Showing papers by "Max Planck Society published in 2001"

Initial sequencing and analysis of the human genome.

Abstract: The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells

Abstract: RNA interference (RNAi) is the process of sequence-specific, post-transcriptional gene silencing in animals and plants, initiated by double-stranded RNA (dsRNA) that is homologous in sequence to the silenced gene. The mediators of sequence-specific messenger RNA degradation are 21- and 22-nucleotide small interfering RNAs (siRNAs) generated by ribonuclease III cleavage from longer dsRNAs. Here we show that 21-nucleotide siRNA duplexes specifically suppress expression of endogenous and heterologous genes in different mammalian cell lines, including human embryonic kidney (293) and HeLa cells. Therefore, 21-nucleotide siRNA duplexes provide a new tool for studying gene function in mammalian cells and may eventually be used as gene-specific therapeutics.

Learning with Kernels: Support Vector Machines, Regularization, Optimization, and Beyond

Abstract: From the Publisher: In the 1990s, a new type of learning algorithm was developed, based on results from statistical learning theory: the Support Vector Machine (SVM). This gave rise to a new class of theoretically elegant learning machines that use a central concept of SVMs—-kernels--for a number of learning tasks. Kernel machines provide a modular framework that can be adapted to different tasks and domains by the choice of the kernel function and the base algorithm. They are replacing neural networks in a variety of fields, including engineering, information retrieval, and bioinformatics. Learning with Kernels provides an introduction to SVMs and related kernel methods. Although the book begins with the basics, it also includes the latest research. It provides all of the concepts necessary to enable a reader equipped with some basic mathematical knowledge to enter the world of machine learning using theoretically well-founded yet easy-to-use kernel algorithms and to understand and apply the powerful algorithms that have been developed over the last few years.

Neurophysiological investigation of the basis of the fMRI signal

Abstract: Functional magnetic resonance imaging (fMRI) is widely used to study the operational organization of the human brain, but the exact relationship between the measured fMRI signal and the underlying neural activity is unclear. Here we present simultaneous intracortical recordings of neural signals and fMRI responses. We compared local field potentials (LFPs), single- and multi-unit spiking activity with highly spatio-temporally resolved blood-oxygen-level-dependent (BOLD) fMRI responses from the visual cortex of monkeys. The largest magnitude changes were observed in LFPs, which at recording sites characterized by transient responses were the only signal that significantly correlated with the haemodynamic response. Linear systems analysis on a trialby-trial basis showed that the impulse response of the neurovascular system is both animal- and site-specific, and that LFPs yield a better estimate of BOLD responses than the multi-unit responses. These findings suggest that the BOLD contrast mechanism reflects the input and intracortical processing of a given area rather than its spiking output.

Identification of novel genes coding for small expressed RNAs.

Abstract: In Caenorhabditis elegans, lin-4 and let-7 encode 22- and 21-nucleotide (nt) RNAs, respectively, which function as key regulators of developmental timing. Because the appearance of these short RNAs is regulated during development, they are also referred to as small temporal RNAs (stRNAs). We show that many 21- and 22-nt expressed RNAs, termed microRNAs, exist in invertebrates and vertebrates and that some of these novel RNAs, similar to let-7 stRNA, are highly conserved. This suggests that sequence-specific, posttranscriptional regulatory mechanisms mediated by small RNAs are more general than previously appreciated.

Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.

Abstract: Microarray analysis has become a widely used tool for the generation of gene expression data on a genomic scale. Although many significant results have been derived from microarray studies, one limitation has been the lack of standards for presenting and exchanging such data. Here we present a proposal, the Minimum Information About a Microarray Experiment (MIAME), that describes the minimum information required to ensure that microarray data can be easily interpreted and that results derived from its analysis can be independently verified. The ultimate goal of this work is to establish a standard for recording and reporting microarray-based gene expression data, which will in turn facilitate the establishment of databases and public repositories and enable the development of data analysis tools. With respect to MIAME, we concentrate on defining the content and structure of the necessary information rather than the technical format for capturing it.

RNA interference is mediated by 21- and 22-nucleotide RNAs

Abstract: Double-stranded RNA (dsRNA) induces sequence-specific posttranscriptional gene silencing in many organisms by a process known as RNA interference (RNAi). Using a Drosophila in vitro system, we demonstrate that 21- and 22-nt RNA fragments are the sequence-specific mediators of RNAi. The short interfering RNAs (siRNAs) are generated by an RNase III–like processing reaction from long dsRNA. Chemically synthesized siRNA duplexes with overhanging 3 ends mediate efficient target RNA cleavage in the lysate, and the cleavage site is located near the center of the region spanned by the guiding siRNA. Furthermore, we provide evidence that the direction of dsRNA processing determines whether sense or antisense target RNA can be cleaved by the siRNA–protein complex.

