bluuebunny/crossref_metadata_2025 huggingface dataset:
Allergic Eosinophil-rich Inflammation Develops in Lungs and Airways of B Cell–deficient Mice
Authors: Korsgren Magnus , ält Jonas S. Erjef , Korsgren Olle , Sundler Frank , Persson Carl G.A.
Published: July 2002

Immunoglobulins (Ig), particularly IgE, are believed to be crucially involved in the pathogenesis of asthma and, equally, in allergic models of the disease. To validate this paradigm we examined homozygous mutant C57BL/6 mice, which are B cell deficient, lacking all Ig. Mice were immunized intraperitoneally with 10 μg ovalbumin (OVA) plus alum, followed by daily (day 14–20) 30 min exposures to OVA aerosol (OVA/OVA group). Three control groups were run: OVA intraperitoneally plus saline (SAL) aerosol (OVA/SAL group); saline intraperitoneally plus saline aerosol; saline intraperitoneally plus OVA aerosol (n = 6–7). Lung and large airway tissues obtained 24 h after the last OVA or SAL exposure were examined by light microscopy and transmission electron microscopy (TEM). The Ig-deficient mice receiving OVA/ OVA treatment had swollen and discolored lungs and exhibited marked eosinophilia both in large airway subepithelial tissue (49.2 ± 12.0 cells/mm basement membrane [BM] versus OVA/ SAL control 1.2 ± 0.3 cells/mm BM; P <0.001), and perivascularly and peribronchially in the lung (49.3 ± 9.0 cells/unit area versus OVA/SAL control 2.6 ± 0.6 cells/unit area; P <0.001). The eosinophilia extended to the regional lymph nodes. TEM confirmed the subepithelial and perivascular localization of eosinophils. Mucus cells in large airway epithelium increased from 1.5 ± 0.8 (OVA/SAL mice) to 39.5 ± 5.7 cells/mm BM in OVA/OVA treated mice (P <0.001). OVA/SAL mice never differed from the other control groups. Corresponding experiments in wild-type mice (n = 6–7 in each group) showed qualitatively similar but less pronounced eosinophil and mucus cell changes. Macrophages and CD4+ T cells increased in lungs of all OVA/OVA-treated mice. Mast cell number did not differ but degranulation was detected only in OVA/OVA-treated wild-type mice. Immunization to OVA followed by OVA challenges thus cause eosinophil-rich inflammation in airways and lungs of mice without involvement of B cells and Ig.
Impaired Plasma Membrane Targeting of Grb2–Murine Son of Sevenless (mSOS) Complex and Differential Activation of the Fyn–T Cell Receptor (TCR)-ζ–Cbl Pathway Mediate T Cell Hyporesponsiveness in Autoimmune Nonobese Diabetic Mice
Authors: Salojin Konstantin , Zhang Jian , Cameron Mark , Gill Bruce , Arreaza Guillermo , Ochi Atsuo , Delovitch Terry L.
Published: July 2002

Nonobese diabetic (NOD) mouse thymocytes are hyporesponsive to T cell antigen receptor (TCR)-mediated stimulation of proliferation, and this T cell hyporesponsiveness may be causal to the onset of autoimmune diabetes in NOD mice. We previously showed that TCR-induced NOD T cell hyporesponsiveness is associated with a block in Ras activation and defective signaling along the PKC/Ras/MAPK pathway. Here, we report that several sequential changes in TCR-proximal signaling events may mediate this block in Ras activation. We demonstrate that NOD T cell hyporesponsiveness is associated with the (a) enhanced TCR-β–associated Fyn kinase activity and the differential activation of the Fyn–TCR-ζ–Cbl pathway, which may account for the impaired recruitment of ZAP70 to membrane-bound TCR-ζ; (b) relative inability of the murine son of sevenless (mSOS) Ras GDP releasing factor activity to translocate from the cytoplasm to the plasma membrane; and (c) exclusion of mSOS and PLC-γ1 from the TCR-ζ–associated Grb2/pp36–38/ZAP70 signaling complex. Our data suggest that altered tyrosine phosphorylation and targeting of the Grb2/pp36–38/ZAP70 complex to the plasma membrane and cytoskeleton and the deficient association of mSOS with this Grb2-containing complex may block the downstream activation of Ras and Ras-mediated amplification of TCR/CD3-mediated signals in hyporesponsive NOD T cells. These findings implicate mSOS as an important mediator of downregulation of Ras signaling in hyporesponsive NOD T cells.
An Alternate Pathway for T Cell Development Supported by the Bone Marrow Microenvironment: Recapitulation of Thymic Maturation
Authors: García-Ojeda Marcos E. , Dejbakhsh-Jones Sussan , Weissman Irving L. , Strober Samuel
Published: July 2002

In the principal pathway of α/β T cell maturation, T cell precursors from the bone marrow migrate to the thymus and proceed through several well-characterized developmental stages into mature CD4+ and CD8+ T cells. This study demonstrates an alternative pathway in which the bone marrow microenvironment also supports the differentiation of T cell precursors into CD4+ and CD8+ T cells. The marrow pathway recapitulates developmental stages of thymic maturation including a CD4+CD8+ intermediary cell and positive and negative selection, and is strongly inhibited by the presence of mature T cells. The contribution of the marrow pathway in vivo requires further study in mice with normal and deficient thymic or immune function.
Antagonist Peptide Selects Thymocytes Expressing a Class II Major Histocompatibility Complex–restricted T Cell Receptor into the CD8 Lineage
Authors: Volkmann Ariane , Barthlott Thomas , Weiss Siegfried , Frank Ronald , Stockinger Brigitta
Published: July 2002

