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All Outputs (19)

Multiple novel caliciviruses identified from stoats (Mustela erminea) in the United Kingdom (2024)
Journal Article
Hinds, J., Apaa, T., Parry, R. H., Withers, A. J., MacKenzie, L., Staley, C., Morrison, J., Bennett, M., Bremner-Harrison, S., Chadwick, E. A., Hailer, F., Harrison, S. W., Lambin, X., Loose, M., Mathews, F., Tarlinton, R., & Blanchard, A. (2024). Multiple novel caliciviruses identified from stoats (Mustela erminea) in the United Kingdom. Access Microbiology, 6(7), Article 000813.v4. https://doi.org/10.1099/acmi.0.000813.v4

The Caliciviridae family, comprising positive-sense RNA viruses, is characterised by its non-enveloped, small virions, broad host range, and notable tendency for host switching. These viruses are primarily associated with gastroenteric disease, thoug... Read More about Multiple novel caliciviruses identified from stoats (Mustela erminea) in the United Kingdom.

Vivaldi: An amplicon-based whole genome sequencing method for the four seasonal human coronaviruses 229E, NL63, OC43 & HKU1, alongside SARS-CoV-2 (2024)
Preprint / Working Paper
McClure, C. P., Tsoleridis, T., Holmes, N., Chappell, J. G., Byaruhanga, T., Duncan, J., Tofan, M., Khater, A., Berry, L., Clark, G., Irving, W. L., Tarr, A. W., Ball, J. K., Astbury, S., & Loose, M. Vivaldi: An amplicon-based whole genome sequencing method for the four seasonal human coronaviruses 229E, NL63, OC43 & HKU1, alongside SARS-CoV-2

Prior to the emergence of SARS-CoV-2 in 2019, Alphacoronaviruses 229E and NL63 and Betacoronaviruses OC43 and HKU1 were already established endemic ‘common cold’ viral infections. Despite their collective contribution towards global respiratory morbi... Read More about Vivaldi: An amplicon-based whole genome sequencing method for the four seasonal human coronaviruses 229E, NL63, OC43 & HKU1, alongside SARS-CoV-2.

A single-cell atlas of pig gastrulation as a resource for comparative embryology (2024)
Journal Article
Simpson, L., Strange, A., Klisch, D., Kraunsoe, S., Azami, T., Goszczynski, D., …Alberio, R. (2024). A single-cell atlas of pig gastrulation as a resource for comparative embryology. Nature Communications, 15(1), Article 5210. https://doi.org/10.1038/s41467-024-49407-6

Cell-fate decisions during mammalian gastrulation are poorly understood outside of rodent embryos. The embryonic disc of pig embryos mirrors humans, making them a useful proxy for studying gastrulation. Here we present a single-cell transcriptomic at... Read More about A single-cell atlas of pig gastrulation as a resource for comparative embryology.

NANOG is required to establish the competence for germ-layer differentiation in the basal tetrapod axolotl (2023)
Journal Article
Simpson, L. A., Crowley, D., Forey, T., Acosta, H., Ferjentsik, Z., Chatfield, J., …Johnson, A. D. (2023). NANOG is required to establish the competence for germ-layer differentiation in the basal tetrapod axolotl. PLoS Biology, 21(6), Article e3002121. https://doi.org/10.1371/journal.pbio.3002121

Pluripotency defines the unlimited potential of individual cells of vertebrate embryos, from which all adult somatic cells and germ cells are derived. Understanding how the programming of pluripotency evolved has been obscured in part by a lack of da... Read More about NANOG is required to establish the competence for germ-layer differentiation in the basal tetrapod axolotl.

Factors affecting turnaround time of SARS-CoV-2 sequencing for inpatient infection prevention and control decision making: analysis of data from the COG-UK HOCI study (2022)
Journal Article
Colton, H., Parker, M. D., Stirrup, O., Blackstone, J., Loose, M., McClure, C. P., …de Silva, T. I. (2023). Factors affecting turnaround time of SARS-CoV-2 sequencing for inpatient infection prevention and control decision making: analysis of data from the COG-UK HOCI study. Journal of Hospital Infection, 131, 34-42. https://doi.org/10.1016/j.jhin.2022.09.022

Background Barriers to rapid return of sequencing results can affect the utility of sequence data for infection prevention and control decisions. Aim To undertake a mixed-methods analysis to identify challenges that sites faced in achieving a ra... Read More about Factors affecting turnaround time of SARS-CoV-2 sequencing for inpatient infection prevention and control decision making: analysis of data from the COG-UK HOCI study.

