Targeted disruption of the Pak5 and Pak6 genes in mice leads to deficits in learning and locomotion

PAK6 is a member of the group B family of PAK serine/threonine kinases, and is highly expressed in the brain. The group B PAKs, including PAK4, PAK5, and PAK6, were first identified as effector proteins for the Rho GTPase Cdc42. They have important roles in filopodia formation, the extension of neurons, and cell survival. Pak4 knockout mice die in utero, and the embryos have several abnormalities, including a defect in the development of motor neurons. In contrast, Pak5 knockout mice do not have any noticeable abnormalities. So far nothing is known about the biological function of Pak6. To address this, we have deleted the Pak6 gene in mice. Since Pak6 and Pak5 are both expressed in the brain, we also generated Pak5/Pak6 double knockout mice. These mice were viable and fertile, but had several locomotor and behavioral deficits. Our results indicate that Pak5 and Pak6 together are not required for viability, but are required for a normal level of locomotion and activity as well as for learning and memory. This is consistent with a role for the group B PAKs in the nervous system.     

Inner city stormwater control using a combination of best management practices

Structural best management practices (BMPs) are now commonplace for stormwater management in new suburban developments; however, their installation in older central areas is limited. Here, the effect of disconnecting impervious areas from a combined sewer in favour of a new open stormwater system is investigated. The site, an inner city suburb of Malmö, Sweden, consists of council offices and apartment blocks separated by courtyards, roads and parking places. The BMPs range from green-roofs and open channels to detention ponds and their choice, size and location was dictated by cost, available land, safety and public expectations. The system was assessed by comparing synthetic hydrographs for the 1/2, 2, 5 and 10-year design-storms assuming wet and dry initial conditions. Direct runoff was simulated using the time–area method; and routing through the BMPs using PondPack. As the BMPs are in series, the outflow of one BMP became part of the inflow to the next in the system. Additionally, the water balance for the year 2001–2002 was investigated. It was found that the green-roofs are effective at lowering the total runoff from Augustenborg and that the ponds should successfully attenuate storm peak flows for even the 10-year rainfall.     

Spatial structure-mediated indirect effects of an aquatic plant, Trapa japonica, on interaction between a leaf beetle, Galerucella nipponensis, and a water strider, Gerris nepalensis

The spatial structure-mediated indirect effects of an aquatic host plant, Trapa japonica (Trapaceae), on survival of a leaf beetle, Galerucella nipponensis (Coleoptera: Chrysomelidae), with regard to predation by a water strider, Gerris nepalensis (Hemiptera: Gerridae), were investigated in an irrigation pond and under indoor conditions. Beetle density, particularly in the first-instar stage of the larvae, became extremely low in the second generation in the pond, even though food resources were abundant. The biological check method, which excludes natural enemies by caging, suggested that a causal factor of the low density was predation by Gerris nepalensis in midsummer and thereafter. Normally growing rosettes extend their leaves horizontally on the water surface. However, some rosettes of T. japonica grew leaves vertically in the later seasons, and such overgrown rosettes were distributed patchily in the ponds. Beetle density was higher on the latter rosettes than on the former ones. The indoor experiment showed that the water strider can feed on the eggs of beetles on normally grown rosettes but not on the overgrown rosettes. Furthermore, female adults of Galerucella nipponensis preferred the overgrown rosettes over the normally grown rosettes for oviposition when water striders were present. These facts suggest that the spatial structure-mediated indirect effects of the host plant modify the interaction between herbivore and predator. Received: November 22, 2001 / Accepted: February 26, 2002     

Extending the Horizon of Homology Detection with Coevolution-based Structure Prediction

