Visual motion: Dendritic integration makes sense of the world

Flies use a system of specialised neurons to read the patterns of visual motion – optic flow – induced by the their movements. Recent experiments illustrate how the dendrites of these neurons reach out to assemble patterns of optic flow and encode them reliably.     

Lymph flow guided irradiation of regional lymph nodes in patients with cervical cancer: Preliminary analysis of scintigraphic data

PurposeTo evaluate patterns of lymph flow from primary lesions in patients with cervical cancer and to determine how useful for radiotherapy planning this information can be.Materials and methodsSPECT–CT visualization of sentinel (SLN) lymph nodes (LNs) was performed in 36 primary patients with IB-IIB cervical cancer. The acquisition started 120–240 min after 4 peritumoral injections of 99mTc-radiocolloids (150–300 MBq in 0.4–1 ml). We determined localization of LN with uptake of radiocolloids, type of lymph flow (mono-, bi-lateral) and lymph flow patterns (supraureteral paracervical, infraureteral paracervical and directly to para-aortic LNs).ResultsSLNs were visualized in 31 of 36 women. Bilateral lymph-flow was detected in 22 (71%), monolateral – in the other 9 (29%) cases. The distribution of SLNs was as follows: external iliac – 64.5%, internal iliac – 54.8%, obturator – 32.2%, common iliac – 35.5% and pre-sacral 3.2%. Para-aortic LNs were visualized in 5 (16.1%) patients. The supraureteral paracervical pattern of lymph flow was identified in 22, infraureteral paracervical – in 4 and their combination – in the other 5 women.ConclusionVisualization of an individual pattern of lymph flow from primary cervical cancer can be considered as a promising tool for optimization of the volume of irradiated regional LNs.     

Determination of lead content in medicinal plants by pre‐concentration flow injection analysis–flame atomic absorption spectrometry

Introduction – Although medicinal plants are widely used throughout the world, few studies have been carried out concerning the levels of heavy metal contaminants present. Such metals are highly toxic to living organisms even in low concentrations owing to their cumulative effect. The present paper describes the the development of a pre‐concentration flow injection analysis‐flame atomic absorption spectrometric system to determine the lead content in medicinal plants at the ppb level. Objective – To develop a pre‐concentration flow injection analysis‐flame atomic absorption spectrometric system to determine the lead content in medicinal plants at the ppb level. Methodology – A pre‐concentration flow system was coupled to a flame atomic absorption spectrometer. The plant samples were analysed after nitroperchloric digestion. The proposed system was optimised by evaluating the following parameters: nature, concentration and volume of the eluent solution, elution flow rate, elution efficiency, pre‐concentration flow rate and pre‐concentration time. Results – The proposed system exhibited good performance with high precision and repeatability (RSD ≤ 2.36%), excellent linearity (r = 0.9999), low sample consumption (10.5 mL per determination) and an analytical throughput of 55 samples/h. Lead concentrations ranged from 3.37 ± 0.25 to 7.03 ± 0.51 μg/g in dry material. This concentration interval is greater than that previously published in the literature. Conclusion – The inclusion of a pre‐concentration column in the flow manifold improved the sensitivity of the spectrometer. Thus, it was possible to determine the analyte at the ng/mL level in sample solutions of medicinal plants. This is a very important accomplishment, especially when the cumulative effect of heavy metals in living organisms is considered. Copyright © 2009 John Wiley & Sons, Ltd.     

Next issue (January 2008): Methods and Advances in Biotech

Edited by Dr. Barbara Janssens, Managing Editor – Recombinant therapeutic proteins – Technical aspects of biocatalysis – Advances in safe and efficient DNA therapy – SeSaM-Tv: A random mutagenesis method – Bioinformatics: Identifying interacting residues using boolean learning and support vector machines – 3D imaging flow cytometry – Flow cytometry technology responding to HIV-tuberculosis coinfections – Stem cell cultures: Technical aspects Many of these exciting articles are already available online under “Early View”! A sneak preview of other content can be found under “News”.     

