Temperature-Controlled Mechanochemistry for the Nickel-Catalyzed Suzuki-Miyaura-Type Coupling of Aryl Sulfamates via Ball Milling and Twin-Screw Extrusion

The use of temperature-controlled mechanochemistry to enable the mechanochemical nickel-catalyzed Suzuki-Miyaura coupling is herein described. Transitioning from a capricious room-temperature protocol, through to a heated, PID-controlled programmable jar heater manifold was required to deliver an efficient method for the coupling of aryl sulfamates (derived from ubiquitous phenols) and aryl boronic acid species. Furthermore, this process is conducted using a base-metal nickel catalyst, in the absence of bulk solvent, and in the absence of air/moisture sensitive reaction set-ups. This methodology is showcased through translation to large-scale twin-screw extrusion methodology enabling 200-fold scale increase, producing decagram quantities of C-C coupled material

Remodeling and control of homologous recombination by DNA helicases and translocases that target recombinases and synapsis

Recombinase enzymes catalyse invasion of single-stranded DNA (ssDNA) into homologous duplex DNA forming "Displacement loops" (D-loops), a process called synapsis. This triggers homologous recombination (HR), which can follow several possible paths to underpin DNA repair and restart of blocked and collapsed DNA replication forks. Therefore, synapsis can be a checkpoint for controlling whether or not, how far, and by which pathway, HR proceeds to overcome an obstacle or break in a replication fork. Synapsis can be antagonized by limiting access of a recombinase to ssDNA and by dissociation of D-loops or heteroduplex formed by synapsis. Antagonists include DNA helicases and translocases that are identifiable in eukaryotes, bacteria and archaea, and which target synaptic and pre-synaptic DNA structures thereby controlling HR at early stages. Here we survey these events with emphasis on enabling DNA replication to be resumed from sites of blockage or collapse. We also note how knowledge of anti-recombination activities could be useful to improve efficiency of CRISPR-based genome editing

DNA binding and unwinding by Hel308 helicase requires dual functions of a winged helix domain

Hel308 helicases promote genome stability linked to DNA replication in archaea, and have homologues in metazoans. In the crystal structure of archaeal Hel308 bound to a tailed DNA duplex, core helicase domains encircle single-stranded DNA (ssDNA) in a “ratchet” for directional translocation. A winged helix domain (WHD) is also present, but its function is mysterious. We investigated the WHD in full-length Hel308, identifying that mutations in a solvent exposed α-helix resulted in reduced DNA binding and unwinding activities. When isolated from the rest of Hel308, the WHD protein alone bound to duplex DNA but not ssDNA, and DNA binding by WHD protein was abolished by the same mutations as were analyzed in full-length Hel308. Isolated WHD from a human Hel308 homologue (HelQ) also bound to duplex DNA. By disrupting the interface between the Hel308 WHD and a RecA-like domain, a topology typical of Ski2 helicases, we show that this is crucial for ATPase and helicase activities. The data suggest a model in which the WHD promotes activity of Hel308 directly, through binding to duplex DNA that is distinct from ssDNA binding by core helicase, and indirectly through interaction with the RecA-like domain. We propose how the WHD may contribute to ssDNA translocation, resulting in DNA helicase activity or in removal of other DNA bound proteins by “reeling” ssDNA

A participatory, farmer-led approach to changing practices around antimicrobial use on UK farms

