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  • Journal article
    Fernandez-Gonzalez A, Cowen S, Kim J, Foy CA, Jimenez J, Huggett JF, Whale ASet al., 2022,

    Applicability of control materials to support gene promoter characterization and expression in engineered cells using digital PCR

    , Analytical Chemistry, Vol: 94, Pages: 5566-5574, ISSN: 0003-2700

    The use of standardized components and processes in engineering underpins the design-build-test model, and the engineering of biological systems is no different. Substantial efforts to standardize both the components and the methods to validate the engineered biological systems is ongoing. This study has developed a panel of control materials encoding the commonly used reporter genes GFP and RFP as DNA or RNA molecules. Each panel contained up to six samples with increasingly small copy number differences between the two reporter genes that ranged from 1- to 2-fold differences. These copy number differences represent the magnitude of changes that may need to be measured to validate an engineered system. Using digital PCR (dPCR), we demonstrated that it is possible to quantify changes in both gene and gene transcript numbers both within and between samples down to 1.05-fold. We corroborated these findings using a simple gene circuit within a bacterial model to demonstrate that dPCR was able to precisely identify small changes in gene expression of two transcripts in response to promoter stimulation. Finally, we used our findings to highlight sources of error that can contributed to the measurement uncertainty in the measurement of small ratios in biological systems. Together, the development of a panel of control materials and validation of a high accuracy method for the measurement of small changes in gene expression, this study can contribute to the engineering biology “toolkit” of methods and materials to support the current standardization efforts.

  • Journal article
    Makrydaki E, Donini R, Krueger A, Royle K, Moya-Ramirez I, Kuntz DA, Rose DR, Haslam SM, Polizzi K, Kontoravdi Cet al., 2022,

    Immobilised enzyme cascade for targeted glycosylation

    <jats:title>Abstract</jats:title><jats:p>Glycosylation is a critical post-translational modification of proteins, improving properties such as folding, half-life and functionality. However, glycosylation is a non-templated and heterogeneous process because of the promiscuity of the enzymes involved. Here we describe a platform for <jats:underline>s</jats:underline>eq<jats:underline>u</jats:underline>ential <jats:underline>g</jats:underline>lycosyl<jats:underline>a</jats:underline>tion <jats:underline>r</jats:underline>eactions for <jats:underline>ta</jats:underline>ilo<jats:underline>r</jats:underline>ed su<jats:underline>g</jats:underline>ar s<jats:underline>t</jats:underline>ructures (SUGAR-TARGET) that allows bespoke, controlled N-linked glycosylation <jats:italic>in vitro</jats:italic>. This novel proof-of-concept system is enabled by immobilised enzymes produced with a “one-step immobilisation/purification” method to express, biotinylate <jats:italic>in vivo</jats:italic> and immobilise glycosyltransferases. The immobilised enzymes are used in a reaction cascade mimicking a human-like N-linked glycosylation pathway where promiscuity naturally exists. The enzyme cascade is applied to free glycans, and a monomeric Fc domain expressed in glycoengineered <jats:italic>Pichia pastoris</jats:italic>, yielding near homogeneous glycoforms (&gt;95% conversion). Finally, immobilised β-1,4 galactosyltransferase is used to enhance the galactosylation profile of three different IgGs yielding 80.2 – 96.3 % terminal galactosylation. Enzyme recycling was further demonstrated for 7 cycles, with a combined reaction time greater than 140 hours. The novel SUGAR-TARGET platform is easy to implement, modular and reusable, and therefore can lead to the development of homogeneous glycan structures fo

  • Journal article
    Henson SA, Laufkotter C, Leung S, Giering SLC, Palevsky H, Cavan ELet al., 2022,

    Uncertain response of ocean biological carbon export in a changing world

    , NATURE GEOSCIENCE, Vol: 15, Pages: 248-254, ISSN: 1752-0894
  • Journal article
    Broto A, Gaspari E, Miravet-Verde S, Martins dos Santos VAP, Isalan Met al., 2022,

    A genetic toolkit and gene switches to limit Mycoplasma growth for biosafety applications

    , Nature Communications, Vol: 13, ISSN: 2041-1723

    Mycoplasmas have exceptionally streamlined genomes and are strongly adapted to their many hosts, which provide them with essential nutrients. Owing to their relative genomic simplicity, Mycoplasmas have been used to develop chassis for biotechnological applications. However, the dearth of robust and precise toolkits for genomic manipulation and tight regulation has hindered any substantial advance. Herein we describe the construction of a robust genetic toolkit for M. pneumoniae, and its successful deployment to engineer synthetic gene switches that control and limit Mycoplasma growth, for biosafety containment applications. We found these synthetic gene circuits to be stable and robust in the long-term, in the context of a minimal cell. With this work, we lay a foundation to develop viable and robust biosafety systems to exploit a synthetic Mycoplasma chassis for live attenuated vectors for therapeutic applications.

