bluuebunny/crossref_metadata_2025 huggingface dataset:
In V
itro
and
In V
ivo
Characterization of the
Pseudomonas aeruginosa
Cyclic AMP (cAMP) Phosphodiesterase CpdA, Required for cAMP Homeostasis and Virulence Factor Regulation
Authors: Fuchs Erin L. , Brutinel Evan D. , Klem Erich R. , Fehr Anthony R. , Yahr Timothy L. , Wolfgang Matthew C.
Published: March 2010

Cyclic AMP (cAMP) is an important second messenger signaling molecule that controls a wide variety of eukaryotic and prokaryotic responses to extracellular cues. For cAMP-dependent signaling pathways to be effective, the intracellular cAMP concentration is tightly controlled at the level of synthesis and degradation. In the opportunistic human pathogen
Pseudomonas aeruginosa
, cAMP is a key regulator of virulence gene expression. To better understand the role of cAMP homeostasis in this organism, we identified and characterized the enzyme CpdA, a putative cAMP phosphodiesterase. We demonstrate that CpdA possesses 3′,5′-cAMP phosphodiesterase activity
in vitro
and that it utilizes an iron-dependent catalytic mechanism. Deletion of
cpdA
results in the accumulation of intracellular cAMP and altered regulation of
P. aeruginosa
virulence traits. Further, we demonstrate that the cAMP-dependent transcription factor Vfr directly regulates
cpdA
expression in response to intracellular cAMP accumulation, thus providing a feedback mechanism for controlling cAMP levels and fine-tuning virulence factor expression.
Expanded Role for the Nitrogen Assimilation Control Protein in the Response of
Klebsiella pneumoniae
to Nitrogen Stress
Authors: Frisch Ryan L. , Bender Robert A.
Published: March 2010

Klebsiella pneumoniae
is able to utilize many nitrogen sources, and the utilization of some of these nitrogen sources is dependent on the nitrogen assimilation control (NAC) protein. Seven NAC-regulated promoters have been characterized in
K. pneumoniae
, and nine NAC-regulated promoters have been found by microarray analysis in
Escherichia coli
. So far, all characterized NAC-regulated promoters have been directly related to nitrogen metabolism. We have used a genome-wide analysis of NAC binding under nitrogen limitation to identify the regions of the chromosome associated with NAC in
K. pneumoniae
. We found NAC associated with 99 unique regions of the chromosome under nitrogen limitation.
In vitro
, 84 of the 99 regions associate strongly enough with purified NAC to produce a shifted band by electrophoretic mobility shift assay. Primer extension analysis of the mRNA from genes associated with 17 of the fragments demonstrated that at least one gene associated with each fragment was NAC regulated under nitrogen limitation. The large size of the NAC regulon in
K. pneumoniae
indicates that NAC plays a larger role in the nitrogen stress response than it does in
E. coli
. Although a majority of the genes with identifiable functions that associated with NAC under nitrogen limitation are involved in nitrogen metabolism, smaller subsets are associated with carbon and energy acquisition (18 genes), and growth rate control (10 genes). This suggests an expanded role for NAC regulation during the nitrogen stress response, where NAC not only regulates genes involved in nitrogen metabolism but also regulates genes involved in balancing carbon and nitrogen pools and growth rate.
Agrobacterium tumefaciensType IV Secretion Protein VirB3 Is an Inner Membrane Protein and Requires VirB4, VirB7, and VirB8 for Stabilization
Authors: Mossey Pamela , Hudacek Andrew , Das Anath
Published: March 2010

