bluuebunny/crossref_metadata_2025 huggingface dataset:
“In the Power of God Christ”: Greek inscriptional evidence for the anti-Arian theology of Ethiopia's first Christian king
Authors: Black Stephanie L
Published: February 2008

Four fourth-century ad inscriptions of Ezana, first Christian king of Aksum (Ethiopia), are surveyed, with special attention to Ezana's only known post-conversion inscription, written in Greek. Greek syntax and terminology in Ezana's inscription point to an anti-Arian Christology which may be associated with Frumentius, first bishop of Aksum, and his connection with Athanasius of Alexandria. The inscription's trinitarian formula “the power of the Father and Son and Holy Spirit” is structured in such a way as to assert the identity of the three members of the Trinity. The phrase “in the power of God Christ” further equates Christ with God. This christological language stands in contrast to the Arian imperial policy of the time, and is historically significant in light of Constantius's attempt to force Frumentius's recall to Alexandria. This inscription serves as the first internal documentary evidence for an anti-Arian Christology in the earliest developments of Ethiopian Christianity.
International Relations and the challenges of global communication
Authors: CONSTANTINOU COSTAS M. , RICHMOND OLIVER P. , WATSON ALISON M. S.
Published: February 2008

We live in an interconnected, hyper-mediated world. A plethora of communications surrounds our everyday lives and polities, whilst new media and technologies have brought forth possibilities for, and ways of, communicating across space and time. Long-distance communication and travelling, the accelerated flow of information, ideas, images and sounds across national and other frontiers, the construction of multinational urban centres and global media corporations, the live broadcasting and commercialisation of major events and crises, the expansion of global advertising, spin and political marketing, and the advent of the Internet, have modified and complicated the reality of national, international and transnational relationships. This very collection of essays was made possible via the Internet to connect the Editors, based in different locations and while they were travelling. This is now the norm. Slightly more unusually, yet underlining the growing potential of this area, a workshop held at the University of St Andrews in November 2006 brought some of the contributors together both physically and virtually through the medium of Skype. Physical presence has long not been necessary in order to communicate, influence, or indeed, coerce.
On order and conflict: International Relations and the ‘communicative turn’
Authors: ALBERT MATHIAS , KESSLER OLIVER , STETTER STEPHAN
Published: February 2008

This article begins from the observation that while communication is a widely used catch-phrase in current IR theorising, the very concept of ‘communication’ is still mainly treated in terms of simple sender-receiver models which do not sufficiently elaborate how the insights of the ‘communicative turn’ can be made fruitful for IR theorising. The argument is developed in three steps. First – particularly drawing on the work of Karl W. Deutsch – we identify those pockets in IR theory, namely conflict studies and theories of ‘communicative action’, in which ‘communication’ plays a considerable theoretical role. Second, it is claimed that placing ‘communication’ at the centre of any theory of IR requires taking full account of the theoretical consequences of the ‘linguistic turn’. To develop this argument requires an examination of the often implicit notion of ‘communication’ in contemporary uses of speech act theory and symbolic interactionism in current IR theory. Such a move necessarily leads to the diagnosis that all social systems and orders of exchange, including international relations, are communicatively constituted. Finally, such a view enables a reconfiguration of the central problems of ‘order’ and ‘conflict’ in IR theory in an innovative fashion: while the problem of order can be restated not as the problem of establishing regularities and patterns but as a problem of disconnecting communications, the problem of conflict can be restated not as a problem of a disruption of communication but as a problem of continuing conflict communication.
Global communication and political culture in the semi-periphery: the rise of the Globo corporation
Authors: WILKIN PETER
Published: February 2008

This article will offer a description and explanation of the rise of the Brazilian media corporation Globo by situating it in the context of the periphery and semi-periphery of the World System and the globalisation of communication. In particular it focuses upon the changing role that Globo has played in the construction of an elite-led political culture in Brazil that has moved through phases of authoritarian and democratic government. The article sets out an historical account of the emergence of Globo from being a regional media organisation in the periphery of the world system to a global broadcaster in the semi-periphery. It moves through three phases: First, 1925–1964, the colonial legacy and Brazil in the periphery; second, 1964–1985, a period of transition and conservative modernisation, into the semi-periphery; and finally, 1985 onwards, the age of globalisation.
Aetiological factors and perception of anaemia in Tunisian women of reproductive age
Authors: Ati Jalila El , Lefèvre Pierre , Béji Chiraz , Ben Rayana Chiheb , Gaigi Sadok , Delpeuch Francis
Published: February 2008

Objectives

To identify aetiological factors in anaemia and to explore knowledge, perceptions and attitudes towards anaemia.

Design

Two cross-sectional surveys and sixteen focus group discussions.

Setting

The two regions with the highest prevalence of anaemia in Tunisia, Greater Tunis (GT) and the South West (SW).

Subjects

Two representative samples of 687 (GT) and 729 (SW) women of reproductive age; 108 women were included in focus group discussions.

Results

Among anaemic women, 63·4 % in the GT region and 80·2 % in the SW displayed iron deficiency (ID). Genetic haemoglobinopathies accounted for 10·0 % and 3·6 % of the cases of anaemia in the two regions, respectively. After adjustment for confounders, the major factors for iron-deficiency anaemia were low dietary Fe intake (OR = 5·0, 95 % CI 3·0, 8·4), drinking tea after eating (OR = 3·4, 95 % CI 2·0, 5·7) and pica (OR = 2·1, 95 % CI 1·1, 3·9). Most of the women related anaemia to the following causes: malnutrition, lack of hygiene, and their heavy workload and responsibilities in the household. Many women connected anaemia with hypotension. Few established a relationship between ID and anaemia. They had confidence in their doctor for treatment, but many complained they were not given sufficient information. Low dietary Fe intake, inappropriate food practices and inadequate perceptions contribute to the aetiology of anaemia in women.

