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  • Journal article
    Gabiane G, Yen P-S, Failloux A-B, 2022,

    Aedes mosquitoes in the emerging threat of urban yellow fever transmission

    , REVIEWS IN MEDICAL VIROLOGY, Vol: 32, ISSN: 1052-9276
  • Journal article
    Katsanos D, Barkoulas M, 2022,

    Targeted DamID in C. elegans reveals a direct role for LIN-22 and NHR-25 in antagonising the epidermal stem cell fate

    , Science Advances, Vol: 8, Pages: 1-15, ISSN: 2375-2548

    Transcription factors are key players in gene networks controlling cell fate specification during development. In multicellular organisms, they often display complex patterns of expression and binding to their targets, hence tissue-specificity is required in the characterisation of transcription factor-target interactions. We introduce here Targeted DamID (TaDa) as a method for tissue-specific transcription factor target identification in intact C. elegans animals. We employ TaDa to recover targets in the epidermis for two key transcription factors, the HES1 homologue LIN-22 and the NR5A1/2 nuclear hormone receptor NHR-25. We demonstrate a direct link between LIN-22 and the Wnt signalling pathway through repression of the Frizzled receptor lin-17. We also find a direct role for NHR-25 in promoting cell differentiation via repressing the expression of stem cell-promoting GATA factors. Our results expand our understanding of the epidermal gene network and highlight the potential of TaDa to dissect the architecture of tissue-specific gene regulatory networks.

  • Journal article
    Colgan TJ, Arce AN, Gill RJ, Ramos Rodrigues A, Kanteh A, Duncan EJ, Li L, Chittka L, Wurm Yet al., 2022,

    Genomic Signatures of Recent Adaptation in a Wild Bumblebee

  • Journal article
    Piot N, Schweiger O, Meeus I, Yañez O, Straub L, Villamar-Bouza L, De la Rúa P, Jara L, Ruiz C, Malmstrøm M, Mustafa S, Nielsen A, Mänd M, Karise R, Tlak-Gajger I, Özgör E, Keskin N, Diévart V, Dalmon A, Gajda A, Neumann P, Smagghe G, Graystock P, Radzevičiūtė R, Paxton RJ, de Miranda JRet al., 2022,

    Honey bees and climate explain viral prevalence in wild bee communities on a continental scale

    , Scientific Reports, Vol: 12, ISSN: 2045-2322

    Viruses are omnipresent, yet the knowledge on drivers of viral prevalence in wild host populations is often limited. Biotic factors, such as sympatric managed host species, as well as abiotic factors, such as climatic variables, are likely to impact viral prevalence. Managed and wild bees, which harbor several multi-host viruses with a mostly fecal-oral between-species transmission route, provide an excellent system with which to test for the impact of biotic and abiotic factors on viral prevalence in wild host populations. Here we show on a continental scale that the prevalence of three broad host viruses: the AKI-complex (Acute bee paralysis virus, Kashmir bee virus and Israeli acute paralysis virus), Deformed wing virus, and Slow bee paralysis virus in wild bee populations (bumble bees and solitary bees) is positively related to viral prevalence of sympatric honey bees as well as being impacted by climatic variables. The former highlights the need for good beekeeping practices, including Varroa destructor management to reduce honey bee viral infection and hive placement. Furthermore, we found that viral prevalence in wild bees is at its lowest at the extreme ends of both temperature and precipitation ranges. Under predicted climate change, the frequency of extremes in precipitation and temperature will continue to increase and may hence impact viral prevalence in wild bee communities.

  • Journal article
    Beal J, Telmer CA, Vignoni A, Boada Y, Baldwin GS, Hallett L, Lee T, Selvarajah V, Billerbeck S, Brown B, Cai G-N, Cai L, Eisenstein E, Kiga D, Ross D, Alperovich N, Sprent N, Thompson J, Young EM, Endy D, Haddock-Angelli Tet al., 2022,

    Multicolor plate reader fluorescence calibration

  • Journal article
    Hao M, Ye F, Jovanovic M, Kotta-Loizou I, Xu Q, Qin X, Buck M, Zhang X, Wang Met al., 2022,

    Structures of Class I and Class II transcription complexes reveal the molecular basis of RamA-dependent transcription activation

