Entropic elasticity in the generation of muscle force--a theoretical model

A novel simplified structural model of sarcomeric force production in striate muscle is presented. Using some simple assumptions regarding the distribution of myosin spring lengths at different sliding velocities it is possible to derive a very simple expression showing the main components of the experimentally observed force-velocity relationship of muscle: nonlinearity during contraction (Hill, 1938), maximal force production during stretching equal to two times the isometric force (Katz, 1939), yielding at high stretching velocity, slightly concave force-extension relationship during sudden length changes (Ford et al., 1977; Lombardi & Piazzesi, 1990), accurate reproduction of the rate of ATP consumption (Shirakawa et al., 2000; He et al., 2000) and of the extra energy liberation rate (Hill, 1964a). Different assumptions regarding the force-length relationship of individual cross-bridges are explored [linear, power function and worm-like chain (WLC) model based], and it is shown that the best results are obtained if the individual myosin-spring forces are modelled using a WLC model, thus hinting that entropic elasticity could be the main source of force in myosin undergoing the conformational changes associated with the power stroke.     

Residual electrostatic effects in the unfolded state of the N-terminal domain of L9 can be attributed to nonspecific nonlocal charge-charge interactions

Residual electrostatic interactions in the unfolded state of the N-terminal domain of L9 (NTL9) were found by Kuhlman et al. [(1999) Biochemistry 38, 4896-4903]. These residual interactions are analyzed here by the Gaussian-chain model [Zhou, H.-X. (2002) Proc. Natl. Acad. Sci. U.S.A. 99, 3569-3574]. The original model is made more realistic by replacing "standard" model-compound pK(a) values for ionizable groups by those measured by Kuhlman et al. in peptide fragments of NTL9. The predicted pH dependence of the unfolding free energy is in agreement with experiment over the pH range of 1-7 at ionic strengths of 100 and 750 mM. This indicates that the residual electrostatic effects in the unfolded state of NTL9 can be attributed to nonspecific nonlocal charge-charge interactions.     

Effects of UV‐B Radiation on Anti‐Predator Behavior in Amphibians: Reply to Cummins

Cummins' (2002) criticism of our paper ( Kats et al. 2000 ) (1) displays a lack of understanding of experimental biology, (2) fails to report our results accurately, (3) places our paper in the wrong context, (4) seems unaware of much of the pertinent literature or selectively avoids certain references, and (5) takes the opportunity to criticize other papers examining the effects of ultraviolet radiation (UV, particularly UV‐B) on amphibians in the field. We address these issues below.     

Liver function parameters in HIV/HCV co-infected patients treated with amprenavir and ritonavir and correlation with plasma levels

Acute liver toxicity is a frequent adverse event that occurs during antiretroviral therapy and was observed in 6-30% of the patients on treatment, especially in presence of HCV coinfection (Cooper et al., 2002, Maida et al., 2006, Sulkowski et al., 2000). A correlation between HCV-associated liver-fibrosis severity and the risk of HAART associated hepatoxicity has been demonstrated (Aranzabal et al., 2005, Sulkowski et al., 2004). This high liver toxicity rate might be due to increased drug exposure in patients with liver disease (Veronese et al., 2000). It has been reported that patients with chronic hepatitis C show significantly reduced CPY3A4 and CYP2D6 activity in comparison with healthy volunteers (Becquemont et al., 2002). The aim of this study was to evaluate the liver function tests in HCV-co-infected patients treated with fos-amprenavir and ritonavir.     

Reprogramming is essential in nuclear transfer

Fertile offspring have been produced by nuclear transfer from adult somatic cells in several mammalian species (Wilmut et al., 1997; Kato et al., 1998; Wakayama et al., 1998; Polejaeva et al., 2000; Chesne et al., 2002; Shin et al., 2002; Zhou et al., 2003). Various possible causes have been suggested for the overall low efficiency (Perry and Wakayama, 2002). Notably, however, it has not yet been clearly demonstrated whether reprogramming after nuclear transfer is necessary for successful cloning. Here we show that reprogramming is essential in nuclear transfer, by comparing the developmental efficiency after the transfer of cumulus cell nuclei with that for zygote nuclei. Nuclear transfers from blastomeres of a series of pre-implantation stages showed further that, as development proceeds, the nuclei progressively lose their potency and become more difficult to reprogram upon their transfer into enucleated MII oocytes. We also found that naturally ovulated oocytes are much better recipients of a nucleus than are superovulated oocytes, which have been used in all the nuclear transfer experiments reported so far. This indicates that cloning efficiency can also be increased to some extent by technical improvements. All these results enable us to distinguish more clearly between the inherent problem of reprogramming and technical problems associated with materials, manipulation, and in vitro culture.     

