白垩纪中期缅甸琥珀昆虫行为生态学研究进展

缅甸琥珀生物群产自距今约98.8Ma的白垩纪中期,该生物群是世界上物种多样性很高的琥珀生物群之一,为了解白垩纪中期生物多样性和古生态提供了重要窗口。文中以近年来缅甸琥珀地层学、琥珀生物学研究为依据,总结缅甸琥珀形成环境,并对缅甸琥珀揭示的昆虫与植物的协同演化、昆虫的捕食、社会性证据、寄生、求偶和结构色等方面的研究结果进行总结,以期较全面地综述缅甸琥珀的古环境和昆虫行为生态学特征。     

Natural and human impact in Mediterranean landscapes: An intriguing puzzle or only a question of time?

Time is a key factor to understand the effects of disturbance on natural communities or ecosystems. In Mediterranean landscapes, where nature and humans have been strongly intermingling since mid-Holocene, the relationships between plant ecology and palaeoecology and their role for the interpretation of natural and anthropogenic changes still needs to be clearly understood. Ecology and palaeoecology are both investigating such problems, but each of them cannot disentangle the specific role played by nature and by humans in shaping the present plant communities and landscapes. A new age of cooperation among researchers in ecology and palaeoecology is needed, and the integration of these closely related but separated research fields is necessary to explain the resulting dynamic puzzle. Plant ecologists should avoid the oversimplification of the actual causes as the exclusive drivers of plant communities and landscapes and force the exploitation of the available data to generate and test new hypotheses for past, present and future environmental reconstructions and management. Even when planning for the future biodiversity conservation, we need to properly use the existing information about millennia of human effects on the natural biotas, to properly set landscape management and conservation priorities.     

Tomographic reconstructions of crab burrows from deltaic tidal flat: Contribution to palaeoecology of decapod trace fossils in coastal settings

Trace fossils play an important role in reconstructing palaeoecology and depositional environment. Their palaeoecological implications can be better understood when the trace makers are correctly identified. Neoichnology studies the burrow morphologies, behavioral ecology of modern organisms and their interaction with the environment. Neoichnology is of great significance in linking burrowing behaviors of extant organisms with interpretation of trace fossil palaeoecology. This paper reports a study on burrows produced by the ocypodid crab (Macrophthalmus japonicus De Haan) in the tidal region of the Yellow River Delta using CT scanning techniques. Our results show that M. japonicus produces abundant I-, U-, and Y-shaped burrows in a mudflat of the delta. These domicile structures are similar in morphological characteristics to the trace fossil Psilonichnus, suggesting M. japonicus as its possible additional trace maker. Our study supports the usage of Psilonichnus as a significant palaeoenvironmental indicator for coastal and shelf environments. Furthermore, this study highlights the great potential of applying CT techniques in future ichnological-related studies.     

Integrating models with data in ecology and palaeoecology: advances towards a model-data fusion approach

It is increasingly being recognized that global ecological research requires novel methods and strategies in which to combine process-based ecological models and data in cohesive, systematic ways. Model-data fusion (MDF) is an emerging area of research in ecology and palaeoecology. It provides a new quantitative approach that offers a high level of empirical constraint over model predictions based on observations using inverse modelling and data assimilation (DA) techniques. Increasing demands to integrate model and data methods in the past decade has led to MDF utilization in palaeoecology, ecology and earth system sciences. This paper reviews key features and principles of MDF and highlights different approaches with regards to DA. After providing a critical evaluation of the numerous benefits of MDF and its current applications in palaeoecology (i.e., palaeoclimatic reconstruction, palaeovegetation and palaeocarbon storage) and ecology (i.e. parameter and uncertainty estimation, model error identification, remote sensing and ecological forecasting), the paper discusses method limitations, current challenges and future research direction. In the ongoing data-rich era of today's world, MDF could become an important diagnostic and prognostic tool in which to improve our understanding of ecological processes while testing ecological theory and hypotheses and forecasting changes in ecosystem structure, function and services.     