Agrobacterium tumefaciensVirB proteins assemble a type IV secretion apparatus and a T-pilus for secretion of DNA and proteins into plant cells. The pilin-like protein VirB3, a membrane protein of unknown topology, is required for the assembly of the T-pilus and for T-DNA secretion. Using PhoA and green fluorescent protein (GFP) as periplasmic and cytoplasmic reporters, respectively, we demonstrate that VirB3 contains two membrane-spanning domains and that both the N and C termini of the protein reside in the cytoplasm. Fusion proteins with GFP at the N or C terminus of VirB3 were fluorescent and, like VirB3, localized to a cell pole. Biochemical fractionation studies demonstrated that VirB3 proteins encoded by three Ti plasmids, the octopine Ti plasmid pTiA6NC, the supervirulent plasmid pTiBo542, and the nopaline Ti plasmid pTiC58, are inner membrane proteins and that VirB4 has no effect on membrane localization of pTiA6NC-encoded VirB3 (pTiA6NC VirB3). The pTiA6NC and pTiBo542 VirB2 pilins, like VirB3, localized to the inner membrane. The pTiC58 VirB4 protein was earlier found to be essential for stabilization of VirB3. Stabilization of pTiA6NC VirB3 requires not only VirB4 but also two additional VirB proteins, VirB7 and VirB8. A binary interaction between VirB3 and VirB4/VirB7/VirB8 is not sufficient for VirB3 stabilization. We hypothesize that bacteria use selective proteolysis as a mechanism to prevent assembly of unproductive precursor complexes under conditions that do not favor assembly of large macromolecular structures.
Structure and Protein-Protein Interaction Studies on
Chlamydia trachomatis
Protein CT670 (YscO Homolog)
Authors: Lorenzini Emily , Singer Alexander , Singh Bhag , Lam Robert , Skarina Tatiana , Chirgadze Nickolay Y. , Savchenko Alexei , Gupta Radhey S.
Published: March 2010

Comparative genomic studies have identified many proteins that are found only in various
Chlamydiae
species and exhibit no significant sequence similarity to any protein in organisms that do not belong to this group. The CT670 protein of
Chlamydia trachomatis
is one of the proteins whose genes are in one of the type III secretion gene clusters but whose cellular functions are not known. CT670 shares several characteristics with the YscO protein of
Yersinia pestis
, including the neighboring genes, size, charge, and secondary structure, but the structures and/or functions of these proteins remain to be determined. Although a BLAST search with CT670 did not identify YscO as a related protein, our analysis indicated that these two proteins exhibit significant sequence similarity. In this paper, we report that the CT670 crystal, solved at a resolution of 2 Å, consists of a single coiled coil containing just two long helices. Gel filtration and analytical ultracentrifugation studies showed that in solution CT670 exists in both monomeric and dimeric forms and that the monomer predominates at lower protein concentrations. We examined the interaction of CT670 with many type III secretion system-related proteins (viz., CT091, CT665, CT666, CT667, CT668, CT669, CT671, CT672, and CT673) by performing bacterial two-hybrid assays. In these experiments, CT670 was found to interact only with the CT671 protein (YscP homolog), whose gene is immediately downstream of
ct670
. A specific interaction between CT670 and CT671 was also observed when affinity chromatography pull-down experiments were performed. These results suggest that CT670 and CT671 are putative homologs of the YcoO and YscP proteins, respectively, and that they likely form a chaperone-effector pair.
Two Distantly Homologous DnaG Primases from
Thermoanaerobacter tengcongensis
Exhibit Distinct Initiation Specificities and Priming Activities
Authors: Li Jie , Liu Jingfang , Zhou Ligang , Pei Huadong , Zhou Jian , Xiang Hua
Published: March 2010

Primase, encoded by
dnaG
in bacteria, is a specialized DNA-dependent RNA polymerase that synthesizes RNA primers
de novo
for elongation by DNA polymerase. Genome sequence analysis has revealed two distantly related
dnaG
genes,
TtdnaG
and
TtdnaG
2
, in the thermophilic bacterium
Thermoanaerobacter tengcongensis
. Both TtDnaG (600 amino acids) and TtDnaG2 (358 amino acids) exhibit primase activities
in vitro
at a wide range of temperatures. Interestingly, the template recognition specificities of these two primases are quite distinctive. When trinucleotide-specific templates were tested, TtDnaG initiated RNA primer synthesis efficiently only on templates containing the trinucleotide 5′-CCC-3′, not on the other 63 possible trinucleotides. When the 5′-CCC-3′ sequence was flanked by additional cytosines or guanines, the initiation efficiency of TtDnaG increased remarkably. Significantly, TtDnaG could specifically and efficiently initiate RNA primer synthesis on a limited set of tetranucleotides composed entirely of cytosines and guanines, indicating that TtDnaG initiated RNA primer synthesis more preferably on GC-containing tetranucleotides. In contrast, it seemed that TtDnaG2 had no specific initiation nucleotides, as it could efficiently initiate RNA primer synthesis on all templates tested. The DNA binding affinity of TtDnaG2 was usually 10-fold higher than that of TtDnaG, which might correlate with its high activity but low template specificity. These distinct priming activities and specificities of TtDnaG and TtDnaG2 might shed new light on the diversity in the structure and function of the primases.
Biochemical Characterization of a Novel Indole Prenyltransferase from
Streptomyces
sp. SN-593
Authors: Takahashi Shunji , Takagi Hiroshi , Toyoda Atsushi , Uramoto Masakazu , Nogawa Toshihiko , Ueki Masashi , Sakaki Yoshiyuki , Osada Hiroyuki
Published: March 2010

