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2. Marmoset and human trophoblast stem cells differ in signaling requirements and recapitulate divergent modes of trophoblast invasion

Author

Siriwardena, Dylan, Munger, Clara, Penfold, Christopher, Kohler, Timo N., Weberling, Antonia, Linneberg-Agerholm, Madeleine, Slatery, Erin, Ellermann, Anna L., Bergmann, Sophie, Clark, Stephen J., Rawlings, Thomas M., Brickman, Joshua M., Reik, Wolf, Brosens, Jan J., Zernicka-Goetz, Magdalena, Sasaki, Erika, Behr, Rüdiger, Hollfelder, Florian, and Boroviak, Thorsten E.

Published
2024
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4. Spatial profiling of early primate gastrulation in utero

Author

Bergmann, Sophie, Penfold, Christopher A., Slatery, Erin, Siriwardena, Dylan, Drummer, Charis, Clark, Stephen, Strawbridge, Stanley E., Kishimoto, Keiko, Vickers, Alice, Tewary, Mukul, Kohler, Timo N., Hollfelder, Florian, Reik, Wolf, Sasaki, Erika, Behr, Rüdiger, and Boroviak, Thorsten E.

Published
2022
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8. Inferring the perturbation time from biological time course data

Author

Yang, Jing, Penfold, Christopher A., Grant, Murray R., and Rattray, Magnus

Subjects
Quantitative Biology - Quantitative Methods
Abstract

Time course data are often used to study the changes to a biological process after perturbation. Statistical methods have been developed to determine whether such a perturbation induces changes over time, e.g. comparing a perturbed and unperturbed time course dataset to uncover differences. However, existing methods do not provide a principled statistical approach to identify the specific time when the two time course datasets first begin to diverge after a perturbation; we call this the perturbation time. Estimation of the perturbation time for different variables in a biological process allows us to identify the sequence of events following a perturbation and therefore provides valuable insights into likely causal relationships. In this paper, we propose a Bayesian method to infer the perturbation time given time course data from a wild-type and perturbed system. We use a non-parametric approach based on Gaussian Process regression. We derive a probabilistic model of noise-corrupted and replicated time course data coming from the same profile before the perturbation time and diverging after the perturbation time. The likelihood function can be worked out exactly for this model and the posterior distribution of the perturbation time is obtained by a simple histogram approach, without recourse to complex approximate inference algorithms. We validate the method on simulated data and apply it to study the transcriptional change occurring in Arabidopsis following inoculation with P. syringae pv. tomato DC3000 versus the disarmed strain DC3000hrpA. An R package, DEtime, implementing the method is available at https://github.com/ManchesterBioinference/DEtime along with the data and code required to reproduce all the results., Comment: 63 pages, 20 figures, paper submitted to Bioinformatics

Published
2016

10. Age‐related and species‐specific methylation changes in the protein‐coding marmoset sperm epigenome.

Author

Dittrich, Marcus, Bernhardt, Laura, Penfold, Christopher A., Boroviak, Thorsten E., Drummer, Charis, Behr, Rüdiger, Müller, Tobias, and Haaf, Thomas

Subjects
PATERNAL age effect, GERM cells, EMBRYONIC stem cells, CELLULAR control mechanisms, MARMOSETS, SPERMATOZOA
Abstract

The sperm epigenome is thought to affect the developmental programming of the resulting embryo, influencing health and disease in later life. Age‐related methylation changes in the sperm of old fathers may mediate the increased risks for reproductive and offspring medical problems. The impact of paternal age on sperm methylation has been extensively studied in humans and, to a lesser extent, in rodents and cattle. Here, we performed a comparative analysis of paternal age effects on protein‐coding genes in the human and marmoset sperm methylomes. The marmoset has gained growing importance as a non‐human primate model of aging and age‐related diseases. Using reduced representation bisulfite sequencing, we identified age‐related differentially methylated transcription start site (ageTSS) regions in 204 marmoset and 27 human genes. The direction of methylation changes was the opposite, increasing with age in marmosets and decreasing in humans. None of the identified ageTSS was differentially methylated in both species. Although the average methylation levels of all TSS regions were highly correlated between marmosets and humans, with the majority of TSS being hypomethylated in sperm, more than 300 protein‐coding genes were endowed with species‐specifically (hypo)methylated TSS. Several genes of the glycosphingolipid (GSL) biosynthesis pathway, which plays a role in embryonic stem cell differentiation and regulation of development, were hypomethylated (<5%) in human and fully methylated (>95%) in marmoset sperm. The expression levels and patterns of defined sets of GSL genes differed considerably between human and marmoset pre‐implantation embryo stages and blastocyst tissues, respectively. [ABSTRACT FROM AUTHOR]

Published
2024
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12. The dynamics of colicin E9 release from Escherichia coli in native conditions.