    , Advanced Science, Vol: 9, Pages: 1-10, ISSN: 2198-3844

    Transcription activator RamA is linked to multidrug resistance of Klebsiella pneumoniae through controlling genes that encode efflux pumps (acrA) and porin-regulating antisense RNA (micF). In bacteria, σ70, together with activators, controls the majority of genes by recruiting RNA polymerase (RNAP) to the promoter regions. RNAP and σ70 form a holoenzyme that recognizes -35 and -10 promoter DNA consensus sites. Many activators bind upstream from the holoenzyme and can be broadly divided into two classes. RamA acts as a class I activator on acrA and class II activator on micF, respectively. The authors present biochemical and structural data on RamA in complex with RNAP-σ70 at the two promoters and the data reveal the molecular basis for how RamA assembles and interacts with core RNAP and activates transcription that contributes to antibiotic resistance. Further, comparing with CAP/TAP complexes reveals common and activator-specific features in activator binding and uncovers distinct roles of the two C-terminal domains of RNAP α subunit.

  • Journal article
    Chik HYJ, Estrada C, Wang Y, Tank P, Lord A, Schroeder Jet al., 2022,

    Individual variation in reaction norms but no directional selection in reproductive plasticity of a wild passerine population

    , ECOLOGY AND EVOLUTION, Vol: 12, ISSN: 2045-7758
  • Journal article
    Sperandio V, Frankel G, 2022,

    Editorial overview: Host-microbe interactions: friends, foes and frenemies

    , CURRENT OPINION IN MICROBIOLOGY, Vol: 65, Pages: VIII-X, ISSN: 1369-5274
  • Journal article
    Mullineaux Sanders C, Kozik Z, Sanchez Garrido J, Hopkins EGD, Choudhary JS, Frankel Get al., 2022,

    Citrobacter rodentium infection induces persistent molecular changes and interferon gamma-dependent major histocompatibility complex class II expression in the colonic epithelium

    , mBio, Vol: 13, Pages: 1-18, ISSN: 2150-7511

    Most studies of infections at mucosal surfaces have focused on the acute phase of the disease. Consequently, little is known about the molecular processes that underpin tissue recovery and the long-term consequences postinfection. Here, we conducted temporal deep quantitative proteomic analysis of colonic intestinal epithelial cells (cIECs) from mice infected with the natural mouse pathogen Citrobacter rodentium over time points corresponding to the late steady-state phase (10 days postinfection [DPI]), the clearance phase (13 to 20 DPI), and 4 weeks after the pathogen has been cleared (48 DPI). C. rodentium, which relies on a type III secretion system to infect, is used to model infections with enteropathogenic and enterohemorrhagic Escherichia coli. We observe a strong upregulation of inflammatory signaling and nutritional immunity responses during the clearance phase of the infection. Despite morphological tissue recovery, chromogranin B (ChgB)-positive endocrine cells remained significantly below baseline levels at 48 DPI. In contrast, we observed an increased abundance of proteins involved in antigen processing and presentation 4 weeks after pathogen clearance. In particular, long-term changes were characterized by a persistent interferon gamma (IFN-γ) response and the expression of major histocompatibility complex class II (MHCII) molecules in 60% of the EpCAM+ cIECs, which were not seen in Ifnγ−/− mice. Nonetheless, both wild-type and Ifnγ−/− mice mounted similar systemic and colonic IgG responses to C. rodentium and were equally protected from rechallenge, suggesting that cIEC MHCII is not necessary for protective immunity against C. rodentium.

  • Journal article
    Wong Y, Rosindell J, 2022,

    Dynamic visualisation of million-tip trees: the OneZoom project

    , Methods in Ecology and Evolution, Vol: 13, Pages: 303-313, ISSN: 2041-210X

    1. The complete tree of life is now available, but methods to visualise it are still needed to meet needs in research, teaching and science communication. Dynamic visualisation of million-tip trees requires many challenges in data synthesis, data handling and computer graphics to be overcome.2. Our approach is to automate data processing, synthesise data from a wide range of available sources, then to feed these data to a client-side visualisation engine in parts. We develop a way to store the whole tree topology locally in a highly compressed form, then dynamically populate metadata such as text and images as the user explores.3. The result is a seamless and smooth way to explore the complete tree of life, including images and metadata, even on relatively old mobile devices.4. The underlying methods developed have applications that transcend tree of life visualisation. For the whole complete tree, we describe automated ID mappings between well known resources without resorting to taxonomic name resolution, automated methods to collate sets of public domain representative images for higher taxa, and an index to measure public interest of individual species. 5. The visualisation layout and the client user interface are both abstracted components of the codebase enabling other zoomable tree layouts to be swapped in, and supporting multiple applications including exhibition kiosks and digital art.6. After 10 years of work, our tree of life explorer is now broadly complete, it has attracted nearly 1.5 million online users, and is backed by a novel long-term sustainability plan. We conclude our description of the OneZoom project by suggesting the next challenges that need to be solved in this field: extinct species and guided tours around the tree.