Genome sequencing of
Streptomyces
species has highlighted numerous potential genes of secondary metabolite biosynthesis. The mining of cryptic genes is important for exploring chemical diversity. Here we report the metabolite-guided genome mining and functional characterization of a cryptic gene by biochemical studies. Based on systematic purification of metabolites from
Streptomyces
sp. SN-593, we isolated a novel compound, 6-dimethylallylindole (DMAI)-3-carbaldehyde. Although many 6-DMAI compounds have been isolated from a variety of organisms, an enzyme catalyzing the transfer of a dimethylallyl group to the C-6 indole ring has not been reported so far. A homology search using known prenyltransferase sequences against the draft sequence of the
Streptomyces
sp. SN-593 genome revealed the
iptA
gene. The IptA protein showed 27% amino acid identity to cyanobacterial LtxC, which catalyzes the transfer of a geranyl group to (−)-indolactam V. A BLAST search against IptA revealed much-more-similar homologs at the amino acid level than LtxC, namely, SAML0654 (60%) from
Streptomyces ambofaciens
ATCC 23877 and SCO7467 (58%) from
S. coelicolor
A3(2). Phylogenetic analysis showed that IptA was distinct from bacterial aromatic prenyltransferases and fungal indole prenyltransferases. Detailed kinetic analyses of IptA showed the highest catalytic efficiency (6.13 min
−1
μM
−1
) for
l
-Trp in the presence of dimethylallyl pyrophosphate (DMAPP), suggesting that the enzyme is a 6-dimethylallyl-
l
-Trp synthase (6-DMATS). Substrate specificity analyses of IptA revealed promiscuity for indole derivatives, and its reaction products were identified as novel 6-DMAI compounds. Moreover, Δ
iptA
mutants abolished the production of 6-DMAI-3-carbaldehyde as well as 6-dimethylallyl-
l
-Trp, suggesting that the
iptA
gene is involved in the production of 6-DMAI-3-carbaldehyde.
Longus, a Type IV Pilus of Enterotoxigenic
Escherichia coli
, Is Involved in Adherence to Intestinal Epithelial Cells
Authors: Mazariego-Espinosa Karina , Cruz Ariadnna , Ledesma Maria A. , Ochoa Sara A. , Xicohtencatl-Cortes Juan
Published: March 2010

Enterotoxigenic
Escherichia coli
(ETEC) is the leading bacterial cause of diarrhea in the developing world, as well as the most common cause of traveler's diarrhea. The main hallmarks of this type of bacteria are the expression of one or more enterotoxins and fimbriae used for attachment to host intestinal cells. Longus is a pilus produced by ETEC. These bacteria grown in pleuropneumonia-like organism (PPLO) broth at 37°C and in 5% CO
2
produced longus, showing that the assembly and expression of the pili depend on growth conditions and composition of the medium. To explore the role of longus in the adherence to epithelial cells, quantitative and qualitative analyses were done, and similar levels of adherence were observed, with values of 111.44 × 10
4
CFU/ml in HT-29, 101.33 × 10
4
CFU/ml in Caco-2, and 107.11 × 10
4
CFU/ml in T84 cells. In addition, the E9034AΔ
lngA
strain showed a significant reduction in longus adherence of 32% in HT-29, 22.28% in Caco-2, and 21.68% in T84 cells compared to the wild-type strain. In experiments performed with nonintestinal cells (HeLa and HEp-2 cells), significant differences were not observed in adherence between E9034A and derivative strains. Interestingly, the E9034A and E9034AΔ
lngA
(pLngA) strains were 30 to 35% more adherent in intestinal cells than in nonintestinal cells. Twitching motility experiments were performed, showing that ETEC strains E9034A and E9034AΔ
lngA
(pLngA) had the capacity to form spreading zones while ETEC E9034AΔ
lngA
does not. In addition, our data suggest that longus from ETEC participates in the colonization of human colonic cells.
Heterogeneous
rpoS
and
rhlR
mRNA Levels and 16S rRNA/rDNA (rRNA Gene) Ratios within
Pseudomonas aeruginosa
Biofilms, Sampled by Laser Capture Microdissection
Authors: Pérez-Osorio Ailyn C. , Williamson Kerry S. , Franklin Michael J.
Published: March 2010

