Binding Specificity of ASHH2 CW Domain Toward H3K4me1 Ligand Is Coupled to Its Structural Stability Through Its α1-Helix

The CW domain binds to histone tail modifications found in different protein families involved in epigenetic regulation and chromatin remodeling. CW domains recognize the methylation state of the fourth lysine on histone 3 and could, therefore, be viewed as a reader of epigenetic information. The specificity toward different methylation states such as me1, me2, or me3 depends on the particular CW subtype. For example, the CW domain of ASHH2 methyltransferase binds preferentially to H3K4me1, and MORC3 binds to both H3K4me2 and me3 modifications, while ZCWPW1 is more specific to H3K4me3. The structural basis for these preferential bindings is not well understood, and recent research suggests that a more complete picture will emerge if dynamical and energetic assessments are included in the analysis of interactions. This study uses fold assessment by NMR in combination with mutagenesis, ITC affinity measurements, and thermal denaturation studies to investigate possible couplings between ASHH2 CW selectivity toward H3K4me1 and the stabilization of the domain and loops implicated in binding. The key elements of the binding site—the two tryptophans and the α1-helix form and maintain the binding pocket— were perturbed by mutagenesis and investigated. Results show that the α1-helix maintains the overall stability of the fold via the I915 and L919 residues and that the correct binding consolidates the loops designated as η1 and η3, as well as the C-terminal. This consolidation is incomplete for H3K4me3 binding to CW, which experiences a decrease in overall thermal stability on binding. Loop mutations not directly involved in the binding site, nonetheless, affect the equilibrium positions of the key residues.publishedVersio

Sensing Archaeology in the North: The Use of Non-Destructive Geophysical and Remote Sensing Methods in Archaeology in Scandinavian and North Atlantic Territories

In August 2018, a group of experts working with terrestrial/marine geophysics and remote sensing methods to explore archaeological sites in Denmark, Finland, Norway, Scotland and Sweden gathered together for the first time at the Workshop ‘Sensing Archaeology in The North’. The goal was to exchange experiences, discuss challenges, and consider future directions for further developing these methods and strategies for their use in archaeology. After the event, this special journal issue was arranged to publish papers that are based on the workshop presentations, but also to incorporate work that is produced by other researchers in the field. This paper closes the special issue and further aims to provide current state-of-the-art for the methods represented by the workshop. Here, we introduce the aspects that inspired the organisation of the meeting, a summary of the 12 presentations and eight paper contributions, as well as a discussion about the main outcomes of the workshop roundtables, including the production of two searchable databases (online resources and equipment). We conclude with the position that the ‘North’, together with its unique cultural heritage and thriving research community, is at the forefront of good practice in the application and development of sensing methods in archaeological research and management. However, further method development is required, so we claim the support of funding bodies to back research efforts based on testing/experimental studies to: explore unknown survey environments and identify optimal survey conditions, as well as to monitor the preservation of archaeological remains, especially those that are at risk. It is demonstrated that remote sensing and geophysics not only have an important role in the safeguarding of archaeological sites from development and within prehistorical-historical research, but the methods can be especially useful in recording and monitoring the increased impact of climate change on sites in the North

Maternal PCOS status and metformin in pregnancy: Steroid hormones in 5–10 years old children from the PregMet randomized controlled study