  • Journal article
    MacGregor-Chatwin C, Nurnberg DJ, Jackson PJ, Vasilev C, Hitchcock A, Ho M-Y, Shen G, Gisriel CJ, Wood WHJ, Mahbub M, Selinger VM, Johnson MP, Dickman MJ, Rutherford AW, Bryant DA, Hunter CNet al., 2022,

    Changes in supramolecular organization of cyanobacterial thylakoid membrane complexes in response to far-red light photoacclimation

    , SCIENCE ADVANCES, Vol: 8, ISSN: 2375-2548
  • Journal article
    Wong Y, Rosindell J, 2022,

    Dynamic visualisation of million‐tip trees: The OneZoom project

    , Methods in Ecology and Evolution, Vol: 13, Pages: 303-313, ISSN: 2041-210X
  • Journal article
    Kirwan GM, Broughton RK, Lees AC, Ottenburghs J, Tobias JAet al., 2022,

    The ‘Meidum geese’ revisited: Early historical art is not a suitable basis for taxonomic speculation

    , Journal of Archaeological Science: Reports, Vol: 41, Pages: 1-5, ISSN: 2352-409X

    Romilio (2021) used a taxonomic scoring system to compare differences between three species of geese (Anseriformes) depicted in the Chapel of Itet, one of which he speculated might represent an undescribed (presumably now extinct) species. Despite some apparently distinctive features, the depiction has traditionally been associated with the well-known modern species, red-breasted goose (Branta ruficollis). We discuss limitations in applying the Tobias et al. (2010) scoring system to cases such as this, for which it was not designed, and we outline the many pitfalls that must be considered when attempting to identify historical artwork of birds using examples discussed recently in the ornithological literature. We conclude that the illustrations proposed by Romilio to represent a new Branta goose species are within the range of known plumage variation and potential artistic licence for red-breasted goose, and that this very probably is the species upon which the artwork was based. More generally, we caution against applying the Tobias criteria to cases where a series of specimens cannot be measured, and highlight the difficulties of using illustrations to inform taxonomy.

  • Journal article
    Au HKE, Isalan M, Mielcarek M, 2022,

    Gene therapy advances: a meta-analysis of AAV usage in clinical settings

    , Frontiers in Medicine, Vol: 8, Pages: 1-14, ISSN: 2296-858X

    Adeno-associated viruses (AAVs) are the safest and most effective gene delivery vehicles to drive long-term transgene expression in gene therapy. While animal studies have shown promising results, the translatability of AAVs into clinical settings has been partly limited due to their restricted gene packaging capacities, off-target transduction, and immunogenicity. In this study, we analysed over two decades of AAV applications, in 136 clinical trials. This meta-analysis aims to provide an up-to-date overview of the use and successes of AAVs in clinical trials, while evaluating the approaches used to address the above challenges. First, this study reveals that the speed of novel AAV development has varied between therapeutic areas, with particular room for improvement in Central Nervous System disorders, where development has been slow. Second, the lack of dose-dependent toxicity and efficacy data indicates that optimal dosing regimes remain elusive. Third, more clinical data on the effectiveness of various immune-modulation strategies and gene editing approaches are required to direct future research and to accelerate the translation of AAV-mediated gene therapy into human applications.

  • Journal article
    Amin H, Ilangovan A, Costa TRD, 2022,

    Publisher Correction: Architecture of the outer-membrane core complex from a conjugative type IV secretion system.