Conclusions

These results point out to the need for a strategy combining food fortification, Fe supplementation for pregnant women, nutritional education for the general public and at-risk specific target groups, and training of health professionals.
Arctic sea ice parameters from AMSR‐E data using two techniques and comparisons with sea ice from SSM/I
Authors: Comiso Josefino C. , Parkinson Claire L.
Published: February 2008

We use two algorithms to process Advanced Microwave Scanning Radiometer for the Earth Observing System (AMSR‐E) data in order to determine algorithm dependence, if any, on the estimates of sea ice concentration, ice extent and area, and trends and to evaluate how AMSR‐E data compare with historical Special Sensor Microwave Imager (SSM/I) data. The monthly ice concentrations derived from the two algorithms from AMSR‐E data (the AMSR‐E bootstrap algorithm, or ABA, and the enhanced NASA team algorithm, or NT2), differ on average by about 1–3%, with data from the consolidated ice region being comparable for ABA and NT2 retrievals while data in the marginal ice zones and thin ice regions show slightly higher values when the NT2 algorithm is used. The iceextents and areas derived separately from AMSR‐E using these two algorithms are, however, in good agreement, with the differences (ABA – NT2) being about 0.07 × 106 km2 on average for ice extents and −0.07 × 106 km2 for ice area, which are small compared with mean seasonal values of 10.5 × 106 and 9.8 × 106 for ice extent and area, respectively. Likewise, extents and areas derived from the same algorithm but from AMSR‐E and SSM/I data are consistent but differ by about 0.24 × 106 km2 and 0.14 × 106 km2, respectively. The discrepancies are larger with the estimates of extents than area mainly because of differences in channel selection and sensor resolutions. Trends in extent during the AMSR‐E era were also estimated, and results from all three data sets are shown to be in good agreement (within errors).
Heregulin β1 promotes breast cancer cell proliferation through Rac/ERK-dependent induction of cyclin D1 and p21Cip1
Authors: Yang Chengfeng , Klein Eric A. , Assoian Richard K. , Kazanietz Marcelo G.
Published: February 2008

Accumulating evidence indicates that heregulins, EGF (epidermal growth factor)-like ligands, promote breast cancer cell proliferation and are involved in the progression of breast cancer towards an aggressive and invasive phenotype. However, there is limited information regarding the molecular mechanisms that mediate these effects. We have recently established that HRG (heregulin β1) promotes breast cancer cell proliferation and migration via cross-talk with EGFR (EGF receptor) that involves the activation of the small GTPase Rac1. In the present paper we report that Rac1 is an essential player for mediating the induction of cyclin D1 and p21Cip1 by HRG in breast cancer cells. Inhibition of Rac function by expressing either the Rac-GAP (GTPase-activating protein) β2-chimaerin or the dominant-negative Rac mutant N17Rac1, or Rac1 depletion using RNAi (RNA interference), abolished the cyclin D1 and p21Cip1 induction by HRG. Interestingly, the proliferative effect of HRG was impaired not only when the expression of Rac1 or cyclin D1 was inhibited, but also when cells were depleted of p21Cip1 using RNAi. Inhibition of EGFR, PI3K (phosphoinositide 3-kinase; kinases required for Rac activation by HRG) or MEK [MAPK (mitogen-activated protein kinase)/ERK (extracellular-signal-regulated kinase) kinase] also blocked the up-regulation of cyclin D1 and p21Cip1 by HRG. In addition, we found that HRG activates NF-κB (nuclear factor κB) in a Rac1- and MEK-dependent fashion, and inhibition of NF-κB abrogates cyclin D1/p21Cip1 induction and proliferation by HRG. Taken together, these findings establish a central role for Rac1 in the control of HRG-induced breast cancer cell-cycle progression and proliferation through up-regulating the expression of cyclin D1 and p21Cip1.
IL-6 and IL-8 increase the expression of glycosyltransferases and sulfotransferases involved in the biosynthesis of sialylated and/or sulfated Lewisx epitopes in the human bronchial mucosa
Authors: Groux-Degroote Sophie , Krzewinski-Recchi Marie-Ange , Cazet Aurélie , Vincent Audrey , Lehoux Sylvain , Lafitte Jean-Jacques , van Seuningen Isabelle , Delannoy Philippe
Published: February 2008

Bronchial mucins from patients suffering from CF (cystic fibrosis) exhibit glycosylation alterations, especially increased amounts of the sialyl-Lewisx (NeuAcα2-3Galβ1-4[Fucα1-3]GlcNAc-R) and 6-sulfo-sialyl-Lewisx (NeuAcα2-3Galβ1-4[Fucα1-3][SO3H-6]GlcNAc-R) terminal structures. These epitopes are preferential receptors for Pseudomonas aeruginosa, the bacteria responsible for the chronicity of airway infection and involved in the morbidity and early death of CF patients. However, these glycosylation changes cannot be directly linked to defects in CFTR (CF transmembrane conductance regulator) gene expression since cells that secrete airway mucins express no or very low amounts of the protein. Several studies have shown that inflammation may affect glycosylation and sulfation of various glycoproteins, including mucins. In the present study, we show that incubation of macroscopically healthy fragments of human bronchial mucosa with IL-6 (interleukin-6) or IL-8 results in a significant increase in the expression of α1,3/4-fucosyltransferases [FUT11 (fucosyltransferase 11 gene) and FUT3], α2-6- and α2,3-sialyltransferases [ST3GAL6 (α2,3-sialyltransferase 6 gene) and ST6GAL2 (α2,6-sialyltransferase 2 gene)] and GlcNAc-6-O-sulfotransferases [CHST4 (carbohydrate sulfotransferase 4 gene) and CHST6] mRNA. In parallel, the amounts of sialyl-Lewisx and 6-sulfo-sialyl-Lewisx epitopes at the periphery of high-molecular-mass proteins, including MUC4, were also increased. In conclusion, our results indicate that IL-6 and -8 may contribute to the increased levels of sialyl-Lewisx and 6-sulfo-sialyl-Lewisx epitopes on human airway mucins from patients with CF.
The dramatically increased chaperone activity of small heat-shock protein IbpB is retained for an extended period of time after the stress condition is removed
Authors: Jiao Wangwang , Hong Weizhe , Li Pulin , Sun Shihu , Ma Jing , Qian Mengding , Hu Mengdie , Chang Zengyi
Published: February 2008

