bluuebunny/crossref_metadata_2025 huggingface dataset:
The transition from quantitative trait loci to diagnostic test in cattle and other livestock
Authors: Barendse W.
Published: August 2005

The efficient identification of the genes that influence quantitative traits requires: large sample sizes; the analysis of large numbers of polymorphisms in and around genes or surrogates for these; repeated testing in independent samples; the realisation that the inheritance patterns of quantitative trait loci will show the full range of effects found for genes that affect discrete traits; and choosing the appropriate genetic structure of the sample and the kind of DNA polymorphism for the different stages in the identification of the quantitative trait loci. The choice of trait is critical to the successful production of diagnostic tests. Since this is the most important single factor affecting whether a test will be commercialised, not only due to the economic importance of the trait, but whether there are easy, alternative methods to improve the trait that are cheaper to implement than a DNA test.
Development successes and issues for the future in deriving and applying selection indexes for beef breeding
Authors: Barwick S. A. , Henzell A. L.
Published: August 2005

Research and development to provide systems for effective derivation and use of selection indexes has been conducted for the Australian beef industry since the late 1980s. This paper reports on development successes and presents evidence of increasing rates of industry genetic gain in beef production profitability. Key factors in success are identified and include the ability of the index development process to capture the full context of selection. The level of performance recording in many cases is the primary limitation to effective index use. Issues that will be more important in future applications of indexes are discussed. They include the need for more specific selection for environments, for extending the breeding objective to encompass additional industry sectors and aims, for greater account of industry supply and demand flow-on effects, and for combining gene marker tests with other criteria in indexes of economic merit. The critical role of selection indexes in targeting multiple-trait economic merit is likely to increase further with the availability of new gene marker test information.
Chicken functional genomics: an overview
Authors: Moore R. J. , Doran T. J. , Wise T. G. , Riddell S. , Granger K. , Crowley T. M. , Jenkins K. A. , Karpala A. J. , Bean A. G. D. , Lowenthal J. W.
Published: August 2005

Chickens have undergone intensive selection to produce highly productive strains with excellent growth rates and feed conversion ratios. There does not appear to be any reduction in the rate of strain improvement. The recently completed chicken genome sequencing project and adjunct projects cataloging single nucleotide polymorphisms demonstrate that there is still a high level of genetic variation present in modern breeds. The information provided by genome and transcriptome studies furnishes the chicken biologist with powerful tools for the functional analysis of gene networks. Gene microarrays have been constructed and used to investigate gene expression patterns associated with certain production traits and changes in expression induced by pathogen challenge. Such studies have the potential to identify important genes involved in biological processes influencing animal productivity and health. Fundamental regulatory mechanisms controlled by non-coding RNAs, such as microRNAs, can now be studied following the identification of many potential genes by homology with previously identified genes from other organisms. We demonstrate here that microarrays and northern blotting can be used to detect expression of microRNAs in chicken tissue. Other tools are being used for functional genomic analysis including the production of transgenic birds, still a difficult process, and the use of gene silencing. Gene silencing via RNA interference is having a large impact in many areas of functional genomics and we and others have shown that the mechanisms needed for its action are functional in chickens. The chicken genome sequence has revealed a large number of immune related genes that had not previously been identified in chickens. Functional analysis of these genes is likely to lead to applications aimed at improving chicken health and productivity.
Challenges with investing in genetic improvement for the Australian extensive livestock industries
Authors: Banks R. G.
Published: August 2005

Investment in animal genetic improvement in Australia involves a diverse range of stakeholders and tackles complexity in a range of markets and production environments. While an excellent range of tools and knowledge for genetic improvement has been developed, industry-wide rates of genetic progress lag well below what is possible. This constitutes a considerable opportunity cost to the investors and to the wider community. It is proposed that this is partly a problem of coordination of effort across many diverse interests, and that this problem will be exacerbated by increasing availability, but complexity of use of genotypic information. Some approaches aimed at improving coordination and hence efficiency of investment are suggested, with consideration of the role of research and development corporations.
Genetic evaluation for the beef industry in Australia
Authors: Graser H-U. , Tier B. , Johnston D. J. , Barwick S. A.
Published: August 2005

Genetic evaluation for beef cattle in Australia has been performed using an animal model with best linear unbiased prediction since 1984. The evaluation procedures have evolved from simple to more complex models and from few to a large number of traits, including traits for reproduction, growth and carcass characteristics. This paper describes in detail the current beef cattle genetic evaluation system ‘BREEDPLAN’ used for the Australian beef cattle industry, the traits analysed and underlying models, and presents a short overview of the challenges and planned developments of coming years.
Crooked tail (
Cd
) model of human folate-responsive neural tube defects is mutated in Wnt coreceptor lipoprotein receptor-related protein 6
Authors: Carter Michelle , Chen Xu , Slowinska Bozena , Minnerath Sharon , Glickstein Sara , Shi Lei , Campagne Fabien , Weinstein Harel , Ross M. Elizabeth
Published: August 2005

A cranial neural tube defect in
Crooked tail
(
Cd
) mice is prevented with prenatal dietary folic acid
Cd
positional cloning reveals a missense mutation of a highly conserved amino acid in the low density lipoprotein receptor-related protein 6 (
Lrp6
), a coreceptor required for Wnt canonical signaling. Molecular modeling predicts that