  • Journal article
    Viola S, Roseby W, Santabarabara S, Nürnberg D, Assunção R, Dau H, Sellés J, Boussac A, Fantuzzi A, Rutherford AWet al., 2022,

    Impact of energy limitations on function and resilience in long-wavelength Photosystem II

    <jats:title>Abstract</jats:title><jats:p>Photosystem II (PSII) uses the energy from red light to split water and reduce quinone, an energy-demanding process based on chlorophyll a (Chl-a) photochemistry. Two kinds of cyanobacterial PSII can use Chl-d and Chl-f to perform the same reactions using lower energy, far-red light. PSII from <jats:italic>Acaryochloris marina</jats:italic> has Chl-d replacing all but one of its 35 Chl-a, while PSII from <jats:italic>Chroococcidiopsis thermalis</jats:italic>, a facultative far-red species, has just 4 Chl-f and 1 Chl-d and 30 Chl-a. From bioenergetic considerations, the far-red PSII were predicted to lose photochemical efficiency and/or resilience to photodamage. Here, we compare enzyme turnover efficiency, forward electron transfer, back-reactions and photodamage in Chl-f-PSII, Chl-d-PSII and Chl-a-PSII. We show that: i) all types of PSII have a comparable efficiency in enzyme turnover; ii) the modified energy gaps on the acceptor side of Chl-d-PSII favor recombination via P<jats:sub>D1</jats:sub><jats:sup>+</jats:sup>Phe<jats:sup>-</jats:sup> repopulation, leading to increased singlet oxygen production and greater sensitivity to high-light damage compared to Chl-a-PSII and Chl-f-PSII; ii) the acceptor-side energy gaps in Chl-f-PSII are tuned to avoid harmful back reactions, favoring resilience to photodamage over efficiency of light usage. The results are explained by the differences in the redox tuning of the electron transfer cofactors Phe and Q<jats:sub>A</jats:sub> and in the number and layout of the chlorophylls that share the excitation energy with the primary electron donor. PSII has adapted to lower energy in two distinct ways, each appropriate for its specific environment but with different functional penalties.</jats:p>

  • Journal article
    Yi L, Liu B, Nixon PJ, Yu J, Chen Fet al., 2022,

    Recent advances in understanding the structural and functional evolution of FtsH proteases

    , Frontiers in Plant Science, Vol: 13, Pages: 1-16, ISSN: 1664-462X

    The FtsH family of proteases are membrane-anchored, ATP-dependent, zinc metalloproteases. They are universally present in prokaryotes and the mitochondria and chloroplasts of eukaryotic cells. Most bacteria bear a single ftsH gene that produces hexameric homocomplexes with diverse house-keeping roles. However, in mitochondria, chloroplasts and cyanobacteria, multiple FtsH homologues form homo and heterocomplexes with specialised functions in maintaining photosynthesis and respiration. The diversification of FtsH homologues combined with selective pairing of FtsH isomers is a versatile strategy to enable functional adaptation. In this article we summarise recent progress in understanding the evolution, structure and function of FtsH proteases with a focus on the role of FtsH in photosynthesis and respiration.

  • Journal article
    Ehsan M, Wang H, Katsube S, Munk CF, Du Y, Youn T, Yoon S, Byrne B, Loland CJ, Guan L, Kobilka BK, Chae PSet al., 2022,

    Glyco-Steroidal Amphiphiles (GSAs) for membrane protein structural study

    , ChemBioChem: a European journal of chemical biology, Vol: 23, Pages: 1-8, ISSN: 1439-4227

    Integral membrane proteins pose considerable challenges to high resolution structural analysis. Maintaining membrane proteins in their native state during protein isolation is essential for structural study of these bio-macromolecules. Detergents are the most commonly used amphiphilic compounds for stabilizing membrane proteins in solution outside a lipid bilayer. We previously introduced a glyco-diosgenin (GDN) detergent that was shown to be highly effective at stabilizing a wide range of membrane proteins. This steroidal detergent has additionally gained attention due to its compatibility with membrane protein structure study via cryo-EM. However, synthetic inconvenience limits widespread use of GDN in membrane protein study. To improve its synthetic accessibility and to further enhance detergent efficacy for protein stabilization, we designed a new class of glyco-steroid-based detergents using three steroid units: cholestanol, cholesterol and diosgenin. These new detergents were efficiently prepared and showed marked efficacy for protein stabilization in evaluation with a few model membrane proteins including two G protein-coupled receptors. Some new agents were not only superior to a gold standard detergent, DDM (n-dodecyl-β-d-maltoside), but were also more effective than the original GDN at preserving protein integrity long term. These agents represent valuable alternatives to GDN, and are likely to facilitate structural determination of challenging membrane proteins.

