In a collaboration between Soochow (China), Institut Pasteur (Shanghai), CDC (China), Liverpool, Georgia (US), and Warwick we investigated the host-specificity of S. enterica based on 362,931 publically accessible genomes in EnteroBase (a database of sequenced enteric bacteria genomes hosted and developed at Warwick). We detected the presence of nine populations that are enriched in pigs and observed frequent intercontinental transmission of genetically almost identical strains in these pig-enriched populations, which cannot be explained solely by natural causes. Therefore, we focused on one population enriched in pigs, serovar Choleraesuis, reconstructing the historical fluctuations in this population, accumulation of antimicrobial-resistant genes, and international transmissions. We revealed a 2-stage expansion in the population of this serovar, the first associated with the development of intensive pig farming in the early 20th century and the second due to the increased frequency of antimicrobial resistance after the 1960s. Additionally, we found that Europe and the USA contributed the most to international transmissions of this serovar.
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Morphogen gradients provide essential positional information to gene networks through their spatially heterogeneous distribution, yet how they form is still hotly contested, with multiple models proposed for different systems. Here, we focus on the transcription factor Bicoid (Bcd), a morphogen that forms an exponential gradient across the anterior-posterior (AP) axis of the early Drosophila embryo. Using fluorescence correlation spectroscopy we find there are spatial differences in Bcd diffusivity along the AP axis, with Bcd diffusing more rapidly in the posterior. We establish that such spatially varying differences in Bcd dynamics are sufficient to explain how Bcd can have a steep exponential gradient in the anterior half of the embryo and yet still have an observable fraction of Bcd near the posterior pole. In the nucleus, we demonstrate that Bcd dynamics are impacted by binding to DNA. Addition of the Bcd homeodomain to eGFP::NLS qualitatively replicates the Bcd concentration profile, suggesting this domain regulates Bcd dynamics. Our results reveal how a long-range gradient can form while retaining a steep profile through much of its range. Read the paper here.

More and more evidence suggest that circadian clock disruption or misalignment is a feature of many diverse chronic diseases including metabolic syndrome, depression but also a number of cancers. For the latter, recent mechanistic studies in cancer models have established an understanding of how the circadian clock influences onset, progression and therapeutic outcomes. Moreover, it has been proposed that tumours might have disrupted circadian oscillators. In patients, however, this is more difficult to establish as usually only single samples, e.g., tumour biopsies, are available. Therefore, novel tools to measure the functional state of the molecular circadian clock are needed.

Here, we introduce TimeTeller, a machine learning tool that analyses the clock as a system and aims to estimate circadian clock function from a single sample’s transcriptome by modelling the multi-dimensional state of the clock. We demonstrate TimeTeller’s utility for analysing experimental in vitro and in vivo, as well as healthy human and patient samples from various platforms (microarray, RNA-Seq and NanoString) and highlight TimeTeller’s potential relevance for advancing circadian medicine. The project is an inter-disciplinary collaboration including significant work by Warwick’s MRCDTP students Laura Usselmann and Vadim Vasilyev and is setting the stage for further applications of TimeTeller in experimental models and human breast tumours.
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This work is based on the discovery of diurnal variations impacting cancer therapy. Especially, use of chronomodulated treatment with 5-fluorouracil (5-FU) has gained significance. Studies indicate high inter-individual variability in diurnal variations in dihydropyrimidine dehydrogenase (DPD) activity – a key enzyme for 5-FU metabolism. However, the influence of individual chronotypes on chronomodulated therapy was unclear but is needed to optimize precision dosing of chronomodulated 5‑FU. Lead by the Thorsten Lehr's PKPD group at the University of Saarland, this collaborative paper is taking a treasure trove of patient 5-FU PK data amalgamated with DPD enzyme activity data from health people to establish a novel PKPD model of 5-FU that captures the extent of diurnal variations in DPD activity and can help investigate individualized chronomodulated 5-FU therapy through testing alternative personalized dosing strategies. Read the paper here.

Work by recent WMS PhD graduate Agnieszka Nagorska and PDRA Andreas Zaucker shows that translational control of an enzyme, FurinA, is important for normal positioning of the heart, and for cardiac valve function. FurinA cleaves the growth factor signal and morphogen, Nodal. Mutant zebrafish embryos with mis-regulated furina show premature and increased levels of FurinA, ectopic Nodal signalling, and defects in heart positioning and valve development. This is similar to human patients with mitral valve regurgitation. The findings pave the way for potential diagnostic tests for patients with heart valve dysfunctions. The work was supported by grants from the Leverhulme Trust, UKRI-BBSRC, MLSRF, and doctoral studentships from Warwick Medical School, MRC DTP, and Warwick-ARAP.
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Gram negative bacterial pathogens use so called Type VI secretion systems (T6SSs) to deliver virulence effectors into target cells (either animal cells or other bacteria). Besides structural and effector proteins, many other proteins, such as adaptors, co-effectors and accessory proteins, are involved in this process. MIX domains can assist in the delivery of T6SS effectors when encoded as a stand-alone gene or fused at the N-terminal of the effector. However, whether there are other conserved domains exhibiting similar encoding forms to MIX in T6SS remains obscure.

In this work, we scanned publicly available bacterial genomes and established a database which include 130,825 T6SS vgrG loci from 45,041 bacterial genomes. Based on this, we revealed six domain families encoded within vgrG loci, which are either fused at the C-terminus of VgrG/N-terminus of T6SS toxin or encoded by an independent gene. Among them, DUF2345 was further validated and shown to be indispensable for the T6SS effector delivery and LysM was confirmed to assist the interaction between VgrG and the corresponding effector. Together, our results implied that these widely distributed domain families with similar genetic configurations may be required for the T6SS effector recruitment process.

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The dramatic global impact of the coronavirus pandemic has increased consideration on epidemiological progressions of pandemics. Measures implemented to reduce viral transmission have been largely historical, comparable in nature with the 1918 and 2009 influenza pandemics, demonstrating the importance of clinicians’ awareness on historical pandemics.

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Liver hepatocytes are the front-line cells for screening new compounds for toxicity. However, hepatocytes are stored frozen in vials, not in monolayers meaning they need substantial processing to be ‘usable’ especially for high throughput screening. To solve this the Gibson and Dallman groups have collaborated, so show that immortalised and primary hepatocytes can be cryopreserved whilst attached to 96 well microplates. These can then be taken from the freezer, and simple thawed and are ready to use in under 24 hours. Post-thaw the cells show equal performance to fresh. This was achieved by careful consideration of the molecular mechanism damage during freezing, with the team using patent-pending controlled ice nucleation technology, rather than a traditional re-formulation of cryoprotectants approach. This work was in collaboration with Cryologyx, a University of Warwick Spin out, which has commercialised aspects of this technology.  
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Trafficking of proteins, lipids, and other molecules between cellular compartments is carried out by vesicular carriers. Material destined for transfer is packaged into a small trafficking vesicle at the donor compartment; the vesicle must then travel to its destination, before fusing with the target compartment to deliver the material.

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