The local environmental conditions in biofilms are dependent on the impinging aqueous solution, chemical diffusion, and the metabolic activities of cells within the biofilms. Chemical gradients established in biofilms lead to physiological heterogeneities in bacterial gene expression. Previously, we used laser capture microdissection (LCM) and quantitative reverse transcription (RT)-PCR to target defined biofilm subpopulations for gene expression studies. Here, we combined this approach with quantitative PCR of bacterial DNA to normalize the amount of gene expression per cell. By comparing the ratio of 16S rRNA to 16S rDNA (rRNA gene), we demonstrated that cells at the top of thick
Pseudomonas aeruginosa
biofilms have 16S rRNA/genome ratios similar to those of cells in a transition from the exponential phase to the stationary phase. Cells in the middle and bottom layers of these biofilms have ratios that are not significantly different from those of stationary-phase planktonic cultures. Since much of each biofilm appeared to be in a stationary-phase-like state, we analyzed the local amounts of the stationary-phase sigma factor
rpoS
gene and the quorum-sensing regulator
rhlR
gene per cell. Surprisingly, the amount of
rpoS
mRNA was largest at the top of the biofilms at the air-biofilm interface. Less than one
rpoS
mRNA transcript per cell was observed in the middle or base of the biofilms. The
rhlR
mRNA content was also greatest at the top of the biofilms, and there was little detectable
rhlR
expression at the middle or bottom of the biofilms. While the cell density was slightly greater at the bottom of the biofilms, expression of the quorum-sensing regulator occurred primarily at the top of the biofilms, where the cell metabolic activity was greatest, as indicated by local expression of the housekeeping gene
acpP
and by expression from a constitutive P

trc

promoter. The results indicate that in thick
P. aeruginosa
biofilms, cells in the 30 μm adjacent to the air-biofilm interface actively express genes associated with stationary phase, while cells in the interior portions do not express these genes and therefore are in a late-stationary-phase-like state and may be dormant.
Negative Regulation of Expression of the Nitrate AssimilationnirAOperon in the Heterocyst-Forming CyanobacteriumAnabaenasp. Strain PCC 7120
Authors: Frías José Enrique , Flores Enrique
Published: March 2010

In the filamentous, heterocyst-forming cyanobacteriumAnabaenasp. strain PCC 7120, expression of the nitrate assimilationnirAoperon takes place in the absence of ammonium and the presence of nitrate or nitrite. Several positive-action proteins that are required for expression of thenirAoperon have been identified. Whereas NtcA and NtcB exert their action by direct binding to thenirAoperon promoter, CnaT acts by an as yet unknown mechanism. In the genome of this cyanobacterium, open reading frame (ORF)all0605(thenirBgene) is found between thenirA(encoding nitrite reductase) andntcBgenes. AnirBmutant was able to grow at the expense of nitrate as a nitrogen source and showed abnormally high levels ofnirAoperon mRNA both in the presence and in the absence of nitrate. This mutant showed increased nitrate reductase activity but decreased nitrite reductase activity, an imbalance that resulted in excretion of nitrite, which accumulated in the extracellular medium, when thenirBmutant was grown in the presence of nitrate. AnirAin-frame deletion mutant also showed a phenotype of increased expression of thenirAoperon in the absence of ammonium, independent of the presence of nitrate in the medium. Both NirB and NirA are therefore needed to keep low levels of expression of thenirAoperon in the absence of an inducer. Because NirB is also needed to attain high levels of nitrite reductase activity, NirA appears to be a negative element in the nitrate regulation of expression of thenirAoperon inAnabaenasp. strain PCC 7120.
Bacterial rRNA-Targeted Reverse Transcription-PCR Used To Identify Pathogens Responsible for Fever with Neutropenia
Authors: Sakaguchi Sachi , Saito Masahiro , Tsuji Hirokazu , Asahara Takashi , Takata Oto , Fujimura Junya , Nagata Satoru , Nomoto Koji , Shimizu Toshiaki
Published: March 2010