CD4/CD8 lineage decision is an important event during T cell maturation in the thymus. CD8 T cell differentiation usually requires corecognition of major histocompatibility complex (MHC) class I by the T cell receptor (TCR) and CD8, whereas CD4 T cells differentiate as a consequence of MHC class II recognition by the TCR and CD4. The involvement of specific peptides in the selection of T cells expressing a particular TCR could be demonstrated so far for the CD8 lineage only. We used mice transgenic for an MHC class II-restricted TCR to investigate the role of antagonistic peptides in CD4 T cell differentiation. Interestingly, antagonists blocked the development of CD4+ cells that normally differentiate in thymus organ culture from those mice, and they induced the generation of CD8+ cells in thymus organ culture from mice impaired in CD4+ cell development (invariant chain–deficient mice). These results are in line with recent observations that antagonistic signals direct differentiation into the CD8 lineage, regardless of MHC specificity.
Premature Expression of T Cell Receptor (Tcr)αβ Suppresses Tcrγδ Gene Rearrangement but Permits Development of γδ Lineage T Cells
Authors: Terrence Kathleen , Pavlovich Christian P. , Matechak Errin O. , Fowlkes B.J.
Published: July 2002

The T cell receptor (TCR)γδ and the pre-TCR promote survival and maturation of early thymocyte precursors. Whether these receptors also influence γδ versus αβ lineage determination is less clear. We show here that TCRγδ gene rearrangements are suppressed in TCRαβ transgenic mice when the TCRαβ is expressed early in T cell development. This situation offers the opportunity to examine the outcome of γδ versus αβ T lineage commitment when only the TCRαβ is expressed. We find that precursor thymocytes expressing TCRαβ not only mature in the αβ pathway as expected, but also as CD4−CD8− T cells with properties of γδ lineage cells. In TCRαβ transgenic mice, in which the transgenic receptor is expressed relatively late, TCRγδ rearrangements occur normally such that TCRαβ+CD4−CD8− cells co-express TCRγδ. The results support the notion that TCRαβ can substitute for TCRγδ to permit a γδ lineage choice and maturation in the γδ lineage. The findings could fit a model in which lineage commitment is determined before or independent of TCR gene rearrangement. However, these results could be compatible with a model in which distinct signals bias lineage choice and these signaling differences are not absolute or intrinsic to the specific TCR structure.
Structure–Function Relationship of Cytokine Induction by Lipoteichoic Acid fromStaphylococcus aureus
Authors: Morath Siegfried , Geyer Armin , Hartung Thomas
Published: July 2002

Lipoteichoic acids (LTAs) have been proposed as putative Gram-positive immunostimulatory counterparts to Gram-negative lipopolysaccharides. However, LTA from Staphylococcus aureus, the clinically most frequent Gram-positive pathogen, was inactive after purification. Here, a novel isolation procedure to prepare pure (>99%) biologically active LTA, allowing the first structural analysis by nuclear magnetic resonance and mass spectrometry, is described. A comparison with LTA purified by standard techniques revealed that alanine substituents are lost during standard purification, resulting in attenuated cytokine induction activity. In line with this finding, hydrolysis of alanine substituents of active LTA decimated cytokine induction. LTA represents a major immunostimulatory component of S. aureus.
Anuria, Omphalocele, and Perinatal Lethality in Mice Lacking the Cd34-Related Protein Podocalyxin
Authors: Doyonnas Regis , Kershaw David B. , Duhme Christian , Merkens Helen , Chelliah Shierley , Graf Thomas , McNagny Kelly M.
Published: July 2002

Podocalyxin is a CD34-related sialomucin that is expressed at high levels by podocytes, and also by mesothelial cells, vascular endothelia, platelets, and hematopoietic stem cells. To elucidate the function of podocalyxin, we generated podocalyxin-deficient (podxl−/−) mice by homologous recombination. Null mice exhibit profound defects in kidney development and die within 24 hours of birth with anuric renal failure. Although podocytes are present in the glomeruli of the podxl−/− mice, they fail to form foot processes and slit diaphragms and instead exhibit cell–cell junctional complexes (tight and adherens junctions). The corresponding reduction in permeable, glomerular filtration surface area presumably leads to the observed block in urine production. In addition, podxl−/− mice frequently display herniation of the gut (omphalocele), suggesting that podocalyxin may be required for retraction of the gut from the umbilical cord during development. Hematopoietic and vascular endothelial cells develop normally in the podocalyxin-deficient mice, possibly through functional compensation by other sialomucins (such as CD34). Our results provide the first example of an essential role for a sialomucin in development and suggest that defects in podocalyxin could play a role in podocyte dysfunction in renal failure and omphalocele in humans.
Interference with Immunoglobulin (Ig)α Immunoreceptor Tyrosine–Based Activation Motif (Itam) Phosphorylation Modulates or Blocks B Cell Development, Depending on the Availability of an Igβ Cytoplasmic Tail
Authors: Kraus Manfred , Pao Lily I. , Reichlin Amy , Hu Yun , Canono Beth , Cambier John C. , Nussenzweig Michel C. , Rajewsky Klaus
Published: July 2002

