The binding specificity of the marker antibodies Tra-1-60 and Tra-1-81 reveals a novel pluripotency-associated type 1 lactosamine epitope

The expression of the epitopes recognized by the monoclonal antibodies Tra-1-60 and Tra-1-81 is routinely used to assess the pluripotency status of human embryonic stem cells (hESCs) and induced pluripotent stem (iPS) cells. Although it is known that the epitopes recognized by Tra-1-60 and Tra-1-81 are carbohydrates, the exact molecular identity of these epitopes has been unclear. Glycan array analysis with more than 500 oligosaccharide structures revealed specific binding of Tra-1-60 and Tra-1-81 to two molecules containing terminal type 1 lactosamine: Galβ1-3GlcNAcβ1-3Galβ1-4GlcNAc and Galβ1-3GlcNAcβ1-3Galβ1-4GlcNAcβ1-6(Galβ1-3GlcNAcβ1-3)Galβ1-4Glc. The type 1 disaccharide in itself was not sufficient for binding, indicating that the complete epitope requires an extended tetrasaccharide structure where the type 1 disaccharide is β1,3-linked to type 2 lactosamine. Our mass spectrometric analysis complemented with glycosidase digestions of hESC O-glycans indicated the presence of the extended tetrasaccharide epitope on an O-glycan with the likely structure Galβ1-3GlcNAcβ1-3Galβ1-4GlcNAcβ1-6(Galβ1-3)GalNAc. Thus, the present data indicate that the pluripotency marker antibodies Tra-1-60 and Tra-1-81 recognize the minimal epitope Galβ1-3GlcNAcβ1-3Galβ1-4GlcNAc, which is present in hESCs as a part of a mucin-type O-glycan structure. The exact molecular identity of Tra-1-60 and Tra-1-81 is important for the development of improved tools to characterize the pluripotent phenotype.     

Crystal structure of the N-terminal NC4 domain of collagen IX, a zinc binding member of the laminin-neurexin-sex hormone binding globulin (LNS) domain family

Collagen IX, located on the surface of collagen fibrils, is crucial for cartilage integrity and stability. The N-terminal NC4 domain of the alpha1(IX) chain is probably important in this because it interacts with various macromolecules such as proteoglycans and cartilage oligomeric matrix protein. At least 17 distinct collagen polypeptides carry an NC4-like unit near their N terminus, but this report, describing the crystal structure of NC4 at 1.8-A resolution, represents the first atomic level structure for these domains. The structure is similar to previously characterized laminin-neurexin-sex hormone binding globulin (LNS) structures, dominated by an antiparallel beta-sheet sandwich. In addition, a zinc ion was found in a position similar to that of the metal binding site of other LNS domains. A partial backbone NMR assignment of NC4 was obtained and utilized in NMR titration studies to investigate the zinc binding in solution state and to quantitate the affinity of metal binding. The K(d) of 11.5 mM suggests a regulatory rather than a structural role for zinc in solution. NMR titration with a heparin tetrasaccharide revealed the presence of a secondary binding site for heparin on NC4, showing structural and functional conservation with thrombospondin-1, but a markedly reduced affinity for the ligand. Also the overall arrangement of the N and C termini of NC4 resembles most closely the N-terminal domain of thrombospondin-1, distinguishing the two from the majority of the published LNS structures.     

Homogeneous TR-FRET high-throughput screening assay for calcium-dependent multimerization of sorcin

A homogeneous high-throughput screening method based on time-resolved fluorescence resonance energy transfer (TR-FRET) for the measurement of calcium-dependent multimerization of an EF-hand protein, sorcin, is described. The assay is based on a specific sorcin binding peptide conjugated either with an intrinsically highly fluorescent europium chelate (donor) or an Alexa Fluor 700 fluorophore (acceptor). Addition of calcium results in multimerization of sorcin, allowing several peptides to bind simultaneously to the epitopes of the multimeric protein complex, and the proximity of peptides labeled either with donor or acceptor label results in fluorescence resonance energy transfer between the 2 labels. When no calcium is present, the protein remains in a monomer form, and thus no FRET can take place. In the optimized assay construct, the assay was performed in 45 min, and a more than 20-fold signal-to-background ratio was achieved. The reversibility of sorcin multimerization was shown by chelating free calcium with ethylenediamine tetraacetic acid (EDTA). The developed homogeneous assay can be used in screening molecules that either inhibit or enhance multimerization of sorcin, and the assay format is applicable to various noncompetitive high-throughput screening assays detecting protein multimerization reactions.     

Empowering her guardians to nurture our Ocean’s future

Reviews in Fish Biology and Fisheries - Coastal Indigenous and Traditional communities are starting to see changes to their lives from climate change, whether this is from species range changes or...     

Opposite latitudinal patterns for bird and arthropod predation revealed in experiments with differently colored artificial prey

The strength of biotic interactions is generally thought to increase toward the equator, but support for this hypothesis is contradictory. We explored whether predator attacks on artificial prey of eight different colors vary among climates and whether this variation affects the detection of latitudinal patterns in predation. Bird attack rates negatively correlated with model luminance in cold and temperate environments, but not in tropical environments. Bird predation on black and on white (extremes in luminance) models demonstrated different latitudinal patterns, presumably due to differences in prey conspicuousness between habitats with different light regimes. When attacks on models of all colors were combined, arthropod predation decreased, whereas bird predation increased with increasing latitude. We conclude that selection for prey coloration may vary geographically and according to predator identity, and that the importance of different predators may show contrasting patterns, thus weakening the overall latitudinal trend in top‐down control of herbivorous insects.     

