Article
Multidisciplinary Sciences
Jason M. Neal-McKinney, Kun C. Liu, Christopher M. Lock, Wen-Hsin Wu, Jinxin Hu
Summary: The study compared Campylobacter genome assemblies generated from MiSeq and MinION data independently, as well as hybrid genome assemblies combining both data types. SPAdes assemblies had the most accurate nucleotide identity, while hybrid assemblies were the most contiguous. Assemblies generated only from MinION data using Canu were the least accurate. The hybrid sequencing approach was the most useful for detecting plasmids, large genome rearrangements, and repetitive elements.
SCIENTIFIC REPORTS
(2021)
Article
Cardiac & Cardiovascular Systems
Tomoya Takashima, Sophie Brisset, Asuka Furukawa, Hirohisa Taniguchi, Rika Takeyasu, Akio Kawamura, Yuichi Tamura
Summary: The study demonstrated the feasibility of using MinION nanopore sequencer for genetic analysis of PAH patients, particularly in detecting BMPR2 mutations. The portable nanopore sequencer showed promise as a screening tool for BMPR2 mutations, especially in small laboratories and research groups.
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2021)
Article
Biotechnology & Applied Microbiology
Syeed Md Iskander, Yamrot M. Amha, Phillip Wang, Qin Dong, Juhe Liu, Michael Corbett, Adam L. Smith
Summary: Co-digestion of fats, oils, and grease (FOG) with food waste (FW) can improve energy recovery in anaerobic membrane bioreactors (AnMBRs), especially by introducing more biogas production through a two-phase (TP-MP) reactor. Co-digestion of FW with FOG can also significantly increase daily biogas production and have a positive impact on microbial communities.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Article
Microbiology
Waleed Aljabr, Muhannad Alruwaili, Rebekah Penrice-Randal, Abdulrahman Alrezaihi, Abbie Jasmine Harrison, Yan Ryan, Eleanor Bentley, Benjamin Jones, Bader Y. Alhatlani, Dayel AlShahrani, Zana Mahmood, Natasha Y. Rickett, Bandar Alosaimi, Asif Naeem, Saad Alamri, Hadel Alsran, Maaweya E. Hamed, Xiaofeng Dong, Abdullah M. Assiri, Abdullah R. Alrasheed, Muaawia Hamza, Miles W. Carroll, Matthew Gemmell, Alistair Darby, I'ah Donovan-Banfield, James P. Stewart, David A. Matthews, Andrew D. Davidson, Julian A. Hiscox
Summary: MERS-CoV is a zoonotic infection originating in the Middle East with severe symptoms and high fatality rate, affecting both camels and humans. Rapid sequencing and metagenomic analysis are crucial in monitoring and studying this virus.
Article
Biotechnology & Applied Microbiology
Tomas Nohejl, Jana Palkovicova, Kristina Nesporova, Adam Valcek, Jarmila Lausova, Monika Dolejska
Summary: The fos operon enables bacteria to thrive in challenging environments, and its global distribution in bacterial genomes is still unknown. The presence of plasmid-harbored fos operons in resistant bacteria may contribute to the spread of antibiotic resistance.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
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
Microbiology
Cora M. M. Holicki, Felicitas Bergmann, Franziska Stoek, Ansgar Schulz, Martin H. H. Groschup, Ute Ziegler, Balal Sadeghi
Summary: This study compares different sequencing platforms for Usutu virus (USUV) and finds that amplicon-based MinION Nanopore sequencing is a cost- and time-effective alternative with optimal genome coverage. It can be used for various lab and field-based research objectives.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Cell Biology
Yong-Xin Liu, Yuan Qin, Tong Chen, Meiping Lu, Xubo Qian, Xiaoxuan Guo, Yang Bai
Summary: This article systematically summarizes the advantages and limitations of methods in microbiome research, recommends specific analysis flows and common software, introduces statistical and visualization methods suitable for microbiome analysis, and provides a reproducible analysis guide. The goal is to help researchers conduct data analysis more effectively and efficiently mine the biological significance behind the data.