Lrp6
Cd

alters a hinge region of the second YWTD β-propeller domain. Mutant LRP6 binds to Wnt and Dickkopf1 (Dkk1) but not Mesd1, and Dkk1 cannot antagonize Wnt in
Cd
/
Cd
cells, resulting in hyperactivity. NIH 3T3 cells transfected with a mutant Lrp6 plasmid resist Dkk1 antagonism much like
Cd
/+ cells, confirming the significance of the mutation. The
Lrp6
mutation in
Cd
mice provides evidence for a functional connection between Wnt signaling and folate rescue of neural tube defects.
Central IL-1 receptor signaling regulates bone growth and mass
Authors: Bajayo Alon , Goshen Inbal , Feldman Sharon , Csernus Valer , Iverfeldt Kerstin , Shohami Esther , Yirmiya Raz , Bab Itai
Published: August 2005

The proinflammatory cytokine IL-1, acting via the hypothalamic IL-1 receptor type 1 (IL-1RI), activates pathways known to suppress bone formation such as the hypothalamo pituitary-adrenocortical axis and the sympathetic nervous system. In addition, peripheral IL-1 has been implicated as a mediator of the bone loss induced by sex hormone depletion and TNF. Here, we report an unexpected low bone mass (LBM) phenotype, including impairment of bone growth, in IL-1RI-deficient mice (IL-1rKO mice). Targeted overexpression of human IL-1 receptor antagonist to the central nervous system using the murine glial fibrillary acidic protein promoter (IL-1raTG mice) resulted in a similar phenotype, implying that central IL-1RI silencing is the causative process in the LBM induction. Analysis of bone remodeling indicates that the process leading to the LBM in both IL-1rKO and IL-1raTG is characterized mainly by doubling the osteoclast number. Either genetic modification does not decrease testosterone or increase corticosterone serum levels, suggesting that systems other than the gonads and hypothalamo pituitary-adrenocortical axis mediate the central IL-1RI effect on bone. We further demonstrate that WT mice express mouse IL-1ra in bone but not in the hypothalamus. Because low levels of IL-1 are present in both tissues, it is suggested that skeletal IL-1 activity is normally suppressed, whereas central IL-1 produces a constant physiologic stimulation of IL-1RI signaling. Although the pathway connecting the central IL-1RI signaling to bone remodeling remains unknown, the outburst of osteoclastogenesis in its absence suggests that normally it controls bone growth and mass by tonically restraining bone resorption.
Glucose transporter 1 expression identifies a population of cycling CD4+CD8+human thymocytes with high CXCR4-induced chemotaxis
Authors: Swainson Louise , Kinet Sandrina , Manel Nicolas , Battini Jean-Luc , Sitbon Marc , Taylor Naomi
Published: August 2005

GLUT1, the major glucose transporter in peripheral T lymphocytes, is induced upon T cell receptor activation. However, the role of GLUT1 during human thymocyte differentiation remains to be evaluated. Our identification of GLUT1 as the human T lymphotrophic virus (HTLV) receptor has enabled us to use tagged HTLV-receptor-binding domain fusion proteins to specifically monitor surface GLUT1 expression. Here, we identify a unique subset of CD4+CD8+double-positive (DP) thymocytes, based on their GLUT1 surface expression. Whereas these cells express variable levels of CD8, they express uniformly high levels of CD4. Glucose uptake was 7-fold higher in CD4hiDP thymocytes than in CD4loDP thymocytes (P= 0.0002). Further analyses indicated that these GLUT1+thymocytes are early post-β-selection, as demonstrated by low levels of T cell receptor (TCR)αβ and CD3. This population of immature GLUT1+DP cells is rapidly cycling and can be further distinguished by specific expression of the transferrin receptor. Importantly, the CXCR4 chemokine receptor is expressed at 15-fold higher levels on GLUT1+DP thymocytes, as compared with the DP GLUT1-subset, and the former cells show enhanced chemotaxis to the CXCR4 ligand CXCL12. Thus, during human thymopoiesis, GLUT1 is up-regulated after β-selection, and these immature DP cells constitute a population with distinct metabolic and chemotactic properties.
Evolution of human-chimpanzee differences in malaria susceptibility: Relationship to human genetic loss of
N
-glycolylneuraminic acid
Authors: Martin Maria J. , Rayner Julian C. , Gagneux Pascal , Barnwell John W. , Varki Ajit
Published: August 2005

Chimpanzees are the closest evolutionary cousins of humans, sharing >99% identity in most protein sequences.
Plasmodium falciparum
is the major worldwide cause of malaria mortality.
Plasmodium reichenowi
, a morphologically identical and genetically very similar parasite, infects chimpanzees but not humans. Conversely, experimental
P
.
falciparum
infection causes brief moderate parasitization and no severe infection in chimpanzees. This surprising host specificity remains unexplained. We modified and enhanced traditional methods for measuring sialic acid (Sia)-dependent recognition of glycophorins by merozoite erythrocyte-binding proteins, eliminating interference caused by endogenous Sias on transfected cells, and by using erythroleukemia cells to allow experimental manipulation of Sia content. We present evidence that these remarkable differences among such closely related host-parasite pairs is caused by species-specific erythrocyte-recognition profiles, apparently related to the human-specific loss of the common primate Sia
N
-glycolylneuraminic acid. The major merozoite-binding protein erythrocyte-binding antigen-175 of
P
.
falciparum
apparently evolved to take selective advantage of the excess of the Sia
N
-acetylneuraminic acid (the precursor of
N
-glycolylneuraminic acid) on human erythrocytes. The contrasting preference of
P
.
reichenowi
erythrocyte-binding antigen-175 for
N
-glycolylneuraminic acid is likely the ancestral condition. The surprising ability of
P
.
falciparum
to cause disease in New World
Aotus
monkeys (geographically isolated from
P
.
falciparum
until arrival of peoples from the Old World) can be explained by parallel evolution of a human-like Sia expression pattern in these distantly related primates. These results also have implications for the prehistory of hominids and for the genetic origins and recent emergence of
P
.
falciparum
as a major human pathogen.
The plant cell wall matrix harbors a precursor of defense signaling peptides
Authors: Narváez-Vásquez Javier , Pearce Gregory , Ryan Clarence A.
Published: August 2005