The purpose of this study was to evaluate the clinical utility of bacterial rRNA-targeted reverse transcription-quantitative PCR (BrRNA RT-qPCR) assays for identifying the bacterial pathogens that cause fever with neutropenia in pediatric cancer patients, by comparing the bacterial detection rate of this technique with that of blood culture. One milliliter of blood was collected from pediatric patients who developed fever with neutropenia following cancer chemotherapy. BrRNA RT-qPCR was performed using 16 primer sets, each designed for a specific type of bacteria. The entire BrRNA RT-qPCR procedure took less than 5 h. Blood culture was performed at the same time, following the standard institutional procedure. Blood from 13 patients was collected during 23 febrile neutropenic episodes. Of these samples, bacteria were identified in 16 by BrRNA RT-qPCR (69.6%) and in 4 by blood culture (17.4%,
P
< 0.001). In all 4 blood culture-positive samples, BrRNA RT-qPCR detected the same type of bacteria as that identified by culture. In 9 samples, more than 4 types of bacteria were identified simultaneously by BrRNA RT-qPCR, most of which were anaerobic bacteria known to be part of the gut flora. We conclude that BrRNA RT-qPCR could be useful in the diagnosis of fever with neutropenia, given its high bacterial detection rate, short turnaround time, and the small blood sample required compared with the standard blood culture techniques. Our findings also indicate that anaerobic intestinal bacteria, which are difficult to detect by standard culture techniques, may be responsible for some cases of febrile neutropenia.
Rubella Virus Genotypes in the People's Republic of China between 1979 and 2007: a Shift in Endemic Viruses during the 2001 Rubella Epidemic
Authors: Zhu Zhen , Abernathy Emily , Cui Aili , Zhang Yan , Zhou Shujie , Zhang Zhenying , Wang Changyin , Wang Tongzhan , Ling Hua , Zhao Chunfang , Chen Yingqiong , He Jilan , Sun Li , Chen Xia , Tang Jihai , Feng Daxin , Wang Yan , Ba Zhuoma , Fan Lixia , Chen Haiyun , Pan Zhengfan , Zhan Jun , Chen Hui , Zhou Shunde , Zheng Lei , Gao Hui , Liang Yong , Dai Defang , Icenogle Joseph , Xu Wenbo
Published: March 2010

The incidence of rubella cases in China from 1991 to 2007 was reviewed, and the nucleotide sequences from 123 rubella viruses collected during 1999 to 2007 and 4 viral sequences previously reported from 1979 to 1984 were phylogenetically analyzed. Rubella vaccination was not included in national immunization programs in China before 2007. Changes in endemic viruses were compared with incidences of rubella epidemics. The results showed that rubella epidemics occur approximately every 6 to 8 years (1993/1994, 2001, and 2007), and a shift of disease burden to susceptible young adults was observed. The Chinese rubella virus sequences were categorized into 5 of the 13 rubella virus genotypes, 1a, 1E, 1F, 2A, and 2B; cocirculations of these different genotypes were found in China. In Anhui province, a shift in the predominant genotype from 1F and 2B to 1E coincided with the 2001 rubella epidemic. This shift may have occurred throughout China during 2001 to 2007. This study investigated the genotype distribution of rubella viruses in China over a 28-year period to establish an important genetic baseline in China during its prevaccination era.
Fear of dying in an ethnically diverse society: cross-sectional studies of people aged 65+ in Britain
Authors: Bowling Ann , Iliffe Steve , Kessel Anthony , Higginson Irene J
Published: March 2010

Aim

To examine fears about dying in an ethnically diverse population sample, and a more homogeneous population sample, aged 65 and over.

Methods

Personal interviews with people aged 65+ living at home responding to two Office for National Statistics Omnibus Surveys in Britain, and two Ethnibus Surveys of ethnically diverse populations in Britain.

Results

Ethnically diverse respondents were more likely than British population respondents to express fears about dying on all measures used. Respondents in both samples with better, compared with worse, quality of life had significantly reduced odds of having extreme fears of dying (ethnically diverse sample, OR 0.924 (95% CI 0.898 to 0.951); British population sample, OR 0.981 (95% CI 0.966 to 0.996); both p<0.001). In the latter sample only, older age was protective (OR 0.957; 95% CI 0.930 to 0.985; p<0.001), whereas in the Ethnibus sample, having a longstanding illness (OR 2.024; 95% CI 1.158 to 3.535; p<0.05) and having more relatives to help them (OR 1.134; 95% CI 1.010 to 1.274; p<0.05) increased fears about dying.

