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  • Journal article
    Waring B, Gurgel A, Koberle A, Paltsev S, Rogelj Jet al., 2023,

    Natural Climate Solutions must embrace multiple perspectives to ensure synergy with sustainable development

    , Frontiers in Climate, Vol: 5, Pages: 1-7, ISSN: 2624-9553

    To limit global warming to well below 2°C, immediate emissions reductions must be coupled with active removal of greenhouse gases from the atmosphere. 'Natural Climate Solutions' (NCS) achieve atmospheric CO2 reduction through the conservation, restoration, or altered management of natural ecosystems, 1,2 with enormous potential to deliver 'win-win-win' outcomes for climate, nature and society.Yet the supply of high-quality NCS projects does not meet market demand, and projects already underway often fail to deliver their promised benefits, due to a complex set of interacting ecological, social, and financial constraints. How can these cross-sectoral challenges be surmounted? Here we draw from expert elicitation surveys and workshops with professionals across the ecological, sociological, and economic sciences, evaluating differing perspectives on NCS, and suggesting how these might be integrated to address urgent environmental challenges. We demonstrate that funders' perceptions of operational, political, and regulatory risk strongly shape the kinds of NCS projects that are implemented, and the locations where they occur. Because of this, greenhouse gas removal through NCS may fall far short of technical potential.Moreover, socioecological co-benefits of NCS are unlikely to be realized unless the local communities engaged with these projects are granted ownership over implementation and outcomes.

  • Journal article
    Johansson J, Arce A, Gill R, 2023,

    How competition between overlapping generations can influence optimal egg-laying strategies in annual social insects

    , Oecologia, Vol: 202, Pages: 535-547, ISSN: 0029-8549

    Annual social insects are an integral functional group of organisms, particularly in temperate environments. An emblematic part of their annual cycle is the social phase, during which the colony-founding queen rears workers that later assist her in rearing sexual progeny (gynes and drones). In many annual social insects, such as species of bees, wasps, and other groups, developing larvae are provisioned gradually as they develop (progressive provisioning) leading to multiple larval generations being reared simultaneously. We present a model for how the queen in such cases should optimize her egg-laying rate throughout the social phase depending on number-size trade-offs, colony age-structure, and energy balance. Complementing previous theory on optimal allocation between workers vs. sexuals in annual social insects and on temporal egg-laying patterns in solitary insects, we elucidate how resource competition among overlapping larval generations can influence optimal egg-laying strategies. With model parameters informed by knowledge of a common bumblebee species, the optimal egg-laying schedule consists of two temporally separated early broods followed by a more continuous rearing phase, matching empirical observations. However, eggs should initially be laid continuously at a gradually increasing rate when resources are scarce or mortality risks high and in cases where larvae are fully supplied with resources at the egg-laying stage (mass-provisioning). These factors, alongside sexual:worker body size ratios, further determine the overall trend in egg-laying rates over the colony cycle. Our analysis provides an inroad to study and mechanistically understand variation in colony development strategies within and across species of annual social insects.

  • Journal article
    Clive J, Flintham E, Savolainen V, 2023,

    Same-sex sociosexual behaviour is widespread and heritable in male rhesus macaques

    , Nature Ecology and Evolution, Vol: 7, Pages: 1287-1301, ISSN: 2397-334X

    Numerous reports have documented the occurrence of same-sex sociosexual behaviour (SSB) across animal species. However, the distribution of the behaviour within a species is needed to test the theories describing its evolution and maintenance, in particular whether the behaviour is heritable and can therefore evolve by natural selection. Here, we collected detailed observations across three years of social and mounting behaviour of 236 male semi-wild rhesus macaques, which we combined with a pedigree dating back to 1938, to show that SSB was both repeatable (19.35%) and heritable (6.4%). Demographic factors (age and group structure) explained SSB variation only marginally. Furthermore, we found a positive genetic correlation between same-sex mounter and mountee activities, indicating a common basis to different forms of SSB. Finally, we found no evidence of fitness costs to SSB, but show instead that the behaviour mediated coalitionary partnerships that have been linked with improved reproductive success. Together, our results demonstrate that SSB is frequent in rhesus macaques, can evolve, and is not costly, indicating that SSB may be a common feature of primate reproductive ecology.