Article
Forestry
Dwi Wahyuni, Fifi Gus Dwiyanti, Rahadian Pratama, Muhammad Majiidu, Henti Hendalastuti Rachmat, Iskandar Zulkarnaen Siregar
Summary: This study utilized ONT technology to generate a large amount of DNA sequence data for Kapur, successfully constructing a partial chloroplast genome and identifying the close genetic relationships between species of the genus Dryobalanops.
Article
Microbiology
Ansgar Schulz, Balal Sadeghi, Franziska Stoek, Jacqueline King, Kerstin Fischer, Anne Pohlmann, Martin Eiden, Martin H. Groschup
Summary: By sequencing samples of arboviruses circulating in Africa, we demonstrated the effectiveness of a nonspecific sequencing technique, SISPA, in generating complete genomes without the need for virus-specific whole-genome PCRs. The results of this study may contribute to a better understanding of the genetic diversity of neglected arboviruses.
Article
Microbiology
Hiroto Miura, Masayuki Takeda, Megumi Yamaguchi, Yoshihisa Ohtani, Go Endo, Yasuhisa Masuda, Kaede Ito, Yoshio Nagura, Kunihiro Iwashita, Tomohiro Mitani, Yutaka Suzuki, Yasuo Kobayashi, Satoshi Koike
Summary: This study established a high-resolution and high-throughput rumen microbial profiling approach by combining the MinION platform and buccal swab samples, which could potentially be applied in large-scale studies for rumen microbial analysis.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Yoshiyuki Matsuo, Shinnosuke Komiya, Yoshiaki Yasumizu, Yuki Yasuoka, Katsura Mizushima, Tomohisa Takagi, Kirill Kryukov, Aisaku Fukuda, Yoshiharu Morimoto, Yuji Naito, Hidetaka Okada, Hidemasa Bono, So Nakagawa, Kiichi Hirota
Summary: This study demonstrates that full-length 16S rRNA gene sequencing using the MinION(TM) long-read sequencer provides better resolution for bacterial classification, especially in complex gut microbiota.
Article
Immunology
Yan-Ying Huang, Qiu-Shi Li, Zhao-Dong Li, Ai-Hua Sun, Sheng-Ping Hu
Summary: This study reports the use of nanopore sequencing for the diagnosis of M. marinum. Nanopore sequencing offers advantages such as rapid identification, low cost, long read lengths, and small equipment size.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Parasitology
Luz Helena Patino, Nathalia Ballesteros, Marina Munoz, Jesus Jaimes, Adriana C. Castillo-Castaneda, Roy Madigan, Alberto Paniz-Mondolfi, Juan David Ramirez
Summary: The study introduced a new 771 bp HSP70-Long marker based on the 70-kDa heat shock protein gene for accurate identification of diverse Leishmania species and coinfection events in clinical samples. Both the HSP70-Long and HSP70-Short markers demonstrated strong discriminatory capabilities in distinguishing different Leishmania species and detecting instances of coinfection.
PARASITES & VECTORS
(2023)
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
Oncology
Devika Ganesamoorthy, Alan James Robertson, Wenhan Chen, Michael B. Hall, Minh Duc Cao, Kaltin Ferguson, Sunil R. Lakhani, Katia Nones, Peter T. Simpson, Lachlan J. M. Coin
Summary: This study conducted deep sequencing analysis of plasma samples, revealing a higher fraction of unique somatic mutations in plasma samples that were not detected in matched tumour samples. Sequencing of di-nucleosome bound cfDNA fragments may increase recovery of tumour mutations from plasma.
