Benjamin G. Davis
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Biocompatible ligand balancing in transition metal coordination enables benign in-cell protein arylation Open
Metal-mediated chemistries now find increasing application in in vitro biomolecule modification. However, the perceived and potential toxicity of some metals has limited the application of organometallic reagents in more complex biological…
View article: Toward a global research agenda for preventing multiple sclerosis
Toward a global research agenda for preventing multiple sclerosis Open
Background: Considerable progress has been made in understanding genetic and environmental risk factors for multiple sclerosis (MS), yet we still cannot prevent MS. Objectives: To drive progress in primary and secondary prevention of MS by…
View article: Gluebodies Offer a Route To Improve Crystal Reliability and Diversity through Transferable Nanobody Mutations That Introduce Constitutive Close Contacts
Gluebodies Offer a Route To Improve Crystal Reliability and Diversity through Transferable Nanobody Mutations That Introduce Constitutive Close Contacts Open
Design of modular, transferable protein assemblies has broad applicability and in structural biology could help with the ever-troublesome crystallization bottleneck, including finding robustly behaved protein crystals for rapidly character…
View article: Biomolecular tracking by FIRESCAPE reveals distinct modes of clearance, damage induction and cellular uptake for extracellular histone H3
Biomolecular tracking by FIRESCAPE reveals distinct modes of clearance, damage induction and cellular uptake for extracellular histone H3 Open
In attempting to observe the behaviour of a protein of interest in vivo , akin to other observer effects, current techniques require modifications or interventions that inherently alter the protein or its host, leaving one uncertain as to …
Seedless: on-the-fly pulse calculation for NMR experiments Open
NMR experiments require sequences of radio frequency (RF) pulses to manipulate nuclear spins. Signal is lost due to non-uniform excitation of nuclear spins resonating at different energies (chemical shifts) and inhomogeneity in the RF unav…
Live-cell 3D-SIM of Rift Valley fever virus NSs filaments reveals a polygonal web architecture Open
A defining feature of Rift Valley fever virus (RVFV) is the incorporation of the NSs protein into large filamentous assemblies inside infected nuclei 1 , as judged from fixed specimens. To gain insight into the three-dimensional (3D) struc…
Radiology resident education during the COVID-19 pandemic in the United States Open
The COVID-19 pandemic presented unprecedented challenges to healthcare systems, including radiology residency programs. This study aims to examine the impact of COVID-19 on radiology residency education and identify interventions implement…
View article: Membrane-permeable trehalose 6-phosphate precursor spray increases wheat yields in field trials
Membrane-permeable trehalose 6-phosphate precursor spray increases wheat yields in field trials Open
Trehalose 6-phosphate (T6P) is an endogenous sugar signal in plants that promotes growth, yet it cannot be introduced directly into crops or fully genetically controlled. Here we show that wheat yields were improved using a timed microdose…
Addressing NHS Chemistry: Efficient Quenching of Excess TMT Reagent and Reversing TMT Overlabeling in Proteomic Samples by Methylamine Open
N-hydroxysuccinimide (NHS) ester chemistry is used extensively across proteomics sample preparation. One of its increasingly prevalent applications is in isobaric reagent-based quantitation such as isobaric tags for relative and absolute q…
View article: Sugar signal manipulation by T6P for yield on wheat grain - whole grain RNA-seq
Sugar signal manipulation by T6P for yield on wheat grain - whole grain RNA-seq Open
Trehalose 6-phosphate (T6P) is a powerful internal sugar signal in plants yet cannot be directly added norfully genetically controlled. A timed microdose of a plant-permeable T6P signalling precursor, DMNB-T6P, causes substantial yield imp…
View article: Sugar signal manipulation by T6P for yield on wheat grain - whole grain RNA-seq
Sugar signal manipulation by T6P for yield on wheat grain - whole grain RNA-seq Open
Trehalose 6-phosphate (T6P) is a powerful internal sugar signal in plants yet cannot be directly added norfully genetically controlled. A timed microdose of a plant-permeable T6P signalling precursor, DMNB-T6P, causes substantial yield imp…
View article: Isostere <sup>18</sup> F-protein post-translational editing enables dynamic tracking of neurodegeneration biomarkers
