Species’ roles in food webs show fidelity across a highly variable oak forest

Ecological communities are composed of many species and an intricate network of interactions between them. Because of their overall complexity, an intriguing approach to understanding network structure is by breaking it down into the structural roles of its constituent species. The structural role of a species can be directly measured based on how it appears in network motifs – the basic building blocks of complex networks. Here, we study the distribution of species’ roles at three distinct spatio‐temporal scales (i.e. species, network, and temporal) in host–parasitoid networks collected across 22 sites over two years within a fragmented landscape of oaks in southern Finland. We found that species’ roles for hosts and parasitoids were heterogeneously distributed across the study system but that roles are strongly conserved over spatial scales. In addition, we found that species’ roles were remarkably consistent between years even in the presence of disturbances (e.g. species turnover). Overall, our results suggest that species’ roles are an intrinsic property of species that may be predictable over spatial and temporal scales.     

A systematic review of MRI studies of language development from birth to 2 years of age

Neurocognitive functions supporting language development start to develop well before first words are spoken during the first years of life. This process coincides with the initial growth spurt of the brain. While the core components of the language network are well characterized in adults and children, the initial neural correlates of language skills are still relatively unknown. We reviewed 10 studies identified via a systematic search that combined magnetic resonance imaging and language‐related measures in healthy infants from birth to 2 years of age. We aimed to describe the current knowledge as well as point out viable future directions for similar studies. Expectedly, the implicated cerebral areas included many established components of the language networks, including frontal and temporal regions. A volumetric leftward asymmetry of the brain was suggested as a determinant of language skills, yet with marked interindividual variation. Overall, temporal and frontal brain volumes associated positively with language skills. Positive associations were described between the maturation of language related white matter tracts and language skills. The language networks showed adult‐like structural similarities already in neonates, with weaker asymmetry compared to adults. In summary, we found some evidence that the language circuit described in older age groups is also associated to language skills during the first 2 years of life. However, across the reviewed studies there were no systematic neural correlates of language skills, which is partly explained by a modest number of studies, scattered representation of ages in measurements and the variance in the used methods.     

Identification of a Novel Bacterial Outer Membrane Interleukin-1Β-Binding Protein from Aggregatibacter actinomycetemcomitans

Aggregatibacter actinomycetemcomitans is a gram-negative opportunistic oral pathogen. It is frequently associated with subgingival biofilms of both chronic and aggressive periodontitis, and the diseased sites of the periodontium exhibit increased levels of the proinflammatory mediator interleukin (IL)-1β. Some bacterial species can alter their physiological properties as a result of sensing IL-1β. We have recently shown that this cytokine localizes to the cytoplasm of A. actinomycetemcomitans in co-cultures with organotypic gingival mucosa. However, current knowledge about the mechanism underlying bacterial IL-1β sensing is still limited. In this study, we characterized the interaction of A. actinomycetemcomitans total membrane protein with IL-1β through electrophoretic mobility shift assays. The interacting protein, which we have designated bacterial interleukin receptor I (BilRI), was identified through mass spectrometry and was found to be Pasteurellaceae specific. Based on the results obtained using protein function prediction tools, this protein localizes to the outer membrane and contains a typical lipoprotein signal sequence. All six tested biofilm cultures of clinical A. actinomycetemcomitans strains expressed the protein according to phage display-derived antibody detection. Moreover, proteinase K treatment of whole A. actinomycetemcomitans cells eliminated BilRI forms that were outer membrane specific, as determined through immunoblotting. The protein was overexpressed in Escherichia coli in both the outer membrane-associated form and a soluble cytoplasmic form. When assessed using flow cytometry, the BilRI-overexpressing E. coli cells were observed to bind 2.5 times more biotinylated-IL-1β than the control cells, as detected with avidin-FITC. Overexpression of BilRI did not cause binding of a biotinylated negative control protein. In a microplate assay, soluble BilRI bound to IL-1β, but this binding was not specific, as a control protein for IL-1β also interacted with BilRI. Our findings suggest that A. actinomycetemcomitans expresses an IL-1β-binding surface-exposed lipoprotein that may be part of the bacterial IL-1β-sensing system.     

A Novel Feeder-Free Culture System for Human Pluripotent Stem Cell Culture and Induced Pluripotent Stem Cell Derivation

Correct interactions with extracellular matrix are essential to human pluripotent stem cells (hPSC) to maintain their pluripotent self-renewal capacity during in vitro culture. hPSCs secrete laminin 511/521, one of the most important functional basement membrane components, and they can be maintained on human laminin 511 and 521 in defined culture conditions. However, large-scale production of purified or recombinant laminin 511 and 521 is difficult and expensive. Here we have tested whether a commonly available human choriocarcinoma cell line, JAR, which produces high quantities of laminins, supports the growth of undifferentiated hPSCs. We were able to maintain several human pluripotent stem cell lines on decellularized matrix produced by JAR cells using a defined culture medium. The JAR matrix also supported targeted differentiation of the cells into neuronal and hepatic directions. Importantly, we were able to derive new human induced pluripotent stem cell (hiPSC) lines on JAR matrix and show that adhesion of the early hiPSC colonies to JAR matrix is more efficient than to matrigel. In summary, JAR matrix provides a cost-effective and easy-to-prepare alternative for human pluripotent stem cell culture and differentiation. In addition, this matrix is ideal for the efficient generation of new hiPSC lines.     