To determine the function of immunoglobulin (Ig)α immunoreceptor tyrosine–based activation motif (ITAM) phosphorylation, we generated mice in which Igα ITAM tyrosines were replaced by phenylalanines (IgαFF/FF). IgαFF/FFmice had a specific reduction of B1 and marginal zone B cells, whereas B2 cell development appeared to be normal, except that λ1 light chain usage was increased. The mutants responded less efficiently to T cell–dependent antigens, whereas T cell–independent responses were unaffected. Upon B cell receptor ligation, the cells exhibited heightened calcium flux, weaker Lyn and Syk tyrosine phosphorylation, and phosphorylation of Igα non-ITAM tyrosines. Strikingly, when the Igα ITAM mutation was combined with a truncation of Igβ, B cell development was completely blocked at the pro-B cell stage, indicating a crucial role of ITAM phosphorylation in B cell development.
Effector Contributions to Gβγ-mediated Signaling as Revealed by Muscarinic Potassium Channel Gating
Authors: Ivanova-Nikolova Tatyana T. , Breitwieser Gerda E.
Published: July 2002

Receptor-mediated activation of heterotrimeric G proteins leading to dissociation of the Gα subunit from Gβγ is a highly conserved signaling strategy used by numerous extracellular stimuli. Although Gβγ subunits regulate a variety of effectors, including kinases, cyclases, phospholipases, and ion channels (Clapham, D.E., and E.J. Neer. 1993. Nature (Lond.). 365:403–406), few tools exist for probing instantaneous Gβγ-effector interactions, and little is known about the kinetic contributions of effectors to the signaling process. In this study, we used the atrial muscarinic K+ channel, which is activated by direct interactions with Gβγ subunits (Logothetis, D.E., Y. Kurachi, J. Galper, E.J. Neer, and D.E. Clap. 1987. Nature (Lond.). 325:321–326; Wickman, K., J.A. Iniguez-Liuhi, P.A. Davenport, R. Taussig, G.B. Krapivinsky, M.E. Linder, A.G. Gilman, and D.E. Clapham. 1994. Nature (Lond.). 366: 654–663; Huang, C.-L., P.A. Slesinger, P.J. Casey, Y.N. Jan, and L.Y. Jan. 1995. Neuron. 15:1133–1143), as a sensitive reporter of the dynamics of Gβγ-effector interactions. Muscarinic K+ channels exhibit bursting behavior upon G protein activation, shifting between three distinct functional modes, characterized by the frequency of channel openings during individual bursts. Acetylcholine concentration (and by inference, the concentration of activated Gβγ) controls the fraction of time spent in each mode without changing either the burst duration or channel gating within individual modes. The picture which emerges is of a Gβγ effector with allosteric regulation and an intrinsic “off” switch which serves to limit its own activation. These two features combine to establish exquisite channel sensitivity to changes in Gβγ concentration, and may be indicative of the factors regulating other Gβγ-modulated effectors.
Onset of Feedback Reactions Underlying Vertebrate Rod Photoreceptor Light Adaptation
Authors: Calvert Peter D. , Ho Theresa W. , LeFebvre Yvette M. , Arshavsky Vadim Y.
Published: July 2002

Light adaptation in vertebrate photoreceptors is thought to be mediated through a number of biochemical feedback reactions that reduce the sensitivity of the photoreceptor and accelerate the kinetics of the photoresponse. Ca2+ plays a major role in this process by regulating several components of the phototransduction cascade. Guanylate cyclase and rhodopsin kinase are suggested to be the major sites regulated by Ca2+. Recently, it was proposed that cGMP may be another messenger of light adaptation since it is able to regulate the rate of transducin GTPase and thus the lifetime of activated cGMP phosphodiesterase. Here we report measurements of the rates at which the changes in Ca2+ and cGMP are followed by the changes in the rates of corresponding enzymatic reactions in frog rod outer segments. Our data indicate that there is a temporal hierarchy among reactions that underlie light adaptation. Guanylate cyclase activity and rhodopsin phosphorylation respond to changes in Ca2+ very rapidly, on a subsecond time scale. This enables them to accelerate the falling phase of the flash response and to modulate flash sensitivity during continuous illumination. To the contrary, the acceleration of transducin GTPase, even after significant reduction in cGMP, occurs over several tens of seconds. It is substantially delayed by the slow dissociation of cGMP from the noncatalytic sites for cGMP binding located on cGMP phosphodiesterase. Therefore, cGMP-dependent regulation of transducin GTPase is likely to occur only during prolonged bright illumination.
Model of Sarcomeric Ca2+ Movements, Including ATP Ca2+ Binding and Diffusion, during Activation of Frog Skeletal Muscle
Authors: Baylor S.M. , Hollingworth S.
Published: July 2002

Cannell and Allen (1984. Biophys. J. 45:913–925) introduced the use of a multi-compartment model to estimate the time course of spread of calcium ions (Ca2+) within a half sarcomere of a frog skeletal muscle fiber activated by an action potential. Under the assumption that the sites of sarcoplasmic reticulum (SR) Ca2+ release are located radially around each myofibril at the Z line, their model calculated the spread of released Ca2+ both along and into the half sarcomere. During diffusion, Ca2+ was assumed to react with metal-binding sites on parvalbumin (a diffusible Ca2+- and Mg2+-binding protein) as well as with fixed sites on troponin. We have developed a similar model, but with several modifications that reflect current knowledge of the myoplasmic environment and SR Ca2+ release. We use a myoplasmic diffusion constant for free Ca2+ that is twofold smaller and an SR Ca2+ release function in response to an action potential that is threefold briefer than used previously. Additionally, our model includes the effects of Ca2+ and Mg2+ binding by adenosine 5′-triphosphate (ATP) and the diffusion of Ca2+-bound ATP (CaATP). Under the assumption that the total myoplasmic concentration of ATP is 8 mM and that the amplitude of SR Ca2+ release is sufficient to drive the peak change in free [Ca2+] (Δ[Ca2+]) to 18 μM (the approximate spatially averaged value that is observed experimentally), our model calculates that (a) the spatially averaged peak increase in [CaATP] is 64 μM; (b) the peak saturation of troponin with Ca2+ is high along the entire thin filament; and (c) the half-width of Δ[Ca2+] is consistent with that observed experimentally. Without ATP, the calculated half-width of spatially averaged Δ[Ca2+] is abnormally brief, and troponin saturation away from the release sites is markedly reduced. We conclude that Ca2+ binding by ATP and diffusion of CaATP make important contributions to the determination of the amplitude and the time course of Δ[Ca2+].
Mechanism of Inhibition of Cyclic Nucleotide–Gated Ion Channels by Diacylglycerol
Authors: Crary Jennifer I. , Dean Dylan M. , Nguitragool Wang , Kurshan Peri T. , Zimmerman Anita L.
Published: July 2002