Differential and defective transcription of koala retrovirus indicates the complexity of host and virus evolution (2022)
Journal Article
Tarlinton, R. E., Legione, A. R., Sarker, N., Fabijan, J., Meers, J., McMichael, L., …Emes, R. D. (2022). Differential and defective transcription of koala retrovirus indicates the complexity of host and virus evolution. Journal of General Virology, 103(6), Article 001749. https://doi.org/10.1099/jgv.0.001749

Koala retrovirus (KoRV) is unique amongst endogenous (inherited) retroviruses in that its incorporation to the host genome is still active, providing an opportunity to study what drives this fundamental process in vertebrate genome evolution. Animals... Read More about Differential and defective transcription of koala retrovirus indicates the complexity of host and virus evolution.

Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements (2022)
Journal Article
Cahyani, I., Putro, E. W., Ridwanuloh, A. M., Wibowo, S., Hariyatun, H., Syahputra, G., …Susanti, S. (2022). Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements. Viruses, 14(4), Article 778. https://doi.org/10.3390/v14040778

Whole-genome sequencing (WGS) has played a significant role in understanding the epidemiology and biology of SARS-CoV-2 virus. Here, we investigate the use of SARS-CoV-2 WGS in Southeast and East Asian countries as a genomic surveillance during the C... Read More about Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements.

Specification and epigenomic resetting of the pig germline exhibit conservation with the human lineage (2021)
Journal Article
Zhu, Q., Sang, F., Withey, S., Tang, W., Dietmann, S., Klisch, D., …Alberio, R. (2021). Specification and epigenomic resetting of the pig germline exhibit conservation with the human lineage. Cell Reports, 34(6), Article 108735. https://doi.org/10.1016/j.celrep.2021.108735

Investigations of the human germline and programming are challenging because of limited access to embryonic material. However, the pig as a model may provide insights into transcriptional network and epigenetic reprogramming applicable to both specie... Read More about Specification and epigenomic resetting of the pig germline exhibit conservation with the human lineage.

Readfish enables targeted nanopore sequencing of gigabase-sized genomes (2020)
Journal Article
Payne, A., Holmes, N., Clarke, T., Munro, R., Debebe, B., & Loose, M. (2021). Readfish enables targeted nanopore sequencing of gigabase-sized genomes. Nature Biotechnology, 39, 442-450. https://doi.org/10.1038/s41587-020-00746-x

© 2020, The Author(s), under exclusive licence to Springer Nature America, Inc. Nanopore sequencers can be used to selectively sequence certain DNA molecules in a pool by reversing the voltage across individual nanopores to reject specific sequences,... Read More about Readfish enables targeted nanopore sequencing of gigabase-sized genomes.

Nanopore native RNA sequencing of a human poly(A) transcriptome (2019)
Journal Article
Workman, R. E., Tang, A. D., Tang, P. S., Jain, M., Tyson, J. R., Razaghi, R., …Timp, W. (2019). Nanopore native RNA sequencing of a human poly(A) transcriptome. Nature Methods, https://doi.org/10.1038/s41592-019-0617-2

High-throughput complementary DNA sequencing technologies have advanced our understanding of transcriptome complexity and regulation. However, these methods lose information contained in biological RNA because the copied reads are often short and mod... Read More about Nanopore native RNA sequencing of a human poly(A) transcriptome.

BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files (2018)
Journal Article
Payne, A., Holmes, N., Rakyan, V., & Loose, M. (2018). BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files. Bioinformatics, 35(13), 2193-2198. https://doi.org/10.1093/bioinformatics/bty841

Motivation: The Oxford Nanopore Technologies (ONT) MinION is used for sequencing a wide variety of sample types with diverse methods of sample extraction. Nanopore sequencers output FAST5 files containing signal data subsequently base called to FASTQ... Read More about BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files.

