From Diversity, Equity, and Inclusion to an Antiracism Strategic Plan: An Academic Department of Psychiatry's Journey.

The efforts of an academic psychiatry department to embark on an antiracism strategic planning process are outlined, including the establishment of an antiracism task force charged with the development of an antiracism strategic plan. The initial process of the task force is described, recommendations are summarized, and future directions are outlined.

Clonal expansion and rapid characterization of Klebsiella pneumoniae ST1788, an otherwise uncommon strain spreading in Wales, UK.

A multidrug-resistant strain of Klebsiella pneumoniae (Kp) sequence type (ST) 1788, an otherwise uncommon ST worldwide, was isolated from 65 patients at 11 hospitals and 11 general practices across South and West Wales, UK, between February 2019 and November 2021. A collection of 97 Kp ST1788 isolates (including 94 from Wales) was analysed to investigate the diversity and spread across Wales and to identify molecular marker(s) to aid development of a strain-specific real-time PCR. Whole genome sequencing (WGS) was performed with Illumina technology and the data were used to perform phylogenetic analyses. Pan-genome analysis of further Kp genome collections was used to identify an ST1788-specific gene target; a real-time PCR was then validated against a panel of 314 strains and 218 broth-enriched screening samples. Low genomic diversity was demonstrated amongst the 94 isolates from Wales. Evidence of spread within and across healthcare facilities was found. A yersiniabactin locus and the KL2 capsular locus were identified in 85/94 (90.4 %) and 94/94 (100 %) genomes respectively; bla SHV-232, bla TEM-1, bla CTX-M-15 and bla OXA-1 were simultaneously carried by 86/94 (91.5 %) isolates; 4/94 (4.3 %) isolates also carried bla OXA-48 carbapenemase. Aminoglycoside and fluoroquinolone resistance markers were found in 94/94 (100 %) and 86/94 (91.5 %) isolates respectively. The ST1788-specific real-time PCR was 100 % sensitive and specific. Our analyses demonstrated recent clonal expansion and spread of Kp ST1788 in the community and across healthcare facilities in South and West Wales with isolates carrying well-defined antimicrobial resistance and virulence markers. An ST1788-specific marker was also identified, enabling rapid and reliable preliminary characterization of isolates by real-time PCR. This study confirms the utility of WGS in investigating novel strains and in aiding proactive implementation of molecular tools to assist infection control specialists.

Substrate promiscuity of a de novo designed peroxidase.

The design and construction of de novo enzymes offer potentially facile routes to exploiting powerful chemistries in robust, expressible and customisable protein frameworks, while providing insight into natural enzyme function. To this end, we have recently demonstrated extensive catalytic promiscuity in a heme-containing de novo protein, C45. The diverse transformations that C45 catalyses include substrate oxidation, dehalogenation and carbon­carbon bond formation. Here we explore the substrate promiscuity of C45's peroxidase activity, screening the de novo enzyme against a panel of peroxidase and dehaloperoxidase substrates. Consistent with the function of natural peroxidases, C45 exhibits a broad spectrum of substrate activities with selectivity dictated primarily by the redox potential of the substrate, and by extension, the active oxidising species in peroxidase chemistry, compounds I and II. Though the comparison of these redox potentials provides a threshold for determining activity for a given substrate, substrate:protein interactions are also likely to play a significant role in determining electron transfer rates from substrate to heme, affecting the kinetic parameters of the enzyme. We also used biomolecular simulation to screen substrates against a computational model of C45 to identify potential interactions and binding sites. Several sites of interest in close proximity to the heme cofactor were discovered, providing insight into the catalytic workings of C45.

Female birds monitor the activity of their mates while brooding nest-bound young.

In addition to food and protection, altricial young in many species are ectothermic and require that endothermic parents provide warmth to foster growth, yet only one parent-typically the female-broods these young to keep them warm. When this occurs, reduced provisioning by males obliges females to forage instead of providing warmth for offspring, favoring the temporal mapping of male activities. We assessed this in a wild house wren population while experimentally feeding nestlings to control offspring satiety. While brooding, females look out from the nest to inspect their surroundings, and we hypothesized that this helps to determine if their mate is nearby and likely to deliver food to the brood (males pass food to brooding females, which pass the food to nestlings). Females looked out from the nest less often when their partner was singing nearby and when his singing and provisioning were temporally linked, signaling his impending food delivery. Females also left to forage less often when their mate was nearby and likely to deliver food. Nestling begging did not affect these behaviors. Females looking out from the nest more often also provisioned at a higher rate and were more likely to divorce and find a new mate prior to nesting again within seasons, as expected if females switch mates when a male fails to meet expectations. Our results suggest anticipatory effects generated by male behavior and that brooding females temporally map male activity to inform decisions about whether to continue brooding or to leave the nest to forage.

The Thyroid Tumor Microenvironment: Potential Targets for Therapeutic Intervention and Prognostication.