  • Journal article
    Hui L, Ippolito K, Sarsfield M, Charalambous Met al., 2023,

    Using a self-reflective ePortfolio and feedback dialogue to understand and address problematic feedback expectations

  • Journal article
    Granville NR, Banks-Leite C, 2023,

    Mangrove propagules are limited in their capacity to disperse across long distances

    , JOURNAL OF TROPICAL ECOLOGY, Vol: 39, ISSN: 0266-4674
  • Journal article
    de Lorm TA, Horswill C, Rabaiotti D, Ewers RM, Groom RJ, Watermeyer J, Woodroffe Ret al., 2023,

    Optimizing the automated recognition of individual animals to support population monitoring

    , Ecology and Evolution, Vol: 13, ISSN: 2045-7758

    Reliable estimates of population size and demographic rates are central to assessing the status of threatened species. However, obtaining individual-based demographic rates requires long-term data, which is often costly and difficult to collect. Photographic data offer an inexpensive, noninvasive method for individual-based monitoring of species with unique markings, and could therefore increase available demographic data for many species. However, selecting suitable images and identifying individuals from photographic catalogs is prohibitively time-consuming. Automated identification software can significantly speed up this process. Nevertheless, automated methods for selecting suitable images are lacking, as are studies comparing the performance of the most prominent identification software packages. In this study, we develop a framework that automatically selects images suitable for individual identification, and compare the performance of three commonly used identification software packages; Hotspotter, I3S-Pattern, and WildID. As a case study, we consider the African wild dog, Lycaon pictus, a species whose conservation is limited by a lack of cost-effective large-scale monitoring. To evaluate intraspecific variation in the performance of software packages, we compare identification accuracy between two populations (in Kenya and Zimbabwe) that have markedly different coat coloration patterns. The process of selecting suitable images was automated using convolutional neural networks that crop individuals from images, filter out unsuitable images, separate left and right flanks, and remove image backgrounds. Hotspotter had the highest image-matching accuracy for both populations. However, the accuracy was significantly lower for the Kenyan population (62%), compared to the Zimbabwean population (88%). Our automated image preprocessing has immediate application for expanding monitoring based on image matching. However, the difference in accuracy between population

  • Journal article
    Voisin TB, Couves EC, Tate EW, Bubeck Det al., 2023,

    Dynamics and molecular interactions of GPI-anchored CD59

    , Toxins, Vol: 15, ISSN: 2072-6651

    CD59 is a GPI-anchored cell surface receptor that serves as a gatekeeper to controlling pore formation. It is the only membrane-bound inhibitor of the complement membrane attack complex (MAC), an immune pore that can damage human cells. While CD59 blocks MAC pores, the receptor is co-opted by bacterial pore-forming proteins to target human cells. Recent structures of CD59 in complexes with binding partners showed dramatic differences in the orientation of its ectodomain relative to the membrane. Here, we show how GPI-anchored CD59 can satisfy this diversity in binding modes. We present a PyLipID analysis of coarse-grain molecular dynamics simulations of a CD59-inhibited MAC to reveal residues of complement proteins (C6:Y285, C6:R407 C6:K412, C7:F224, C8β:F202, C8β:K326) that likely interact with lipids. Using modules of the MDAnalysis package to investigate atomistic simulations of GPI-anchored CD59, we discover properties of CD59 that encode the flexibility necessary to bind both complement proteins and bacterial virulence factors.

  • Journal article
    Morissette O, Trueman CN, Sturrock AM, Geffen AJ, Shirai Ket al., 2023,

    Limited evidence for species-specific sensitivity of temperature-dependent fractionation of oxygen stable isotope in biominerals: A meta-analysis

    , METHODS IN ECOLOGY AND EVOLUTION, Vol: 14, Pages: 1719-1731, ISSN: 2041-210X
  • Journal article
    Dong N, Dechant B, Wang H, Wright IJ, Prentice ICet al., 2023,