Proteins of plant cell walls serve as structural macromolecules and play important roles in morphogenesis and development but have not been reported to be the origins of peptide signals that activate genes for plant defense. We report here that the mRNA coding the tomato leaf polyprotein precursor of three hydroxyproline-rich glycopeptide defense signals (called
Le
HypSys I, II, and III) is synthesized in phloem parenchyma cells in response to wounding, systemin, and methyl jasmonate, and the nascent protein is sequestered in the cell wall matrix. These findings indicate that the plant cell wall can play an active role in defense as a source of peptide signals for systemic wound signaling.
Domestication of a Mesoamerican cultivated fruit tree,
Spondias purpurea
Authors: Miller Allison , Schaal Barbara
Published: August 2005

Contemporary patterns of genetic variation in crops reflect historical processes associated with domestication, such as the geographic origin(s) of cultivated populations. Although significant progress has been made in identifying several global centers of domestication, few studies have addressed the issue of multiple origins of cultivated plant populations from different geographic regions within a domestication center. This study investigates the domestication history of jocote (
Spondias purpurea
), a Mesoamerican cultivated fruit tree. Sequences of the chloroplast spacer
trn
G–
trn
S were obtained for cultivated and wild
S. purpurea
trees, two sympatric taxa (
Spondias mombin
var.
mombin
and
Spondias radlkoferi
), and two outgroups (
S. mombin
var.
globosa
and
Spondias testudinus
). A phylogeographic approach was used and statistically significant associations of clades and geographical location were tested with a nested clade analysis. The sequences confirm that wild populations of
S. purpurea
are the likely progenitors of cultivated jocote trees. This study provides phylogeographic evidence of multiple domestications of this Mesoamerican cultivated fruit tree. Haplotypes detected in
S. purpurea
trees form two clusters, each of which includes alleles recovered in both cultivated and wild populations from distinct geographic regions. Cultivated
S. purpurea
populations have fewer unique
trn
G–
trn
S alleles than wild populations; however, five haplotypes were absent in the wild. The presence of unique alleles in cultivation may reflect contemporary extinction of the tropical dry forests of Mesoamerica. These data indicate that some agricultural habitats may be functioning as reservoirs of genetic variation in
S. purpurea
.
Orogeny can be very short
Authors: Dewey John F.
Published: August 2005

In contrast to continent/continent collision, arc–continent collision generates very short-lived orogeny because the buoyancy-driven impedance of the subduction of continental lithosphere, accompanied by arc/suprasubduction-zone ophiolite obduction, is relieved by subduction polarity reversal (flip). This tectonic principle is illustrated by the early Ordovician Grampian Orogeny in the British and Irish Caledonides, in which a wealth of detailed sedimentologic, heavy mineral, and geochronologic data pin the Orogeny to a very short Arenig/Llanvirn event. The Orogeny, from the initial subduction of continental margin sediments to the end of postflip shortening, lasted ≈18 million years (my). The collisional shortening, prograde-metamorphic phase of the Orogeny lasted 8 my, extensional collapse and exhumation of midcrustal rocks lasted 1.5 my, and postflip shortening lasted 4.5 my. Strain rates were a typical plate-boundary-zone 10
-15
. Metamorphism, to the second sillimanite isograd, with extensive partial melting, occurred within a few my after initial collision, indicating that conductive models for metamorphic heat transfer in Barrovian terrains are incorrect and must be replaced by advective models in which large volumes of mafic/ultramafic magma are emplaced, syn-tectonically, below and into evolving nappe stacks. Arc/continent collision generates fast and very short orogeny, regional metamorphism, and exhumation.
CTLA-4 up-regulation of lymphocyte function-associated antigen 1 adhesion and clustering as an alternate basis for coreceptor function
Authors: Schneider Helga , Valk Elke , da Rocha Dias Silvy , Wei Bin , Rudd Christopher E.
Published: August 2005

Although cytotoxic T lymphocyte antigen-4 (CTLA-4) negatively regulates T cell activation, the full range of functions mediated by this coreceptor has yet to be established. In this study, we report the surprising finding that CTLA-4 engagement by soluble antibody or CD80 potently up-regulates lymphocyte function-associated antigen 1 (LFA-1) adhesion to intercellular adhesion molecule-1 (ICAM-1) and receptor clustering concurrent with IL-2 inhibition. This effect was also observed with CTLA-4 ligation and not with other coreceptors. T cell antigen receptor (TcR)-induced lymphocyte function-associated antigen 1 function was also dependent on CTLA-4 expression as observed with reduced adhesion/clustering onCTLA-4-/-primary T cells. CTLA-4 up-regulated adhesion was mediated by regulator for cell adhesion and polarization type 1 (Rap-1) as shown by anti-CTLA-4-induced Rap-1 activation as well as Rap-1-N17 blockade and Rap-1-V12 mimicry of adhesion/clustering. Our findings identify a potent role for CTLA-4 in directing integrin adhesion and provide an alternate mechanism to account for aspects of CTLA-4 function in T cell immunity.
Gliding ghosts of
Mycoplasma mobile
Authors: Uenoyama Atsuko , Miyata Makoto
Published: August 2005