Palaeoniches get stitches: analyses of niches informing macroevolutionary theory

The concept of the niche is fundamental to ecology and palaeoecology, and an extensive body of scientific literature exists on the subject Here we discuss how recent palaeontological studies, particularly those focusing on species’ niche dynamics through time, continue to integrate palaeoecology with macroevolutionary theory.     

BILDUNG UND GEBRAUCH VON BEGRIFFEN IN DER PALÄOÖKOLOGIE

During the past 20 years, palaeoecology has established itself as a concept in palaeontology and geology. As in other interdisciplinary sciences, the interchange of methods and terminology between the branches involved has led to changes in the meaning of the terms, and changes or confusion in the corresponding scientific concepts. This calls for stricter adherence to the original definition of the terms in many cases and for their redefinition in others. Starting with a critical review of the scientific and methodological range of palaeoecology, this paper presents a reconsideration of its basic concepts, with proposals concerning the conservation or redefinition of terms and with special regard to terms coined in German literature. It is desirable that similar revisions be undertaken in other language areas in order to attain a stricter, internationalized terminology, preferably substantiated in a dictionary.     

Certain organism-substrate relationships affecting the distribution of Uca minax (Crustacea: Decapoda)

The involvement of substrate in the ecology of the fiddler crab Uca minax was investigated by means of both field and laboratory studies. These included determination of the oxygen-holding capacities of five types of substrates on which this organism lives, as well as experiments to determine if there is substrate selection. The effect of population density on burrowing was also studied to determine the optimum number of individuals needed in the selection experiments, and to delineate the mechanisms these organisms use for avoiding dispersion onto less favorable substrates. Results indicate that Uca minax prefers substrates with high organic content, although these were shown to contain the lowest substrate oxygen. This evidence suggests that Uca minax prefers substrates of high energy value, and explains the significance of this species' adaptation in withstanding low oxygen tensions. Population density experiments indicate that at high population densities these crabs reduce intraspecific encounter and competition by burrowing and subsequently covering their burrows. Seasonal monitoring of burrow temperatures indicate the stability of this microenvironment as compared with the surrounding air temperature. These data also demonstrate the significance of the adjacent water in the habitat ecology of Uca minax.     

Phylogeny and palaeoecology of Polyommatus blue butterflies show Beringia was a climate-regulated gateway to the New World

Transcontinental dispersals by organisms usually represent improbable events that constitute a major challenge for biogeographers. By integrating molecular phylogeny, historical biogeography and palaeoecology, we test a bold hypothesis proposed by Vladimir Nabokov regarding the origin of Neotropical Polyommatus blue butterflies, and show that Beringia has served as a biological corridor for the dispersal of these insects from Asia into the New World. We present a novel method to estimate ancestral temperature tolerances using distribution range limits of extant organisms, and find that climatic conditions in Beringia acted as a decisive filter in determining which taxa crossed into the New World during five separate invasions over the past 11 Myr. Our results reveal a marked effect of the Miocene-Pleistocene global cooling, and demonstrate that palaeoclimatic conditions left a strong signal on the ecology of present-day taxa in the New World. The phylogenetic conservatism in thermal tolerances that we have identified may permit the reconstruction of the palaeoecology of ancestral organisms, especially mobile taxa that can easily escape from hostile environments rather than adapt to them.     

