Cryptic enzymatic assembly of peptides armed with ß-lactone warheads.

Nature has evolved biosynthetic pathways to molecules possessing reactive warheads that inspired the development of many therapeutic agents, including penicillin antibiotics. Peptides armed with electrophilic warheads have proven to be particularly effective covalent inhibitors, providing essential antimicrobial, antiviral and anticancer agents. Here we provide a full characterization of the pathways that nature deploys to assemble peptides with ß-lactone warheads, which are potent proteasome inhibitors with promising anticancer activity. Warhead assembly involves a three-step cryptic methylation sequence, which is likely required to reduce unfavorable electrostatic interactions during the sterically demanding ß-lactonization. Amide-bond synthetase and adenosine triphosphate (ATP)-grasp enzymes couple amino acids to the ß-lactone warhead, generating the bioactive peptide products. After reconstituting the entire pathway to ß-lactone peptides in vitro, we go on to deliver a diverse range of analogs through enzymatic cascade reactions. Our approach is more efficient and cleaner than the synthetic methods currently used to produce clinically important warhead-containing peptides.

Thermal Transport and Mechanical Stress Mapping of a Compression Bonded GaN/Diamond Interface for Vertical Power Devices.

Bonding diamond to the back side of gallium nitride (GaN) electronics has been shown to improve thermal management in lateral devices; however, engineering challenges remain with the bonding process and characterizing the bond quality for vertical device architectures. Here, integration of these two materials is achieved by room-temperature compression bonding centimeter-scale GaN and a diamond die via an intermetallic bonding layer of Ti/Au. Recent attempts at GaN/diamond bonding have utilized a modified surface activation bonding (SAB) method, which requires Ar fast atom bombardment immediately followed by bonding within the same tool under ultrahigh vacuum (UHV) conditions. The method presented here does not require a dedicated SAB tool yet still achieves bonding via a room-temperature metal-metal compression process. Imaging of the buried interface and the total bonding area is achieved via transmission electron microscopy (TEM) and confocal acoustic scanning microscopy (C-SAM), respectively. The thermal transport quality of the bond is extracted from spatially resolved frequency-domain thermoreflectance (FDTR) with the bonded areas boasting a thermal boundary conductance of >100 MW/m2·K. Additionally, Raman maps of GaN near the GaN-diamond interface reveal a low level of compressive stress, <80 MPa, in well-bonded regions. FDTR and Raman were coutilized to map these buried interfaces and revealed some poor thermally bonded areas bordered by high-stress regions, highlighting the importance of spatial sampling for a complete picture of bond quality. Overall, this work demonstrates a novel method for thermal management in vertical GaN devices that maintains low intrinsic stresses while boasting high thermal boundary conductances.

Inversion for Thermal Properties with Frequency Domain Thermoreflectance.

3D integration of multiple microelectronic devices improves size, weight, and power while increasing the number of interconnections between components. One integration method involves the use of metal bump bonds to connect devices and components on a common interposer platform. Significant variations in the coefficient of thermal expansion in such systems lead to stresses that can cause thermomechanical and electrical failures. More advanced characterization and failure analysis techniques are necessary to assess the bond quality between components. Frequency domain thermoreflectance (FDTR) is a nondestructive, noncontact testing method used to determine thermal properties in a sample by fitting the phase lag between an applied heat flux and the surface temperature response. The typical use of FDTR data involves fitting for thermal properties in geometries with a high degree of symmetry. In this work, finite element method simulations are performed using high performance computing codes to facilitate the modeling of samples with arbitrary geometric complexity. A gradient-based optimization technique is also presented to determine unknown thermal properties in a discretized domain. Using experimental FDTR data from a GaN-diamond sample, thermal conductivity is then determined in an unknown layer to provide a spatial map of bond quality at various points in the sample.

Phosphoregulation of the checkpoint kinase Mec1ATR.

Yeast Mec1, and its mammalian ortholog, Ataxia-Telangiectasia and Rad3-related, are giant protein kinases central to replication stress and double strand DNA break repair. Mec1ATR, in complex with Ddc2ATRIP, is a 'sensor' of single stranded DNA, and phosphorylates numerous cell cycle and DNA repair factors to enforce cell cycle arrest and facilitate repair. Over the last several years, new techniques - particularly in structural biology - have provided molecular mechanisms for Mec1ATR function. It is becoming increasingly clear how post-translational modification of Mec1ATR and its interaction partners modulates the DNA damage checkpoint. In this review, we summarise the most recent work unravelling Mec1ATR function in the DNA damage checkpoint and provide a molecular context for its regulation by phosphorylation.