Objective: Polycystic ovary syndrome (PCOS) is a common endocrine disorder, with potential effects on offspring both genetically and through altered intrauterine environment. Metformin, which ameliorate hormonal disturbances in non-pregnant women with PCOS is increasingly used in pregnancy. It passes the placenta, and the evidence on potential consequences for offspring endocrine development is scarce. We explore the potential effects of maternal PCOS status and intrauterine metformin exposure on offspring steroid hormone levels. Design: This is a follow-up study of 5–10 years old children from the PregMet-study–a randomized controlled trial comparing metformin (2000 mg/day) to placebo during PCOS pregnancies. Of the 255 children invited, 117 (46%) were included. Methods: There was no intervention in this follow-up study. Outcomes were serum levels of androstenedione, testosterone, SHBG, cortisol, 17-hydroxyprogesterone, 11-deoxycortisol and calculated free testosterone converted to gender-and age adjusted z-scores from a Norwegian reference population. These were compared in i) placebo-exposed children versus children from the reference population (z-score zero) by the deviation in z-score by one-sample t-tests and ii) metformin versus placebo-exposed children by two-sample t-tests. Holm-Bonferroni adjustments were performed to account for multiple endpoints. Results: Girls of mothers with PCOS (n = 30) had higher mean z-scores of androstenedione (0.73 (95% confidence interval (CI) 0.41 to 1.06), p<0.0001), testosterone (0.76 (0.51 to 1.00), p<0.0001), and free testosterone (0.99 (0.67 to 1.32), p<0.0001) than the reference population. Metformin-exposed boys (n = 31) tended to have higher 11-deoxycortisol z-score than placebo-exposed boys (n = 24) (mean difference 0.65 (95% CI 0.14–1.17), p = 0.014). Conclusion: Maternal PCOS status was associated with elevated androgens in 5- to 10-year-old daughters, which might indicate earlier maturation and increased risk of developing PCOS. An impact of metformin in pregnancy on steroidogenesis in children born to mothers with PCOS cannot be excluded. Our findings need confirmation in studies that include participants that have entered puberty.publishedVersio

Non-conserved C-terminal regions in the histone recognition module CW, determines specificity, stability and affinity towards monomethylated histone tails

Histone modifications have an important role in epigenetic gene regulation and contribute to the cellular memory system. It has been well documented that certain patterns of histone modifications are associated with different states of gene expression. The mechanisms underlying these associations are, however, still poorly understood. Many nuclear proteins have histone recognition modules that can serve to recruit the proteins to relevant sites in chromatin. The CW domain is a family of histone recognition modules found in chromatin-related proteins. While all known CW domains have specificity for histone H3 methylated on lysine 4, different subfamilies of CW domains have different specificities for different methylation states. The C-terminal lid regions" of the CW domains are highly variable and they have been proposed to contribute to the ligand specificity. To explore how the C-terminal "lid regions" contribute to ligand specificity, this project aims to measure the relative mobility of these regions in A. thaliana ASHH2 CW domain using NMR experiments. To support our claims, intrinsic tryptophan fluorescence thermal denaturation and ITC have been used. We have engineered three ASHH2 CW domain variants, which differ in length in their N- and C-terminal regions. We show that the lid regions are important for the stability of the domain, and that the protein adopts a more stable confirmation upon ligand binding. The C-terminal helix is mobile in the unbound state but becomes less mobile upon binding. We also show that K9 has a small effect on binding since doubly modified H3K4me1K9ac has a higher KD than H3K4me1. Furthermore, the implications for the binding mechanisms are discussed

A multi-camera system for the integrated documentation of Underwater Cultural Heritage of high structural complexity; The case study of M/S Helma wreck

High structural complexity is quite common in underwater archaeological sites and perhaps on top of the list when it comes to challenges regarding 3D reconstruction. Advances in underwater robotics and optical sensors are providing solutions for high quality data acquisition for mapping and documentation of underwater cultural heritage (UCH) sites. This paper presents a workflow for the detailed 3D reconstruction of a disintegrated shipwreck from the 1920’s in Trondheimsfjord, Norway, a wreck site of high 3D structural complexity at 55 meters depth. The work focuses on the use of seven multi-purpose optical sensors, like low-cost action cameras, omnidirectional cameras, a depth camera and an RGB camera attached to an Underwater Hyperspectral Imaging sensor, all mounted on a Remotely Operated Vehicle (ROV). The 3D reconstruction of the wreck site was carried out offline, through the implementation of a typical Structure-from-Motion pipeline. Only one camera, considered as the master camera of the system, was connected to the ROV’s control system and to the navigation sensors, hence providing georeferenced images. With the assumption that all seven cameras were moving jointly in 3D space, an approach for estimating the relative positions of the six stand-alone cameras, with respect to the master camera, was followed. The geometric configuration of the multi-sensor system allowed scaling and georeferencing of all created 3D models, and a more rapid alignment process of the big amount of collected imagery data. The presented case study highlights the advantages of multi-vision setups for UCH documentation, such as near 360° field of view with robust geometry; full 3D coverage of challenging objects of interest; the possibility of sensor’s synchronization invariant approaches, and not least minimization of maneuvering and bottom time

