bluuebunny/crossref_metadata_2025 huggingface dataset:
Extracellular signal-regulated kinase 2 is necessary for mesoderm differentiation
Authors: Yao Yao , Li Wei , Wu Junwei , Germann Ursula A. , Su Michael S. S. , Kuida Keisuke , Boucher Diane M.
Published: October 2003

The extracellular signal-regulated kinase (ERK) is a component of the mitogen-activated protein kinase cascade. Exon 2 of
erk2
was deleted by homologous recombination and resulted in embryonic lethality at embryonic day 6.5.
erk2
mutant embryos did not form mesoderm and showed increased apoptosis but comparable levels of BrdUrd incorporation, indicating a defect in differentiation.
erk2
null embryonic stem (ES) cells exhibited reduced total ERK activity upon serum stimulation, augmented ERK1 phosphorylation, and decreased downstream p90Rsk phosphorylation and activity; yet ES cell proliferation was unaffected. Mutant ES cells were capable of forming mesoderm; however, treatment of mutant ES cells with the mitogen-activated protein kinase kinase inhibitor PD184352 decreased total ERK activity and expression of the mesodermal marker
brachyury
, suggesting that ERK1 can compensate for ERK2
in vitro
. Normal embryos at embryonic day 6.5 expressed activated ERK1/2 in the extraembryonic ectoderm, whereas
erk2
mutant embryos had no detectable activated ERK1/2 in this region, suggesting that activated ERK1 was not expressed, and therefore cannot compensate for loss of ERK2
in vivo
. These data indicate that ERK2 plays an essential role in mesoderm differentiation during embryonic development.
The energetic cost of domain reorientation in maltose-binding protein as studied by NMR and fluorescence spectroscopy
Authors: Millet Oscar , Hudson Rhea P. , Kay Lewis E.
Published: October 2003

Maltose-binding protein (MBP) is a two-domain protein that undergoes a ligand-mediated conformational rearrangement from an “open” to a “closed” structure on binding to maltooligosaccharides. To characterize the energy landscape associated with this transition, we have generated five variants of MBP with mutations located in the hinge region of the molecule. Residual dipolar couplings, measured in the presence of a weak alignment medium, have been used to establish that the average structures of the mutant proteins are related to each other by domain rotation about an invariant axis, with the rotation angle varying from 5° to 28°. Additionally, the domain orientations observed in the wild-type apo and ligand-bound (maltose, maltotriose, etc.) structures are related through a rotation of 35° about the same axis. Remarkably, the free energy of unfolding, measured by equilibrium denaturation experiments and monitored by fluorescence spectroscopy, shows a linear correlation with the rotation angle, with the stability of the (apo)protein decreasing with domain closure by 212 ± 16 cal·mol
–1
per degree of rotation. The apparent binding energy for maltose also shows a similar correlation with the interdomain angle, suggesting that the mutations, as they relate to binding, affect predominantly the ligand-free structure. The linearity of the energy change is interpreted in terms of an increase in the extent of hydrophobic surface that becomes solvent accessible on closure. The combination of structural, stability, and binding data allows separation of the energetics of domain reorientation from ligand binding. This work presents a near quantitative structure-energy-binding relationship for a series of mutants of MBP, illustrating the power of combined studies involving protein engineering and solution NMR spectroscopy.
Nitric oxide-donating aspirin inhibits β-catenin/T cell factor (TCF) signaling in SW480 colon cancer cells by disrupting the nuclear β-catenin–TCF association
Authors: Nath Niharika , Kashfi Khosrow , Chen Jie , Rigas Basil
Published: October 2003

Dysregulation of the Wnt pathway and altered β-catenin expression are central early events in colorectal carcinogenesis. We studied the
ortho
,
meta
, and
para (o
-,
m
-, and
p
-) positional isomers of NO-donating aspirin (NO-ASA), a chemopreventive agent against colon cancer, for their effect on β-catenin/T cell factor (TCF) signaling. In human SW480 colon carcinoma cells, cell-growth inhibition by NO-ASA [IC
50
values for
p
-,
o
-, and
m
were 48.1 ± 4.3 (mean ± SEM), 60.4 ± 2.1, and 900 ± 50 μM, respectively] was accompanied by significant inhibition of β-catenin signaling. We determined β-catenin-dependent TCF-4 transcriptional activity by measuring the activity of the luciferase gene placed under the control of TCF-4 regulatory sequences. The IC
50
values for β-catenin/TCF-4-signaling inhibition by NO-ASA were:
o
-, 2.6 ± 0.4;
m
-, 15 ± 5;
p
-, 1.1 ± 0.1 μM; and for ASA, >5,000 μM. Total or nuclear levels of β-catenin and its distribution in the cell were not altered by NO-ASA, as judged by protein expression levels and semiquantitative immunofluorescence analysis. NO-ASA disrupted the association of β-catenin and TCF-4 in the nucleus, whereas ASA did not affect it. NO-ASA reduced the expression of
cyclin D1
, a downstream target gene that plays an important role in colon carcinogenesis. In contrast, a structural analog of NO-ASA lacking the —NO
2
moiety did not affect TCF-4 transcriptional activity. Thus, NO-ASA inhibits β-catenin-mediated TCF activity by preventing the formation of the β-catenin/TCF-4 complex. This effect, occurring at NO-ASA concentrations far below those required to inhibit cell growth, may be a critical early event in the chemopreventive activity of NO-ASA against colon cancer.
Ancient maize from Chacoan great houses: Where was it grown?
Authors: Benson Larry , Cordell Linda , Vincent Kirk , Taylor Howard , Stein John , Farmer G. Lang , Futa Kiyoto
Published: October 2003