sHSP (small heat-shock protein) IbpB (inclusion-body-binding protein B) from Escherichia coli is known as an ATP-independent holding chaperone which prevents the insolubilization of aggregation-prone proteins by forming stable complexes with them. It was found that the chaperone function of IbpB is greatly modulated by the ambient temperature, i.e. when the temperature increases from normal to heat-shock, the chaperone activity of IbpB is dramatically elevated to a level that allows it to effectively bind the aggregation-prone client proteins. Although it is generally believed that the release and refolding of the client protein from the sHSPs depends on the aid of the ATP-dependent chaperones such as Hsp (heat-shock protein) 70 and Hsp100 when the ambient temperature recovers from heat-shock to normal, the behaviour of the sHSPs during this recovery stage has not yet been investigated. In the present study, we examined the behaviour and properties of IbpB upon temperature decrease from heat-shock to normal. We found that IbpB, which becomes functional only under heat-shock conditions, retains the chaperone activity for an extended period of time after the heat-shock stress condition is removed. A detail comparison demonstrates that such preconditioned IbpB is distinguished from the non-preconditioned IbpB by a remarkable conformational transformation, including a significant increase in the flexibility of the N- and C-terminal regions, as well as enhanced dynamic subunit dissociation/reassociation. Intriguingly, the preconditioned IbpB displayed a dramatic decrease in its surface hydrophobicity, suggesting that the exposure of hydrophobic sites might not be the sole determinant for IbpB to exhibit chaperone activity. We propose that the maintenance of the chaperone activity for such ‘holdases’ as sHSPs would be important for cells to recover from heat-shock stress.
La
Al
O
3
gate dielectric with ultrathin equivalent oxide thickness and ultralow leakage current directly deposited on Si substrate
Authors: Suzuki Masamichi , Yamaguchi Takeshi , Fukushima Noburu , Koyama Masato
Published: February 2008

By a careful choice of film deposition conditions, LaAlO3 (LAO) gate dielectric film with equivalent oxide thickness (EOT) of 0.31nm and gate leakage current density (Jg) of 0.1A∕cm2 (at Vfb+1V) has been successfully demonstrated. Elimination of interfacial low-k layer at LAO/Si and reduction of defect density in LAO has been realized through both LAO film deposition at high-temperature (700°C) and subsequent low-temperature (200°C) annealing. By using thermal desorption spectroscopy technique, we find that our process reduces remnant H2O or OH− species in the LAO film, which are responsible for the degradation of EOT and Jg.
Ferromagnetism in Cu-doped ZnO films: Role of charge carriers
Authors: Tiwari Ashutosh , Snure Michael , Kumar Dhananjay , Abiade Jeremiah T.
Published: February 2008

We report the observation of room temperature ferromagnetism in Cu-doped (5%) ZnO films grown on c-plane sapphire substrates. Films were prepared by pulsed laser deposition technique and were thoroughly characterized using several state-of-the-art characterization techniques. Hall measurements showed that the films are of n-type with a carrier concentration of 3×1017cm−3. Magnetization measurements showed that the films exhibit room temperature ferromagnetism with a saturation magnetization of ∼1.45μB∕Cu atom. When additional carriers were introduced in the films, ferromagnetism was completely vanished. Our results show that the p-type nature of the film is not essential for realizing ferromagnetic characteristics; however, the concentration of n-type carriers should not exceed a critical value.
Sustained surface wave propagation induced by surface diffusion driven by strain relaxation in a heteroepitaxial film
Authors: Liu P. , Zhang Y. W. , Gao H. J. , Lam K. Y.
Published: February 2008

We examine the dynamics of surface pattern formation during both annealing and vapor deposition of a heteroepitaxial thin film on prepatterned substrate surfaces, predicting a sustained propagation of regular surface waves via surface diffusion driven by strain relaxation. Both the wavelength and propagation speed are found to be insensitive to the surface prepatterns, growth rate and film thickness.
SOX2-expressing progenitor cells generate all of the major cell types in the adult mouse pituitary gland
Authors: Fauquier Teddy , Rizzoti Karine , Dattani Mehul , Lovell-Badge Robin , Robinson Iain C. A. F.
Published: February 2008