Farmer-led, participatory approaches are being increasingly employed in agricultural research with promising results. This study aimed to understand how a participatory approach based on the Danish Stable Schools could help to achieve practical, farmer-led changes that reduced reliance on antimicrobials in the UK. Five facilitated Farmer Action Groups comprising 30 dairy farms across South West England met on farm at regular intervals between 2016 – 2018 and worked collaboratively within their groups to discuss how to reduce antimicrobial use. Qualitative data from group discussions and individual semi-structured interviews were collected and analysed using thematic analysis to explore how the approach helped farmers address and deal with changes to their on-farm practices. Facilitator-guided reviews of antimicrobial use and benchmarking were carried out on each farm to assess any change in usage and help farmers review their practices. The pattern of antimicrobial use changed over the 2 years of the study with 21 participating farms reducing their use of highest priority critically important antibiotics (6 farms were not using any of these critical medicines from the outset). Thirty practical action plans were co-developed by the groups with an average implementation rate of 54.3% within a year. All assessed farms implemented 1 recommendation, and many were still ongoing at the end of the study. Farmers particularly valued the peer-to-peer learning during farm walks. Farmers reported how facilitated discussions and action planning as a peer group had empowered them to change practices. Participants identified knowledge gaps during the project, particularly on highest priority critically important antibiotics where they were not getting information from their veterinarians. The study demonstrated that facilitation has a valuable role to play in participatory approaches beyond moderating discussion; facilitators encouraged knowledge mobilization within the groups and were participants in the research as well. Facilitated, farmer-led, participatory approaches that mobilize different forms of knowledge and encourage peer learning are a promising way of helping farmers to adapt and develop responsible practices

The HelQ human DNA repair helicase utilizes a PWI-like domain for DNA loading through interaction with RPA, triggering DNA unwinding by the HelQ helicase core

Genome instability is a characteristic enabling factor for carcinogenesis. HelQ helicase is a component of human DNA maintenance systems that prevent or reverse genome instability arising during DNA replication. Here, we provide details of the molecular mechanisms that underpin HelQ function — its recruitment onto ssDNA through interaction with RPA, and subsequent translocation of HelQ along ssDNA. We describe for the first time a functional role for the non-catalytic N-terminal region of HelQ, by identifying and characterising its PWI-like domain. We present evidence that this domain of HelQ mediates interaction with RPA that orchestrates loading of the helicase domains onto ssDNA. Once HelQ is loaded onto the ssDNA, ATP-Mg2+ binding in the catalytic site activates the helicase core and triggers translocation along ssDNA as a dimer. Furthermore, we identify HelQ-ssDNA interactions that are critical for the translocation mechanism. Our data are novel and detailed insights into the mechanisms of HelQ function relevant for understanding how human cells avoid genome instability provoking cancers, and also how cells can gain resistance to treatments that rely on DNA crosslinking agents

IRC/The Hague:

Contract HRN-I-00-99-00011-0

A spatially resolved atlas of the human lung characterizes a gland-associated immune niche

Single-cell transcriptomics has allowed unprecedented resolution of cell types/states in the human lung, but their spatial context is less well defined. To (re)define tissue architecture of lung and airways, we profiled five proximal-to-distal locations of healthy human lungs in depth using multi-omic single cell/nuclei and spatial transcriptomics (queryable at lungcellatlas.org ). Using computational data integration and analysis, we extend beyond the suspension cell paradigm and discover macro and micro-anatomical tissue compartments including previously unannotated cell types in the epithelial, vascular, stromal and nerve bundle micro-environments. We identify and implicate peribronchial fibroblasts in lung disease. Importantly, we discover and validate a survival niche for IgA plasma cells in the airway submucosal glands (SMG). We show that gland epithelial cells recruit B cells and IgA plasma cells, and promote longevity and antibody secretion locally through expression of CCL28, APRIL and IL-6. This new 'gland-associated immune niche' has implications for respiratory health

A cell atlas of human thymic development defines T cell repertoire formation.

The thymus provides a nurturing environment for the differentiation and selection of T cells, a process orchestrated by their interaction with multiple thymic cell types. We used single-cell RNA sequencing to create a cell census of the human thymus across the life span and to reconstruct T cell differentiation trajectories and T cell receptor (TCR) recombination kinetics. Using this approach, we identified and located in situ CD8αα+ T cell populations, thymic fibroblast subtypes, and activated dendritic cell states. In addition, we reveal a bias in TCR recombination and selection, which is attributed to genomic position and the kinetics of lineage commitment. Taken together, our data provide a comprehensive atlas of the human thymus across the life span with new insights into human T cell development