In this article, we compare chemical (
87
Sr/
86
Sr and elemental) analyses of archaeological maize from dated contexts within Pueblo Bonito, Chaco Canyon, New Mexico, to potential agricultural sites on the periphery of the San Juan Basin. The oldest maize analyzed from Pueblo Bonito probably was grown in an area located 80 km to the west at the base of the Chuska Mountains. The youngest maize came from the San Juan or Animas river floodplains 90 km to the north. This article demonstrates that maize, a dietary staple of southwestern Native Americans, was transported over considerable distances in pre-Columbian times, a finding fundamental to understanding the organization of pre-Columbian southwestern societies. In addition, this article provides support for the hypothesis that major construction events in Chaco Canyon were made possible because maize was brought in to support extra-local labor forces.
Interaction between the Alzheimer's survival peptide humanin and insulin-like growth factor-binding protein 3 regulates cell survival and apoptosis
Authors: Ikonen Maaria , Liu Bingrong , Hashimoto Yuichi , Ma Liqun , Lee Kuk-Wha , Niikura Takako , Nishimoto Ikuo , Cohen Pinchas
Published: October 2003

Insulin-like growth factor-binding protein-3 (IGFBP-3) regulates IGF bioactivity and also independently modulates cell growth and survival. By using a yeast two-hybrid screen to identify IGFBP-3-interacting proteins, we cloned humanin (HN) as an IGFBP-3-binding partner. HN is a 24-aa peptide that has been shown to specifically inhibit neuronal cell death induced by familial Alzheimer's disease mutant genes and amyloid-β (Aβ). The physical interaction of HN with IGFBP-3 was determined to be of high affinity and specificity and was confirmed by yeast mating, displaceable pull-down experiments with (His)-6-tagged HN, and ligand blot experiments. Coimmunoprecipitation of IGFBP-3 and HN from mouse testes confirmed the interactionin vivo. In cross-linking experiments, HN bound IGFBP-3 but did not compete with IGF-I–IGFBP-3 binding; competitive ligand dot blot experiments revealed the 18-aa heparin-binding domain of IGFBP-3 as the binding site for HN. Alanine scanning determined that F6A-HN mutant does not bind IGFBP-3. HN but not F6A-HN inhibited IGFBP-3-induced apoptosis in human glioblastoma-A172. In contrast, HN did not suppress IGFBP-3 response in SH-SY5Y neuroblastoma and mouse cortical primary neurons. In primary neurons, IGFBP-3 markedly potentiated HN rescue ability from Aβ1–43toxicity. In summary, we have identified an interaction between the survival peptide HN and IGFBP-3 that is pleiotrophic in nature and is capable of both synergistic and antagonistic interaction. This interaction may prove to be important in neurological disease processes and could provide important targets for drug development.
β-Adrenergic regulation requires direct anchoring of PKA to cardiac Ca
V
1.2 channels via a leucine zipper interaction with A kinase-anchoring protein 15
Authors: Hulme Joanne T. , Lin Teddy W.-C. , Westenbroek Ruth E. , Scheuer Todd , Catterall William A.
Published: October 2003

Activation of β-adrenergic receptors and consequent phosphorylation by cAMP-dependent protein kinase A (PKA) greatly increases the L-type Ca
2+
current through Ca
V
1.2 channels in isolated cardiac myocytes. A kinase-anchoring protein 15 (AKAP15) coimmunoprecipitates with Ca
V
1.2 channels isolated from rat heart membrane extracts and transfected cells, and it colocalizes with Ca
V
1.2 channels and PKA in the transverse tubules of isolated ventricular myocytes. Site-directed mutagenesis studies reveal that AKAP15 directly interacts with the distal C terminus of the cardiac Ca
V
1.2 channel via a leucine zipper-like motif. Disruption of PKA anchoring to Ca
V
1.2 channels via AKAP15 using competing peptides markedly inhibits the β-adrenergic regulation of Ca
V
1.2 channels via the PKA pathway in ventricular myocytes. These results identify a conserved leucine zipper motif in the C terminus of the Ca
V
1 family of Ca
2+
channels that directly anchors an AKAP15-PKA signaling complex to ensure rapid and efficient regulation of L-type Ca
2+
currents in response to β-adrenergic stimulation and local increases in cAMP.
Distinct roles of Bazooka and Stardust in the specification of
Drosophila
photoreceptor membrane architecture
Authors: Hong Yang , Ackerman Larry , Jan Lily Yeh , Jan Yuh-Nung
Published: October 2003

Photoreceptors form during
Drosophila
pupal development and acquire elaborate membrane structures, including the rhabdomeres and stalk membranes. Here, we show that the development of these cellular structures involves two distinct processes: the establishment of apical–basal polarity that requires Bazooka (Baz), and the regionalization of apical membrane into stalk membranes and rhabdomeres that requires Stardust (Sdt). In the absence of Baz, the apical–basal polarity is compromised in early pupal photoreceptors, and no identifiable apical membrane domain is formed. Sdt, in contrast, plays a more limited role in apical–basal polarity but is essential for the proper localization of transmembrane protein Crumbs (Crb), known to be required in the biogenesis of stalk membrane. Loss of Sdt causes strong defects in stalk membrane and rhabdomere resembling
crb
mutant phenotype. Thus, proteins required for establishing the early embryonic epithelial polarity are used later for the morphogenesis of photoreceptors, with Baz and Sdt functioning in different aspects of the formation of the apical–basal cellular architecture.
A plant virus replication system to assay the formation of RNA pseudotriloop motifs in RNA–protein interactions
Authors: Haasnoot P. C. Joost , Bol John F. , Olsthoorn René C. L.
Published: October 2003