Cyclic nucleotide–gated (CNG) channels are critical components in the visual and olfactory signal transduction pathways, and they primarily gate in response to changes in the cytoplasmic concentration of cyclic nucleotides. We previously found that the ability of the native rod CNG channel to be opened by cGMP was markedly inhibited by analogues of diacylglycerol (DAG) without a phosphorylation reaction (Gordon, S.E., J. Downing-Park, B. Tam, and A.L. Zimmerman. 1995. Biophys. J. 69:409–417). Here, we have studied cloned bovine rod and rat olfactory CNG channels expressed in Xenopus oocytes, and have determined that they are differentially inhibited by DAG. At saturating [cGMP], DAG inhibition of homomultimeric (α subunit only) rod channels was similar to that of the native rod CNG channel, but DAG was much less effective at inhibiting the homomultimeric olfactory channel, producing only partial inhibition even at high [DAG]. However, at low open probability (Po), both channels were more sensitive to DAG, suggesting that DAG is a closed state inhibitor. The Hill coefficients for DAG inhibition were often greater than one, suggesting that more than one DAG molecule is required for effective inhibition of a channel. In single-channel recordings, DAG decreased the Po but not the single-channel conductance. Results with chimeras of rod and olfactory channels suggest that the differences in DAG inhibition correlate more with differences in the transmembrane segments and their attached loops than with differences in the amino and carboxyl termini. Our results are consistent with a model in which multiple DAG molecules stabilize the closed state(s) of a CNG channel by binding directly to the channel and/or by altering bilayer–channel interactions. We speculate that if DAG interacts directly with the channel, it may insert into a putative hydrophobic crevice among the transmembrane domains of each subunit or at the hydrophobic interface between the channel and the bilayer.
K Depletion Enhances the Extracellular Ca2+-Induced Inhibition of the Apical K Channels in the Mtal of Rat Kidney
Authors: Gu Rui-Min , Wei Yuan , Jiang Ho-Lin , Lin Dao-Hong , Sterling Hyacinth , Bloom Peter , Balazy Micheal , Wang Wen-Hui
Published: July 2002

We have shown previously that raising extracellular Ca2+ inhibited the apical 70-pS K channel in the thick ascending limb (TAL; Wang, W.H., M. Lu, and S.C. Hebert. 1996. Am. J. Physiol. 270:C103–C111). We now used the patch-clamp technique to study the effect of increasing the extracellular Ca2+ on the 70-pS K channel in the mTAL from rats on a different K diet. Increasing the extracellular Ca2+ from 10 μM to 0.5, 1, and to 1.5 mM in the mTAL from rats on a K-deficient (KD) diet inhibited the channel activity by 30, 65, and 90%, respectively. In contrast, raising the extracellular Ca2+ to 1.5 mM had no significant effect on channel activity in the mTAL from animals on a high K (HK) diet and further increasing the extracellular Ca2+ to 2.5, 3.5, and 5.5 mM decreased the channel activity by 29, 55, and 90%, respectively. Inhibition of the cytochrome P450 monooxygenase completely abolished the effect of the extracellular Ca2+ on channel activity in the mTAL from rats on a different K diet. In contrast, blocking cyclooxygenase did not significantly alter the responsiveness of the 70-pS K channel to the extracellular Ca2+. Moreover, addition of sodium nitropruside, a nitric oxide (NO) donor, not only increased the channel activity, but also blunted the inhibitory effect of the extracellular Ca2+ on the 70-pS K channel and decreased 20-hydroxyeicosatetraenoic acid (20-HETE) concentration in the mTAL from rats on a KD diet. In contrast, inhibiting NOS with L-NAME enhanced the inhibitory effect of the extracellular Ca2+ on the channel activity and increased 20-HETE concentration in the mTAL from rats on a high K diet. Western blot has further shown that the expression of inducible NO synthase (iNOS) is significantly higher in the renal medulla from rats on an HK diet than that on a KD diet. Also, addition of S-nitroso-N-acetylpenicillamine abolished the inhibitory effect of arachidonic acid on channel activity in the mTAL, whereas it did not block the inhibitory effect of 20-HETE. We conclude that a low dietary K intake increases the sensitivity of the 70-pS K channel to the extracellular Ca2+, and that a decrease in NOS activity is involved in enhancing the inhibitory effect of the extracellular Ca2+ on channel activity in the mTAL during K depletion.
Unbundled journals: trying to predict the future
Authors: Berin Andrew
Published: July 2002

The variety of publishing models and ways to publish online suggests that there is plenty of room for varying viewpoints. However, there is also a consensus that online publishing will come to mean online access to articles – the fundamental whole unit of information in academic publishing. This article's main thrust is to catalogue the variety of ways to access journals online, where no subscription to the print edition is needed. If one then looks at the current array of unbundled products from the vantage point of single‐article access, one may predict which of today's online‐only offerings will remain viable into the future.
Jacobi sums and new families of irreducible polynomials of Gaussian periods
Authors: Thaine F.
Published: July 2002

