bluuebunny/crossref_metadata_2025 huggingface dataset:
CAST: an iterative algorithm for the complexity analysis of
sequence tracts
Authors: Promponas Vasilis J. , Enright Anton J. , Tsoka Sophia , Kreil David P. , Leroy Christophe , Hamodrakas Stavros , Sander Chris , Ouzounis Christos A.
Published: July 2002

Motivation: Sensitive detection and masking of low-complexity regions in protein sequences. Filtered sequences can be used in sequence comparison without the risk of matching compositionally biased regions. The main advantage of the method over similar approaches is the selective masking of single residue types without affecting other, possibly important, regions.

Results: A novel algorithm for low-complexity region detection and selective masking. The algorithm is based on multiple-pass Smith–Waterman comparison of the query sequence against twenty homopolymers with infinite gap penalties. The output of the algorithm is both the masked query sequence for further analysis, e.g. database searches, as well as the regions of low complexity. The detection of low-complexity regions is highly specific for single residue types. It is shown that this approach is sufficient for masking database query sequences without generating false positives. The algorithm is benchmarked against widely available algorithms using the 210 genes of Plasmodium falciparum chromosome 2, a dataset known to contain a large number of low-complexity regions.

Availability: CAST (version 1.0) executable binaries are available to academic users free of charge under license. Web site entry point, server and additional material: http://www.ebi.ac.uk/research/cgg/services/cast/

Contact: ouzounis@ebi.ac.uk

To whom correspondence should be addressed.
A knowledge model for analysis and simulation of regulatory

networks
Authors: Rzhetsky Andrey , Koike Tomohiro , Kalachikov Sergey , Gomez Shawn M. , Krauthammer Michael , Kaplan Sabina H. , Kra Pauline , Russo James J. , Friedman Carol
Published: July 2002

Motivation: In order to aid in hypothesis-driven experimental gene discovery, we are designing a computer application for the automatic retrieval of signal transduction data from electronic versions of scientific publications using natural language processing (NLP) techniques, as well as for visualizing and editing representations of regulatory systems. These systems describe both signal transduction and biochemical pathways within complex multicellular organisms, yeast, and bacteria. This computer application in turn requires the development of a domain-specific ontology, or knowledge model.

Results: We introduce an ontological model for the representation of biological knowledge related to regulatory networks in vertebrates. We outline a taxonomy of the concepts, define their ‘whole-to-part’ relationships, describe the properties of major concepts, and outline a set of the most important axioms. The ontology is partially realized in a computer system designed to aid researchers in biology and medicine in visualizing and editing a representation of a signal transduction system.

Availability: The knowledge model can be reviewed at http://genome6.cpmc.columbia.edu/tkoike/ontology/

Contact: ar345@columbia.edu

* To whom correspondence should be addressed.
The Human Transcript Database: a catalogue of full length cDNA
inserts
Authors: Bouck John , McLeod Michael P. , Worley Kim , Gibbs Richard A.
Published: July 2002

Summary: Full length cDNA sequences are an important resource for the research community but are currently intermingled with other sequences. We have identified the human full length insert cDNA sequences in GenBank and placed them in a single location, the Human Transcript Database.

Availability: The Human Transcript Database is available at http://www.hgsc.bcm.tmc.edu/HTDB/.

Contact: John Bouck: jbouck@bcm.tmc.edu
Estimating the rate of molecular evolution: incorporating
non-contemporaneous sequences into maximum likelihood phylogenies
Authors: Rambaut Andrew
Published: July 2002

Motivation: TipDate is a program that will use sequences that have been isolated at different dates to estimate their rate of molecular evolution. The program provides a maximum likelihood estimate of the rate and also the associated date of the most recent common ancestor of the sequences, under a model which assumes a constant rate of substitution (molecular clock) but which accommodates the dates of isolation. Confidence intervals for these parameters are also estimated.

Results: The approach was applied to a sample of 17 dengue virus serotype 4 sequences, isolated at dates ranging from 1956 to 1994. The rate of substitution for this serotype was estimated to be 7.91 × 10−4 substitutions per site per year (95% confidence intervals of 6.07 × 10−4, 9.86 × 10−4). This is compatible with a date of 1922 (95% confidence intervals of 1900–1936) for the most recent common ancestor of these sequences.

Availability: TipDate can be obtained by WWW from http://evolve.zoo.ox.ac.uk/software. The package includes the source code, manual and example files. Both UNIX and Apple Macintosh versions are available from the same site.

Contact: andrew.rambaut@zoo.ox.ac.uk
Conceptual modelling of genomic information
Authors: Paton Norman W. , Khan Shakeel A. , Hayes Andrew , Moussouni Fouzia , Brass Andy , Eilbeck Karen , Goble Carole A. , Hubbard Simon J. , Oliver Stephen G.
Published: July 2002

Motivation: Genome sequencing projects are making available complete records of the genetic make-up of organisms. These core data sets are themselves complex, and present challenges to those who seek to store, analyse and present the information. However, in addition to the sequence data, high throughput experiments are making available distinctive new data sets on protein interactions, the phenotypic consequences of gene deletions, and on the transcriptome, proteome, and metabolome. The effective description and management of such data is of considerable importance to bioinformatics in the post-genomic era. The provision of clear and intuitive models of complex information is surprisingly challenging, and this paper presents conceptual models for a range of important emerging information resources in bioinformatics. It is hoped that these can be of benefit to bioinformaticians as they attempt to integrate genetic and phenotypic data with that from genomic sequences, in order to both assign gene functions and elucidate the different pathways of gene action and interaction.