Author

Bano, Shaista, Tunio, Sarfraz Ali, Penfold, Christopher N, and James, Richard

Subjects
ESCHERICHIA coli, MITOMYCIN C, PLASMIDS, CELL populations, LYSIS, CELL death
Abstract

Colicin (Col) plasmid contains colicin encoding genes arranged in an operon controlled by an SOS inducible promoter. Therefore, any external stresses to the host cell can induce the expression of the downstream genes in the Col operon, including a lysis gene. The lysis protein is involved in the extracellular release of colicin through lysis of the producer cells, which causes a decline in culture turbidity. However, it is not yet known that E. coli cells with the native pColE9-J plasmid hold the same level of cell death at the population level following a set of induced conditions. In this study, using a mitomycin C sensitivity assay along with a live dead staining method of detection, we showed that the native pColE9-J plasmid, which unusually carries an extended Col operon (ColE9) containing two lysis genes, did not confer a rapid decline in the culture turbidity following induction with mitomycin C. Interestingly a subset of the cells suffered perturbation of their outer membrane, which was not observed from single lysis mutant (∆ celE or ∆ celI) cells. This observed heterogeneity in the colicin E9 release leading to differential outer membrane perforation may bring a competitive advantage to these cells in a mixed population. [ABSTRACT FROM AUTHOR]

Published
2024
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14. Elizaveta Svilova and Soviet documentary film

Author

Penfold, Christopher, Bergfelder, Tim, and Dunn, David

Subjects
791.436, DK Russia. Soviet Union. Former Soviet Republics, PN1993 Motion Pictures, ZA Information resources
Abstract

The focus of my research is Soviet documentary filmmaker, Elizaveta Svilova (1900-75), most commonly remembered, if at all, as the wife and collaborator of acclaimed Soviet film pioneer, Dziga Vertov (1896-1954). Having worked with her husband for many years, Svilova continued her career as an independent director-editor after Vertov fell out of favour with the Central Committee. Employed at the Central Studio for Documentary Film, a state-initiated studio, Svilova’s films were vehicles of rhetoric, mobilised to inform, educate and persuade the masses. She draws on visual symbols familiar to audiences and organises them according to the semiotic theories – namely techniques of dialecticism and linkage – attributed to the Soviet montage school of the 1920s. On-screen credits indicate that, during the period 1939 to 1956, Svilova was the director-editor of over 100 documentaries and newsreel episodes, yet this corpus of films has received very little critical attention. As my thesis aims to demonstrate, the reasons for the lack of attention to Svilova’s films are partly due to her husband’s eminent status – the rules whereby we construct film history have resulted in Svilova’s contribution being absorbed into Vertov’s – and this is related to the long-standing tendency within film criticism to marginalise the female artist. My thesis also touches on issues regarding curatorial and archival policies, and provides an opportunity to rethink early film history and the modes through which historiographic and filmographic knowledge are transmitted.

Published
2013

15. DNA methylation derived systemic inflammation indices are associated with head and neck cancer development and survival

Author

Ambatipudi, Srikant, Langdon, Ryan, Richmond, Rebecca C., Suderman, Matthew, Koestler, Devin C., Kelsey, Karl T., Kazmi, Nabila, Penfold, Christopher, Ho, Karen M., McArdle, Wendy, Ring, Susan M., Pring, Miranda, Waterboer, Tim, Pawlita, Michael, Gaunt, Tom R., Davey Smith, George, Thomas, Steve, Ness, Andy R., and Relton, Caroline L.

Published
2018
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16. Patient copayments in primary medical care

Author

Penfold, Christopher M.