A pseudotriloop is formed by transloop base pairing between the first (5′) and the fifth nucleotide in a hexanucleotide RNA loop (“hexaloop”) to subtend a triloop of nucleotides 2–4. This structure has been found in hairpins involved in the regulation of iron metabolism in mammalian cells and in transcription of plant virus subgenomic RNA. Several hexaloop hairpins, including HIV-transactivation-responsive element and hepatitis B virus ε, potentially adopt a pseudotriloop conformation. Here we show that an RNA plant virus whose replication depends on a conventional triloop hairpin can be used to verify the existence of pseudotriloop structures
in vivo
. Our data suggest that the pseudotriloop may represent a common motif in RNA–protein recognition.
Dynamic structures inEscherichia coli: Spontaneous formation of MinE rings and MinD polar zones
Authors: Huang Kerwyn Casey , Meir Yigal , Wingreen Ned S.
Published: October 2003

InEscherichia coli, division site selection is regulated in part by the Min-protein system. Oscillations of the Min proteins from pole to pole every ≈40 sec have been revealed byin vivostudies of GFP fusions. The dynamic oscillatory structures produced by the Min proteins, including a ring of MinE protein, compact polar zones of MinD, and zebra-striped oscillations in filamentous cells, remain unexplained. We show that the Min oscillations, including mutant phenotypes, can be accounted for byin vitro-observed interactions involving MinD and MinE, with a crucial role played by the rate of nucleotide exchange. Recent discoveries suggest that protein oscillations may play a general role in proper chromosome and plasmid partitioning.
Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins
Authors: Miyashita O. , Onuchic J. N. , Wolynes P. G.
Published: October 2003

Large-scale motions of biomolecules involve linear elastic deformations along low-frequency normal modes, but for function nonlinearity is essential. In addition, unlike macroscopic machines, biological machines can locally break and then reassemble during function. We present a model for global structural transformations, such as allostery, that involve large-scale motion and possible partial unfolding, illustrating the method with the conformational transition of adenylate kinase. Structural deformation between open and closed states occurs via low-frequency modes on separate reactant and product surfaces, switching from one state to the other when energetically favorable. The switching model is the most straightforward anharmonic interpolation, which allows the barrier for a process to be estimated from a linear normal mode calculation, which by itself cannot be used for activated events. Local unfolding, or cracking, occurs in regions where the elastic stress becomes too high during the transition. Cracking leads to a counterintuitive catalytic effect of added denaturant on allosteric enzyme function. It also leads to unusual relationships between equilibrium constant and rate like those seen recently in single-molecule experiments of motor proteins.
Principles of cell-free genetic circuit assembly
Authors: Noireaux Vincent , Bar-Ziv Roy , Libchaber Albert
Published: October 2003

Cell-free genetic circuit elements were constructed in a transcription–translation extract. We engineered transcriptional activation and repression cascades, in which the protein product of each stage is the input required to drive or block the following stage. Although we can find regions of linear response for single stages, cascading to subsequent stages requires working in nonlinear regimes. Substantial time delays and dramatic decreases in output production are incurred with each additional stage because of a bottleneck at the translation machinery. Faster turnover of RNA message can relieve competition between genes and stabilize output against variations in input and parameters.
Mutations in human complement regulator, membrane cofactor protein (CD46), predispose to development of familial hemolytic uremic syndrome
Authors: Richards Anna , Kemp Elizabeth J. , Liszewski M. Kathryn , Goodship Judith A. , Lampe Anne K. , Decorte Ronny , Müslümanogğlu M. Hamza , Kavukcu Salih , Filler Guido , Pirson Yves , Wen Leana S. , Atkinson John P. , Goodship Timothy H. J.
Published: October 2003

Membrane cofactor protein (MCP; CD46) is a widely expressed transmembrane complement regulator. Like factor H it inhibits complement activation by regulating C3b deposition on targets. Factor H mutations occur in 10–20% of patients with hemolytic uremic syndrome (HUS). We hypothesized that MCP mutations could predispose to HUS, and we sequenced MCP coding exons in affected individuals from 30 families. MCP mutations were detected in affected individuals of three families: a deletion of two amino acids (D237/S238) in family 1 (heterozygous) and a substitution, S206P, in families 2 (heterozygous) and 3 (homozygous). We evaluated protein expression and function in peripheral blood mononuclear cells from these individuals. An individual with the D237/S238 deletion had reduced MCP levels and ≈50% C3b binding compared with normal controls. Individuals with the S206P change expressed normal quantities of protein, but demonstrated ≈50% reduction in C3b binding in heterozygotes and complete lack of C3b binding in homozygotes. MCP expression and function was evaluated in transfectants reproducing these mutations. The deletion mutant was retained intracellularly. S206P protein was expressed on the cell surface but had a reduced ability to prevent complement activation, consistent with its reduced C3b binding and cofactor activity. This study presents further evidence that complement dysregulation predisposes to development of thrombotic microangiopathy and that screening patients for such defects could provide informed treatment strategies.
Elevated gene expression levels distinguish human from non-human primate brains
Authors: Cáceres Mario , Lachuer Joel , Zapala Matthew A. , Redmond John C. , Kudo Lili , Geschwind Daniel H. , Lockhart David J. , Preuss Todd M. , Barlow Carrolee
Published: October 2003

