Functional transitions in enzyme evolution: Balancing stability, folding and catalytic specificity

Evolutionary pathways by which proteins have evolved in Nature over billions of years have resulted in an impressive diversity of structures that carry out many functions with unrivalled efficiency. Directed protein evolution in the test tube can emulate natural evolution, but is often limited by low hit rates and small improvements during evolutionary cycles. Furthermore, the combination of mutations that is needed for large improvements cannot always be reached by one-by-one mutational steps due to the occurrence of general loss-of-function mutations or epistatic ratchets. The question then arises how evolutionary dead ends can be avoided. Important parameters that shape these fitness landscapes are e.g. expression level, stability and catalytic activity/specificity. We are currently probing these parameters for ancestral sequences inferred from phylogenetic relationships between members of the catalytically diverse metallo-β-lactamase1 and alkaline phosphatase2-4 superfamilies. Mapping of substrate specificity profiles on the genetic relationships allowed the identification of the ancestral nodes between which transitions in primary function most likely occur. The latter is one of the key processes in evolution of new functions. The substrate specificity profiles of the current enzymes suggest that the change in primary function is the result of a shift in substrate preference rather than de novo evolutionary invention of a novel activity. Furthermore several characterized ancestral sulfatases suggest a shift toward increased specificity over evolutionary time, as well as a trend that ancestral enzymes are more stable than present day enzymes. References 1 Baier & Tokuriki (2014) Connectivity between catalytic landscapes of the metallo-β-lactamase superfamily. J. Mol. Biol. 426, 2442-2456. 2 Jonas & Hollfelder (2009) Mapping catalytic promiscuity in the alkaline phosphatase superfamily. Pure. Appl. Chem. 81, 731-742. 3 van Loo et al. (2010) An efficient, multiply promiscuous hydrolase in the alkaline phosphatase superfamily, Proc. Natl. Acad. Sci. U. S. A. 107, 2740-2745. 4 van Loo et al (2017) Balancing specificity and promiscuity in enzyme superfamily evolution: multidimensional activity transitions. submitted

Life Cycle Assessment of Composites Additive Manufacturing Using Recycled Materials

Additive manufacturing (AM) of composite materials is promising to create customizable products with enhanced properties, utilizing materials like carbon fibers (CFs). To increase their circularity, composite recycling has been proposed to re-introduce the recovered components in AM. A careful evaluation of recycling is necessary, considering the sustainability and functionality (i.e., mechanical properties) of the recovered components. Thus, Life Cycle Assessment (LCA) is applied to estimate the environmental impacts of AM via Fused Filament Fabrication (FFF), using virgin or recycled CFs via solvolysis at a laboratory scale. This study aims to provide a detailed Life Cycle Inventory (LCI) of FFF and evaluate the sustainability of using recycled CFs in AM. For both virgin CF manufacturing and CF recycling, electricity consumption was the main contributor to environmental impacts. CF recovery via solvolysis resulted in lower impacts across most impact categories compared to AM with virgin CFs. Different scenarios were examined to account for the mechanical properties of recycled CFs. AM with 75% recycled CFs, compared to 100% virgin CFs undergoing landfilling, resulted in over 22% reduction in climate change potential, even after a 50% loss of recycled CF functionality. Overall, this study offers insights into the LCI of FFF and shows that CF recycling from composites is worth pursuing

Divergent COVID-19 vaccine policies: policy mapping of ten European countries

Background: The COVID-19 pandemic highlighted the fragmented nature of governmental policy decisions in Europe. However, the extent to which COVID-19 vaccination policies differed between European countries remains unclear. Here, we mapped the COVID-19 vaccination policies that were in effect in January 2022 as well as booster regulations in April 2022 in Austria, Denmark, England, France, Germany, Ireland, Italy, the Netherlands, Poland, and Spain. Methods: National public health and health policy experts from these ten European nations developed and completed an electronic questionnaire. The questionnaire included a series of questions that addressed six critical components of vaccine implementation, including (1) authorization, (2) prioritization, (3) procurement and distribution, (4) data collection, (5) administration, and (6) mandate requirements. Results: Our findings revealed significant variations in COVID-19 vaccination policies across Europe. We observed critical differences in COVID-19 vaccine formulations authorized for use, as well as the specific groups that were provided with priority access. We also identified discrepancies in how vaccination-related data were recorded in each country and what vaccination requirements were implemented. Conclusion: Each of the ten European nations surveyed in this study reported different COVID-19 vaccination policies. These differences complicated efforts to provide a coordinated pandemic response. These findings might alert policymakers in Europe of the need to coordinate their efforts to avoid fostering divergent and socially disruptive policies

Tumor Growth Rate Estimates Are Independently Predictive of Therapy Response and Survival in Recurrent High-Grade Serous Ovarian Cancer Patients

