bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Intestinal Protozoan ParasiteEntamoeba histolyticaContains 20 Cysteine Protease Genes, of Which Only a Small Subset Is Expressed during In Vitro Cultivation
Authors: Bruchhaus Iris , Loftus Brendan J. , Hall Neil , Tannich Egbert 
Published: June 2003

ABSTRACTCysteine proteases are known to be important pathogenicity factors of the protozoan parasiteEntamoeba histolytica. So far, a total of eight genes coding for cysteine proteases have been identified inE. histolytica, two of which are absent in the closely related nonpathogenic speciesE. dispar.However, present knowledge is restricted to enzymes expressed during in vitro cultivation of the parasite, which might represent only a subset of the entire repertoire. Taking advantage of the currentE. histolyticagenome-sequencing efforts, we analyzed databases containing more than 99% of all ameba gene sequences for the presence of cysteine protease genes. A total of 20 full-length genes was identified (including all eight genes previously reported), which show 10 to 86% sequence identity. The various genes obviously originated from two separate ancestors since they form two distinct clades. Despite cathepsin B-like substrate specificities, all of the ameba polypeptides are structurally related to cathepsin L-like enzymes. None of the previously described enzymes but 7 of the 12 newly identified proteins are unique compared to cathepsins of higher eukaryotes in that they are predicted to have transmembrane or glycosylphosphatidylinositol anchor attachment domains. Southern blot analysis revealed that orthologous sequences for all of the newly identified proteases are present inE. dispar.Interestingly, the majority of the various cysteine protease genes are not expressed inE. histolyticaorE. dispartrophozoites during in vitro cultivation. Therefore, it is likely that at least some of these enzymes are required for infection of the human host and/or for completion of the parasite life cycle.
RNA Polymerase I Transcribes Procyclin Genes and Variant Surface Glycoprotein Gene Expression Sites in
Trypanosoma brucei
Authors: Günzl Arthur , Bruderer Thomas , Laufer Gabriele , Schimanski Bernd , Tu Lan-Chun , Chung Hui-Min , Lee Pei-Tseng , Lee Mary Gwo-Shu 
Published: June 2003

ABSTRACT

In eukaryotes, RNA polymerase (pol) I exclusively transcribes the large rRNA gene unit (rDNA) and mRNA is synthesized by RNA pol II. The African trypanosome,
Trypanosoma brucei
, represents an exception to this rule. In this organism, transcription of genes encoding the variant surface glycoprotein (VSG) and the procyclins is resistant to α-amanitin, indicating that it is mediated by RNA pol I, while other protein-coding genes are transcribed by RNA pol II. To obtain firm proof for this concept, we generated a
T. brucei
cell line which exclusively expresses protein C epitope-tagged RNA pol I. Using an anti-protein C immunoaffinity matrix, we specifically depleted RNA pol I from transcriptionally active cell extracts. The depletion of RNA pol I impaired in vitro transcription initiated at the rDNA promoter, the GPEET procyclin gene promoter, and a VSG gene expression site promoter but did not affect transcription from the spliced leader (SL) RNA gene promoter. Fittingly, induction of RNA interference against the RNA pol I largest subunit in insect-form trypanosomes significantly reduced the relative transcriptional efficiency of rDNA, procyclin genes, and VSG expression sites in vivo whereas that of SL RNA, αβ-tubulin, and heat shock protein 70 genes was not affected. Our studies unequivocally show that
T. brucei
harbors a multifunctional RNA pol I which, in addition to transcribing rDNA, transcribes procyclin genes and VSG gene expression sites.
A Region within a Lumenal Loop of
Saccharomyces cerevisiae
Ycf1p Directs Proteolytic Processing and Substrate Specificity
Authors: Mason Deborah L. , Mallampalli Monica P. , Huyer Gregory , Michaelis Susan 
Published: June 2003