Little is known about how the human brain differs from that of our closest relatives. To investigate the genetic basis of human specializations in brain organization and cognition, we compared gene expression profiles for the cerebral cortex of humans, chimpanzees, and rhesus macaques by using several independent techniques. We identified 169 genes that exhibited expression differences between human and chimpanzee cortex, and 91 were ascribed to the human lineage by using macaques as an outgroup. Surprisingly, most differences between the brains of humans and non-human primates involved up-regulation, with ≈90% of the genes being more highly expressed in humans. By contrast, in the comparison of human and chimpanzee heart and liver, the numbers of up- and down-regulated genes were nearly identical. Our results indicate that the human brain displays a distinctive pattern of gene expression relative to non-human primates, with higher expression levels for many genes belonging to a wide variety of functional classes. The increased expression of these genes could provide the basis for extensive modifications of cerebral physiology and function in humans and suggests that the human brain is characterized by elevated levels of neuronal activity.
A subset of membrane-associated proteins is ubiquitinated in response to mutations in the endoplasmic reticulum degradation machinery
Authors: Hitchcock Amy L. , Auld Kathryn , Gygi Steven P. , Silver Pamela A.
Published: October 2003

Ubiquitination of membrane-associated proteins can direct their proteasome-mediated degradation or activation at the endoplasmic reticulum (ER), as well as their endocytosis and intracellular sorting. However, the full spectrum of ubiquitinated membrane proteins has not been determined. Here we combined proteomic analysis with yeast genetics to identify 211 ubiquitinated membrane-associated proteins in
Saccharomyces cerevisiae
and map >30 precise sites of ubiquitination. Major classes of identified ubiquitinated proteins include ER-resident membrane proteins, plasma membrane-localized permeases, receptors, and enzymes, and surprisingly, components of the actin cytoskeleton. By determining the differential abundance of ubiquitinated proteins in yeast mutated for
NPL4
and
UBC7
, which are major components of ER-associated degradation (ERAD), we furthermore were able to classify 83 of these identified ubiquitinated membrane proteins as potential endogenous substrates of the ERAD pathway. These substrates are highly enriched for proteins that localize to or transit through the ER. Interestingly, we also identified novel membrane-bound transcription factors that may be subject to ubiquitin/proteasome-mediated cleavage and activation at the ER membrane.
Structure of tRNA pseudouridine synthase TruB and its RNA complex: RNA recognition through a combination of rigid docking and induced fit
Authors: Pan Hu , Agarwalla Sanjay , Moustakas Demetri T. , Finer-Moore Janet , Stroud Robert M.
Published: October 2003

RNA pseudouridine synthase, TruB, catalyzes pseudouridine formation at U55 in tRNA. This posttranscriptional modification is almost universally conserved and occurs in the T arm of most tRNAs. We determined the crystal structure of
Escherichia coli
TruB apo enzyme, as well as the structure of
Thermotoga maritima
TruB in complex with RNA. Comparison of the RNA-free and -bound forms of TruB reveals that this enzyme undergoes significant conformational changes on binding to its substrate. These conformational changes include the ordering of the “thumb loop,” which binds right into the RNA hairpin loop, and a 10° hinge movement of the C-terminal domain. Along with the result of docking experiments performed on apo TruB, we conclude that TruB recognizes its RNA substrate through a combination of rigid docking and induced fit, with TruB first rigidly binding to its target and then maximizing the interaction by induced fit.
RNA-editing cytidine deaminase Apobec-1 is unable to induce somatic hypermutation in mammalian cells
Authors: Eto Tomonori , Kinoshita Kazuo , Yoshikawa Kiyotsugu , Muramatsu Masamichi , Honjo Tasuku
Published: October 2003

Antibody diversification by somatic hypermutation, gene conversion, and class switch recombination is completely dependent on activation-induced cytidine deaminase (AID). A recent report showing induction of DNA mutations in
Escherichia coli
by overexpression of AID, Apobec-1, and related members of the RNA-editing cytidine deaminase family suggested that they may directly modify deoxycytidine in DNA in mammalian cells (DNA-editing model). We therefore examined whether Apobec-1 bona fide RNA-editing enzyme could show somatic hypermutation and class switching activities in murine B lymphocytes and fibroblasts. Unlike AID, Apobec-1 was unable to induce somatic hypermutation or class switching. The results force a reevaluation of the physiological significance of the DNA deaminase activities of AID and Apobec-1 in
E. coli
and
in vitro
.
Helical Lévy walks: Adjusting searching statistics to resource availability in microzooplankton
Authors: Bartumeus Frederic , Peters Francesc , Pueyo Salvador , Marrasé Cèlia , Catalan Jordi
Published: October 2003

The searching trajectories of different animals can be described with a broad class of flight length (

l
j

) distributions with
P
(

l
j

) =

l
j

–μ
. Theoretical studies have shown that changes in these distributions (i.e., different μ values) are key to optimizing the long-term encounter statistics under certain searcher–resource scenarios. In particular, they predict the advantage of Lévy searching (μ ≈ 2) over Brownian motion (μ ≥ 3) for low-prey-density scenarios. Here, we present experimental evidence of predicted optimal changes in the flight-time distribution of a predator's walk in response to gradual density changes of its moving prey. Flight times of the dinoflagellate
Oxyrrhis marina
switched from an exponential to an inverse square power-law distribution when the prey (
Rhodomonas
sp.) decreased in abundance. Concomitantly, amplitude and frequency of the short-term helical path increased. The specific biological mechanisms involved in these searching behavioral changes are discussed. We suggest that, in a three-dimensional environment, a stronger helical component combined with a Lévy walk searching strategy enhances predator's encounter rates. Our results support the idea of universality of the statistical laws in optimal searching processes despite variations in the biological details of the organisms.
The development of diabetes in
E2f1/E2f2
mutant mice reveals important roles for bone marrow-derived cells in preventing islet cell loss
Authors: Li Feng X. , Zhu Jing W. , Tessem Jeffery S. , Beilke Joshua , Varella-Garcia Marileila , Jensen Jan , Hogan Christopher J. , DeGregori James
Published: October 2003