This study aimed to assess the predictive value of tumor growth rate estimates based on serial cancer antigen-125 (CA-125) levels on therapy response and survival of patients with recurrent high-grade serous ovarian cancer (HGSOC). In total, 301 consecutive patients with advanced HGSOC (exploratory cohort: n = 155, treated at the Medical University of Vienna; external validation cohort: n = 146, from the Ovarian Cancer Therapy–Innovative Models Prolong Survival (OCTIPS) consortium) were enrolled. Tumor growth estimates were obtained using a validated two-phase equation model involving serial CA-125 levels, and their predictive value with respect to treatment response to the next chemotherapy and the prognostic value with respect to disease-specific survival and overall survival were assessed. Tumor growth estimates were an independent predictor for response to second-line chemotherapy and an independent prognostic factor for second-line chemotherapy use in both univariate and multivariable analyses, outperforming both the predictive (second line: p = 0.003, HR 5.19 [1.73–15.58] vs. p = 0.453, HR 1.95 [0.34–11.17]) and prognostic values (second line: p = 0.042, HR 1.53 [1.02–2.31] vs. p = 0.331, HR 1.39 [0.71–2.27]) of a therapy-free interval (TFI) < 6 months. Tumor growth estimates were a predictive factor for response to third- and fourth-line chemotherapy and a prognostic factor for third- and fourth-line chemotherapy use in the univariate analysis. The CA-125-derived tumor growth rate estimate may be a quantifiable and easily assessable surrogate to TFI in treatment decision making for patients with recurrent HGSOC

DNA Methylation Profiles of Ovarian Clear Cell Carcinoma

BACKGROUND: Ovarian clear cell carcinoma (OCCC) is a rare ovarian cancer histotype that tends to be resistant to standard platinum-based chemotherapeutics. We sought to better understand the role of DNA methylation in clinical and biological subclassification of OCCC. METHODS: We interrogated genome-wide methylation using DNA from fresh frozen tumors from 271 cases, applied non-smooth non-negative matrix factorization (nsNMF) clustering, and evaluated clinical associations and biological pathways. RESULTS: Two approximately equally sized clusters that associated with several clinical features were identified. Compared to Cluster 2 (N=137), Cluster 1 cases (N=134) presented at a more advanced stage, were less likely to be of Asian ancestry, and tended to have poorer outcomes including macroscopic residual disease following primary debulking surgery (p-values <0.10). Subset analyses of targeted tumor sequencing and immunohistochemical data revealed that Cluster 1 tumors showed TP53 mutation and abnormal p53 expression, and Cluster 2 tumors showed aneuploidy and ARID1A/PIK3CA mutation (p-values <0.05). Cluster-defining CpGs included 1,388 CpGs residing within 200 bp of the transcription start sites of 977 genes; 38% of these genes (N=369 genes) were differentially expressed across cluster in transcriptomic subset analysis (p-values <10(−4)). Differentially expressed genes were enriched for six immune-related pathways, including interferon alpha and gamma responses (p-values < 10(−6)). CONCLUSIONS: DNA methylation clusters in OCCC correlate with disease features and gene expression patterns among immune pathways. IMPACT: This work serves as a foundation for integrative analyses that better understand the complex biology of OCCC in an effort to improve potential for development of targeted therapeutics

Connexin43 Modulates Cell Polarity and Directional Cell Migration by Regulating Microtubule Dynamics

Knockout mice deficient in the gap junction gene connexin43 exhibit developmental anomalies associated with abnormal neural crest, primordial germ cell, and proepicardial cell migration. These migration defects are due to a loss of directional cell movement, and are associated with abnormal actin stress fiber organization and a loss of polarized cell morphology. To elucidate the mechanism by which Cx43 regulates cell polarity, we used a wound closure assays with mouse embryonic fibroblasts (MEFs) to examine polarized cell morphology and directional cell movement. Studies using embryonic fibroblasts from Cx43 knockout (Cx43KO) mice showed Cx43 deficiency caused cell polarity defects as characterized by a failure of the Golgi apparatus and the microtubule organizing center to reorient with the direction of wound closure. Actin stress fibers at the wound edge also failed to appropriately align, and stabilized microtubule (Glu-tubulin) levels were markedly reduced. Forced expression of Cx43 with deletion of its tubulin-binding domain (Cx43dT) in both wildtype MEFs and neural crest cell explants recapitulated the cell migration defects seen in Cx43KO cells. However, forced expression of Cx43 with point mutation causing gap junction channel closure had no effect on cell motility. TIRF imaging revealed increased microtubule instability in Cx43KO cells, and microtubule targeting of membrane localized Cx43 was reduced with expression of Cx43dT construct in wildtype cells. Together, these findings suggest the essential role of Cx43 gap junctions in development is mediated by regulation of the tubulin cytoskeleton and cell polarity by Cx43 via a nonchannel function

Citrullination regulates pluripotency and histone H1 binding to chromatin.