Traditional sequence analysis algorithms fail to identify distant homologies when they lie beyond a detection horizon. In this review, we discuss how co-evolution-based contact and distance prediction methods are pushing back this homology detection horizon, thereby yielding new functional insights and experimentally testable hypotheses. Based on correlated substitutions, these methods divine three-dimensional constraints among amino acids in protein sequences that were previously devoid of all annotated domains and repeats. The new algorithms discern hidden structure in an otherwise featureless sequence landscape. Their revelatory impact promises to be as profound as the use, by archaeologists, of ground-penetrating radar to discern long-hidden, subterranean structures. As examples of this, we describe how triplicated structures reflecting longin domains in MON1A-like proteins, or UVR-like repeats in DISC1, emerge from their predicted contact and distance maps. These methods also help to resolve structures that do not conform to a “beads-on-a-string” model of protein domains. In one such example, we describe CFAP298 whose ubiquitin-like domain was previously challenging to perceive owing to a large sequence insertion within it. More generally, the new algorithms permit an easier appreciation of domain families and folds whose evolution involved structural insertion or rearrangement. As we exemplify with α1-antitrypsin, coevolution-based predicted contacts may also yield insights into protein dynamics and conformational change. This new combination of structure prediction (using innovative co-evolution based methods) and homology inference (using more traditional sequence analysis approaches) shows great promise for bringing into view a sea of evolutionary relationships that had hitherto lain far beyond the horizon of homology detection.     

To share or not to share: Incentivizing data sharing in life science communities

Most scientists recognize the importance of sharing data online in an open fashion. Nonetheless, many studies have documented the concerns that accompany data sharing activities, including loss of credit or IP, misuse and the time needed to curate interoperable data. To this end, discussions around data sharing often identify incentives that could potentially ameliorate these disincentivising concerns. Nonetheless, current Open Data discussions often rely on evidence‐based studies to identify the disincentives to overcome. This results in highly specific and directed interventions. In contrast, this paper offers a different interpretation of these concerns. To do so, it makes use of the Thomas Theorem which suggests that: “If men define situations as real, they are real in their consequences”. Using empirical evidence from sub‐Saharan African (bio)chemistry laboratories, this paper illustrates how individual perceptions of research environments – whether associated with evidence or not – are highly influential in shaping data sharing practices. It concludes with the suggestion that discussion on incentivising data sharing amongst scientific communities need to take a broader set of concerns into account and offer a more creative approach to ameliorating environmental disincentives.     

Open exchange of scientific knowledge and European copyright: The case of biodiversity information

Background. The 7^th Framework Programme for Research and Technological Development is helping the European Union to prepare for an integrative system for intelligent management of biodiversity knowledge. The infrastructure that is envisaged and that will be further developed within the Programme “Horizon 2020” aims to provide open and free access to taxonomic information to anyone with a requirement for biodiversity data, without the need for individual consent of other persons or institutions. Open and free access to information will foster the re-use and improve the quality of data, will accelerate research, and will promote new types of research. Progress towards the goal of free and open access to content is hampered by numerous technical, economic, sociological, legal, and other factors. The present article addresses barriers to the open exchange of biodiversity knowledge that arise from European laws, in particular European legislation on copyright and database protection rights.We present a legal point of view as to what will be needed to bring distributed information together and facilitate its re-use by data mining, integration into semantic knowledge systems, and similar techniques. We address exceptions and limitations of copyright or database protection within Europe, and we point to the importance of data use agreements. We illustrate how exceptions and limitations have been transformed into national legislations within some European states to create inconsistencies that impede access to biodiversity information.Conclusions. The legal situation within the EU is unsatisfactory because there are inconsistencies among states that hamper the deployment of an open biodiversity knowledge management system. Scientists within the EU who work with copyright protected works or with protected databases have to be aware of regulations that vary from country to country. This is a major stumbling block to international collaboration and is an impediment to the open exchange of biodiversity knowledge. Such differences should be removed by unifying exceptions and limitations for research purposes in a binding, Europe-wide regulation.     

