Methods
Karim Rahimi, Anne Faerch Nielsen, Morten T. Veno, Jorgen Kjems
Summary: Circular RNA (circRNA) are highly stable RNA molecules with suggested roles in development and disease, derived from linear pre-mRNAs through a process called back-splicing. Identification of circRNAs depends on the detection of unique back-splice-junction sequence reads. Long-read nanopore sequencing has expanded our understanding of circRNA size distribution and internal splicing patterns.
Article
Microbiology
Kai Peng, Yi Yin, Yan Li, Shangshang Qin, Yuan Liu, Xiaorong Yang, Zhiqiang Wang, Ruichao Li
Summary: In this study, we comprehensively evaluated the feasibility of QitanTech nanopore long-read sequencing technology in assembling complete genomes of MDR pathogens. The results showed that QitanTech sequencing technology has the potential to generate high-quality sequencing data and assemble complete bacterial genomes.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Theodore M. Nelson, Sankar Ghosh, Thomas S. Postler
Summary: Long-read sequencing (LRS) provides more accurate and quantitative records of RNA, including splicing patterns, compared to conventional high-throughput sequencing. However, mining and analyzing publicly available LRS data can be challenging due to the complexity of software tools and difficulties in comparing results across different studies. To address these challenges, we have developed a user-friendly and free pipeline for the rapid and standardized analysis of LRS datasets.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Juan-Carlos A. Padilla, Seda Barutcu, Ludovic Malet, Gabrielle Deschamps-Francoeur, Virginie Calderon, Eunjeong Kwon, Eric Lecuyer
Summary: This study provides novel insights into the compositional diversity of poly-A transcript isoforms enriched within EVs and highlights the potential usefulness of nanopore sequencing in interrogating secreted RNA transcriptomes.
Article
Microbiology
Limiao Hu, Xi Zeng, Qi Ai, Caijuan Liu, Xiaotuan Zhang, Yajun Chen, Logen Liu, Guo-Qing Li
Summary: In this study, the authors investigated the antibiotic resistance pattern of H. pylori in a Chinese medical center. The results showed high rates of resistance to clarithromycin, metronidazole, and levofloxacin. The study also compared short-read- and long-read-based whole-genome sequencing methods for identifying genotypes and found that both methods were effective in predicting antibiotic resistance. Furthermore, the study discovered the heterozygous status of the 23S rRNA gene in H. pylori strains, which is important for clarithromycin resistance. Overall, the study provides important evidence for empirical treatment of H. pylori and demonstrates the potential of Nanopore sequencing in predicting clarithromycin resistance.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biochemical Research Methods
Francesco E. Emiliani, Ian Hsu, Aaron McKenna
Summary: Recombinant DNA is a crucial tool in biotechnology and medicine, and validation of plasmid sequences is a critical and time-consuming step. In this study, a high-throughput plasmid sequencing approach using DNA transposition and Oxford Nanopore sequencing was developed, resulting in robust and accurate plasmid assemblies.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemical Research Methods
Francesco E. Emiliani, Ian Hsu, Aaron McKenna
Summary: Circuit-seq is a high-throughput plasmid sequencing method using DNA transposition and Oxford Nanopore sequencing. It can rapidly and accurately generate complete plasmid assemblies, analyze plasmid size and complexity, and estimate plasmid contamination levels.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Plant Sciences
Alessia Russo, Baptiste Mayjonade, Daniel Frei, Giacomo Potente, Roman T. Kellenberger, Lea Frachon, Dario Copetti, Bruno Studer, Juerg E. Frey, Ueli Grossniklaus, Philipp M. Schluter
Summary: This article describes a method for extracting high molecular weight (HMW) DNA from low input plant material, which is easy to follow and quick. It successfully enables HMW DNA extraction from different plant species and is suitable for long-read sequencing on the Oxford Nanopore Technologies PromethION(R) platform.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Obstetrics & Gynecology
Anna Oberle, Lara Urban, Stefanie Falch-Leis, Chiara Ennemoser, Yoko Nagai, Kyota Ashikawa, Patricia A. Ulm, Markus Hengstschlaeger, Michael Feichtinger
Summary: This study investigated the feasibility of using nanopore technology for full-length 16S rRNA gene sequencing as an alternative approach for endometrial microbiome analysis. Results from experiments on 33 patients seeking infertility treatment showed that nanopore sequencing was reliable and could accurately assess and compare the microbiome composition of different patients.
REPRODUCTIVE BIOMEDICINE ONLINE
(2021)
Article
Biochemistry & Molecular Biology
Scott Ferguson, Ashley Jones, Kevin Murra, Benjamin Schwessinger, Justin O. Borevitz
Summary: Synteny loss, primarily caused by unequal homologous recombination, is commonly observed when comparing closely related species. In this study, the genomes of three closely related Eucalyptus species were analyzed, revealing that approximately 48% of the genomes remained syntenic while approximately 36% underwent rearrangements. It was found that rearrangements highly fragmented microsynteny and potentially altered the phenotypes of the Eucalyptus species. This study highlights the importance of using an unbiased framework in genomic variation studies and emphasizes the potential impact of rearrangements on species differentiation and adaptation.