Several species of mycoplasmas glide on solid surfaces, in the direction of their membrane protrusion at a cell pole, by an unknown mechanism. Our recent studies on the fastest species,
Mycoplasma mobile
, suggested that the gliding machinery, localized at the base of the membrane protrusion (the “neck”), is composed of two huge proteins. This machinery forms spikes sticking out from the neck and propels the cell by alternately binding and unbinding the spikes to a solid surface. Here, to study the intracellular mechanisms for gliding, we established a permeabilized gliding ghost model, analogous to the “Triton model” of the eukaryotic axoneme. Treatment with Triton X-100 stopped the gliding and converted the cells to permeabilized “ghosts.” When ATP was added exogenously, ≈85% of the ghosts were reactivated, gliding at speeds similar to those of living cells. The reactivation activity and inhibition by various nucleotides and ATP analogs, as well as their kinetic parameters, showed that the machinery is driven by the hydrolysis of ATP to ADP plus phosphate, caused by an unknown ATPase.
Membrane metabolism mediated by Sec14 family members influences Arf GTPase activating protein activity for transport from the trans-Golgi
Authors: Wong Tania A. , Fairn Gregory D. , Poon Pak P. , Shmulevitz Maya , McMaster Christopher R. , Singer Richard A. , Johnston Gerald C.
Published: August 2005

The budding yeast
Saccharomyces cerevisiae
contains a family of Arf (ADP-ribosylation factor) GTPase activating protein (GAP) proteins with the Gcs1 + Age2 ArfGAP pair providing essential overlapping function for the movement of transport vesicles from the trans-Golgi network. We have generated a temperature-sensitive but stable version of the Gcs1 protein that is impaired only for trans-Golgi transport and find that deleterious effects of this enfeebled Gcs1-4 mutant protein are relieved by increased gene dosage of the
gcs1-4
mutant gene itself or by the
SFH2
gene (also called
CSR1
), encoding a phosphatidylinositol transfer protein (PITP). This effect was not seen for the
SEC14
gene, encoding the founding member of the yeast PITP protein family, even though the Gcs1 and Age2 ArfGAPs are known to be downstream effectors of Sec14-mediated activity for trans-Golgi transport. Sfh2-mediated suppression of inadequate Gcs1-4 function depended on phospholipase D, whereas inadequate Gcs1-4 activity was relieved by increasing levels of diacylglycerol (DAG). Recombinant Gcs1 protein was found to bind certain phospholipids but not DAG. Our findings favor a model of Gcs1 localization through binding to specific phospholipids and activation of ArfGAP activity by DAG-mediated membrane curvature as the transport vesicle is formed. Thus, ArfGAPs are subject to both temporal and spatial regulation that is facilitated by Sfh2-mediated modulation of the lipid environment.
Distinct regulation of Ubc13 functions by the two ubiquitin-conjugating enzyme variants Mms2 and Uev1A
Authors: Andersen Parker L. , Zhou Honglin , Pastushok Landon , Moraes Trevor , McKenna Sean , Ziola Barry , Ellison Michael J. , Dixit Vishva M. , Xiao Wei
Published: August 2005

Ubc13, a ubiquitin-conjugating enzyme (Ubc), requires the presence of a Ubc variant (Uev) for polyubiquitination. Uevs, although resembling Ubc in sequence and structure, lack the active site cysteine residue and are catalytically inactive. The yeast Uev (Mms2) incites noncanonical Lys63-linked polyubiquitination by Ubc13, whereas the increased diversity of Uevs in higher eukaryotes suggests an unexpected complication in ubiquitination. In this study, we demonstrate that divergent activities of mammalian Ubc13 rely on its pairing with either of two Uevs, Uev1A or Mms2. Structurally, we demonstrate that Mms2 and Uev1A differentially modulate the length of Ubc13-mediated Lys63-linked polyubiquitin chains. Functionally, we describe that Ubc13–Mms2 is required for DNA damage repair but not nuclear factor κB (NF-κB) activation, whereas Ubc13–Uev1A is involved in NF-κB activation but not DNA repair. Our finding suggests a novel regulatory mechanism in which different Uevs direct Ubcs to diverse cellular processes through physical interaction and alternative polyubiquitination.
Plx1 is the 3F3/2 kinase responsible for targeting spindle checkpoint proteins to kinetochores
Authors: Wong Oi Kwan , Fang Guowei
Published: August 2005

Dynamic attachment of microtubules to kinetochores during mitosis generates pulling force, or tension, required for the high fidelity of chromosome separation. A lack of tension activates the spindle checkpoint and delays the anaphase onset. A key step in the tension–response pathway involves the phosphorylation of the 3F3/2 epitope by an unknown kinase on untensed kinetochores. Using a rephosphorylation assay in Xenopus laevis extracts, we identified the kinetochore-associated Polo-like kinase Plx1 as the kinase both necessary and sufficient for this phosphorylation. Indeed, Plx1 is the physiological 3F3/2 kinase involved in checkpoint response, as immunodepletion of Plx1 from checkpoint extracts abolished the 3F3/2 signal and blocked association of xMad2, xBubR1, xNdc80, and xNuf2 with kinetochores. Interestingly, the kinetochore localization of Plx1 is under the control of the checkpoint protein xMps1, as immunodepletion of xMps1 prevents binding of Plx1 to kinetochores. Thus, Plx1 couples the tension signal to cellular responses through phosphorylating the 3F3/2 epitope and targeting structural and checkpoint proteins to kinetochores.
Regulation of ubiquitin ligase dynamics by the nucleolus
Authors: Mekhail Karim , Khacho Mireille , Carrigan Amanda , Hache Robert R.J. , Gunaratnam Lakshman , Lee Stephen
Published: August 2005

