Dipeptide interactions with Zn(II)–cyclen artificial model for molecular recognition

The Zn(II)–cyclen–dipeptide ternary systems (where cyclen is abbreviated as L and dipeptide is glycylglycine (HL¹) or glycyl‐(S)‐alanine (HL²)) were investigated by potentiometry applying both “out‐of‐cell” and direct titrations and by ¹H NMR spectroscopy. Especially, the ¹H NMR study was found to be very efficient to estimate speciation in the systems. The results obtained under full equilibria indicated two main species, [Zn(L)(HL^1,2)]²⁺ and [Zn(L)(L^1,2)]⁺, in both the systems. In the [Zn(L)(HL^1,2)]²⁺ complex, presence of carbonyl‐carboxylate chelate was confirmed, and in the [Zn(L)(L^1,2)]⁺ species, the peptide coordination is re‐organized to carbonyl‐amine chelate or only terminal amino group is coordinated. Equilibrium constants describing [Zn(L)]²⁺–dipeptide interaction are relatively low, log K = 3.4 for Gly‐Gly and 4.1 for Gly‐(S)‐Ala, respectively. Nevertheless, the values are slightly higher than stability constants for interaction of Zn(II) with the dipeptides (i.e. [Zn(L^1,2)]⁺ species) where a chelate formation is expected. It indicates that interaction between Zn(II) ion in [Zn(L)]²⁺ and the dipeptides should be supported by some additional interactions. Potentiometry carried out under non‐equilibrum condition showed different species where these additional stabilizing forces play more important role. Copyright © 2015 John Wiley & Sons, Ltd.     

A comparison of methods to calculate a total merit index using stochastic simulation

Background

Modern dairy cattle breeding goals include several production and more and more functional traits. Estimated breeding values (EBV) that are combined in the total merit index usually come from single-trait models or from multivariate models for groups of traits. In most cases, a multivariate animal model based on phenotypic data for all traits is not feasible and approximate methods based on selection index theory are applied to derive the total merit index. Therefore, the objective of this study was to compare a full multitrait animal model with two approximate multitrait models and a selection index approach based on simulated data.

Methods

Three production and two functional traits were simulated to mimic the national Austrian Brown Swiss population. The reference method for derivation of the total merit index was a multitrait evaluation based on all phenotypic data. Two of the approximate methods were variations of an approximate multitrait model that used either yield deviations or de-regressed breeding values. The final method was an adaptation of the selection index method that is used in routine evaluations in Austria and Germany. Three scenarios with respect to residual covariances were set up: residual covariances were equal to zero, or half of or equal to the genetic covariances.

Results

Results of both approximate multitrait models were very close to those of the reference method, with rank correlations of 1. Both methods were nearly unbiased. Rank correlations for the selection index method showed good results when residual covariances were zero but correlations with the reference method decreased when residual covariances were large. Furthermore, EBV were biased when residual covariances were high.

Conclusions

We applied an approximate multitrait two-step procedure to yield deviations and de-regressed breeding values, which led to nearly unbiased results. De-regressed breeding values gave even slightly better results. Our results confirmed that ignoring residual covariances when a selection index approach is applied leads to remarkable bias. This could be relevant in terms of selection accuracy. Our findings suggest that the approximate multitrait approach applied to de-regressed breeding values can be used in routine genetic evaluation.     

Generalized pollination system: Are floral traits adapted to different pollinators?

Flowers that are pollinated both during the day and at night could exhibit two different groups of pollinators and produce two different sets of attractants and rewards. We explored the patterns of emission of flower scents and production of nectar in the cactus Echinopsis chiloensis ssp. chiloensis, in relation to the patterns of activity of its diurnal and nocturnal pollinators. We measured frequency of flower visitors, analyzed floral scents, measured nectar production and sugar concentration, and performed pollination exclusion experiments. Bees were the main visitors at daytime and hawkmoths at nighttime. Diurnal scents were dominated by several compounds that can attract a wide range of pollinators, whereas nocturnal scents were less diverse and were dominated by (E)-nerolidol, a compound eliciting antennal responses in hawkmoths. Nectar volume and sugar concentration at night were similar to those recorded in hawkmoth-pollinated flowers. Daytime nectar volume was higher than those commonly found in bee-pollinated flowers, but similar to those found in flowers pollinated by several pollinators. Daytime sugar concentration was similar to those recorded in bee-pollinated flowers. Flowers of E. chiloensis ssp. chiloensis seem morphologically adapted to hawkmoth pollination, but diurnal and nocturnal pollinators contribute to similar extents to reproductive success. Additionally, diurnal and nocturnal pollinators showed a synergic effect on the product of fruit set and seed set. The results are discussed in terms of the linkage between floral traits and perception abilities and requirements of pollinators.     

