bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative Determination of Surface Concentration of Human Apolipoprotein H with Capillary Electrophoresis
Authors: Wang Shao‐xiong , Sun Yu‐Tong , Ru Qin‐hua , Luo Guo‐an , Sui Sen‐fang 
Published: July 2002

AbstractThe phospholipid monolayer at an air/water interface is widely used to mimic the biological membrane. The dynamic process of the protein or peptide interacting with lipid molecules can be reflected in the change in surface pressure of the monolayer. But the conventional method used to measure the surface pressure change gives results that cannot easily be correlated with the contribution of a single protein molecule. Previously, measuring the surface concentration of the protein molecules at the air/water interface has required the protein to be labeled with radioactivity or fluorescence. Here, a new method using capillary electrophoresis is introduced to measure the surface concentration of the protein. The results show at least two advantages of the new method: The numerical results of protein concentration can be obtained in a more precise and rapid way; and there is no need to label the protein sample or to build a special monolayer setup.
Effect of Buffer Solutions on Activation of Shamouti Orange Pyrophosphate‐Dependent Phosphofructokinase by Fructose 2,6‐Bisphosphate
Authors: Van Praag Esther , Tzur Assaf , Zehavi Uri , Goren Raphael 
Published: July 2002

AbstractShamouti phosphofructokinase (PFP) activation depends on the presence of fructose 2,6‐bisphosphate (Fru‐2,6‐P2) in the glycolytic reaction. The effect of activation by Fru‐2,6‐P2 differs considerably, however, according to the buffer (pH 8.0) in which the reaction is performed: Ka = 2.77 plus/minus 0.3 nM in Hepes‐NaOH and 7.75 plus/minus 1.49 nM in Tris‐HCl. The presence of chloride ions (39 mM) in the Tris‐HCl buffer inhibits PFP. Indeed, when using a Hepes‐NaOH buffer and then adding 39 mM NaCl, Ka = 8.12 plus/minus 0.52 nM. The Ki for chloride ions is approximately 21.7 mM. In the gluconeogenic reaction, Shamouti PFP generally showed a high endogenous activity. Addition of Fru‐2,6‐P2 did not modify the velocity and the Vmax of the enzyme; however, its presence increased the affinity of the enzyme for Fru‐1,6‐P2 from 200 plus/minus 15.6 muM in absence of Fru‐2,6‐P2 to 89 plus/minus 10.3 muM in its presence (10 muM). In the presence of chloride (39 mM), the affinity for the substrate decreased with Km = 150 plus/minus 14 muM. The calculated Ki for chloride ions equals 56.9 mM. In both the glycolytic and the gluconeogenic reactions, Vmax is not affected; therefore, the inhibition mode of chloride is competitive.
Selection of Peptide Ligands That Bind to Acid Fibroblast Growth Factor
Authors: Fan Hongkuan , Liu Ying , Zhou Hui , Wang Liping , Li Wei , Guo Lili , Roeske Roger W. 
Published: July 2002

AbstractAcid fibroblast growth factor (aFGF) binds to its cell‐surface receptors in a heparin‐dependent manner. In an attempt to define the aFGF recognition site on fibroblast growth factor receptor 1 (FGFR1), we developed a screening strategy for identifying FGF ligands that bind to the receptor‐binding region of FGF. To retain the natural conformation of aFGF during screening, we used biotinylated heparin to immobilize aFGF on a streptavidincoated dish. A 15‐mer phage display peptide library was then screened in the dish and a group of related peptide sequences was identified. These peptide sequences contain two conserved motifs, SSG and VPS, corresponding to two protein sequences of the immunoglobulin‐like (Ig‐like) domain II of FGFR1 at amino acids 180‐182 and 221‐223 (CPSSG‐VPSDKGNYTC). Further experiments demonstrate that the phage displaying these sequences can specifically bind to aFGF and that the synthesized peptide corresponding in sequence can inhibit mitogenic activity of aFGF.These sequences may thus constitute part of the aFGF‐binding region on FGFR1, and the synthesized peptide has the potential to become a therapeutic agent as an aFGF antagonist.
The Isolated Comet Tail Pseudopodium of Listeria monocytogenes: A Tail of Two Actin Filament Populations, Long and Axial and Short and Random
Authors: Sechi Antonio S. , Wehland Jürgen , Small J. Victor 
Published: July 2002

