RecQ helicase-catalyzed DNA unwinding detected by fluorescence resonance energy transfer

A fluorometric assay was used to study the DNA unwinding kinetics induced by Escherichiacoli RecQ helicase.This assay was based on fluorescence resonance energy transfer and carried out onstopped-flow,in which DNA unwinding was monitored by fluorescence emission enhancement of fluoresceinresulting from helicase-catalyzed DNA unwinding.By this method,we determined the DNA unwinding rateof RecQ at different enzyme concentrations.We also studied the dependences of DNA unwinding magnitudeand rate on magnesium ion concentration.We showed that this method could be used to determine thepolarity of DNA unwinding.This assay should greatly facilitate further study of the mechanism for RecQ-catalyzed DNA unwinding.     

Influence of visual targets and landmarks on honey bee foraging and waggle dancing

Animals use diverse sensory stimuli to navigate their environment and to recognize rewarding food sources.Honey bees use visual atributes of the targeted food source,such as its color,shape,size,direction and distance from the hive,and the landmarks around it to navigate during foraging.They transmit the location information of the food source to other bees if it is highly rewarding.To investigate the relative importance of these attributes,we trained bees to feeders in two different experiments.In the first experiment,we asked whether bees prefer to land on(a)a similar feeder at a different distance on the same heading or on(b)a visually distinct feeder located at the exact same location.We found that,within a short foraging range,bees relied heavily on the color and the shape of the food source and to a lesser extent on its distance from the hive.In the second experiment,we asked if moving the main landmark or the feeder(visual target)influenced recruitment dancing for the feeder.We found that foragers took longer to land and danced fewer circuits when the location of the food source,or a major landmark associated with it,changed.These results demonstrate that prominent visual atributes of food sources and landmarks are evidently more reliable than distance information and that foraging bees heavily utilize these visual cues at the later stages of their journey.     

Relative importance of long‐term changes in climate and land‐use on the phenology and abundance of legume crop specialist and generalist aphids

Abstract Insect populations are prone to respond to global changes through shifts in phenology, distribution and abundance. However, global changes cover several factors such as climate and land-use, the relative importance of these being largely unknown. Here, we aim at disentangling the effects of climate, land-use, and geographical drivers on aphid abundance and phenology in France, at a regional scale and over the last 40 years. We used aerial data obtained from suction traps between 1978 and 2015 on five aphid species varying in their degree of specialization to legumes, along with climate, legume crop area and geographical data. Effects of environmental and geographical variables on aphid annual abundance and spring migration dates were analyzed using generalized linear mixed models. We found that within the last four decades, aphids have advanced their spring migration by a month, mostly due to the increase in temperature early in the year, and their abundance decreased by half on average, presumably in response to a combination of factors. The influence of legume crop area decreased with the degree of specialization of the aphid species to such crops. The effect of geographical variation was high even when controlling for environmental variables, suggesting that many other spatially structured processes act on aphid population characteristics. Multifactorial analyses helped to partition the effects of different global change drivers. Climate and land-use changes have strong effects on aphid populations, with important implications for future agriculture. Additionally, trait-based response variation could have major consequences at the community scale.     

Designing a Biomimetic Ornithopter Capable of Sustained and Controlled Flight

We describe the design of four ornithopters ranging in wing span from 10 cm to 40 cm, and in weight from 5 g to 45 g. The controllability and power supply are two major considerations, so we compare the efficiency and characteristics between different types of subsystems such as gearbox and tail shape. Our current omithopter is radio-controlled with inbuilt visual sensing and capable of takeoff and landing. We also concentrate on its wing efficiency based on design inspired by a real insect wing and consider that aspects of insect flight such as delayed stall and wake capture are essential at such small size. Most importantly, the advance ratio, controlled either by enlarging the wing beat amplitude or raising the wing beat frequency, is the most significant factor in an ornithopter which mimics an insect.     

A Biomimetic Approach to Robot Locomotion in Unstructured and Slippery Environments

While much attention has been given to bio-robotics in recent years, not much of this has been given to the challenging subject of locomotion in slippery conditions. This study begins to rectify this by proposing a biomimetic approach to generating the friction required to give sufficient propulsive force on a slippery substrate. We took inspiration from a successful biological solution-that of applying hair-like structures to the propulsive appendages, similar to the setae found in nereid polychaetes living in muddy habitats. We began by examining the morphology and the mean locomotion parameters of one of the most common nereids: Nereis diversicolor. Following this study, we designed and fabricated a robotic system with appendages imitating the biological shape found in the worm. A flexible control system was developed to allow most of the locomotion parameters observed in the real worm to be applied to the robot. Experiments on three different natural substrates ranging from fine sand to gravel showed     

Different paths to sexual size dimorphism in two praying mantids,Pseudomantis albofimbriata and Hierodula majuscula