Let

m
>
2

m> 2

,

ζ
m

\zeta _m

an

m
m

-th primitive root of 1,

q
≡
1

q\equiv 1

mod

2
m

2m

a prime number,

s
=

s

q

s=s_{q}

a primitive root modulo

q
q

and

f
=

f

q

=
(
q
−
1
)

/

m

f=f_{q}=(q-1)/m

. We study the Jacobi sums
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="upper J Subscript a comma b Baseline equals minus sigma-summation Underscript k equals 2 Overscript q minus 1 Endscripts zeta Subscript m Superscript a ind Super Subscript s Superscript left-parenthesis k right-parenthesis plus b ind Super Subscript s Superscript left-parenthesis 1 minus k right-parenthesis">

J

a
,
b

=
−

∑

k
=
2

q
−
1

ζ
m

a

ind

s

(
k
)
+
b

ind

s

(
1
−
k
)

J_{a,b}=-\sum _{k=2}^{q-1}\zeta _m ^{\, a\, \text {ind}_{s}(k)+b\, \text {ind}_{s}(1-k)}

,

0
≤
a
,
b
≤
m
−
1

0\leq a, b\leq m-1

, where

ind

s

(
k
)

\text {ind}_{s}(k)

is the least nonnegative integer such that

s

ind

s

(
k
)

≡
k

s^{\, \text {ind}_{s}(k)}\equiv k

mod

q
q

. We exhibit a set of properties that characterize these sums, some congruences they satisfy, and a MAPLE program to calculate them. Then we use those results to show how one can construct families

P

q

(
x
)

P_{q}(x)

,

q
∈

P

q\in \mathcal {P}

, of irreducible polynomials of Gaussian periods,

η

i

=

∑

j
=
0

f
−
1

ζ
q

s

i
+
m
j

\eta _{i}=\sum _{j=0}^{f-1}\zeta _q^{s^{i+mj}}

, of degree

m
m

, where

P

\mathcal {P}

is a suitable set of primes

≡
1

\equiv 1

mod

2
m

2m

. We exhibit examples of such families for several small values of

m
m

, and give a MAPLE program to construct more of them.
Composition constants for raising the orders of unconventional schemes for ordinary differential equations
Authors: Kahan William , Li Ren-Cang
Published: July 2002

Many models of physical and chemical processes give rise to ordinary differential equations with special structural properties that go unexploited by general-purpose software designed to solve numerically a wide range of differential equations. If those properties are to be exploited fully for the sake of better numerical stability, accuracy and/or speed, the differential equations may have to be solved by unconventional methods. This short paper is to publish composition constants obtained by the authors to increase efficiency of a family of mostly unconventional methods, called reflexive.
Gauss periods: orders and cryptographical applications
Authors: Gao Shuhong , von zur Gathen Joachim , Panario Daniel
Published: July 2002

Experimental results on the multiplicative orders of Gauss periods in finite fields are presented. These results indicate that Gauss periods have high order and are often primitive (self-dual) normal elements in finite fields. It is shown that Gauss periods can be exponentiated in quadratic time. An application is an efficient pseudorandom bit generator.
The Spindle Pole Body Protein Cdc11p Links Sid4p to the Fission Yeast Septation Initiation Network
Authors: Tomlin Gregory C. , Morrell Jennifer L. , Gould Kathleen L.
Published: July 2002

The Schizosaccharomyces pombe septation initiation network (SIN) signals the onset of cell division from the spindle pole body (SPB) and is regulated by the small GTPase Spg1p. The localization of SIN components including Spg1p to the SPB is required for cytokinesis and is dependent on Sid4p, a constitutive resident of SPBs. However, a direct interaction between Sid4p and other members of the SIN has not been detected. To understand how Sid4p is linked to other SIN components, we have begun to characterize an S. pombe homolog of the Saccharomyces cerevisiaeSPB protein Nud1p. We have determined that this S. pombeNud1p homolog corresponds to Cdc11p, a previously uncharacterized SIN element. We report that Cdc11p is present constitutively at SPBs and that its function appears to be required for the localization of all other SIN components to SPBs with the exception of Sid4p. The Cdc11p C terminus localizes the protein to SPBs in a Sid4p-dependent manner, and we demonstrate a direct Cdc11p-Sid4p interaction. The N-terminus of Cdc11p is required for Spg1p binding to SPBs. Our studies indicate that Cdc11p provides a physical link between Sid4p and the Spg1p signaling pathway.
HICLAS: a taxonomic database system for displaying and comparing biological classification and phylogenetic trees.
Authors: Zhong Y , Luo Y , Pramanik S , Beaman J H
Published: July 2002

MOTIVATION: Numerous database management systems have been developed for processing various taxonomic data bases on biological classification or phylogenetic information. In this paper, we present an integrated system to deal with interacting classifications and phylogenies concerning particular taxonomic groups. RESULTS: An information-theoretic view (taxon view) has been applied to capture taxonomic concepts as taxonomic data entities. A data model which is suitable for supporting semantically interacting dynamic views of hierarchic classifications and a query method for interacting classifications have been developed. The concept of taxonomic view and the data model can also be expanded to carry phylogenetic information in phylogenetic trees. We have designed a prototype taxonomic database system called HICLAS (HIerarchical CLAssification System) based on the concept of taxon view, and the data models and query methods have been designed and implemented. This system can be effectively used in the taxonomic revisionary process, especially when databases are being constructed by specialists in particular groups, and the system can be used to compare classifications and phylogenetic trees. AVAILABILITY: Freely available at the WWW URL: http://aims.cps.msu.edu/hiclas/ CONTACT: pramanik@cps.msu.edu; lotus@wipm.whcnc.ac.cn
TargetFinder: searching annotated sequence databases for target genes of transcription factors.
Authors: Lavorgna G , Guffanti A , Borsani G , Ballabio A , Boncinelli E
Published: July 2002