Subjects
617.60068
Abstract

This research was carried out to assess the feasibility of studying the effects of introducing copayments in primary medical care via studying the effects of copayments in primary dental care. Quantitative methods were used to investigate the impact of primary dental care copayments on patients and to compare predictors of primary medical and dental care uptake. Qualitative methods were used to investigate attitudes towards copayments for NHS primary health services and their extension to include primary medical consultations. Regression models, chi-square analyses and ANOVA were applied to the England and Wales sub-sample of nationally representative self-report data from the 1998 Adult Dental Health Survey (ADHS) (n=3628) to investigate the impact of copayments on primary dental care uptake. Regression models and chi-square analyses were applied to the England and Wales sub-sample of nationally representative self-report data from the 1997/98 British Household Panel Survey (BHPS) (n=8526) and the 1998 ADHS (n=3641) to compare predictors of primary medical and dental consultations. Semi- structured interviews were undertaken in Bristol and Somerset with purposively sampled frequent and infrequent primary medical care users (n=19). Predictors of primary medical and dental care utilisation differed across predisposing, enabling and illness level factors. Private and NHS dental copayments were perceived to be expensive and this perception was associated with lower preventive-led dental consultation rates, but not with treatment-led consultation rates. Copayments for services affected the nature of the patient-practitioner relationship. Findings were inconclusive regarding the effect of copayment exemption status on people's decisions to consult a dentist and on dental treatments received. It was not feasible to study the effects of introducing copayments in primary medical care via studying the effects of copayments in primary dental care.

Published
2011

19. Epigenetic resetting in the human germ line entails histone modification remodeling

Author

Gruhn, Wolfram H, Tang, Walfred WC, Dietmann, Sabine, Alves-Lopes, João P, Penfold, Christopher A, Wong, Frederick CK, Ramakrishna, Navin B, Surani, M Azim, Gruhn, Wolfram H [0000-0001-6072-1916], Tang, Walfred WC [0000-0002-5803-1681], Dietmann, Sabine [0000-0001-6672-8457], Alves-Lopes, João P [0000-0003-3042-6988], Penfold, Christopher A [0000-0001-5823-4705], Wong, Frederick CK [0000-0002-0503-4360], Ramakrishna, Navin B [0000-0003-2974-9886], Surani, M Azim [0000-0002-8640-4318], and Apollo - University of Cambridge Repository

Subjects
Histone Code, Mammals, Germ Cells, DNA Transposable Elements, Animals, Humans, DNA Methylation, Epigenesis, Genetic
Abstract

Epigenetic resetting in the mammalian germ line entails acute DNA demethylation, which lays the foundation for gametogenesis, totipotency, and embryonic development. We characterize the epigenome of hypomethylated human primordial germ cells (hPGCs) to reveal mechanisms preventing the widespread derepression of genes and transposable elements (TEs). Along with the loss of DNA methylation, we show that hPGCs exhibit a profound reduction of repressive histone modifications resulting in diminished heterochromatic signatures at most genes and TEs and the acquisition of a neutral or paused epigenetic state without transcriptional activation. Efficient maintenance of a heterochromatic state is limited to a subset of genomic loci, such as evolutionarily young TEs and some developmental genes, which require H3K9me3 and H3K27me3, respectively, for efficient transcriptional repression. Accordingly, transcriptional repression in hPGCs presents an exemplary balanced system relying on local maintenance of heterochromatic features and a lack of inductive cues.

Published
2023
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20. Origin and segregation of the human germline

Author

Castillo-Venzor, Aracely, primary, Penfold, Christopher A, additional, Morgan, Michael D, additional, Tang, Walfred WC, additional, Kobayashi, Toshihiro, additional, Wong, Frederick CK, additional, Bergmann, Sophie, additional, Slatery, Erin, additional, Boroviak, Thorsten E, additional, Marioni, John C, additional, and Surani, M Azim, additional

Published
2023
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21. Time-Series Transcriptomics Reveals That AGAMOUS-LIKE22 Affects Primary Metabolism and Developmental Processes in Drought-Stressed Arabidopsis

Author

Bechtold, Ulrike, Penfold, Christopher A., Jenkins, Dafyd J., Legaie, Roxane, Moore, Jonathan D., Lawson, Tracy, Matthews, Jack S.A., Vialet-Chabrand, Silvere R.M., Baxter, Laura, Subramaniam, Sunitha, Hickman, Richard, Florance, Hannah, Sambles, Christine, Salmon, Deborah L., Feil, Regina, Bowden, Laura, Hill, Claire, Baker, Neil R., Lunn, John E., Finkenstädt, Bärbel, Mead, Andrew, Buchanan-Wollaston, Vicky, Beynon, Jim, Rand, David A., Wild, David L., Denby, Katherine J., Ott, Sascha, Smirnoff, Nicholas, and Mullineaux, Philip M.