Red‐ and green‐emitting nano‐clay materials doped with Eu3+ and/or Tb3+

Trivalent europium (Eu³⁺) and terbium (Tb³⁺) ions are important activator centers used in different host lattices to produce red and green emitting materials. The current work shows the design of new clay minerals to act as host lattices for rare earth (RE) ions. Based on the hectorite structure, nano‐chlorohectorites and nano‐fluorohectorites were developed by replacing the OH^? present in the hectorite structure with Cl^? or F^?, thus avoiding the luminescence quenching expected due to the OH^? groups. The produced matrices were characterized through X‐ray powder diffraction (XPD), transmission electron microscopy (TEM), FT‐IR, ²⁹Si MAS (magic angle spinning) NMR, nitrogen sorption, thermogravimetry‐differential scanning calorimetry (TGA‐DSC) and luminescence measurements, indicating all good features expected from a host lattice for RE ions. The nano‐clay materials were successfully doped with Eu³⁺ and/or Tb³⁺ to yield materials preserving the hectorite crystal structure and showing the related luminescence emissions. Thus, the present work shows that efficient RE³⁺ luminescence can be obtained from clays without the use of organic ‘antenna’ molecules.     

Application of alkali-activated materials for water and wastewater treatment: a review

Alkali-activation (or geopolymer) technology has gained a great deal of interest for its potential applications in water and wastewater treatment during the last decade. Alkali-activated materials can be prepared via a relatively simple and low-energy process, most commonly by treating aluminosilicate precursors with concentrated alkali hydroxide and/or silicate solutions at (near) ambient conditions. The resulting materials are, in general, amorphous, have good physical and chemical stability, ion-exchange properties, and a porous structure. Several of the precursors are industrial by-products or other readily available low-cost materials, which further enhances the environmental and economic feasibility. The application areas of alkali-activated materials in water and wastewater treatment are adsorbents/ion-exchangers, photocatalysts, high-pressure membranes, filter media, anti-microbial materials, pH buffers, carrier media in bioreactors, and solidification/stabilization of water treatment residues. The purpose of this review is to present a comprehensive evaluation of the rapidly growing prospects of alkali-activation technology in water and wastewater treatment.

     

Precise construction of oligonucleotide–Fab fragment conjugate for homogeneous immunoassay using HaloTag technology

The use of oligonucleotide–protein conjugates enables the development of novel types of bioanalytical assays. However, convenient methods for producing covalent and stoichiometric oligonucleotide–protein conjugates are still rare. Here we demonstrate, for the first time, covalent conjugation of DNA oligonucleotide to Fab fragments with a 1:1 ratio using HaloTag self-labeling technology. The oligonucleotide coupling was carried out while the Fab was attached to protein G matrix, thereby enabling straightforward production of covalent conjugates. Furthermore, it allowed convenient purification of the product because the unreacted components were easily removed before the elution of the high-purity conjugate. The prepared conjugate was employed in a homogeneous immunoassay where prostate-specific antigen was used as a model analyte. Switchable lanthanide luminescence was used for detection, and the obtained limit of detection was 0.27 ng/ml. In the future, the developed method for covalent conjugation and successive purification in protein G column could also be applied for introducing other kinds of modifications to Fab fragments in a simple and site-specific manner.     

Fast but ephemeral effects of ecological restoration on forest beetle community

Many protected areas have a long history of human intervention before being protected. In protected forests, the past land use has reduced the amount of natural structures, which are crucial substrates for thousands of species. We evaluate the short-term ecological effect of forest restoration (dead wood creation) on conifer-associated saproxylic (dead-wood dependent) beetles. More specifically, we analyze the effect of dead wood creation on the number of beetle species and individuals 1 and 5 years after restoration in spruce and pine forests, using a large-scale monitoring network over Finland. The number of saproxylic beetle species and individuals was larger at restored than at control plots both 1 and 5 years after restoration in both spruce and pine forests. Community composition in restored plots was different from control plots 1 year after restoration, but had returned towards the control plot composition 5 years after restoration, while control plots remained largely unchanged. Both in spruce and pine forests, there were more red-listed and rare saproxylic beetles in restored than in control plots 1 and 5 years after restoration. Our results indicate that restoration has an overall positive influence on saproxylic beetle diversity immediately after dead wood creation, but this effect is rather short-lived. Long term monitoring of restored dead wood is crucial in investigating successional pathways as well as biotic communities in advanced decay stages, and in fully evaluating the ecological effect of dead wood creation as a forest restoration measure.     

Integrating genetic data and population viability analyses for the identification of harbour seal (Phoca vitulina) populations and management units

Identification of populations and management units is an essential step in the study of natural systems. Still, there is limited consensus regarding how to define populations and management units, and whether genetic methods allow for inference at the relevant spatial and temporal scale. Here, we present a novel approach, integrating genetic, life history and demographic data to identify populations and management units in southern Scandinavian harbour seals. First, 15 microsatellite markers and model‐ and distance‐based genetic clustering methods were used to determine the population genetic structure in harbour seals. Second, we used harbour seal demographic and life history data to conduct population viability analyses (PVAs) in the vortex simulation model in order to determine whether the inferred genetic units could be classified as management units according to Lowe and Allendorf's (Molecular Ecology, 19, 2010, 3038) ‘population viability criterion’ for demographic independence. The genetic analyses revealed fine‐scale population structuring in southern Scandinavian harbour seals and pointed to the existence of several genetic units. The PVAs indicated that the census population size of each of these genetic units was sufficiently large for long‐term population viability, and hence that the units could be classified as demographically independent management units. Our study suggests that population genetic inference can offer the same degree of temporal and spatial resolution as ‘nongenetic’ methods and that the combined use of genetic data and PVAs constitutes a promising approach for delineating populations and management units.