  • Journal article
    Cavender-Bares J, Nelson E, Meireles JE, Lasky J, Miteva DA, Nowak D, Pearse W, Helmus M, Zanne AE, Fagan W, otherset al., 2022,

    The hidden value of trees: quantifying the ecosystem services of tree lineages and their major threats across the continental US

    , PLoS
  • Journal article
    Giannos P, Triantafyllidis KK, Geropoulos G, Kechagias Ket al., 2022,

    Persistent hiccups as an atypical presentation of SARS-CoV-2 infection: a systematic review of case reports

    , Frontiers in Neurology, Vol: 13, ISSN: 1664-2295

    Symptoms such as fever, dry cough, dyspnoea, and respiratory distress are commonly described in patients infected with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Recently, a growing number of cases pertained to persistent hiccups have been reported by SARS-CoV-2 infected patients. The aim of this systematic review was to screen the current literature and provide a summary of the reported cases of SARS-CoV-2 infected patients presenting with persistent hiccups. The PubMed, Scoups and Web of Science databases were searched according to PRISMA guidelines from inception until 1, 2020 and December 31, 2020. Case reports or case series that provided a separate clinical description for patients with presenting complaints of persistent hiccups before or after COVID-19 diagnosis, were retrieved. The critical appraisal checklist for case reports provided by the Joanna Briggs Institute (JBI) was employed to evaluate the overall quality of the eligible studies. We identified 13 eligible studies that included 16 patients in which presenting complaints of hiccups were reported by hospitalised and emergency department-admitted COVID-19 patients. The mean duration of hiccups was 4.6 days reported in 87% (14/16) patients. Hypertension was the most common comorbidity present in 50% (8/16) of patients followed by diabetes mellitus (4/16). Moreover, 43% (7/16) of patients received only one medication for managing the hiccups with metoclopramide (5/16) followed by chlorpromazine and baclofen (4/16) used as primary treatment. Equally, 43% of patients (7/16) received dexamethasone followed by azithromycin (5/16), ivermectin (4/16) and ceftriaxone (4/16) for managing the infection from SARS-CoV-2. The majority of patients (14/16) improved after initiation of treatment. Persistent hiccups are possibly a rare symptom clinicians may expect to encounter in patients infected with SARS-CoV-2. Although there is not ample proof to propose causation, increased awareness about the

  • Journal article
    McKenna S, Huse KK, Giblin S, Pearson M, Majid Al Shibar MS, Sriskandan S, Matthews S, Pease JEet al., 2022,

    The role of streptococcal cell-envelope proteases in bacterial evasion of the innate immune system

    , Journal of Innate Immunity, Vol: 14, Pages: 69-88, ISSN: 1662-811X

    Bacteria possess the ability to evolve varied and ingenious strategies to outwit the host immune system, instigating an evolutionary arms race. Proteases are amongst the many weapons employed by bacteria, which specifically cleave and neutralize key signalling molecules required for a coordinated immune response. In this article, we focus on a family of S8 subtilisin-like serine proteases expressed as cell-envelope proteases (CEPs) by group A and group B streptococci. Two of these proteases known as Streptococcus pyogenes CEP (SpyCEP) and C5a peptidase cleave the chemokine CXCL8 and the complement fragment C5a, respectively. Both CXCL8 and C5a are potent neutrophil-recruiting chemokines, and by neutralizing their activity, streptococci evade a key defence mechanism of innate immunity. We review the mechanisms by which CXCL8 and C5a recruit neutrophils and the characterization of SpyCEP and C5a peptidase, including both in vitro and in vivo studies. Recently described structural insights into the function of this CEP family are also discussed. We conclude by examining the progress of prototypic vaccines incorporating SpyCEP and C5a peptidase in their preparation. Since streptococci-producing SpyCEP and C5a peptidase are responsible for a considerable global disease burden, targeting these proteases by vaccination strategies or by small-molecule antagonists should provide protection from and promote the resolution of streptococcal infections.