The pituitary gland adapts the proportion of each of its endocrine cell types to meet differing hormonal demands throughout life. There is circumstantial evidence that multipotent adult progenitor cells contribute to this plasticity, but these cells have not been identified. Here, we describe a small (<0.05%) population of progenitor cells in the adult pituitary gland. We show that these cells express SOX2, a marker of several early embryonic progenitor and stem cell types, and form “pituispheres” in culture, which can grow, form secondary spheres, and differentiate to all of the pituitary endocrine cell types, as well as folliculostellate cells. Differentiation of cells in the pituispheres was associated with the expression of nestin, SOX9, and S100. Cells expressing SOX2 and E-cadherin are found throughout Rathke's pouch (RP) in embryos but persist in the adult gland, mostly in a narrow zone lining the pituitary cleft, but also are scattered throughout the pituitary. However, unlike in embryonic RP, most of these SOX2
+
cells in the adult gland also express SOX9 and S100. We suggest that this SOX2
+
/SOX9
+
population represents transit-amplifying cells, whereas the SOX2
+
/SOX9
−
cells we identify are multipotent progenitor/stem cells persisting in the adult pituitary.
A systems approach to delineate functions of paralogous transcription factors: Role of the Yap family in the DNA damage response
Authors: Tan Kai , Feizi Hoda , Luo Colin , Fan Stephanie H. , Ravasi Timothy , Ideker Trey G.
Published: February 2008

Duplication of genes encoding transcription factors plays an essential role in driving phenotypic variation. Because regulation can occur at multiple levels, it is often difficult to discern how each duplicated factor achieves its regulatory specificity. In these cases, a “systems approach” may distinguish the role of each factor by integrating complementary large-scale measurements of the regulatory network. To explore such an approach, we integrate growth phenotypes, promoter binding profiles, and gene expression patterns to model the DNA damage response network controlled by the Yeast-specific AP-1 (YAP) family of transcription factors. This analysis reveals that YAP regulatory specificity is achieved by at least three mechanisms: (
i
) divergence of DNA-binding sequences into two subfamilies; (
ii
) condition-specific combinatorial regulation by multiple Yap factors; and (
iii
) interactions of Yap 1, 4, and 6 with chromatin remodeling proteins. Additional microarray experiments establish that Yap 4 and 6 regulate gene expression through interactions with the histone deacetylase, Hda1. The data further highlight differences among Yap paralogs in terms of their regulatory mode of action (activation vs. repression). This study suggests how other large TF families might be disentangled in the future.
Independent evolution of an antiviral TRIMCyp in rhesus macaques
Authors: Wilson Sam J. , Webb Benjamin L. J. , Ylinen Laura M. J. , Verschoor Ernst , Heeney Jonathan L. , Towers Greg J.
Published: February 2008

The antiretroviral restriction factor TRIM5 has recently emerged as an important mediator of innate immunity and species-specific inhibition of retroviral replication in mammals. Selection pressure from pathogenic infection has driven rapid evolution of TRIM5 genes, leading to the antiviral specificities we see today. Remarkably, the New World owl monkey (
Aotus trivirgatus
) encodes a TRIM5 protein in which the antiviral determinants in the B30.2 domain have been replaced by cyclophilin A (CypA) encoded by a retrotransposed cDNA. The owl monkey TRIMCyp protein restricts infection by a subset of lentiviruses that recruit CypA to their capsids, including HIV-1 and feline immunodeficiency virus. Here, we show that the Old World monkey, rhesus macaque (
Macaca mulatta
), also encodes a TRIMCyp protein that has arisen independently from that in owl monkeys. The rhesus TRIMCyp is encoded by a single, but common, allele (
Mamu7
) of the rhesus TRIM5 gene, among at least six further alleles that encode full-length TRIM5 proteins with no homology to CypA. The antiviral specificity of the rhesus TRIMCyp is distinct, restricting infection of HIV-2 and feline immunodeficiency virus but not HIV-1. Restriction by rhesus TRIMCyp is before reverse transcription and inhibited by blocking CypA binding, with cyclosporine A, or by mutation of the capsid CypA binding site. These observations suggest a mechanism of restriction that is conserved between TRIMCyp proteins. The lack of activity against HIV-1 suggests that
Mamu7
homozygous animals will be null for TRIM5-mediated restriction of HIV-1 and could contribute to improved animal models for HIV/AIDS.
PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis
Authors: Mosher Rebecca A. , Schwach Frank , Studholme David , Baulcombe David C.
Published: February 2008

DNA-dependent RNA polymerase (Pol)IV in
Arabidopsis
exists in two isoforms (PolIVa and PolIVb), with NRPD1a and NRPD1b as their respective largest subunits. Both isoforms are implicated in production and activity of siRNAs and in RNA-directed DNA methylation (RdDM). Deep sequence analysis of siRNAs in WT
Arabidopsis
flowers and in
nrpd1a
and
nrpd1b
mutants identified >4,200 loci producing siRNAs in a PolIV-dependent manner, with PolIVb reinforcing siRNA production by PolIVa. Transposable element identity and pericentromeric localization are both features that predispose a locus for siRNA production via PolIV proteins and determine the extent to which siRNA production relies on PolIVb. Detailed analysis of DNA methylation at PolIV-dependent loci revealed unexpected deviations from the previously noted association of PolIVb-dependent siRNA production and RdDM. Notably, PolIVb functions independently in DNA methylation and siRNA generation. Additionally, we have uncovered siRNA-directed loss of DNA methylation, a process requiring both PolIV isoforms. From these findings, we infer that the role of PolIVb in siRNA production is secondary to a role in chromatin modification and is influenced by chromatin context.
CNK and HYP form a discrete dimer by their SAM domains to mediate RAF kinase signaling
Authors: Rajakulendran Thanashan , Sahmi Malha , Kurinov Igor , Tyers Mike , Therrien Marc , Sicheri Frank
Published: February 2008