    , Nature Communications, Vol: 13, Pages: 1-1, ISSN: 2041-1723
  • Journal article
    Russell M, Cator L, 2022,

    No impact of biocontrol agent’s predation cues on development time or size of surviving Aedes al-bopictus under optimal nutritional availability

    , Insects, Vol: 13, ISSN: 2075-4450

    Cyclopoid copepods have been applied successfully to limit populations of highly invasive Aedes albopictus mosquitoes that can transmit diseases of public health importance. However, there is concern that changes in certain mosquito traits, induced by exposure to copepod predation, might increase the risk of disease transmission. In this study, third instar Ae. albopictus larvae (focal individuals) were exposed to Megacyclops viridis predator cues associated with both the consumption of newly hatched mosquito larvae and attacks on focal individuals. The number of newly hatched larvae surrounding each focal larva was held constant to control for density effects on size, and the focal individual’s day of pupation and wing length were recorded for each replicate. Exposing late instar Ae. albopictus to predation decreased their chances of surviving to adulthood, and three focal larvae that died in the predator treatment showed signs of melanisation, indicative of wounding. Among surviving focal Ae. albopictus, no significant difference in either pupation day or wing length was observed due to copepod predation. The absence of significant sublethal impacts from M. viridis copepod predation on surviving later stage larvae in this analysis supports the use of M. viridis as a biocontrol agent against Ae. albopictus.

  • Journal article
    Mandela E, Stubenrauch CJ, Ryoo D, Hwang H, Cohen EJ, Torres VL, Deo P, Webb CT, Huang C, Schittenhelm RB, Beeby M, Gumbart JC, Lithgow T, Hay IDet al., 2022,

    Adaptation of the periplasm to maintain spatial constraints essential for cell envelope processes and cell viability

    , ELIFE, Vol: 11, ISSN: 2050-084X
  • Journal article
    Turnbull C, Carrington S, 2022,

    A hard graft problem solved for key global food crops

    , Nature, Vol: 602, Pages: 214-215, ISSN: 0028-0836
  • Journal article
    Dwijayanti A, Storch M, Stan G-B, Baldwin GSet al., 2022,

    A modular RNA interference system for multiplexed gene regulation

    , Nucleic Acids Research, Vol: 50, ISSN: 0305-1048

    The rational design and realisation of simple-to-use genetic control elements that are modular, orthogonal and robust is essential to the construction of predictable and reliable biological systems of increasing complexity. To this effect, we introduce modular Artificial RNA interference (mARi), a rational, modular and extensible design framework that enables robust, portable and multiplexed post-transcriptional regulation of gene expression in Escherichia coli. The regulatory function of mARi was characterised in a range of relevant genetic contexts, demonstrating its independence from other genetic control elements and the gene of interest, and providing new insight into the design rules of RNA based regulation in E. coli, while a range of cellular contexts also demonstrated it to be independent of growth-phase and strain type. Importantly, the extensibility and orthogonality of mARi enables the simultaneous post-transcriptional regulation of multi-gene systems as both single-gene cassettes and poly-cistronic operons. To facilitate adoption, mARi was designed to be directly integrated into the modular BASIC DNA assembly framework. We anticipate that mARi-based genetic control within an extensible DNA assembly framework will facilitate metabolic engineering, layered genetic control, and advanced genetic circuit applications.

  • Conference paper
    Martinez-Gili L, Gordon H, Blad W, McDonald JAK, Holmes E, Marchesi JR, Harbord Met al., 2022,

    Gut bacteria composition and familiality echo Inflammatory Bowel Disease type and pathological spectrum

    , 17th Congress of ECCO, Publisher: Oxford University Press, Pages: I601-I602, ISSN: 1873-9946

    BackgroundInflammatory bowel disease (IBD) aetiology encompasses genetic and environmental factors. Twin studies provide valuable insights to the familial degree (shared genetics and environment) of observed phenotypes. We characterised the gut bacterial composition of twins with IBD to find taxa associated with disease and estimate their familiality.MethodsFaecal samples were collected from 88 monozygotic (MZ) and dizygotic (DZ) twin pairs concordant or discordant for Crohn’s disease (CD; 26 MZ; 19 DZ) or ulcerative colitis (UC; 16 MZ; 27 DZ). The 16S rRNA gene was sequenced and amplicon sequence variants (ASV) generated. ANCOM software was used to assess differences in IBD vs. non-IBD, stratifying by disease type (CD/UC) and adjusting for age, gender and smoking. Twin pair and zygosity were added as random effects to estimate familiality, defined as percentage of variation due to common environment and genetics. IBD-affected twins were used for differences in disease location or treatment. Participants reporting antibiotic/probiotic treatment within the last 3 months or with a stoma/pouch were not included. In UC, surgery-naive patients were compared to an excluded subset who underwent ileostomy or pouch surgery without any recent antibiotic courses.ResultsDisease concordance in MZ twins was higher in CD (54%) than UC (19%). Alpha diversity was lower in CD, but not UC, and in ileostomy and pouch vs. surgery-naive UC. Principal component analysis showed that CD-affected twins clustered apart from non-IBD ones (Figure 1A). Familiality was lower in CD, with 5% of ASVs having familiality > 50%, compared to 17% in UC (Figure 1B). Two Lachnospirales order ASVs were less abundant in UC, while 15 ASVs from Clostridia, Bacteroidia, Bacilli and Coriobacteriia classes differentiated CD from non-IBD. Firmicutes were higher in CD (β= 0.95; 95%CI [0.34,1.56]), while no phyla changed in UC. Veillonella, Barnesiella, Faecalimonas and Holdemania genera had opposite t