  • Journal article
    Creedy TJ, Andújar C, Meramveliotakis E, Noguerales V, Overcast I, Papadopoulou A, Morlon H, Vogler AP, Emerson BC, Arribas Pet al., 2022,

    Coming of age for COI metabarcoding of whole organism community DNA: towards bioinformatic harmonisation

    , Molecular Ecology Resources, Vol: 22, Pages: 847-861, ISSN: 1471-8278

    Metabarcoding of DNA extracted from community samples of whole organisms (whole organism community DNA, wocDNA) is increasingly being applied to terrestrial, marine and freshwater metazoan communities to provide rapid, accurate and high resolution data for novel molecular ecology research. The growth of this field has been accompanied by considerable development that builds on microbial metabarcoding methods to develop appropriate and efficient sampling and laboratory protocols for whole organism metazoan communities. However, considerably less attention has focused on ensuring bioinformatic methods are adapted and applied comprehensively in wocDNA metabarcoding. In this study we examined over 600 papers and identified 111 studies that performed COI metabarcoding of wocDNA. We then systematically reviewed the bioinformatic methods employed by these papers to identify the state-of-the-art. Our results show that the increasing use of wocDNA COI metabarcoding for metazoan diversity is characterised by a clear absence of bioinformatic harmonisation, and the temporal trends show little change in this situation. The reviewed literature showed (i) high heterogeneity across pipelines, tasks and tools used, (ii) limited or no adaptation of bioinformatic procedures to the nature of the COI fragment, and (iii) a worrying underreporting of tasks, software and parameters. Based upon these findings we propose a set of recommendations that we think the metabarcoding community should consider to ensure that bioinformatic methods are appropriate, comprehensive and comparable. We believe that adhering to these recommendations will improve the long-term integrative potential of wocDNA COI metabarcoding for biodiversity science.

  • Journal article
    Dechantsreiter S, Ambrose AR, Worboys JD, Lim JME, Liu S, Shah R, Montero MA, Quinn AM, Hussell T, Tannahill GM, Davis DMet al., 2022,

    Heterogeneity in extracellular vesicle secretion by single human macrophages revealed by super-resolution microscopy

  • Journal article
    Curio S, Edwards SC, Suzuki T, McGovern J, Triulzi C, Yoshida N, Jonsson G, Glauner T, Rami D, Wiesheu R, Kilbey A, Purcell RV, Coffelt SB, Guerra Net al., 2022,

    NKG2D signaling regulates IL-17A-producing γδT cells in mice to promote cancer progression

    , Discovery Immunology, ISSN: 2754-2483

    γδT cells are unconventional T cells particularly abundant in mucosal tissues that play an important role in tissue surveillance, homeostasis and cancer. γδT cells recognize stressed cells or cancer cells through the NKG2D receptor to kill these cells and maintain normality. Contrary to the well-established anti-tumor function of these NKG2D-expressing γδT cells, we show here that, in mice, NKG2D regulates a population of pro-tumor γδT cells capable of producing IL-17A. Germline deletion of Klrk1, the gene encoding NKG2D, reduced the frequency of γδT cells in the tumor microenvironment and delayed tumor progression. We further show that blocking NKG2D reduced the capability of γδT cells to produce IL-17A in the pre-metastatic lung and that co-culture of lung T cells with NKG2D ligand-expressing tumor cells specifically increased the frequency of γδT cells. Together, these data support the hypothesis that in a tumor microenvironment where NKG2D ligands are constitutively expressed, γδT cells accumulate in an NKG2D-dependent manner and drive tumor progression by secreting pro-inflammatory cytokines, such as IL-17A.

  • Journal article
    Dobson B, Barry S, Maes-Prior R, Mijic A, Woodward G, Pearse WDet al., 2022,

    Predicting catchment suitability for biodiversity at national scales

    <jats:title>Abstract</jats:title><jats:p>Biomonitoring of water quality and catchment management are often disconnected, due to mismatching scales. Great effort and money is spent each year on routine reach-scale surveying across many sites, particularly in the UK, and typically with a focus on pre-defined indicators of organic pollution to compare observed vs expected subsets of common macroinvertebrate indicator species. Threatened species are often ignored due to their rarity as are many invasive species, which are seen as undesirable even though they are increasingly common in freshwaters, especially in urban ecosystems. However, these taxa are monitored separately for reasons related to biodiversity concerns rather than for gauging water quality. Repurposing such monitoring data could therefore provide important new biomonitoring tools that can help catchment managers to directly link the water quality that they aim to control with the biodiversity that they are trying to protect. Here we used the England Non-Native and Rare/Protected species records that track these two groups of species as a proof-of-concept for linking catchment scale management of freshwater ecosystems and biodiversity to a range of potential drivers across England. We used national land use (Centre for Ecology and Hydrology land cover map) and water quality indicator (Environment Agency water quality data archive) datasets to predict the presence or absence of 48 focal threatened or invasive species of concern routinely sampled by the English Environment Agency at catchment scale, with a median accuracy of 0.81 area under the receiver operating characteristic curve. A variety of water quality indicators and land-use types were useful in predictions, highlighting that future biomonitoring schemes could use such complementary measures to capture a wider spectrum of drivers and responses. In particular, the percentage of a catchment covered by freshwater was the single most