Phosphoregulation of DNA repair via the Rad51 auxiliary factor Swi5-Sfr1.

Homologous recombination (HR) is a major pathway for the repair of DNA double-strand breaks, the most severe form of DNA damage. The Rad51 protein is central to HR, but multiple auxiliary factors regulate its activity. The heterodimeric Swi5-Sfr1 complex is one such factor. It was previously shown that two sites within the intrinsically disordered domain of Sfr1 are critical for the interaction with Rad51. Here, we show that phosphorylation of five residues within this domain regulates the interaction of Swi5-Sfr1 with Rad51. Biochemical reconstitutions demonstrated that a phosphomimetic mutant version of Swi5-Sfr1 is defective in both the physical and functional interaction with Rad51. This translated to a defect in DNA repair, with the phosphomimetic mutant yeast strain phenocopying a previously established interaction mutant. Interestingly, a strain in which Sfr1 phosphorylation was blocked also displayed sensitivity to DNA damage. Taken together, we propose that controlled phosphorylation of Sfr1 is important for the role of Swi5-Sfr1 in promoting Rad51-dependent DNA repair.

A DNA damage-induced phosphorylation circuit enhances Mec1ATR Ddc2ATRIP recruitment to Replication Protein A.

The cell cycle checkpoint kinase Mec1ATR and its integral partner Ddc2ATRIP are vital for the DNA damage and replication stress response. Mec1-Ddc2 "senses" single-stranded DNA (ssDNA) by being recruited to the ssDNA binding Replication Protein A (RPA) via Ddc2. In this study, we show that a DNA damage-induced phosphorylation circuit modulates checkpoint recruitment and function. We demonstrate that Ddc2-RPA interactions modulate the association between RPA and ssDNA and that Rfa1-phosphorylation aids in the further recruitment of Mec1-Ddc2. We also uncover an underappreciated role for Ddc2 phosphorylation that enhances its recruitment to RPA-ssDNA that is important for the DNA damage checkpoint in yeast. The crystal structure of a phosphorylated Ddc2 peptide in complex with its RPA interaction domain provides molecular details of how checkpoint recruitment is enhanced, which involves Zn2+. Using electron microscopy and structural modeling approaches, we propose that Mec1-Ddc2 complexes can form higher order assemblies with RPA when Ddc2 is phosphorylated. Together, our results provide insight into Mec1 recruitment and suggest that formation of supramolecular complexes of RPA and Mec1-Ddc2, modulated by phosphorylation, would allow for rapid clustering of damage foci to promote checkpoint signaling.

Dominant carnivore loss benefits native avian and invasive mammalian scavengers.

Scavenging by large carnivores is integral for ecosystem functioning by limiting the build-up of carrion and facilitating widespread energy flows. However, top carnivores have declined across the world, triggering trophic shifts within ecosystems. Here, we compare findings from previous work on predator decline against areas with recent native mammalian carnivore loss. Specifically, we investigate top-down control on utilization of experimentally placed carcasses by two mesoscavengers-the invasive feral cat and native forest raven. Ravens profited most from carnivore loss, scavenging for five times longer in the absence of native mammalian carnivores. Cats scavenged on half of all carcasses in the region without dominant native carnivores. This was eight times more than in areas where other carnivores were at high densities. All carcasses persisted longer than the three-week monitoring period in the absence of native mammalian carnivores, while in areas with high carnivore abundance, all carcasses were fully consumed. Our results reveal that top-carnivore loss amplifies impacts associated with carnivore decline-increased carcass persistence and carrion access for smaller scavengers. This suggests that even at low densities, native mammalian carnivores can fulfil their ecological functions, demonstrating the significance of global carnivore conservation and supporting management approaches, such as trophic rewilding.

Spatial pattern analysis of line-segment data in ecology.