Sexual size dimorphism （SSD） is widespread among diverse animal taxa and has attracted the attention of evolutionary biologists for over a century. SSD is likely to be adaptive and the result of divergent selection on different size optima for males and females, given their different roles in reproduction. The developmental trajectory leading to SSD may help us to understand how selection acts on male and female size. Here, we describe the growth and development of two Australian praying mantids, Pseudomantis albofimbriata and Hierodula majuscula including the number of moults, time to adulthood, size at each moult, and the degree of SSD. While both species exhibit the common pattern of female-biased SSD, the number of moults required for individuals to reach adulthood differed between males and females and between species. Despite their larger adult size, P. albofimbriata females require fewer moults and less time than males to reach adulthood, but are significantly larger than males from the second instar onwards. In contrast, H. majuscula males reached adulthood in fewer moults, and less time than females, however males and females did not differ in size until females went through their final moult into adulthood. H. majuscula also required more time and more moults to reach adulthood than 17. albofimbriata. We discuss these different developmental pathways in light of the existing knowledge of reproductive biology for each species. We also suggest that these differences may relate to the different phenologies that occur in strongly seasonal temperate environments compared with those in the tropics. This study provides evidence that SSD can result from two different patterns of growth and development in closely related species.     

Use of a Digital Image Correlation Technique for Measuring the Material Properties of Beetle Wing

Beetle wings are very specialized flight organs consisting of the veins and membranes.Therefore it is necessary from abionic view to investigate the material properties of a beetle wing experimentally.In the present study,we have used a DigitalImage Correlation (DIC) technique to measure the elastic modulus of a beetle wing membrane.Specimens were prepared bycarefully cutting a beetle hind wing into 3.0 mm by 7.0 mm segments (the gage length was 5 mm).We used a scanning electronmicroscope for a precise measurement of the thickness of the beetle wing membrane.The specimen was attached to a designedfixture to induce a uniform displacement by means of a micromanipulator.We used an ARAMISTM system based on the digitalimage correlation technique to measure the corresponding displacement of a specimen.The thickness of the beetle wing variedat different points of the membrane.The elastic modulus differed in relation to the membrane arrangement showing a structuralanisotropy;the elastic modulus in the chordwise direction is approximately 2.65 GPa,which is three times larger than the elasticmodulus in the spanwise direction of 0.84 GPa.As a result,the digital image correlation-based ARAMIS system was suc-cessfully used to measure the elastic modulus of a beetle wing.In addition to membrane’s elastic modulus,we considered thePoisson’s ratio of the membrane and measured the elastic modulus of a vein using an Instron universal tensile machine.Theresult reveals the Poisson’s ratio is nearly zero and the elastic modulus of a vein is about 11 GPa.     

Numerical and Experimental Research on Modular Oscillating Fin

Fishes are famous for their ability to position themselves accurately even in turbulent flows. This ability is the result of the coordinated movement of fins which extend from the body. We have embarked on a research program designed to develop an agile and high efficient biologically inspired robotic fish based on the performance of hybrid mechanical fms. To accomplish this goal, a mechanical ray-like fin actuated by Shape Memory Alloy （SMA） is developed, which can realize both oscillatory locomotion and undulatory locomotion. We first give a brief introduction on the mechanical structure of our fin and then carry out theoretic analysis on force generation. Detailed information of these theoretical results is later revealed by Computational Huid Dynamic （CFD）, and is final validated by experiments. This robotic fin has potential application as a propulsor for future underwater vehicles in addition to being a valuable scientific instrument.     

Towards Kinetic Modeling of Global Metabolic Networks: Methylobacterium extorquens AM1 Growth as Validation

Here we report a systematic method for constructing a large scale kinetic metabolic model and its initial application to the modeling of central metabolism of Methylobacterium extorquens AM1, a methylotrophic and environmental important bacterium. Its central metabolic network includes formaldehyde metabolism, serine cycle, citric acid cycle, pentose phosphate pathway, gluconeogensis, PHB synthesis and acetyl-CoA conversion pathway, respiration and energy metabolism. Through a systematic and consistent procedure of finding a set of parameters in the physiological range we overcome an outstanding difficulty in large scale kinetic modeling: the requirement for a massive number of enzymatic reaction parameters. We are able to construct the kinetic model based on general biological considerations and incomplete experimental kinetic parameters. Our method consists of the following major steps: 1) using a generic enzymatic rate equation to reduce the number of enzymatic parameters to a minimum set while still preserving their characteristics; 2) using a set of steady state fluxes and metabolite concentrations in the physiological range as the expected output steady state fluxes and metabolite concentrations for the kinetic model to restrict the parametric space of enzymatic reactions; 3) choosing enzyme constants K’s and K’eqs optimized for reactions under physiological concentrations, if their experimental values are unknown; 4) for models which do not cover the entire metabolic network of the organisms, designing a dynamical exchange for the coupling between the metabolism represented in the model and the rest not included.     