Modeling and Estimation of Kinetic Parameters and Replicative Fitness of HIV-1 from Flow-Cytometry-Based Growth Competition Experiments

Growth competition assays have been developed to quantify the relative fitness of HIV-1 mutants. In this article, we develop mathematical models to describe viral/cellular dynamic interactions in the assay system from which the competitive fitness indices or parameters are defined. In our previous HIV-viral fitness experiments, the concentration of uninfected target cells was assumed to be constant (Wu et al. 2006). But this may not be true in some experiments. In addition, dual infection may frequently occur in viral fitness experiments and may not be ignorable. Here, we relax these two assumptions and extend our earlier viral fitness model (Wu et al. 2006). The resulting models then become nonlinear ODE systems for which closed-form solutions are not achievable. In the new model, the viral relative fitness is a function of time since it depends on the target cell concentration. First, we studied the structure identifiability of the nonlinear ODE models. The identifiability analysis showed that all parameters in the proposed models are identifiable from the flow-cytometry-based experimental data that we collected. We then employed a global optimization approach (the differential evolution algorithm) to directly estimate the kinetic parameters as well as the relative fitness index in the nonlinear ODE models using nonlinear least square regression based on the experimental data. Practical identifiability was investigated via Monte Carlo simulations.     

The public world of insect vibrational communication

Food webs involving plants, herbivorous insects and their predators account for 75% of terrestrial biodiversity (Price 2002). Within the abundant arthropod community on plants, myriad ecological and social interactions depend on the perception and production of plant-borne mechanical vibrations (Hill 2008). Study of ecological relationships has shown, for example, that termites monitor the vibrations produced by competing colonies in the same tree trunk (Evans et al. 2009), that stink bugs and spiders attend to the incidental vibrations produced by insects feeding or walking on plants (Pfannenstiel et al. 1995, Barth 1998) and that caterpillars can distinguish among the foraging-related vibrations produced by their invertebrate predators (Castellanos & Barbosa 2006). Study of social interactions has revealed that many insects and spiders have evolved the ability to generate intricate patterns of substrate vibration, allowing them to communicate with potential mates or members of their social group (Cokl & Virant-Doberlet 2003; Hill 2008). Surprisingly, research on the role of substrate vibrations in social and ecological interactions has for the most part proceeded independently, in spite of evidence from other communication modalities – acoustic, visual, chemical and electrical – that predators attend to the signals of their prey (Zuk & Kolluru 1998; Stoddard 1999). The study by Virant-Doberlet et al. (2011) in this issue of Molecular Ecology now helps bring these two areas of vibration research together, showing that the foraging behaviour of a spider is influenced by the vibrational mating signals of its leafhopper prey.     

Biological functions of maspin

Maspin (Mammary Serine Protease Inhibitor) was first reported in 1994 as a serpin with tumor suppressive properties. Maspin was initially isolated through subtractive hybridization and differential display analysis as a 42-kDa protein that is expressed in normal mammary epithelial cells but reduced or absent in breast carcinomas (Zou et al., 1994). Further research led to maspin's characterization as a class II tumor suppressor based on its ability to inhibit cell invasion, promote apoptosis, and inhibit angiogenesis (Sheng et al., 1996; Zhang et al., 2000b; Jiang et al., 2002). Since then, efforts have been made to characterize maspin's tumor suppressive mechanisms. In particular, researchers have studied maspin localization, the regulation of maspin expression, and more recently, maspin protein interactions. By elucidating these mechanisms, researchers are beginning to understand the complex, pleiotropic nature of maspin and the pathways through which maspin exerts its tumor suppressive properties. These new findings not only further enhance our understanding of cancer biology but also provide an avenue to develop maspin's potential as a diagnostic marker for cancer progression, and as a potentially powerful therapeutic agent in the fight against breast cancer.     