Our studies of mice deficient for the E2F1 and E2F2 transcription factors have revealed essential roles for these proteins in the cell cycle control of pancreatic exocrine cells and the regulation of pancreatic beta cell maintenance. Pancreatic exocrine cells in
E2f1/E2f2
mutant mice become increasingly polyploid with age, coinciding with severe exocrine atrophy. Furthermore, mice deficient for both E2F1 and E2F2 develop nonautoimmune, insulin-dependent diabetes with high penetrance. Surprisingly, transplantation of wild-type bone marrow can prevent or rescue diabetes in
E2f1
-/-
E2f2
-/-
mice. We hypothesize that exocrine degeneration results in a destructive environment for beta cells, which can be alleviated by restoration of the hematopoietic system that is also defective in
E2f1
-/-
E2f2
-/-
mice. The demonstration that beta cell maintenance under conditions of stress is influenced by bone marrow-derived cells may provide important insight into the design of therapies to boost islet mass and function in diabetic patients.
Identification of T cell-signaling pathways that stimulate latent HIV in primary cells
Authors: Brooks David G. , Arlen Philip A. , Gao Lianying , Kitchen Christina M. R. , Zack Jerome A.
Published: October 2003

Eradication of HIV infection depends on the elimination of a small, but stable population of latently infected T cells. After the discontinuation of therapy, activation of latent virus can rekindle infection. To purge this reservoir, it is necessary to define cellular signaling pathways that lead to activation of latent HIV. We used the SCID-hu (Thy/Liv) mouse model of HIV latency to analyze a broad array of T cell-signaling pathways and show in primary, quiescent cells that viral induction depends on the activation of two primary intracellular signaling pathways, protein kinase C or nuclear factor of activated T cells (NF-AT). In contrast, inhibition or activation of other important T cell stimulatory pathways (such as mitogen-activated protein kinase, calcium flux, or histone deacetylation) do not significantly induce virus expression. We found that the activation of NF-κB is critical to viral reactivation; however, all pathways that stimulate NF-κBdonot reactivate latent virus. Our studies further show that inhibition of NF-κB does not prevent activation of HIV by NF-AT, indicating that these pathways can function independently to activate the HIV LTR. Thus, we define several molecular pathways that trigger HIV reactivation from latency and provide evidence that latent HIV infection is maintained by the functional lack of particular transcription factors in quiescent cells.
The detection and quantitation of free desmosine and isodesmosine in human urine and their peptide-bound forms in sputum
Authors: Ma Shuren , Lieberman Seymour , Turino Gerard M. , Lin Yong Y.
Published: October 2003

Desmosine (D) and isodesmosine (I), the intramolecular crosslinking amino acids that occur in chains of elastin, have now been found in free form in human urine. Until now, these amino acids (
M
r
= 526) were found to occur in urine only as higher molecular weight (
M
r
= 1,000–1,500) peptides. Thus, the previously used analytical methods required, as the first step, acid hydrolysis of the urine at elevated temperature to liberate D and I from their peptides. The analytical method described here uses HPLC followed by electrospray ionization MS for the detection and quantitation of free D and I in unhydrolyzed urine. Identities of both D and I were established by their retention times on LC and by their mass ion at 526 atomic mass units, characteristic of each compound. The sensitivity of the method is 0.10 ng. The average values of free D and I in the urine of seven healthy subjects were 1.42 ± 1.16 and 1.39 ± 1.04 μg/g of creatinine, respectively. After acid hydrolysis of the urine, the amounts of D and I were 8.67 ± 3.75 and 6.28 ± 2.87 μg/g of creatinine, respectively. The method was also successfully used to measure peptide-bound D and I levels in the sputum of patients with chronic obstructive pulmonary disease.
Biodiversity as spatial insurance in heterogeneous landscapes
Authors: Loreau Michel , Mouquet Nicolas , Gonzalez Andrew
Published: October 2003

The potential consequences of biodiversity loss for ecosystem functioning and services at local scales have received considerable attention during the last decade, but little is known about how biodiversity affects ecosystem processes and stability at larger spatial scales. We propose that biodiversity provides spatial insurance for ecosystem functioning by virtue of spatial exchanges among local systems in heterogeneous landscapes. We explore this hypothesis by using a simple theoretical metacommunity model with explicit local consumer–resource dynamics and dispersal among systems. Our model shows that variation in dispersal rate affects the temporal mean and variability of ecosystem productivity strongly and nonmonotonically through two mechanisms: spatial averaging by the intermediate-type species that tends to dominate the landscape at high dispersal rates, and functional compensations between species that are made possible by the maintenance of species diversity. The spatial insurance effects of species diversity are highest at the intermediate dispersal rates that maximize local diversity. These results have profound implications for conservation and management. Knowledge of spatial processes across ecosystems is critical to predict the effects of landscape changes on both biodiversity and ecosystem functioning and services.
Evolution of the yeast protein interaction network
Authors: Qin Hong , Lu Henry H. S. , Wu Wei B. , Li Wen-Hsiung
Published: October 2003