SUMMARY: TargetFinder is a new software tool to search a database of annotated sequences for transcription factor binding sites located in context with other important transcription regulatory signals and regions, like the TATA element, the promoter, and so on, thereby greatly reducing the background usually associated with this kind of search. AVAILABILITY: The TargetFinder Web service is available at http://hercules.tigem.it/TargetFinder.html CONTACT: giovanni.lavorgna@hsr.it
Optimizing reduced-space sequence analysis
Authors: Wheeler Raymond , Hughey Richard
Published: July 2002

Motivation: Dynamic programming is the core algorithm of sequence comparison, alignment and linear hidden Markov model (HMM) training. For a pair of sequence lengths m and n, the problem can be solved readily in O(mn)time and O(mn)space. The checkpoint algorithm introduced by Grice et al. (CABIOS , 13, 45–53, 1997) runs in O(Lmn)time and O(LmL√n)space, where Lis a positive integer determined by m, n, and the amount of available workspace. The algorithm is appropriate for many string comparison problems, including all-paths and single-best-path hidden Markov model training, and is readily parallelizable. The checkpoint algorithm has a diagonal version that can solve the single-best-path alignment problem in O(mn)time and O(m + n)space.

Results: In this work, we improve performance by analyzing optimal checkpoint placement. The improved row checkpoint algorithm performs up to one half the computation of the original algorithm. The improved diagonal checkpoint algorithm performs up to 35% fewer computational steps than the original. We modified the SAM hidden Markov modeling package to use the improved row checkpoint algorithm. For a fixed sequence length, the new version is up to 33% faster for all-paths and 56% faster for single-best-path HMM training, depending on sequence length and allocated memory. Over a typical set of protein sequence lengths, the improvement is ~10%.

Availability: The SAM hidden Markov modeling package is freely available for academic use from http://www.cse.ucsc.edu/research/compbio/sam.html. The C++code used to find optimal checkpoint placements is available from http://www.cse.ucsc.edu/research/kestrel.

Contact: rph@cse.ucsc.edu

2 Current address: Neomorphic, 2612 8th St., Berkeley, CA 94710, USA.

3 To whom correspondence may be addressed.
PROF_ PAT 1.3: Updated database of patterns used to detect
local similarities
Authors: Bachinsky A. G. , Frolov A. S. , Naumochkin A. N. , Nizolenko L. Ph. , Yarigin A. A.
Published: July 2002

Motivation: When analysing novel protein sequences, it is now essential to extend search strategies to include a range of ‘secondary’ databases. Pattern databases have become vital tools for identifying distant relationships in sequences, and hence for predicting protein function and structure. The main drawback of such methods is the relatively small representation of proteins in trial samples at the time of their construction. Therefore, a negative result of an amino acid sequence comparison with such a databank forces a researcher to search for similarities in the original protein banks. We developed a database of patterns constructed for groups of related proteins with maximum representation of amino acid sequences of SWISS-PROT in the groups.

Results: Software tools and a new method have been designed to construct patterns of protein families. By using such method, a new version of databank of protein family patterns, PROF_ PAT 1.3, is produced. This bank is based on SWISS-PROT (r1.38) and TrEMBL (r1.11), and contains patterns of more than 13 000 groups of related proteins in a format similar to that of the PROSITE. Motifs of patterns, which had the minimum level of probability to be found in random sequences, were selected. Flexible fast search program accompanies the bank. The researcher can specify a similarity matrix (the type PAM, BLOSUM and other). Variable levels of similarity can be set (permitting search strategies ranging from exact matches to increasing levels of ‘fuzziness’).

Availability: The Internet address for comparing sequences with the bank is: http://wwwmgs.bionet.nsc.ru/mgs/programs/prof_pat/. The local version of the bank and search programs (approximately 50 Mb) is available via ftp: ftp://ftp.bionet.nsc.ru/pub/biology/vector/prof_pat/, and ftp://ftp.ebi.ac.uk/pub/databases/prof_pat/. Another appropriate way for its external use is to mail amino acid sequences to bachin@vector.nsc.ru for comparison with PROF_ PAT 1.3.

Contact: bachin@vector.nsc.ru
Clustalnet: the joining of Clustal and CORBA
Authors: Campagne F.
Published: July 2002

Motivation: Performing sequence alignment operations from a different program than the original sequence alignment code, and/or through a network connection, is often required. Interactive alignment editors and large-scale biological data analysis are common examples where such a flexibility is important. Interoperability between the alignment engine and the client should be obtained regardless of the architectures and programming languages of the server and client.

Results: Clustalnet, a Clustal alignment CORBA server is described, which was developed on the basis of Clustalw. This server brings the robustness of the algorithms and implementations of Clustal to a new level of reuse. A Clustalnet server object can be accessed from a program, transparently through the network. We present interfaces to perform the alignment operations and to control these operations via immutable contexts. The interfaces that select the contexts do not depend on the nature of the operation to be performed, making the design modular. The IDL interfaces presented here are not specific to Clustal and can be implemented on top of different sequence alignment algorithm implementations.