Neural networks in the cockpit of the fly

Flies have been buzzing around on earth for over 300 million years. During this time they have radiated into more than 125,000 different species (Yeates and Wiegmann 1999), so that, by now, roughly every tenth described species is a fly. They thus represent one of the most successful animal groups on our planet. This evolutionary success might, at least in part, be a result of their acrobatic maneuverability, which enables them, for example, to chase mates at turning velocities of more than 3000 degrees s(-1) with delay times of less than 30 ms (Land and Collett 1974; Wagner 1986). It is this fantastic behavior, which has initiated much research during the last decades, both on its sensory control and the biophysical and aerodynamic principles of the flight output (Dickinson et al. 1999, 2000). Here, we review the current state of knowledge about the neural processing of visual motion, which represents one sensory component intimately involved in flight control. Other reviews on this topic have been published with a similar (Hausen 1981, 1984; Hausen and Egelhaaf 1989; Borst 1996) or different emphasis (Frye and Dickinson 2001; Borst and Dickinson 2002). Because of space limitations, we do not review the extensive work that has been done on fly motion-sensitive neurons to advance our understanding of neural coding (Bialek et al. 1991; Rieke et al. 1997; de Ruyter et al. 1997, 2000; Haag and Borst 1997, 1998; Borst and Haag 2001). Unless stated otherwise, all data presented in the following were obtained on the blowfly Calliphora vicina which we will often casually refer to as 'the fly'.     

贵州下寒武统牛蹄塘生物群中海绵新材料

描述了贵州下寒武统牛蹄塘生物群中海绵化石1新属(Zunyispongiagen.nov.),2新种(Zunyispongiatriangulariagen.etsp.nov.,Choiafanensis.sp.nov.),通过对其形态功能的分析和讨论证实了寒武纪早期海绵动物的骨骼是由细小骨针向粗大骨针演变,骨架结构从不稳定型向稳定型发展。     

Assessing protected area network effectiveness through the temporal change in avian communities’ composition

Current rates of land use are driving temporal changes in avian communities. Thus, it is essential to properly designate and manage protected areas since they mitigate the adverse effects of temporal changes on species populations. By using common bird monitoring data in Czechia from two periods (2005/2006 and 2014/2015), we calculated two indices of temporal change per each site, the Jaccard dissimilarity index (temporal dissimilarity between the community composition) and the difference in bird species richness between both periods (delta bird species richness). We tested three main predictions on temporal change in bird communities between protected and unprotected areas: (i) bird species richness will be higher inside protected areas, (ii) temporal changes in avian communities will be lower inside protected areas, (iii) the effect of protected areas will interact with land-use types, land-use richness, and altitudinal zones. Bird species richness was higher inside protected areas in 2014/2015, ten years after the implementation of Natura 2000 in Czechia. Both indices of temporal change were lower inside protected areas. The interactions of protected areas and land-use types on the indices of temporal change were not significant. However, interactions with altitudinal zones had a significant positive effect on the indices, i.e., in higher altitudes, delta bird species richness and higher dissimilarity levels. Our study underlines the importance of protected areas for conservation by buffering the consequences of factors driving temporal community changes. Together, our results indicate a positive ‘umbrella’ effect of protected areas on avian communities that was likely facilitated by the implementation of Natura 2000.     