Emission of trace gases and aerosols from biomass burning

Abstract: A large body of information on emissions from the various types of biomass burning has been accumulated over the past decade, to a large extent as a result of International Geosphere-Biosphere Programme/International Global Atmospheric Chemistry research activities. Yet this information has not been readily accessible to the atmospheric chemistry community because it was scattered over a large number of publications and reported in numerous different units and reference systems. We have critically evaluated the presently available data and integrated these into a consistent format. On the basis of this analysis we present a set of emission factors for a large variety of species emitted from biomass fires. Where data were not available, we have proposed estimates based on appropriate extrapolation techniques. We have derived global estimates of pyrogenic emissions for important species emitted by the various types of biomass burning and compared our estimates with results from inverse modeling studies.

Aerosols, climate, and the hydrological cycle

Abstract: Human activities are releasing tiny particles (aerosols) into the atmosphere. These human-made aerosols enhance scattering and absorption of solar radiation. They also produce brighter clouds that are less efficient at releasing precipitation. These in turn lead to large reductions in the amount of solar irradiance reaching Earth's surface, a corresponding increase in solar heating of the atmosphere, changes in the atmospheric temperature structure, suppression of rainfall, and less efficient removal of pollutants. These aerosol effects can lead to a weaker hydrological cycle, which connects directly to availability and quality of fresh water, a major environmental issue of the 21st century.

Rab proteins as membrane organizers

Abstract: Cellular organelles in the exocytic and endocytic pathways have a distinctive spatial distribution and communicate through an elaborate system of vesiculo-tubular transport. Rab proteins and their effectors coordinate consecutive stages of transport, such as vesicle formation, vesicle and organelle motility, and tethering of vesicles to their target compartment. These molecules are highly compartmentalized in organelle membranes, making them excellent candidates for determining transport specificity and organelle identity.

Dynamic predictions: Oscillations and synchrony in top–down processing

Abstract: Classical theories of sensory processing view the brain as a passive, stimulus-driven device. By contrast, more recent approaches emphasize the constructive nature of perception, viewing it as an active and highly selective process. Indeed, there is ample evidence that the processing of stimuli is controlled by top-down influences that strongly shape the intrinsic dynamics of thalamocortical networks and constantly create predictions about forthcoming sensory events. We discuss recent experiments indicating that such predictions might be embodied in the temporal structure of both stimulus-evoked and ongoing activity, and that synchronous oscillations are particularly important in this process. Coherence among subthreshold membrane potential fluctuations could be exploited to express selective functional relationships during states of expectancy or attention, and these dynamic patterns could allow the grouping and selection of distributed neuronal responses for further processing.

The European Photon Imaging Camera on XMM-Newton: The pn-CCD camera

Abstract: The European Photon Imaging Camera (EPIC) consortium has provided the focal plane instruments for the three X-ray mirror systems on XMM-Newton. Two cameras with a reflecting grating spectrometer in the optical path are equipped with MOS type CCDs as focal plane detectors (Turner 2001), the telescope with the full photon flux operates the novel pn-CCD as an imaging X-ray spectrometer. The pn-CCD camera system was developed under the leadership of the Max-Planck-Institut fur extraterrestrische Physik (MPE), Garching. The concept of the pn-CCD is described as well as the dierent operational modes of the camera system. The electrical, mechanical and thermal design of the focal plane and camera is briefly treated. The in-orbit performance is described in terms of energy resolution, quantum eciency, time resolution, long term stability and charged particle background. Special emphasis is given to the radiation hardening of the devices and the measured and expected degradation due to radiation damage of ionizing particles in the rst 9 months of in orbit operation.

A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA.

Abstract: The 21-nucleotide small temporal RNA (stRNA) let-7 regulates developmental timing in Caenorhabditis elegans and probably in other bilateral animals We present in vivo and in vitro evidence that in Drosophila melanogaster a developmentally regulated precursor RNA is cleaved by an RNA interference-like mechanism to produce mature let-7 stRNA Targeted destruction in cultured human cells of the messenger RNA encoding the enzyme Dicer, which acts in the RNA interference pathway, leads to accumulation of the let-7 precursor Thus, the RNA interference and stRNA pathways intersect Both pathways require the RNA-processing enzyme Dicer to produce the active small-RNA component that represses gene expression

The Theory of Event Coding (TEC): a framework for perception and action planning.