The spatial analysis of linear features (lines and curves) is a challenging and rarely attempted problem in ecology. Existing methods are typically expressed in abstract mathematical formalism, making it difficult to assess their relevance and transferability into an ecological setting. We introduce a set of concrete and accessible methods to analyze the spatial patterning of line-segment data. The methods include Monte Carlo techniques based on a new generalization of Ripley's K -function and a class of line-segment processes that can be used to specify parametric models: parameters are estimated using maximum likelihood and models compared using information-theoretic principles. We apply the new methods to fallen tree (dead log) data collected from two 1-ha Australian tall eucalypt forest plots. Our results show that the spatial pattern of the fallen logs is best explained by plot-level spatial heterogeneity in combination with a slope-dependent nonuniform distribution of fallen-log orientations. These methods are of a general nature and are applicable to any line-segment data. In the context of forest ecology, the integration of fallen logs as linear structural features in a landscape with the point locations of living trees, and a quantification of their interactions, can yield new insights into the functional and structural role of tree fall in forest communities and their enduring post-mortem ecological legacy as spatially distributed decomposing logs.

Steady-state methods for measuring in-plane thermal conductivity of thin films for heat spreading applications.

The development of high thermal conductivity thin film materials for the thermal management of electronics requires accurate and precise methods for characterizing heat spreading capability, namely, in-plane thermal conductivity. However, due to the complex nature of thin film thermal property measurements, resolving the in-plane thermal conductivity of high thermal conductivity anisotropic thin films with high accuracy is particularly challenging. Capable transient techniques exist; however, they usually measure thermal diffusivity and require heat capacity and density to deduce thermal conductivity. Here, we present an explicit uncertainty analysis framework for accurately resolving in-plane thermal conductivity via two independent steady-state thermometry techniques: particle-assisted Raman thermometry and electrical resistance thermometry. Additionally, we establish error-based criteria to determine the limiting experimental conditions that permit the simplifying assumption of one-dimensional thermal conduction to further reduce thermal analysis. We demonstrate the accuracy and precision (<5% uncertainty) of both steady-state techniques through in-plane thermal conductivity measurements of anisotropic nanocrystalline diamond thin films.

Parsimonious model selection using information theory: a modified selection rule.

Information-theoretic approaches to model selection, such as Akaike's information criterion (AIC) and cross validation, provide a rigorous framework to select among candidate hypotheses in ecology, yet the persistent concern of overfitting undermines the interpretation of inferred processes. A common misconception is that overfitting is due to the choice of criterion or model score, despite research demonstrating that selection uncertainty associated with score estimation is the predominant influence. Here we introduce a novel selection rule that identifies a parsimonious model by directly accounting for estimation uncertainty, while still retaining an information-theoretic interpretation. The new rule, which is a modification of the existing one-standard-error rule, mitigates overfitting and reduces the likelihood that spurious effects will be included in the selected model, thereby improving its inferential properties. We present the rule and illustrative examples in the context of maximum-likelihood estimation and Kullback-Leibler discrepancy, although the rule is applicable in a more general setting, including Bayesian model selection and other types of discrepancy.

Roadkill islands: Carnivore extinction shifts seasonal use of roadside carrion by generalist avian scavenger.

Global road networks facilitate habitat modification and are integral to human expansion. Many animals, particularly scavengers, use roads as they provide a reliable source of food, such as carrion left after vehicle collisions. Tasmania is often cited as the 'roadkill capital of Australia', with the isolated offshore islands in the Bass Strait experiencing similar, if not higher, levels of roadkill. However, native mammalian predators on the islands are extirpated, meaning the remaining scavengers are likely to experience lower interference competition. In this study, we used a naturally occurring experiment to examine how the loss of mammalian carnivores within a community impacts roadside foraging behaviour by avian scavengers. We monitored the locations of roadkill and forest ravens Corvus tasmanicus, an abundant scavenger species, on eight road transects across the Tasmanian mainland (high scavenging competition) and the Bass Strait islands (low scavenging competition). We represented raven observations as one-dimensional point patterns, using hierarchical Bayesian models to investigate the dependence of raven spatial intensity on habitat, season, distance to roadkill and route location. We found that roadkill carcasses were a strong predictor of raven presence along road networks. The effect of roadkill was amplified on roads on the Bass Strait islands, where roadside carrion was a predictor of raven presence across the entire year. In contrast, ravens were more often associated with roadkill on Tasmanian mainland roads in the autumn, when other resources were low. This suggests that in the absence of competing mammalian scavengers, ravens choose to feed on roadside carrion throughout the year, even in seasons when other resources are available. This lack of competition could be disproportionately benefiting forest ravens, leading to augmented raven populations and changes to the vertebrate community structure. Our study provides evidence that scavengers modify their behaviour in response to reduced scavenger species diversity, potentially triggering trophic shifts and highlighting the importance of conserving or reintroducing carnivores within ecosystems.

Regulation of DNA break repair by RNA.