RAF kinase functions in the mitogen-activated protein kinase (MAPK) pathway to transmit growth signals to the downstream kinases MEK and ERK. Activation of RAF catalytic activity is facilitated by a regulatory complex comprising the proteins CNK (
C
onnector e
n
hancer of
K
SR), HYP (Hyphen), and KSR (
K
inase
S
uppressor of
R
as). The sterile α-motif (SAM) domain found in both CNK and HYP plays an essential role in complex formation. Here, we have determined the x-ray crystal structure of the SAM domain of CNK in complex with the SAM domain of HYP. The structure reveals a single-junction SAM domain dimer of 1:1 stoichiometry in which the binding mode is a variation of polymeric SAM domain interactions. Through
in vitro
and
in vivo
mutational analyses, we show that the specific mode of dimerization revealed by the crystal structure is essential for RAF signaling and facilitates the recruitment of KSR to form the CNK/HYP/KSR regulatory complex. We present two docking-site models to account for how SAM domain dimerization might influence the formation of a higher-order CNK/HYP/KSR complex.
Natal dispersal driven by environmental conditions interacting across the annual cycle of a migratory songbird
Authors: Studds Colin E. , Kyser T. Kurt , Marra Peter P.
Published: February 2008

Natal dispersal, the process through which immature individuals permanently depart their natal area in search of new sites, is integral to the ecology and evolution of animals. Insights about the underlying causes of natal dispersal arise mainly from research on species whose short dispersal distances or restricted distributions make them relatively easy to track. However, for small migratory animals, the causes of natal dispersal remain poorly understood because individuals are nearly impossible to track by using conventional mark–recapture approaches. Using stable-hydrogen isotope ratios in feathers of American redstarts (Setophaga ruticilla) captured as immature birds and again as adults, we show that habitat use during the first tropical nonbreeding season appears to interact with latitudinal gradients in spring phenology on the temperate breeding grounds to influence the distance traveled on the initial spring migration and the direction of natal dispersal. In contrast, adult redstarts showed considerable site fidelity between breeding seasons, indicating that environmental conditions did not affect dispersal patterns after the first breeding attempt. Our findings suggest that habitat occupancy during the first nonbreeding season helps determine the latitude at which this species of Neotropical–Nearctic migratory bird breeds throughout its life and emphasize the need to understand how events throughout the annual cycle interact to shape fundamental biological processes.
Quorum size of
Pseudomonas syringae
is small and dictated by water availability on the leaf surface
Authors: Dulla Glenn , Lindow Steven E.
Published: February 2008

The paradigm of bacterial quorum sensing (QS), which mediates cell-density-dependent gene expression, usually has been studied in high-cell-density planktonic liquid cultures or in biofilms in which signal concentrations accumulate to sufficiently high levels to induce QS. Presumably under conditions with restricted diffusion of the signal molecule, smaller population sizes could achieve such a state of QS induction. The plant-pathogenic bacterium
Pseudomonas syringae
, in which QS controls traits involved in epiphytic fitness and virulence, occurs on leaf surfaces in aggregates of various sizes. Because leaves often harbor limited surface water, we investigated the size of aggregates that would permit QS in a nonsaturated environment. QS induction was visualized via dual fluorescence of
P. syringae
cells harboring a transcriptional fusion of mRFP1 with
ahlI
, which exhibits
N
-acyl homoserine lactone-dependent transcriptional activity, and a constitutive GFP marker to account for all
P. syringae
cells on a leaf. Confocal microscopy revealed that, on wet leaves, no QS induction was evident within 2 days after inoculation, but it increased rapidly with increasing aggregate sizes >40 and 22 cells per aggregate by 3 and 4 days, respectively. In contrast, QS induction was common in aggregates >33 cells by 2 days after inoculation on dry leaves and increased rapidly with increasing aggregate sizes >35 and 13 cells after 3 and 4 days, respectively. These observations demonstrate that small groups of cells experience QS conditions on dry leaves where signal diffusion is restricted. Quorum size of bacteria in non-water-saturated environments such as on leaves is small, and QS induction may be commonly operative.
HLA alleles determine differences in human natural killer cell responsiveness and potency
Authors: Kim Sungjin , Sunwoo John B. , Yang Liping , Choi Taewoong , Song Yun-Jeong , French Anthony R. , Vlahiotis Anna , Piccirillo Jay F. , Cella Marina , Colonna Marco , Mohanakumar Thalachallour , Hsu Katharine C. , Dupont Bo , Yokoyama Wayne M.
Published: February 2008

Epidemiological studies have associated certain human disease outcomes with particular killer cell Ig-like receptor (KIR) and HLA genotypes. However, the functional explanation for these associations is poorly understood, because the KIRs were initially described as natural killer (NK) cell inhibitory receptors with specificity for HLA molecules on their cellular targets. Yet resolution of infections is often associated with genotypic pairing of inhibitory KIRs with their cognate HLA ligands. Recent studies in mice indicate a second role for MHC-specific inhibitory receptors, i.e., self-MHC recognition confers functional competence on the NK cell to be triggered through their activation receptors, a process termed licensing. As a result, licensed NK cells with self-MHC-specific receptors are more readily activated as compared with unlicensed NK cells without self-MHC-specific receptors. Such results predict that human NK cells may undergo a similar process. Here, we examined the human NK cell subset expressing KIR3DL1, the only known KIR specific for HLA-Bw4 alleles. The KIR3DL1
+
subset in normal donors with two HLA-B-Bw4 genes displayed increased responsiveness to tumor stimulation compared with the KIR3DL1
+
subset from individuals with only one or no Bw4 genes. By contrast, NK cells lacking KIR3DL1 showed no differences. Therefore, these data indicate that particular KIR and HLA alleles are associated with more responsive NK cells, strongly suggesting that human NK cells are also subjected to NK cell licensing, and providing a potential functional explanation for the influence of KIR and HLA genes in disease as well as interindividual differences in NK cell potency.
Functional interactions among Orai1, TRPCs, and STIM1 suggest a STIM-regulated heteromeric Orai/TRPC model for SOCE/Icrac channels
Authors: Liao Yanhong , Erxleben Christian , Abramowitz Joel , Flockerzi Veit , Zhu Michael Xi , Armstrong David L. , Birnbaumer Lutz
Published: February 2008