  • Journal article
    Russell MC, Herzog C, Gajewskic Z, Ramsayd C, El Moustaid F, Even MV, Gottdenkere NL, Hermanni SL, Power AG, McCall Aet al., 2022,

    Both consumptive and non-consumptive effects of predators impact mosquito populations and have implications for disease transmission

    , eLife, Vol: 11, Pages: 1-23, ISSN: 2050-084X

    Predator-prey interactions influence prey traits through both consumptive and non-consumptive effects, and variation in these traits can shape vector-borne disease dynamics. Meta-analysis methods were employed to generate predation effect sizes by different categories of predators and mosquito prey. This analysis showed that multiple families of aquatic predators are effective in consumptively reducing mosquito survival, and that the survival of Aedes, Anopheles, and Culex mosquitoes is negatively impacted by consumptive effects of predators. Mosquito larval size was found to play a more important role in explaining the heterogeneity of consumptive effects from predators than mosquito genus. Mosquito survival and body size were reduced by non-consumptive effects of predators, but development time was not significantly impacted. In addition, Culex vectors demonstrated predator avoidance behavior during oviposition. The results of this meta-analysis suggest that predators limit disease transmission by reducing both vector survival and vector size, and that associations between drought and human West Nile virus cases could be driven by the vector behavior of predator avoidance during oviposition. These findings are likely to be useful to infectious disease modelers who rely on vector traits as predictors of transmission.

  • Journal article
    Huxley PJ, Murray KA, Pawar S, Cator LJet al., 2022,

    Competition and resource depletion shape the thermal response of population fitness in Aedes aegypti

  • Journal article
    Tuomela K, Mukherjee D, Ambrose AR, Harikrishnan A, Mole H, Hurlstone A, Onfelt B, Honeychurch J, Davis DMet al., 2022,

    Radiotherapy transiently reduces the sensitivity of cancer cells to lymphocyte cytotoxicity

  • Journal article
    Fantuzzi A, Haniewicz P, Farci D, Loi MC, Park K, Büchel C, Bochtler M, Rutherford AW, Piano Det al., 2022,

    Bicarbonate Activation of Monomeric Photosystem II-PsbS/Psb27 Complex

    <jats:title>Abstract</jats:title><jats:p>In thylakoid membranes, Photosystem II monomers from the stromal lamellae contain the subunits PsbS and Psb27 (PSIIm-S/27), while Photosystem II monomers from granal regions (PSIIm) lack these subunits. Here, we have isolated and characterised these two types of Photosystem II complexes. The PSIIm-S/27 showed enhanced fluorescence, the near-absence of oxygen evolution, as well as limited and slow electron transfer from Q<jats:sub>A</jats:sub> to Q<jats:sub>B</jats:sub> compared to the near-normal activities in the granal PSIIm. However, when bicarbonate was added to the PSIIm-S/27, water splitting and Q<jats:sub>A</jats:sub> to Q<jats:sub>B</jats:sub> electron transfer rates were comparable to those in granal PSIIm. The findings suggest that the binding of PsbS and/or Psb27 inhibits forward electron transfer and lowers the binding affinity for the bicarbonate. This can be rationalized in terms of the recently discovered photoprotection role played by bicarbonate binding via the redox tuning of the Q<jats:sub>A</jats:sub>/Q<jats:sub>A</jats:sub><jats:sup>•−</jats:sup> couple, which controls the charge recombination route, and this limits chlorophyll triplet mediated <jats:sup>1</jats:sup>O<jats:sub>2</jats:sub> formation (Brinkert K et al. (2016) Proc Natl Acad Sci U S A. 113(43):12144-12149). These findings suggest that PSIIm-S/27 is an intermediate in the assembly of PSII in which PsbS and/or Psb27 restrict PSII activity while in transit, by using a bicarbonate-mediated switch and protective mechanism.</jats:p><jats:sec><jats:title>One sentence summary</jats:title><jats:p>A photosystem II monomer with PsbS and Psb27 as additional subunits, is inactive as isolated but activated by bicarbonate, and is attributed to be a late-stage intermediate in photoassembly.&l