ABSTRACT

Ycf1p, a member of the yeast multidrug resistance-associated protein (MRP) subfamily of ATP-binding cassette proteins, is a vacuolar membrane transporter that confers resistance to a variety of toxic substances such as cadmium and arsenite. Ycf1p undergoes a
PEP4
-dependent processing event to yield N- and C-terminal cleavage products that remain associated with one another. In the present study, we sought to determine whether proteolytic cleavage is required for Ycf1p activity. We have identified a unique region within lumenal loop 6 of Ycf1p, designated the loop 6 insertion (L6
ins
), which appears to be necessary and sufficient for proteolytic cleavage, since L6
ins
can promote processing when moved to new locations in Ycf1p or into a related transporter, Bpt1p. Surprisingly, mutational results indicate that proteolytic processing is not essential for Ycf1p transport activity. Instead, the L6
ins
appears to regulate substrate specificity of Ycf1p, since certain mutations in this region lower cellular cadmium resistance with a concomitant gain in arsenite resistance. Although some of these L6
ins
mutations block processing, there is no correlation between processing and substrate specificity. The activity profiles of the Ycf1p L6
ins
mutants are dramatically affected by the strain background in which they are expressed, raising the possibility that another cellular component may functionally impact Ycf1p activity. A candidate component may be a new full-length MRP-type transporter (
NFT1
), reported in the
Saccharomyces
Genome Database as two adjacent open reading frames,
YKR103w
and
YKR104w
, but which we show here is present in most
Saccharomyces
strains as a single open reading frame.
Identification of In Vivo Enzyme Activities in the Cometabolism of Glucose and Acetate by
Saccharomyces cerevisiae
by Using
13
C-Labeled Substrates
Authors: dos Santos Margarida Moreira , Gombert Andreas Karoly , Christensen Bjarke , Olsson Lisbeth , Nielsen Jens 
Published: June 2003

ABSTRACT

A detailed characterization of the central metabolic network of
Saccharomyces cerevisiae
CEN.PK 113-7D was carried out during cometabolism of different mixtures of glucose and acetate, using aerobic C-limited chemostats in which one of these two substrates was labeled with
13
C. To confirm the role of malic enzyme, an isogenic strain with the corresponding gene deleted was grown under the same conditions. The labeling patterns of proteinogenic amino acids were analyzed and used to estimate metabolic fluxes and/or make inferences about the in vivo activities of enzymes of the central carbon metabolism and amino acid biosynthesis. Malic enzyme flux increased linearly with increasing acetate fraction. During growth on a very-high-acetate fraction, the activity of malic enzyme satisfied the biosynthetic needs of pyruvate in the mitochondria, while in the cytosol pyruvate was supplied via pyruvate kinase. In several cases enzyme activities were unexpectedly detected, e.g., the glyoxylate shunt for a very-low-acetate fraction, phosphoenolpyruvate carboxykinase for an acetate fraction of 0.46 C-mol of acetate/C-mol of substrate, and glucose catabolism to CO
2
via the tricarboxylic acid cycle for a very-high-acetate fraction. Cytoplasmic alanine aminotransferase activity was detected, and evidence was found that α-isopropylmalate synthase has two active forms in vivo, one mitochondrial and the other a short cytoplasmic form.
Histone-Like Proteins of the Dinoflagellate
Crypthecodinium cohnii
Have Homologies to Bacterial DNA-Binding Proteins
Authors: Wong J. T. Y. , New D. C. , Wong J. C. W. , Hung V. K. L. 
Published: June 2003

ABSTRACT

The dinoflagellates have very large genomes encoded in permanently condensed and histoneless chromosomes. Sequence alignment identified significant similarity between the dinoflagellate chromosomal histone-like proteins of
Crypthecodinium cohnii
(HCCs) and the bacterial DNA-binding and the eukaryotic histone H1 proteins. Phylogenetic analysis also supports the origin of the HCCs from histone-like proteins of bacteria.
Geographical pattern of brain cancer incidence in the Navarre and Basque Country regions of Spain
Authors: López-Abente G , Pollán M , Ardanaz E , Errezola M 
Published: June 2003

Background:The study of the distribution of brain cancer mortality in Spain shows a grouping of highest risk provinces corresponding to the autonomous regions of Navarre and the Basque Country.Aim:To explore the possible existence of geographical patterns in these areas.Methods:Municipal maps of brain cancer incidence were drawn up and the influence of land use related variables on the distribution of the disease duly analysed. Autoregressive conditional models were used to plot smoothed municipal maps. The influence of explanatory land use variables, ascertained by remote sensing, was assessed.Results:The maps revealed that certain towns situated in the “Media” and “Cantábrica-Baja Montaña” districts of Navarre were areas of highest risk. Among the towns in question, those in the “Media” district lie very close to the city of Pamplona. However, the pattern of brain cancer incidence in Navarre and the Basque Country could not be conclusively said to be determined by any specific type of land cover and/or crop.Conclusions:Results suggest a possible increase of risk linked to areas devoted to a high percentage of non-irrigated arable land.
Integral Geometry in Statistical Physics
Authors: Mecke Klaus R. 
Published: June 2003