Genomic stability is critical for cell survival and its effective repair when damaged is a vital process for preserving genetic information. Failure to correctly repair the genome can lead to the accumulation of mutations that ultimately drives carcinogenesis. Life has evolved sophisticated surveillance, repair pathways, and mechanisms to recognize and mend genomic lesions to preserve its integrity. Many of these pathways involve a cascade of protein effectors that act to identify the type of damage, such as double-strand (ds) DNA breaks, propagate the damage signal, and recruit an array of other protein factors to resolve the damage without loss of genetic information. It is now becoming increasingly clear that there are a number of RNA processing factors, such as the transcriptional machinery, and microRNA biogenesis components, as well as RNA itself, that facilitate the repair of DNA damage. Here, some of the recent work unravelling the role of RNA in the DNA Damage Response (DDR), in particular the dsDNA break repair pathway, will be reviewed.

Mechanism of auto-inhibition and activation of Mec1ATR checkpoint kinase.

In response to DNA damage or replication fork stalling, the basal activity of Mec1ATR is stimulated in a cell-cycle-dependent manner, leading to cell-cycle arrest and the promotion of DNA repair. Mec1ATR dysfunction leads to cell death in yeast and causes chromosome instability and embryonic lethality in mammals. Thus, ATR is a major target for cancer therapies in homologous recombination-deficient cancers. Here we identify a single mutation in Mec1, conserved in ATR, that results in constitutive activity. Using cryo-electron microscopy, we determine the structures of this constitutively active form (Mec1(F2244L)-Ddc2) at 2.8 Å and the wild type at 3.8 Å, both in complex with Mg2+-AMP-PNP. These structures yield a near-complete atomic model for Mec1-Ddc2 and uncover the molecular basis for low basal activity and the conformational changes required for activation. Combined with biochemical and genetic data, we discover key regulatory regions and propose a Mec1 activation mechanism.

Continuing to look in the mirror: A review of neuroscientific evidence for the broken mirror hypothesis, EP-M model and STORM model of autism spectrum conditions.

LAY ABSTRACT: The mirror neuron system has been argued to be a key brain system responsible for understanding the actions of others and for imitation. It has therefore been proposed that problems within this system could explain the social difficulties experienced by people with autism spectrum condition. This idea is referred to as the broken mirror hypothesis. However, research has produced insufficient evidence to support the broken mirror hypothesis in its original form. Therefore, two other models have been suggested: EP-M model and the social top-down response modulation (STORM) model. All models suggest something is different regarding the mirror neuron system in autism spectrum condition: either within the mirror neuron system itself or within the systems that control the activity of the mirror neuron system. This literature review compares these three models in regard to recent neuroscientific investigations. This review concludes that there is insufficient support for both the broken mirror hypothesis, but converging evidence supports an integrated EP-M and STORM model.

Bulk-like Intrinsic Phonon Thermal Conductivity of Micrometer-Thick AlN Films.

Aluminum nitride (AlN) has garnered much attention due to its intrinsically high thermal conductivity. However, engineering thin films of AlN with these high thermal conductivities can be challenging due to vacancies and defects that can form during the synthesis. In this work, we report on the cross-plane thermal conductivity of ultra-high-purity single-crystal AlN films with different thicknesses (∼3-22 µm) via time-domain thermoreflectance (TDTR) and steady-state thermoreflectance (SSTR) from 80 to 500 K. At room temperature, we report a thermal conductivity of ∼320 ± 42 W m-1 K-1, surpassing the values of prior measurements on AlN thin films and one of the highest cross-plane thermal conductivities of any material for films with equivalent thicknesses, surpassed only by diamond. By conducting first-principles calculations, we show that the thermal conductivity measurements on our thin films in the 250-500 K temperature range agree well with the predicted values for the bulk thermal conductivity of pure single-crystal AlN. Thus, our results demonstrate the viability of high-quality AlN films as promising candidates for the high-thermal-conductivity layers in high-power microelectronic devices. Our results also provide insight into the intrinsic thermal conductivity of thin films and the nature of phonon-boundary scattering in single-crystal epitaxially grown AlN thin films. The measured thermal conductivities in high-quality AlN thin films are found to be constant and similar to bulk AlN, regardless of the thermal penetration depth, film thickness, or laser spot size, even when these characteristic length scales are less than the mean free paths of a considerable portion of thermal phonons. Collectively, our data suggest that the intrinsic thermal conductivity of thin films with thicknesses less than the thermal phonon mean free paths is the same as bulk so long as the thermal conductivity of the film is sampled independent of the film/substrate interface.