Published
2016

23. Transcriptional Dynamics Driving MAMP-Triggered Immunity and Pathogen Effector-Mediated Immunosuppression in Arabidopsis Leaves Following Infection with Pseudomonas syringae pv tomato DC3000

Author

Lewis, Laura A., Polanski, Krzysztof, de Torres-Zabala, Marta, Jayaraman, Siddharth, Bowden, Laura, Moore, Jonathan, Penfold, Christopher A., Jenkins, Dafyd J., Hill, Claire, Baxter, Laura, Kulasekaran, Satish, Truman, William, Littlejohn, George, Prusinska, Justyna, Mead, Andrew, Steinbrenner, Jens, Hickman, Richard, Rand, David, Wild, David L., Ott, Sascha, Buchanan-Wollaston, Vicky, Smirnoff, Nick, Beynon, Jim, Denby, Katherine, and Grant, Murray

Published
2015

27. Spatial embryo profiling (STEP) of primate implantation stages

Author

Bergmann Sophie, Penfold Christopher, Slatery Erin, and Boroviak Thorsten

Abstract

Spatial embryo profiling (STEP) combines laser capture microdissection (LCM)-assisted sample collection for Smart-Seq2 profiling with virtual reconstruction of stereological immunofluorescence images of implanted primate embryos. Frozen, unfixed embryos O.C.T.-embedded in utero are cryosectioned, with every second to third embryo-containing section subjected to LCM for collection of tissue samples of one-to-three cells and processed individually for full-length transcriptome profiling. Remaining sections are fixed and processed for immunofluorescence staining, followed by stereological confocal microscopy, image registration, tissue segmentation and surface generation to create virtual 3D embryo models. Gaussian process regression following the integration of discrete, spatially defined transcriptome samples allows modelling of 3D gene expression patterns across the entire embryo model.

Published
2022
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29. Mapping the biogenesis of forward programmed megakaryocytes from induced pluripotent stem cells

Author

Lawrence, Moyra, Shahsavari, Arash, Borneloev, Susanne, Moreau, Thomas, McDonald, Rebecca, Vallance, Thomas, Kania, Katarzyna, Paramor, Maike, Baye, James, Perrin, Marion, Steindel, Maike, Jimenez-Gomez, Paula, Penfold, Christopher, Mohorianu, Irina, Ghevaert, Cedric, Lawrence, Moyra [0000-0001-9386-5633], Borneloev, Susanne [0000-0001-9276-9981], Moreau, Thomas [0000-0003-1090-6685], McDonald, Rebecca [0000-0002-6131-1748], Vallance, Thomas [0000-0003-4433-9025], Kania, Katarzyna [0000-0001-8206-1349], Paramor, Maike [0000-0002-8523-3588], Baye, James [0000-0002-0078-3688], Perrin, Marion [0000-0003-0996-8918], Steindel, Maike [0000-0002-1170-1318], Penfold, Christopher [0000-0001-5823-4705], Mohorianu, Irina [0000-0003-4863-761X], Ghevaert, Cedric [0000-0002-9251-0934], and Apollo - University of Cambridge Repository

Subjects
Blood Platelets, Pluripotent Stem Cells, CambridgeStemCellInstitute, Multidisciplinary, Induced Pluripotent Stem Cells, Cell Differentiation, Megakaryocytes
Abstract

Platelet deficiency, known as thrombocytopenia, can cause hemorrhage and is treated with platelet transfusions. We developed a system for the production of platelet precursor cells, megakaryocytes, from pluripotent stem cells. These cultures can be maintained for >100 days, implying culture renewal by megakaryocyte progenitors (MKPs). However, it is unclear whether the MKP state in vitro mirrors the state in vivo, and MKPs cannot be purified using conventional surface markers. We performed single-cell RNA sequencing throughout in vitro differentiation and mapped each state to its equivalent in vivo. This enabled the identification of five surface markers that reproducibly purify MKPs, allowing us insight into their transcriptional and epigenetic profiles. Last, we performed culture optimization, increasing MKP production. Together, this study has mapped parallels between the MKP states in vivo and in vitro and allowed the purification of MKPs, accelerating the progress of in vitro–derived transfusion products toward the clinic.