Cellular pathways relay information through dynamic protein interactions. We have assessed the kinetic properties of the murine double minute protein (MDM2) and von Hippel-Lindau (VHL) ubiquitin ligases in living cells under physiological conditions that alter the stability of their respective p53 and hypoxia-inducible factor substrates. Photobleaching experiments reveal that MDM2 and VHL are highly mobile proteins in settings where their substrates are efficiently degraded. The nucleolar architecture converts MDM2 and VHL to a static state in response to regulatory cues that are associated with substrate stability. After signal termination, the nucleolus is able to rapidly release these proteins from static detention, thereby restoring their high mobility profiles. A protein surface region of VHL's β-sheet domain was identified as a discrete [H+]-responsive nucleolar detention signal that targets the VHL/Cullin-2 ubiquitin ligase complex to nucleoli in response to physiological fluctuations in environmental pH. Data shown here provide the first evidence that cells have evolved a mechanism to regulate molecular networks by reversibly switching proteins between a mobile and static state.
Functional Architecture of the Inner Pore of a Voltage-gated Ca2+ Channel
Authors: Zhen Xiao-guang , Xie Cheng , Fitzmaurice Aileen , Schoonover Carl E. , Orenstein Eleza T. , Yang Jian
Published: August 2005

The inner pore of voltage-gated Ca2+ channels (VGCCs) is functionally important, but little is known about the architecture of this region. In K+ channels, this part of the pore is formed by the S6/M2 transmembrane segments from four symmetrically arranged subunits. The Ca2+ channel pore, however, is formed by four asymmetric domains of the same (α1) subunit. Here we investigated the architecture of the inner pore of P/Q-type Ca2+ channels using the substituted-cysteine accessibility method. Many positions in the S6 segments of all four repeats of the α1 subunit (Cav2.1) were modified by internal methanethiosulfonate ethyltrimethylammonium (MTSET). However, the pattern of modification does not fit any known sequence alignment with K+ channels. In IIS6, five consecutive positions showed clear modification, suggesting a likely aqueous crevice and a loose packing between S6 and S5 segments, a notion further supported by the observation that some S5 positions were also accessible to internal MTSET. These results indicate that the inner pore of VGCCs is indeed formed by the S6 segments but is different from that of K+ channels. Interestingly some residues in IIIS6 and IVS6 whose mutations in L-type Ca2+ channels affect the binding of dihydropyridines and phenylalkylamines and are thought to face the pore appeared not to react with internal MTSET. Probing with qBBr, a rigid thiol-reactive agent with a dimension of 12 Å × 10 Å × 6 Å suggests that the inner pore can open to >10 Å. This work provides an impetus for future studies on ion permeation, gating, and drug binding of VGCCs.
Localization of the Activation Gate of a Voltage-gated Ca2+ Channel
Authors: Xie Cheng , Zhen Xiao-guang , Yang Jian
Published: August 2005

Ion channels open and close in response to changes in transmembrane voltage or ligand concentration. Recent studies show that K+ channels possess two gates, one at the intracellular end of the pore and the other at the selectivity filter. In this study we determined the location of the activation gate in a voltage-gated Ca2+ channel (VGCC) by examining the open/closed state dependence of the rate of modification by intracellular methanethiosulfonate ethyltrimethylammonium (MTSET) of pore-lining cysteines engineered in the S6 segments of the α1 subunit of P/Q type Ca2+ channels. We found that positions above the putative membrane/cytoplasm interface, including two positions below the corresponding S6 bundle crossing in K+ channels, showed pronounced state-dependent accessibility to internal MTSET, reacting ∼1,000-fold faster with MTSET in the open state than in the closed state. In contrast, a position at or below the putative membrane/cytoplasm interface was modified equally rapidly in both the open and closed states. Our results suggest that the S6 helices of the α1 subunit of VGCCs undergo conformation changes during gating and the activation gate is located at the intracellular end of the pore.
Functional Role and Affinity of Inorganic Cations in Stabilizing the Tetrameric Structure of the KcsA K+ Channel
Authors: Krishnan Manoj N. , Bingham Jon-Paul , Lee Siew Hwee , Trombley Patrick , Moczydlowski Edward
Published: August 2005

Crystal structures of the tetrameric KcsA K+ channel reveal seven distinct binding sites for K+ ions within the central pore formed at the fourfold rotational symmetry axis. Coordination of an individual K+ ion by eight protein oxygen atoms within the selectivity filter suggests that ion-subunit bridging by cation–oxygen interactions contributes to structural stability of the tetramer. To test this hypothesis, we examined the effect of inorganic cations on the temperature dependence of the KcsA tetramer as monitored by SDS-PAGE. Inorganic cations known to permeate or strongly block K+ channels (K+, Rb+, Cs+, Tl+, NH4+, Ba2+, and Sr2+) confer tetramer stability at higher temperatures (T0.5 range = 87°C to >99°C) than impermeant cations and weak blockers (Li+, Na+, Tris+, choline+; T0.5 range = 59°C to 77°C). Titration of K+, Ba2+, and other stabilizing cations protects against rapid loss of KcsA tetramer observed in 100 mM choline Cl at 90°C. Tetramer protection titrations of K+, Rb+, Cs+, Tl+, and NH4+ at 85°C or 90°C exhibit apparent Hill coefficients (N) ranging from 1.7 to 3.3 and affinity constants (K0.5) ranging from 1.1 to 9.6 mM. Ba2+ and Sr2+ titrations exhibit apparent one-site behavior (N ≅ 1) with K0.5 values of 210 nM and 11 μM, respectively. At 95°C in the presence of 5 mM K+, titration of Li+ or Na+ destabilizes the tetramer with K0.5 values of 57 mM and 109 mM, respectively. We conclude that specific binding interactions of inorganic cations with the selectivity filter are an important determinant of tetramer stability of KscA.
Riemann-Roch-Hirzebruch integral formula for characters of reductive Lie groups
Authors: Libine Matvei
Published: August 2005