Abstract: Traditional approaches to human information processing tend to deal with perception and action planning in isolation, so that an adequate account of the perception-action interface is still missing On the perceptual side, the dominant cognitive view largely underestimates, and thus fails to account for, the impact of action-related processes on both the processing of perceptual information and on perceptual learning On the action side, most approaches conceive of action planning as a mere continuation of stimulus processing, thus failing to account for the goal-directedness of even the simplest reaction in an experimental task We propose a new framework for a more adequate theoretical treatment of perception and action planning, in which perceptual contents and action plans are coded in a common representational medium by feature codes with distal reference Perceived events (perceptions) and to-be-produced events (actions) are equally represented by integrated, task-tuned networks of feature codes – cognitive structures we call event codes We give an overview of evidence from a wide variety of empirical domains, such as spatial stimulus-response compatibility, sensorimotor synchronization, and ideomotor action, showing that our main assumptions are well supported by the data

Nanoengineering of particle surfaces.

Abstract: The creation of core–shell particles is attracting a great deal of interest because of the diverse applicability of these colloidal particles; e.g., as building blocks for photonic crystals, in multi-enzyme biocatalysis, and in drug delivery. This review presents the state-of-the-art in strategies for engineering particle surfaces, such as the layer-by-layer deposition process (see Figure), which allows fine control over shell thickness and composition.

Self-Organized Discotic Liquid Crystals for High-Efficiency Organic Photovoltaics

Abstract: Self-organization of liquid crystalline and crystalline-conjugated materials has been used to create, directly from solution, thin films with structures optimized for use in photodiodes. The discotic liquid crystal hexa-peri-hexabenzocoronene was used in combination with a perylene dye to produce thin films with vertically segregated perylene and hexabenzocoronene, with large interfacial surface area. When incorporated into diode structures, these films show photovoltaic response with external quantum efficiencies of more than 34 percent near 490 nanometers. These efficiencies result from efficient photoinduced charge transfer between the hexabenzocoronene and perylene, as well as from effective transport of charges through vertically segregated perylene and hexabenzocoronene pi systems. This development demonstrates that complex structures can be engineered from novel materials by means of simple solution-processing steps and may enable inexpensive, high-performance, thin-film photovoltaic technology.

Genomic imprinting: parental influence on the genome

Abstract: Genomic imprinting affects several dozen mammalian genes and results in the expression of those genes from only one of the two parental chromosomes. This is brought about by epigenetic instructions--imprints--that are laid down in the parental germ cells. Imprinting is a particularly important genetic mechanism in mammals, and is thought to influence the transfer of nutrients to the fetus and the newborn from the mother. Consistent with this view is the fact that imprinted genes tend to affect growth in the womb and behaviour after birth. Aberrant imprinting disturbs development and is the cause of various disease syndromes. The study of imprinting also provides new insights into epigenetic gene modification during development.

Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate.

Abstract: Duplexes of 21–23 nucleotide (nt) RNAs are the sequence‐specific mediators of RNA interference (RNAi) and post‐transcriptional gene silencing (PTGS). Synthetic, short interfering RNAs (siRNAs) were examined in Drosophila melanogaster embryo lysate for their requirements regarding length, structure, chemical composition and sequence in order to mediate efficient RNAi. Duplexes of 21 nt siRNAs with 2 nt 3′ overhangs were the most efficient triggers of sequence‐specific mRNA degradation. Substitution of one or both siRNA strands by 2′‐deoxy or 2′‐ O ‐methyl oligonucleotides abolished RNAi, although multiple 2′‐deoxynucleotide substitutions at the 3′ end of siRNAs were tolerated. The target recognition process is highly sequence specific, but not all positions of a siRNA contribute equally to target recognition; mismatches in the centre of the siRNA duplex prevent target RNA cleavage. The position of the cleavage site in the target RNA is defined by the 5′ end of the guide siRNA rather than its 3′ end. These results provide a rational basis for the design of siRNAs in future gene targeting experiments.

In search of homo economicus: Behavioral experiments in 15 small-scale societies

Abstract: We can summarize our results as follows. First, the canonical model is not supported in any society studied. Second, there is considerably more behavioral variability across groups than had been found in previous cross-cultural research, and the canonical model fails in a wider variety of ways than in previous experiments. Third, group-level differences in economic organization and the degree of market integration explain a substantial portion of the behavioral variation across societies: the higher the degree of market integration and the higher the payoffs to cooperation, the greater the level of cooperation in experimental games. Fourth, individual-level economic and demographic variables do not explain behavior either within or across groups. Fifth, behavior in the experiments is generally consistent with economic patterns of everyday life in these societies.