Listeria monocytogenes is driven through infected host cytoplasm by a comet tail of actin filaments that serves to project the bacterium out of the cell surface, in pseudopodia, to invade neighboring cells. The characteristics of pseudopodia differ according to the infected cell type. In PtK2 cells, they reach a maximum length of ∼15 μm and can gyrate actively for several minutes before reentering the same or an adjacent cell. In contrast, the pseudopodia of the macrophage cell line DMBM5 can extend to &gt;100 μm in length, with the bacteria at their tips moving at the same speed as when at the head of comet tails in bulk cytoplasm. We have now isolated the pseudopodia from PtK2 cells and macrophages and determined the organization of actin filaments within them. It is shown that they possess a major component of long actin filaments that are more or less splayed out in the region proximal to the bacterium and form a bundle along the remainder of the tail. This axial component of filaments is traversed by variable numbers of short, randomly arranged filaments whose number decays along the length of the pseudopodium. The tapering of the tail is attributed to a grading in length of the long, axial filaments.
The exit of a comet tail from bulk cytoplasm into a pseudopodium is associated with a reduction in total F-actin, as judged by phalloidin staining, the shedding of α-actinin, and the accumulation of ezrin. We propose that this transition reflects the loss of a major complement of short, random filaments from the comet, and that these filaments are mainly required to maintain the bundled form of the tail when its borders are not restrained by an enveloping pseudopodium membrane. A simple model is put forward to explain the origin of the axial and randomly oriented filaments in the comet tail.
Rapid Movements of Vimentin on Microtubule Tracks: Kinesin-dependent Assembly of Intermediate Filament Networks
Authors: Prahlad Veena , Yoon Miri , Moir Robert D. , Vale Ronald D. , Goldman Robert D. 
Published: July 2002

The assembly and maintenance of an extended intermediate filament (IF) network in fibroblasts requires microtubule (MT) integrity. Using a green fluorescent protein–vimentin construct, and spreading BHK-21 cells as a model system to study IF–MT interactions, we have discovered a novel mechanism involved in the assembly of the vimentin IF cytoskeleton. This entails the rapid, discontinuous, and MT-dependent movement of IF precursors towards the peripheral regions of the cytoplasm where they appear to assemble into short fibrils. These precursors, or vimentin dots, move at speeds averaging 0.55 ± 0.24 μm/s. The vimentin dots colocalize with MT and their motility is inhibited after treatment with nocodazole.
Our studies further implicate a conventional kinesin in the movement of the vimentin dots. The dots colocalize with conventional kinesin as shown by indirect immunofluorescence, and IF preparations from spreading cells are enriched in kinesin. Furthermore, microinjection of kinesin antibodies into spreading cells prevents the assembly of an extended IF network. These studies provide insights into the interactions between the IF and MT systems. They also suggest a role for conventional kinesin in the distribution of non-membranous protein cargo, and the local regulation of IF assembly.
Characterization and Expression of the Laminin γ3 Chain: A Novel, Non-Basement Membrane–associated, Laminin Chain
Authors: Koch Manuel , Olson Pamela F. , Albus Anne , Jin William , Hunter Dale D. , Brunken William J. , Burgeson Robert E. , Champliaud Marie-France 
Published: July 2002

Laminins are heterotrimeric molecules composed of an α, a β, and a γ chain; they have broad functional roles in development and in stabilizing epithelial structures. Here, we identified a novel laminin, composed of known α and β chains but containing a novel γ chain, γ3. We have cloned gene encoding this chain, LAMC3, which maps to chromosome 9 at q31-34. Protein and cDNA analyses demonstrate that γ3 contains all the expected domains of a γ chain, including two consensus glycosylation sites and a putative nidogen-binding site. This suggests that γ3-containing laminins are likely to exist in a stable matrix.
Studies of the tissue distribution of γ3 chain show that it is broadly expressed in: skin, heart, lung, and the reproductive tracts. In skin, γ3 protein is seen within the basement membrane of the dermal-epidermal junction at points of nerve penetration. The γ3 chain is also a prominent element of the apical surface of ciliated epithelial cells of: lung, oviduct, epididymis, ductus deferens, and seminiferous tubules. The distribution of γ3-containing laminins on the apical surfaces of a variety of epithelial tissues is novel and suggests that they are not found within ultrastructurally defined basement membranes. It seems likely that these apical laminins are important in the morphogenesis and structural stability of the ciliated processes of these cells.
Mycobacterium tuberculosis Expresses a Novel Ph-Dependent Divalent Cation Transporter Belonging to the Nramp Family
Authors: Agranoff Daniel , Monahan Irene M. , Mangan Joseph A. , Butcher Philip D. , Krishna Sanjeev 
Published: July 2002

