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RNA-seq data- 12 hrs and 24 hrs for C. beijerinckii NCIMB 8052 WT versus agrB mutants
No full textRNA-seq data from three independent agrB mutants made in C. beijerinckii NCIMB 8052. Mutations were made in three different Agr systems, denoted by Agr2, Agr4 and Agr5. Total RNA was extracted from three replicates of each agrB mutant and the WT. RNA sequencing and analysis was carried out by DeepSeq (University of Nottingham). Mutants were compared to the WT gene expression at both 12 and 24 hour sampling points (Grown in glucose containing media)
Rapid and accurate mapping of ligand binding and structural changes in the β-1 adrenergic receptor using carbene footprinting and mass spectrometry
No full textG protein coupled receptors (GPCRs) control many physiological processes and are major targets for therapeutic intervention. As transmembrane proteins with inherent instability they are often difficult study with more conventional structural methods. Here we report the use of carbene footprinting to map ligand binding and structural changes in the β1-adrenergic receptor, β1AR, a GPCR target of beta-blocker drugs. The method revealed differences between binding of the agonist, isoprenaline, and the reverse agonist, carazalol, both in terms of their occupancy of the orthosteric ligand binding site and their effects on key regulatory structural features of β1AR including the ‘ionic lock’ between transmembrane (TM) helicies 3 and 6. Addition of nanobodies (Nbs) known to stabilise the activated complex (Nb80) and inactivated complex (Nb60) of β1AR induced further structural changes above those seen with the ligands alone. This repository entry contains the raw MS data in support of this work
Functional characterization of DEEPGENES to enhance deeper rooting in cereal crops
No full textGlobal food security and climate change represent major challenges faced by humankind during this century. Developing deeper rooting, more resource efficient crops represents an attractive solution to increase crop production sustainably whilst also enhancing soil carbon (C) sequestration. For example, planting maize varieties with a root system 0.5m deeper than currently sown in USA is predicted to improve foraging for water and nitrogen resources in sub-soil layers whilst burying up to two thirds of carbon related to US transportation emissions. The aim of this PhD project is to identify and characterise key genes that control anatomical and architectural traits contributing to deeper rooting in cereal crops such as maize and barley (as part of the DEEPER project funded by the ARPA-E ROOTS initiative).
A DEEPGENES discovery pipeline was initially developed to pinpoint candidate genes that controlled key traits determining deeper rooting in maize. Root anatomical traits included cortical cell number, cortical cell file number, total cortical area and root cortical aerenchyma plus architectural traits such as crown root angle. Promising DEEPGENE candidates where then shortlisted based on root expression and tissue specificity using maize and cross-species transcriptomic datasets in model plants such as rice and Arabidopsis thaliana. Loss of function mutants in candidate DEEPGENES were designed and/or developed in maize and the cereal model Brachypodium distachyon using CRISPR-Cas9 based approaches, respectively. Phenotypic analysis revealed a candidate regulator for root cortical cell number encoded by the QKY gene.
In parallel with maize studies, a forward genetics approach was used to pinpoint root angle or root length mutants in the barley TILLMore population. Two mutants were characterised which disrupted either: 1) HvPIN1A, encoding an auxin-efflux carrier, which controls root growth and vascular patterning in cereal roots; and 2) A novel Tubby1-like gene called HvEGT1 (Enhancing Gravitropism 1) which regulates root gravitropic set point angle in cereals. Barley and wheat mutant lines disrupting EGT1 function exhibited a deeper rooting phenotype, revealing this sequence as a promising DEEPGENE target to create novel cereal varieties
Microplastic - Bacteria interaction in aquatic environments
No full textStudy on the impact of bacterial attachment to microplastics in wate
Further evidence for the role of temporal contiguity as a determinant of overshadowing
No full textThree experiments explored whether weakening temporal contiguity between auditory cues and an outcome attenuated cue-competition in an avoidance learning task with human participants. Overall, with strong temporal contiguity between auditory cues and the outcome during training (the offset of the predictive auditory signals concurred with the onset of the outcome), the target cue trained as part of a compound yielded less avoidance behaviour than the control cue trained alone, an instance of overshadowing. However, weakening temporal contiguity during training (inserting a 5s trace) attenuated overshadowing, resulting in similar avoidance behaviour in response to the control and the target cues. Moreover, as predicted by a recent modification of Pearce’s configural theory (Pearce, 1987; see Herrera et al., 2022), temporal contiguity was critical in determining cue competition
TrustScapes transcripts: exploring young people's trust-related concerns about co-created online resources to promote mental health literacy
No full textThe objective of the present study was to explore young people’s trust-related concerns about and recommendations for the co-created mental health website by using TrustScapes. The findings was used to improve the trustworthiness of the website and to inform future creators of online mental health resources