Let

G

R

G_{\mathbb R}

be a real reductive Lie group acting on a manifold

M
M

. M. Kashiwara and W. Schmid constructed representations of

G

R

G_{\mathbb R}

using sheaves and quasi-

G

R

G_{\mathbb R}

-equivariant

D

{\mathcal D}

-modules on

M
M

. In this article we prove an integral character formula for these representations (Theorem 1). Our main tools will be the integral localization formula recently proved by the author and the integral character formula proved by W. Schmid and K. Vilonen (originally established by W. Rossmann) in the important special case when the manifold

M
M

is the flag variety of

C

⊗

R

g

R

\mathbb C \otimes _{\mathbb R} \mathfrak {g}_{\mathbb R}

—the complexified Lie algebra of

G

R

G_{\mathbb R}

. In the special case when

G

R

G_{\mathbb R}

is commutative and the

D

{\mathcal D}

-module is the sheaf of sections of a

G

R

G_{\mathbb R}

-equivariant line bundle over

M
M

this integral character formula will reduce to the classical Riemann-Roch-Hirzebruch formula. As an illustration we give a concrete example on the enhanced flag variety.
The Pharmacological Potential of Mushrooms
Authors: Lindequist Ulrike , Niedermeyer Timo H. J. , Jülich Wolf-Dieter
Published: August 2005

This review describes pharmacologically active compounds from mushrooms. Compounds and complex substances with antimicrobial, antiviral, antitumor, antiallergic, immunomodulating, anti‐inflammatory, antiatherogenic, hypoglycemic, hepatoprotective and central activities are covered, focusing on the review of recent literature. The production of mushrooms or mushroom compounds is discussed briefly.
Investigating Acupuncture Using Brain Imaging Techniques: The Current State of Play
Authors: Lewith George T. , White Peter J. , Pariente Jeremie
Published: August 2005

We have systematically researched and reviewed the literature looking at the effect of acupuncture on brain activation as measured by functional magnetic resonance imaging and positron emission tomography. These studies show that specific and largely predictable areas of brain activation and deactivation occur when considering the traditional Chinese functions attributable to certain specific acupuncture points. For example, points associated with hearing and vision stimulates the visual and auditory cerebral areas respectively. Pain, however, is a complex matrix that is intimately intertwined with expectation. Acupuncture clearly affects this matrix in both specific and non‐specific manner that is consistent with its specific clinical effects, as well as the effects of expectation on pain relief. This article summarizes the current imaging literature.
Finding the Evidence in CAM: a Student′s Perspective
Authors: Ghassemi Jeffrey
Published: August 2005

This commentary offers a future health care provider′s perspective on the role of complementary and alternative medicine (CAM) in Western (namely, in US) medical education and practice. As a student of both public health and medicine in the United States, Jeffrey Ghassemi is interested in CAM′s contribution to improving medical practice and teaching. The commentary highlights the ambiguous definitions of CAM to Westerners despite the rising popularity of and expenditures for alternative modalities of care. It then argues for collaboration between alternative and established medical communities to ascertain the scientific merits of CAM. It concludes by calling for a new medical paradigm that embraces the philosophies of both communities to advance education and patient care.
Growth Inhibition of Cultured Human Liver Carcinoma Cells by Ki‐energy (Life‐energy): Scientific Evidence for Ki‐effects on Cancer Cells
Authors: Ohnishi Tsuyoshi , Ohnishi Tomoko , Nishino Kozo , Tsurusaki Yoshinori , Yamaguchi Masayoshi
Published: August 2005

‘Ki‐energy’ (life‐energy) is believed to increase the immune activity of its practitioners. It has also been shown to cause neuropsychological effects. We undertook this study to obtain objective and scientific evidence as to whether or not a ‘Ki‐effect’ could inhibit the growth of cultured cancer cells. Cultured human liver carcinoma cells, HepG2, were used. A Japanese Ki‐expert held his fingers toward the cells in culture dishes for 5 or 10 min. After culturing for 24 h, we measured cell numbers, protein concentration per cell, certain mRNA expressions and the synthesis of regucalcin. The results were compared with those for control cells (non‐treated cells). We found that the number of cells in the Ki‐exposed groups were less than those in the controls by 30.3 and 40.6% with 5 and 10 min Ki‐exposure, respectively. The protein content per cell in the Ki‐exposed groups (5 and 10 min) was higher than that in the control groups by 38.8 and 62.9%, respectively. These results were statistically significant. Using RT–PCR, we found that the mRNA expression for c-myc, a tumor stimulator gene, was decreased, while that for regucalcin, which suppresses DNA synthesis, was increased. Our molecular biological studies and mathematical model analysis demonstrated that Ki‐energy inhibited cancer cell division. The data also indicate that the Ki‐effects involve some form of infrared radiation from the human body. This study suggests the possibility that Ki‐energy may be beneficial for cancer patients because it suppresses cancer cell growth, and at the same time, it stimulates immune functions of the patients.
Biological Basis for the Use of Botanicals in Osteoarthritis and Rheumatoid Arthritis: A Review
Authors: Ahmed Salahuddin , Anuntiyo Jeremy , Malemud Charles J. , Haqqi Tariq M.
Published: August 2005