To study the evolution of the yeast protein interaction network, we first classified yeast proteins by their evolutionary histories into isotemporal categories, then analyzed the interaction tendencies within and between the categories, and finally reconstructed the main growth path. We found that two proteins tend to interact with each other if they are in the same or similar categories, but tended to avoid each other otherwise, and that network evolution mirrors the universal tree of life. These observations suggest synergistic selection during network evolution and provide insights into the hierarchical modularity of cellular networks.
Induction of crossreactive antibodies against the Plasmodium falciparum variant protein
Authors: Gratepanche Sylvie , Gamain Benoit , Smith Joseph D. , Robinson Bridget A. , Saul Allan , Miller Louis H.
Published: October 2003

The variant antigenPlasmodium falciparumerythrocyte membrane protein 1 (PfEMP1), present on the surface ofP. falciparum-parasitized erythrocytes (PE), plays a central role in naturally acquired immunity, although antibodies to PfEMP1 are predominantly variant specific. To overcome this major limitation for vaccine development, we immunized mice with three cysteine-rich interdomain 1 (CIDR1) domains of PfEMP1 that have the critical function of binding the PE to CD36 on endothelium and thus preventing spleen-dependent killing of the parasite. The immunizations consisted of different combinations of three CIDR1 encoded by DNA followed by recombinant protein boost. Immunizations with a single variant in a prime-boost regimen induced no or low cross-reactivity toward heterologous CIDR1; however, a broad range of crossreactivity was detected in mice that were immunized with all three variants simultaneously. The induced crossreactivity suggests that an anti-PfEMP1 vaccine may be possible.
The contribution of protease-activated receptor 1 to neuronal damage caused by transient focal cerebral ischemia
Authors: Junge Candice E. , Sugawara Taku , Mannaioni Guido , Alagarsamy Sudar , Conn P. Jeffrey , Brat Daniel J. , Chan Pak H. , Traynelis Stephen F.
Published: October 2003

The serine proteases tissue plasminogen activator, plasmin, and thrombin and their receptors have previously been suggested to contribute to neuronal damage in certain pathological situations. Here we demonstrate that mice lacking protease-activated receptor 1 (PAR1) have a 3.1-fold reduction in infarct volume after transient focal cerebral ischemia. Intracerebroventricular injection of PAR1 antagonist BMS-200261 reduced infarct volume 2.7-fold. There are no detectable differences between PAR1-/-and WT mice in cerebrovascular anatomy, capillary density, or capillary diameter, demonstrating that the neuroprotective phenotype is not likely related to congenital abnormalities in vascular development. We also show that the exogenously applied serine proteases thrombin, plasmin, and tissue plasminogen activator can activate PAR1 signaling in brain tissue. These data together suggest that if blood-derived serine proteases that enter brain tissue in ischemic situations can activate PAR1, this sequence of events may contribute to the harmful effects observed. Furthermore, PAR1 immunoreactivity is present in human brain, suggesting that inhibition of PAR1 may provide a novel potential therapeutic strategy for decreasing neuronal damage associated with ischemia and blood–brain barrier breakdown.
Elevated mutagenesis and decreased DNA repair at a transgene are associated with proliferation but not apoptosis in p53-deficient cells
Authors: Bielas Jason H. , Heddle John A.
Published: October 2003

p53, the most commonly mutated gene in human tumors, is believed to play a crucial role in the prevention of cancer by protecting cells from mutation, a theory commonly known as the “Guardian of the Genome” hypothesis. There are two hypotheses as to how this can occur. In the first, p53 protects the genome by retarding the cell cycle, thus allowing more time for DNA repair. In the second, p53 reduces cancer by initiating apoptosis in damaged cells, thus making it impossible for these cells to become carcinogenic. This study directly tested these two theories in primary murine embryonic fibroblasts on a common genetic background with and without p53, using a
lacI
transgene as a mutational target. The data demonstrate that, as a direct consequence of cell cycle delay, p53 slowed the induction of mutations and decreased their frequency but had little effect on the frequency of apoptosis. This indicates that the function of p53 in cell cycle control is more important than the role of p53 in apoptosis, for mutation prevention, in any uniform cell population. Moreover, p53-mediated protection is further improved in slowly dividing cells, suggesting that p53 may be particularly important in protecting stem cells from mutation. The role of apoptosis
in vivo
, however, may be to remove whole tissue subpopulations that can be renewed by less sensitive stem cells.
Conformational changes in the C terminus of
Shaker
K
+
channel bound to the rat Kvβ2-subunit
Authors: Sokolova Olga , Accardi Alessio , Gutierrez David , Lau Adrian , Rigney Mike , Grigorieff Nikolaus
Published: October 2003

We studied the structure of the C terminus of the
Shaker
potassium channel. The 3D structures of the full-length and a C-terminal deletion (ΔC) mutant of
Shaker
were determined by electron microscopy and single-particle analysis. The difference map between the full-length and the truncated channels clearly shows a compact density, located on the sides of the T1 domain, that corresponds to a large part of the C terminus. We also expressed and purified both WT and ΔC
Shaker
, assembled with the rat Kvβ2-subunit. By using a difference map between the full-length and truncated
Shaker
α–β complexes, a conformational change was identified that shifts a large part of the C terminus away from the membrane domain and into close contact with the β-subunit. This conformational change, induced by the binding of the Kvβ2-subunit, suggests a possible mechanism for the modulation of the K
+
voltage-gated channel function by its β-subunit.
Supramolecular aggregation in 4,4′-bipyridin-1,1′-ium dichloride, 4,4′-bipyridin-1,1′-ium dinitrate and 4,4′-bipyridin-1-ium bromide
Authors: Iyere Peter Abeta , Boadi William Y , Atwood David , Parkin Sean
Published: October 2003