Results: This paper presents a collection of conceptual (i.e. implementation-independent) data models for genomic data. These conceptual models are amenable to (more or less direct) implementation on different computing platforms.

Availability: Most of the information models presented here have been implemented by the authors using an object database. The implementation of a public interface to this database is in progress. We hope to have a public release in the autumn of 2000, available from http://img.cs.man.ac.uk/gims.

Contact: norm@cs.man.ac.uk
A comparison of signal sequence prediction methods using a test
set of signal peptides
Authors: Menne Kerstin M.L. , Hermjakob Henning , Apweiler Rolf
Published: July 2002

Summary: We describe the creation of a test set containing secretory and non-secretory proteins. Five existing prediction programs for signal sequences and their cleavage sites are compared on the basis of this test set: SPScan, SigCleave, SignalP V1.1, SignalP V2.0.b2-HMM and SignalP V2.0.b2-NN.

Availability: Detailed results, the test set and the script to create the test set are available at ftp://ftp.ebi.ac.uk/pub/contrib/swissprot/testsets/signal/

Contact: hhe@ebi.ac.uk
Consumer Behavior in the United States: Implications for Social Security Reform
Authors: Evans Paul
Published: July 2002

This article shows theoretically and empirically that an aggregate Euler equation relates the growth rate of per capita consumption to the real interest rate, the ratio of private wealth plus asset income to consumption, and the ratio of social security wealth to consumption. Using the estimated Euler equation, the paper then calculates the steady‐state effects of social security reform. Reforms that reduce the ratio of social security wealth to consumption are found to shift the balanced growth paths for the capital stock, output, and consumption upward appreciably.
The DNA segregation mechanism of Epstein–Barr virus nuclear antigen 1
Authors: Wu Hong , Ceccarelli Derek F J , Frappier Lori
Published: July 2002

Latent Epstein–Barr virus (EBV) genomes are maintained in human cells as low copy number episomes that are thought to be partitioned by attachment to the cellular mitotic chromosomes through the viral EBNA1 protein. We have identified a human protein, EBP2, which interacts with the EBNA1 sequences that govern EBV partitioning. Here we show that, in mitosis, EBP2 localizes to the condensed cellular chromosomes producing a staining pattern that is indistinguishable from that of EBNA1. The localization of EBNA1 proteins with mutations in the EBP2 binding region was also examined. An EBNA1 mutant (Δ325–376) disrupted for EBP2 binding and segregation function was nuclear but failed to attach to the cellular chromosomes in mitosis. Our results indicate that amino acids 325–376 mediate the binding of EBNA1 to mitotic chromosomes and strongly suggest that EBNA1 mediates EBV segregation by attaching to EBP2 on the cellular mitotic chromosomes.
Synergy between estrogen receptor α activation functions AF1 and AF2 mediated by transcription intermediary factor TIF2
Authors: Benecke Arndt , Chambon Pierre , Gronemeyer Hinrich
Published: July 2002

The activation function AF2 in the ligand‐binding domain of estrogen receptors ERα and ERβ signals through the recruitment of nuclear receptor coactivators. Recent evidence indicates that coactivators, such as the transcription intermediary factor TIF2, also bind to and transactivate the N‐terminal AF1 function of the two ERs. We have generated TIF2 mutant proteins that are deficient in either AF1 or AF2 interaction and use these mutants to investigate the relative contribution of both AFs to TIF2 recruitment and transactivation. We observe that TIF2 is capable of interacting simultaneously with both the isolated N‐ and C‐terminus of ERα in transfected mammalian cells and in vitro, indicating that TIF2 can bridge both receptor domains. The concomitant interaction of TIF2 with both AFs results in synergistic activation of transcription. Thus, synergy between ERα AF1 and AF2 is a result of the cooperative recruitment of TIF2 and/or other members of the p160 coactivator family.
Biologically active APRIL is secreted following intracellular processing in the Golgi apparatus by furin convertase
Authors: López‐Fraga M , Fernández R , Albar J P , Hahne M
Published: July 2002

Tumor necrosis factor (TNF) ligand family members are synthesized as transmembrane proteins, and cleavage of the membrane‐anchored proteins from the cell surface is frequently observed. The TNF‐related ligands APRIL and BLyS and their cognate receptors BCMA/TACI form a two ligand/two receptor system that has been shown to participate in B‐ and T‐cell stimulation. In contrast to BLyS, which is known to be cleaved from the cell surface, we found that APRIL is processed intracellularly by furin convertase. Blockage of protein transport from the endoplasmic reticulum to the Golgi apparatus by Brefeldin A treatment abrogated APRIL processing, whereas monensin, an inhibitor of post‐Golgi transport, did not interfere with cleavage of APRIL, but blocked secretion of processed APRIL. Thus, APRIL shows a unique maturation pathway among the TNF ligand family members, as it not detectable as a membrane‐anchored protein at the cell surface, but is processed in the Golgi apparatus prior to its secretion.
The processivity factor β controls DNA polymerase IV traffic during spontaneous mutagenesis and translesion synthesis in vivo
Authors: Lenne‐Samuel Nathalie , Wagner Jérôme , Etienne Hélène , Fuchs Robert P P
Published: July 2002