Flow‐mediated plasticity in the expression of stickleback nesting glue genes

Nest construction is an essential component of the reproductive behavior of many species, and attributes of nests – including their location and structure – have implications for both their functional capacity as incubators for developing offspring, and their attractiveness to potential mates. To maximize reproductive success, nests must therefore be suited to local environmental conditions. Male three‐spined sticklebacks (Gasterosteus aculeatus) build nests from collected materials and use an endogenous, glue‐like multimeric protein – “spiggin” – as an adhesive. Spiggin is encoded by a multigene family, and differential expression of spiggin genes potentially allows plasticity in nest construction in response to variable environments. Here, we show that the expression of spiggin genes is affected significantly by both the flow regime experienced by a fish and its nesting status. Further, we show the effects of flow on expression patterns are gene‐specific. Nest‐building fish exhibited consistently higher expression levels of the three genes under investigation (Spg‐a, Spg‐1, and Spg‐2) than non‐nesting controls, irrespective of rearing flow treatment. Fish reared under flowing‐water conditions showed significantly increased levels of spiggin gene expression compared to those reared in still water, but this effect was far stronger for Spg‐a than for Spg‐1 or Spg‐2. The strong effect of flowing water on Spg‐a expression, even among non‐nesters, suggests that the increased production of spiggin – or of spiggin rich in the component contributed by Spg‐a – may allow more rapid and/or effective nest construction under challenging high flow conditions.     

Haemodynamic analysis of femoral artery bifurcation models under different physiological flow waveforms

Thrombus in a femoral artery may form under stagnant flow conditions which vary depending on the local arterial waveform. Four different physiological flow waveforms – poor (blunt) monophasic, sharp monophasic, biphasic and triphasic – can exist in the femoral artery as a result of different levels of peripheral arterial disease progression. This study aims to examine the effect of different physiological waveforms on femoral artery haemodynamics. In this regard, a fluid–structure interaction analysis was carried out in idealised models of bifurcated common femoral artery. The results showed that recirculation zones occur in almost all flow waveforms; however, the sites at where these vortices are initiated, the size and structure of vortices are highly dependent on the type of flow waveform being used. It was shown that the reverse diastolic flow in biphasic and triphasic waveforms leads to the occurrence of a retrograde flow which aids in ‘washout’ of the disturbed flow regions. This may limit the likelihood of thrombus formation, indicating the antithrombotic role of retrograde flow in femoral arteries. Furthermore, our data revealed that the flow particles experience considerably higher residence time under blunt and sharp monophasic waveforms than under biphasic and triphasic waveforms. This confirms that the risk of atherothrombotic plaque initiation and development in femoral arteries is higher under blunt and sharp monophasic waveforms than under biphasic and triphasic flow waveforms.     

Jasminum polyanthum Franch. as a natural source of (−)‐methyl jasmonate: an alternative to the use of the synthetic standard

Introduction – Methyl jasmonate (MJ) contains two chiral centres at C‐3 and C‐7 in its chemical structure, which implies that it can exist in four possible stereoisomeric forms, namely (+)‐MJ, (?)‐MJ, (+)‐epiMJ and (?)‐epiMJ. The absolute configuration of the two side chains of MJ affects the biological activity associated with this compound. Objective – To isolate pure (?)‐MJ from a natural source, Jasminum polyanthum Franch., with the intention of increasing the knowledge about its biological properties, including its effect on the biosynthesis of plant metabolites. Methodology – The method used was based on steam distillation extraction (SDE) as an extraction technique followed by high‐performance liquid chromatography (HPLC) as a purification procedure. The HPLC flow‐rate as well as the number of fractions accumulated were optimised to achieve the concentration and purity required. Results – The employment of 0.3 mL/min as HPLC flow‐rate and the accumulation of three HPLC fractions allowed the required enantiomeric purity (95%) and concentration (0.36 mg/L in each HPLC fraction) to efficiently obtain (?)‐methyl jasmonate from Jasminum polyanthum Franch. to be achieved. Conclusion – The approach proposed may enable the properties and effect of pure (?)‐MJ on plant responses to be studied. The use of a natural source to obtain (?)‐MJ is presented as an alternative to the enantioselective synthesis and enantiomeric resolution from the standard racaemic mixture. Copyright © 2009 John Wiley & Sons, Ltd.     