The aim of this paper is to point out the importance of a morphological characterization of patterns in Statistical Physics. Integral geometry furnishes a suitable family of morphological descriptors, known as Minkowski functionals. They characterize not only the connectivity (topology) but also the content and shape (geometry) of spatial patterns. Integral geometry provides also powerful theorems and formulae, which makes the calculus convenient for many models of stochastic geometries, for instance, for the Boolean grain model. This model generates random structures in space by overlapping bodies or "grains" (balls, sticks) each with arbitrary location and orientation. We illustrate the integral geometric approach to stochastic geometries by applying morphological measures to such diverse topics as percolation, complex fluids, and the large-scale structure of the universe: (A) Porous media may be generated by overlapping holes of arbitrary shape distributed uniformly in space. The percolation thresold of such porous media can be estimated accurately in terms of the morphology of the distributed pores. (B) Under rather natural assumptions a general expression for the Hamiltonian of complex fluids can be derived that includes energy contributions related to the morphology of the spatial domains of homogeneous mesophases. We find that the Euler characteristic in the Hamiltonian stabilizes a highly connected bicontinuous structure resembling the middle-phase in oil-water microemulsions, for instance. (C) Morphological measures are a novel method for the description of complex spatial structures aiming for relevant order parameters and structure information complement to correlation functions. Typical applications address Turing patterns in chemical reaction diffusion systems, homogeneous phases evolving during spinodal decomposition, and the distribution of galaxies and clusters of galaxies in the Universe as a prominent example of a point process in nature.
Dynamics of a Pair of Interacting Spins Coupled to an Environmental Sea
Authors: Dubé M. , Stamp P. C. E. 
Published: June 2003

We solve for the dynamics of a pair of spins, coupled to each other and also to an environmental sea of oscillators. The environment mediates an indirect interaction between the spins, causing both mutual coherence effects and dissipation. This model describes a wide variety of physical systems, ranging from 2 coupled microscopic systems (e.g. magnetic impurities, chromophores, etc.), to 2 coupled macroscopic quantum systems. We obtain analytic results for 3 regimes, viz., (i) The "locked" regime, where the 2 spins lock together; (ii) The "correlated relaxation" regime (mutually correlated incoherent relaxation); and (iii) The "mutual coherence" regime, with correlated damped oscillations. These results cover most of the parameter space of the system.
ECOLOGICAL HOLISM AND THEOLOGICAL DUALISM AS ROOTS OF ENVIRONMENTAL RACISM: MEDIEVAL LESSONS FOR MODERN RELIGIOUS SCHOLARS
Authors: Power Bratton Susan 
Published: June 2003

AbstractThe central hypothesis of this paper is that idealization of nature may fuel environmental racism when combined with dual interpretation of human religious or spiritual states. Medieval typological Biblical exegesis, originally based on historic rather than racial differentiation, encouraged presentation of Christianity as "natural" and Judaism as contra-natural. During the Gothic period, the stained glass of St. Denis Cathedral presented Judaism as occupying the material rather than the transcendent spheres of existence. In numerous stained glass windows, Jews appear as threats to nature by attacking Christ on a green cross, which symbolizes the renewal of all life, or the Lignum Vitae. As Christian architects and scientists increased their focus on the divine light of creation, prejudicial portrayals depicted Judaism as blind Synagogue, unable to fully appreciate nature. Pagan motifs, such as the Green Man, syncretized with Christian theological dualism, also serve to separate Judaism from living nature. These depictions purposefully conflict with Gothic aesthetic emphasis on proportion, clarity, and integrity and were intended to imply that religious minorities have no legitimate role in Christian European society. Modern religious scholarship must be cautious not to describe some religions as natural or nature religion, while neglecting others, particularly Judaism and Islam.
BIOTIC COMMUNITY—REAL OR UNREAL: A PHILOSOPHICAL DILEMMA
Authors: Landen Laura 
Published: June 2003