Conclusions

Enabling older people to express fears about dying is likely to be important when planning supportive end-of-life care. Practitioners should not assume that fears about dying are the same in different social groups, or that extensive family support is protective against such anxiety. Older people from ethnic minorities had more anxieties about dying than others, and were more likely to express fears the more extensive their family support. These findings have implications for commissioners and practitioners of primary and secondary care.
THE STUDY OF $^3_{\Sigma}{\rm HE}$ HYPERNUCLEUS BASED ON THE CHIRAL SU(3) QUARK MODEL
Authors: LV S. T. , CAO H. Y. , LU X.
Published: March 2010

With the resonating group method, we study the non-local Σ - N interaction and spin–isospin dependence of Σ - N in the chiral SU (3) quark model. Meanwhile, the binding energy of hypernucleus [Formula: see text] is calculated based on the non-local Σ - N interaction in the union of channels with (S = 0, T = 1/2), (S = 1, T = 1/2) and (S = 0, T = 3/2). The result shows that there theoretically exists bound state of [Formula: see text]. Furthermore, we analyze the effect of various potentials and relative motion energy between hyperon and core on the binding energy in the model.
NEW CALCULATION FOR SOME GROUND STATE FEATURES OF 40Ca, 48Ca32S AND 39K NUCLEI
Authors: AYTEKIN H. , BALDIK R. , TEL E. , AYDIN A.
Published: March 2010

Some ground states features of 32 S , 39 K , 40 Ca and 48 Ca nuclei are investigated using the Hartree–Fock method with the Skyrme SKM * and SLy4 forces calculated in two different code implementations. The calculated total binding energies per particle and root mean square (rms) nuclear charge radii using the Skyrme–Hartree–Fock (SHF) + BCS method are compared with relativistic mean-field (RMF) theory and experimental values. The obtained charge density distributions from these code implementations are compared with the experimental data. Pairing effects are also included in calculations for the same nuclei. Variations of the total binding energies per particle and rms nuclear charge radii were investigated as the last shell nucleons were carried to the upper shell.
FRACTAL INTERPOLATION FUNCTIONS ON POST CRITICALLY FINITE SELF-SIMILAR SETS
Authors: RUAN HUO-JUN
Published: March 2010

In this paper, we introduce fractal interpolation functions (FIFs) and linear FIFs on a post critically finite (p.c.f. for short) self-similar set K. We present a sufficient condition such that linear FIFs have finite energy and prove that the solution of Dirichlet problem -Δμ u = f,u|∂K = 0 is a linear FIF on K if f is a linear FIF.
HOMOTOPIES OF EIGENFUNCTIONS AND THE SPECTRUM OF THE LAPLACIAN ON THE SIERPINSKI CARPET
Authors: HEILMAN STEVEN M. , STRICHARTZ ROBERT S.
Published: March 2010

Consider a family of bounded domains Ωt in the plane (or more generally any Euclidean space) that depend analytically on the parameter t, and consider the ordinary Neumann Laplacian Δt on each of them. Then we can organize all the eigenfunctions into continuous families [Formula: see text] with eigenvalues [Formula: see text] also varying continuously with t, although the relative sizes of the eigenvalues will change with t at crossings where [Formula: see text]. We call these families homotopies of eigenfunctions. We study two explicit examples. The first example has Ω0 equal to a square and Ω1 equal to a circle; in both cases the eigenfunctions are known explicitly, so our homotopies connect these two explicit families. In the second example we approximate the Sierpinski carpet starting with a square, and we continuously delete subsquares of varying sizes. (Data available in full at ).
In the Virtual Extension
Authors: CACM Staff
Published: March 2010

Communications
' Virtual Extension brings more quality articles to ACM members. These articles are now available in the ACM Digital Library.
Robots gear up for disaster response
Authors: Anthes Gary
Published: March 2010

After 15 years of research, robots for search and rescue may be nearing prime time.
Be careful what you wish for
Authors: Campbell-Kelly Martin
Published: March 2010

Reflections on the decline of mathematical tables.
CTO roundtable
Authors: Creeger Mache
Published: March 2010

The battle is bigger than most of us realize.
A History of the Liberal Arts Computer Science Consortium and its Model Curricula
Authors: Bruce Kim B. , Cupper Robert D. , Drysdale Robert L. Scot
Published: March 2010

