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  • Journal article
    Saunders T, Adkins J, Beard KH, Atwood TB, Waring BGet al., 2023,

    Herbivores influence biogeochemical processes by altering litter quality and quantity in a subarctic wetland

    , BIOGEOCHEMISTRY, Vol: 166, Pages: 67-85, ISSN: 0168-2563
  • Journal article
    Bailey AJ, Ukegbu CV, Giorgalli M, Besson TRB, Christophides GK, Vlachou Det al., 2023,

    Intracellular<i> Plasmodium</i> aquaporin 2 is important for sporozoite production in the mosquito vector and malaria transmission

    , PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 120, ISSN: 0027-8424
  • Journal article
    Sammon D, Krueger A, Busse-Wicher M, Morgan RM, Haslam S, Schumann B, Briggs D, Hohenester Eet al., 2023,

    Molecular mechanism of decision-making in glycosaminoglycan biosynthesis

    , Nature Communications, Vol: 14, ISSN: 2041-1723

    Two major glycosaminoglycan types, heparan sulfate (HS) and chondroitin sulfate (CS), control many aspects of development and physiology in a type-specific manner. HS and CS are attached to core proteins via a common linker tetrasaccharide, but differ in their polymer backbones. How core proteins are specifically modified with HS or CS has been an enduring mystery. By reconstituting glycosaminoglycan biosynthesis in vitro, we establish that the CS-initiating N-acetylgalactosaminyltransferase CSGALNACT2 modifies all glycopeptide substrates equally, whereas the HS-initiating N-acetylglucosaminyltransferase EXTL3 is selective. Structure-function analysis reveals that acidic residues in the glycopeptide substrate and a basic exosite in EXTL3 are critical for specifying HS biosynthesis. Linker phosphorylation by the xylose kinase FAM20B accelerates linker synthesis and initiation of both HS and CS, but has no effect on the subsequent polymerisation of the backbone. Our results demonstrate that modification with CS occurs by default and must be overridden by EXTL3 to produce HS.
  • Journal article
    Liang G, Reed SC, Stark JM, Waring BGet al., 2023,

    Unraveling mechanisms underlying effects of wetting-drying cycles on soil respiration in a dryland

    , BIOGEOCHEMISTRY, ISSN: 0168-2563
  • Journal article
    El Omari K, Duman R, Mykhaylyk V, Orr CM, Latimer-Smith M, Winter G, Grama V, Qu F, Bountra K, Kwong HS, Romano M, Reis RI, Vogeley L, Vecchia L, Owen CD, Wittmann S, Renner M, Senda M, Matsugaki N, Kawano Y, Bowden TA, Moraes I, Grimes JM, Mancini EJ, Walsh MA, Guzzo CR, Owens RJ, Jones EY, Brown DG, Stuart DI, Beis K, Wagner Aet al., 2023,

    Experimental phasing opportunities for macromolecular crystallography at very long wavelengths

    , COMMUNICATIONS CHEMISTRY, Vol: 6, ISSN: 2399-3669
  • Journal article
    Blackhurst L, Gilestro G, 2023,

    Ethoscopy and ethoscope-lab: a framework for behavioural analysis to lower entrance barrier and aid reproducibility behavioural analysis to lower entrance barrier and aidreproducibility

    , Bioinformatics Advances, Vol: 3, ISSN: 2635-0041

    High-throughput analysis of behaviour is a pivotal instrument in modern neuroscience, allowing researchers to combine modern genetics breakthrough to unbiased, objective, reproducible experimental approaches. To this extent, we recently created an open-source hardware platform (ethoscope (Geissmann et al., 2017)) that allows for inexpensive, accessible, high-throughput analysis of behaviour in Drosophila or other animal models. Here we equip ethoscopes with a Python framework for data analysis, ethoscopy, designed to be a user-friendly yet powerful platform, meeting the requirements of researchers with limited coding expertise as well as experienced data scientists. Ethoscopy is best consumed in a prebakedJupyter-based docker container, ethoscope-lab, to improve accessibility and to encourage the use of notebooks as anatural platform to share post-publication data analysis. Ethoscopy is a Python package available on GitHub and PyPi. Ethoscope-lab is a docker container available on DockerHub. A landing page aggregating all the code and documentation is available at https://lab.gilest.ro/ethoscopy.
  • Journal article
    Costa TRD, Patkowski JB, Mace K, Christie PJ, Waksman Get al., 2023,

