Scrambling of bands in gel electrophoresis of DNA.

Under certain conditions of agarose gel electrophoresis, larger DNA molecules migrate faster than smaller ones. This anomalous mobility of DNA, which can lead to serious errors in the measurement of DNA fragment lengths, is related to near-zero velocity conformations which can trap DNA chains during electrophoresis. Intermittent electric fields can be used to alter the chain conformations so as to restore the monotonic mobility-size relationship which is necessary for a correct interpretation of the gel. These data are in agreement with the results of a computer simulation based on a theoretical model of electrophoresis.     

What is the role of local landscape structure in the vegetation composition of field boundaries?

Question: How distinct is the flora of field boundaries? How does the structure of field boundaries determine the composition of vegetation? Location: Estonia, six 4 km × 4 km agricultural areas. Methods: We studied the vegetation of fields and field boundaries using 2 m × 2 m sample plots. We estimated the frequency of species in both habitat types, applied an MRPP test to analyse the vegetation composition of field boundaries with various combinations of landscape features (ditches, roads, tree and bush layers) illustrating this by DCA ordination, and used indicator species analysis to determine the characteristic species of each boundary type. Results: Ca. 45% of the flora of field boundaries comprised species found on agricultural land. Most typical species in fields — agrotolerants — were also the most common in field boundaries. The vegetation of road verges and grassy boundaries consisted mainly of disturbance‐tolerant species. Woody boundaries were characterised by shade‐tolerant and nitrophilous species. Ditch banks included species typical of moist habitats and semi‐natural grasslands. Few threatened or protected species were observed. Conclusion: The vegetation composition of field boundaries varied due to the complex effects of landscape structure around and in these boundaries. Plant species in agricultural landscapes can be classified into two broad emergent groups on the basis of their different responses to agricultural disturbances — agrotolerant species and nature‐value species. Agrotolerant species are promoted by agriculture, nature‐value species include rare weeds and habitat specialists. We suggest that high‐nature‐value species should prevail in monitoring the effects of land‐use intensification on biodiversity rather than total species richness.     

Evidence for Divisome Localization Mechanisms Independent of the Min System and SlmA in Escherichia coli

Cell division in Escherichia coli starts with assembly of FtsZ protofilaments into a ring-like structure, the Z-ring. Positioning of the Z-ring at midcell is thought to be coordinated by two regulatory systems, nucleoid occlusion and the Min system. In E. coli, nucleoid occlusion is mediated by the SlmA proteins. Here, we address the question of whether there are additional positioning systems that are capable of localizing the E. coli divisome with respect to the cell center. Using quantitative fluorescence imaging we show that slow growing cells lacking functional Min and SlmA nucleoid occlusion systems continue to divide preferentially at midcell. We find that the initial Z-ring assembly occurs over the center of the nucleoid instead of nucleoid-free regions under these conditions. We determine that Z-ring formation begins shortly after the arrival of the Ter macrodomain at the nucleoid center. Removal of either the MatP, ZapB, or ZapA proteins significantly affects the accuracy and precision of Z-ring positioning relative to the nucleoid center in these cells in accordance with the idea that these proteins link the Ter macrodomain and the Z-ring. Interestingly, even in the absence of Min, SlmA, and the putative Ter macrodomain – Z-ring link, there remains a weak midcell positioning bias for the Z-ring. Our work demonstrates that additional Z-ring localization systems are present in E. coli than are known currently. In particular, we identify that the Ter macrodomain acts as a landmark for the Z-ring in the presence of MatP, ZapB and ZapA proteins.     

Species’ traits influence ground beetle responses to farm and landscape level agricultural intensification in Europe