Thyroid cancer is the most common endocrine malignancy and incidences are rising rapidly, in both pediatric and adult populations. Many thyroid tumors are successfully treated which results in low mortality rates, but there is often a significant morbidity associated with thyroid cancer treatments. For patients with tumors that are not successfully treated with surgical resection or radioactive iodine treatment, prognosis is dramatically reduced. Patients diagnosed with anaplastic thyroid cancer face a very grim prognosis with a median survival of 6 months post-diagnosis. There is a critical need to identify patients who are at greatest risk of developing persistent disease and progressing to poorly differentiated or anaplastic disease. Furthermore, development of treatments associated with less morbidity would represent a significant improvement for thyroid cancer survivors. It is well established the stromal cells and components of the tumor microenvironment can drive tumor progression and resistance to therapy. Here we review the current state of what is known regarding the thyroid tumor microenvironment and how these factors may contribute to thyroid tumor pathogenesis. Study of the tumor microenvironment within thyroid cancer is a relatively new field, and more studies are needed to dissect the complex and dynamic crosstalk between thyroid tumor cells and its tumor niche.

Condition-Dependent Begging Elicits Increased Parental Investment in a Wild Bird Population.

The coevolution of parental supply and offspring demand has long been thought to involve offspring need driving begging and parental care, leaving other hypotheses underexplored. In a population of wild birds, we experimentally tested whether begging serves as a negatively condition-dependent signal of need or a positively condition-dependent signal of quality. Across multiple years, we supplemented nestling house wrens with food shortly after hatching and simultaneously manipulated corticosterone levels to simulate the hunger-induced increase in glucocorticoids thought to mediate begging. This allowed us to also test whether begging is simply a proximate signal of hunger. Days after supplementation ended, food-supplemented nestlings were in better condition than nonsupplemented nestlings and begged for food at an increased rate; their parents, in turn, increased provisioning to a greater extent than parents of nonsupplemented young, as begging positively predicted provisioning. Food-supplemented nestlings therefore attained above-average condition, which predicted their recruitment as breeding adults in the local population. Glucocorticoids increased begging in the short term, but this transient effect depended on satiety. Thus, glucocorticoids promoted begging as a proximate response to hunger, whereas the longer-term changes in nestling condition, begging, and food provisioning suggest that begging ultimately signals offspring quality to elicit increased investment, thereby enhancing offspring survival.

Construction and in vivo assembly of a catalytically proficient and hyperthermostable de novo enzyme.

Although catalytic mechanisms in natural enzymes are well understood, achieving the diverse palette of reaction chemistries in re-engineered native proteins has proved challenging. Wholesale modification of natural enzymes is potentially compromised by their intrinsic complexity, which often obscures the underlying principles governing biocatalytic efficiency. The maquette approach can circumvent this complexity by combining a robust de novo designed chassis with a design process that avoids atomistic mimicry of natural proteins. Here, we apply this method to the construction of a highly efficient, promiscuous, and thermostable artificial enzyme that catalyzes a diverse array of substrate oxidations coupled to the reduction of H2O2. The maquette exhibits kinetics that match and even surpass those of certain natural peroxidases, retains its activity at elevated temperature and in the presence of organic solvents, and provides a simple platform for interrogating catalytic intermediates common to natural heme-containing enzymes.Catalytic mechanisms of enzymes are well understood, but achieving diverse reaction chemistries in re-engineered proteins can be difficult. Here the authors show a highly efficient and thermostable artificial enzyme that catalyzes a diverse array of substrate oxidations coupled to the reduction of H2O2.

A suite of de novo c-type cytochromes for functional oxidoreductase engineering.

Central to the design of an efficient de novo enzyme is a robust yet mutable protein scaffold. The maquette approach to protein design offers precisely this, employing simple four-α-helix bundle scaffolds devoid of evolutionary complexity and with proven tolerance towards iterative protein engineering. We recently described the design of C2, a de novo designed c-type cytochrome maquette that undergoes post-translational modification in E. coli to covalently graft heme onto the protein backbone in vivo. This de novo cytochrome is capable of reversible oxygen binding, an obligate step in the catalytic cycle of many oxygen-activating oxidoreductases. Here we demonstrate the flexibility of both the maquette platform and the post-translational machinery of E. coli by creating a suite of functional de novo designed c-type cytochromes. We explore the engineering tolerances of the maquette by selecting alternative binding sites for heme C attachment and creating di-heme maquettes either by appending an additional heme C binding motif to the maquette scaffold or by binding heme B through simple bis-histidine ligation to a second binding site. The new designs retain the essential properties of the parent design but with significant improvements in structural stability. Molecular dynamics simulations aid the rationalization of these functional improvements while providing insight into the rules for engineering heme C binding sites in future iterations. This versatile, functional suite of de novo c-type cytochromes shows significant promise in providing robust platforms for the future engineering of de novo oxygen-activating oxidoreductases. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electron transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.