Review
Biochemical Research Methods
Fuyi Li, Shuangyu Dong, Andre Leier, Meiya Han, Xudong Guo, Jing Xu, Xiaoyu Wang, Shirui Pan, Cangzhi Jia, Yang Zhang, Geoffrey Webb, Lachlan J. M. Coin, Chen Li, Jiangning Song
Summary: Conventional supervised binary classification algorithms have been widely used in biological and biomedical data analysis. However, labeling data can be laborious, leading to the proposal of the positive unlabeled (PU) learning scheme. This approach allows for learning from limited positive samples and a large number of unlabeled samples, contributing to the development of various PU learning algorithms for addressing biological questions.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Genetics & Heredity
Vikrant Kumar, Richard B. Pouw, Matias Autio, Manfred G. Sagmeister, Zai Yang Phua, Lisa Borghini, Victoria J. Wright, Clive Hoggart, Bangfen Pan, Antson Kiat Yee Tan, Alexander Binder, Mieke C. Brouwer, Ellie Pinnock, Ronald De Groot, Jan Hazelzet, Marieke Emonts, Michiel van der Flier, Karl Reiter, Markus M. Nothen, Per Hoffmann, Luregn J. Schlapbach, Evangelos Bellos, Suzanne Anderson, Fatou Secka, Federico Martinon-Torres, Antonio Salas, Colin Fink, Enitan D. Carrol, Andrew J. Pollard, Lachlan J. Coin, Werner Zenz, Diana Wouters, Lay Teng Ang, Martin L. Hibberd, Michael Levin, Taco W. Kuijpers, Sonia Davila
Summary: This study identified a single nucleotide polymorphism (SNP) in CFHR3, rs75703017, which is associated with decreased levels of complement factor H (FH) in the blood and provides protection against Neisseria meningitidis-induced meningococcal disease. Functional experiments showed that the deletion of rs75703017 increased FH expression in hepatocytes by preventing promoter inhibition.
AMERICAN JOURNAL OF HUMAN GENETICS
(2022)
Article
Cell Biology
Mark A. T. Blaskovich, Karl A. Hansford, Mark S. Butler, Soumya Ramu, Angela M. Kavanagh, Angie M. Jarrad, Anggia Prasetyoputri, Miranda E. Pitt, Johnny X. Huang, Fredrik Lindahl, Zyta M. Ziora, Tanya Bradford, Craig Muldoon, Premraj Rajaratnam, Ruby Pelingon, David J. Edwards, Bing Zhang, Maite Amado, Alysha G. Elliott, Johannes Zuegg, Lachlan Coin, Anne-Kathrin Woischnig, Nina Khanna, Elena Breidenstein, Anna Stincone, Clive Mason, Nawaz Khan, Hye-Kyung Cho, Melissa J. Karau, Kerryl E. Greenwood-Quaintance, Robin Patel, Mandy Wootton, Meagan L. James, Melanie L. Hutton, Dena Lyras, Abiodun D. Ogunniyi, Layla K. Mahdi, Darren J. Trott, Xiaoqian Wu, Samantha Niles, Kim Lewis, Jordan R. Smith, Katie E. Barber, Juwon Yim, Seth Alan Rice, Michael J. Rybak, Chad R. Ishmael, Kellyn R. Hori, Nicholas M. Bernthal, Kevin P. Francis, Jason A. Roberts, David L. Paterson, Matthew A. Cooper
Summary: Drug-resistant Gram-positive bacterial infections remain a significant burden on the public health system. We have developed an effective antibiotic, MCC5145, which shows excellent potency against MRSA and other Gram-positive bacteria, with low toxicity and improved activity against biofilms. It also has a low propensity for developing drug resistance.