Agricultural intensification may result in important shifts in insect community composition and function, but this remains poorly explored. Studying how groups of species with shared traits respond to local and landscape scale land-use management can reveal mechanisms behind such observed impacts. We tested if ground beetles (Coleoptera: Carabidae) divided into trait groups based on body sizes, wing morphologies and dietary preferences respond differently to farming practise (organic and conventional), farming intensity (measured as yield) and landscape complexity (measured as the proportion of arable land within a 1,000 m radius) across Europe. We used data from 143 farms in five regions in northern and central Europe. Organic farms did not differ in abundance or richness of any trait group compared to conventional farms. As farm scale intensity (yield) increased, overall abundance of beetles decreased, but abundances of small and medium sized beetles, as well as that of wingless beetles, were unaffected. Overall species richness was not affected by yield, whereas consideration of traits revealed that phytophagous and omnivorous beetles were less species rich on farms with high yields. Increasing the proportion of arable land in the landscape increased overall beetle abundance. This was driven by an increase in omnivorous beetles. The total species richness was not affected by an increase in the proportion arable land, although the richness of wingless beetles was found to increase. Potential effects on ecosystem functioning need to be taken into account when designing schemes to maintain agricultural biodiversity, because species with different ecological traits respond differently to local management and landscape changes.     

Persistent negative effects of pesticides on biodiversity and biological control potential on European farmland

During the last 50 years, agricultural intensification has caused many wild plant and animal species to go extinct regionally or nationally and has profoundly changed the functioning of agro-ecosystems. Agricultural intensification has many components, such as loss of landscape elements, enlarged farm and field sizes and larger inputs of fertilizer and pesticides. However, very little is known about the relative contribution of these variables to the large-scale negative effects on biodiversity. In this study, we disentangled the impacts of various components of agricultural intensification on species diversity of wild plants, carabids and ground-nesting farmland birds and on the biological control of aphids.In a Europe-wide study in eight West and East European countries, we found important negative effects of agricultural intensification on wild plant, carabid and bird species diversity and on the potential for biological pest control, as estimated from the number of aphids taken by predators. Of the 13 components of intensification we measured, use of insecticides and fungicides had consistent negative effects on biodiversity. Insecticides also reduced the biological control potential. Organic farming and other agri-environment schemes aiming to mitigate the negative effects of intensive farming on biodiversity did increase the diversity of wild plant and carabid species, but – contrary to our expectations – not the diversity of breeding birds.We conclude that despite decades of European policy to ban harmful pesticides, the negative effects of pesticides on wild plant and animal species persist, at the same time reducing the opportunities for biological pest control. If biodiversity is to be restored in Europe and opportunities are to be created for crop production utilizing biodiversity-based ecosystem services such as biological pest control, there must be a Europe-wide shift towards farming with minimal use of pesticides over large areas.     

Raman Spectroscopy Analysis of Botryococcene Hydrocarbons from the Green Microalga Botryococcus braunii

Botryococcus braunii, B race is a unique green microalga that produces large amounts of liquid hydrocarbons known as botryococcenes that can be used as a fuel for internal combustion engines. The simplest botryococcene (C₃₀) is metabolized by methylation to give intermediates of C₃₁, C₃₂, C₃₃, and C₃₄, with C₃₄ being the predominant botryococcene in some strains. In the present work we have used Raman spectroscopy to characterize the structure of botryococcenes in an attempt to identify and localize botryococcenes within B. braunii cells. The spectral region from 1600–1700 cm⁻¹ showed ν(C=C) stretching bands specific for botryococcenes. Distinct botryococcene Raman bands at 1640 and 1647 cm⁻¹ were assigned to the stretching of the C=C bond in the botryococcene branch and the exomethylene C=C bonds produced by the methylations, respectively. A Raman band at 1670 cm⁻¹ was assigned to the backbone C=C bond stretching. Density function theory calculations were used to determine the Raman spectra of all botryococcenes to compare computed theoretical values with those observed. The analysis showed that the ν(C=C) stretching bands at 1647 and 1670 cm⁻¹ are actually composed of several closely spaced bands arising from the six individual C=C bonds in the molecule. We also used confocal Raman microspectroscopy to map the presence and location of methylated botryococcenes within a colony of B. braunii cells based on the methylation-specific 1647 cm⁻¹ botryococcene Raman shift.     