    Global leaf-trait mapping based on optimality theory

    , Global Ecology and Biogeography, Vol: 32, Pages: 1152-1162, ISSN: 1466-822X

    AimLeaf traits are central to plant function, and key variables in ecosystem models. However recently published global trait maps, made by applying statistical or machine-learning techniques to large compilations of trait and environmental data, differ substantially from one another. This paper aims to demonstrate the potential of an alternative approach, based on eco-evolutionary optimality theory, to yield predictions of spatio-temporal patterns in leaf traits that can be independently evaluated.InnovationGlobal patterns of community-mean specific leaf area (SLA) and photosynthetic capacity (Vcmax) are predicted from climate via existing optimality models. Then leaf nitrogen per unit area (Narea) and mass (Nmass) are inferred using their (previously derived) empirical relationships to SLA and Vcmax. Trait data are thus reserved for testing model predictions across sites. Temporal trends can also be predicted, as consequences of environmental change, and compared to those inferred from leaf-level measurements and/or remote-sensing methods, which are an increasingly important source of information on spatio-temporal variation in plant traits.Main conclusionsModel predictions evaluated against site-mean trait data from > 2,000 sites in the Plant Trait database yielded R2 = 73% for SLA, 38% for Nmass and 28% for Narea. Declining species-level Nmass, and increasing community-level SLA, have both been recently reported and were both correctly predicted. Leaf-trait mapping via optimality theory holds promise for macroecological applications, including an improved understanding of community leaf-trait responses to environmental change.

  • Journal article
    Pal D, Patel M, Boulet F, Sundarraj J, Grant OA, Branco MR, Basu S, Santos SDM, Zabet NR, Scaffidi P, Pradeepa MMet al., 2023,

    H4K16ac activates the transcription of transposable elements and contributes to their <i>cis</i>-regulatory function

    , NATURE STRUCTURAL & MOLECULAR BIOLOGY, Vol: 30, Pages: 935-+, ISSN: 1545-9993
  • Journal article
    Hunt ESE, Felice RN, Tobias JA, Goswami Aet al., 2023,

    Ecological and life-history drivers of avian skull evolution

    , EVOLUTION, Vol: 77, Pages: 1720-1729, ISSN: 0014-3820
  • Other
    Mengoli G, Harrison SP, Prentice IC, 2023,

    Supplementary material to "A global function of climatic aridity accounts for soil moisture stress on carbon assimilation"

  • Journal article
    Tan C, Trew J, Peacock T, Mok KY, Hart C, Lau K, Ni D, Orme CDL, Ransome E, Pearse W, Coleman C, Bailey D, Thakur N, Quantrill J, Sukhova K, Richard D, Kahane L, Woodward G, Bell T, Worledge L, Nunez-Mino J, Barclay W, van Dorp L, Balloux F, Savolainen Vet al., 2023,

    Genomic screening of 16 UK native bat species through conservationist networks uncovers coronaviruses with zoonotic potential

    , Nature Communications, Vol: 14, Pages: 1-13, ISSN: 2041-1723

    There has been limited characterisation of bat-borne coronaviruses in Europe. Here, we screened for coronaviruses in 48 faecal samples from 16 of the 17 bat species breeding in the UK, collected through a bat rehabilitation and conservationist network. We recovered nine (two novel) complete genomes across six bat species: four alphacoronaviruses, a MERS-related betacoronavirus, and four closely related sarbecoviruses. We demonstrate that at least one of these sarbecoviruses can bind and use the human ACE2 receptor for infecting human cells, albeit suboptimally. Additionally, the spike proteins of these sarbecoviruses possess an R-A-K-Q motif, which lies only one nucleotide mutation away from a furin cleavage site (FCS) that enhances infectivity in other coronaviruses, including SARS-CoV-2. However, mutating this motif to an FCS does not enable spike cleavage. Overall, while UK sarbecoviruses would require further molecular adaptations to infect humans, their zoonotic risk is unknown and warrants closer surveillance.