Same-day diagnostic and surveillance data for tuberculosis via whole genome sequencing of direct respiratory samples (2017)
Journal Article
Votintseva, A. A., Bradley, P., Pankhurst, L., Elias, C. D. O., Loose, M., Nilgiriwala, K., …Iqbal, Z. (2017). Same-day diagnostic and surveillance data for tuberculosis via whole genome sequencing of direct respiratory samples. Journal of Clinical Microbiology, 55(5), https://doi.org/10.1128/JCM.02483-16

Routine full characterization of Mycobacterium tuberculosis (TB) is culture-based, taking many weeks. Whole-genome sequencing (WGS) can generate antibiotic susceptibility profiles to inform treatment, augmented with strain information for global surv... Read More about Same-day diagnostic and surveillance data for tuberculosis via whole genome sequencing of direct respiratory samples.

Real-time selective sequencing using nanopore technology (2016)
Journal Article
Loose, M., Malla, S., & Stout, M. (in press). Real-time selective sequencing using nanopore technology. Nature Methods, 13(9), https://doi.org/10.1038/nmeth.3930

The Oxford Nanopore Technologies MinION sequencer enables the selection of specific DNA molecules for sequencing by reversing the driving voltage across individual nanopores. To directly select molecules for sequencing, we used dynamic time warping t... Read More about Real-time selective sequencing using nanopore technology.

Stochastic specification of primordial germ cells from mesoderm precursors in axolotl embryos (2014)
Journal Article
Chatfield, J., O'Reilly, M.-A., Bachvarova, R. F., Ferjentsik, Z., Redwood, C., Walmsley, M., …JOhnson, A. D. (2014). Stochastic specification of primordial germ cells from mesoderm precursors in axolotl embryos. Development, 141(12), 2429-2440. https://doi.org/10.1242/dev.105346

A common feature of development in most vertebrate models is the early segregation of the germ line from the soma. For example, in Xenopus and zebrafish embryos primordial germ cells (PGCs) are specified by germ plasm that is inherited from the egg;... Read More about Stochastic specification of primordial germ cells from mesoderm precursors in axolotl embryos.

Transient Accumulation of 5-Carboxylcytosine Indicates Involvement of Active Demethylation in Lineage Specification of Neural Stem Cells (2014)
Journal Article
Wheldon, L. M., Abakir, A., Ferjentsik, Z., Dudnakova, T., Strohbuecker, S., Christie, D., …Ruzov, A. (2014). Transient Accumulation of 5-Carboxylcytosine Indicates Involvement of Active Demethylation in Lineage Specification of Neural Stem Cells. Cell Reports, 7(5), 1353-1361. https://doi.org/10.1016/j.celrep.2014.05.003

5-Methylcytosine (5mC) is an epigenetic modification involved in regulation of gene activity during differentiation. Tet dioxygenases oxidize 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). Both 5fC and 5... Read More about Transient Accumulation of 5-Carboxylcytosine Indicates Involvement of Active Demethylation in Lineage Specification of Neural Stem Cells.

Kinetochore assembly and heterochromatin formation occur autonomously in Schizosaccharomyces pombe (2014)
Journal Article
Brown, W. R., Thomas, G., Lee, N. C., Blythe, M., Liti, G., Warringer, J., & Loose, M. W. (2014). Kinetochore assembly and heterochromatin formation occur autonomously in Schizosaccharomyces pombe. Proceedings of the National Academy of Sciences, 111(5), https://doi.org/10.1073/pnas.1216934111

Kinetochores in multicellular eukaryotes are usually associated with heterochromatin. Whether this heterochromatin simply promotes the cohesion necessary for accurate chromosome segregation at cell division or whether it also has a role in kinetochor... Read More about Kinetochore assembly and heterochromatin formation occur autonomously in Schizosaccharomyces pombe.

5-hydroxymethyl-cytosine enrichment of non-committed cells is not a universal feature of vertebrate development (2012)
Journal Article
Almeida, R. D., Loose, M., Sottile, V., Matsa, E., Denning, C., Young, L., …Ruzov, A. (2012). 5-hydroxymethyl-cytosine enrichment of non-committed cells is not a universal feature of vertebrate development. Epigenetics, 7(4), https://doi.org/10.4161/epi.19375

5-hydroxymethyl-cytosine (5-hmc) is a cytosine modification that is relatively abundant in mammalian pre-implantation embryos and embryonic stem cells (Esc) derived from mammalian blastocysts. Recent observations imply that both 5-hmc and Tet1/2/... Read More about 5-hydroxymethyl-cytosine enrichment of non-committed cells is not a universal feature of vertebrate development.