Receptor-operated Ca
2+
entry (ROCE) and store-operated Ca
2+
entry (SOCE) into cells are functions performed by all higher eukaryotic cells, and their impairment is life-threatening. The main molecular components of this pathway appear to be known. However, the molecular make-up of channels mediating ROCE and SOCE is largely unknown. One hypothesis proposes SOCE channels to be formed solely by Orai proteins. Another proposes SOCE channels to be composed of both Orai and C-type transient receptor potential (TRPC) proteins. Both hypotheses propose that the channels are activated by STIM1, a sensor of the filling state of the Ca
2+
stores that activates Ca
2+
entry when stores are depleted. The role of Orai in SOCE has been proven. Here we show the TRPC-dependent reconstitution of Icrac, the electrophysiological correlate to SOCE, by expression of Orai1; we also show that R91W-Orai1 can inhibit SOCE and ROCE and that Orai1 and STIM1 expression leads to functional expression of Gd-resistant ROCE. Because channels that mediate ROCE are accepted to be formed with the participation of TRPCs, our data show functional interaction between ROCE and SOCE components. We propose that SOCE/Icrac channels are composed of heteromeric complexes that include TRPCs and Orai proteins.
Arabidopsis
LEAFY COTYLEDON2 induces maturation traits and auxin activity: Implications for somatic embryogenesis
Authors: Stone Sandra L. , Braybrook Siobhan A. , Paula Stephanie L. , Kwong Linda W. , Meuser Jonathan , Pelletier Julie , Hsieh Tzung-Fu , Fischer Robert L. , Goldberg Robert B. , Harada John J.
Published: February 2008

LEAFY COTYLEDON2 (LEC2) is a central regulator of embryogenesis sufficient to induce somatic cells to form embryos when expressed ectopically. Here, we analyze the cellular processes induced by LEC2, a B3 domain transcription factor, that may underlie its ability to promote somatic embryogenesis. We show auxin-responsive genes are induced after LEC2 activation in seedlings. Genes encoding enzymes involved in auxin biosynthesis,
YUC2
and
YUC4
, are activated within 1 h after induction of LEC2 activity, and
YUC4
appears to be a direct transcriptional target of LEC2. We also show ectopic
LEC2
expression induces accumulation of seed storage protein and oil bodies in vegetative and reproductive organs, events that normally occur during the maturation phase of embryogenesis. Furthermore, LEC2 activates seed protein genes before an increase in RNAs encoding LEC1 or FUS3 is observed. Thus, LEC2 causes rapid changes in auxin responses and induces cellular differentiation characteristic of the maturation phase. The relevance of these changes to the ability of LEC2 to promote somatic embryogenesis is discussed.
The
stumpy
gene is required for mammalian ciliogenesis
Authors: Town Terrence , Breunig Joshua J. , Sarkisian Matthew R. , Spilianakis Charalampos , Ayoub Albert E. , Liu Xiuxin , Ferrandino Anthony F. , Gallagher A. Rachel , Li Ming O. , Rakic Pasko , Flavell Richard A.
Published: February 2008

Cilia are present on nearly all cell types in mammals and perform remarkably diverse functions. However, the mechanisms underlying ciliogenesis are unclear. Here, we cloned a previously uncharacterized highly conserved gene,
stumpy
, located on mouse chromosome 7.
Stumpy
was ubiquitously expressed, and conditional loss in mouse resulted in complete penetrance of perinatal hydrocephalus (HC) and severe polycystic kidney disease (PKD). We found that cilia in
stumpy
mutant brain and kidney cells were absent or markedly deformed, resulting in defective flow of cerebrospinal fluid.
Stumpy
colocalized with ciliary basal bodies, physically interacted with γ-tubulin, and was present along ciliary axonemes, suggesting that
stumpy
plays a role in ciliary axoneme extension. Therefore,
stumpy
is essential for ciliogenesis and may be involved in the pathogenesis of human congenital malformations such as HC and PKD.
Dysregulation of IL-32 in myelodysplastic syndrome and chronic myelomonocytic leukemia modulates apoptosis and impairs NK function
Authors: Marcondes A. Mario , Mhyre Andrew J. , Stirewalt Derek L. , Kim Soo-Hyun , Dinarello Charles A. , Deeg H. Joachim
Published: February 2008

