Acetylation of histone H3 lysine 56 regulates replication-coupled nucleosome assembly.

Chromatin assembly factor 1 (CAF-1) and Rtt106 participate in the deposition of newly synthesized histones onto replicating DNA to form nucleosomes. This process is critical for the maintenance of genome stability and inheritance of functionally specialized chromatin structures in proliferating cells. However, the molecular functions of the acetylation of newly synthesized histones in this DNA replication-coupled nucleosome assembly pathway remain enigmatic. Here we show that histone H3 acetylated at lysine 56 (H3K56Ac) is incorporated onto replicating DNA and, by increasing the binding affinity of CAF-1 and Rtt106 for histone H3, H3K56Ac enhances the ability of these histone chaperones to assemble DNA into nucleosomes. Genetic analysis indicates that H3K56Ac acts in a nonredundant manner with the acetylation of the N-terminal residues of H3 and H4 in nucleosome assembly. These results reveal a mechanism by which H3K56Ac regulates replication-coupled nucleosome assembly mediated by CAF-1 and Rtt106.

Fetal ascites in cloacal malformations-a red flag.

INTRODUCTION: Cloacal malformation is a rare anomaly that remains a diagnostic challenge prenatally, despite the current advances in ultrasonography and MRI. This condition can in some, present with isolated ascites or with other findings, such as a pelvic cyst or upper urinary tract dilatation. In a minority, the ascites may be progressive, questioning the role of antenatal intervention. METHODS: We report on ten patients that have been identified from our Cloaca database between 2010 and 2022. RESULTS: The presence of ascites was associated with extensive bowel adhesions and matting, leading to a challenging initial laparotomy and peri-operative course. CONCLUSIONS: Antenatal finding of ascites in newborns with cloacal malformations should raise a red flag. The surgeon and anaesthetist should be prepared for the operative difficulties secondary to bowel adhesions and the higher risk of haemodynamic instability at the initial surgery. An experienced team at initial laparotomy in such patients is vital. LEVEL OF EVIDENCE: II.

Quantitative skin exposure assessment of metals: a systematic literature review of current approaches for risk assessment using the construction industry as an exposure scenario.

PURPOSE: This article summarises a systematic literature review of skin exposure assessment methods and concepts for deriving skin (dermal) exposure limits for metals, using the construction industry, where there is a high prevalence of occupational skin exposures as a test environment. METHODS: A systematic literature review was undertaken across ten databases key to Occupational Health and Safety. Articles were considered for inclusion if they evaluated skin or surface exposure to metals or discussed the feasibility of establishing skin or surface exposure limits in an occupational setting. Only full text, peer-reviewed articles were retrieved. All publications up to 30/06/2019 were considered. The quality of evidence was evaluated based on methodology. RESULTS: A total of 71 studies were selected for inclusion in the review with 49 on skin exposure assessment methods for metals and 22 relating to the derivation of skin exposure limits. The use of wipe sampling methodologies was shown to be standardised and effective for sampling skin exposures to metals. In contrast, there was no scientific consensus on the concept of quantitative skin exposure limits. CONCLUSION: There was greater strength of evidence that wipe methods for the measurement of metals would work well. A research gap with respect to the development of health-based skin exposure limits for metals was identified. Frameworks currently proposed for devising quantitative skin exposure limits are provided. These approaches could be adapted to improve the risk assessment of skin exposures to surface metal contaminants.

Structural basis for recognition of H3K56-acetylated histone H3-H4 by the chaperone Rtt106.

Dynamic variations in the structure of chromatin influence virtually all DNA-related processes in eukaryotes and are controlled in part by post-translational modifications of histones. One such modification, the acetylation of lysine 56 (H3K56ac) in the amino-terminal α-helix (αN) of histone H3, has been implicated in the regulation of nucleosome assembly during DNA replication and repair, and nucleosome disassembly during gene transcription. In Saccharomyces cerevisiae, the histone chaperone Rtt106 contributes to the deposition of newly synthesized H3K56ac-carrying H3-H4 complex on replicating DNA, but it is unclear how Rtt106 binds H3-H4 and specifically recognizes H3K56ac as there is no apparent acetylated lysine reader domain in Rtt106. Here, we show that two domains of Rtt106 are involved in a combinatorial recognition of H3-H4. An N-terminal domain homodimerizes and interacts with H3-H4 independently of acetylation while a double pleckstrin-homology (PH) domain binds the K56-containing region of H3. Affinity is markedly enhanced upon acetylation of K56, an effect that is probably due to increased conformational entropy of the αN helix of H3. Our data support a mode of interaction where the N-terminal homodimeric domain of Rtt106 intercalates between the two H3-H4 components of the (H3-H4)(2) tetramer while two double PH domains in the Rtt106 dimer interact with each of the two H3K56ac sites in (H3-H4)(2). We show that the Rtt106-(H3-H4)(2) interaction is important for gene silencing and the DNA damage response.