  • Journal article
    Matthews S, 2022,

    Secondary structure and X-ray crystallographic analysis of the Glideosome-Associated Connector (GAC) from Toxoplasma gondii

    , Crystals, Vol: 12, Pages: 1-6, ISSN: 2073-4352

    A model for parasitic motility has been proposed in which parasite filamentous actin (F-actin) is attached to surface adhesins by a large component of the glideosome, known as the glideosome-associated connector protein (GAC). This large 286 kDa protein interacts at the cytoplasmic face of the plasma membrane with the phosphatidic acid-enriched inner leaflet and cytosolic tails of surface adhesins to connect them to the parasite actomyosin system. GAC is observed initially to the conoid at the apical pole and re-localised with the glideosome to the basal pole in gliding parasite. GAC presumably functions in force transmission to surface adhesins in the plasma membrane and not in force generation. Proper connection between F-actin and the adhesins is as important for motility and invasion as motor operation itself. This notion highlights the need for new structural information on GAC interactions, which has eluded the field since its discovery. We have obtained crystals that diffracted to 2.6–2.9 Å for full-length GAC from Toxoplasma gondii in native and selenomethionine-labelled forms. These crystals belong to space group P212121; cell dimensions are roughly a = 119 Å, b = 123 Å, c = 221 Å, α = 90°, β = 90° and γ = 90° with 1 molecule per asymmetric unit, suggesting a more compact conformation than previously proposed

  • Journal article
    Leimberger KG, Dalsgaard B, Tobias JA, Wolf C, Betts MGet al., 2022,

    The evolution, ecology, and conservation of hummingbirds and their interactions with flowering plants

    , Biological Reviews, Vol: 97, ISSN: 1464-7931

    The ecological co-dependency between plants and hummingbirds is a classic example of a mutualistic interaction: hummingbirds rely on floral nectar to fuel their rapid metabolisms, and more than 7000 plant species rely on hummingbirds for pollination. However, threats to hummingbirds are mounting, with 10% of 366 species considered globally threatened and 60% in decline. Despite the important ecological implications of these population declines, no recent review has examined plant–hummingbird interactions in the wider context of their evolution, ecology, and conservation. To provide this overview, we (i) assess the extent to which plants and hummingbirds have coevolved over millions of years, (ii) examine the mechanisms underlying plant–hummingbird interaction frequencies and hummingbird specialization, (iii) explore the factors driving the decline of hummingbird populations, and (iv) map out directions for future research and conservation. We find that, despite close associations between plants and hummingbirds, acquiring evidence for coevolution (versus one-sided adaptation) is difficult because data on fitness outcomes for both partners are required. Thus, linking plant–hummingbird interactions to plant reproduction is not only a major avenue for future coevolutionary work, but also for studies of interaction networks, which rarely incorporate pollinator effectiveness. Nevertheless, over the past decade, a growing body of literature on plant–hummingbird networks suggests that hummingbirds form relationships with plants primarily based on overlapping phenologies and trait-matching between bill length and flower length. On the other hand, species-level specialization appears to depend primarily on local community context, such as hummingbird abundance and nectar availability. Finally, although hummingbirds are commonly viewed as resilient opportunists that thrive in brushy habitats, we find that range size and forest dependency are key predic

  • Journal article
    Furniss RCD, Kaderabkova N, Barker D, Bernal P, Maslova E, Antwi AAA, McNeil HE, Pugh HL, Dortet L, Blair JMA, Larrouy-Maumus G, McCarthy RR, Gonzalez D, Mavridou DAet al., 2022,

    Breaking antimicrobial resistance by disrupting extracytoplasmic protein folding

    , ELIFE, Vol: 11, ISSN: 2050-084X
  • Journal article
    Budzak J, Jones R, Tschudi C, Kolev N, Rudenko Get al., 2022,

    An assembly of nuclear bodies associates with the active VSG expression site in African trypanosomes