    Structural and functional diversity of type IV secretion systems

    , Nature Reviews Microbiology, ISSN: 1740-1526

    Considerable progress has been made in recent years in the structural and molecular biology of type IV secretion systems in Gram-negative bacteria. The latest advances have substantially improved our understanding of the mechanisms underlying the recruitment and delivery of DNA and protein substrates to the extracellular environment or target cells. In this Review, we aim to summarize these exciting structural and molecular biology findings and to discuss their functional implications for substrate recognition, recruitment and translocation, as well as the biogenesis of extracellular pili. We also describe adaptations necessary for deploying a breadth of processes, such as bacterial survival, host–pathogen interactions and biotic and abiotic adhesion. We highlight the functional and structural diversity that allows this extremely versatile secretion superfamily to function under different environmental conditions and in different bacterial species. Additionally, we emphasize the importance of further understanding the mechanism of type IV secretion, which will support us in combating antimicrobial resistance and treating type IV secretion system-related infections.
  • Journal article
    O'Gorman EJ, Zhao L, Kordas RL, Dudgeon S, Woodward Get al., 2023,

    Warming indirectly simplifies food webs through effects on apex predators

    , NATURE ECOLOGY & EVOLUTION, ISSN: 2397-334X
  • Journal article
    Kikuchi C, Antonopoulos A, Wang S, Maemura T, Karamanska R, Lee C, Thompson AJ, Dell A, Kawaoka Y, Haslam SM, Paulson JCet al., 2023,

    Glyco-engineered MDCK cells display preferred receptors of H3N2 influenza absent in eggs used for vaccines

    , Nature Communications, Vol: 14, ISSN: 2041-1723

    Evolution of human H3N2 influenza viruses driven by immune selection has narrowed the receptor specificity of the hemagglutinin (HA) to a restricted subset of human-type (Neu5Acα2-6 Gal) glycan receptors that have extended poly-LacNAc (Galβ1-4GlcNAc) repeats. This altered specificity has presented challenges for hemagglutination assays, growth in laboratory hosts, and vaccine production in eggs. To assess the impact of extended glycan receptors on virus binding, infection, and growth, we have engineered N-glycan extended (NExt) cell lines by overexpressing β3-Ν-acetylglucosaminyltransferase 2 in MDCK, SIAT, and hCK cell lines. Of these, SIAT-NExt cells exhibit markedly increased binding of H3 HAs and susceptibility to infection by recent H3N2 virus strains, but without impacting final virus titers. Glycome analysis of these cell lines and allantoic and amniotic egg membranes provide insights into the importance of extended glycan receptors for growth of recent H3N2 viruses and relevance to their production for cell- and egg-based vaccines.
  • Journal article
    Jonsson R, Bjorling A, Midtgaard SR, Jensen GV, Skar-Gislinge N, Arleth L, Matthews S, Krogfelt KA, Jenssen Het al., 2023,

    Aggregative adherence fimbriae form compact structures as seen by SAXS

    , SCIENTIFIC REPORTS, Vol: 13, ISSN: 2045-2322
  • Journal article
    Bentham AR, De la Concepcion JC, Benjumea JV, Kourelis J, Jones S, Mendel M, Stubbs J, Stevenson CEM, Maidment JHR, Youles M, Zdrzałek R, Kamoun S, Banfield MJet al., 2023,

    Allelic compatibility in plant immune receptors facilitates engineering of new effector recognition specificities