AbstractAs defined over time, biotic community has meant anything from superorganism to ecosystem. Some ecologists entirely reject any such holistic concept. This spectrum of positions—from holism to reductionism—reflects a divide among ecologists. Ordinarily, such battles pass with little notice beyond the confines of science. Ecology, however, has impact well outside its borders. In the popular arena the expression "biotic community" is widely, albeit sometimes uncritically, accepted. Even though both scientists and philosophers disagree about the validity of the concept, arguments for or against rely upon a common principle: novel properties signify a new reality. Conclusions divide based upon what may count as real. Must the new entity be a material object or is it merely conceptual? I review the evolution of meanings for biotic community and examine representative objections to either the reality or the utility of the concept. I argue that what is lacking in all discussions of biotic community is attention to the mode of existence of community, and conclude that biotic community is real, although its mode of existence is relational, not material.
TOWARD A VALUE-ORIENTED METAPHYSICS OF NATURE
Authors: Bracken Joseph 
Published: June 2003

AbstractThe English philosopher/theologian Colin Gunton argues that many of the problems besetting the contemporary Western world, including those dealing with the environment, are traceable to a mistaken understanding of the relationship between the One and the Many in practical life. A solution, however, is available in retrieval of the doctrine of the Trinity promoted by the early Greek Fathers, in particular the notion of perichoresis as the dynamic bond of unity among the divine persons. While agreeing with Gunton on this point, the author believes that perichoresis can only be applied to the world of creation in terms of a metaphysics of universal intersubjectivity such as he developed in a recent book. After laying out the basic contours of this new 'relational ontology', the author concludes by calling attention to the work of another process-oriented thinker, Douglas Sturm, with the latter's work on the 'politics of relationality' and an ethic of solidarity.
OVERPOPULATION: ECOLOGICAL AND BIBLICAL PRINCIPLES CONCERNING LIMITATION
Authors: Boorse Dorothy 
Published: June 2003

AbstractThere is an increasing consensus among ecologists that global ecosystems are under strain from unsustainable consumption habits and human overpopulation. However, there is no such consensus among many religious persons. Many Christians for example, are quite concerned about both overconsumption and overpopulation while others are uncomfortable with any discussion of either, or specifically with discussions about overpopulation. This discomfort may be due to concerns about undermining God's sovereignty or opposition to specific family planning policies. Two other reasons for this lack of consensus are misunderstandings of science and of Scripture. Central to the ecological understanding of the world is a belief in the concept of limitation. Some Christians, however, appear to believe that natural laws and limitations do not act on human populations. Furthermore, some Christians interpret the Bible as promoting high fertility. In contrast, I describe the ecological principles of allocation, optima, and limiting factors, which derive from the limitation of matter and energy. I propose to integrate these scientific principles with three scriptural principles: balance, wisdom, and corporate responsibility and to apply them to the current issue of overpopulation.
THE VIRTUOUS COOPERATOR: MODELING THE HUMAN IN AN ECOLOGICALLY ENDANGERED AGE
Authors: Schaefer Jame 
Published: June 2003

AbstractA theological model of the human is needed to prompt responsible thinking about and acting within the physical world. Some basic components for modeling the human as a virtuous cooperator appear in the teachings of Thomas Aquinas. When appropriated cautiously and informed broadly by contemporary scientific findings, this model provides a promising way of thinking about humans in relation to other species and ecological systems, a framework for acting responsibly, and the motivation for making this behavior habitual.
A family of vortex wakes generated by a thrush nightingale in free flight in a wind tunnel over its entire natural range of flight speeds
Authors: Spedding G. R. , Rosén M. , Hedenström A. 
Published: June 2003