The dinB‐encoded DNA polymerase IV (Pol IV) belongs to the recently identified Y‐family of DNA polymerases. Like other members of this family, Pol IV is involved in translesion synthesis and mutagenesis. Here, we show that the C‐terminal five amino acids of Pol IV are essential in targeting it to the β‐clamp, the processivity factor of the replicative DNA polymerase (Pol III) of Escherichia coli. In vivo, the disruption of this interaction obliterates the function of Pol IV in both spontaneous and induced mutagenesis. These results point to the pivotal role of the processivity clamp during DNA polymerase trafficking in the vicinity of damaged‐template DNA.
Mapping and identification of essential gene functions on the X chromosome of Drosophila
Authors: Peter Annette , Schöttler Petra , Werner Meike , Beinert Nicole , Dowe Gordon , Burkert Peter , Mourkioti Foteini , Dentzer Lore , He Yuchun , Deak Peter , Benos Panayiotis V , Gatt Melanie K , Murphy Lee , Harris David , Barrell Bart , Ferraz Concepcion , Vidal Sophie , Brun Christine , Demaille Jacques , Cadieu Edouard , Dreano Stephane , Gloux Stéphanie , Lelaure Valerie , Mottier Stephanie , Galibert Francis , Borkova Dana , Miñana Belen , Kafatos Fotis C , Bolshakov Slava , Sidén‐Kiamos Inga , Papagiannakis George , Spanos Lefteris , Louis Christos , Madueño Encarnación , de Pablos Beatriz , Modolell Juan , Bucheton Alain , Callister Debbie , Campbell Lorna , Henderson Nadine S , McMillan Paul J , Salles Cathy , Tait Evelyn , Valenti Phillipe , Saunders Robert D C , Billaud Alain , Pachter Lior , Klapper Robert , Janning Wilfried , Glover David M , Ashburner Michael , Bellen Hugo J , Jäckle Herbert , Schäfer Ulrich
Published: July 2002

The Drosophila melanogaster genome consists of four chromosomes that contain 165 Mb of DNA, 120 Mb of which are euchromatic. The two Drosophila Genome Projects, in collaboration with Celera Genomics Systems, have sequenced the genome, complementing the previously established physical and genetic maps. In addition, the Berkeley Drosophila Genome Project has undertaken large‐scale functional analysis based on mutagenesis by transposable P element insertions into autosomes. Here, we present a large‐scale P element insertion screen for vital gene functions and a BAC tiling map for the X chromosome. A collection of 501 X‐chromosomal P element insertion lines was used to map essential genes cytogenetically and to establish short sequence tags (STSs) linking the insertion sites to the genome. The distribution of the P element integration sites, the identified genes and transcription units as well as the expression patterns of the P‐element‐tagged enhancers is described and discussed.
Cellular and molecular partners involved in gut morphogenesis and differentiation
Authors: Kedinger M. , Lefebvre O. , Duluc I. , Freund J. N. , Simon–Assmann P.
Published: July 2002

The intestinal mucosa represents an interesting model to study the cellular and molecular basis of epithelial–mesenchymal cross–talk participating in the development and maintenance of the digestive function. This cross–talk involves extracellular matrix molecules, cell–cell and cell–matrix adhesion molecules as well as paracrine factors and their receptors. The cellular and molecular unit is additionally regulated by hormonal, immune and neural inputs. Such integrated cell interactions are involved in pattern formation, in proximodistal regionalization, in maintenance of a gradient of epithelial proliferation and differentiation, and in epithelial cell migration. We focus predominantly on two aspects of these integrated interactions in this paper: (i) the role of basement membrane molecules, namely laminins, in the developmental and spatial epithelial behaviour; and (ii) the importance of the mesenchymal cell compartment in these processes.
Wound healing in the liver with particular reference to stem cells
Authors: Alison Malcolm , Golding Matthew , Lalani El–Nasir , Sarraf Catherine
Published: July 2002

The efficiency of liver regeneration in response to the loss of hepatocytes is widely acknowledged, and this is usually accomplished by the triggering of normally proliferatively quiescent hepatocytes into the cell cycle. However, when regeneration is defective, tortuous ductular structures, initially continuous with the biliary tree, proliferate and migrate into the surrounding hepatocyte parenchyma. In humans, these biliary cells have variously been referred to as ductular structures, neoductules and neocholangioles, and have been observed in many forms of chronic liver disease, including cancer. In experimental animals, similar ductal cells are usually called oval cells, and their association with impaired regeneration has led to the conclusion that they are the progeny of facultative stem cells. Oval cells are of considerable biological interest as they may represent a target population for hepatic carcinogens, and they may also be useful vehicles for
ex vivo
gene therapy for the correction of inborn errors of metabolism. This review proposes that the liver harbours stem cells that are located in the biliary epithelium, that oval cells are the progeny of these stem cells, and that these cells can undergo massive expansion in their numbers before differentiating into hepatocytes. This is a conditional process that only occurs when the regenerative capacity of hepatocytes is overwhelmed, and thus, unlike the intestinal epithelium, the liver is not behaving as a classical, continually renewing, stem cell–fed lineage. We focus on the biliary network, not merely as a conduit for bile, but also as a cell compartment with the ability to proliferate under appropriate conditions and give rise to fully differentiated hepatocytes and other cell types.
Dynamics of arthropod filiform hairs. V. The response of spider trichobothria to natural stimuli
Authors: Barth Friedrich G. , Höller Andreas
Published: July 2002