  • Journal article
    McClure C, Aughey G, Hassan A, Butt K, Estacio Gomez A, Duggal A, Ying Sia C, Barber A, Southall Tet al., 2022,

    An auxin-inducible, GAL4-compatible, gene expression system for Drosophila

    , eLife, Vol: 11, Pages: 1-18, ISSN: 2050-084X

    The ability to control transgene expression, both spatially and temporally, is essential for studying model organisms. In Drosophila, spatial control is primarily provided by the GAL4/UAS system, whilst temporal control relies on a temperature-sensitive GAL80 (which inhibits GAL4) and drug-inducible systems. However, these are not ideal. Shifting temperature can impact on many physiological and behavioural traits, and the current drug-inducible systems are either leaky, toxic, incompatible with existing GAL4-driver lines, or do not generate effective levels of expression. Here, we describe the auxin-inducible gene expression system (AGES). AGES relies on the auxin-dependent degradation of a ubiquitously expressed GAL80, and therefore, is compatible with existing GAL4-driver lines. Water-soluble auxin is added to fly food at a low, non-lethal, concentration, which induces expression comparable to uninhibited GAL4 expression. The system works in both larvae and adults, providing a stringent, non-lethal, cost-effective, and convenient method for temporally controlling GAL4 activity in Drosophila.

  • Journal article
    Yordanova M, Evison SEF, Gill RJ, Graystock Pet al., 2022,

    The threat of pesticide and disease co-exposure to managed and wild bee larvae

    , International Journal for Parasitology: Parasites and Wildlife, Vol: 17, Pages: 319-326, ISSN: 2213-2244

    Brood diseases and pesticides can reduce the survival of bee larvae, reduce bee populations, and negatively influence ecosystem biodiversity. However, major gaps persist in our knowledge regarding the routes and implications of co-exposure to these stressors in managed and wild bee brood. In this review, we evaluate the likelihood for co-exposure to brood pathogen and pesticide stressors by examining the routes of potential co-exposure and the possibility for pollen and nectar contaminated with pathogens and pesticides to become integrated into brood food. Furthermore, we highlight ways in which pesticides may increase brood disease morbidity directly, through manipulating host immunity, and indirectly through disrupting microbial communities in the guts of larvae, or compromising brood care provided by adult bees. Lastly, we quantify the brood research bias towards Apis species and discuss the implications the bias has on brood disease and pesticide risk assessment in wild bee communities. We advise that future studies should place a higher emphasis on evaluating bee brood afflictions and their interactions with commonly encountered stressors, especially in wild bee species.

  • Conference paper
    Bell RV, Clarke NK, Isalan M, Alton EWFW, Griesenbach Uet al., 2022,

    Regulated Expression of Lentiviral Vectors Following Administration of an Inducing Molecule

    , Publisher: CELL PRESS, Pages: 419-419, ISSN: 1525-0016
  • Journal article
    Galas A, Haghighat-Khah RE, Cuber P, Benavente M, Gorfinkiel D, Galas Set al., 2022,

    The Impact of COVID-19 Pandemic on Halting Sustainable Development in the Colca y Volcanes de Andagua UNESCO Global Geopark in Peru-Prospects and Future

  • Journal article
    Prentice IC, Villegas-Diaz R, Harrison SP, 2022,

    Accounting for atmospheric carbon dioxide variations in pollen-based reconstructions of past hydroclimates.