    , Nature Communications, Vol: 13, Pages: 1-17, ISSN: 2041-1723

    A Variant Surface Glycoprotein (VSG) coat protects bloodstream form Trypanosomabrucei. Prodigious amounts of VSG mRNA (~7-10% total) are generated from a single RNApolymerase I (Pol I) transcribed VSG expression site (ES), necessitating extremely highlevels of localised splicing. We show that splicing is required for processive ES transcription,and describe novel ES-associated T. brucei nuclear bodies. In bloodstream formtrypanosomes, the expression site body (ESB), spliced leader array body (SLAB), NUFIPbody and Cajal bodies all frequently associate with the active ES. This assembly of nuclearbodies appears to facilitate the extraordinarily high levels of transcription and splicing at theactive ES. In procyclic form trypanosomes, the NUFIP body and SLAB do not appear tointeract with the Pol I transcribed procyclin locus. The congregation of a restricted numberof nuclear bodies at a single active ES, provides an attractive mechanism for how monoallelicES transcription is mediated.

  • Journal article
    Anthony MA, Crowther TW, van der Linde S, Suz LM, Bidartondo MI, Cox F, Schaub M, Rautio P, Ferretti M, Vesterdal L, De Vos B, Dettwiler M, Eickenscheidt N, Schmitz A, Meesenburg H, Andreae H, Jacob F, Dietrich H-P, Waldner P, Gessler A, Frey B, Schramm O, van den Bulk P, Hensen A, Averill Cet al., 2022,

    Forest tree growth is linked to mycorrhizal fungal composition and function across Europe

    , The ISME Journal: multidisciplinary journal of microbial ecology, Vol: 16, ISSN: 1751-7362

    Most trees form symbioses with ectomycorrhizal fungi (EMF) which influence access to growth-limiting soil resources. Mesocosm experiments repeatedly show that EMF species differentially affect plant development, yet whether these effects ripple up to influence the growth of entire forests remains unknown. Here we tested the effects of EMF composition and functional genes relative to variation in well-known drivers of tree growth by combining paired molecular EMF surveys with high-resolution forest inventory data across 15 European countries. We show that EMF composition was linked to a three-fold difference in tree growth rate even when controlling for the primary abiotic drivers of tree growth. Fast tree growth was associated with EMF communities harboring high inorganic but low organic nitrogen acquisition gene proportions and EMF which form contact versus medium-distance fringe exploration types. These findings suggest that EMF composition is a strong bio-indicator of underlying drivers of tree growth and/or that variation of forest EMF communities causes differences in tree growth. While it may be too early to assign causality or directionality, our study is one of the first to link fine-scale variation within a key component of the forest microbiome to ecosystem functioning at a continental scale.

  • Journal article
    Haines MC, Carling B, Marshall J, Shenshin VA, Baldwin GS, Storch M, Freemont Pet al., 2022,

    basicsynbio and the BASIC SEVA collection: Software and vectors for an established DNA assembly method

    <jats:title>Abstract</jats:title><jats:p>Standardized DNA assembly methods utilizing modular components provide a powerful framework to explore design spaces and iterate through Design-Build-Test-Learn cycles. Biopart Assembly Standard for Idempotent Cloning (BASIC) DNA assembly uses modular parts and linkers, is highly accurate, easy to automate, free for academic and commercial use, while enabling simple hierarchical assemblies through an idempotent format. These features facilitate various applications including pathway engineering, ribosome binding site tuning, fusion protein engineering and multiplexed gRNA expression. In this work we present basicsynbio, an open-source software encompassing a Web App (<jats:ext-link xmlns:xlink="" ext-link-type="uri" xlink:href=""></jats:ext-link>) and Python Package (<jats:ext-link xmlns:xlink="" ext-link-type="uri" xlink:href=""></jats:ext-link>). With basicsynbio, users can access commonly used BASIC parts and linkers while robustly designing new parts and assemblies with exception handling for common design errors. Users can export sequence data and create build instructions for manual or acoustic liquid-handling platforms. The generation of build instructions relies on the BasicBuild Open Standard which is easily parsed for bespoke workflows and is serializable in Java Script Object Notation for transfer and storage. We demonstrate basicsynbio by assembling a collection of 30 vectors using various sequences including modules from the Standard European Vector Architecture (SEVA). The BASIC SEVA collection is compatible with BASIC and Golden Gate using BsaI. It encompasses vectors containing six antibiotic resistance mark

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