Covalent Post-Assembly Modification: A Synthetic Multipurpose Tool in Supramolecular Chemistry.

The use of covalent post-assembly modification (PAM) in supramolecular chemistry has grown significantly in recent years, to the point where PAM is now a versatile synthesis tool for tuning, modulating, and expanding the functionality of self-assembled complexes and materials. PAM underpins supramolecular template-synthesis strategies, enables modular derivatization of supramolecular assemblies, permits the covalent 'locking' of unstable structures, and can trigger controlled structural transformations between different assembled morphologies. This Review discusses key examples of PAM spanning a range of material classes, including discrete supramolecular complexes, self-assembled soft nanostructures and hierarchically ordered polymeric and framework materials. As such, we hope to highlight how PAM has continued to evolve as a creative and functional addition to the synthetic chemist's toolbox for constructing bespoke self-assembled complexes and materials.

New horizons in iron deficiency anaemia in older adults.

Iron deficiency anaemia (IDA) is common in older adults and associated with a range of adverse outcomes. Differentiating iron deficiency from other causes of anaemia is important to ensure appropriate investigations and treatment. It is possible to make the diagnosis reliably using simple blood tests. Clinical evaluation and assessment are required to help determine the underlying cause and to initiate appropriate investigations. IDA in men and post-menopausal females is most commonly due to occult gastrointestinal blood loss until proven otherwise, although there is a spectrum of underlying causative pathologies. Investigation decisions should take account of the wishes of the patient and their competing comorbidities, individualising the approach. Management involves supplementation using oral or intravenous (IV) iron then consideration of treatment of the underlying cause of deficiency. Future research areas are outlined including the role of Hepcidin and serum soluble transferrin receptor measurement, quantitative faecal immunochemical testing, alternative dosing regimens and the potential role of IV iron preparations.

Interfacial Thermal Conductance across Room-Temperature-Bonded GaN/Diamond Interfaces for GaN-on-Diamond Devices.

The wide bandgap, high-breakdown electric field, and high carrier mobility makes GaN an ideal material for high-power and high-frequency electronics applications, such as wireless communication and radar systems. However, the performance and reliability of GaN-based high-electron-mobility transistors (HEMTs) are limited by the high channel temperature induced by Joule heating in the device channel. Integration of GaN with high thermal conductivity substrates can improve the heat extraction from GaN-based HEMTs and lower the operating temperature of the device. However, heterogeneous integration of GaN with diamond substrates presents technical challenges to maximize the heat dissipation potential brought by the ultrahigh thermal conductivity of diamond substrates. In this work, two modified room-temperature surface-activated bonding (SAB) techniques are used to bond GaN and single-crystal diamond. Time-domain thermoreflectance (TDTR) is used to measure the thermal properties from room temperature to 480 K. A relatively large thermal boundary conductance (TBC) of the GaN/diamond interfaces with a ∼4 nm interlayer (∼90 MW/(m2 K)) was observed and material characterization was performed to link the interfacial structure with the TBC. Device modeling shows that the measured TBC of the bonded GaN/diamond interfaces can enable high-power GaN devices by taking full advantage of the ultrahigh thermal conductivity of single-crystal diamond. For the modeled devices, the power density of GaN-on-diamond can reach values ∼2.5 times higher than that of GaN-on-SiC and ∼5.4 times higher than that of GaN-on-Si with a maximum device temperature of 250 °C. Our work sheds light on the potential for room-temperature heterogeneous integration of semiconductors with diamond for applications of electronics cooling, especially for GaN-on-diamond devices.

Structures and regulations of ATM and ATR, master kinases in genome integrity.

Homologous recombination (HR) is a faithful repair mechanism for double stranded DNA breaks. Two highly homologous master kinases, the tumour suppressors ATM and ATR (Tel1 and Mec1 in yeast), coordinate cell cycle progression with repair during HR. Despite their importance, our molecular understanding of these apical coordinators has been limited, in part due to their large sizes. With the recent development in cryo-electron microscopy, significant advances have been made in structural characterisation of these proteins in the last two years. These structures, combined with new biochemical studies, now provide a more detailed understanding of how a low basal activity is maintained and how activation may occur. In this review, we summarize recent advances in the structural and molecular understanding of these key components in HR, compare the common and distinct features of these kinases and suggest aspects of structural components that are likely to be involved in regulating its activity.