Binding Specificity of ASHH2 CW Domain Toward H3K4me1 Ligand Is Coupled to Its Structural Stability Through Its α1-Helix

The CW domain binds to histone tail modifications found in different protein families involved in epigenetic regulation and chromatin remodeling. CW domains recognize the methylation state of the fourth lysine on histone 3 and could, therefore, be viewed as a reader of epigenetic information. The specificity toward different methylation states such as me1, me2, or me3 depends on the particular CW subtype. For example, the CW domain of ASHH2 methyltransferase binds preferentially to H3K4me1, and MORC3 binds to both H3K4me2 and me3 modifications, while ZCWPW1 is more specific to H3K4me3. The structural basis for these preferential bindings is not well understood, and recent research suggests that a more complete picture will emerge if dynamical and energetic assessments are included in the analysis of interactions. This study uses fold assessment by NMR in combination with mutagenesis, ITC affinity measurements, and thermal denaturation studies to investigate possible couplings between ASHH2 CW selectivity toward H3K4me1 and the stabilization of the domain and loops implicated in binding. The key elements of the binding site—the two tryptophans and the α1-helix form and maintain the binding pocket— were perturbed by mutagenesis and investigated. Results show that the α1-helix maintains the overall stability of the fold via the I915 and L919 residues and that the correct binding consolidates the loops designated as η1 and η3, as well as the C-terminal. This consolidation is incomplete for H3K4me3 binding to CW, which experiences a decrease in overall thermal stability on binding. Loop mutations not directly involved in the binding site, nonetheless, affect the equilibrium positions of the key residues

Underwater hyperspectral imaging: a new tool for marine archaeology

By applying an underwater hyperspectral imager (UHI) to a selection of archaeological artifacts, we have found spectral signatures that are representative of materials likely to be present at wreck sites. By successfully using the signatures to classify a subset of said artifacts placed on the seabed at 61 m depth, we demonstrate that it is possible to detect archaeological objects of interest in UHI data acquired by a remotely operated vehicle. Correct UHI classification of rust and glass bottles in situ on a historical wreck site further supports the viability of the method for marine archaeological applications

Genotype by environment interaction for growth in Atlantic Cod (Gadus morhua L.) in four farms of Norway

We studied genotype by environment interaction (G × E) for body weight (BW) of Atlantic cod (Gadus morhua L.) from the National cod breeding program in Norway. Records of 13,811 fish in a nucleus farm (NUC) and two test farms (PENorth, PESouth) in year-class (YC) 2007, and for 9149 fish in NUC and one test farm in YC 2010 were available. Heterogeneity of variances and heritabilities ( ) were estimated using a univariate animal model with environmental effects common to full-sibs (full-model). Genetic correlations ( ) between farms were estimated using a multivariate full-model and a reduced-model (without ) for each YC. Heterogeneity of  was observed in both YC 2007 (0.10 to 0.16) and YC 2010 (0.08 to 0.26). The estimates of  between NUC and test farms were relatively high for both models (0.81 ± 0.19 to 0.96 ± 0.17) and (0.81 ± 0.08 to 0.86 ± 0.04), suggesting low re-ranking of genotypes. Strong re-ranking of genotypes between PESouth and PENorth may be less important because most cod producers are situated close to the breeding nucleus. In conclusion, G × E between NUC and test farms were low and at present there is no need for separate breeding programs for BW in cod