Osteoarthritis (OA) of the knee and hip is a debilitating disease affecting more women than men and the risk of developing OA increases precipitously with aging. Rheumatoid arthritis (RA), the most common form of inflammatory joint diseases, is a disease of unknown etiology and affects ∼1% of the population worldwide, and unlike OA, generally involves many joints because of the systemic nature of the disease. Non‐steroidal anti‐inflammatory drugs (NSAIDs) are the first drugs of choice for the symptomatic treatment of both OA and RA. Because of the risks associated with the use of NSAIDs and other limitations, the use of alternative therapies, such as acupuncture and medicinal herbs, is on the rise and according to reports ∼60–90% of dissatisfied arthritis patients are likely to seek the option of complementary and alternative medicine (CAM). This paper reviews the efficacy of some of the common herbs that have a history of human use and their anti‐inflammatory or antiarthritic properties have been evaluated in animal models of inflammatory arthritis, in studies employing well defined and widely accepted in vitro models that use human chondrocytes/cartilage explants or in clinical trials. Available data suggests that the extracts of most of these herbs or compounds derived from them may provide a safe and effective adjunctive therapeutic approach for the treatment of OA and RA. This, in turn, argues for trials to establish efficacy and optimum dosage of these compounds for treating human inflammatory and degenerative joint diseases.
ACADEMIC TENURE, POSTTENURE EFFORT, AND CONTRACTUAL DAMAGES
Authors: Dnes Antony , Garoupa Nuno
Published: August 2005

In this article we explore the incentive properties of academic tenure relative to alternatives that might be substitutes for tenure, in particular contractual damages. We emphasize the role of tenure in providing an incentive for incumbent faculty to reveal the characteristics of recruits and to maintain their own performance posttenure. Our results suggest that tenure is just one of many mechanisms potentially able to achieve honest revelation. (JEL I2, K0, L2)
Organization and Metabolism of Plastids and Mitochondria in Arbuscular Mycorrhizal Roots of Medicago truncatula
Authors: Lohse Swanhild , Schliemann Willibald , Ammer Christian , Kopka Joachim , Strack Dieter , Fester Thomas
Published: August 2005

Colonization of root cortical cells by arbuscular mycorrhizal fungi leads to marked cytological changes of plastids and mitochondria. Plastids in particular are forming tubular extensions partially connecting individual organelles in a network-like way. These cytological changes correspond to an increased need for plastid and mitochondrial products during establishment and functioning of the symbiosis. The analysis of metabolite and transcript levels in mycorrhizal and nonmycorrhizal roots from Medicago truncatula revealed concomitant changes regarding a number of metabolic pathways. Our results indicate the activation of the mitochondrial tricarboxylic acid cycle and of plastid biosynthetic pathways producing fatty acids, amino acids, and apocarotenoids. These observations provide a general overview of structural and metabolic changes of plastids and mitochondria during colonization of root cortical cells by arbuscular mycorrhizal fungi.
NpPDR1, a Pleiotropic Drug Resistance-Type ATP-Binding Cassette Transporter from Nicotiana plumbaginifolia, Plays a Major Role in Plant Pathogen Defense
Authors: Stukkens Yvan , Bultreys Alain , Grec Sébastien , Trombik Tomasz , Vanham Delphine , Boutry Marc
Published: August 2005

Nicotiana plumbaginifolia NpPDR1, a plasma membrane pleiotropic drug resistance-type ATP-binding cassette transporter formerly named NpABC1, has been suggested to transport the diterpene sclareol, an antifungal compound. However, direct evidence for a role of pleiotropic drug resistance transporters in the plant defense is still lacking. In situ immunolocalization and histochemical analysis using the gusA reporter gene showed that NpPDR1 was constitutively expressed in the whole root, in the leaf glandular trichomes, and in the flower petals. However, NpPDR1 expression was induced in the whole leaf following infection with the fungus Botrytis cinerea, and the bacteria Pseudomonas syringae pv tabaci, Pseudomonas fluorescens, and Pseudomonas marginalis pv marginalis, which do not induce a hypersensitive response in N. plumbaginifolia, whereas a weaker response was observed using P. syringae pv syringae, which does induce a hypersensitive response. Induced NpPDR1 expression was more associated with the jasmonic acid than the salicylic acid signaling pathway. These data suggest that NpPDR1 is involved in both constitutive and jasmonic acid-dependent induced defense. Transgenic plants in which NpPDR1 expression was prevented by RNA interference showed increased sensitivity to sclareol and reduced resistance to B. cinerea. These data show that NpPDR1 is involved in pathogen resistance and thus demonstrate a new role for the ATP-binding cassette transporter family.
Loss of Function of OsDCL1 Affects MicroRNA Accumulation and Causes Developmental Defects in Rice
Authors: Liu Bin , Li PingChuan , Li Xin , Liu ChunYan , Cao ShouYun , Chu ChengCai , Cao XiaoFeng
Published: August 2005

MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are two types of noncoding RNAs involved in developmental regulation, genome maintenance, and defense in eukaryotes. The activity of Dicer or Dicer-like (DCL) proteins is required for the maturation of miRNAs and siRNAs. In this study, we cloned and sequenced 66 candidate rice (Oryza sativa) miRNAs out of 1,650 small RNA sequences (19 to approximately 25 nt), and they could be further grouped into 21 families, 12 of which are newly identified and three of which, OsmiR528, OsmiR529, and OsmiR530, have been confirmed by northern blot. To study the function of rice DCL proteins (OsDCLs) in the biogenesis of miRNAs and siRNAs, we searched genome databases and identified four OsDCLs. An RNA interference approach was applied to knock down two OsDCLs, OsDCL1 and OsDCL4, respectively. Strong loss of function of OsDCL1IR transformants that expressed inverted repeats of OsDCL1 resulted in developmental arrest at the seedling stage, and weak loss of function of OsDCL1IR transformants caused pleiotropic developmental defects. Moreover, all miRNAs tested were greatly reduced in OsDCL1IR but not OsDCL4IR transformants, indicating that OsDCL1 plays a critical role in miRNA processing in rice. In contrast, the production of siRNA from transgenic inverted repeats and endogenous CentO regions were not affected in either OsDCL1IR or OsDCL4IR transformants, suggesting that the production of miRNAs and siRNAs is via distinct OsDCLs.
Interaction of Auxin and ERECTA in Elaborating Arabidopsis Inflorescence Architecture Revealed by the Activation Tagging of a New Member of the YUCCA Family Putative Flavin Monooxygenases
Authors: Woodward Claire , Bemis Shannon M. , Hill Emi J. , Sawa Shinichiro , Koshiba Tomokazu , Torii Keiko U.
Published: August 2005

The aboveground body of higher plants has a modular structure of repeating units, or phytomers. As such, the position, size, and shape of the individual phytomer dictate the plant architecture. The Arabidopsis (Arabidopsis thaliana) ERECTA (ER) gene regulates the inflorescence architecture by affecting elongation of the internode and pedicels, as well as the shape of lateral organs. A large-scale activation-tagging genetic screen was conducted in Arabidopsis to identify novel genes and pathways that interact with the ER locus. A dominant mutant, super1-D, was isolated as a nearly complete suppressor of a partial loss-of-function allele er-103. We found that SUPER1 encodes YUCCA5, a novel member of the YUCCA family of flavin monooxygenases. The activation tagging of YUCCA5 conferred increased levels of free indole acetic acid, increased auxin response, and mild phenotypic characteristics of auxin overproducers, such as elongated hypocotyls, epinastic cotyledons, and narrow leaves. Both genetic and cellular analyses indicate that auxin and the ER pathway regulate cell division and cell expansion in a largely independent but overlapping manner during elaboration of inflorescence architecture.
Gibberellin Biosynthesis in Developing Pumpkin Seedlings
Authors: Lange Theo , Kappler Jeannette , Fischer Andreas , Frisse Andrea , Padeffke Tania , Schmidtke Sabine , Lange Maria João Pimenta
Published: August 2005

A gibberellin (GA) biosynthetic pathway was discovered operating in root tips of 7-d-old pumpkin (Cucurbita maxima) seedlings. Stepwise analysis of GA metabolism in cell-free systems revealed the conversion of GA12-aldehyde to bioactive GA4 and inactive GA34. Highest levels of endogenous GA4 and GA34 were found in hypocotyls and root tips of 3-d-old seedlings. cDNA molecules encoding two GA oxidases, CmGA20ox3 and CmGA3ox3, were isolated from root tips of 7-d-old LAB150978-treated seedlings. Recombinant CmGA20ox3 fusion protein converted GA12 to GA9, GA24 to GA9, GA14 to GA4, and, less efficiently, GA53 to GA20, and recombinant CmGA3ox3 protein oxidized GA9 to GA4. Transcript profiles were determined for four GA oxidase genes from pumpkin revealing relatively high transcript levels for CmGA7ox in shoot tips and cotyledons, for CmGA20ox3 in shoot tips and hypocotyls, and for CmGA3ox3 in hypocotyls and roots of 3-d-old seedlings. Transcripts of CmGA2ox1 were mainly found in roots of 7-d-old seedlings. In roots of 7-d-old seedlings, transcripts of CmGA7ox, CmGA20ox3, and CmGA3ox3 were localized in the cap and the rhizodermis by in situ hybridization. We conclude that hypocotyls and root tips are important sites of GA biosynthesis in the developing pumpkin seedling.
Aleurone Cell Identity Is Suppressed following Connation in Maize Kernels
Authors: Geisler-Lee Jane , Gallie Daniel R.
Published: August 2005

Expression of the cytokinin-synthesizing isopentenyl transferase enzyme under the control of the Arabidopsis (Arabidopsis thaliana) SAG12 senescence-inducible promoter reverses the normal abortion of the lower floret from a maize (Zea mays) spikelet. Following pollination, the upper and lower floret pistils fuse, producing a connated kernel with two genetically distinct embryos and the endosperms fused along their abgerminal face. Therefore, ectopic synthesis of cytokinin was used to position two independent endosperms within a connated kernel to determine how the fused endosperm would affect the development of the two aleurone layers along the fusion plane. Examination of the connated kernel revealed that aleurone cells were present for only a short distance along the fusion plane whereas starchy endosperm cells were present along most of the remainder of the fusion plane, suggesting that aleurone development is suppressed when positioned between independent starchy endosperms. Sporadic aleurone cells along the fusion plane were observed and may have arisen from late or imperfect fusion of the endosperms of the connated kernel, supporting the observation that a peripheral position at the surface of the endosperm and not proximity to maternal tissues such as the testa and pericarp are important for aleurone development. Aleurone mosaicism was observed in the crown region of nonconnated SAG12-isopentenyl transferase kernels, suggesting that cytokinin can also affect aleurone development.