Island biology: looking towards the future

Oceanic islands are renowned for the profound scientific insights that their fascinating biotas have provided to biologists during the past two centuries. Research presented at Island Biology 2014—an international conference, held in Honolulu, Hawaii (7–11 July 2014), which attracted 253 presenters and 430 participants from at least 35 countries¹—demonstrated that islands are reclaiming a leading role in ecology and evolution, especially for synthetic studies at the intersections of macroecology, evolution, community ecology and applied ecology. New dynamics in island biology are stimulated by four major developments. We are experiencing the emergence of a truly global and comprehensive island research community incorporating previously neglected islands and taxa. Macroecology and big-data analyses yield a wealth of global-scale synthetic studies and detailed multi-island comparisons, while other modern research approaches such as genomics, phylogenetic and functional ecology, and palaeoecology, are also dispersing to islands. And, increasingly tight collaborations between basic research and conservation management make islands places where new conservation solutions for the twenty-first century are being tested. Islands are home to a disproportionate share of the world''s rare (and extinct) species, and there is an urgent need to develop increasingly collaborative and innovative research to address their conservation requirements.     

Activity of mushroom polyphenol oxidase in organic medium

A kinetic study of the activity of mushroom polyphenol oxidase in an organic system was carried out to obtain detailed enzyme kinetic data in relation to optimization of reaction conditions and substrate specificity. A simple method for consistent measurement of reaction rates in the heterogeneous enzyme/organic solvent system (consisting of immobilized polyphenol oxidase and a hydrated solution of the substrate in chloroform) was designed. The aqueous content of the system was optimized using p-cresol as the substrate. With this system, a crude extract of Agaricus bisporus was used to hydroxylate and oxidize a range of selected p-substituted phenolic substrates, yielding o-quinone products. Michaelis-Menten kinetics were used to obtain apparent K(M) and V(max) values with respect to each of these substrates. Results from this analysis indicated a correlation between the enzymic kinetic parameters obtained and the steric requirements of the substrates, which could be rationalized in terms of the restricted flexibility of the enzyme when it is in chloroform and also in terms of substrate and solvent hydrophobicity. In the course of the investigation UV molar absorption coefficients of several o-quinones were measured by a novel method: (1)H nuclear magnetic resonance (NMR) spectroscopy was employed to determine component concentrations in reaction mixtures resulting from the transformation of phenols by polyphenol oxidase in chloroform. Thus the UV molar absorption coefficients could be obtained directly, avoiding the necessity to isolate the water-sensitive, unstable o-quinones. (c) 1993 John Wiley & Sons, Inc.     

Intraspecific Colour Variation among Lizards in Distinct Island Environments Enhances Local Camouflage

Within-species colour variation is widespread among animals. Understanding how this arises can elucidate evolutionary mechanisms, such as those underlying reproductive isolation and speciation. Here, we investigated whether five island populations of Aegean wall lizards (Podarcis erhardii) have more effective camouflage against their own (local) island substrates than against other (non-local) island substrates to avian predators, and whether this was linked to island differences in substrate appearance. We also investigated whether degree of local substrate matching varied among island populations and between sexes. In most populations, both sexes were better matched against local backgrounds than against non-local backgrounds, particularly in terms of luminance (perceived lightness), which usually occurred when local and non-local backgrounds were different in appearance. This was found even between island populations that historically had a land connection and in populations that have been isolated relatively recently, suggesting that isolation in these distinct island environments has been sufficient to cause enhanced local background matching, sometimes on a rapid evolutionary time-scale. However, heightened local matching was poorer in populations inhabiting more variable and unstable environments with a prolonged history of volcanic activity. Overall, these results show that lizard coloration is tuned to provide camouflage in local environments, either due to genetic adaptation or changes during development. Yet, the occurrence and extent of selection for local matching may depend on specific conditions associated with local ecology and biogeographic history. These results emphasize how anti-predator adaptations to different environments can drive divergence within a species, which may contribute to reproductive isolation among populations and lead to ecological speciation.     