SCIENCE TRANSLATIONAL MEDICINE
(2022)
Article
Computer Science, Information Systems
Hardik A. Jain, Vinti Agarwal, Chaarvi Bansal, Anupama Kumar, Faheem FaheemFaheem, Muzaffar-Ur-Rehman Mohammed, Sankaranarayanan Murugesan, Moana M. Simpson, Avinash V. Karpe, Rohitash Chandra, Christopher A. MacRaild, Ian K. Styles, Amanda L. Peterson, Matthew A. Cooper, Carl M. J. Kirkpatrick, Rohan M. Shah, Enzo A. Palombo, Natalie L. Trevaskis, Darren J. Creek, Seshadri S. Vasan
Summary: Repurposing approved drugs is an excellent strategy to quickly obtain safe and effective COVID-19 treatments. To address this, the CoviRx.org platform provides a user-friendly interface for analyzing and filtering large quantities of data, while encouraging users to submit their findings. This will help combat the pandemic and expand to other diseases.
Article
Biochemistry & Molecular Biology
Ramar Perumal Samy, Stephen P. P. Mackessy, Alagarmalai Jeyasankar, Mano Ranjana Ponraj, Octavio Luiz Franco, Matthew A. A. Cooper, Matheswaran Kandasamy, Tapan Kumar Mohanta, Jebasingh Bhagavathsingh, Sakthivel Vaiyapuri
Summary: PaTx-II, an active component from the venom of the Mulga Snake, showed potent antimicrobial activity and promoted wound healing.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Engineering, Environmental
Shuxin Zhang, Jiahua Shi, Elipsha Sharma, Xuan Li, Shuhong Gao, Xu Zhou, Jake O'Brien, Lachlan Coin, Yanchen Liu, Muttucumaru Sivakumar, Faisal Hai, Guangming Jiang
Summary: This study investigated the recovery of Campylobacter spp. from wastewater and their decay under different simulated sewer reactor conditions. The results showed that the recovery of Campylobacter spp. varied with their concentrations in wastewater and the detection limit of quantification methods. The concentration reduction of Campylobacter spp. in sewers followed a two-phase reduction model, with the faster reduction in the first phase mainly due to partitioning onto sewer biofilms. The total decay of Campylobacter spp. varied in different types of sewer reactors.
Article
Multidisciplinary Sciences
Mark R. R. Davies, Nadia Keller, Stephan Brouwer, Magnus G. G. Jespersen, Amanda J. J. Cork, Andrew J. Hayes, Miranda E. E. Pitt, David M. P. De Oliveira, Nichaela Harbison-Price, Olivia M. M. Bertolla, Daniel G. G. Mediati, Bodie F. F. Curren, George Taiaroa, Jake A. A. Lacey, Helen V. V. Smith, Ning-Xia Fang, Lachlan J. M. Coin, Kerrie Stevens, Steven Y. C. Tong, Martina Sanderson-Smith, Jai J. J. Tree, Adam D. D. Irwin, Keith Grimwood, Benjamin P. P. Howden, Amy V. V. Jennison, Mark J. J. Walker
Summary: A new variant of Streptococcus pyogenes serotype M1 (M1(UK)) has been reported in the UK, which exhibits enhanced expression of the superantigen SpeA. A single SNP in the 5' leader sequence of ssrA is responsible for the upregulation of SpeA expression. This variant has also been observed in Australia and is associated with epidemic scarlet fever in Asia.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Andrew Chen, Jiaman Sun, Guillaume Martin, Lesley-Ann Gray, Eva Hribova, Pavla Christelova, Nabila Yahiaoui, Steve Rounsley, Rebecca Lyons, Jacqueline Batley, Ning Chen, Sharon Hamill, Subash K. Rai, Lachlan Coin, Brigitte Uwimana, Angelique D'Hont, Jaroslav Dolezel, David Edwards, Rony Swennen, Elizabeth A. B. Aitken
Summary: In this study, the resistance to Fusarium oxysporum f. sp. cubense Tropical Race 4 (Foc TR4) in Musa acuminata ssp. malaccensis was characterized. QTL-seq analysis of an F2 population segregating for resistance revealed a major QTL on the long arm of chromosome 3. This research provides a foundation for marker assisted selection in breeding programs and identification of resistance genes.