Availability: This implementation is freely available for non-commercial use for a variety of architectures. Clustalnet can be downloaded from http://transport.physbio.mssm.edu/clustalnet.

Contact: campagne@inka.mssm.edu

Supplementary Information: Alignment encoding description and full IDL in the documentation, with the distribution.
Digital reviews in molecular biology: approaches to structured
digital publication
Authors: Steffen D. L. , Levine A. E. , Yarus S. , Baasiri R. A. , Wheeler D. A.
Published: July 2002

Motivation: It is widely appreciated that it is no longer possible for biomedical research scientists to keep up with as much of what is published in their field as they ought. One solution to this problem is to increase the efficiency of information use by moving away from the classical browsing model for scientific information dissemination towards an information on demand model which would allow researchers to access information quickly and efficiently only as they need it. The most common approach to this goal has been to use information retrieval technology to improve access to text databases of biomedical information. We are interested in exploring an alternative; encoding this information for storage in structured databases for efficient retrieval.

Results: Two small databases described here are test beds for development of structured digital publication software; the Tumor Gene Database, containing information about genes which are the sites for cancer-causing mutations, and the Mammary Transgene Database, containing information about expression of transgenes in agriculturally important animals. Both have been successfully searched by users and edited by curators via the World Wide Web.

Availability: These databases can be accessed at http://www.tumor-gene.org/drmb.html

Contact: For further information on these databases, contact the individual database owners, listed on the page above, or David Steffen, Biomedical Computing, Inc., 6626 Westchester, Houston, Texas 77005, steffen@biomedcomp.com
Combining frequency and positional information to predict
transcription factor binding sites
Authors: Kiełbasa Szymon
   M. , Korbel Jan O. , Beule Dieter , Schuchhardt Johannes , Herzel Hanspeter
Published: July 2002

Motivation: Even though a number of genome projects have been finished on the sequence level, still only a small proportion of DNA regulatory elements have been identified. Growing amounts of gene expression data provide the possibility of finding coregulated genes by clustering methods. By analysis of the promoter regions of those genes, rather weak signals of transcription factor binding sites may be detected.

Results: We introduce the new algorithm ITB, an Integrated Tool for Box finding, which combines frequency and positional information to predict transcription factor binding sites in upstream regions of coregulated genes. Motifs are extracted by exhaustive analysis of regular expression-like patterns and by estimating probabilities of positional clusters of motifs. ITB detects consensus sequences of experimentally verified transcription factor binding sites of the yeast Saccharomyces cerevisiae. Moreover, a number of new binding site candidates with significant scores are predicted. Besides applying ITB on yeast upstream regions, the program is run on human promoter sequences.

Availability: ITB is available upon request.

Contact: s.kielbasa@itb.biologie.hu-berlin.de

* Both authors contributed equally.
Using clusters of computers for large QU-GENE simulation

experiments
Authors: Micallef Kevin P. , Cooper Mark , Podlich Dean W.
Published: July 2002

Summary: The QU-GENE Computing Cluster (QCC) is a hardware and software solution to the automation and speedup of large QU-GENE (QUantitative GENEtics) simulation experiments that are designed to examine the properties of genetic models, particularly those that involve factorial combinations of treatment levels. QCC automates the management of the distribution of components of the simulation experiments among the networked single-processor computers to achieve the speedup.

Contact: k.micallef@mailbox.uq.edu.au

Supplementary information: http://pig.ag.uq.edu.au/qu-gene/cluster.htm

* To whom correspondence should be addressed.
Dynamic simulation of the human red blood cell metabolic

network
Authors: Jamshidi Neema , Edwards Jeremy S. , Fahland Tom , Church George M. , Palsson Bernhard O.
Published: July 2002

Summary: We have developed a Mathematica®application package to perform dynamic simulations of the red blood cell (RBC) metabolic network. The package relies on, and integrates, many years of mathematical modeling and biochemical work on red blood cell metabolism. The extensive data regarding the red blood cell metabolic network and the previous kinetic analysis of all the individual components makes the human RBC an ideal ‘model’ system for mathematical metabolic models. The Mathematica package can be used to understand the dynamics and regulatory characteristics of the red blood cell.

Availability: The Mathematica package and an example file can be downloaded from http://gcrg.ucsd.edu
ProDDO: a database of disordered proteins from the Protein Data

Bank (PDB)
Authors: Sim Kim Lan , Uchida Tomoyuki , Miyano Satoru
Published: July 2002

Summary: ProDDO represents a ‘pre-screened’ database that denotes disorder (or possible disorder) in proteins from the PDB.

Availability: ProDDO is available at http://bonsai.ims.u-tokyo.ac.jp/~klsim/database.html

Contact: klsim@plato.gws.uky.edu

* To whom correspondence should be addressed. Present address: Kentucky Center for Structural Biology, Department of Biochemistry, University of Kentucky, 800 Rose Street, Lexington, KY 40536-0298, USA.
ADAPTSITE: detecting natural selection at single amino acid

sites
Authors: Suzuki Yoshiyuki , Gojobori Takashi , Nei Masatoshi
Published: July 2002

Summary: ADAPTSITE is a program package for detecting natural selection at single amino acid sites, using a multiple alignment of protein-coding sequences for a given phylogenetic tree. The program infers ancestral codons at all interior nodes, and computes the total numbers of synonymous (cS) and nonsynonymous (cN) substitutions as well as the average numbers of synonymous (sS) and nonsynonymous (sN) sites for each codon site. The probabilities of occurrence of synonymous and nonsynonymous substitutions are approximated by sS / (sS + sN) and sN / (sS + sN), respectively. The null hypothesis of selective neutrality is tested for each codon site, assuming a binomial distribution for the probability of obtaining cS and cN.