Trichobothria are cuticular filiform hairs of arachnids, which respond to air movements. In the wandering spider,
Cupiennius salei
, about 900 trichobothria form characteristic groups on the pedipalps and legs and are used to detect and localize flying insect prey. We analyse the response of the receptor cells of metatarsal trichobothria of different lengths (200 to 800 μm) to both natural and synthetic stimuli to understand what the single receptor can contribute to the detection of natural signals. (i) The receptor cells are not spontaneously active. Their response to hair deflection is strictly phasic. The airflow produced by a tethered flying fly (
Calliphora sp.
) elicits a physiological response up to a distance of 55 cm. The response strength, however, strongly depends on the orientation and position of the fly. The receptor cells encode a wide range of airflow velocities (1 mm s
−1
to 1 m s
−1
). The time–course and frequency content of the strongly fluctuating air movements characterizing a fly signal are well represented in the spiking pattern of the receptor cells. There is almost no adaptation to a broad–band noise stimulus but strong adaptation to monofrequency stimulation. The presence of a platform below the spider (corresponding to its dwelling plant) strongly enhances the response of the trichobothrium due to its ‘amplifying’ effect on flow velocity. Without the platform, the sensory space of the trichobothrium decreases from 55 cm to 15 cm. (ii) With the hair directly coupled to the stimulating device, threshold curves do not depend on hair length (200 to 800 μm). Physiologically and irrespective of their length, the trichobothria are all broadly tuned to a frequency range between about 50 and 100 Hz where threshold deflection angles are
ca
. 0.1° and sometimes as small as 0.01°. This contrasts the length dependence of the mechanical frequency tuning of trichobothria. Above threshold the band pass characteristics of the cell reponse is much more pronounced than at threshold. (iii) Due to their low thresholds, their tuning and the highly phasic character of their response, the receptor cells of the trichobothria are well suited to detect and encode air particle movements produced by flying prey. Low–frequency background air movements (wind) are filtered by both the mechanical and the physiological properties of the trichobothria.
Milestones in research on tobacco mosaic virus
Authors: Harrison B. D. , Wilson T. M. A.
Published: July 2002

Beijerinck's (1898) recognition that the cause of tobacco mosaic disease was a novel kind of pathogen became the breakthrough which led eventually to the establishment of virology as a science. Research on this agent, tobacco mosaic virus (TMV), has continued to be at the forefront of virology for the past century.

After an initial phase, in which numerous biological properties of TMV were discovered, its particles were the first shown to consist of RNA and protein, and X–ray diffraction analysis of their structure was the first of a helical nucleoprotein. In the molecular biological phase of research, TMV RNA was the first plant virus genome to be sequenced completely, its genes were found to be expressed by cotranslational particle disassembly and the use of subgenomic mRNA, and the mechanism of assembly of progeny particles from their separate parts was discovered. Molecular genetical and cell biological techniques were then used to clarify the roles and modes of action of the TMV non–structural proteins: the 126 kDa and 183 kDa replicase components and the 30 kDa cell–to–cell movement protein. Three different TMV genes were found to act as avirulence genes, eliciting hypersensitive responses controlled by specific, but different, plant genes. One of these (the
N
gene) was the first plant gene controlling virus resistance to be isolated and sequenced. In the biotechnological sphere, TMV has found several applications: as the first source of transgene sequences conferring virus resistance, in vaccines consisting of TMV particles genetically engineered to carry foreign epitopes, and in systems for expressing foreign genes.

TMV owes much of its popularity as a research model to the great stability and high yield of its particles. Although modern methods have much decreased the need for such properties, and TMV may have a less dominant role in the future, it continues to occupy a prominent position in both fundamental and applied research.
Intracellular membrane traffic: getting proteins sorted. The 1999 Croonian Lecture
Authors: Pelham Hugh R. B.
Published: July 2002

The secretory and endocytic pathways within higher cells consist of multiple membrane-bound compartments, each with a characteristic composition, through which proteins move on their way to or from the cell surface. Sorting of proteins within this system is achieved by their selective incorporation into budding vesicles and the specific fusion of these with an appropriate target membrane. Cytosolic coat proteins help to select vesicle contents, while fusion is mediated by membrane proteins termed SNAREs present in both vesicles and target membranes. SNAREs are not the sole determinants of target specificity, but they lie at the heart of the fusion process. The complete set of SNAREs is known in yeast, and analysis of their locations, interactions and functions in vivo gives a comprehensive picture of the traffic routes and the ways in which organelles such as the Golgi apparatus are formed. The principles of protein and lipid sorting revealed by this analysis are likely to apply to a wide variety of eukaryotic cells. The 1999 Croonian Lecture held at Imperial College, London on 28 January 1999.
The role of Mid-Palaeozoic mesofossils in the detection of early bryophytes
Authors: Edwards Dianne
Published: July 2002