Single session exercises and concurrent functional electrical stimulation are more effective on muscles’ force generation than only exercises in spinal cord injured persons: a feasibility study

Objectives:To evaluate impact of first therapy session, containing functional electrical stimulation (FES) and therapeutic exercises (TE) on erector spinae (ES) and rectus abdominis (RA) force generation in persons with spinal cord injury (SCI).Methods:Five men with SCI were divided in two groups - FES+TE received concurrent FES on ES and RA and TE, TE only TE. Participants performed exercises for improving sitting balance and posture. Muscles’ electrical activity was evaluated by electromyography; amplitude (AEMG) and median frequency (MF) were used for analysis.Results:AEMG of ES left (L) increased 292.9% (g=-0.92), right (R) 175% (g=-1.01), RA L 314.3% (g=-0,81, P<0.05), R 266.7% (g=-0.08) in FES+TE. AEMG of ES L increased 47.6% (g=-0.46), R 96.4% (g=-0.95); RA L 7.1% (g=-0.97), but R decreased 6.7% (g=0.12) in TE. MF of ES L increased 108.5% (g=-0.74), R 184% (g=-1.25); RA L 886.7% (g=3-05, P<0.05), R 817.6% (g=-2.55, P<0.05) in FES+TE. MF of ES L increased 95.2% (g=-1.02), R 161.4% (g=-1.64); RA L 3,2% (g=-0.06), R 30.8% (g=-0.46) in TE.Conclusions:In SCI persons, single session exercises and concurrent functional electrical stimulation may be more effective on muscles` force generation than only exercises. However, replication of the results is needed before clinical implementation.     

Activin A and Wnt-dependent specification of human definitive endoderm cells

Activin/Nodal and Wnt signaling are known to play important roles in the regional specification of endoderm. Here we have investigated the effect of the length of stimulation with Activin A plus Wnt3a on the development of hepatic and pancreatic progenitors from the definitive endoderm (DE) cells derived from human pluripotent stem cells (hPSC). We show that DE-cells derived from hPSC with 3 days high Activin A and Wnt3a treatment were able to differentiate further into both tested endodermal lineages. When prolonging the DE-induction protocol from 3 to 5 or 7 days, almost pure DE-marker positive cell populations were obtained. However, these cells had an impaired pancreatic differentiation capacity, while they still developed into hepatocyte-like cells. Further propagation of the DE-cells in the presence of Wnt3a and Activin A led to the complete loss of differentiation capacity into hepatic or pancreatic lineages. When Wnt3a was removed after 24 h from the initiation of the differentiation, the cells were able to differentiate into PDX1+/NKX6.1+ pancreatic progenitors even with longer DE induction time while efficiency of hepatic differentiation was lower. Our results suggest that both the length and the timing of Wnt3a treatment during DE induction are crucial for the final differentiation outcome. Although it is possible to derive apparently pure DE cells with prolonged Activin A/Wnt-stimulation, their progenitor capacity is restricted to a limited time window.     

The conservation of ground layer lichen communities in alvar grasslands and the relevance of substitution habitats

Semi-natural calcareous grasslands (alvars) are biodiversity hotspots in Northern Europe, particularly for herb layer plants. In the last century, traditional management has ceased, and the area of grasslands has declined due to extensive encroachment. We were interested in the drivers of ground layer (alias terricolous or epigeic) lichen communities. Our survey consisted of 86 habitat fragments in western Estonia, covering four types of historic alvar grasslands and three types of alvar-like habitats. We found that the ground lichen communities were primarily soil-type-specific, but were also affected by historic disturbances and land use change. In contrast to knowledge about herb layer communities, for which shrub encroachment has been shown to be main driver, the increased density of the herb layer and the reduced diversity of microhabitats were major drivers for the ground layer lichen community. These drivers caused a decrease in species richness, but only within the species of conservation value, and also led to a shift in the composition of lichen growth form from the dominance of squamulose and crustose towards fruticose lichens. We conclude that the traditional practice of restoring alvars by cutting shrubs is insufficient to maintain ground layer lichen biodiversity. Alvar maintenance practices should include grazing, which creates various small-scale ground disturbances and increases microhabitat heterogeneity. Alvar-like habitats originating from large-scale historic disturbances appeared to be suitable for calcicolous epigeic lichens, and can therefore be considered to be temporary substitution habitats, i.e. refugia for the regional species pool.     

Delineating Novel Therapeutic Drug and Vaccine Targets for Staphylococcus cornubiensis NW1T Through Computational Analysis

International Journal of Peptide Research and Therapeutics - Staphylococcal multidrug resistance is an emerging future threat. Among staphylococci species, Staphylococcus intermedius group (SIG)...