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.     

Biogenic volatile organic compound emissions in four vegetation types in high arctic Greenland

Biogenic volatile organic compounds (BVOCs) emitted from terrestrial vegetation participate in oxidative reactions in the atmosphere, leading to the formation of secondary organic aerosols and longer lifetime of methane. Global models of BVOC emissions have assumed minimal emissions from the high latitudes. However, measurements from this region are lacking, and studies from the high arctic are yet to be published. This study aimed to obtain estimates for BVOC emissions from the high arctic, and hereby to add new knowledge to the understanding of global BVOC emissions. Measurements were conducted in four vegetation types dominated by Cassiope tetragona, Salix arctica, Vaccinium uliginosum and a mixture of Kobresia myosuroides, Dryas spp. and Poa arctica. Emissions were measured by an enclosure technique and collection of volatiles into adsorbent cartridges in August. Volatiles were analyzed by gas chromatography–mass spectrometry following thermal desorption. Isoprene showed highest emissions in S. arctica heath. Monoterpene and sesquiterpene emissions were especially associated with C. tetragona heath. Total observed emissions were comparable in magnitude to emissions previously found in the subarctic, whereas isoprene emissions were lower. This study shows that considerable amounts of BVOCs are emitted from the high arctic. The results are also of importance as the emissions from this region are expected to increase in the future as a result of the predicted climate warming in the high arctic. We suggest further studies to assess the effects of climate changes in the region in order to gain new knowledge and understanding of future global BVOC emissions.     

An improved amplified fragment length polymorphism (AFLP) protocol for discrimination of Listeria isolates

Nine restriction enzyme combinations and 108 different primer combinations were initially tested for suitability for amplified fragment length polymorphism (AFLP) analysis of Listeria monocytogenes; the combination of HindIII and HpyCH4IV showed consistently strong signals on gels, amplified an adequate number of DNA fragments and detected polymorphism among closely related strains based on AscI macrorestriction profiles. AFLP also distinguished between L. monocytogenes, L. innocua, L. ivanovii, L. seeligeri, L. welshimeri and L. grayi species. All Listeria species showed species-specific clusters, with less than 33% similarity between different species. A total of 34 L. monocytogenes strains were characterised by using both AFLP and pulsed-field gel electrophoresis (PFGE). The results of AFLP analysis of L. monocytogenes strains were in concordance with those obtained by PFGE. Both methods identified 29 different genotypes of L. monocytogenes and had a high discrimination index (> 0.999). By combining the results of AFLP and PFGE, subtype discrimination was further improved. Numerical analysis of both AFLP and PFGE profiles yielded three genomic groups of L. monocytogenes strains. AFLP was found to be faster and less labour-intensive than PFGE. We conclude that the AFLP protocol is a highly discriminatory, reproducible and valuable tool in characterisation of Listeria strains and may also be suitable for Listeria species identification.     

A parasitoid wasp uses landmarks while monitoring potential resources

Social insects and insects that provision nests are well known to have complex foraging behaviour involving repeated visits to learned locations. Other insects do not forage from a central location and are generally assumed to respond to resources by simple attraction without spatial memory. This simple response to resource cues is generally taken as giving rise to patterns of resource use that correspond directly to resource distribution. By contrast, the solitary parasitoid wasp Hyposoter horticola monitors the locations of multiple potential hosts (butterfly eggs) for up to several weeks, until the hosts become susceptible to parasitism. Essentially all hosts in the landscape are found, and one-third of them are parasitized, independent of host density. Here, we show that the wasps do not relocate hosts using odour markers previously left by themselves or other foragers, nor do they find the eggs anew repeatedly. Instead, the wasps relocate host eggs by learning the position of the eggs relative to visual landmarks. The anticipatory foraging behaviour presented here is a key to the wasp's exceptionally stable population dynamics.     

16S rDNA PCR-denaturing gradient gel electrophoresis in determining proportions of coexisting Actinobacillus actinomycetemcomitans strains

Certain serotypes of Actinobacillus actinomycetemcomitans seem to prefer coexistence in vivo. The 16S rDNA PCR-denaturing gradient gel electrophoresis (DGGE) was tested for its capability to distinguish coexisting A. actinomycetemcomitans strains of different serotypes or genetic lineages and to determine their proportions in vitro. The migration pattern of the PCR amplicon from serotype c differed from those of the other serotypes. Contrary to the strains of serotypes c, d, and e, strains of serotypes a, b, and f consistently demonstrated intra-serotype migration patterns similar to each other. Since the migration patterns differed between serotype c and b strains a strain of each was used to determine their proportional representation in a strain mixture. The strains were distinguishable from each other above the 5% PCR-DGGE detection level (12.5 ng DNA/1.5 x 10(6) cells). DGGE provides a promising tool for in vitro studies on the coexistence of different genetic lineages of A. actinomycetemcomitans.