Recently discovered Silurian and Devonian coalified mesofossils provide an additional source of data on early embryophytes. Those reviewed in this paper are considered of some relevance to understanding the early history of bryophytes while highlighting the difficulties of recognizing bryophytes in often very fragmentary fossils. The first group comprises sporophytes in which terminal sporangia contain permanent dyads and tetrads. Such spores (cryptospores) are similar to those found dispersed in older Ordovician and Silurian strata, when they are considered evidence for a land vegetation of embryophytes at a bryophyte grade. The phylogenetic significance of plants, where the axes associated with both dyadand tetrad–containing sporangia are branching, a character state not found in extant bryophytes, is discussed. The second group comprises axial fossils, many with occasional stomata, in which central conducting strands include G–type tracheids and a number of novel types of elongate elements not readily compared with those of any tracheophyte. They include smooth–walled, evenly thickened elongate elements as well as those with numerous branching +/− anastomosing projections into the lumen. Some of the latter bear an additional microporate layer, but the homogenized lateral walls between adjacent cells are never perforate. Such cells, which occur in various combinations in central strands, are compared with the leptoids and hydroids of mosses, hydroids of liverworts and presumed water–conducting cells in coeval Lower Devonian plants such as Aglaophyton . It is concluded that lack of information on the chemistry of their walls hampers sensible assessment of their functions and the affinities of the plants. Finally, a minute fossil, comprising an elongate sporangium in which a central cylindrical cavity containing spores and possible elaters terminates in a complex poral dehiscence apparatus, is used to exemplify problems of identifying early bryophytes. It is concluded that further progress necessitates the discovery of pre–Upper Silurian fossils with well–preserved anatomy, as well as a re–evaluation of criteria used to assess existing and new Devonian fossils for bryophyte affinity.
Prions and the lymphoreticular system
Authors: Weissmann Charles , Raeber Alex J. , Montrasio Fabio , Hegyi Ivan , Frigg Rico , Klein Michael A. , Aguzzi Adriano
Published: July 2002

Following intracerebral or peripheral inoculation of mice with scrapie prions, infectivity accumulates first in the spleen and only later in the brain. In the spleen of scrapie–infected mice, prions were found in association with T and B lymphocytes and to a somewhat lesser degree with the stroma, which contains the follicular dendritic cells (FDCs) but not with non–B, non–T cells; strikingly, no infectivity was found in lymphocytes from blood of the same mice. Transgenic PrP knockout mice expressing PrP restricted to either B or T lymphocytes show no prion replication in the lymphoreticular system. Therefore, splenic lymphocytes either acquire prions from another source or replicate them in dependency on other PrP–expressing cells. The essential role of FDCs in prion replication in spleen was shown by treating mice with soluble lymphotoxin–β receptor, which led to disappearance of mature FDCs from the spleen and concomitantly abolished splenic prion accumulation and retarded neuroinvasion following intraperitoneal scrapie inoculation.
Treatment with immunotoxin
Authors: Knechtle Stuart J.
Published: July 2002

T–cell depletion prior to or beginning at the time of transplantation has been shown to be a valuable adjunct to the induction of immunological unresponsiveness. Both total lymphoid irradiation and anti–lymphocyte globulin have been used for this purpose in experimental models of transplantation as well as in human organ transplant recipients. However, these methods of T–cell depletion are limited in their ability to deplete T cells selectively due to non–specific targeting and limited efficacy. A new anti–CD3 immunotoxin has been developed with a far more potent ability to deplete T cells selectively as measured by flow cytometry analysis of peripheral blood T lymphocytes as well as lymph node lymphocytes. This immunotoxin is well tolerated by rhesus monkeys when administeredin vivo. When administered as a single immunosuppressive agent pretransplant, it substantially promotes allograft survival, inducing tolerance in at least one–third of recipients as measured by subsequent acceptance of donor skin grafts and rejection of third–party skin grafts. When administered on the day of transplant in combination with steroid pretreatment and a brief course of deoxyspergualin or mycophenolate mofetil (4 to 14 days), long–term unresponsiveness is also produced and in a more reliable manner than using immunotoxin alone. A new immunotoxin directed at the human CD3ε has been developed with excellent potency in T–cell killing and lacking the Fc portion of the CD3 antibody. This construct may be useful for T–cell depletion in humans and has a potential application in tolerance induction in human organ transplantation. Lessons learned from anti–CD3 immunotoxin in the non–human primate model to date include (i) profound (2–3 log) depletion of T–cells can be accomplished safely without inducing lymphoma or infection, (ii) such depletion is a useful adjunct for tolerance induction to allogeneic organ transplants, and (iii) tolerance to both allogeneic renal transplants and xenogeneic islet transplants has been accomplished using such strategies to date in non–human primates and in pigs. Immunotoxin may be useful for the induction of chimerism using strategies that include donor bone marrow infusion. Successful strategies for tolerance induction have also been developed using immunotoxin without the adjunct of donor bone marrow or stem cell infusion. Clinical application of immunotoxin will use a newly engineered construct with the potential for causing cytokine release, less susceptibility to neutralization by anti–diphtheria antibody and not dependent on chemical conjugation of an antibody and toxin. The usefulness of immunotoxin is directly related to its tremendous potency for depleting T cells. Based on results in nonhuman primates, it is anticipated that it will become a useful agent in tolerance induction in humans.
The KH-type RNA-binding protein PSI is required for Drosophila viability, male fertility, and cellular mRNA processing
Authors: Labourier Emmanuel , Blanchette Marco , Feiger Jennie W. , Adams Melissa D. , Rio Donald C.
Published: July 2002