Mammalian natural resistance–associated macrophage protein (Nramp) homologues are important determinants of susceptibility to infection by diverse intracellular pathogens including mycobacteria. Eukaryotic Nramp homologues transport divalent cations such as Fe2+, Mn2+, Zn2+, and Cu2+. Mycobacterium tuberculosis and Mycobacterium bovis (bacillus Calmette-Guérin [BCG]) also encode an Nramp homologue (Mramp).
RNA encoding Mramp induces ∼20-fold increases in 65Zn2+ and 55Fe2+ uptake when injected into Xenopus laevis oocytes. Transport is dependent on acidic extracellular pH and is maximal between pH 5.5 and 6.5. Mramp-mediated 65Zn2+ and 55Fe2+ transport is abolished by an excess of Mn2+ and Cu2+, confirming that Mramp interacts with a broad range of divalent transition metal cations.
Using semiquantitative reverse transcription PCR, we show that Mramp mRNA levels in M. tuberculosis are upregulated in response to increases in ambient Fe2+ and Cu2+ between &lt;1 and 5 μM concentrations and that this upregulation occurs in parallel with mRNA for y39, a putative metal-transporting P-type ATPase. Using a quantitative ratiometric PCR technique, we demonstrate a fourfold decrease in Mramp/y39 mRNA ratios from organisms grown in 5–70 μM Cu2+. M. bovis BCG cultured axenically and within THP-1 cells also expresses mRNA encoding Mramp.
Mramp exemplifies a novel prokaryotic class of metal ion transporter. Within phagosomes, Mramp and Nramp1 may compete for the same divalent cations, with implications for intracellular survival of mycobacteria.
Promises and challenges of electronic journals: academic libraries surveyed
Authors: Chu Heting 
Published: July 2002

ABSTRACTIn spring 1997, a questionnaire was mailed to 95 major academic libraries in the United States to explore how serials librarians are responding to the boom of electronic journals (e‐journals). Fifty librarians (52.6%) answered the survey with one follow‐up. The study found that over 70% of the libraries that returned the survey had participated in e‐journal‐related activities. Questions relating to ‘access’ were consistently ranked high in explaining why librarians in major academic libraries think e‐journals are valuable, yet ‘cost’ seems to be a critical factor in determining e‐journal adoption. For most of the libraries surveyed, the figure for e‐journals appears modest, although some institutions claimed to have more than 1,100 titles in their e‐journal collections.
On 𝜙-amicable pairs
Authors: Cohen Graeme , te Riele Herman 
Published: July 2002

Let

ϕ
(
n
)

\phi (n)

denote Euler’s totient function, i.e., the number of positive integers

>
n

>n

and prime to

n
n

. We study pairs of positive integers

(

a

0

,

a

1

)

(a_{0},a_{1})

with

a

0

≤

a

1

a_{0}\le a_{1}

such that

ϕ
(

a

0

)
=
ϕ
(

a

1

)
=
(

a

0

+

a

1

)

/

k

\phi (a_{0})=\phi (a_{1})=(a_{0}+a_{1})/k

for some integer

k
≥
1

k\ge 1

. We call these numbers

ϕ
\phi

–amicable pairs with multiplier

k
k

, analogously to Carmichael’s multiply amicable pairs for the

σ
\sigma

–function (which sums all the divisors of

n
n

). We have computed all the

ϕ
\phi

–amicable pairs with larger member

≤

10

9

\le 10^{9}

and found

812
812

pairs for which the greatest common divisor is squarefree. With any such pair infinitely many other

ϕ
\phi

–amicable pairs can be associated. Among these

812
812

pairs there are

499
499

so-called primitive

ϕ
\phi

–amicable pairs. We present a table of the

58
58

primitive

ϕ
\phi

–amicable pairs for which the larger member does not exceed

10

6

10^{6}

. Next,

ϕ
\phi

–amicable pairs with a given prime structure are studied. It is proved that a relatively prime

ϕ
\phi

–amicable pair has at least twelve distinct prime factors and that, with the exception of the pair

(
4
,
6
)

(4,6)

, if one member of a

ϕ
\phi

–amicable pair has two distinct prime factors, then the other has at least four distinct prime factors. Finally, analogies with construction methods for the classical amicable numbers are shown; application of these methods yields another 79 primitive

ϕ
\phi

–amicable pairs with larger member

>

10

9

>10^{9}

, the largest pair consisting of two 46-digit numbers.
Comprehensive, comprehensible, distributed and intelligent databases: current status.
Authors: Frishman D , Heumann K , Lesk A , Mewes H W 
Published: July 2002