Isostere <sup>18</sup> F-protein post-translational editing enables dynamic tracking of neurodegeneration biomarkers Open
The neurofilament light chain protein (NfL) is a suggested general marker for neuronal loss. Its release from brain parenchyma into cerebral spinal fluid, and presumed detection in blood has seen it established as a first blood-based marke…
Structure of WzxE the lipid III flippase for Enterobacterial Common Antigen polysaccharide Open
The enterobacterial common antigen (ECA) is conserved in Gram-negative bacteria of the Enterobacterales order although its function is debated. ECA biogenesis depends on the Wzx/Wzy-dependent strategy whereby the newly synthesized lipid-li…
Lipid-Modulated, Graduated Inhibition of N-Glycosylation Pathway Priming Suggests Wide Tolerance of ER Proteostasis to Stress Open
Protein N-glycosylation is a cotranslational modification that takes place in the endoplasmic reticulum (ER). Disruption of this process can result in accumulation of misfolded proteins, known as ER stress. In response, the unfolded protei…
Removal of NHS-labelling by-products in Proteomic Samples Open
N-Hydroxysuccinimide (NHS) ester chemistry is used extensively across proteomics sample preparation. One of its increasingly prevalent applications is in isobaric reagent-based quantitation such as the iTRAQ (isobaric tags for relative and…
Covalent penicillin-protein conjugates elicit anti-drug antibodies that are clonally and functionally restricted Open
Many archetypal and emerging classes of small-molecule therapeutics form covalent protein adducts. In vivo, both the resulting conjugates and their off-target side-conjugates have the potential to elicit antibodies, with implications for a…
View article: Vibrational Electron Energy Loss Spectroscopy for Zero-Size Labeling of Amino Acids
Vibrational Electron Energy Loss Spectroscopy for Zero-Size Labeling of Amino Acids Open
Vibrational electron energy-loss spectroscopy (vibEELS) measures the bonding environment of molecules with high spatial resolution. Here, we demonstrate that vibEELS can be used to identify site-specific vibrational signatures of selective…
Macaw: A Machine Code Toolbox for the Busy Binary Analyst Open
When attempting to understand the behavior of an executable, a binary analyst can make use of many different techniques. These include program slicing, dynamic instrumentation, binary-level rewriting, symbolic execution, and formal verific…
View article: Distributable, metabolic PET reporting of tuberculosis
Distributable, metabolic PET reporting of tuberculosis Open
Tuberculosis remains a large global disease burden for which treatment regimens are protracted and monitoring of disease activity difficult. Existing detection methods rely almost exclusively on bacterial culture from sputum which limits s…
Standalone hybrid PV/MHP/BES system sizing with complementarity adjustment Open
The paper proposes a method to size a standalone hybrid PV/MHP/BES (photovoltaic/micro-hydro/battery energy storage) system. The proposed method is simple and easy to use. The size and location decoupled proposed approach can effectively s…
View article: Di-Gluebodies as covalently-rigidified, modular protein assemblies enable simultaneous determination of high-resolution, low-size, cryo-EM structures
Di-Gluebodies as covalently-rigidified, modular protein assemblies enable simultaneous determination of high-resolution, low-size, cryo-EM structures Open
Cryo-EM has become a routine structural biology method, yet elucidation of small proteins (<100 kDa) and increasing throughput remain challenging. Here, we describe covalently-dimerized engineered nanobodies, Di-Gluebodies, as novel and mo…
Seedless: On-the-fly pulse calculation for NMR experiments Open
All NMR experiments require sequences of RF ‘pulses’ to manipulate nuclear spins. Signal is lost due to non-uniform excitation of nuclear spins resonating at different energies (chemical shifts) and inhomogeneity in the RF actually generat…
Late-Stage Functionalization of Living Organisms: Rethinking Selectivity in Biology Open
With unlimited selectivity, full post-translational chemical control of biology would circumvent the dogma of genetic control. The resulting direct manipulation of organisms would enable atomic-level precision in "editing" of function. We …
The Minimum Protein Staple? – Towards ‘bio’-Baldwin's rules <i>via</i> inter-phosphosite linking in the MEK1 activation loop Open
One-out-of-six regioselectivity allows the use of poly-Cys arrays to report on protein structure and reactivity in a biological extension of the Baldwin rules.