Article
Medicine, General & Internal
Sanaz Pournajaf, Rocco Salvatore Calabro, Antonino Naro, Michela Goffredo, Irene Aprile, Federica Tamburella, Serena Filoni, Andreas Waldner, Stefano Mazzoleni, Antonella Focacci, Francesco Ferraro, Donatella Bonaiuti, Marco Franceschini
Summary: This study investigated the efficacy of stationary robot-assisted gait rehabilitation in comparison to conventional overground gait training for subacute stroke survivors. The results showed that robot-assisted training improved walking ability better than conventional training, with significant improvements in walking speed observed.
JOURNAL OF CLINICAL MEDICINE
(2023)
Article
Automation & Control Systems
Francesco Infarinato, Paola Romano, Francesco Adinolfi, Marco Franceschini, Roberta Ginocchi, Michela Goffredo, Marco Ottaviani, Marianna Valente, Sanaz Pournajaf
Summary: By emphasizing the importance of right care for all people in their community, the World Health Organization provides a fundamental assumption for primary health care. In this study, a home-rehabilitation system was developed to provide intensive care to chronic stroke patients with aphasia, utilizing an information and communication technologies ecosystem. The analysis of the system showed that it is an acceptable and effective alternative to standard face-to-face speech therapy, providing speech and language rehabilitation.
IEEE ROBOTICS & AUTOMATION MAGAZINE
(2023)
Article
Clinical Neurology
Marco Franceschini, Lorenzo Cecconi, Jacopo Bonavita, Sanaz Pournajaf, Salvatore Ferro, Maria Cristina Pagliacci, Italian SCI Study Grp
Summary: This study investigated the reasons for hospital readmission and the influence of length of stay in individuals with spinal cord injury. The results showed that urological problems, pressure injuries, and spasticity were the most common causes of re-hospitalization. Additionally, residents from the South frequently sought medical treatment in northern healthcare facilities. This study provides valuable information for preventing hospital readmissions and highlights the need for attention to specific geographic regions.
Article
Rehabilitation
Sanaz Pournajaf, Leonardo Pellicciari, Stefania Proietti, Francesco Agostini, Debora Gabbani, Michela Goffredo, Carlo Damiani, Marco Franceschini
Summary: This study aimed to determine whether the mBI items collected at admission can predict the total mBI at discharge in large cohorts of orthopedic and neurological patients. In neurological patients, a shorter time between the acute event and rehabilitation admission, shorter length of stay, and independence with feeding, personal hygiene, bladder, and transfers were associated with higher mBI at discharge. In orthopedic patients, age, a shorter time between the acute event and rehabilitation admission, shorter length of stay, and independence with personal hygiene, dressing, and bladder were associated with higher mBI at discharge. These findings suggest that clinicians should consider these predictors of functionality when planning rehabilitation treatment.
INTERNATIONAL JOURNAL OF REHABILITATION RESEARCH
(2023)
Article
Medicine, General & Internal
Matteo Cioeta, Sanaz Pournajaf, Michela Goffredo, Giuseppe Giovannico, Marco Franceschini
Summary: This case report describes a 57-year-old woman who suffered from neck pain for 15 months. After poor compliance with traditional physiotherapy treatments, home exercise training through virtual reality was proposed to improve patient adherence to the treatment plan. The personalized treatment allowed the patient to quickly resolve her problem and return to a peaceful life with her family.
JOURNAL OF CLINICAL MEDICINE
(2023)
Article
Medicine, General & Internal
Michela Goffredo, Chiara Pagliari, Andrea Turolla, Cristina Tassorelli, Sonia Di Tella, Sara Federico, Sanaz Pournajaf, Johanna Jonsdottir, Roberto De Icco, Leonardo Pellicciari, Rocco Salvatore Calabro, Francesca Baglio, Marco Franceschini
Summary: This study aimed to expand the research on the impact of telerehabilitation on quality of life to a larger sample of neurological patients, including those with Parkinson's Disease. The results showed that telerehabilitation positively affected static and dynamic balance and gait in people with Parkinson's Disease and Multiple Sclerosis.