  • Journal article
    Liu Y, Kaffah N, Pandor S, Sartain MJ, Larrouy-Maumus Get al., 2023,

    Ion mobility mass spectrometry for the study of mycobacterial mycolic acids

    , Scientific Reports, Vol: 13, Pages: 1-8, ISSN: 2045-2322

    Lipids are highly structurally diverse molecules involved in a wide variety of biological processes. The involvement of lipids is even more pronounced in mycobacteria, including the human pathogen Mycobacterium tuberculosis, which produces a highly complex and diverse set of lipids in the cell envelope. These lipids include mycolic acids, which are among the longest fatty acids in nature and can contain up to 90 carbon atoms. Mycolic acids are ubiquitously found in mycobacteria and are alpha branched and beta hydroxylated lipids. Discrete modifications, such as alpha, alpha’, epoxy, methoxy, keto, and carboxy, characterize mycolic acids at the species level. Here, we used high precision ion mobility-mass spectrometry to build a database including 206 mass-resolved collision cross sections (CCSs) of mycolic acids originating from the strict human pathogen M. tuberculosis, the opportunistic strains M. abscessus, M. marinum and M. avium, and the nonpathogenic strain M. smegmatis. Primary differences between the mycolic acid profiles could be observed between mycobacterial species. Acyl tail length and modifications were the primary structural descriptors determining CCS magnitude. As a resource for researchers, this work provides a detailed catalogue of the mass-resolved collision cross sections for mycolic acids along with a workflow to generate and analyse the dataset generated.

  • Journal article
    Sharma S, Roy T, Kashyap Y, Buck M, Schumacher J, Goswami D, Gang S, Saraf Met al., 2023,

    Characterizing and demonstrating the role of <i>Klebsiella</i> SSN1 exopolysaccharide in osmotic stress tolerance using neutron radiography

    , SCIENTIFIC REPORTS, Vol: 13, ISSN: 2045-2322
  • Journal article
    Otero-Muras I, Perez-Carrasco R, Banga JR, Barnes CPet al., 2023,

    Automated design of gene circuits with optimal mushroom-bifurcation behaviour

    , iScience, Vol: 26, Pages: 1-15, ISSN: 2589-0042

    Recent advances in synthetic biology are enabling exciting technologies, including the next generation of biosensors, the rational design of cell memory, modulated synthetic cell differentiation and generic multifunctional biocircuits. These novel applications require the design of gene circuits leading to sophisticated behaviours and functionalities. At the same time, designs need to be kept minimal to avoid compromising cell viability. Bifurcation theory addresses such challenges by associating circuit dynamical properties with molecular details of its design. Nevertheless, incorporating bifurcation analysis into automated design processes has not been accomplished yet. This work presents an optimization-based method for the automated design of synthetic gene circuits with specified bifurcation diagrams that employ minimal network topologies. Using this approach, we designed circuits exhibiting the mushroom bifurcation, distilled the most robust topologies and explored its multi-functional behavior. We then outline potential applications in biosensors, memory devices, and synthetic cell differentiation.

  • Journal article
    Gutierrez GV, Perez-Aviles D, Raczka N, Pereira-Arias D, Tijerin-Trivino J, Pereira-Arias LD, Medvigy D, Waring BG, Morrisey E, Brzostek E, Powers JSet al., 2023,

    Throughfall exclusion and fertilization effects on tropical dry forest tree plantations, a large-scale experiment

    , BIOGEOSCIENCES, Vol: 20, Pages: 2143-2160, ISSN: 1726-4170
  • Journal article
    Wu X, Azizan EAB, Goodchild E, Garg S, Hagiyama M, Cabrera CP, Fernandes-Rosa FL, Boulkroun S, Kuan JL, Tiang Z, David A, Murakami M, Mein CA, Wozniak E, Zhao W, Marker A, Buss F, Saleeb RS, Salsbury J, Tezuka Y, Satoh F, Oki K, Udager AM, Cohen DL, Wachtel H, King PJ, Drake WM, Gurnell M, Ceral J, Ryska A, Mustangin M, Wong YP, Tan GC, Solar M, Reincke M, Rainey WE, Foo RS, Takaoka Y, Murray SA, Zennaro M-C, Beuschlein F, Ito A, Brown MJet al., 2023,

    Somatic mutations of CADM1 in aldosterone-producing adenomas and gap junction-dependent regulation of aldosterone production