    , Global and Planetary Change, Vol: 211, Pages: 1-9, ISSN: 0921-8181

    Changes in atmospheric carbon dioxide (CO2) concentration directly influence the ratio of stomatal water loss to carbon uptake. This ratio (e) is a fundamental quantity for terrestrial ecosystems, as it defines the water requirement for plant growth. Statistical and analogue-based methods used to reconstruct past hydroclimate variables from fossil pollen assemblages do not take account of the effect of CO2 variations on e. Here we present a general, globally applicable method to correct for this effect. The method involves solving an equation that relates e to a climatic moisture index (MI, the ratio of mean annual precipitation to mean annual potential evapotranspiration), mean growing-season temperature, and ambient CO2. The equation is based on the least-cost optimality hypothesis, which predicts how the ratio (χ) of leaf-internal to ambient CO2 varies with vapour pressure deficit (vpd), growing-season temperature and atmospheric pressure, combined with experimental evidence on the response of χ to the CO2 level at which plants have been grown. An empirical relationship based on global climate data is used to relate vpd to MI and growing-season temperature. The solution to the equation allows past MI to be estimated from pollen-reconstructed MI, given past CO2 and temperature. This MI value can be used to estimate mean annual precipitation, accounting for the effects of orbital variations, temperature and cloud cover (inferred from MI) on potential evapotranspiration. A pollen record from semi-arid Spain that spans the last glacial interval is used to illustrate the method. Low CO2 leads to estimated MI being larger than reconstructed MI during glacial times. The CO2 effect on inferred precipitation was partly offset by increased cloud cover; nonetheless, inferred precipitation was greater than present almost throughout the glacial period. This method allows a more robust reconstruction of past hydroclimatic variations than currently available tools.

  • Journal article
    Duncombe L, Howells L, Haughey A, Taylor AV, Kaveh D, Erdenliğ Gϋrbilek S, Dell A, Hitchen PG, Haslam SM, Mandal SS, Ganesh NV, Bundle DR, McGiven Jet al., 2022,

    The tip of brucella O-Polysaccharide is a potent epitope in response to brucellosis infection and enables short synthetic antigens to be superior diagnostic reagents

    , Microorganisms, Vol: 10, Pages: 1-19, ISSN: 2076-2607

    Brucellosis is a global disease and the world’s most prevalent zoonosis. All cases in livestock and most cases in humans are caused by members of the genus Brucella that possess a surface O-polysaccharide (OPS) comprised of a rare monosaccharide 4-deoxy-4-formamido-D-mannopyranose assembled with α1,2 and α1,3 linkages. The OPS of the bacterium is the basis for serodiagnostic tests for brucellosis. Bacteria that also contain the same rare monosaccharide can induce antibodies that cross-react in serological tests. In previous work we established that synthetic oligosaccharides, representing elements of the Brucella A and M polysaccharide structures, were excellent antigens to explore the antibody response in the context of infection, immunisation and cross reaction. These studies suggested the existence of antibodies that are specific to the tip of the Brucella OPS. Sera from naturally and experimentally Brucella abortus-infected cattle as well as from cattle experimentally infected with the cross-reactive bacterium Yersinia enterocolitica O:9 and field sera that cross react in conventional serological assays were studied here with an expanded panel of synthetic antigens. The addition of chemical features to synthetic antigens that block antibody binding to the tip of the OPS dramatically reduced their polyclonal antibody binding capability providing conclusive evidence that the OPS tip (non-reducing end) is a potent epitope. Selected short oligosaccharides, including those that were exclusively α1,2 linked, also demonstrated superior specificity when evaluated with cross reactive sera compared to native smooth lipopolysaccharide (sLPS) antigen and capped native OPS. This surprising discovery suggests that the OPS tip epitope, even though common to both Brucella and Y. enterocolitica O:9, has more specific diagnostic properties than the linear portion of the native antigens. This finding opens the way to the development of improved serological

  • Journal article
    Tuomela K, Ambrose AR, Davis DM, 2022,

    Escaping death: how cancer cells and infected cells resist cell-mediated cytotoxicity

    , Frontiers in Immunology, Vol: 13, ISSN: 1664-3224

    Cytotoxic lymphocytes are critical in our immune defence against cancer and infection. Cytotoxic T lymphocytes and Natural Killer cells can directly lyse malignant or infected cells in at least two ways: granule-mediated cytotoxicity, involving perforin and granzyme B, or death receptor-mediated cytotoxicity, involving the death receptor ligands, tumour necrosis factor-related apoptosis-inducing ligand (TRAIL) and Fas ligand (FasL). In either case, a multi-step pathway is triggered to facilitate lysis, relying on active pro-death processes and signalling within the target cell. Because of this reliance on an active response from the target cell, each mechanism of cell-mediated killing can be manipulated by malignant and infected cells to evade cytolytic death. Here, we review the mechanisms of cell-mediated cytotoxicity and examine how cells may evade these cytolytic processes. This includes resistance to perforin through degradation or reduced pore formation, resistance to granzyme B through inhibition or autophagy, and resistance to death receptors through inhibition of downstream signalling or changes in protein expression. We also consider the importance of tumour necrosis factor (TNF)-induced cytotoxicity and resistance mechanisms against this pathway. Altogether, it is clear that target cells are not passive bystanders to cell-mediated cytotoxicity and resistance mechanisms can significantly constrain immune cell-mediated killing. Understanding these processes of immune evasion may lead to novel ideas for medical intervention.