Parallel Force Assay for Protein-Protein Interactions

Quantitative proteome research is greatly promoted by high-resolution parallel format assays. A characterization of protein complexes based on binding forces offers an unparalleled dynamic range and allows for the effective discrimination of non-specific interactions. Here we present a DNA-based Molecular Force Assay to quantify protein-protein interactions, namely the bond between different variants of GFP and GFP-binding nanobodies. We present different strategies to adjust the maximum sensitivity window of the assay by influencing the binding strength of the DNA reference duplexes. The binding of the nanobody Enhancer to the different GFP constructs is compared at high sensitivity of the assay. Whereas the binding strength to wild type and enhanced GFP are equal within experimental error, stronger binding to superfolder GFP is observed. This difference in binding strength is attributed to alterations in the amino acids that form contacts according to the crystal structure of the initial wild type GFP-Enhancer complex. Moreover, we outline the potential for large-scale parallelization of the assay.     

An Integrated Computational/Experimental Model of Lymphoma Growth

Non-Hodgkin''s lymphoma is a disseminated, highly malignant cancer, with resistance to drug treatment based on molecular- and tissue-scale characteristics that are intricately linked. A critical element of molecular resistance has been traced to the loss of functionality in proteins such as the tumor suppressor p53. We investigate the tissue-scale physiologic effects of this loss by integrating in vivo and immunohistological data with computational modeling to study the spatiotemporal physical dynamics of lymphoma growth. We compare between drug-sensitive Eμ-myc Arf-/- and drug-resistant Eμ-myc p53-/- lymphoma cell tumors grown in live mice. Initial values for the model parameters are obtained in part by extracting values from the cellular-scale from whole-tumor histological staining of the tumor-infiltrated inguinal lymph node in vivo. We compare model-predicted tumor growth with that observed from intravital microscopy and macroscopic imaging in vivo, finding that the model is able to accurately predict lymphoma growth. A critical physical mechanism underlying drug-resistant phenotypes may be that the Eμ-myc p53-/- cells seem to pack more closely within the tumor than the Eμ-myc Arf-/- cells, thus possibly exacerbating diffusion gradients of oxygen, leading to cell quiescence and hence resistance to cell-cycle specific drugs. Tighter cell packing could also maintain steeper gradients of drug and lead to insufficient toxicity. The transport phenomena within the lymphoma may thus contribute in nontrivial, complex ways to the difference in drug sensitivity between Eμ-myc Arf-/- and Eμ-myc p53-/- tumors, beyond what might be solely expected from loss of functionality at the molecular scale. We conclude that computational modeling tightly integrated with experimental data gives insight into the dynamics of Non-Hodgkin''s lymphoma and provides a platform to generate confirmable predictions of tumor growth.     

ATP Impedes the Inhibitory Effect of Hsp90 on Aβ40 Fibrillation

Heat shock protein 90 (Hsp90) is a molecular chaperone that assists protein folding in an Adenosine triphosphate (ATP)-dependent way. Hsp90 has been reported to interact with Alzheime?s disease associated amyloid-β (Aβ) peptides and to suppress toxic oligomer- and fibril formation. However, the mechanism remains largely unclear. Here we use a combination of atomic force microscopy (AFM) imaging, circular dichroism (CD) spectroscopy and biochemical analysis to quantify this interaction and put forward a microscopic picture including rate constants for the different transitions towards fibrillation. We show that Hsp90 binds to Aβ₄₀ monomers weakly but inhibits Aβ₄₀ from growing into fibrils at substoichiometric concentrations. ATP impedes this interaction, presumably by modulating Hsp90’s conformational dynamics and reducing its hydrophobic surface. Altogether, these results might indicate alternative ways to prevent Aβ₄₀ fibrillation by manipulating chaperones that are already abundant in the brain.     

Ecosystem based modeling and indication of ecological integrity in the German North Sea—Case study offshore wind parks

Human exploitation and use of marine and coastal areas are apparent and growing in many regions of the world. For instance, fishery, shipping, military, raw material exploitation, nature protection and the rapidly expanding offshore wind power technology are competing for limited resources and space. The development and implementation of Integrated Coastal Zone Management (ICZM) strategies could help to solve these problems. Therefore, suitable spatial assessment, modeling, planning and management tools are urgently needed. These tools have to deal with data that include complex information on different spatial and temporal scales. A systematic approach based on the development of future scenarios which are assessed by combining different simulation models, GIS methods and an integrating set of ecological integrity indicators, was applied in a case study in the German North Sea. Here, the installation of huge offshore wind parks within the near future is planned. The aim was to model environmental effects of altered sea-use patterns on marine biota. Indicators of ecological integrity were used to assess altering conditions and possible ecosystem shifts ranging from systems’ degradations to the development of highly productive and diverse artificial reef systems. The results showed that some ecosystem processes and properties and related indicators are sensitive to changes generated by offshore wind park installations while others did not react as hypothesized.     

Five challenges to bringing single-molecule force spectroscopy into living cells

In recent years, single-molecule force spectroscopy techniques have been used to study how inter- and intramolecular interactions control the assembly and functional state of biomolecular machinery in vitro. Here we discuss the problems and challenges that need to be addressed to bring these technologies into living cells and to learn how cellular machinery is controlled in vivo.