Towards Kinetic Modeling of Global Metabolic Networks: Methylobacterium extorquens AM1 Growth as Validation

Here we report a systematic method for constructing a large scale kinetic metabolic model and its initial application to the modeling of central metabolism of Methylobacterium extorquens AM1, a methylotrophic and environmental important bacterium. Its central metabolic network includes formaldehyde metabolism, serine cycle, citric acid cycle, pentose phosphate pathway, gluconeogensis, PHB synthesis and acetyl-CoA conversion pathway, respiration and energy metabolism. Through a systematic and consistent procedure of finding a set of parameters in the physiological range we overcome an outstanding difficulty in large scale kinetic modeling: the requirement for a massive number of enzymatic reaction parameters. We are able to construct the kinetic model based on general biological considerations and incomplete experimental kinetic parameters. Our method consists of the following major steps: 1) using a generic enzymatic rate equation to reduce the number of enzymatic parameters to a minimum set while still preserving their characteristics; 2) using a set of steady state fluxes and metabolite concentrations in the physiological range as the expected output steady state fluxes and metabolite concentrations for the kinetic model to restrict the parametric space of enzymatic reactions; 3) choosing enzyme constants K’s and K’eqs optimized for reactions under physiological concentrations, if their experimental values are unknown; 4) for models which do not cover the entire metabolic network of the organisms, designing a dynamical exchange for the coupling between the metabolism represented in the model and the rest not included.     

B-cell ligand processing pathways detected by large-scale comparative analysis

The initiation of B-cell ligand recognition is a critical step for the generation of an immune response against foreign bodies.We sought to identify the biochemical pathways involved in the B-cell ligand recognition cascade and sets of ligands that trigger similar immunological responses.We utilized several comparative approaches to analyze the gene coexpression networks generated from a set of microarray experiments spanning 33 different ligands.First,we compared the degree distributions of the generated networks.Second,we utilized a pairwise network alignment algorithm,BiNA,to align the networks based on the hubs in the networks.Third,we aligned the networks based on a set of K_EGG pathways.We summarized our results by constructing a consensus hierarchy of pathways that are involved in B cell ligand recognition.The resulting pathways were further validated through literature for their common physiological responses.Collectively,the results based on our comparative analyses of degree distributions,alignment of hubs,and alignment based on KEGG pathways provide a basis for molecular characterization of the immune response states of B-cells and demonstrate the power of comparative approaches(e.g.,gene coexpression network alignment algorithms) in elucidating biochemical pathways involved in complex signaling events in cells.     

Spontaneous modulation of a dynamic balance between bacterial genomic stability and mutability: roles and molecular mechanisms of the genetic switch

Bacteria need a high degree of genetic stability to maintain their species identities over long evolutionary times while retaining some mutability to adapt to the changing environment.It is a long unanswered question that how bacteria reconcile these seemingly contradictory biological properties.We hypothesized that certain mechanisms must maintain a dynamic balance between genetic stability and mutability for the survival and evolution of bacterial species.To identify such mechanisms,we analyzed bacterial genomes,focusing on the Salmonella mismatch repair(MMR)system.We found that the MMR gene mutL functions as a genetic switch through a slipped-strand mispairing mechanism,modulating and maintaining a dynamic balance between genetic stability and mutability during bacterial evolution.This mechanism allows bacteria to maintain their phylogenetic status,while also adapting to changing environments by acquiring novel traits.In this review,we outline the history of research into this genetic switch,from its discovery to the latest findings,and discuss its potential roles in the genomic evolution of bacteria.     

Structure for energy cycle: a unique status of the second law of thermodynamics for living systems

Distinguishing things from beings, or matters from lives, is a fundamental question. Extending E. Schr?dinger's neg-entropy and I. Prigogine's dissipative structure, we propose a chemical kinetic view that the earliest "live" process is embedded essentially in a special interaction between a pair of specific components under a particular, corresponding environmental conditions. The interaction exists as an inter-molecular-force-bond complex(IMFBC) that couples two separate chemical processes: one is the spontaneous formation of the IMFBC driven by a decrease of Gibbs free energy as a dissipative process; while the other is the disassembly of the IMFBC driven thermodynamically by free energy input from the environment. The two chemical processes coupled by the IMFBC originated independently and were considered non-living on Earth, but the IMFBC coupling of the two can be considered as the earliest form of metabolism: the first landmark on the path from things to a being. The dynamic formation and disassembly of the IMFBC, as a composite individual, follows a principle designated as "… structure for energy for structure for energy…", the cycle continues; and for short it will be referred to as "structure for energy cycle". With additional features derived from this starting point, the IMFBC-centered "live" process spontaneously evolved into more complex living organisms with the characteristics currently known.     

Comparative analysis of splice site regions by information content

We have applied concepts from information theory for a comparative analysis of donor （gt） and acceptor （ag） splice site regions in the genes of five different organisms by calculating their mutual information content （relative entropy） over a selected block of nucleotides. A similar pattern that the information content decreases as the block size increases was observed for both regions in all the organisms studied. This result suggests that the information required for splicing might be contained in the consensus of -6-8 nt at both regions. We assume from our study that even though the nucleotides are showing some degrees of conservation in the flanking regions of the splice sites, certain level of variability is still tolerated, which leads the splicing process to occur normally even if the extent of base pairing is not fully satisfied. We also suggest that this variability can be compensated by recognizing different splice sites with different spliceosomal factors.