  • Journal article
    Hidalgo D, Martinez-Ortiz CA, Palsson BO, Jimenez J, Utrilla Jet al., 2022,

    Regulatory perturbations of ribosome allocation in bacteria reshape the growth proteome with a trade-off in adaptation capacity

    , iScience, Vol: 25, ISSN: 2589-0042

    Bacteria regulate their cellular resource allocation to enable fast growth-adaptation to a variety of environmental niches. We studied the ribosomal allocation, growth, and expression profiles of two sets of fast-growing mutants of Escherichia coli K-12 MG1655. Mutants with only three of the seven copies of ribosomal RNA operons grew faster than the wild-type strain in minimal media and show similar phenotype to previously studied fast-growing rpoB mutants. Comparing these two different regulatory perturbations (rRNA promoters or rpoB mutations), we show how they reshape the proteome for growth with a concomitant fitness cost. The fast-growing mutants shared downregulation of hedging functions and upregulated growth functions. They showed longer diauxic shifts and reduced activity of gluconeogenic promoters during glucose-acetate shifts, suggesting reduced availability of the RNA polymerase for expressing hedging proteome. These results show that the regulation of ribosomal allocation underlies the growth/hedging phenotypes obtained from laboratory evolution experiments.

  • Journal article
    Kaplan M, Oikonomou CM, Wood CR, Chreifi G, Subramanian P, Ortega DR, Chang Y-W, Beeby M, Shaffer CL, Jensen GJet al., 2022,

    Novel transient cytoplasmic rings stabilize assembling bacterial flagellar motors

    , EMBO JOURNAL, Vol: 41, ISSN: 0261-4189
  • Journal article
    Kreutzberger MAB, Sobe RC, Sauder AB, Chatterjee S, Peña A, Wang F, Giron JA, Kiessling V, Costa TRD, Conticello VP, Frankel G, Kendall MM, Scharf BE, Egelman EHet al., 2022,

    Flagellin outer domain dimerization modulates motility in pathogenic and soil bacteria from viscous environments.

    , Nature Communications, Vol: 13, Pages: 1-13, ISSN: 2041-1723

    Flagellar filaments function as the propellers of the bacterial flagellum and their supercoiling is key to motility. The outer domains on the surface of the filament are non-critical for motility in many bacteria and their structures and functions are not conserved. Here, we show the atomic cryo-electron microscopy structures for flagellar filaments from enterohemorrhagic Escherichia coli O157:H7, enteropathogenic E. coli O127:H6, Achromobacter, and Sinorhizobium meliloti, where the outer domains dimerize or tetramerize to form either a sheath or a screw-like surface. These dimers are formed by 180° rotations of half of the outer domains. The outer domain sheath (ODS) plays a role in bacterial motility by stabilizing an intermediate waveform and prolonging the tumbling of E. coli cells. Bacteria with these ODS and screw-like flagellar filaments are commonly found in soil and human intestinal environments of relatively high viscosity suggesting a role for the dimerization in these environments.

  • Journal article
    Gregory N, Ewers RM, Chung AYC, Cator LJet al., 2022,

    Oil palm expansion increases the vectorial capacity of dengue vectors in Malaysian Borneo

    , PLoS Neglected Tropical Diseases, Vol: 16, ISSN: 1935-2727

    Changes in land-use and the associated shifts in environmental conditions can have large effects on the transmission and emergence of mosquito-borne disease. Mosquito-borne disease are particularly sensitive to these changes because mosquito growth, reproduction, survival and susceptibility to infection are all thermally sensitive traits, and land use change dramatically alters local microclimate. Predicting disease transmission under environmental change is increasingly critical for targeting mosquito-borne disease control and for identifying hotspots of disease emergence. Mechanistic models offer a powerful tool for improving these predictions. However, these approaches are limited by the quality and scale of temperature data and the thermal response curves that underlie predictions. Here, we used fine-scale temperature monitoring and a combination of empirical, laboratory and temperature-dependent estimates to estimate the vectorial capacity of Aedes albopictus mosquitoes across a tropical forest-oil palm plantation conversion gradient in Malaysian Borneo. We found that fine-scale differences in temperature between logged forest and oil palm plantation sites were not sufficient to produce differences in temperature-dependent demographic trait estimates using published thermal performance curves. However, when measured under field conditions a key parameter, adult abundance, differed significantly between land-use types, resulting in estimates of vectorial capacity that were 1.5 times higher in plantations than in forests. The prediction that oil palm plantations would support mosquito populations with higher vectorial capacity was robust to uncertainties in our adult survival estimates. These results provide a mechanistic basis for understanding the effects of forest conversion to agriculture on mosquito-borne disease risk, and a framework for interpreting emergent relationships between land-use and disease transmission. As the burden of Ae. albopictus-vectored d