Article
Biology
Bing Zhang, Wanida Phetsang, M. Rhia L. Stone, Sanjaya Kc, Mark S. S. Butler, Matthew A. A. Cooper, Alysha G. G. Elliott, Urszula Lapinska, Margaritis Voliotis, Krasimira Tsaneva-Atanasova, Stefano Pagliara, Mark A. T. Blaskovich
Summary: Antimicrobial resistance is a critical concern for human health, and this study presents the development of vancomycin fluorescent probes that can be used for detecting and visualizing Gram-positive bacteria as well as for measuring outer membrane permeabilization in Gram-negative bacteria. The probes were synthesized by modifying vancomycin with an azide substituent, enabling it to undergo copper-catalyzed azide-alkyne cycloaddition reactions. The probes exhibited similar antibacterial profiles to the parent vancomycin antibiotic and were versatile tools for various detection and imaging techniques.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biology
Fuyi Li, Xudong Guo, Yue Bi, Runchang Jia, Miranda E. Pitt, Shirui Pan, Shuqin Li, Robin B. Gasser, Lachlan JM. Coin, Jiangning Song
Summary: A deep learning-based approach called Digerati was developed for the rapid and accurate identification of PE and PPE family proteins. Digerati achieved a significantly better performance (-18-20%) than alignment-based methods. It is expected to facilitate high-throughput identification and analysis of PE/PPE family members.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Genetics & Heredity
Michael B. Hall, Leandro Lima, Lachlan J. M. Coin, Zamin Iqbal
Summary: Tuberculosis, a global pandemic disease, is facing an increasing challenge of antimicrobial resistance. The World Health Organization (WHO) aims to achieve universal access to drug susceptibility testing (DST), and whole-genome sequencing followed by genotype-based prediction of DST is a promising approach. In this study, we developed DrPRG (Drug resistance Prediction with Reference Graphs) by constructing a reference graph for Mycobacterium tuberculosis drug resistance using a global dataset of isolates. We compared DrPRG with existing graph-based and haplotype-based tools and found that DrPRG performs better in terms of sensitivity, specificity, computational memory usage, and runtime.
MICROBIAL GENOMICS
(2023)
Article
Medicine, Research & Experimental
Dominic Habgood-Coote, Clare Wilson, Chisato Shimizu, Anouk M. Barendregt, Ria Philipsen, Rachel Galassini, Irene Rivero Calle, Lesley Workman, Philipp K. A. Agyeman, Gerben Ferwerda, Suzanne T. Anderson, J. Merlijn van den Berg, Marieke Emonts, Enitan D. Carrol, Colin G. Fink, Ronald de Groot, Martin L. Hibberd, John Kanegaye, Mark P. Nicol, Stephane Paulus, Andrew J. Pollard, Antonio Salas, Fatou Secka, Luregn J. Schlapbach, Adriana H. Tremoulet, Michael Walther, Werner Zenz, Michiel van der Flier, Heather J. Zar, Taco Kuijpers, Jane C. Burns, Federico Martinon-Torres, Victoria J. Wright, Lachlan J. M. Coin, Aubrey J. Cunnington, Jethro A. Herberg, Michael Levin, Myrsini Kaforou
Summary: A panel of genes in blood can be used to discriminate various infectious and inflammatory diseases, allowing for reliable prediction of categories such as bacterial infection, viral infection, malaria, tuberculosis, or inflammatory disease.
Article
Biochemistry & Molecular Biology
Fuyi Li, Xudong Guo, Dongxu Xiang, Miranda E. Pitt, Arnold Bainomugisa, Lachlan J. M. Coin
Summary: In this study, a machine learning-based bioinformatics approach called PEPPER was developed to rapidly and accurately identify PE_PGRS proteins. Experimental results showed that PEPPER outperformed existing methods in terms of prediction accuracy and speed.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