Conformational Changes in the Endosomal Sorting Complex Required for the Transport III Subunit Ist1 Lead to Distinct Modes of ATPase Vps4 Regulation.

Intralumenal vesicle formation of the multivesicular body is a critical step in the delivery of endocytic cargoes to the lysosome for degradation. Endosomal sorting complex required for transport III (ESCRT-III) subunits polymerize on endosomal membranes to facilitate membrane budding away from the cytoplasm to generate these intralumenal vesicles. The ATPase Vps4 remodels and disassembles ESCRT-III, but the manner in which Vps4 activity is coordinated with ESCRT-III function remains unclear. Ist1 is structurally homologous to ESCRT-III subunits and has been reported to inhibit Vps4 function despite the presence of a microtubule-interacting and trafficking domain-interacting motif (MIM) capable of stimulating Vps4 in the context of other ESCRT-III subunits. Here we report that Ist1 inhibition of Vps4 ATPase activity involves two elements in Ist1: the MIM itself and a surface containing a conserved ELYC sequence. In contrast, the MIM interaction, in concert with a more open conformation of the Ist1 core, resulted in stimulation of Vps4. Addition of the ESCRT-III subunit binding partner of Ist1, Did2, also converted Ist1 from an inhibitor to a stimulator of Vps4 ATPase activity. Finally, distinct regulation of Vps4 by Ist1 corresponded with altered ESCRT-III disassembly in vitro. Together, these data support a model in which Ist1-Did2 interactions during ESCRT-III polymerization coordinate Vps4 activity with the timing of ESCRT-III disassembly.

Efficiency of Respirator Filter Media against Diesel Particulate Matter: A Comparison Study Using Two Diesel Particulate Sources.

Diesel engines have been a mainstay within many industries since the early 1900s. Exposure to diesel particulate matter (DPM) is a major issue in many industrial workplaces given the potential for serious health impacts to exposed workers; including the potential for lung cancer and adverse irritant and cardiovascular effects. Personal respiratory protective devices are an accepted safety measure to mitigate worker exposure against the potentially damaging health impacts of DPM. To be protective, they need to act as effective filters against carbon and other particulates. In Australia, the filtering efficiency of respiratory protective devices is determined by challenging test filter media with aerosolised sodium chloride to determine penetration at designated flow rates. The methodology outlined in AS/NZS1716 (Standards Australia International Ltd and Standards New Zealand 2012. Respiratory protective devices. Sydney/Wellington: SAI Global Limited/Standards New Zealand) does not account for the differences between characteristics of workplace contaminants like DPM and sodium chloride such as structure, composition, and particle size. This study examined filtering efficiency for three commonly used AS/NZS certified respirator filter models, challenging them with two types of diesel emissions; those from a diesel generator and a diesel engine. Penetration through the filter media of elemental carbon (EC), total carbon (TC), and total suspended particulate (TSP) was calculated. Results indicate that filtering efficiency assumed by P2 certification in Australia was achieved for two of the three respirator models for DPM generated using the small diesel generator, whilst when the larger diesel engine was used, filtering efficiency requirements were met for all three filter models. These results suggest that the testing methodology specified for certification of personal respiratory protective devices by Standards Australia may not ensure adequate protection for respirator users against DPM under all circumstances of diesel generated particles.

Vps4 stimulatory element of the cofactor Vta1 contacts the ATPase Vps4 α7 and α9 to stimulate ATP hydrolysis.

The endosomal sorting complexes required for transport (ESCRTs) function in a variety of membrane remodeling processes including multivesicular body sorting, abscission during cytokinesis, budding of enveloped viruses, and repair of the plasma membrane. Vps4 ATPase activity modulates ESCRT function and is itself modulated by its cofactor Vta1 and its substrate ESCRT-III. The carboxyl-terminal Vta1/SBP-1/Lip5 (VSL) domain of Vta1 binds to the Vps4 ß-domain to promote Vps4 oligomerization-dependent ATP hydrolysis. Additionally, the Vps4 stimulatory element (VSE) of Vta1 contributes to enhancing Vps4 oligomer ATP hydrolysis. The VSE is also required for Vta1-dependent stimulation of Vps4 by ESCRT-III subunits. However, the manner by which the Vta1 VSE contributes to Vps4 activation is unknown. Existing structural data were used to generate a model of the Vta1 VSE in complex with Vps4. This model implicated residues within the small ATPase associated with various activities (AAA) domain, specifically α-helices 7 and 9, as relevant contact sites. Rational generation of Vps4 mutants defective for VSE-mediated stimulation, as well as intergenic compensatory mutations, support the validity of this model. These findings have uncovered the Vps4 surface responsible for coordinating ESCRT-III-stimulated Vta1 input during ESCRT function and identified a novel mechanism of Vps4 stimulation.