4,4′-Bipyridin-1,1′-ium dichloride [C10H10Cl2N2 (I)] and 4,4′-bipyridin-1,1′-ium dinitrate [C10H10N4O6 (II)] have been prepared and the crystal structures determined at 90.0 (2) K. Molecules of (I) are linked by two chlorine-bridged, three-centered N—H...Cl hydrogen bonds into chains along the b axis. The chains are coupled by weak C—H...Cl interactions into a molecular ladder along the c direction. In (II) each nitrate is coordinated to four bipyridinium ions through the interplay of the N—H...O and C—H...O contacts, resulting in a three-dimensional zigzag sheet on the ab plane. The sheets stack along the c axis. In 4,4′-bipyridin-1-ium bromide monohydrate [C10H9N2
+·Br−·H2O (III)] the bipyridinium ions are linked by three-center N—H...N′ hydrogen bonds in a head-to-tail fashion to form chains along the b axis. The chains are linked by C—H...Br and C—H...OH2 into a three-dimensional framework.
Structure–property correlation over five phases and four transitions in Pb5Al3F19
Authors: Abrahams S. C. , Ravez J. , Ritter H. , Ihringer J.
Published: October 2003

The calorimetric and dielectric properties of Pb5Al3F19 in the five phases stable under ambient pressure are correlated with structure for fuller characterization of each phase. The first-order transition between ferroelectric phase V and antiferroelectric phase IV at T
V,IV = 260 (5) K exhibits a thermal hysteresis of 135 (5) K on heating, with a maximum atomic displacement Δ(xyz)max = 1.21 (6) Å; the transition from phase IV to ferroelastic phase III at 315 (5) K is also first order but with a thermal hysteresis of 10 (5) K and Δ(xyz)max = 0.92 (7)  Å; that from phase III to paraelastic phase II at 360 (5) K is second order without hysteresis and has Δ(xyz)max = 0.69 (4) Å; and the transition from phase II to paraelectric phase I at 670 (5) K is second or higher order, with Δ(xyz)max = 0.7 (4) Å. The measured entropy change ΔS at T
V,IV agrees well with ΔS as derived from the increased configurational energy by Stirling's approximation. For all other phase transitions, 0.5 ≥ ΔS > 0 J mol−1 K−1 is consistent with an entropy change caused primarily by the changes in the vibrational energy. The structure of phase III is determined both by group theoretical/normal mode analysis and by consideration of the structures of phases II, IV and V reported previously; refinement is by simultaneous Rietveld analysis of the X-ray and neutron diffraction powder profiles. The structure of prototypic phase I is predicted on the basis of the atomic arrangement in phases II, III, IV and V. The introduction of 3d electrons into the Pb5Al3F19 lattice disturbs the structural equilibrium, the addition of 0.04% Cr3+ causing significant changes in atomic positions and increasing T
IV,III by ∼15 K. Substitution of Al3+ by 20% or more Cr3+ eliminates the potential minima that otherwise stabilize phases IV, III and II.
Features of the electron density in magnesium diboride: reconstruction from X-ray diffraction data and comparison with TB-LMTO and FPLO calculations
Authors: Tsirelson V. , Stash A. , Kohout M. , Rosner H. , Mori H. , Sato S. , Lee S. , Yamamoto A. , Tajima S. , Grin Yu.
Published: October 2003

Features of the electron density in MgB2 reconstructed from room-temperature single-crystal X-ray diffraction intensities using a multipole model are considered. Topological analysis of the total electron density has been applied to characterize the atomic interactions in magnesium diboride. The shared-type B—B interaction in the B-atom layer reveals that both σ and π components of the bonding are strong. A closed-shell-type weak B—B π interaction along the c axis of the unit cell has also been found. The Mg—B closed-shell interaction exhibits a bond path that is significantly curved towards the vertical Mg-atom chain ([110] direction). The latter two facts reflect two sorts of bonding interactions along the [001] direction. Integration of the electron density over the zero-flux atomic basins reveals a charge transfer of ∼1.4 (1) electrons from the Mg atoms to the B-atom network. The calculated electric-field gradients at nuclear positions are in good agreement with experimental NMR values. The anharmonic displacement of the B atoms is also discussed. Calculations of the electron density by tight-binding linear muffin-tin orbital (TB-LMTO) and full-potential non-orthogonal local orbital (FPLO) methods confirm the results of the reconstruction from X-ray diffraction; for example, a charge transfer of 1.5 and 1.6 electrons, respectively, was found.
Synthesis and structure of M
0.5Bi3P2O10 (M = Ca, Sr, Ba, Pb) series
Authors: Porob Digamber G. , Guru Row T. N.
Published: October 2003

A series of M
0.5Bi3P2O10 compounds with M = Ca, Sr, Ba and Pb have been synthesized in MO–Bi2O3–P2O5 ternary systems by the ceramic method and the crystal structures were then solved using single-crystal X-ray diffraction data. These compounds are isostructural with Bi6.67P4O20 (triclinic, space group P\bar 1, Z = 2). The structures consist of infinite chains of Bi2O2 units along the c axis formed by linking BiO8 and BiO6 polyhedra. These chains are interconnected by MO8 polyhedra forming two-dimensional layers in the ac plane. The phosphate tetrahedra are sandwiched between these layers.
A database survey of molecular and crystallographic symmetry
Authors: Pidcock Elna , Motherwell W. D. Samuel , Cole Jason C.
Published: October 2003