Published
2022
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34. Arabidopsis Defense against Botrytis cinerea: Chronology and Regulation Deciphered by High-Resolution Temporal Transcriptomic Analysis

Author

Windram, Oliver, Madhou, Priyadharshini, McHattie, Stuart, Hill, Claire, Hickman, Richard, Cooke, Emma, Jenkins, Dafyd J., Penfold, Christopher A., Baxter, Laura, Breeze, Emily, Kiddle, Steven J., Rhodes, Johanna, Atwell, Susanna, Kliebenstein, Daniel J., Kim, Youn-sung, Stegle, Oliver, Borgwardt, Karsten, Zhang, Cunjin, Tabrett, Alex, Legaie, Roxane, Moore, Jonathan, Finkenstadt, Bärbel, Wild, David L., Mead, Andrew, Rand, David, Beynon, Jim, Ott, Sascha, Buchanan-Wollaston, Vicky, and Denby, Katherine J.

Published
2012

36. Origin and segregation of the human germline

Author

Castillo-Venzor, Aracely, primary, Penfold, Christopher Andrew, additional, Morgan, Michael David, additional, Tang, Walfred W.C., additional, Kobayashi, Toshihiro, additional, Wong, Frederick C. K., additional, Bergmann, Sophie, additional, Slatery, Erin, additional, Boroviak, Thorsten Edwin, additional, Marioni, John, additional, and Surani, M. Azim, additional

Published
2022
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39. High-Resolution Temporal Profiling of Transcripts during Arabidopsis Leaf Senescence Reveals a Distinct Chronology of Processes and Regulation

Author

Breeze, Emily, Harrison, Elizabeth, McHattie, Stuart, Hughes, Linda, Hickman, Richard, Hill, Claire, Kiddle, Steven, Kim, Youn-sung, Penfold, Christopher A., Jenkins, Dafyd, Zhang, Cunjin, Morris, Karl, Jenner, Carol, Jackson, Stephen, Thomas, Brian, Tabrett, Alexandra, Legaie, Roxane, Moore, Jonathan D., Wild, David L., Ott, Sascha, Rand, David, Beynon, Jim, Denby, Katherine, Mead, Andrew, and Buchanan-Wollaston, Vicky

Published
2011

45. Time‐series transcriptomics reveals a BBX32 ‐directed control of acclimation to high light in mature Arabidopsis leaves

Author

Alvarez‐Fernandez, Ruben, primary, Penfold, Christopher A., additional, Galvez‐Valdivieso, Gregorio, additional, Exposito‐Rodriguez, Marino, additional, Stallard, Ellie J., additional, Bowden, Laura, additional, Moore, Jonathan D., additional, Mead, Andrew, additional, Davey, Phillip A., additional, Matthews, Jack S. A., additional, Beynon, Jim, additional, Buchanan‐Wollaston, Vicky, additional, Wild, David L., additional, Lawson, Tracy, additional, Bechtold, Ulrike, additional, Denby, Katherine J., additional, and Mullineaux, Philip M., additional

Published
2021
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47. Investigating early events in receptor binding and translocation of colicin E9 using synchronized cell killing and proteolytic cleavage

Author

Zhang, Ying, Vankemmelbeke, Mireille N., Holland, Lisa E., Walker, David C., James, Richard, and Penfold, Christopher N.