    , Nature Genetics, Vol: 55, Pages: 1009-1021, ISSN: 1061-4036

    Aldosterone-producing adenomas (APAs) are the commonest curable cause of hypertension. Most have gain-of-function somatic mutations of ion channels or transporters. Herein we report the discovery, replication and phenotype of mutations in the neuronal cell adhesion gene CADM1. Independent whole exome sequencing of 40 and 81 APAs found intramembranous p.Val380Asp or p.Gly379Asp variants in two patients whose hypertension and periodic primary aldosteronism were cured by adrenalectomy. Replication identified two more APAs with each variant (total, n = 6). The most upregulated gene (10- to 25-fold) in human adrenocortical H295R cells transduced with the mutations (compared to wildtype) was CYP11B2 (aldosterone synthase), and biological rhythms were the most differentially expressed process. CADM1 knockdown or mutation inhibited gap junction (GJ)-permeable dye transfer. GJ blockade by Gap27 increased CYP11B2 similarly to CADM1 mutation. Human adrenal zona glomerulosa (ZG) expression of GJA1 (the main GJ protein) was patchy, and annular GJs (sequelae of GJ communication) were less prominent in CYP11B2-positive micronodules than adjacent ZG. Somatic mutations of CADM1 cause reversible hypertension and reveal a role for GJ communication in suppressing physiological aldosterone production.

  • Journal article
    Tobias JA, 2023,

    First record of Campina Thrush Turdus arthuri for Bolivia

    , Bulletin of the British Ornithologists' Club, Vol: 143, Pages: 260-264, ISSN: 0007-1595

    An adult thrush trapped in a mist-net near Guayaramerin, dpto. Beni, Bolivia, in April 2005, was initially identified as Black-billed Thrush Turdus ignobilis although several subtle plumage features appeared to differ from the expected race T. i. debilis. These features match those of Campina Thrush T. arthuri, a cryptic species subsequently split from Black-billed Thrush based on molecular evidence, and now known to occur widely in shrubby thickets and stunted campina forest across much of Amazonia. This record extends the known distribution of T. arthuri south-west from the nearest known localities in Amazonas and Rondônia, Brazil. T. arthuri is presumably resident in north-west dpto. Beni in suitable habitat, and potentially occurs elsewhere in Bolivia from Pando to eastern Santa Cruz in similar campina-like habitats associated with weathered outcrops of the Brazilian Shield.

  • Journal article
    Mozaheb N, Rasouli P, Kaur M, Van Der Smissen P, Larrouy-Maumus G, Mingeot-Leclercq M-Pet al., 2023,

    A Mildly Acidic Environment Alters Pseudomonas aeruginosa Virulence and Causes Remodeling of the Bacterial Surface

  • Journal article
    Illukkumbura R, Hirani N, Borrego-Pinto J, Bland T, Ng K, Hubatsch L, McQuade J, Endres RG, Goehring NWet al., 2023,

    Design principles for selective polarization of PAR proteins by cortical flows

    , JOURNAL OF CELL BIOLOGY, Vol: 222, ISSN: 0021-9525
  • Journal article
    Cocker ATH, Guethlein LA, Parham P, 2023,

    The CD56-CD16+NK cell subset in chronic infections

    , BIOCHEMICAL SOCIETY TRANSACTIONS, Vol: 51, Pages: 1201-1212, ISSN: 0300-5127
  • Journal article
    Tan S, Wang H, Prentice IC, Yang K, Nóbrega RLB, Liu X, Wang Y, Yang Yet al., 2023,

    Towards a universal evapotranspiration model based on optimality principles

    , Agricultural and Forest Meteorology, Vol: 336, Pages: 1-11, ISSN: 0168-1923

    Natural resource management requires knowledge of terrestrial evapotranspiration (ET). Most existing numeric models for ET include multiple plant- or ecosystem-type specific parameters that require calibration. This is a significant source of uncertainty under changing environmental conditions. A novel ET model with no type−specific parameters was developed recently. Based on the coupling the diffusion (via stomata) of water and carbon dioxide (CO2), this model predicts canopy conductance based on environmental conditions using eco-evolutionary optimality principles that apply to all plant types. Transpiration (T) and ET are calculated from canopy conductance using the Penman-Monteith equation for T and a universal empirical function for the T:ET ratio. Here, the model is systematically evaluated at globally distributed eddy-covariance sites and river basins. Site-scale modelled ET agrees well with flux data (r = 0.81, root mean square error = 0.73 mm day–1 in 23,623 records) and modelled ET in 39 river basins agrees well with the ET estimated by monthly water budget using two runoff datasets (r = 0.62 and 0.66, respectively). Modelled global patterns of ET are consistent with existing global ET products. The model's universality, parsimony and accuracy combine to indicate a broad potential field of application in resource management and global change science.