The point of contact between molecular and crystallographic symmetries is that of the Wyckoff position, the position at which a molecule resides in a crystal structure. These Wyckoff positions may have the same symmetry as the molecules, some symmetry in common with the molecules or no symmetry at all. Using CSDSymmetry [Yao et al. (2002). Acta Cryst. B58, 640–646], a relational database containing information pertaining to the symmetry of molecules and the crystal structures that play host to them, the distribution of molecules over Wyckoff positions and the occupancy of Wyckoff positions in crystal structures is presented. Analysis of these data has led to the characterization of some relationships between molecular and crystallographic symmetry.
Sodium percarbonate between 293 and 100 K
Authors: Pritchard Robin Gavin , Islam Emran
Published: October 2003

Sodium carbonate perhydrate, Na2CO3·1.5H2O2, commonly known as sodium percarbonate, has been structurally characterized at temperatures ranging from 293 down to 100 K. As the temperature drops, there is a reversible phase change between 250 and 240 K, in which the crystallographic mirror plane of the room-temperature space group, Cmca, is lost, transforming it to Pbca. This transformation is accompanied by a reversal in the expansion coefficient of cell side b, which, like the other two sides, initially contracts on cooling. The two crystallographically independent hydrogen peroxide sites undergo the largest change, where the disorder seen at room temperature gradually diminishes and is almost completely absent at 100 K, thus indicating dynamic rather than static disorder. It is noteworthy that, despite Cmca being the preferred room-temperature space group in the current work, two previous single-crystal studies rejected this space group in favour of non-centrosymmetric Aba2 [Carrondo et al. (1977). J. Chem. Soc. Dalton Trans. pp. 2323–2331; Adams & Pritchard (1977). Acta Cryst. B33, 3650–3653]. A re-evaluation of these determinations indicates that they are identical to the current structure and should be re-assigned to Cmca.
X-ray studies on crystalline complexes involving amino acids and peptides. XLI. Commonalities in aggregation and conformation revealed by the crystal structures of the pimelic acid complexes of L-arginine and DL-lysine
Authors: Saraswathi N. T. , Roy Siddhartha , Vijayan M.
Published: October 2003

The complexes of L-arginine and DL-lysine with pimelic acid are made up of singly positively charged zwitterionic amino acid cations and doubly negatively charged pimelate ions in a 2:1 ratio. In both structures, the amino acid molecules form twofold symmetric or centrosymmetric pairs that are stabilized by hydrogen bonds involving α-amino and α-carboxylate groups. In the L-arginine complex, these pairs form columns along the shortest cell dimension, stabilized by intermolecular hydrogen bonds involving α-amino and α-carboxylate groups. The columns are connected by hydrogen bonds and water bridges to give rise to an amino acid layer. Adjacent layers are then connected by pimelate ions. Unlike molecular ions aggregate into alternating distinct layers in the DL-lysine complex. In the amino acid layer, hydrogen-bonded lysinium dimers related by a glide plane are connected by hydrogen bonds involving α-amino and α-carboxylate groups into head-to-tail sequences. Interestingly, the aggregation pattern observed in L-arginine hemipimelate monohydrate is very similar to those in DL-arginine formate dihydrate, DL-arginine acetate monohydrate and L-arginine hemiglutarate monohydrate. Similarly, the aggregation of amino acid molecules is very similar in DL-lysine hemipimelate 0.53-hydrate, DL-lysine formate and DL-lysine hydrochloride. The complexes thus demonstrate how, in related structures, the effects of a change in composition, and sometimes even those of reversal in chirality, can be accommodated by minor adjustments in essentially the same aggregation pattern. It also transpires that the conformation of the argininium ion is the same in the four argininium complexes; the same is true about the conformation of the lysinium ion in the three lysinium complexes. This result indicates a relation between, and mutual dependence of, conformation and aggregation.
Monitoring structural transformations in crystals. 5. A topotactic [2 + 2]-photodimerization reaction
Authors: Turowska-Tyrk Ilona
Published: October 2003

The structural changes in a crystal of 5-benzylidene-2-(4-chlorobenzyl)cyclopentanone during [2 + 2]-photodimerization were monitored by means of X-ray diffraction. It was observed that the monomers moved gradually from the position occupied in the crystal at the initial stage of the photoreaction and the dimers moved towards the position assumed at the final step. The movements of the molecules possess a rotational component. Moreover, with the progress of the phototransformation the monomers in the reacting pair gradually move closer and change their relative orientation to resemble more the product molecule. The behaviour of the molecules and also the variation of the cell constants for the studied compound were compared with data for 5-benzylidene-2-benzylcyclopentanone.
Temperature-resolved study of the structural behaviour of nickel octahexyl phthalocyanine up to the liquid crystal transition
Authors: Helliwell Madeleine , Teat Simon J. , Coles Simon J. , Reeve William
Published: October 2003

This paper describes a temperature-resolved crystallographic investigation into the behaviour of the title compound as the temperature is increased stepwise from room temperature up to 418 K, which is the temperature at which a transition to a discotic columnar mesophase takes place. The experiments were conducted using synchrotron radiation on Station 9.8 at the SRS at the Daresbury Laboratory. An intermediate transition to a less well ordered crystal form was seen at 326 K and differential scanning calorimetry (DSC) measurements confirmed the transition temperature of this change. Also, a new improved room-temperature crystal structure was obtained, as well as further structure determinations at 323, 328 and 353 K. These showed that as the mobility, particularly of the hexyl groups, increases with temperature, the packing of the molecules adjusts from pseudohexagonal layers to a rectangular arrangement.