Abstract
MOTIVATION: It is only a matter of time until a user will see not many but one integrated database of information for molecular biology. Is this true? Is it a good thing? Why will it happen? Where are we now? What developments are fostering and what developments are impeding progress towards this end? SUPPLEMENTARY INFORMATION: A list of WWW resources devoted to database issues in molecular biology is available at http://www.mips.biochem.mpg.de CONTACT: frishman@mips.biochem.mpg.de
BLAST Search Updater: a notification system for new database
matches
Authors: Boone Matthew , Upton Chris 
Published: July 2002

Abstract
Summary: BLAST Search Updater (BSU) can help molecular biologists perform large numbers of BLAST searches routinely and screen the results for novel matches. The search result files (HTML format) and delta files (novel matches) are WWW viewable and BSU also emails users alignments of new matches.
Availability: BSU runs on UNIX machines and is freely available to academic users at http://athena.bioc.uvic.ca/genomes/. Additional figures and description are also available.
Contact: cupton@uvic.ca
To whom correspondence should be addressed.
ASAP: analysis of peptide composition
Authors: Serra-Hartmann Xavier , Rebordosa Xavier , Piñol Jaume , Querol Enrique , Martı́-Renom Marc

A. 
Published: July 2002

Abstract
Summary: ASAP is a web tool designed to search for specific dipeptides, tripeptides and tetrapeptides in a protein sequence database. The server allows for: (a) identification of frequent and infrequent peptides and the creation of peptide probability tables for a given database of sequences (GenerNet program), (b) determination of the compatibility of an amino-acid sequence to the given peptide probability tables (ClonErrNet program); and (c) comparison of different protein databases based on peptide composition (CompNet program). ASAP server can be useful in protein engineering and/or protein classification studies.
Availability: http://guitar.rockefeller.edu/~marcius/ASAP.html
Contact: martim@rockefeller.edu
* To whom correspondence should be addressed.
Storing biological sequence databases in relational form
Authors: Xie Guochun , DeMarco Reynold , Blevins Richard , Wang Yuhong 
Published: July 2002

Abstract
Summary: We have created a set of applications using Perl and Java in combination with XML technology to install biological sequence databases into an Oracle RDBMS. An easy-to-use interface using Java has been created for database query and other tools developed to integrate with our in-house bioinformatics applications.
Availability: The database schema, DTD file, and source codes are available from the authors via email.
Contact: guochun_xie@merck.com
GESTALT: a workbench for automatic integration and
visualization of large-scale genomic sequence analyses
Authors: Glusman Gustavo , Lancet Doron 
Published: July 2002

Abstract
Summary: The GESTALT Workbench is a WWW-based tool for genomic sequence analysis, comparison and annotation, with strong emphasis on visualization. GESTALT integrates graphically the output of diverse sequence analysis algorithms producing an information-rich, interactive genomic map.
Availability: The GESTALT Workbench, as well as a more detailed description, are available at http://bioinfo.weizmann.ac.il/GESTALT/.
Contact: Gustavo@bioinfo.weizmann.ac.il, Doron.Lancet@weizmann.ac.il
Viral Genome DataBase: storing and analyzing genes and proteins
from complete viral genomes
Authors: Hiscock David , Upton Chris 
Published: July 2002

Abstract
* To whom correspondence should be addressed.
Summary: The Viral Genome DataBase (VGDB) contains detailed information of the genes and predicted protein sequences from 15 completely sequenced genomes of large (&100 kb) viruses (2847 genes). The data that is stored includes DNA sequence, protein sequence, GenBank and user-entered notes, molecular weight (MW), isoelectric point (pI), amino acid content, A + T%, nucleotide frequency, dinucleotide frequency and codon use. The VGDB is a mySQL database with a user-friendly JAVA GUI. Results of queries can be easily sorted by any of the individual parameters.
Availability: The software and additional figures and information are available at http://athena.bioc.uvic.ca/genomes/index.html.
Contact: cupton@uvic.ca
Browsing the SLoop database of structurally classified loops connecting elements of protein secondary structure
Authors: Burke David F. , Deane Charlotte M. , Blundell Tom L. 
Published: July 2002

Abstract
We describe a web server, which provides easy access to the SLoop database of loop conformations connecting elements of protein secondary structure. The loops are classified according to their length, the type of bounding secondary structures and the conformation of the mainchain. The current release of the database consists of over 8000 loops of up to 20 residues in length. A loop prediction method, which selects conformers on the basis of the sequence and the positions of the elements of secondary structure, is also implemented. These web pages are freely accessible over the internet at http://www-cryst.bioc.cam.ac.uk/~sloop.
IMpRH Server: an RH mapping server available on the Web
Authors: Milan Denis , Hawken Rachel , Cabau Cédric , Leroux Sophie , Genet Carine , Lahbib Yvette , Tosser Gwenola , Robic Annie , Hatey Francois , Alexander Lee , Beattie Craig , Schook Larry , Yerle Martine , Gellin Joël 
Published: July 2002