Positive species interactions shape species' range limits

The relationship between niche and distribution, and especially the role of biotic interactions in shaping species' geographic distributions, has gained increasing interest in the last two decades. Most ecological research has focused on negative species interactions, especially competition, predation and parasitism. Yet the relevance of positive interactions – mutualisms and commensalisms – have been brought to the fore in recent years by an increasing number of empirical studies exploring their impact on range limits. Based on a review of 73 studies from a Web of Science search, we found strong evidence that positive interactions can influence the extent of species' geographic or ecological ranges through a diversity of mechanisms. More specifically, we found that while obligate interactions, and especially obligate mutualisms, tend to constrain the ranges of one or both partners, facultative positive interactions tend to widen ranges. Nonetheless, there was more variation in effects of facultative interactions on range limits, pointing to important context-dependencies. Therefore, we propose that conceptual development in this field will come from studying ecological interactions in the context of networks of many species across environmental gradients, since pairwise interactions alone might overlook the indirect and environmentally-contingent effects that species have on each other in communities of many interacting species. Finally, our study also revealed key data gaps that limit our current understanding of the pervasiveness of effects that positive interactions have on species' ranges, highlighting potential avenues for future theoretical and experimental work.     

Evolution of metal hyperaccumulation and phytoremediation hype

Cadmium accumulation and tolerance are discussed in a New Phytologist article by Krämer (2000), which comments on a paper by Lombi et al . (2000). In this context, a number of additional points should be made, putting the role of humans in the evolution of metal resistance into context and emphasizing what is the 'hype' of phytoremediation.
It is important that sites created by humans should not be overemphasized in considering the evolution of metal resistance. Plants resistant to heavy metals have their primary sites not on these, but on soils where ores are outcropping, the so-called metalliferous or orogenic soils (Ernst, 1974). Over thousands of years, natural exposure to a surplus of various metals, depending on the mineralization process, has driven the evolution of metal resistance in many plant species under the local environmental conditions. Many publications have shown that Thlaspi caerulescens can hyperaccumulate Zn (e.g. Vázquez et al ., 1992), and accumulate other heavy metals such as Cu and Pb depending on soil chemistry (e.g. Baker et al ., 1994). It has been known for more than 30 years that T. caerulescens gives a good response to experimentally supplied high Zn levels (Ernst, 1968). One of the ecological effects of hyperaccumulation of heavy metals is a defence against herbivorous insects (Boyd & Martens, 1994). This effect is enhanced by a preferential accumulation of heavy metals in the epidermal leaf layer (Heath et al ., 1997).     