    , The Plant Cell, Vol: 35, Pages: 3809-3827, ISSN: 1040-4651

    Engineering the plant immune system offers genetic solutions to mitigate crop diseases caused by diverse agriculturally significant pathogens and pests. Modification of intracellular plant immune receptors of the nucleotide-binding leucine-rich repeat (NLR) receptor superfamily for expanded recognition of pathogen virulence proteins (effectors) is a promising approach for engineering disease resistance. However, engineering can cause NLR autoactivation, resulting in constitutive defense responses that are deleterious to the plant. This may be due to plant NLRs associating in highly complex signaling networks that coevolve together, and changes through breeding or genetic modification can generate incompatible combinations, resulting in autoimmune phenotypes. The sensor and helper NLRs of the rice (Oryza sativa) NLR pair Pik have coevolved, and mismatching between noncoevolved alleles triggers constitutive activation and cell death. This limits the extent to which protein modifications can be used to engineer pathogen recognition and enhance disease resistance mediated by these NLRs. Here, we dissected incompatibility determinants in the Pik pair in Nicotiana benthamiana and found that heavy metal-associated (HMA) domains integrated in Pik-1 not only evolved to bind pathogen effectors but also likely coevolved with other NLR domains to maintain immune homeostasis. This explains why changes in integrated domains can lead to autoactivation. We then used this knowledge to facilitate engineering of new effector recognition specificities, overcoming initial autoimmune penalties. We show that by mismatching alleles of the rice sensor and helper NLRs Pik-1 and Pik-2, we can enable the integration of synthetic domains with novel and enhanced recognition specificities. Taken together, our results reveal a strategy for engineering NLRs, which has the potential to allow an expanded set of integrations and therefore new disease resistance specificities in plants.
  • Journal article
    Tossell K, Yu X, Giannos P, Anuncibay Soto B, Nollet M, Yustos R, Miracca G, Vicente M, Miao A, Hsieh B, Ma Y, Vysstoski A, Constandinou T, Franks N, Wisden Wet al., 2023,

    Somatostatin neurons in prefrontal cortex initiate sleep preparatory behavior and sleep via the preoptic and lateral hypothalamus

    , Nature Neuroscience, Vol: 26, Pages: 1805-1819, ISSN: 1097-6256

    The prefrontal cortex (PFC) enables mammals to respond to situations, including internal states, with appropriate actions. One such internal state could be ‘tiredness’. Here, using activity tagging in the mouse PFC, we identified particularly excitable, fast-spiking, somatostatin-expressing, γ-aminobutyric acid (GABA) (PFCSst-GABA) cells that responded to sleep deprivation. These cells projected to the lateral preoptic (LPO) hypothalamus and the lateral hypothalamus (LH). Stimulating PFCSst-GABA terminals in the LPO hypothalamus caused sleep-preparatory behavior (nesting, elevated theta power and elevated temperature), and stimulating PFCSst-GABA terminals in the LH mimicked recovery sleep (non-rapid eye-movement sleep with higher delta power and lower body temperature). PFCSst-GABA terminals had enhanced activity during nesting and sleep, inducing inhibitory postsynaptic currents on diverse cells in the LPO hypothalamus and the LH. The PFC also might feature in deciding sleep location in the absence of excessive fatigue. These findings suggest that the PFC instructs the hypothalamus to ensure that optimal sleep takes place in a suitable place.
  • Journal article
    Savolainen V, 2023,

    Environmental DNA helps reveal reef shark distribution across a remote archipelago

    , Ecological Indicators, Vol: 154, Pages: 1-10, ISSN: 1470-160X

    Environmental DNA (eDNA) methods are being increasingly used in proof-of-concept studies to detect shark species, many populations of which are experiencing severe declines. These methods are widely seen as the future of biodiversity monitoring, but they have yet to become established as routine monitoring techniques for elasmobranch species. Here, we developed species-specific quantitative PCR assays for the detection of grey reef shark (Carcharhinus amblyrhynchos) and silvertip shark (Carcharhinus albimarginatus). We assessed whether species-specific eDNA methods could infer the distribution of the two species around the atolls of the Chagos Archipelago, which, despite being surrounded by a large marine protected area, experience contrasting levels of illegal fishing leading to heterogeneity in shark population densities. We found that eDNA detections were significantly reduced and sporadic around the northern atolls, which are under high pressure from illegal fishing. By contrast eDNA detections of both species were ubiquitous and consistent around the highly protected atoll Diego Garcia. We postulate that current levels of illegal, unreported and unregulated (IUU) fishing is having a significant impact on the shark community in the northern atolls and suppressing local reef shark populations. In the northern atolls we also employed visual and acoustic telemetry techniques to reveal the distribution of reef sharks. We found that despite eDNA samples being taken directly after visual surveys, detection results did not correlate, suggesting a need for further optimisation of eDNA methods for detecting sharks. However, both species were detected by eDNA in sites where they were not observed, highlighting that the scale of the sampling environment must be considered when inferring eDNA results and showing that eDNA methods can be used to fill gaps in data from more established monitoring techniques. We conclude that eDNA methods should be used in combination with oth
  • Journal article
    Devenish AJM, Schmitter P, Jellason NP, Esmail N, Abdi NM, Adanu SK, Adolph B, Al-Zubi M, Amali AA, Barron J, Chapman ASA, Chausson AM, Chibesa M, Davies J, Dugan E, Edwards GI, Egeru A, Gebrehiwot T, Griffiths GH, Haile A, Hunga HG, Igbine L, Jarju OM, Keya F, Khalifa M, Ledoux WA, Lejissa LT, Loupa P, Lwanga J, Mapedza ED, Marchant R, McLoud T, Mukuyu P, Musah LM, Mwanza M, Mwitwa J, Neina D, Newbold T, Njogo S, Robinson EJZ, Singini W, Umar BB, Wesonga F, Willcock S, Yang J, Tobias JAet al., 2023,