Direct interactions between RNA-binding proteins and snRNP particles modulate eukaryotic pre-mRNA processing patterns to control gene expression. Here, we report that the conserved U1 snRNP-interacting RNA-binding protein PSI is essential for Drosophila viability. A null PSI mutation is recessive lethal at the first-instar larval stage, and lethality is fully rescued by transgenes expressing the PSI protein. A mutant transgene that lacks the PSI–U1 snRNP-interaction domain restores viability but shows courtship behavior abnormalities and meiosis defects during spermatogenesis, resulting in a complete male sterility phenotype. Using cDNA microarrays, we have identified specific target mRNAs with altered expression profiles in these mutant males. A subset of these transcripts is also found associated with PSI in endogenous immunopurified ribonucleoprotein complexes. One specific target, the hrp40/squid transcript, shows an altered pre-mRNA splicing pattern in PSI mutant testes. We conclude that a functional association between the PSI protein and the spliceosomal U1 snRNP particle is required for normal Drosophila development and for the processing of specific PSI-interacting cellular transcripts. These results also validate the use of cDNA microarrays to characterize in vivo RNA-processing defects and alternative pre-mRNA splicing patterns.
Comparative Genomics Between Rice and Arabidopsis Shows Scant Collinearity in Gene Order
Authors: Liu Hong , Sachidanandam Ravi , Stein Lincoln
Published: July 2002

We have investigated possible collinearity between the genomes of rice and Arabidopsis by comparing 126 annotated and mapped rice BAC sequences (∼20 Mb of sequence) with the annotated and complete Arabidopsis genome (∼115 Mb). Although we were able to identify several regions in which gene order is preserved, they are relatively small, and are interrupted by noncollinear genes. Computer simulation showed that these microscale collinearities are above the expectation for a random process. On the other hand, the order of exons within homologous genes (<2.5 kb) was preserved, as expected.
Identification of Genes Encoding Amino Acid Permeases by Inactivation of Selected ORFs from the Synechocystis Genomic Sequence
Authors: Quintero Marı́a José , Montesinos Marı́a Luz , Herrero Antonia , Flores Enrique
Published: July 2002

Genes encoding elements of four amino acid permeases were identified by insertional inactivation of ORFs from the genomic sequence of the cyanobacterium Synechocystis sp. strain PCC 6803 whose putative products are homologous to amino acid permease proteins from other bacteria. A transport system for neutral amino acids and histidine and a transport system for basic amino acids and glutamine were identified as ABC-type transporters, whereas Na+-dependent transport of glutamate was found to be mediated by at least two systems, the secondary permease GltS and a TRAP-type transporter. Except for GltS, substrate specificities of the identified permeases do not match those of previously characterized systems homologous to these permeases.
Computational Detection and Location of Transcription Start Sites in Mammalian Genomic DNA
Authors: Down Thomas A. , Hubbard Tim J. P.
Published: July 2002

Transcription, the process whereby RNA copies are made from sections of the DNA genome, is directed by promoter regions. These define the transcription start site, and also the set of cellular conditions under which the promoter is active. At least in more complex species, it appears to be common for genes to have several different transcription start sites, which may be active under different conditions. Eukaryotic promoters are complex and fairly diffuse structures, which have proven hard to detect in silico. We show that a novel hybrid machine-learning method is able to build useful models of promoters for >50% of human transcription start sites. We estimate specificity to be >70%, and demonstrate good positional accuracy. Based on the structure of our learned models, we conclude that a signal resembling the well known TATA box, together with flanking regions of C-G enrichment, are the most important sequence-based signals marking sites of transcriptional initiation at a large class of typical promoters.
Binding of Phosphate and pyrophosphate ions at the active site of human angiogenin as revealed by X‐ray crystallography
Authors: Leonidas Demetres D. , Chavali Gayatri B. , Jardine Anwar M. , Li Songlin , Shapiro Robert , Acharya K. Ravi
Published: July 2002