Populating a cluster of galaxies - I. Results at z=0

Abstract: ABSTRA C T We simulate the assembly of a massive rich cluster and the formation of its constituent galaxies in a flat, low-density universe. Our most accurate model follows the collapse, the star formation history and the orbital motion of all galaxies more luminous than the Fornax dwarf spheroidal, while dark halo structure is tracked consistently throughout the cluster for all galaxies more luminous than the SMC. Within its virial radius this model contains about 2 10 7 dark matter particles and almost 5000 distinct dynamically resolved galaxies. Simulations of this same cluster at a variety of resolutions allow us to check explicitly for numerical convergence both of the dark matter structures produced by our new parallel N-body and substructure identification codes, and of the galaxy populations produced by the phenomenological models we use to follow cooling, star formation, feedback and stellar aging. This baryonic modelling is tuned so that our simulations reproduce the observed properties of isolated spirals outside clusters. Without further parameter adjustment our simulations then produce a luminosity function, a mass-to-light ratio, luminosity, number and velocity dispersion profiles, and a morphology ‐radius relation which are similar to those observed in real clusters. In particular, since our simulations follow galaxy merging explicitly, we can demonstrate that it accounts quantitatively for the observed cluster population of bulges and elliptical galaxies.

Bounded rationality: The adaptive toolbox

Abstract: In a complex and uncertain world, humans and animals make decisions under the constraints of limited knowledge, resources, and time. Yet models of rational decision making in economics, cognitive science, biology, and other fields largely ignore these real constraints and instead assume agents with perfect information and unlimited time. About forty years ago, Herbert Simon challenged this view with his notion of "bounded rationality." Today, bounded rationality has become a fashionable term used for disparate views of reasoning. This book promotes bounded rationality as the key to understanding how real people make decisions. Using the concept of an "adaptive toolbox," a repertoire of fast and frugal rules for decision making under uncertainty, it attempts to impose more order and coherence on the idea of bounded rationality. The contributors view bounded rationality neither as optimization under constraints nor as the study of people's reasoning fallacies. The strategies in the adaptive toolbox dispense with optimization and, for the most part, with calculations of probabilities and utilities. The book extends the concept of bounded rationality from cognitive tools to emotions; it analyzes social norms, imitation, and other cultural tools as rational strategies; and it shows how smart heuristics can exploit the structure of environments.

Global response of terrestrial ecosystem structure and function to CO2 and climate change: results from six dynamic global vegetation models

Abstract: The possible responses of ecosystem processes to rising atmospheric CO2 concentration and climate change are illustrated using six dynamic global vegetation models that explicitly represent the interactions of ecosystem carbon and water exchanges with vegetation dynamics. The models are driven by the IPCC IS92a scenario of rising CO2 (Wigley et al. 1991), and by climate changes resulting from effective CO2 concentrations corresponding to IS92a, simulated by the coupled ocean atmosphere model HadCM2-SUL. Simulations with changing CO2 alone show a widely distributed terrestrial carbon sink of 1.4‐3.8 Pg C y ‐1 during the 1990s, rising to 3.7‐8.6 Pg C y ‐1 a century later. Simulations including climate change show a reduced sink both today (0.6‐ 3.0 Pg C y ‐1 ) and a century later (0.3‐6.6 Pg C y ‐1 ) as a result of the impacts of climate change on NEP of tropical and southern hemisphere ecosystems. In all models, the rate of increase of NEP begins to level off around 2030 as a consequence of the ‘diminishing return’ of physiological CO2 effects at high CO2 concentrations. Four out of the six models show a further, climate-induced decline in NEP resulting from increased heterotrophic respiration and declining tropical NPP after 2050. Changes in vegetation structure influence the magnitude and spatial pattern of the carbon sink and, in combination with changing climate, also freshwater availability (runoff). It is shown that these changes, once set in motion, would continue to evolve for at least a century even if atmospheric CO2 concentration and climate could be instantaneously stabilized. The results should be considered illustrative in the sense that the choice of CO2 concentration scenario was arbitrary and only one climate model scenario was used. However, the results serve to indicate a range of possible biospheric responses to CO2 and climate change. They reveal major uncertainties about the response of NEP to climate

Defensive function of herbivore-induced plant volatile emissions in nature.