Extreme weather events threaten biodiversity and functions of river ecosystems: evidence from a meta-analysis

Both gradual and extreme weather changes trigger complex ecological responses in river ecosystems. It is still unclear to what extent trend or event effects alter biodiversity and functioning in river ecosystems, adding considerable uncertainty to predictions of their future dynamics. Using a comprehensive database of 71 published studies, we show that event – but not trend – effects associated with extreme changes in water flow and temperature substantially reduce species richness. Furthermore, event effects – particularly those affecting hydrological dynamics – on biodiversity and primary productivity were twice as high as impacts due to gradual changes. The synthesis of the available evidence reveals that event effects induce regime shifts in river ecosystems, particularly affecting organisms such as invertebrates. Among extreme weather events, dryness associated with flow interruption caused the largest effects on biota and ecosystem functions in rivers. Effects on ecosystem functions (primary production, organic matter decomposition and respiration) were asymmetric, with only primary production exhibiting a negative response to extreme weather events. Our meta-analysis highlights the disproportionate impact of event effects on river biodiversity and ecosystem functions, with implications for the long-term conservation and management of river ecosystems. However, few studies were available from tropical areas, and our conclusions therefore remain largely limited to temperate river systems. Further efforts need to be directed to assemble evidence of extreme events on river biodiversity and functioning.     

The spatial scale of local adaptation in a stochastic environment

The distribution of phenotypes in space will be a compromise between adaptive plasticity and local adaptation increasing the fit of phenotypes to local conditions and gene flow reducing that fit. Theoretical models on the evolution of quantitative characters on spatially explicit landscapes have only considered scenarios where optimum trait values change as deterministic functions of space. Here, these models are extended to include stochastic spatially autocorrelated aspects to the environment, and consequently the optimal phenotype. Under these conditions, the regression of phenotype on the environmental variable becomes steeper as the spatial scale on which populations are sampled becomes larger. Under certain deterministic models – such as linear clines – the regression is constant. The way in which the regression changes with spatial scale is informative about the degree of phenotypic plasticity, the relative scale of effective gene flow and the environmental dependency of selection. Connections to temporal models are discussed.     

Species: a praxiographic study

Taxonomists, who describe new species, are acutely aware of how political, economic, and ecological forces bring new forms of life into being. Conducting ethnographic research among taxonomic specialists – experts who bring order to categories of animals, plants, fungi, and microbes – I found that they pay careful attention to the ebb and flow of agency in multispecies worlds. Emergent findings from genomics and information technologies are transforming existing categories and bringing new ones into being. This article argues that the concept of species remains a valuable sense‐making tool despite recent attacks from cultural critics.     

Visualizing protein motion in Couette flow by all-atom molecular dynamics

In living cells, biomacromolecules are exposed to a highly crowded environment. The cytoplasm, the nucleus, and other organelles are highly viscous fluids that differ from dilute in vitro conditions. Viscosity, a measure of fluid internal friction, directly affects the forces that act on immersed macromolecules. Although active motion of this viscous fluid – cytoplasmic streaming – occurs in many plant and animal cells, the effect of fluid motion (flow) on biomolecules is rarely discussed. Recently NMR experiments that apply a shearing flow in situ have been used for protein studies. While these NMR experiments have succeeded in spectroscopically tracking protein aggregation in real time, they do not provide a visual picture of protein motion under shear. To fill this gap, here we have used molecular dynamics simulations to study the motion of three proteins of different size and shape in a simple shearing flow. The proteins exhibit a superposition of random diffusion and shear-flow-induced rotational motion. Random rotational diffusion dominates at lower shear stresses, whereas an active “rolling motion” along the axis of the applied flow occurs at higher shear stress. Even larger shear stresses perturb protein secondary structure elements resulting in local and global unfolding. Apart from shear-induced unfolding, our results imply that, in an ideal Couette flow field biomolecules undergo correlated motion, which should enhance the probability of inter-molecular interaction and aggregation. Connecting biomolecular simulation with experiments applying shear flow in situ appears to be a promising strategy to study protein alignment, deformation, and dynamics under shear.     