SUMMARYIn view of the complexity of the wing-beat kinematics and geometry, an important class of theoretical models for analysis and prediction of bird flight performance entirely, or almost entirely, ignores the action of the wing itself and considers only the resulting motions in the air behind the bird. These motions can also be complicated, but some success has previously been recorded in detecting and measuring relatively simple wake structures that can sometimes account for required quantities used to estimate aerodynamic power consumption. To date, all bird wakes, measured or presumed,seem to fall into one of two classes: the closed-loop, discrete vortex model at low flight speeds, and the constant-circulation, continuous vortex model at moderate to high speeds. Here, novel and accurate quantitative measurements of velocity fields in vertical planes aligned with the freestream are used to investigate the wake structure of a thrush nightingale over its entire range of natural flight speeds. At most flight speeds, the wake cannot be categorised as one of the two standard types, but has an intermediate structure, with approximations to the closed-loop and constant-circulation models at the extremes. A careful accounting for all vortical structures revealed with the high-resolution technique permits resolution of the previously unexplained wake momentum paradox. All the measured wake structures have sufficient momentum to provide weight support over the wingbeat. A simple model is formulated and explained that mimics the correct, measured balance of forces in the downstroke- and upstroke-generated wake over the entire range of flight speeds. Pending further work on different bird species, this might form the basis for a generalisable flight model.
Sweeping and striking: a kinematic study of the trunk during prey capture in three thamnophiine snakes
Authors: Alfaro Michael E. 
Published: June 2003

SUMMARYThe trunk plays an obvious and important role in the prey capture behavior of many species of snake, yet trunk function during predatory strikes is poorly understood. Axial kinematics of three thamnophiine snakes(Thamnophis couchii, Thamnophis elegans and Nerodia rhombifer) were studied to quantify differences between sideways-directed and forward-directed attacks and to investigate strike diversity at relatively low phylogenetic levels. Feeding strikes were filmed at 60 Hz, and 13 points along the head and body were digitized. These points were used to calculate body segment displacement, rotation and velocity during predatory strikes. Kinematic analysis revealed significant differences in the foraging modes of these aquatic-feeding species. T. couchii displayed a stereotypical pre-strike posture in which the entire body was arranged in a series of loops directed towards the prey. Forward displacement of body segments sometimes occurred over the entire body in T. couchii but was restricted to the anterior one-third of the trunk in T. elegans and N. rhombifer. T. couchii and N. rhombifer both struck rapidly compared with T. elegans, although N. rhombifer typically had a short strike distance. N. rhombifer struck significantly faster than T. elegans. Aquatic prey capture diversity appears to reflect ecological diversity in thamnophiine snakes.
Structural colouration of avian skin: convergent evolution of coherently scattering dermal collagen arrays
Authors: Prum Richard O. , Torres Rodolfo 
Published: June 2003

SUMMARYStructural colours of avian skin have long been hypothesized to be produced by incoherent (Rayleigh/Tyndall) scattering. We investigated the colour,anatomy, nanostructure and biophysics of structurally coloured skin,ramphotheca and podotheca from 31 species of birds from 17 families in 10 orders from across Aves. Integumentary structural colours of birds include ultraviolet, dark blue, light blue, green and yellow hues. The discrete peaks in reflectance spectra do not conform to the inverse fourth power relationship predicted by Rayleigh scattering. The dermis of structurally coloured skin consists of a thick (100–500 μm) layer of collagen that is usually underlain by a layer of melanin granules. Transmission electron micrographs(TEMs) of this colour-producing dermal collagen layer revealed quasi-ordered arrays of parallel collagen fibres. Two-dimensional (2-D) Fourier analysis of TEMs of the collagen arrays revealed a ring of peak spatial frequencies in the spatial variation in refractive index that are the appropriate size to make the observed ultraviolet–yellow colours by coherent scattering alone. One species, Philepitta castanea (Eurylaimidae), has exceptionally ordered, hexagonal arrays of collagen fibres that produce a hexagonal pattern of spatial frequency peaks in the power spectra. Ultraviolet, blue, green and yellow structural colours of avian skin are produced by coherent scattering(i.e. constructive interference) by arrays of collagen fibres in the dermis. Some yellow and orange skin colours are produced with a combination of structural and pigmentary mechanisms. These combined colours can have reflectance spectra with discrete peaks that are more saturated than hues produced by carotenoid pigments alone. Bluish facial skin from two species of Neotropical antbirds (Thamnophilidae) are nanostructurally too small to produce visible light by coherent scattering, and the colour production mechanism in these species remains unknown. Based on the phylogenetic distribution of structurally coloured skin in Aves, this mechanism of colour production has evolved convergently more than 50 independent times within extant birds.