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A simple approach to digital control design is the local discretisation of an effective continuous-time control law, such as well-tuned PID (proportional-integral-derivative). There are rules of thumb (e.g. the sample rate should be at least 25× the closed-loop bandwidth) that ensure only marginal degradation in performance, but these often require fast and accurate implementations. Low-power microcontrollers, on the other hand, might be slow and have restricted word-length. An approach to discretisation is thus to employ a mixed realisation using an ‘analogue wrap-around’ in which a proportional signal bypasses the computer and is added to the computer's digitally-evaluated component. Analysis and simulated examples indicate that this can lead to a significant reduction of the sample rate required for good closed-loop control when compared with the classical methods of Tustin, step- and ramp-invariant transformations. [ABSTRACT FROM AUTHOR]

Background: The malaria parasite Plasmodium falciparum replicates within red blood cells, then ruptures the cell in a process called egress in order to continue its life cycle. Egress is regulated by a proteolytic cascade involving an essential parasite subtilisin-like serine protease called SUB1. Maturation of SUB1 initiates in the parasite endoplasmic reticulum with autocatalytic cleavage of an N-terminal prodomain (p31), which initially remains non-covalently bound to the catalytic domain, p54. Further trafficking of the p31-p54 complex results in formation of a terminal p47 form of the SUB1 catalytic domain. Recent work has implicated a parasite aspartic protease, plasmepsin X (PMX), in maturation of the SUB1 p31-p54 complex through controlled cleavage of the prodomain p31., Methods: Here we use biochemical and enzymatic analysis to examine the activation of SUB1 by PMX., Results: We show that both p31 and p31-p54 are largely dimeric under the relatively acidic conditions to which they are likely exposed to PMX in the parasite. We confirm the sites within p31 that are cleaved by PMX and determine the order of cleavage. We find that cleavage by PMX results in rapid loss of the capacity of p31 to act as an inhibitor of SUB1 catalytic activity and we directly demonstrate that exposure to PMX of recombinant p31-p54 complex activates SUB1 activity., Conclusions: Our results confirm that precise, PMX-mediated cleavage of the SUB1 prodomain activates SUB1 enzyme activity., General Significance: Our findings elucidate the role of PMX in activation of SUB1, a key effector of malaria parasite egress., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

RAD52 is important for the repair of DNA double-stranded breaks 1,2 , mitotic DNA synthesis 3-5 and alternative telomere length maintenance 6,7 . Central to these functions, RAD52 promotes the annealing of complementary single-stranded DNA (ssDNA) 8,9 and provides an alternative to BRCA2/RAD51-dependent homologous recombination repair 10 . Inactivation of RAD52 in homologous-recombination-deficient BRCA1- or BRCA2-defective cells is synthetically lethal 11,12 , and aberrant expression of RAD52 is associated with poor cancer prognosis 13,14 . As a consequence, RAD52 is an attractive therapeutic target against homologous-recombination-deficient breast, ovarian and prostate cancers 15-17 . Here we describe the structure of RAD52 and define the mechanism of annealing. As reported previously 18-20 , RAD52 forms undecameric (11-subunit) ring structures, but these rings do not represent the active form of the enzyme. Instead, cryo-electron microscopy and biochemical analyses revealed that ssDNA annealing is driven by RAD52 open rings in association with replication protein-A (RPA). Atomic models of the RAD52-ssDNA complex show that ssDNA sits in a positively charged channel around the ring. Annealing is driven by the RAD52 N-terminal domains, whereas the C-terminal regions modulate the open-ring conformation and RPA interaction. RPA associates with RAD52 at the site of ring opening with critical interactions occurring between the RPA-interacting domain of RAD52 and the winged helix domain of RPA2. Our studies provide structural snapshots throughout the annealing process and define the molecular mechanism of ssDNA annealing by the RAD52-RPA complex., (© 2024. The Author(s).)