    One hundred priority questions for the development of sustainable food systems in Sub-Saharan Africa

    , Land, Vol: 12, ISSN: 2073-445X

    Sub-Saharan Africa is facing an expected doubling of human population and tripling of food demand over the next quarter century, posing a range of severe environmental, political, and socio-economic challenges. In some cases, key Sustainable Development Goals (SDGs) are in direct conflict, raising difficult policy and funding decisions, particularly in relation to trade-offs between food production, social inequality, and ecosystem health. In this study, we used a horizon-scanning approach to identify 100 practical or research-focused questions that, if answered, would have the greatest positive impact on addressing these trade-offs and ensuring future productivity and resilience of food-production systems across sub-Saharan Africa. Through direct canvassing of opinions, we obtained 1339 questions from 331 experts based in 55 countries. We then used online voting and participatory workshops to produce a final list of 100 questions divided into 12 thematic sections spanning topics from gender inequality to technological adoption and climate change. Using data on the background of respondents, we show that perspectives and priorities can vary, but they are largely consistent across different professional and geographical contexts. We hope these questions provide a template for establishing new research directions and prioritising funding decisions in sub-Saharan Africa.
  • Journal article
    Egli M, Rapp Wright H, Oloyede O, Francis W, Preston-Allen R, Friedman S, Woodward G, Piel FB, Barron LPet al., 2023,

    A One-Health environmental risk assessment of contaminants of emerging concern in London’s waterways throughout the SARS-CoV-2 pandemic

    , Environment International, Vol: 180, ISSN: 0160-4120

    The SARS-CoV-2 pandemic had huge impacts on global urban populations, activity and health, yet little is known about attendant consequences for urban river ecosystems. We detected significant changes in occurrence and risks from contaminants of emerging concern (CECs) in waterways across Greater London (UK) during the pandemic. We were able to rapidly identify and monitor large numbers of CECs in n=390 samples across 2019–2021 using novel direct-injection liquid chromatography-mass spectrometry methods for scalable targeted analysis, suspect screening and prioritisation of CEC risks. At total of 10,029 measured environmental concentrations (MECs) were obtained for 66 unique CECs. Pharmaceutical MECs decreased during lockdown in 2020 in the R. Thames (p≤0.001), but then increased significantly in 2021 (p ≤0.01). For the tributary rivers, the R. Lee, Beverley Brook, R. Wandle and R. Hogsmill were the most impacted primarily via wastewater treatment plant effluent and combined sewer overflows. For the R. Hosgmill in particular, pharmaceutical MEC trends were generally correlated with NHS prescription statistics, likely reflecting limited wastewater dilution. Suspect screening of ∼1,200 compounds tentatively identified 25 additional CECs at the five impacted sites, including metabolites such as O-desmethylvenlafaxine, an EU Watch List compound. Lastly, risk quotients (RQs) ≥0.1 were calculated for 21 compounds across the whole Greater London freshwater catchment, of which 7 were of medium risk (RQ ≥1.0) and three were in the high-risk category (RQ ≥10), including imidacloprid (RQ=19.6), azithromycin (15.7) and diclofenac (10.5). This is the largest spatiotemporal dataset of its kind for any major capital city globally and the first for Greater London, representing ∼16 % of the population of England, and delivering a foundational One Health case study in the third largest city in Europe across a global pandemic.
  • Journal article
    de Ceglia R, Ledonne A, Litvin DG, Lind BL, Carriero G, Latagliata EC, Bindocci E, Di Castro MA, Savtchouk I, Vitali I, Ranjak A, Congiu M, Canonica T, Wisden W, Harris K, Mameli M, Mercuri N, Telley L, Volterra Aet al., 2023,

    Specialized astrocytes mediate glutamatergic gliotransmission in the CNS.