Subjects
Escherichia coli -- Physiological aspects, Escherichia coli -- Genetic aspects, Escherichia coli -- Research, Translocation (Genetics) -- Physiological aspects, Translocation (Genetics) -- Research, Bacteriocins -- Physiological aspects, Bacteriocins -- Research, Biological sciences
Abstract

Enzymatic colicins such as colicin E9 (ColE9) bind to BtuB on the cell surface of Escherichia coli and rapidly recruit a second coreceptor, either OmpF or OmpC, through which the N-terminal natively disordered region (NDR) of their translocation domain gains entry into the cell periplasm and interacts with TolB. Previously, we constructed an inactive disulfide-locked mutant ColE9 ([ColE9.sup.s-s]) that binds to BtuB and can be reduced with dithiothreitol (DTT) to synchronize cell killing. By introducing unique enterokinase (EK) cleavage sites in [ColE9.sup.s-s], we showed that the first 61 residues of the NDR were inaccessible to cleavage when bound to BtuB, whereas an EK cleavage site inserted at residue 82 of the NDR remained accessible. This suggests that most of the NDR is occluded by OmpF shortly after binding to BtuB, whereas the extreme distal region of the NDR is surface exposed before unfolding of the receptor-binding domain occurs. EK cleavage of unique cleavage sites located in the ordered region of the translocation domain or in the distal region of the receptor-binding domain confirmed that these regions of ColE9 remained accessible at the E. coli cell surface. Lack of EK cleavage of the DNase domain of the cell-bound, oxidized ColE9/Im9 complex, and the rapid detection of Alexa Fluor 594-labeled Im9 ([Im9.sup.AF]) in the cell supernatant following treatment of cells with DTT, suggested that immunity release occurred immediately after unfolding of the colicin and was not driven by binding to BtuB.

Published
2008

48. Consensus-based antimicrobial resistance and stewardship competencies for UK undergraduate medical students

Author

McMaster, David, Courtenay, Molly, Santucci, Catherine, Davies, Angharad P, Kirby, Andrew, Seddon, Owen, Price, David A, Barlow, Gavin, Lim, Felicia H, Davies, Bethany S, O'Shea, Matthew K, Collini, Paul, Basarab, Marina, Ahmad, Afshan, Albur, Mahableshwar, Hemsley, Carolyn, Brown, Nicholas M, O'Gorman, Ciaran, Rautemaa-Richardson, Riina, Davies, Geraint R, Penfold, Christopher N, Patel, Sanjay, Keep Antibiotics Working (KAW) Group, McMaster, David [0000-0003-1900-8785], Rautemaa-Richardson, Riina [0000-0002-1071-6040], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, Response rate (survey), Medical education, 030106 microbiology, education, Modified delphi, MEDLINE, Keep Antibiotics Working (KAW) group, 03 medical and health sciences, Qualitative feedback, 0302 clinical medicine, Antibiotic resistance, AcademicSubjects/MED00290, Antimicrobial stewardship, AcademicSubjects/MED00740, Original Article, 030212 general & internal medicine, Stewardship, Psychology, AcademicSubjects/MED00230, Curriculum
Abstract

Background In the UK there is limited coverage of antimicrobial stewardship across postgraduate curricula and evidence that final year medical students have insufficient and inconsistent antimicrobial stewardship teaching. A national undergraduate curriculum for antimicrobial resistance and stewardship is required to standardize an adequate level of understanding for all future doctors. Objectives To provide a UK national consensus on competencies for antimicrobial resistance and stewardship for undergraduate medical education. Methods Using the modified Delphi method over two online survey rounds, an expert panel comprising leads for infection teaching from 25 UK medical schools reviewed competency descriptors for antimicrobial resistance and stewardship education. Results There was a response rate of 100% with all 28 experts who agreed to take part completing both survey rounds. Following the first-round survey, of the initial 55 descriptors, 43 reached consensus (78%). The second-round survey included the 12 descriptors from the first round in which agreement had not been reached, four amended descriptors and 12 new descriptors following qualitative feedback from the panel members. Following the second-round survey, a total of 58 consensus-based competency descriptors within six overarching domains were identified. Conclusions The consensus-based competency descriptors defined here can be used to inform standards, design curricula, develop assessment tools and direct UK undergraduate medical education.

Published
2020
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49. Mapping the biogenesis of forward programmed megakaryocytes from induced pluripotent stem cells

Author

Lawrence, Moyra, primary, Shahsavari, Arash, additional, Bornelöv, Susanne, additional, Moreau, Thomas, additional, Kania, Katarzyna, additional, Paramor, Maike, additional, McDonald, Rebecca, additional, Baye, James, additional, Perrin, Marion, additional, Steindel, Maike, additional, Jimenez-Gomez, Paula, additional, Penfold, Christopher, additional, Mohorianu, Irina, additional, and Ghevaert, Cedric, additional

Published
2021
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