Human angiogenin (Ang) is an unusual homolog of bovine pancreatic RNase A that utilizes its ribonucleolytic activity to induce the formation of new blood vessels. The pyrimidine‐binding site of Ang was shown previously to be blocked by glutamine 117, indicating that Ang must undergo a conformational change to bind and cleave RNA. The mechanism and nature of this change are not known, and no Ang‐inhibitor complexes have been characterized structurally thus far. Here, we report crystal structures for the complexes of Ang with the inhibitors phosphate and pyrophosphate, and the structure of the complex of the superactive Ang variant Q117G with phosphate, all at 2.0 Å resolution. Phosphate binds to the catalytic site of both Ang and Q117G in essentially the same manner observed in the RNase A–phosphate complex, forming hydrogen bonds with the side chains of His 13, His 114, and Gln 12, and the main chain of Leu 115; it makes an additional interaction with the Lys 40 ammonium group in the Ang complex. One of the phosphate groups of pyrophosphate occupies a similar position. The other phosphate extends toward Gln 117, and lies within hydrogen‐bonding distance from the side‐chain amide of this residue as well as the imidazole group of His 13 and the main‐chain oxygen of Leu 115. The pyrimidine site remains obstructed in all three complex structures, that is, binding to the catalytic center is not sufficient to trigger the conformational change required for catalytic activity, even in the absence of the Gln 117 side chain. The Ang–pyrophosphate complex structure suggests how nucleoside pyrophosphate inhibitors might bind to Ang; this information may be useful for the design of Ang antagonists as potential anti‐angiogenic drugs.
Recursive domains in proteins
Authors: Przytycka Teresa , Srinivasan Rajgopal , Rose George D.
Published: July 2002

The domain is a fundamental unit of protein structure. Numerous studies have analyzed folding patterns in protein domains of known structure to gain insight into the underlying protein folding process. Are such patterns a haphazard assortment or are they similar to sentences in a language, which can be generated by an underlying grammar? Specifically, can a small number of intuitively sensible rules generate a large class of folds, including feasible new folds? In this paper, we explore the extent to which four simple rules can generate the known all‐β folds, using tools from graph theory. As a control, an exhaustive set of β‐sandwiches was tested and found to be largely incompatible with such a grammar. The existence of a protein grammar has potential implications for both the mechanism of folding and the evolution of domains.
Involvement of the amino‐terminal β‐hairpin of the Aspergillus ribotoxins on the interaction with membrances and nonspecific ribonuclease activity
Authors: García‐ortega Lucía , Lacadena Javier , Mancheño José M. , Oñaderra Mercedes , Kao Richard , Davies Julian , Olmo Nieves , Martínez Álvaro , Pozo Del , Gavilanes José G.
Published: July 2002

Ribotoxins are a family of potent cytotoxic proteins from Aspergillus whose members display a high sequence identity (85% for about 150 amino acid residues). The three‐dimensional structures of two of these proteins, α‐sarcin and restrictocin, are known. They interact with phospholipid bilayers, according to their ability to enter cells, and cleave a specific phosphodiester bond in the large subunit of ribosome thus inhibiting protein biosynthesis. Two nonconservative sequence changes between these proteins are located at the amino‐terminal β‐hairpin of α‐sarcin, a characteristic structure that is absent in other nontoxic structurally related microbial RNases. These two residues of α‐sarcin, Lys 11 and Thr 20, have been substituted with the equivalent amino acids in restrictocin. The single mutants (K11L and T20D) and the corresponding K11L/T20D double mutant have been produced in Escherichia coli and purified to homogeneity. The spectroscopic characterization of the purified proteins reveals that the overall native structure is preserved. The ribonuclease and lipid‐perturbing activities of the three mutants and restrictocin have been evaluated and compared with those of α‐sarcin. These proteins exhibit the same ability to specifically inactivate ribosomes, although they show different activity against nonspecific substrate analogs such as poly(A). The mutant variant K11L and restrictocin display a lower phospholipid‐interacting ability correlated with a decreased cytotoxicity. The results obtained are interpreted in terms of the involvement of the amino‐terminal β‐hairpin in the interaction with both membranes and polyadenylic acid.
Beam characteristics of a retrofitted double‐focused multileaf collimator
Authors: Das Indra J. , Desobry Gregory E. , McNeeley Shawn W. , Cheng Elizabeth C. , Schultheiss Timothy E.
Published: July 2002

Multileaf collimators (MLCs) are generally believed to be convenient and cost‐effective tools for intensity modulation and conformal therapy. They are becoming a standard feature on new accelerators; however, the older units can be retrofitted with modern MLCs. Before such a unit can be clinically used, the beam characteristics must be verified. In this study the beam characteristics of a Siemens double‐focused MLC retrofitted to an MD2 linear accelerator are presented. The head leakage along with inter‐ and intra‐leaf radiation transmission were measured using film. The collimator phantom total scatter factors, central axis depth dose, beam profiles for off‐axis ratios, penumbra, and surface dose were evaluated for square, rectangular, and irregularly shaped fields. The maximum head leakage was estimated to be <0.05% in any plane at a distance of 1 m and maximum transmission through the MLC leaves was estimated to be <1.4% and <1.1% for the 10 MV and 6 MV beams, respectively. The maximum differences between pre‐ and post‐MLC installation data for the and were ⩽0.7% and ⩽1.4%, respectively. Similarly, the percent depth dose data for all fields and both beam energies were within 1.5% of the original data. The beam profiles measured at various depths were also in agreement with those of the pre‐MLC installation data. The measured beam penumbra (20%–80%) showed a range of 7.8 mm–11.0 mm for the 6 MV and 8.4 mm–11.1 mm for the 10 MV beams from smallest to largest fields. These ranges differ by less than a millimeter from those of the old data. The surface dose measurements were slightly lower than the conventional jaw values suggesting that MLC does not produce significant electron contamination. It is concluded that the retrofitted MLC maintains the integrity of the original beam and may provide a cost‐effective conformal therapy.
A general methodology for three‐dimensional analysis of variation in target volume delineation
Authors: Remeijer Peter , Rasch Coen , Lebesque Joos V. , van Herk Marcel
Published: July 2002