  • Journal article
    Kelsall IR, McCrory EH, Xu Y, Scudamore CL, Nanda SK, Mancebo-Gamella P, Wood NT, Knebel A, Matthews SJ, Cohen Pet al., 2022,

    HOIL-1 ubiquitin ligase activity targets unbranched glucosaccharides and is required to prevent polyglucosan accumulation

    , EMBO JOURNAL, Vol: 41, ISSN: 0261-4189
  • Report
    Morris O, Barquín J, Belgrano A, Blanchard J, Bull C, Layer-Dobra K, Lauridsen R, O’Gorman E, Guõbergsson G, Woodward Get al., 2022,

    New strategies for sustainable fisheries management: A case study of Atlantic salmon

    , New strategies for sustainable fisheries management: A case study of Atlantic salmon,, Publisher: The Grantham Institute, 37

    This briefing paper considers the alarming declines in fish stocks in recent years, and how holistic, integrated approaches can help manage fish stocks within biologically sustainable limits. Using Atlantic salmon as a case study, the authors highlight the challenges facing fisheries management and conservation, and the implications for policy and management.

  • Journal article
    Ceballos Escalera Fernandez A, Richards J, Arias MB, Inward DJG, Vogler Aet al., 2022,

    Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers

    , MycoKeys, Vol: 88, Pages: 1-33, ISSN: 1314-4057

    Full taxonomic characterisation of fungal communities is necessary for establishing ecological associations and early detection of pathogens and invasive species. Complex communities of fungi are regularly characterised by metabarcoding using the Internal Transcribed Spacer (ITS) and the Large-Subunit (LSU) gene of the rRNA locus, but reliance on a single short sequence fragment limits the confidence of identification. Here we link metabarcoding from the ITS2 and LSU D1-D2 regions to characterise fungal communities associated with bark beetles (Scolytinae), the likely vectors of several tree pathogens. Both markers revealed similar patterns of overall species richness and response to key variables (beetle species, forest type), but identification against the respective reference databases using various taxonomic classifiers revealed poor resolution towards lower taxonomic levels, especially the species level. Thus, Operational Taxonomic Units (OTUs) could not be linked via taxonomic classifiers across ITS and LSU fragments. However, using phylogenetic trees (focused on the epidemiologically important Sordariomycetes) we placed OTUs obtained with either marker relative to reference sequences of the entire rRNA cistron that includes both loci and demonstrated the largely similar phylogenetic distribution of ITS and LSU-derived OTUs. Sensitivity analysis of congruence in both markers suggested the biologically most defensible threshold values for OTU delimitation in Sordariomycetes to be 98% for ITS2 and 99% for LSU D1-D2. Studies of fungal communities using the canonical ITS barcode require corroboration across additional loci. Phylogenetic analysis of OTU sequences aligned to the full rRNA cistron shows higher success rate and greater accuracy of species identification compared to probabilistic taxonomic classifiers.

  • Journal article
    Adzhar R, Kelley DI, Dong N, George C, Torello Raventos M, Veenendaal E, Feldpausch TR, Phillips OL, Lewis SL, Sonke B, Taedoumg H, Schwantes Marimon B, Domingues T, Arroyo L, Djagbletey G, Saiz G, Gerard Fet al., 2022,

    MODIS Vegetation Continuous Fields tree cover needs calibrating in tropical savannas

    , BIOGEOSCIENCES, Vol: 19, Pages: 1377-1394, ISSN: 1726-4170
  • Journal article
    Ward D, Melbourne-Thomas J, Pecl GT, Evans K, Green M, McCormack PC, Novaglio C, Trebilco R, Bax N, Brasier MJ, Cavan EL, Edgar G, Hunt HL, Jansen J, Jones R, Lea M-A, Makomere R, Mull C, Semmens JM, Shaw J, Tinch D, van Steveninck TJ, Layton Cet al., 2022,

    Safeguarding marine life: conservation of biodiversity and ecosystems

    , REVIEWS IN FISH BIOLOGY AND FISHERIES, Vol: 32, Pages: 65-100, ISSN: 0960-3166

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