Population structure and history of the Welsh sheep breeds determined by whole genome genotyping.

BACKGROUND: One of the most economically important areas within the Welsh agricultural sector is sheep farming, contributing around £230 million to the UK economy annually. Phenotypic selection over several centuries has generated a number of native sheep breeds, which are presumably adapted to the diverse and challenging landscape of Wales. Little is known about the history, genetic diversity and relationships of these breeds with other European breeds. We genotyped 353 individuals from 18 native Welsh sheep breeds using the Illumina OvineSNP50 array and characterised the genetic structure of these breeds. Our genotyping data were then combined with, and compared to, those from a set of 74 worldwide breeds, previously collected during the International Sheep Genome Consortium HapMap project. RESULTS: Model based clustering of the Welsh and European breeds indicated shared ancestry. This finding was supported by multidimensional scaling analysis (MDS), which revealed separation of the European, African and Asian breeds. As expected, the commercial Texel and Merino breeds appeared to have extensive co-ancestry with most European breeds. Consistently high levels of haplotype sharing were observed between native Welsh and other European breeds. The Welsh breeds did not, however, form a genetically homogeneous group, with pairwise F ST between breeds averaging 0.107 and ranging between 0.020 and 0.201. Four subpopulations were identified within the 18 native breeds, with high homogeneity observed amongst the majority of mountain breeds. Recent effective population sizes estimated from linkage disequilibrium ranged from 88 to 825. CONCLUSIONS: Welsh breeds are highly diverse with low to moderate effective population sizes and form at least four distinct genetic groups. Our data suggest common ancestry between the native Welsh and European breeds. These findings provide the basis for future genome-wide association studies and a first step towards developing genomics assisted breeding strategies in the UK.

Extensive Necrotising Enterocolitis: Objective Evaluation of the Role of Second-Look Laparotomy in Bowel Salvage and Survival.

AIM: We investigated the role and outcome of a planned second-look laparotomy (SLL) in preserving bowel in extensive necrotizing enterocolitis (NEC). METHODS: Extensive NECs managed surgically in a tertiary centre in 2006-2009 were retrospectively studied to include patients planned for an SLL. End points were bowel salvage rate and survival outcomes. Results were median (ranges), and statistical significance was P < 0.05. MAIN RESULTS: In 4 years, 34 NECs required a laparotomy, and 9 extensive NECs who required an SLL were included. The gestation at birth was 27 (24-38) weeks, birth weight was 1120 (580-2835) g, and first laparotomy performed on day 34 (2-77) of life, with SLL performed 2 (1-3) days after initial laparotomy. Commonest indications for SLL were doubtful bowel viability and physiological instability. 3 died before SLL. Patients who survived to have an SLL (n = 6) had remaining small bowel length of 41 (25-70) cm, overall small bowel salvage rate 51 % (0-100 %), and 30-day survival 5/6 (83 %). Four patients survived for 1 year, their length of NICU stay was 114 (76-120) postoperative days, time on PN was 84 postoperative days (71 days-17 months), including one patient with short bowel syndrome who achieved enteral autonomy at 17 months; one late mortality had short bowel syndrome after further bowel resection for bowel obstruction, developed intestinal failure associated liver disease, and died before 1 year of life following liver transplant. CONCLUSION: SLL is a viable approach for extensive NEC. It offered bowel salvage rate of 51 % and long-term PN-free survival of 44 %, in the patient group who would have had significant risk of mortality and major morbidity.

A PBPK model describing a xenobiotic with a short PK event scale.