Investigating biological control over soil carbon temperature sensitivity

Understanding the temperature sensitivity of soil respiration is critical for predicting the response of ecosystems to climate change, yet the microbial communities responsible are rarely considered explicitly in studies or models. In this study, we assessed total microbial community composition, quantified bacterial respiration temperature response, and investigated the temperature dependence of bacterial carbon substrate utilization in tropical, temperate, and taiga soils (from Puerto Rico, California, and Alaska). Microbial community composition was characterized using phospholipid fatty acid analysis. Bacterial community respiration on a standardized set of substrates was ascertained using the BiOLOG^™ substrate utilization assay incubated at four temperatures: 4, 12, 28, and 40 °C. First, we found that microbial communities from the three latitudes were compositionally distinct and that the bacterial component of the three communities had markedly different respiration temperature–response curves corresponding with their experienced temperature regimes. We use these data to highlight limitations of widely used temperature–response equations and investigate temperature-dependent patterns of substrate utilization. We found that temperature response, in terms of both respiration rates and substrate use, varied for these bacterial communities independent of substrate quality or quantity interactions such as labile depletion. In contrast to the common assumption of heterotrophic microbial ubiquity, we found that bacterial community differences from these diverse systems appeared to determine both rates of respiration and patterns of carbon substrate usage. We suggest that microbial community composition-specific responses to changing climate may be important in predicting the long-term role of ecosystems in atmospheric CO₂ dynamics.     

Studies on the properties of P1 site-specific recombination: evidence for topologically unlinked products following recombination

Bacteriophage P1 encodes its own site-specific recombination system consisting of a site at which recombination takes place called loxP and a recombinase called Cre. A number of lambda and plasmid substrates containing two loxP sites have been constructed. Using these substrates we have shown both in vivo and in vitro that a fully functional loxP site is composed of no more than 60 bp. In vitro, when an extract containing Cre is used, recombination between loxP sites on supercoiled, nicked-circle or linear DNA occurs efficiently. The most surprising result from the in vitro studies is that 50% of the products of recombination between loxP sites on a supercoiled DNA substrate are present as free supercoiled circles. The ability to produce free products starting with a supercoiled substrate suggests a rather unique property of Cre-mediated lox recombination, the implications of which are discussed in terms of possible effects of the protein on the topology of the DNA molecule.     

Inhibition of mitochondrial respiration by loss of intra-mitochondrial K

1. A system is described in which intra-mitochondrial K⁺ concentration can be manipulated by the use of dinitrophenol and valinomycin.

2. As mitochondria lose K⁺ a striking inhibition of O₂ consumption occurs with both succinate and DPN-linked substrates, but not if tetramethyl-p-phenylenediamine + ascorbate serves as substrate. Respiration can be re-activated by adding K⁺ to the medium.

3. Results are discussed in terms of sensitivity of electron transport or substrate dehydrogenation to intra-mitochondrial K⁺ content.     

Lipase-catalyzed acyl exchange of soybean phosphatidylcholine in n-Hexane: a critical evaluation of both acyl incorporation and product recovery

Lipase-catalyzed acidolysis was examined for the production of structured phospholipids in a hexane system. In a practical operation of the reaction system, the formation of lyso-phospholipids from hydrolysis is often a serious problem, as demonstrated from previous studies. A clear elucidation of the issue and optimization of the system are essential for the practical applications in reality. The effects of enzyme dosage, reaction temperature, solvent amount, reaction time, and substrate ratio were optimized in terms of the acyl incorporation, which led to the products, and lyso-phospholipids formed by hydrolysis, which led to the low yields. The biocatalyst used was the commercial immobilized lipase Lipozyme TL IM and substrates used were phosphatidylcholine (PC) from soybean and caprylic acid. A response surface design was used to evaluate the influence of selected parameters and their relationships on the incorporation of caprylic acid and the corresponding recovery of PC. Incorporation of fatty acids increased with increasing enzyme dosage, reaction temperature, solvent amount, reaction time, and substrate ratio. Enzyme dosage had the most significant effect on the incorporation, followed by reaction time, reaction temperature, solvent amount, and substrate ratio. However the parameters had also a negative influence on the PC recovery. Solvent amount had the most negative effect on recovery, followed by enzyme dosage, temperature, and reaction time. Individually substrate ratio had no significant effect on the PC recovery. Interactions were observed between different parameters. On the basis of the models, the reaction was optimized for the maximum incorporation and maximum PC recovery. With all of the considerations, the optimal conditions are recommended as enzyme dosage 29%, reaction time 50 h, temperature 54 degrees C, substrate ratio 15 mol/mol caprylic acid/PC, and 5 mL of hexane per 3 g substrate. No additional water is necessary. Under these conditions, an incorporation of caprylic acid up to 46% and recovery of PC up to 60% can be obtained from the prediction. The prediction was confirmed from the verification experiments.     