  • Journal article
    David A, Sternberg MJE, 2023,

    Protein structure-based evaluation of missense variants: Resources, challenges and future directions.

    , Current Opinion in Structural Biology, Vol: 80, Pages: 1-8, ISSN: 0959-440X

    We provide an overview of the methods that can be used for protein structure-based evaluation of missense variants. The algorithms can be broadly divided into those that calculate the difference in free energy (ΔΔG) between the wild type and variant structures and those that use structural features to predict the damaging effect of a variant without providing a ΔΔG. A wide range of machine learning approaches have been employed to develop those algorithms. We also discuss challenges and opportunities for variant interpretation in view of the recent breakthrough in three-dimensional structural modelling using deep learning.

  • Journal article
    Germain RR, Feng S, Chen G, Graves GR, Tobias JA, Rahbek C, Lei F, Fjeldsa J, Hosner PA, Gilbert MTP, Zhang G, Nogues-Bravo Det al., 2023,

    Species-specific traits mediate avian demographic responses under past climate change

    , NATURE ECOLOGY & EVOLUTION, Vol: 7, Pages: 862-872, ISSN: 2397-334X
  • Journal article
    Matthews TJ, Wayman JP, Whittaker RJ, Cardoso P, Hume JP, Sayol F, Proios K, Martin TE, Baiser B, Borges PAV, Kubota Y, dos Anjos L, Tobias JA, Soares FC, Si X, Ding P, Mendenhall CD, Sin YCK, Rheindt FE, Triantis KA, Guilhaumon F, Watson DM, Brotons L, Battisti C, Chu O, Rigal Fet al., 2023,

    A global analysis of avian island diversity-area relationships in the Anthropocene

    , ECOLOGY LETTERS, Vol: 26, Pages: 965-982, ISSN: 1461-023X
  • Journal article
    Larrouy-Maumus G, Dortet L, Nix ID, Maier T, Oberheitmann B, Sparbier K, Kostrzewa Met al., 2023,

    Two-site study on performances of a commercially available MALDI-TOF MS-based assay for the detection of colistin resistance in Escherichia coli

    , European Journal of Clinical Microbiology and Infectious Diseases: an international journal on pathogenesis, diagnosis, epidemiology, therapy, and prevention of infectious diseases, Vol: 42, Pages: 669-679, ISSN: 0934-9723

    Colistin is a last resort drug for the treatment of multiple drug-resistant (MDR) Gram-negative bacterial infections. Rapid methods to detect resistance are highly desirable. Here, we evaluated the performance of a commercially available MALDI-TOF MS-based assay for colistin resistance testing in Escherichia coli at two different sites. Ninety clinical E. coli isolates were provided by France and tested in Germany and UK using a MALDI-TOF MS-based colistin resistance assay. Lipid A molecules of the bacterial cell membrane were extracted using the MBT Lipid Xtract Kit™ (RUO; Bruker Daltonics, Germany). Spectra acquisition and evaluation were performed by the MBT HT LipidART Module of MBT Compass HT (RUO; Bruker Daltonics) on a MALDI Biotyper® sirius system (Bruker Daltonics) in negative ion mode. Phenotypic colistin resistance was determined by broth microdilution (MICRONAUT MIC-Strip Colistin, Bruker Daltonics) and used as a reference. Comparing the results of the MALDI-TOF MS-based colistin resistance assay with the data of the phenotypic reference method for the UK, sensitivity and specificity for the detection of colistin resistance were 97.1% (33/34) and 96.4% (53/55), respectively. Germany showed 97.1% (33/34) sensitivity and 100% (55/55) specificity for the detection of colistin resistance by MALDI-TOF MS. Applying the MBT Lipid Xtract™ Kit in combination with MALDI-TOF MS and dedicated software showed excellent performances for E. coli. Analytical and clinical validation studies must be performed to demonstrate the performance of the method as a diagnostic tool.