Physiologically-based pharmacokinetic (PBPK) modeling has been widely used in human risk assessment and in early drug development to predict human PK from in vitro and/or in vivo animal data. Recently, the application of PBPK modeling has been extended to the evaluation of drug-drug interactions. For most xenobiotic agents, the PK event scale such as elimination is in hours or days. This is much longer than the transit time of the agent in the body, and a PBPK model can be significantly simplified through lumping based on the physiochemical properties, mass transfer, and biotransformation. However, for a xenobiotic agent with a short PK event scale, e.g. in minutes, such an approach is not applicable. In this manuscript, the authors used the observed PK data from an ultrasound contrast agent to illustrate the role of a short PK event scale in the development of a suitable PBPK model. The model development process showed that a PBPK model assuming uniform venous and arterial blood pools, with a static lung model including alveolar and tissue regions, was unable to adequately capture the characteristics of the PK of the agent. Detailed information describing the pulmonary and cardiovascular circulation, and a heterogeneous dynamic lung model became necessary for the model. This exercise once again demonstrates the importance of the principles and methodologies that have been established since the 1960s that need to be followed during PBPK model development.

The linker region plays a regulatory role in assembly and activity of the Vps4 AAA ATPase.

The AAA-type ATPase Vps4 functions with components of the ESCRT (endosomal sorting complex required for transport) machinery in membrane fission events that are essential for endosomal maturation, cytokinesis, and the formation of retroviruses. A key step in these events is the assembly of monomeric Vps4 into the active ATPase complex, which is aided in part by binding of Vps4 via its N-terminal MIT (microtubule interacting and trafficking) domain to its substrate ESCRT-III. We found that the 40-amino acid linker region between the MIT and the ATPase domain of Vps4 is not required for proper function but plays a role in regulating Vps4 assembly and ATPase activity. Deletion of the linker is expected to bring the MIT domains into close proximity to the central pore of the Vps4 complex. We propose that this localization of the MIT domain in linker-deleted Vps4 mimics a repositioning of the MIT domain normally caused by binding of Vps4 to ESCRT-III. This structure would allow the Vps4 complex to engage ESCRT-III subunits with both the pore and the MIT domain simultaneously, which might be essential for the ATP-driven disassembly of ESCRT-III.

Relief of autoinhibition enhances Vta1 activation of Vps4 via the Vps4 stimulatory element.

The endosomal sorting complexes required for transport (ESCRTs) impact multiple cellular processes including multivesicular body sorting, abscission, and viral budding. The AAA-ATPase Vps4 is required for ESCRT function, and its full activity is dependent upon the co-factor Vta1. The Vta1 carboxyl-terminal Vta1 SBP1 Lip5 (VSL) domain stimulates Vps4 function by facilitating oligomerization of Vps4 into its active state. Here we report the identification of the Vps4 stimulatory element (VSE) within Vta1 that is required for additional stimulation of Vps4 activity in vitro and in vivo. VSE activity is autoinhibited in a manner dependent upon the unstructured linker region joining the amino-terminal microtubule interacting and trafficking domains and the carboxyl-terminal VSL domain. The VSE is also required for Vta1-mediated Vps4 stimulation by ESCRT-III subunits Vps60 and Did2. These results suggest that ESCRT-III binding to the Vta1 microtubule interacting and trafficking domains relieves linker region autoinhibition of the VSE to produce maximal activation of Vps4 during ESCRT function.

Exploring various measures of the area under the curve for the assessment of dose-proportionality and estimation of bioavailability.

OBJECTIVE: In pharmacokinetics, the area under the concentration versus time curve (AUC) extrapolated to infinity (AUC0-∞) is the preferred metric but it is not always possible to have a reliable estimate of the terminal phase half-life. Here we sought to explore the accuracy of three different area measures to accurately identify dose proportionality and bioavailability. METHODS: One to three compartment model simulations with different doses for dose-proportionality or different rates and/or extents of bioavailability. Area measures evaluated were AUC0-∞, to the last quantifiable concentration (AUCtlast), and to a common time value (AUCt'). RESULTS: Under linear pharmacokinetics, AUCt' provided the most accurate measure of dose proportionality. Except for the one compartment model where AUC0-∞ provided the best predictor of the true measure, there was no clear advantage to the use of either of the three measures of AUC. CONCLUSION: With uncertainty about the terminal phase half-life, the use of AUCt' can be a very useful and even the preferred measure of exposure for use in assessing proportionality in exposure between doses. The choice of AUC measure in bioavailability is less clear and may depend on compartmental nature of the drug, and study parameters including assay sensitivity and sampling protocols.

Real-time active constraint generation and enforcement for surgical tools using 3D detection and localisation network.