A generic method for three‐dimensional (3‐D) evaluation of target volume delineation in multiple imaging modalities is presented. The evaluation includes geometrical and statistical methods to estimate observer differences and variability in defining the Gross Tumor Volume (GTV) in relation to the diagnostic CT and MRI modalities. The geometrical method is based on mapping the 3‐D shape of the target volume to a scalar representation, thus enabling a one‐dimensional statistical analysis. The statistical method distinguishes observer and modality related uncertainties, which are expressed in terms of three error components: random observer deviations, systematic observer differences, and systematic modality differences. Monte Carlo simulations demonstrate that the standard errors of each of the three model parameters are inversely proportional to the square root of the product of the patient group size and the number of observers and proportional to the intraobserver variation. For 18 patients and 3 observers the standard errors of the estimated systematic modality and observer differences are 19% and 14% of the intraobserver standard deviation, respectively. A scalar representation of the shape of the prostate, delineated by 3 observers for 18 patients, was obtained by sampling the distance between the average center of gravity of the prostate in CT and the prostate surface for a large number of directions (2500), using polar coordinates. Observer variability and differences were obtained by applying the statistical method to the samples independently. The intraobserver variation for CT was largest in regions near the seminal vesicles (s.d: 3 mm) and the apex (s.d: 3 mm). The systematic observer variation in CT was largest in a region near the plexus Santorini, at the caudal‐anterior side of the prostate (s.d.: 2 mm). The sensitivity for the choice of origin was tested by using the average center of gravity from axial MRI instead of CT. The results were almost identical. The polar map measures distances in the scanning directions. A correction procedure to get the variability in directions perpendicular to the surface of the prostate yielded variations that were a factor of 0.85 smaller for all directions. It is concluded that by separating the shape evaluation in a geometrical and a statistical part, the complexity of the analysis of 3‐D shape differences can be significantly reduced. The method was successfully applied to a group of prostate patients, where we demonstrated that delineation variability is nonhomogeneous, with the largest variations occurring near the seminal vesicles and the apex.
TLD dose measurement: A simplified accurate technique for the dose range from 0.5 cGy to 1000 cGy
Authors: Yu C. , Luxton G.
Published: July 2002

A simplified TLD technique characterized by high precision and reproducibility of dose measurement is presented. One hundred eighty LiF TLD rods 1 mm diam ×3 mm length as obtained from the manufacturer were annealed for 1 h at 400 °C followed immediately by 2 h at 105 °C. After exposure to a dose of 1 Gy of 4 MV x rays, TLDs were annealed for 15 min at 105 °C, then read out. TLDs were then sorted into five groups, ranging from 26 to 50 rods each with approximately equal sensitivity after correcting for the drift in the sensitivity of the TLD reader during the readout session. Maintaining group identity, the TLDs were again annealed, irradiated and read out. Fewer than 10% of the TLDs were removed from each group because the corrected readings differed from the respective group mean by more than 3.5%. The standard deviation of the readout was approximately 1.5% within each group. The planchet heater was not flushed with nitrogen gas. Various tests were performed to assess the stability of the group sorting technique and the linearity of TLD dose response. After reannealing, five TLDs were randomly drawn from one of the presorted groups, and subjected to various dose of 4 MV radiation over the range from 0.5 to 1000 cGy. This resulted in an average readout standard deviation of 1.2%. Response per unit dose was almost flat over the range from 0.5 cGy to 100 cGy, and increased by 15% over the range from 100 cGy to 1000 cGy. TLD sensitivity was affected by the duration of the anneal, but was virtually independent of the various time delays between irradiation, prereadout anneal, and readout. The group annealing and sorting (GAS) procedure provides a simple, reliable, precise, convenient, and accurate method for TLD measurements.
The mystery of the fifteenth Bravais lattice
Authors: Nussbaum Allen
Published: July 2002

An understanding of the principles of crystal structure is necessary for the study of solids. There are contradictions in the literature dealing with the nature of crystal lattices, and there is also a miscounting of the number of possible lattices. This paper clarifies the situation in a systematic and simple way.
Tilted boxes on inclined planes
Authors: Nunes A. M. , Silva J. P.
Published: July 2002

We propose the study of a box placed on an inclined plane, with an initial tilt with respect to the plane. This is a paradigmatic example of the role played by friction as a link between translational and rotational motion. This example has two advantages over the usual example of a sphere (or cylinder) rolling down an inclined plane. First, it provides a good model for a much greater variety of “real-life” situations. Second, it exhibits a much richer structure in parameter space, even when the box starts from rest.
Noninertial trajectories on a fast rotating planet
Authors: Amengual Antoni
Published: July 2002

The trajectory of a particle thrown horizontally on the surface of a planet rotating at an arbitrary speed, as viewed by an observer on the planet, is calculated numerically and is subsequently compared to the trivially calculated trajectory viewed by an inertial observer. This provides an excellent example when motion in noninertial frames is explained in a mechanics course.