Abstract: Herbivore attack is known to increase the emission of volatiles, which attract predators to herbivore-damaged plants in the laboratory and agricultural systems. We quantified volatile emissions fromNicotiana attenuata plants growing in natural populations during attack by three species of leaf-feeding herbivores and mimicked the release of five commonly emitted volatiles individually. Three compounds (cis-3-hexen-1-ol, linalool, and cis-α-bergamotene) increased egg predation rates by a generalist predator; linalool and the complete blend decreased lepidopteran oviposition rates. As a consequence, a plant could reduce the number of herbivores by more than 90% by releasing volatiles. These results confirm that indirect defenses can operate in nature.

Perzentile für den Body-mass-Index für das Kindes- und Jugendalter unter Heranziehung verschiedener deutscher Stichproben

Abstract: Fragestellung. Sowohl die Childhood Group der International Obesity Task Force (IOTF) als auch die European Childhood Obesity Group (ECOG) empfehlen den Body-mass-Index als Beurteilungskriterium fur Ubergewicht und Adipositas bei Kindern und Jugendlichen. Im Erwachsenenalter erfolgt die Definition von Ubergewicht und Adipositas anhand fester Grenzwerte, bei der Beurteilung von Kindern und Jugendlichen mussen die alters- und geschlechtsspezifischen Veranderungen des BMI berucksichtigt werden. Methode. Unter Heranziehung von 17 bereits durchgefuhrten Untersuchungen aus verschiedenen Regionen Deutschlands wurden BMI-Perzentile fur Kinder und Jugendliche erstellt. Die Berechnung der Perzentile basiert auf den Korperhohen- und Korpergewichtsdaten von 17.147 Jungen und 17.275 Madchen im Alter von 0–18 Jahren. Ergebnisse und Schlussfolgerung. Die vorgestellten Perzentile sollten als Referenz fur deutsche Kinder und Jugendliche angewendet werden. Die Arbeitsgemeinschaft “Adipositas im Kindes- und Jugendalter” (AGA) hat in ihren Leitlinien die Anwendung der hier vorgestellten 90. und 97. Perzentile zur Definition von Ubergewicht und Adipositas empfohlen.

Large-scale forest girdling shows that current photosynthesis drives soil respiration

Abstract: The respiratory activities of plant roots, of their mycorrhizal fungi and of the free-living microbial heterotrophs (decomposers) in soils are significant components of the global carbon balance, but their relative contributions remain uncertain. To separate mycorrhizal root respiration from heterotrophic respiration in aboreal pine forest, we conducted a large-scale tree-girdling experiment, comprising 9 plots each containing about 120 trees. Tree-girdling involves stripping the stem bark to the depth of the current xylem at breast height terminating the supply of current photosynthates to roots and their mycorrhizal fungi without physically disturbing the delicate root-microbe-soil system. Here we report that girdling reduced soil respiration within 1-2 months by about 54% relative to respiration on ungirdled control plots, and that decreases of up to 37% were detected within 5 days. These values clearly show that the flux of current assimilates to roots is a key driver of soil respiration; they are conservative estimates of root respiration, however, because girdling increased the use of starch reserves in the roots. Our results indicate that models of soil respiration should incorporate measures of photosynthesis and of seasonal patterns of photosynthate allocation to roots.

Sources and distributions of dust aerosols simulated with the GOCART model

Abstract: The global distribution of dust aerosol is simulated with the Georgia Tech/Goddard Global Ozone Chemistry Aerosol Radiation and Transport (GOCART) model. In this model all topographic lows with bare ground surface are assumed to have accumulated sediments which are potential dust sources. The uplifting of dust particles is expressed as a function of surface wind speed and wetness. The GOCART model is driven by the assimilated meteorological fields from the Goddard Earth Observing System Data Assimilation System (GEOS DAS) which facilitates direct comparison with observations. The model includes seven size classes of mineral dust ranging from 0.1–6 μm radius. The total annual emission is estimated to be between 1604 and 1960 Tg yr−1 in a 5-year simulation. The model has been evaluated by comparing simulation results with ground-based measurements and satellite data. The evaluation has been performed by comparing surface concentrations, vertical distributions, deposition rates, optical thickness, and size distributions. The comparisons show that the model results generally agree with the observations without the necessity of invoking any contribution from anthropogenic disturbances to soils. However, the model overpredicts the transport of dust from the Asian sources to the North Pacific. This discrepancy is attributed to an overestimate of small particle emission from the Asian sources.