Introduction: Collaborative robots, designed to work alongside humans for manipulating end-effectors, greatly benefit from the implementation of active constraints. This process comprises the definition of a boundary, followed by the enforcement of some control algorithm when the robot tooltip interacts with the generated boundary. Contact with the constraint boundary is communicated to the human operator through various potential forms of feedback. In fields like surgical robotics, where patient safety is paramount, implementing active constraints can prevent the robot from interacting with portions of the patient anatomy that shouldn't be operated on. Despite improvements in orthopaedic surgical robots, however, there exists a gap between bulky systems with haptic feedback capabilities and miniaturised systems that only allow for boundary control, where interaction with the active constraint boundary interrupts robot functions. Generally, active constraint generation relies on optical tracking systems and preoperative imaging techniques. Methods: This paper presents a refined version of the Signature Robot, a three degrees-of-freedom, hands-on collaborative system for orthopaedic surgery. Additionally, it presents a method for generating and enforcing active constraints "on-the-fly" using our previously introduced monocular, RGB, camera-based network, SimPS-Net. The network was deployed in real-time for the purpose of boundary definition. This boundary was subsequently used for constraint enforcement testing. The robot was utilised to test two different active constraints: a safe region and a restricted region. Results: The network success rate, defined as the ratio of correct over total object localisation results, was calculated to be 54.7% ± 5.2%. In the safe region case, haptic feedback resisted tooltip manipulation beyond the active constraint boundary, with a mean distance from the boundary of 2.70 mm ± 0.37 mm and a mean exit duration of 0.76 s ± 0.11 s. For the restricted-zone constraint, the operator was successfully prevented from penetrating the boundary in 100% of attempts. Discussion: This paper showcases the viability of the proposed robotic platform and presents promising results of a versatile constraint generation and enforcement pipeline.

Regulation of Vps4 during MVB sorting and cytokinesis.

Multivesicular body (MVB) formation is the result of invagination and budding of the endosomal limiting membrane into its intralumenal space. These intralumenal vesicles (ILVs) contain a subset of endosomal transmembrane cargoes destined for degradation within the lysosome, the result of active selection during MVB sorting. Membrane bending and scission during ILV formation is topologically similar to cytokinesis in that both events require the abscission of a membrane neck that is oriented away from the cytoplasm. The endosomal sorting complexes required for transport (ESCRTs) represent cellular machinery whose function makes essential contributions to both of these processes. In particular, the AAA-ATPase Vps4 and its substrate ESCRT-III are key components that seem to execute the membrane abscission reaction. This review summarizes current knowledge about the Vps4-ESCRT-III system and discusses a model for how the recruitment of Vps4 to the different sites of function might be regulated.

Structural basis of Vta1 function in the multivesicular body sorting pathway.

The MVB pathway plays essential roles in several eukaryotic cellular processes. Proper function of the MVB pathway requires reversible membrane association of the ESCRTs, a process catalyzed by Vps4 ATPase. Vta1 regulates the Vps4 activity, but its mechanism of action was poorly understood. We report the high-resolution crystal structures of the Did2- and Vps60-binding N-terminal domain and the Vps4-binding C-terminal domain of S. cerevisiae Vta1. The C-terminal domain also mediates Vta1 dimerization and both subunits are required for its function as a Vps4 regulator. Emerging from our analysis is a mechanism of regulation by Vta1 in which the C-terminal domain stabilizes the ATP-dependent double ring assembly of Vps4. In addition, the MIT motif-containing N-terminal domain, projected by a long disordered linker, allows contact between the Vps4 disassembly machinery and the accessory ESCRT-III proteins. This provides an additional level of regulation and coordination for ESCRT-III assembly and disassembly.

ESCRT-III family members stimulate Vps4 ATPase activity directly or via Vta1.

The AAA-ATPase Vps4 is critical for function of the MVB sorting pathway, which in turn impacts cellular phenomena ranging from receptor downregulation to viral budding to cytokinesis. Vps4 dissociates ESCRTs from endosomal membranes during MVB sorting, but it is unclear how Vps4 ATPase activity is synchronized with ESCRT release. Vta1 potentiates Vps4 activity and interacts with ESCRT-III family members. We have investigated the impact of Vta1 and ESCRT-III family members on Vps4 ATPase activity. Two distinct mechanisms of Vps4 stimulation are described: Vps2 can directly stimulate Vps4 via its MIT domain, whereas Vps60 stimulates via Vta1. Moreover, Did2 can stimulate Vps4 by both mechanisms in distinct contexts. Recent structural determination of the ESCRT-III-binding region of Vta1 unexpectedly revealed a MIT-like region. These data support a model wherein a network of MIT and MIT-like domain interactions with ESCRT-III subunits contributes to the regulation of Vps4 activity during MVB sorting.