    , Nature, Vol: 622, Pages: 120-129

    Multimodal astrocyte-neuron communications govern brain circuitry assembly and function1. For example, through rapid glutamate release, astrocytes can control excitability, plasticity and synchronous activity2,3 of synaptic networks, while also contributing to their dysregulation in neuropsychiatric conditions4-7. For astrocytes to communicate through fast focal glutamate release, they should possess an apparatus for Ca2+-dependent exocytosis similar to neurons8-10. However, the existence of this mechanism has been questioned11-13 owing to inconsistent data14-17 and a lack of direct supporting evidence. Here we revisited the astrocyte glutamate exocytosis hypothesis by considering the emerging molecular heterogeneity of astrocytes18-21 and using molecular, bioinformatic and imaging approaches, together with cell-specific genetic tools that interfere with glutamate exocytosis in vivo. By analysing existing single-cell RNA-sequencing databases and our patch-seq data, we identified nine molecularly distinct clusters of hippocampal astrocytes, among which we found a notable subpopulation that selectively expressed synaptic-like glutamate-release machinery and localized to discrete hippocampal sites. Using GluSnFR-based glutamate imaging22 in situ and in vivo, we identified a corresponding astrocyte subgroup that responds reliably to astrocyte-selective stimulations with subsecond glutamate release events at spatially precise hotspots, which were suppressed by astrocyte-targeted deletion of vesicular glutamate transporter 1 (VGLUT1). Furthermore, deletion of this transporter or its isoform VGLUT2 revealed specific contributions of glutamatergic astrocytes in cortico-hippocampal and nigrostriatal circuits during normal behaviour and pathological processes. By uncovering this atypical subpopulation of specialized astrocytes in the adult brain, we provide insights into the complex roles of astrocytes in central nervous system (CNS) physiology and diseases, and ide
  • Journal article
    Hazra S, Moulick D, Mukherjee A, Sahib S, Chowardhara B, Majumdar A, Upadhyay MK, Yadav P, Roy P, Santra SC, Mandal S, Nandy S, Dey Aet al., 2023,

    Evaluation of efficacy of non-coding RNA in abiotic stress management of field crops: Current status and future prospective.

    , Plant Physiol Biochem, Vol: 203

    Abiotic stresses are responsible for the major losses in crop yield all over the world. Stresses generate harmful ROS which can impair cellular processes in plants. Therefore, plants have evolved antioxidant systems in defence against the stress-induced damages. The frequency of occurrence of abiotic stressors has increased several-fold due to the climate change experienced in recent times and projected for the future. This had particularly aggravated the risk of yield losses and threatened global food security. Non-coding RNAs are the part of eukaryotic genome that does not code for any proteins. However, they have been recently found to have a crucial role in the responses of plants to both abiotic and biotic stresses. There are different types of ncRNAs, for example, miRNAs and lncRNAs, which have the potential to regulate the expression of stress-related genes at the levels of transcription, post-transcription, and translation of proteins. The lncRNAs are also able to impart their epigenetic effects on the target genes through the alteration of the status of histone modification and organization of the chromatins. The current review attempts to deliver a comprehensive account of the role of ncRNAs in the regulation of plants' abiotic stress responses through ROS homeostasis. The potential applications ncRNAs in amelioration of abiotic stresses in field crops also have been evaluated.
  • Conference paper
    Yong H, Chan KLA, Larrouy-Maumus G, Okor J, Munday M, Hall AR, Quaglia A, Oben JAet al., 2023,

    URINARY METABOLITE BIOMARKERS CHANGES IN OBESITY- INDUCED NAFLD AND OBESITY- INDUCED NAFLD PLUS XX.