TNFα levels are elevated in the marrows of patients with myelodysplastic syndrome (MDS) and are associated with high rates of apoptosis, which contributes to hematopoietic failure. We observed that exposure of human marrow stroma cell lines HS5 and HS27a to TNFα increases levels of IL-32 mRNA. IL-32, in turn, induces TNFα. Marrow stroma from patients with MDS expressed 14- to 17-fold higher levels of IL-32 mRNA than healthy controls. In contrast, cells from patients with chronic myelomonocytic leukemia (CMML) expressed only one tenth the level of IL-32 measured in healthy controls. Human KG1a leukemia cells underwent apoptosis when cocultured with HS5 stromal cells, but knockdown of IL-32 in the stromal cells by using siRNA abrogated apoptosis in the leukemia cells. IL-32 knockdown cells also showed dysregulation of VEGF and other cytokines. Furthermore, CD56+natural killer cells from patients with MDS and CMML expressed IL-32 at lower levels than controls and exhibited reduced cytotoxic activity, which was unaffected by IL-2 treatment. We propose that IL-32 is a marrow stromal marker that distinguishes patients with MDS and CMML. Furthermore, IL-32 appears to contribute to the pathophysiology of MDS and may be a therapeutic target.
ParCrys: a Parzen window density estimation approach to protein crystallization propensity prediction
Authors: Overton Ian M. , Padovani Gianandrea , Girolami Mark A. , Barton Geoffrey J.
Published: February 2008

The ability to rank proteins by their likely success in crystallization is useful in current Structural Biology efforts and in particular in high-throughput Structural Genomics initiatives. We present ParCrys, a Parzen Window approach to estimate a protein's propensity to produce diffraction-quality crystals. The Protein Data Bank (PDB) provided training data whilst the databases TargetDB and PepcDB were used to define feature selection data as well as test data independent of feature selection and training. ParCrys outperforms the OB-Score, SECRET and CRYSTALP on the data examined, with accuracy and Matthews correlation coefficient values of 79.1% and 0.582, respectively (74.0% and 0.227, respectively, on data with a ‘real-world’ ratio of positive:negative examples). ParCrys predictions and associated data are available from www.compbio.dundee.ac.uk/parcrys.

Contact:  geoff@compbio.dundee.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.
On mobile assemblies of Bennett linkages
Authors: Chen Y , You Z
Published: February 2008

This paper deals with deployable structures formed by interconnected Bennett linkages. A total of eight cases that allow mobile assemblies of Bennett linkages being built have been found by considering the links that may contain sections with negative length. Among the eight assemblies, four are distinct ones, including the one that we reported previously, and the remaining can be obtained by modifying the four cases. All these assemblies consist of a grid of nested Bennett linkages. The layout of the assemblies can be repeated to form a large deployable structure. When the Bennett linkages are equilateral, the assemblies expand to form arches. For a non-equilateral case, the assemblies deploy into a helical shape with a cylindrical profile. They are geometrically overconstrained with a single degree of mobility. The newly found assemblies provide more choices in the design of deployable structures.
Group velocity of wave propagation in carbon nanotubes
Authors: Wang Lifeng , Guo Wanlin , Hu Haiyan
Published: February 2008

The group velocities of longitudinal and flexural wave propagations in single- and multi-walled carbon nanotubes are studied in the frame of continuum mechanics. The dispersion relations between the group velocity and the wavenumber for flexural and longitudinal waves, described by a beam model and a cylindrical shell model, are established for both single- and multi-walled carbon nanotubes. The effect of microstructures in carbon nanotubes on the wave dispersion is revealed through the non-local elastic models of a beam and a cylindrical shell, including the second-order gradient of strain and a parameter of microstructure. It is shown that the microstructures in the carbon nanotubes play an important role in the dispersion of both longitudinal and flexural waves. In addition, the non-local elastic models predict that the cut-off wavenumber of the dispersion relation between the group velocity and the wavenumber is approximately 2×10
10
 m
−1
for the longitudinal and flexural wave propagations in both single- and multi-walled carbon nanotubes. This may explain why the direct molecular dynamics simulation cannot give a proper dispersion relation between the phase velocity and the wavenumber when the wavenumber approaches approximately 2×10
10
 m
−1
, much lower than the cut-off wavenumber for the dispersion relation between the phase velocity and the wavenumber predicted by continuum mechanics.
Early Eocene lagomorph (Mammalia) from Western India and the early diversification of Lagomorpha
Authors: Rose Kenneth D , DeLeon Valerie Burke , Missiaen Pieter , Rana R.S , Sahni Ashok , Singh Lachham , Smith Thierry
Published: February 2008

We report the oldest known record of Lagomorpha, based on distinctive, small ankle bones (calcaneus and talus) from Early Eocene deposits (Middle Ypresian equivalent,ca53 Myr ago) of Gujarat, west-central India. The fossils predate the oldest previously known crown lagomorphs by several million years and extend the record of lagomorphs on the Indian subcontinent by 35 Myr. The bones show a mosaic of derived cursorial adaptations found in gracile Leporidae (rabbits and hares) and primitive traits characteristic of extant Ochotonidae (pikas) and more robust leporids. Together with gracile and robust calcanei from the Middle Eocene of Shanghuang, China, also reported here, the Indian fossils suggest that diversification within crown Lagomorpha and possibly divergence of the family Leporidae were already underway in the Early Eocene.
The fate of assimilated carbon during drought: impacts on respiration in Amazon rainforests
Authors: Meir P , Metcalfe D.B , Costa A.C.L , Fisher R.A
Published: February 2008