JOURNAL OF CLINICAL MEDICINE
(2023)
Article
Neurosciences
Sanaz Pournajaf, Giovanni Morone, Sofia Straudi, Michela Goffredo, Maria Rosaria Leo, Rocco Salvatore Calabro, Giorgio Felzani, Stefano Paolucci, Serena Filoni, Andrea Santamato, Marco Franceschini
Summary: This study aims to investigate the clinical effects of an exoskeleton robotic system for upper limb rehabilitation compared with conventional therapy in people with subacute stroke. It also aims to identify patient characteristics that can predict better recovery after robotic-assisted therapy and whether it could elicit greater brain stimulation. A total of 84 subacute stroke patients will be randomly allocated to either the control group or experimental group, and the outcomes will be recorded at different time points.
Article
Health Care Sciences & Services
Peppino Tropea, Francesco Infarinato, Irma Sterpi, Marco Ottaviani, Paola Antoniotti, Paola Romano, Michela Picardi, Michela Goffredo, Riccardo Re, Sanaz Pournajaf, Agnese Seregni, Antonio Caronni, Marco Franceschini, Massimo Corbo
Summary: This study aims to investigate the effectiveness of action observation treatment (AOT) in patients with stroke, with a particular focus on the predictive value of neurophysiological biomarkers. A 3-arm, assessor-blinded, randomized controlled trial will be conducted, enrolling chronic stroke patients for 15 sessions of AOT, with different protocols. The primary outcome will be assessed using the Fugl-Meyer Assessment-Upper Extremity scores.
JMIR RESEARCH PROTOCOLS
(2023)
Article
Public, Environmental & Occupational Health
Robyn N. Hall, Ashley Jones, Emma Crean, Victoria Marriott, Nevada Pingault, Alexandra Marmor, Timothy Sloan-Gardner, Karina Kennedy, Kerryn Coleman, Vanessa Johnston, Benjamin Schwessinger
Summary: The Australian Capital Territory (ACT) detected an incursion of the SARS-CoV-2 Delta variant. Public health interventions, including a territory-wide lockdown and comprehensive contact tracing, were rapidly implemented. Genomic sequencing revealed at least 13 independent incursions with onward spread in the community, and different incursions affected distinct cohorts.
EPIDEMIOLOGY AND INFECTION
(2023)
Article
Agronomy
John Lagergren, Mirko Pavicic, Hari B. Chhetri, Larry M. York, Doug Hyatt, David Kainer, Erica M. Rutter, Kevin Flores, Jack Bailey-Bale, Marie Klein, Gail Taylor, Daniel Jacobson, Jared Streich
Summary: This study applies few-shot learning and convolutional neural networks to segment Populus trichocarpa leaf images, extracting features related to leaf morphology and vein topology for genome-wide association study. The work provides the plant phenotyping community with fast and accurate image-based feature extraction methods and a dataset containing diverse leaf phenotypes.
Article
Multidisciplinary Sciences
Muralikrishnan Gopalakrishnan Meena, Matthew J. Lane, Joanna Tannous, Alyssa A. Carrell, Paul E. Abraham, Richard J. Giannone, Jean-Michel Ane, Nancy P. Keller, Jesse L. Labbe, Armin G. Geiger, David Kainer, Daniel A. Jacobson, Tomas A. Rush
Summary: Fungal specialized metabolites are important sources of beneficial compounds. This study introduces a data-driven algorithm based on network analysis to characterize the production of specialized fungal metabolites triggered by different exogenous compounds. The algorithm consists of two routes, the direct route and the auxiliary route, which provide insights into the influence of treatments on metabolite production. The algorithm was validated using chitooligosaccharides and lipids on the fungal pathogen Aspergillus fumigatus, and it was found to be effective in discovering new compounds for drug discovery.
Article
Biochemical Research Methods
Jiri C. Moravec, Robert Lanfear, David L. Spector, Sarah D. Diermeier, Alex Gavryushkin
Summary: This article demonstrates for the first time that scRNA-seq data contain sufficient evolutionary signal and can be utilized for phylogenetic analyses. Both expression levels and SNVs derived from scRNA-seq data are shown to be useful for reconstructing phylogenetic relationships between cells and reflecting the clonal composition of a tumor.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Yu K. Mo, Robert Lanfear, Matthew W. Hahn, Bui Quang Minh
Summary: In this study, a new method for calculating site concordance factors (sCFs) is introduced. The updated version uses likelihood to generate probability distributions of ancestral states at internal nodes, thus reducing the effects of homoplasy and taxon sampling.
Article
Genetics & Heredity
David Kainer, Alan R. Templeton, Erica T. Prates, Daniel Jacboson, Euan R. O. Allan, Sharlee Climer, Michael R. Garvin
Summary: This study identifies structural variations in non-Mendelian inheritance patterns that may contribute to the heritability of autism spectrum disorder. These variations, mostly located in non-coding genic space, affect gene regulation and overlap with differentially expressed genes in the postmortem brain tissue of ASD individuals. Additionally, specific structural variations in certain genes are significantly associated with the non-verbal ASD phenotype.
HUMAN GENETICS AND GENOMICS ADVANCES
(2023)