Application of network methods for understanding evolutionary dynamics in discrete habitats

In populations occupying discrete habitat patches, gene flow between habitat patches may form an intricate population structure. In such structures, the evolutionary dynamics resulting from interaction of gene‐flow patterns with other evolutionary forces may be exceedingly complex. Several models describing gene flow between discrete habitat patches have been presented in the population‐genetics literature; however, these models have usually addressed relatively simple settings of habitable patches and have stopped short of providing general methodologies for addressing nontrivial gene‐flow patterns. In the last decades, network theory – a branch of discrete mathematics concerned with complex interactions between discrete elements – has been applied to address several problems in population genetics by modelling gene flow between habitat patches using networks. Here, we present the idea and concepts of modelling complex gene flows in discrete habitats using networks. Our goal is to raise awareness to existing network theory applications in molecular ecology studies, as well as to outline the current and potential contribution of network methods to the understanding of evolutionary dynamics in discrete habitats. We review the main branches of network theory that have been, or that we believe potentially could be, applied to population genetics and molecular ecology research. We address applications to theoretical modelling and to empirical population‐genetic studies, and we highlight future directions for extending the integration of network science with molecular ecology.     

Automated formation of multicomponent-encapuslating vesosomes using continuous flow microcentrifugation

Vesosomes – hierarchical assemblies consisting of membrane-bound vesicles of various scales – are potentially powerful models of cellular compartmentalization. Current methods of vesosome fabrication are labor intensive, and offer little control over the size and uniformity of the final product. In this article, we report the development of an automated vesosome formation platform using a microfluidic device and a continuous flow microcentrifuge. In the microfluidic device, water-in-oil droplets containing nanoscale vesicles in the water phase were formed using T-junction geometry, in which a lipid monolayer is formed at the oil/water interface. These water-in-oil droplets were then immediately transferred to the continuous flow microcentrifuge. When a water-in-oil droplet passed through a second lipid monolayer formed in the continuous flow microcentrifuge, a bilayer-encapsulated vesosome was created, which contained all of the contents of the aqueous phase encapsulated within the vesosome. Encapsulation of nanoscale liposomes within the outer vesosome membrane was confirmed by fluorescence microscopy. Laser diffraction analysis showed that the vesosomes we fabricated were uniform (coefficient of variation of 0.029). The yield of the continuous flow microcentrifuge is high, with over 60% of impinging water droplets being converted to vesosomes. Our system provides a fully automatable route for the generation of vesosomes encapsulating arbitrary contents. The method employed in this work is simple and can be readily applied to a variety of systems, providing a facile platform for fabricating multicomponent carriers and model cells.     

Validated Method for the Quantification of Atractylenolide III in Different Processed Products of Rhizoma Atractylodes Macrocephalae

Introduction – Rhizoma Atractylodes Macrocephalae (RAM) contains several sesquiterpene compounds including atractylenolide III (AO‐III). This bioactive compound may be used as a chemical marker for the quality control of different processed RAM products. Objective – To develop and validate an RP‐HPLC method for the quantitative determination of AO‐III in RAM and in a variety of processed RAM products. Methodology – HPLC was carried out using a Kromssil C₁₈ RP‐column eluted with methanol–water (70:30) at a flow rate of 1.0 mL/min and with UV detection at 220 nm. Full validation was performed using standard methods. Results – The linear range of AO‐III was 5–50 µg/mL; the regression equation was y = 10210x + 11194 (r = 0.9994) and the average recovery was 101.08% (RSD = 0.98%). The detection and quantification limits for AO‐III were determined to be 0.005 and 0.018 µg/mL at signal‐to‐noise ratios of approximately 3:1 and 10:1, respectively. Conclusion – The described HPLC method is appropriate for quality assurance and differentiation of AO‐III in RAM and different processed products.     

Local adaptation to salinity in the three‐spined stickleback?