    , Meeting of the American-Association-for-the-Study-of-Liver-Diseases (AASLD), Publisher: LIPPINCOTT WILLIAMS & WILKINS, Pages: S893-S894, ISSN: 0270-9139
  • Journal article
    Murray J, Smith AP, Simpson M, Elizondo KM, Aitkenhead-Peterson JA, Waring Bet al., 2023,

    Climate, as well as branch-level processes, drive canopy soil abundance and chemistry

    , GEODERMA, Vol: 438, ISSN: 0016-7061
  • Journal article
    Adachi H, Sakai T, Kourelis J, Pai H, Gonzalez Hernandez JL, Utsumi Y, Seki M, Maqbool A, Kamoun Set al., 2023,

    Jurassic NLR: conserved and dynamic evolutionary features of the atypically ancient immune receptor ZAR1

    , The Plant Cell, Vol: 35, Pages: 3662-3685, ISSN: 1040-4651

    Plant nucleotide-binding leucine-rich repeat (NLR) immune receptors generally exhibit hallmarks of rapid evolution, even at the intraspecific level. We used iterative sequence similarity searches coupled with phylogenetic analyses to reconstruct the evolutionary history of HOPZ-ACTIVATED RESISTANCE1 (ZAR1), an atypically conserved NLR that traces its origin to early flowering plant lineages ∼220 to 150 million yrs ago (Jurassic period). We discovered 120 ZAR1 orthologs in 88 species, including the monocot Colocasia esculenta, the magnoliid Cinnamomum micranthum, and most eudicots, notably the Ranunculales species Aquilegia coerulea, which is outside the core eudicots. Ortholog sequence analyses revealed highly conserved features of ZAR1, including regions for pathogen effector recognition and cell death activation. We functionally reconstructed the cell death activity of ZAR1 and its partner receptor-like cytoplasmic kinase (RLCK) from distantly related plant species, experimentally validating the hypothesis that ZAR1 evolved to partner with RLCKs early in its evolution. In addition, ZAR1 acquired novel molecular features. In cassava (Manihot esculenta) and cotton (Gossypium spp.), ZAR1 carries a C-terminal thioredoxin-like domain, and in several taxa, ZAR1 duplicated into 2 paralog families, which underwent distinct evolutionary paths. ZAR1 stands out among angiosperm NLR genes for having experienced relatively limited duplication and expansion throughout its deep evolutionary history. Nonetheless, ZAR1 also gave rise to noncanonical NLRs with integrated domains and degenerated molecular features.
  • Journal article
    Wiggins BG, Wang Y-F, Burke A, Grunberg N, Vlachaki Walker JM, Dore M, Chahrour C, Pennycook BR, Sanchez-Garrido J, Vernia S, Barr AR, Frankel G, Birdsey GM, Randi AM, Schiering Cet al., 2023,

    Endothelial sensing of AHR ligands regulates intestinal homeostasis

    , Nature, Vol: 621, Pages: 821-829, ISSN: 0028-0836

    Endothelial cells (ECs) line the blood and lymphatic vasculature, and act as an essential physical barrier, control nutrient transport, facilitate tissue immunosurveillance, and coordinate angiogenesis/ lymphangiogenesis1,2. In the intestine, dietary and microbial cues are particularly important in the regulation of organ homeostasis. However, whether enteric ECs actively sense and integrate such signals is currently unknown. Here, we show that the aryl hydrocarbon receptor (AHR) acts as a critical node for EC-sensing of dietary metabolites in adult mice and human primary ECs. We first established a comprehensive single-cell endothelial atlas of the mouse small intestine, uncovering the cellular complexity and functional heterogeneity of blood and lymphatic ECs. Analyses of AHR mediated responses at single-cell resolution identified tissue-protective transcriptional signatures and regulatory networks promoting cellular quiescence and vascular normalcy at steady state. Endothelial AHR-deficiency in adult mice resulted in dysregulated inflammatory responses, and the initiation of proliferative pathways. Furthermore, endothelial sensing of dietary AHR ligands was required for optimal protection against enteric infection. In human ECs, AHR signalling promoted quiescence and restrained activation by inflammatory mediators. Together, our data provide a comprehensive dissection of the impact of environmental sensing across the spectrum of enteric endothelia, demonstrating that endothelial AHR signalling integrates dietary cues to maintain tissue homeostasis by promoting EC quiescence and vascular normalcy.
  • Journal article
    Haas O, Prentice IC, Harrison SP, 2023,