Palaeoecological interpretation of the late Miocene landscapes and vegetation of northern Greece: A comment to Merceron et al., 2016 (Geobios 49, 135–146)

Recent works on feeding habits of ungulates, isotopic composition of equid tooth enamel, and phytoliths from late Miocene localities of northern Greece suggested the presence of savannah and excluded dense forests. Furthermore, Mediterranean-like climates were advocated for the late Miocene of Greece. Here, I compare palaeoenvironments inferred for two mammal localities from Chalkidiki and the Axios Valley (Nikiti, upper Vallesian and lower Turolian; Dytiko, upper Turolian) with evidence from contemporaneous plant assemblages from adjacent areas in Greece and Bulgaria. I use vegetation units inferred from pollen and spore, fruit and seed, and leaf assemblages and compare them with the vegetation inferred from mammal and phytolith data. Open vegetation as inferred from mammal and phytolith data is also part of the range of vegetation units discovered from the pollen and spore, seed and fruit, and leaf record (here called the palaeobotanical record). Poaceae are consistently present in late Vallesian to late Turolian pollen records of northern Greece. Further, a number of vegetation units are indicative of forest vegetation ranging from lowland to upland forests dominated by woody angiosperms and mixed coniferous-angiosperm forests. The presence of such forests is not in conflict with the results from mammal and phytolith studies, but it broadens the view on landscapes present in the late Miocene of northern Greece. In addition to a generalized vegetation type commonly inferred by mammal studies, the palaeobotanical record demonstrates the presence of various complementary vegetation types. A comprehensive view on late Miocene landscapes in northern Greece shows that there is no conflict in inferring open herb dominated landscapes and light to dense forests and provides new opportunities for the ecological interpretation of late Miocene ungulates.     

Lignans from leaves,seedlings and micropropagated plants of Rollinia mucosa (Jacq.) Baill. – Annonaceae

Rollinia mucosa produces furofuranic lignans (magnolin, epiyangambin, yangambin) that are antagonists of platelet-activating factor (PAF). The biosynthetic capacity and the potential for the accumulation of furofuranic lignans, including epieudesmin, of the plants cultured both in vivo and in vitro conditions were evaluated. The production and the pattern of lignans accumulated were dependent on the origin of the plant material and the plant organ. The major accumulation of lignans was observed in leaves. In the mature leaves of in vivo grown seedlings magnolin and yangambin predominated, in contrast to leaves from in vitro propagated plants that presented epiyangambin as the major lignan. This revised version was published online in June 2006 with corrections to the Cover Date.     

Chemical Composition,Antibacterial, Antibiofilm and Synergistic Properties of Essential Oils from Eucalyptus globulus Labill. and Seven Mediterranean Aromatic Plants

Essential oils (EOs) from Eucalyptus globulus Labill . ssp. globulus and from Mediterranean autochthonous aromatic plants – Thymus mastichina L., Mentha pulegium L., Rosmarinus officinalis L., Calamintha nepeta (L.) Savi ssp. nepeta, Cistus ladanifer L., Foeniculum vulgare L., Dittrichia viscosa (L.) Greuter ssp. viscosa – were extracted by hydrodistillation and characterized by GC‐FID and NMR spectroscopy. EOs were evaluated for antimicrobial properties against several bacterial strains, using diverse methods, namely, the agar disc‐diffusion method, the microdilution method, the crystal violet assay and the Live/Dead staining for assessment of biofilm formation. Potential synergy was assessed by a checkerboard method. EOs of R. officinalis and C. ladanifer showed a predominance in monoterpene hydrocarbons (> 60%); EOs of C. nepeta, M. pulegium, T. mastichina, E. globulus and F. vulgare were rich in oxygenated monoterpenes (62 – 96%) whereas EO of D. viscosa was mainly composed of oxygenated sesquiterpenes (54%). All EOs showed antimicrobial activity; M. pulegium and E. globulus generally had the strongest antimicrobial activity. EO of C. nepeta was the most promising in hampering the biofilm formation. The combinations D. viscosa/C. nepeta and E. globulus/T. mastichina were synergistic against Staphylococcus aureus. These results support the notion that EOs from the aromatic plants herein reported should be further explored as potential pharmaceuticals and/or food preservatives.