Different lines of evidence suggest that the occurrence and extent of local adaptation in high gene flow marine environments – even in mobile and long‐lived vertebrates with complex life cycles – may be more widespread than earlier thought. We conducted a common garden experiment to test for local adaptation to salinity in Baltic Sea sticklebacks (Gasterosteus aculeatus). Fish from three different native salinity regimes (high, mid and low) were subjected to three salinity treatments (high, mid and low) in a full‐factorial experimental design. Irrespective of their origin, fish subjected to low (and mid) salinity treatments exhibited higher juvenile survival, grew to largest sizes and were in better condition than fish subjected to the high salinity treatment. However, a significant interaction between native and treatment salinities – resulting mainly from the poor performance of fish native to low salinity in the high salinity treatment – provided clear cut evidence for adaptation to local variation in salinity. Additional support for this inference was provided by the fact that the results concur with an earlier demonstration of significant differentiation in a number of genes with osmoregulatory functions across the same populations and that the population‐specific responses to salinity treatments exceeded that to be expected by random genetic drift.     

Effectiveness of Differently Designed Small‐Scale Constructed Wetlands to Decrease the Acidity of Acid Mine Drainage under Field Conditions

Constructed wetlands are a near‐natural method for the treatment of acid mine drainages (AMD). Because of the different site‐specific wastewater qualities and the variability of the used constructed wetlands regarding design, it is difficult to compare their efficiencies on the basis of literature data (often specific removal rates are missing). The AMD treatment efficiencies (pH, acidity) of differently designed planted and unplanted small‐scale constructed wetlands (subsurface flow – SSF, surface flow – SF, and hydroponic – HP systems with an area of 0.55 m² each) were compared under long‐term field conditions. The planted SF was found to be most effective, reaching mean acidity removal in the range of 80–90 %, and most resistant in view of external influences (i.e., heavy rain events). The planted SSF also showed high efficiency (50–90 %), but much more sensitivity to rain events. In both systems, the pH increased from 3.3 (mean of the inflows) to above 4.5 in the outflows. The efficiencies of the unplanted SF were insufficient and in the range of the (planted and unplanted) HP, i.e., smaller than 40 %. In general, the importance of plants for the success of the neutralization processes could be concluded.     

Does character displacement initiate speciation? Evidence of reduced gene flow between populations experiencing divergent selection

Character displacement – trait evolution stemming from selection to lessen resource competition or reproductive interactions between species – has long been regarded as important in finalizing speciation. By contrast, its role in initiating speciation has received less attention. Yet because selection for character displacement should act only where species co‐occur, individuals in sympatry will experience a different pattern of selection than conspecifics in allopatry. Such divergent selection might favour reduced gene flow between conspecific populations that have undergone character displacement and those that have not, thereby potentially triggering speciation. Here, we explore these ideas empirically by focusing on spadefoot toads, Spea multiplicata, which have undergone character displacement, and for which character displacement appears to cause post‐mating isolation between populations that are in sympatry with a heterospecific and those that are in allopatry. Using mitochondrial sequence data and nuclear microsatellite genotypes, we specifically asked whether gene flow is reduced between populations in different selective environments relative to that between populations in the same selective environment. We found a slight, but statistically significant, reduction in gene flow between selective environments, suggesting that reproductive isolation, and potentially ecological speciation, might indeed evolve as an indirect consequence of character displacement. Generally, character displacement may play a largely underappreciated role in instigating speciation.     

The role of allochrony in speciation

The importance of sympatric speciation – the evolution of reproductive isolation between codistributed conspecific individuals – in generating biodiversity is highly controversial. Allochrony, or differences in breeding time (phenology) between conspecific individuals, has the potential to lead to reproductive isolation and therefore speciation. We critically review the literature to test the importance of allochronic speciation over the three timescales over which allochrony can occur – over the day, between seasons or between years – and explore what is known about genomic mechanisms underlying allochrony in the diverse taxa in which it is found. We found that allochrony can be a key contributor to reproductive isolation, especially if populations have little overlap in breeding time and therefore little potential for gene flow, and may sometimes be the initial or key driver of speciation. Shifts in phenology can be caused by several factors, including a new ecological opportunity, environmental change, or reinforcement. The underlying genomic basis of allochrony has been studied mostly in insects, highlighting the need for genomic studies in other taxa; nonetheless, results to date indicate that several cases of allochrony involve changes in circadian genes. This review provides the first comprehensive discussion of the role of allochrony in speciation and demonstrates that allochrony as a contributor to divergence may be more widespread than previously thought. Understanding genomic changes and adaptations allowing organisms to breed at new times may be key in the light of phenological changes required under climate change.