Examining the Cost of Experimentally Imitated Ornaments

Long forked tail ornament in male barn swallows (Hirundo rustica) were suggested to impose a condition‐dependent viability cost ( Møller 1989 ; reviewed in Møller 1994 ; Møller & de Lope 1994 ; Møller et al. 1995 ): long tails impair male flight and foraging ability in terms of mean size of prey captured. In a recent study, we ( Matyjasiak et al. 1999 ) showed such a foraging cost of an experimentally imitated tail ornament in the sand martin (Riparia riparia), which have no tail ornament. We lengthened the tail in females, instead of in males, and thus controlled experimentally for the possible effect of differential allocation of female parental expenditure (differential‐allocation hypothesis, Burley 1986 ). Cuervo (2000) raises important issues in his comments about our paper. He questions the method used in our study ( Matyjasiak et al. 1999 ). He points out that ‘in order to test the cost of flight of an ornament, the trait to be experimentally manipulated has to be an ornament’, and that we should have not only elongated but also shortened tail feathers. Secondly, he suggests that we did not provide, in our article, the exclusive evidence for the handicap model of sexual selection. Thirdly, he disagrees with our suggestion that the results from the barn swallow experiments could be confounded by the differential allocation of female parental expenditure. Here, we outline the areas of agreement and disagreement between Cuervo's critique and our paper. Firstly, we agree with Cuervo regarding the importance of tail shortening in studies of fully developed tail ornaments, which has already been pointed out by other authors ( Thomas & Rowe 1997 ; Evans & Thomas 1997 ). However, shortening of an ornament that is at equilibrium would always produce a decrease in costs. Therefore it will only confirm that an ornament is costly. However, if shortening is done to individuals of various, known condition, it may result in crucial information for distinguishing between hypotheses of sexual selection. We agree that for a character that is not an ornament, as in our experiments, shortening would not give new insights apart from another way of confirming the measures used in the barn swallow studies. However, we disagree with Cuervo's claims of irrelevance of our experiment to the issues of the evolution of signals. We have chosen sand martins as a model species because the shape of its tail resembles that in ancestors of modern tail‐ornamented swallows, from which tail feather elongation under sexual selection may have started ( Matyjasiak et al. 2000 ). Possible scenarios of the early evolution of a tail ornament may be examined by experimentally adding such an ornament, which requires manipulating original, non‐ornamental traits (e.g. Goötmark 1994, 1996 ). We disagree with Cuervo that the existence of traits that may reduce the costs of ornaments (e.g. Møller 1996 ) eliminates the validity of tail manipulation studies in species without ornaments. We believe that such cost‐reducing traits may not have existed during the early stages of evolution of tail ornaments (as well as other sexual traits) but may have developed later, and our experiment may represent such a situation very well. Hence, by imitating the initial development of a forked tail ornament in sand martins, we performed a biologically relevant manipulation. Secondly, we do not state in our paper that we have tested or proved the handicap principle. We only mention in the last paragraph of the Discussion, that our results are consistent with this principle. However, we do admit that mentioning only the handicap hypothesis in the Introduction and Discussion only, and omitting other processes by which costly tail ornaments might arise, was unwarranted, as Cuervo properly argued; this might have left a false impression that our goal was to test the handicap hypothesis. We do believe that we have properly measured the costs of tail elongation, and this was our goal, as stated in the Abstract and in the last paragraph of the Introduction. Nowhere in the paper did we state that we actually aimed to test the differential costs of ornaments that are crucial to the handicap hypothesis. This issue was the objective of a different paper ( Matyjasiak et al. 2000 ) in which we consider conditions important for the early evolution of tail ornaments, with special emphasis on the handicap principle. Thirdly, we are more cautious at interpreting the barn swallow studies and we do not exclude a possibility that differential allocation of parental expenditure can affect the size of prey brought by males. Differential allocation does exist in this species ( Møller 1992 ; de Lope & Møller 1993 ), as shown by the higher feeding rate by females responding to male higher attractiveness (longer tails). We believe that even though simple logical, intuitive reasoning may suggest that prey size should be unaffected by a differential allocation mechanism, it is not just reasoning but empirical proof that is needed here. Because there was no proof for a lack of the effect of differential allocation on the size of prey, we thought of an independent way of illustrating the costs of tail elongation in swallows, using a species without possible differential allocation effects. We thought that if we obtained results confirming the barn swallow studies by Møller and collaborators, we could help in validating the measures of tail elongation costs used in those studies. This was possible using the sand martin females for reasons discussed in the paper, all of which point to the lack of any differential allocation effects in this species. From this point of view, experimentally coupling tail elongation with tail shortening in our study appears unnecessary. Even though, as argued by Cuervo (2000) , it seems likely that the prey size in male swallows is unaffected by a change in feeding rate of females in response to male attractiveness (an assumption inherent in the barn swallow studies), another scenario is also possible. Imagine a female that has increased the amount of food for nestlings, in response to increased sexual attractiveness of her male partner due to experimental elongation of his tail. In such a situation the male has been relieved from a considerable duty of providing the young with a large amount of food. Hence, it is possible that such a male shifts from maximising the energy brought to nestlings per unit time (i.e. maximising foraging rate) to the criterion of obtaining the daily energetic needs at the least expense (i.e. minimising foraging costs). Such shifts may lead to including some non‐preferred, small insects that can be captured quickly and inexpensively in terms of energy, because it does not require the use of expensive flapping flight, which is required to capture larger, preferred insects ( Waugh 1978 ; Bryant & Turner 1982 ; Turner 1980, 1982 ). By including more small insects in their catch at the expense of a reduced foraging rate, attractive males could save energy for future use. Barn swallows appear to compromise between maximising their foraging efficiency (maximising foraging gains per costs) and maximising energy intake per unit time (see fig. 5.7 in Turner 1980 and table IV in Turner 1982 ). Hence, if sexually attractive males aim at minimising foraging costs rather than maximising foraging rate for nestlings, then we cannot exclude the possibility that this may result in smaller insects being caught, on average, by males with experimentally longer tails. By a similar reasoning, it is theoretically possible that differential allocation effects could lead to larger mean prey size in males with experimentally shortened tails ‐ an effect actually shown in the barn swallow studies ( de Lope & Møller 1993 ; Møller & de Lope 1994 ; Møller et al. 1995 ). Hence, whether shortening, elongating or performing both experimental manipulations, in our view we cannot be entirely sure whether the results are affected by differential allocation. This was sufficient motivation for us to investigate, independently, the usefulness of the change in prey size as an indicator of foraging costs due to elongated tails. In contrast to Cuervo's opinion, we believe that our results are relevant to the issues important for the evolution of forked tail ornaments. We have measured the costs of a character that imitates the hypothetical early stages of the evolution of sexual ornaments, and we may use these results to discuss the early evolution of sexual ornaments (see Matyjasiak et al. 2000 ). We also confirmed the validity of measures of tail elongation costs used in the barn swallow studies.     