Citrullination is the post-translational conversion of an arginine residue within a protein to the non-coded amino acid citrulline. This modification leads to the loss of a positive charge and reduction in hydrogen-bonding ability. It is carried out by a small family of tissue-specific vertebrate enzymes called peptidylarginine deiminases (PADIs) and is associated with the development of diverse pathological states such as autoimmunity, cancer, neurodegenerative disorders, prion diseases and thrombosis. Nevertheless, the physiological functions of citrullination remain ill-defined, although citrullination of core histones has been linked to transcriptional regulation and the DNA damage response. PADI4 (also called PAD4 or PADV), the only PADI with a nuclear localization signal, was previously shown to act in myeloid cells where it mediates profound chromatin decondensation during the innate immune response to infection. Here we show that the expression and enzymatic activity of Padi4 are also induced under conditions of ground-state pluripotency and during reprogramming in mouse. Padi4 is part of the pluripotency transcriptional network, binding to regulatory elements of key stem-cell genes and activating their expression. Its inhibition lowers the percentage of pluripotent cells in the early mouse embryo and significantly reduces reprogramming efficiency. Using an unbiased proteomic approach we identify linker histone H1 variants, which are involved in the generation of compact chromatin, as novel PADI4 substrates. Citrullination of a single arginine residue within the DNA-binding site of H1 results in its displacement from chromatin and global chromatin decondensation. Together, these results uncover a role for citrullination in the regulation of pluripotency and provide new mechanistic insights into how citrullination regulates chromatin compaction.Cancer Research UKThis is the author accepted manuscript. The final version is available from the Nature Publishing Group via http://dx.doi.org/10.1038/nature1294

Wdpcp, a PCP Protein Required for Ciliogenesis, Regulates Directional Cell Migration and Cell Polarity by Direct Modulation of the Actin Cytoskeleton

Planar cell polarity (PCP) regulates cell alignment required for collective cell movement during embryonic development. This requires PCP/PCP effector proteins, some of which also play essential roles in ciliogenesis, highlighting the long-standing question of the role of the cilium in PCP. Wdpcp, a PCP effector, was recently shown to regulate both ciliogenesis and collective cell movement, but the underlying mechanism is unknown. Here we show Wdpcp can regulate PCP by direct modulation of the actin cytoskeleton. These studies were made possible by recovery of a Wdpcp mutant mouse model. Wdpcp-deficient mice exhibit phenotypes reminiscent of Bardet-Biedl/Meckel-Gruber ciliopathy syndromes, including cardiac outflow tract and cochlea defects associated with PCP perturbation. We observed Wdpcp is localized to the transition zone, and in Wdpcp-deficient cells, Sept2, Nphp1, and Mks1 were lost from the transition zone, indicating Wdpcp is required for recruitment of proteins essential for ciliogenesis. Wdpcp is also found in the cytoplasm, where it is localized in the actin cytoskeleton and in focal adhesions. Wdpcp interacts with Sept2 and is colocalized with Sept2 in actin filaments, but in Wdpcp-deficient cells, Sept2 was lost from the actin cytoskeleton, suggesting Wdpcp is required for Sept2 recruitment to actin filaments. Significantly, organization of the actin filaments and focal contacts were markedly changed in Wdpcp-deficient cells. This was associated with decreased membrane ruffling, failure to establish cell polarity, and loss of directional cell migration. These results suggest the PCP defects in Wdpcp mutants are not caused by loss of cilia, but by direct disruption of the actin cytoskeleton. Consistent with this, Wdpcp mutant cochlea has normal kinocilia and yet exhibits PCP defects. Together, these findings provide the first evidence, to our knowledge, that a PCP component required for ciliogenesis can directly modulate the actin cytoskeleton to regulate cell polarity and directional cell migration

Narcissism and the strategic pursuit of short-term mating : universal links across 11 world regions of the International Sexuality Description Project-2.

Previous studies have documented links between sub-clinical narcissism and the active pursuit of short-term mating strategies (e.g., unrestricted sociosexuality, marital infidelity, mate poaching). Nearly all of these investigations have relied solely on samples from Western cultures. In the current study, responses from a cross-cultural survey of 30,470 people across 53 nations spanning 11 world regions (North America, Central/South America, Northern Europe, Western Europe, Eastern Europe, Southern Europe, Middle East, Africa, Oceania, Southeast Asia, and East Asia) were used to evaluate whether narcissism (as measured by the Narcissistic Personality Inventory; NPI) was universally associated with short-term mating. Results revealed narcissism scores (including two broad factors and seven traditional facets as measured by the NPI) were functionally equivalent across cultures, reliably associating with key sexual outcomes (e.g., more active pursuit of short-term mating, intimate partner violence, and sexual aggression) and sex-related personality traits (e.g., higher extraversion and openness to experience). Whereas some features of personality (e.g., subjective well-being) were universally associated with socially adaptive facets of Narcissism (e.g., self-sufficiency), most indicators of short-term mating (e.g., unrestricted sociosexuality and marital infidelity) were universally associated with the socially maladaptive facets of narcissism (e.g., exploitativeness). Discussion addresses limitations of these cross-culturally universal findings and presents suggestions for future research into revealing the precise psychological features of narcissism that facilitate the strategic pursuit of short-term mating

Fifth European Dirofilaria and Angiostrongylus Days (FiEDAD) 2016

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