Abstract
Summary: The INRA-Minnesota Porcine Radiation Hybrid (IMpRH) Server provides both a mapping tool (IMpRH mapping tool) and a database (IMpRH database) of officially submitted results. The mapping tool permits the mapping of a new marker relatively to markers previously mapped on the IMpRH panel. The IMpRH database is the official database for submission of new results and queries. The database not only permits the sharing of public data but also semi-private and private data.
Availability: http://imprh.toulouse.inra.fr
Contact: milan@toulouse.inra.fr
Supplementary Information: Details can be found at http://www.toulouse.inra.fr/lgc/pig/RH/help/help.htm
eSAGE: managing and analysing data generated with Serial
Analysis of Gene Expression (SAGE)
Authors: Margulies Elliott H. , Innis Jeffrey W. 
Published: July 2002

Abstract
Summary: eSAGE is a comprehensive set of software tools for managing and analysing data generated with Serial Analysis of Gene Expression (SAGE).
Availability: eSAGE is freely available for non-commercial use.
Contact: ehm@umich.edu
MDB: a database system utilizing automatic construction of
modules and STAR-derived universal language
Authors: Migliavacca Eugenia , Adzhubei Alexei A. , Peitsch Manuel C. 
Published: July 2002

Abstract
Motivation: The value of information greatly increases if stored in databases. The objective was to construct a multi-purpose database system primarily designed to store and provide access to three-dimensional structures of biological molecules including theoretical models.
Results: A dictionary defining data format and structure for three-dimensional models of biological molecules (MDB dictionary) was developed. The dictionary was written using universal, standardized data description language. This language can be applied to describe data with no restrictions on their origin or type, including metadata. Thus both the data definitions (format) and database descriptions are created using the uniform language and processed with universal software. A database and data design technique that allowed use of dictionaries to automatically construct relational databases was developed. This technique was employed to construct the MDB database system. Data design developed and applied in the MDB project makes it possible to carry out data curation utilizing the database engine to identify errors. It also allows storage and query of data at different levels of consistency with the standard format specifications, i.e. both the correctly formatted data, and data that requires further curation.
Availability: The MDB dictionary is available at http://www.gwer.ch/proteinstructure/mdb and as part of the PDB resources at http://pdb.rutgers.edu/mmcif/.
Contact: aaa75196@gsk.com; em96794@gsk.com
* A.A.A. and E.M. are joint first authors.
1 To whom correspondence should be addressed.
Virtual PCR
Authors: Lexa M. , Horak J. , Brzobohaty B. 
Published: July 2002

Abstract
Summary: We present an algorithm that uses public sequence data to predict PCR products. The algorithm is implemented as a CGI script. Output is compared to real-world PCR.
Availability: Perl code and instructions for installation are freely available over the internet at http://www.sci.muni.cz/LMFR/vpcr.html
Contact: m-lexa@sci.muni.cz
* To whom correspondence should be addressed.
COMBOSA3D: combining sequence alignments with three-dimensional

structures
Authors: Stothard P. M. 
Published: July 2002

Abstract
Summary: COMBOSA3D is a program that allows sequence conservation to be viewed in its proper three-dimensional environment. It superimposes sequence alignment information onto a protein structure using a customizable color scheme, which is also applied to a textual sequence alignment for reference.
Availability: The program can be tested at http://www.bioinformatics.org/combosa3d/, and the source code is freely available.
Contact: stothard@ualberta.ca
Supplementary information: Additional COMBOSA3D documentation is available at the above URL.
RCNPRED: prediction of the residue co-ordination numbers in

proteins
Authors: Fariselli Piero , Casadio Rita 
Published: July 2002

Abstract
Summary: The RCNPRED server implements a neural network-based method to predict the co-ordination numbers of residues starting from the protein sequence. Using evolutionary information as input, RCNPRED predicts the residue states of the proteins in the database with 69% accuracy and scores 12 percentage points higher than a simple statistical method. Moreover the server implements a neural network to predict the relative solvent accessibility of each residue. A protein sequence can be directly submitted to RCNPRED: residue co-ordination numbers and solvent accessibility for each chain are returned via e-mail.
Availability: Freely available to non-commercial users at http://prion.biocomp.unibo.it/rcnpred.html
Contact: casadio@alma.unibo.it; piero@lipid.biocomp.unibo.it
* To whom the correspondence should be addressed.