Using a newly introduced framework to measure ecological stressor interactions

Understanding how stressors combine to affect population abundances and trajectories is a fundamental ecological problem with increasingly important implications worldwide. Generalisations about interactions among stressors are challenging due to different categorisation methods and how stressors vary across species and systems. Here, we propose using a newly introduced framework to analyse data from the last 25 years on ecological stressor interactions, for example combined effects of temperature, salinity and nutrients on population survival and growth. We contrast our results with the most commonly used existing method – analysis of variance (ANOVA) – and show that ANOVA assumptions are often violated and have inherent limitations for detecting interactions. Moreover, we argue that rescaling – examining relative rather than absolute responses – is critical for ensuring that any interaction measure is independent of the strength of single‐stressor effects. In contrast, non‐rescaled measures – like ANOVA – find fewer interactions when single‐stressor effects are weak. After re‐examining 840 two‐stressor combinations, we conclude that antagonism and additivity are the most frequent interaction types, in strong contrast to previous reports that synergy dominates yet supportive of more recent studies that find more antagonism. Consequently, measuring and re‐assessing the frequency of stressor interaction types is imperative for a better understanding of how stressors affect populations.     

Role of afferent input in muscle atrophy.

It is well known that soleus muscle of rat atrophies following spaceflight or hindlimb suspension (Ohira et al., 1992). It is, further, reported that the electromyogram (EMG) of soleus muscle disappears immediately in response to unloading by exposure to actual micro-g environment (Kawano et al., 2002; Leterme and Falempin, 1998) and by hindlimb suspension of rats (Alford et al., 1987; Ohira et al., 2000). However, the EMG level is increased gradually to the control level following 7-10 days of continuous hindlimb suspension (Alford et al., 1987; Ohira, 2000), while muscle atrophy is progressing (Winiarski et al., 1987). We previously reported that reduction of the EMG level of rat soleus in response to actual micro-g environment, created by a parabolic flight of a jet airplane, was closely associated with a decrease of the afferent input recorded at the L5 segmental level of spinal cord (Kawano et al., 2002). However, it is still unclear how the EMG level of soleus muscle adapts to unloading condition. The current study was performed to investigate the responses of soleus EMG and both afferent and efferent neurogram at the L5 segmental level of spinal cord to acute (20 seconds) and chronic (14 days) unloading.     

贵州遵义松林黑沙坡早寒武世牛蹄塘生物群中镇巴虫的发现

贵州遵义松林中南村黑沙坡下寒武统牛蹄塘生物群下部层位产有大型三叶虫,计有2属3种,1未定种：Zhenbaspis subconica S. G Zhang in Lu et al. , 1974, Z. longa Zhou in Lee et al. , 1975 ; Zhenbaspis sp. , Runnania similis Lee in Yin et Lee, , 1978, 确认 Zhenbaspis (Zhenxiongaspis) Lin et Yin in Yin et Lee, 1978,为 Zhenbastn‘sChang et Chu in Lu et al. ,1974的同义名。探讨Zhenbaspis的古地理分布及演化趋势。论文还描述与Zhenbaspis,Runnania共生的Tsunyidiscus及Mianxiandiscus,其中Mianxiandiscus产于下生物群即牛蹄塘组近底部,再次证实牛蹄塘下生物群的时代早于澄江生物群。