Availability: ADAPTSITE is available free of charge at the World-Wide Web sites http://mep.bio.psu.edu/adaptivevol.html and http://www.cib.nig.ac.jp/dda/yossuzuk/welcome.html. The package includes the source code written in C, binary files for UNIX operating systems, manual, and example files.

Contact: yis1@psu.edu

* To whom correspondence should be addressed.
Generation of a database containing discordant intron positions
in eukaryotic genes (MIDB)
Authors: Sakharkar Meena K. , Tan Tin Wee , de Souza Sandro J.
Published: July 2002

Motivation: Intron sliding is the relocation of intron–exon boundaries over short distances and is often also referred to as intron slippage or intron migration or intron drift. We have generated a database containing discordant intron positions in homologous genes (MIDB—Mismatched Intron DataBase). Discordant intron positions are those that are either closely located in homologous genes (within a window of 10 nucleotides) or an intron position that is present in one gene but not in any of its homologs. The MIDB database aims at systematically collecting information about mismatched introns in the genes from GenBank and organizing it into a form useful for understanding the genomics and dynamics of introns thereby helping understand the evolution of genes.

Results: Intron displacement or sliding is critically important for explaining the present distribution of introns among orthologous and paralogous genes. MIDB allows examining of intron movements and allows mapping of intron positions from homologous proteins onto a single sequence. The database is of potential use for molecular biologists in general and for researchers who are interested in gene evolution and eukaryotic gene structure. Partial analysis of this database allowed us to identify a few putative cases of intron sliding.

Availability: http://intron.bic.nus.edu.sg/midb/midb.html

Contact: meena@bic.nus.edu.sg

* To whom correspondence should be addressed.
Identification of characteristic oligonucleotides in the
bacterial 16S ribosomal RNA sequence dataset
Authors: Zhang Zhengdong , Willson Richard C. , Fox George E.
Published: July 2002

Motivation: The phylogenetic structure of the bacterial world has been intensively studied by comparing sequences of 16S ribosomal RNA (16S rRNA). This database of sequences is now widely used to design probes for the detection of specific bacteria or groups of bacteria one at a time. The success of such methods reflects the fact that there are local sequence segments that are highly characteristic of particular organisms or groups of organisms. It is not clear, however, the extent to which such signature sequences exist in the 16S rRNA dataset. A better understanding of the numbers and distribution of highly informative oligonucleotide sequences may facilitate the design of hybridization arrays that can characterize the phylogenetic position of an unknown organism or serve as the basis for the development of novel approaches for use in bacterial identification.

Results: A computer-based algorithm that characterizes the extent to which any individual oligonucleotide sequence in 16S rRNA is characteristic of any particular bacterial grouping was developed. A measure of signature quality, Qs, was formulated and subsequently calculated for every individual oligonucleotide sequence in the size range of 5–11 nucleotides and for 15mers with reference to each cluster and subcluster in a 929 organism representative phylogenetic tree. Subsequently, the perfect signature sequences were compared to the full set of 7322 sequences to see how common false positives were. The work completed here establishes beyond any doubt that highly characteristic oligonucleotides exist in the bacterial 16S rRNA sequence dataset in large numbers. Over 16000 15mers were identified that might be useful as signatures. Signature oligonucleotides are available for over 80% of the nodes in the representative tree.

Availability: The programs described herein are available at http://prion.bchs.uh.edu/16S_signatures/programs/. A preliminary database of signature sequences identified in this paper is available at: http://prion.bchs.uh.edu/16S_signatures/.

Contact: zzhang@bayou.uh.edu; fox@uh.edu

* To whom correspondence should be addressed.
PATRI—paternity inference using genetic data
Authors: Signorovitch J. , Nielsen R.
Published: July 2002

Summary: PATRI is a new application for paternity analysis using genetic data that accounts for the sampling fraction of potential fathers.

Availability: Executables are available at www.biom.cornell.edu/Homepages/Rasmus_Nielsen/

Contact: jes48@cornell.edu

* To whom correspondence should be addressed.
Microarray data warehouse allowing for inclusion of experiment
annotations in statistical analysis
Authors: Fellenberg Kurt , Hauser Nicole C. , Brors Benedikt , Hoheisel Jörg
   D. , Vingron Martin
Published: July 2002

Motivation: Microarray technology provides access to expression levels of thousands of genes at once, producing large amounts of data. These datasets are valuable only if they are annotated by sufficiently detailed experiment descriptions. However, in many databases a substantial number of these annotations is in free-text format and not readily accessible to computer-aided analysis.

Results: The Multi-Conditional Hybridization Intensity Processing System (M-CHIPS), a data warehousing concept, focuses on providing both structure and algorithms suitable for statistical analysis of a microarray database’s entire contents including the experiment annotations. It addresses the rapid growth of the amount of hybridization data, more detailed experimental descriptions, and new kinds of experiments in the future. We have developed a storage concept , a particular instance of which is an organism-specific database. Although these databases may contain different ontologies of experiment annotations, they share the same structure and therefore can be accessed by the very same statistical algorithms. Experiment ontologies have not yet reached their final shape, and standards are reduced to minimal conventions that do not yet warrant extensive description. An ontology-independent structure enables updates of annotation hierarchies during normal database operation without altering the structure.

Availability and supplementary information: http://www.dkfz.de/tbi/services/mchips

Contact: k.fellenberg@dkfz.de

* To whom correspondence should be addressed.

3 Present address: Max-Planck-Institute for Molecular Genetics, Ihnestr. 73, D-14195 Berlin, Germany.