  • Journal article
    Wisden W, Franks NP, 2023,

    Biochemical pathways of sleep

    , CELL RESEARCH, Vol: 33, Pages: 417-418, ISSN: 1001-0602
  • Journal article
    Kavil S, Laverick A, Whitfield CJ, Banks AM, Howard TPet al., 2023,

    Methods for embedding cell-free protein synthesis reactions in macro-scale hydrogels

    , Journal of Visualized Experiments, Pages: 1-14, ISSN: 1940-087X

    Synthetic gene networks provide a platform for scientists and engineers to design and build novel systems with functionality encoded at a genetic level. While the dominant paradigm for the deployment of gene networks is within a cellular chassis, synthetic gene networks may also be deployed in cell-free environments. Promising applications of cell-free gene networks include biosensors, as these devices have been demonstrated against biotic (Ebola, Zika, and SARS-CoV-2 viruses) and abiotic (heavy metals, sulfides, pesticides, and other organic contaminants) targets. Cell-free systems are typically deployed in liquid form within a reaction vessel. Being able to embed such reactions in a physical matrix, however, may facilitate their broader application in a wider set of environments. To this end, methods for embedding cell-free protein synthesis (CFPS) reactions in a variety of hydrogel matrices have been developed. One of the key properties of hydrogels conducive to this work is the high-water reconstitution capacity of hydrogel materials. Additionally, hydrogels possess physical and chemical characteristics that are functionally beneficial. Hydrogels can be freeze-dried for storage and rehydrated for use later. Two step-by-step protocols for the inclusion and assay of CFPS reactions in hydrogels are presented. First, a CFPS system can be incorporated into a hydrogel via rehydration with a cell lysate. The system within the hydrogel can then be induced or expressed constitutively for complete protein expression through the hydrogel. Second, cell lysate can be introduced to a hydrogel at the point of polymerization, and the entire system can be freeze-dried and rehydrated at a later point with an aqueous solution containing the inducer for the expression system encoded within the hydrogel. These methods have the potential to allow for cell-free gene networks that confer sensory capabilities to hydrogel materials, with the potential for deployment beyond the laboratory

  • Journal article
    Agirre J, Atanasova M, Bagdonas H, Ballard CB, Basle A, Beilsten-Edmands J, Borges RJ, Brown DG, Burgos-Marmol JJ, Berrisford JM, Bond PS, Caballero I, Catapano L, Chojnowski G, Cook AG, Cowtan KD, Croll TI, Debreczeni JE, Devenish NE, Dodson EJ, Drevon TR, Emsley P, Evans G, Evans PR, Fando M, Foadi J, Fuentes-Montero L, Garman EF, Gerstel M, Gildea RJ, Hatti K, Hekkelman ML, Heuser P, Hoh SW, Hough MA, Jenkins HT, Jimenez E, Joosten RP, Keegan RM, Keep N, Krissinel EB, Kolenko P, Kovalevskiy O, Lamzin VS, Lawson DM, Lebedev AA, Leslie AGW, Lohkamp B, Long F, Maly M, McCoy AJ, McNicholas SJ, Medina A, Millan C, Murray JW, Murshudov GN, Nicholls RA, Noble MEM, Oeffner R, Pannu NS, Parkhurst JM, Pearce N, Pereira J, Perrakis A, Powell HR, Read RJ, Rigden DJ, Rochira W, Sammito M, Rodriguez FS, Sheldrick GM, Shelley KL, Simkovic F, Simpkin AJ, Skubak P, Sobolev E, Steiner RA, Stevenson K, Tews I, Thomas JMH, Thorn A, Trivino Valls J, Uski V, Uson I, Vagin A, Velankar S, Vollmar M, Walden H, Waterman D, Wilson KS, Winn MD, Winter G, Wojdyr M, Yamashita Ket al., 2023,

    The CCP4 suite: integrative software for macromolecular crystallography

    , Acta Crystallographica Section D: Structural Biology, Vol: 79, Pages: 449-461, ISSN: 2059-7983

    The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world.

This data is extracted from the Web of Science and reproduced under a licence from Thomson Reuters. You may not copy or re-distribute this data in whole or in part without the written consent of the Science business of Thomson Reuters.

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