Profiling serine protease substrate specificity with solution phase fluorogenic peptide microarrays

A novel microarray-based proteolytic profiling assay enabled the rapid determination of protease substrate specificities with minimal sample and enzyme usage. A 722-member library of fluorogenic protease substrates of the general format Ac-Ala-X-X-(Arg/Lys)-coumarin was synthesized and microarrayed, along with fluorescent calibration standards, in glycerol nanodroplets on microscope slides. The arrays were then activated by deposition of an aerosolized enzyme solution, followed by incubation and fluorometric scanning. The specificities of human blood serine proteases (human thrombin, factor Xa, plasmin, and urokinase plasminogen activator) were examined. The arrays provided complete maps of protease specificity for all of the substrates tested and allowed for detection of cooperative interactions between substrate subsites. The arrays were further utilized to explore the conservation of thrombin specificity across species by comparing the proteolytic fingerprints of human, bovine, and salmon thrombin. These enzymes share nearly identical specificity profiles despite approximately 390 million years of divergent evolution. Fluorogenic substrate microarrays provide a rapid way to determine protease substrate specificity information that can be used for the design of selective inhibitors and substrates, the study of evolutionary divergence, and potentially, for diagnostic applications.     

Utilization of oriented peptide libraries to identify substrate motifs selected by ATM

The ataxia telangiectasia mutated (ATM) gene encodes a serine/threonine protein kinase that plays a critical role in genomic surveillance and development. Here, we use a peptide library approach to define the in vitro substrate specificity of ATM kinase activity. The peptide library analysis identified an optimal sequence with a central core motif of LSQE that is preferentially phosphorylated by ATM. The contributions of the amino acids surrounding serine in the LSQE motif were assessed by utilizing specific peptide libraries or individual peptide substrates. All amino acids comprising the LSQE sequence were critical for maximum peptide substrate suitability for ATM. The DNA-dependent protein kinase (DNA-PK), a Ser/Thr kinase related to ATM and important in DNA repair, was compared with ATM in terms of peptide substrate selectivity. DNA-PK was found to be unique in its preference of neighboring amino acids to the phosphorylated serine. Peptide library analyses defined a preferred amino acid motif for ATM that permits clear distinctions between ATM and DNA-PK kinase activity. Data base searches using the library-derived ATM sequence identified previously characterized substrates of ATM, as well as novel candidate substrate targets that may function downstream in ATM-directed signaling pathways.     

Substrate Specifity of Chymotrypsin. Study of Induced Strain by Molecular Mechanics

Acylenzyme intermediates, produced by transfer of the acyl portions of selected natural substrates onto the catalytic serine hydroxyl of the serine protease chymotrypsin, were modeled with the AMBER force field. The obtained structures were used to calculate interaction and deformation energies. A set of 32 geometry variables were extracted out of each structure. They describe deformation effects specific for each substrate. It is shown by statistical analyses, that the interaction and deformation energies correspond to measured substrate reactivities. The extracted geometry variables are able to reproduce this dependency through multivariante statistical methods. These analyses suggest that there exist specific deformations of both the substrate and the enzyme portion, which are related to substrate reactivity. The geometry changes observed for high specific substrates are interpreted in terms of mechanistical requirements of the enzymatic reaction. The obtained model validates the hypothesis of induced strain as possible source of substrate specifity of chymotrypsin.