Homologous recombination is a fundamental process of life. It is required for the protection and restart of broken replication forks, the repair of chromosome breaks and the exchange of genetic material during meiosis. Individuals with mutations in key recombination genes, such as BRCA2 (also known as FANCD1), or the RAD51 paralogues RAD51B, RAD51C (also known as FANCO), RAD51D, XRCC2 (also known as FANCU) and XRCC3, are predisposed to breast, ovarian and prostate cancers 1-10 and the cancer-prone syndrome Fanconi anaemia 11-13 . The BRCA2 tumour suppressor protein-the product of BRCA2-is well characterized, but the cellular functions of the RAD51 paralogues remain unclear. Genetic knockouts display growth defects, reduced RAD51 focus formation, spontaneous chromosome abnormalities, sensitivity to PARP inhibitors and replication fork defects 14,15 , but the precise molecular roles of RAD51 paralogues in fork stability, DNA repair and cancer avoidance remain unknown. Here we used cryo-electron microscopy, AlphaFold2 modelling and structural proteomics to determine the structure of the RAD51B-RAD51C-RAD51D-XRCC2 complex (BCDX2), revealing that RAD51C-RAD51D-XRCC2 mimics three RAD51 protomers aligned within a nucleoprotein filament, whereas RAD51B is highly dynamic. Biochemical and single-molecule analyses showed that BCDX2 stimulates the nucleation and extension of RAD51 filaments-which are essential for recombinational DNA repair-in reactions that depend on the coupled ATPase activities of RAD51B and RAD51C. Our studies demonstrate that BCDX2 orchestrates RAD51 assembly on single stranded DNA for replication fork protection and double strand break repair, in reactions that are critical for tumour avoidance., (© 2023. The Author(s), under exclusive licence to Springer Nature Limited.)

Most eukaryotic messenger RNAs (mRNAs) are processed at their 3' end by the cleavage and polyadenylation specificity factor (CPF/CPSF). CPF mediates the endonucleolytic cleavage of the pre-mRNA and addition of a polyadenosine (poly(A)) tail, which together define the 3' end of the mature transcript. The activation of CPF is highly regulated to maintain the fidelity of RNA processing. Here, using cryo-EM of yeast CPF, we show that the Mpe1 subunit directly contacts the polyadenylation signal sequence in nascent pre-mRNA. The region of Mpe1 that contacts RNA also promotes the activation of CPF endonuclease activity and controls polyadenylation. The Cft2 subunit of CPF antagonizes the RNA-stabilized configuration of Mpe1. In vivo, the depletion or mutation of Mpe1 leads to widespread defects in transcription termination by RNA polymerase II, resulting in transcription interference on neighboring genes. Together, our data suggest that Mpe1 plays a major role in accurate 3' end processing, activating CPF, and ensuring timely transcription termination., Competing Interests: Declaration of interests L.A.P. is an inventor on a patent filed by the Medical Research Council for all-gold EM supports, licensed to Quantifoil under the trademark UltrAuFoil. L.A.P. is on the advisory board for Molecular Cell., (Copyright © 2022 MRC Laboratory of Molecular Biology. Published by Elsevier Inc. All rights reserved.)

The amount of any given protein in the brain is determined by the rates of its synthesis and destruction, which are regulated by different cellular mechanisms. Here, we combine metabolic labeling in live mice with global proteomic profiling to simultaneously quantify both the flux and amount of proteins in mouse models of neurodegeneration. In multiple models, protein turnover increases were associated with increasing pathology. This method distinguishes changes in protein expression mediated by synthesis from those mediated by degradation. In the App NL-F knockin mouse model of Alzheimer's disease, increased turnover resulted from imbalances in both synthesis and degradation, converging on proteins associated with synaptic vesicle recycling (Dnm1, Cltc, Rims1) and mitochondria (Fis1, Ndufv1). In contrast to disease models, aging in wild-type mice caused a widespread decrease in protein recycling associated with a decrease in autophagic flux. Overall, this simple multidimensional approach enables a comprehensive mapping of proteome dynamics and identifies affected proteins in mouse models of disease and other live animal test settings., Competing Interests: Conflict of interest The authors declare no competing interests., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)

This paper examines the relationship between conceptual and embodied reasoning in engineering work. In the last decade across multiple research projects on pipeline engineering, we have observed only a few times when engineers have expressed embodied or sensory aspects of their practice, as if the activity itself is disembodied. Yet, they also often speak about the importance of field experience. In this paper, we look at engineers' accounts of the value of field experience showing how it works on their sense of what the technology that they are designing looks, feels, and sounds like in practice, and so what this means for construction and operation, and the management of risk. We show how office-based pipeline engineering work is an exercise in embodied imagination that humanizes the socio-technical system as it manifests in the technical artifacts that they work with. Engineers take the role of the other to reason through the practicability of their designs and risk acceptability., (© The Author(s) 2022.)