Interannual variations in CO
2
exchange across Amazonia, as deduced from atmospheric inversions, correlate with El Niño occurrence. They are thought to result from changes in net ecosystem exchange and fire incidence that are both related to drought intensity. Alterations to net ecosystem production (NEP) are caused by changes in gross primary production (GPP) and ecosystem respiration (
R
eco
). Here, we analyse observations of the components of
R
eco
(leaves, live and dead woody tissue, and soil) to provide first estimates of changes in
R
eco
during short-term (seasonal to interannual) moisture limitation. Although photosynthesis declines if moisture availability is limiting, leaf dark respiration is generally maintained, potentially acclimating upwards in the longer term. If leaf area is lost, then short-term canopy-scale respiratory effluxes from wood and leaves are likely to decline. Using a moderate short-term drying scenario where soil moisture limitation leads to a loss of 0.5 m
2
 m
−2
 yr
−1
in leaf area index, we estimate a reduction in respiratory CO
2
efflux from leaves and live woody tissue of 1.0 (±0.4) t C ha
−1
 yr
−1
. Necromass decomposition declines during drought, but mortality increases; the median mortality increase following a strong El Niño is 1.1% (
n
=46 tropical rainforest plots) and yields an estimated net short-term increase in necromass CO
2
efflux of 0.13–0.18 t C ha
−1
 yr
−1
. Soil respiration is strongly sensitive to moisture limitation over the short term, but not to associated temperature increases. This effect is underestimated in many models but can lead to estimated reductions in CO
2
efflux of 2.0 (±0.5) t C ha
−1
 yr
−1
. Thus, the majority of short-term respiratory responses to drought point to a decline in
R
eco
, an outcome that contradicts recent regional-scale modelling of NEP. NEP varies with both GPP and
R
eco
but robust moisture response functions are clearly needed to improve quantification of the role of
R
eco
in influencing regional-scale CO
2
emissions from Amazonia.
Towards quantifying uncertainty in predictions of Amazon ‘dieback’
Authors: Huntingford Chris , Fisher Rosie A , Mercado Lina , Booth Ben B.B , Sitch Stephen , Harris Phil P , Cox Peter M , Jones Chris D , Betts Richard A , Malhi Yadvinder , Harris Glen R , Collins Mat , Moorcroft Paul
Published: February 2008

Simulations with the Hadley Centre general circulation model (HadCM3), including carbon cycle model and forced by a ‘business-as-usual’ emissions scenario, predict a rapid loss of Amazonian rainforest from the middle of this century onwards. The robustness of this projection to both uncertainty in physical climate drivers and the formulation of the land surface scheme is investigated. We analyse how the modelled vegetation cover in Amazonia responds to (i) uncertainty in the parameters specified in the atmosphere component of HadCM3 and their associated influence on predicted surface climate. We then enhance the land surface description and (ii) implement a multilayer canopy light interception model and compare with the simple ‘big-leaf’ approach used in the original simulations. Finally, (iii) we investigate the effect of changing the method of simulating vegetation dynamics from an area-based model (TRIFFID) to a more complex size- and age-structured approximation of an individual-based model (ecosystem demography).

We find that the loss of Amazonian rainforest is robust across the climate uncertainty explored by perturbed physics simulations covering a wide range of global climate sensitivity. The introduction of the refined light interception model leads to an increase in simulated gross plant carbon uptake for the present day, but, with altered respiration, the net effect is a decrease in net primary productivity. However, this does not significantly affect the carbon loss from vegetation and soil as a consequence of future simulated depletion in soil moisture; the Amazon forest is still lost. The introduction of the more sophisticated dynamic vegetation model reduces but does not halt the rate of forest dieback. The potential for human-induced climate change to trigger the loss of Amazon rainforest appears robust within the context of the uncertainties explored in this paper. Some further uncertainties should be explored, particularly with respect to the representation of rooting depth.
Is lipopolysaccharide a factor in infectivity of Chlamydia trachomatis?
Authors: Fadel Sanaa , Eley Adrian
Published: February 2008

Lipopolysaccharide (LPS) is a major surface component ofChlamydia trachomatis, as with all Gram-negative bacteria. The effect ofC. trachomatisLPS onC. trachomatisinfectivity of human epithelial cells was investigated.C. trachomatisLPS andC. trachomatisLPS antibody significantly reduced infectivity, mostly in a dose-dependent manner. As the structure of LPS inC. trachomatisis simple and consists only of lipid A and 3-deoxy-d-manno-octulosonic acid (Kdo), we investigated whether lipid A or Kdo was inhibitory to chlamydial infectivity. Polymyxin B, as a lipid A inhibitor, and Kdo considerably reducedC. trachomatisinfectivity. With all the LPS inhibitors used, there was greater inhibition against serovar E than serovar LGV. These results suggest a role for LPS in chlamydial infectivity. Elucidation of how LPS acts in infectivity and identification of host-cell receptors would help in understanding pathogenicity.
Neisseria elongata endocarditis complicated by brain embolism and abscess
Authors: Hsiao Ju-Feng , Lee Ming-Hsun , Chia Ju-Hsin , Ho Wan-Jing , Chu Jaw-Ji , Chu Pao-Hsien
Published: February 2008

We report a case of Neisseria elongata endocarditis with thalamic septic embolization and subsequent brain abscess formation, which to the best of our knowledge has never been reported in the literature. The brain abscess completely resolved after a surgical repair of the infected mitral valve and an additional 4 weeks of antimicrobial therapy. Based on a review of all previous reports of N. elongata endocarditis, including ours, this will remind physicians that invasive N. elongata infections should be managed and followed up cautiously, as surgical intervention is often required.
Co-infection with two different strains of Bordetella pertussis in an infant
Authors: Cassiday Pamela K. , Tobin-D'Angelo Melissa , Watson J. Renee , Wu Kai-Hui , Park Mahin M. , Sanden Gary N.
Published: February 2008

We report co-infection with two phenotypically and genotypically distinct strains ofBordetella pertussisin an infant male hospitalized with a 2-week history of cough, paroxysms and vomiting. Colonies from the twoB. pertussisphenotypes were isolated and evaluated by PFGE profile analysis, gene sequence typing and PCR-RFLP of a portion of the 23S rRNA gene. These results demonstrated simultaneous infection with two different strains ofB. pertussis.