    The response of wildfire regimes to Last Glacial Maximum carbon dioxide and climate

    , BIOGEOSCIENCES, Vol: 20, Pages: 3981-3995, ISSN: 1726-4170
  • Journal article
    Caceres C, Bourtzis K, Gouvi G, Vreysen MJB, Somda NSB, Hejnickova M, Marec F, Meza JSet al., 2023,

    Development of a novel genetic sexing strain of Ceratitis capitata based on an X-autosome translocation

    , SCIENTIFIC REPORTS, Vol: 13, ISSN: 2045-2322
  • Journal article
    Boussac A, Sugiura M, Nakamura M, Nagao R, Noguchi T, Viola S, Rutherford AW, Selles Jet al., 2023,

    Absorption changes in Photosystem II in the Soret band region upon the formation of the chlorophyll cation radical [P<sub>D1</sub>P<sub>D2</sub>]<SUP>+</SUP>

    , PHOTOSYNTHESIS RESEARCH, ISSN: 0166-8595
  • Journal article
    Drury F, Grover M, Hintze M, Saunders J, Fasseas MK, Constantinou C, Barkoulas Met al., 2023,

    A PAX6-regulated receptor tyrosine kinase pairs with a pseudokinase to activate immune defense upon oomycete recognition in Caenorhabditis elegans.

    , Proc Natl Acad Sci U S A, Vol: 120

    Oomycetes were recently discovered as natural pathogens of Caenorhabditis elegans, and pathogen recognition alone was shown to be sufficient to activate a protective transcriptional program characterized by the expression of multiple chitinase-like (chil) genes. However, the molecular mechanisms underlying oomycete recognition in animals remain fully unknown. We performed here a forward genetic screen to uncover regulators of chil gene induction and found several independent loss-of-function alleles of old-1 and flor-1, which encode receptor tyrosine kinases belonging to the C. elegans-specific KIN-16 family. We report that OLD-1 and FLOR-1 are both necessary for mounting the immune response and act in the epidermis. FLOR-1 is a pseudokinase that acts downstream of the active kinase OLD-1 and regulates OLD-1 levels at the plasma membrane. Interestingly, the old-1 locus is adjacent to the chil genes in the C. elegans genome, thereby revealing a genetic cluster important for oomycete resistance. Furthermore, we demonstrate that old-1 expression at the anterior side of the epidermis is regulated by the VAB-3/PAX6 transcription factor, well known for its role in visual system development in other animals. Taken together, our study reveals both conserved and species-specific factors shaping the activation and spatial characteristics of the immune response to oomycete recognition.
  • Journal article
    Frankel G, 2023,

    Plasmids pick a bacterial partner before committing to conjugation (vol 51, pg 8925, 2023)

    , NUCLEIC ACIDS RESEARCH, Vol: 51, Pages: 10812-10812, ISSN: 0305-1048
  • Journal article
    Frankel G, David S, Low WW, Seddon C, Wong JLC, Beis Ket al., 2023,

    Plasmids pick a bacterial partner before committing to conjugation

    , NUCLEIC ACIDS RESEARCH, Vol: 51, Pages: 8925-8933, ISSN: 0305-1048
  • Journal article
    Lee S, Seung J, Yang Y, Orr M, Lee M, Tak J-H, Vogler AP, Bai M, Lee Set al., 2023,

    The Water-Exclusion Trap (WET): A 3D printable window trap collector that prevents DNA degradation

    , METHODS IN ECOLOGY AND EVOLUTION, ISSN: 2041-210X
  • Journal article
    Kvasnica J, Matula R, Rejzek M, Ewers RM, Riutta T, Turner EC, Nilus R, Svatek Met al., 2023,

    Multi-stemming enhances tree survival and growth in Borneo's logged forests

    , FOREST ECOLOGY AND MANAGEMENT, Vol: 544, ISSN: 0378-1127
  • Journal article
    Sasidharan S, Davis DM, Dunlop IE, 2023,

    Bioinspired Materials for Immunoengineering of T Cells and Natural Killer Cells

    , ADVANCED FUNCTIONAL MATERIALS, ISSN: 1616-301X

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