With the support of a grant from the Sloan Foundation, nine computer scientists from liberal arts colleges came together in October, 1984 to form the Liberal Arts Computer Science Consortium (LACS) and to create a model curriculum appropriate for liberal arts colleges. Over the years the membership has grown and changed, but the focus has remained on helping to establish and maintain high-quality computer science programs in liberal arts colleges. In this report we discuss briefly the history of the group, the series of three curricula produced by LACS, and other contributions of the members to computer science education.
Ant colony based rule generation for reusable software component retrieval
Authors: Bhatia Rajesh K. , Dave Mayank , Joshi R. C.
Published: March 2010

Storage and representation of reusable software components in software repositories to facilitate convenient identification and retrieval has been always a concern for software reuse researchers. This paper discusses and demonstrated an ant colony algorithm based technique that generates rules to store and then identify the component from software repository for possible reuse. Proposed technique help user in organization and storage of components in repository and later can help in identifying most appropriate component for given context. In first stage while searching it makes use of keywords, their synonyms and their inter-relationships. Then it makes use of ant colony optimization; initial pheromone of one is assigned to all domain representative terms of components. By updating pheromone for participating terms and non-participating terms iteratively and by calculating the quality of each rule generated, it leads to quality rules to represent and retrieve the reusable components
Self-* e-nursing
Authors: Nami Mohammad Reza , Saneipour Jila
Published: March 2010

The rapid advances in Information and Communication Tech-nology (ICT), management, and network technologies have had key role in emerging heterogeneous large-scale distributed sys-tems. The term of E-nursing has been used to refer to the incorpo-ration of ICT into nursing. An Autonomous system has as its vision the creation of self managing systems to address today's concerns of complexity and total cost of ownership while meeting to-morrow's needs for pervasive and ubiquitous computation and communication. Purpose of this paper is to present an autonomous virtual organization for e-nursing describing their characteristics, effects on quality factors, their building blocks architecture, and challenges
Parallel resetting of arterial baroreflex control of renal and cardiac sympathetic nerve activities during upright tilt in rabbits
Authors: Kamiya Atsunori , Kawada Toru , Mizuno Masaki , Shimizu Shuji , Sugimachi Masaru
Published: March 2010

Since humans are under ceaseless orthostatic stress, the mechanisms to maintain arterial pressure (AP) against gravitational fluid shift are important. As one mechanism, it was reported that upright tilt reset baroreflex control of renal sympathetic nerve activity (SNA) to a higher SNA in anesthetized rabbits. In the present study, we tested the hypothesis that upright tilt causes a parallel resetting of baroreflex control of renal and cardiac SNAs in anesthetized rabbits. In anesthetized rabbits ( n = 8, vagotomized and aortic denervated) with 0° supine and 60° upright tilt postures, renal and cardiac SNAs were simultaneously recorded while isolated intracarotid sinus pressure (CSP) was increased stepwise from 40 to 160 mmHg with increments of 20 mmHg. Upright tilt shifted the reverse-sigmoidal curve of the CSP-SNA relationship to higher SNA similarly in renal and cardiac SNAs. Although upright tilt increased the maximal gain, the response range and the minimum value of SNA, the curves were almost superimposable in these SNAs regardless of postures. Scatter plotting of cardiac SNA over renal SNA during the stepwise changes in CSP was close to the line of identity in 0° supine and 60° upright tilt postures. In addition, upright tilt also shifted the reverse-sigmoidal curve of the CSP-heart rate relationship to a higher heart rate, with increases in the maximal gain and the response range. In conclusion, upright posture caused a resetting of arterial baroreflex control of SNA similarly in renal and cardiac SNAs in anesthetized rabbits.
Integrated control of pulmonary vascular tone by endothelin and angiotensin II in exercising swine depends on gender
Authors: de Beer Vincent J. , de Graaff Henri J. D. , Hoekstra Maaike , Duncker Dirk J. , Merkus Daphne
Published: March 2010

The lungs are now recognized as an active metabolic organ that is a major determinant of the plasma concentrations of the vasoconstrictors endothelin (ET) and ANG II. Several studies have suggested a complex interaction between ET and ANG II in the systemic and coronary vascular beds that is different at rest and during exercise. To date, the interaction between these vasoconstrictor peptides has barely been investigated in relation to the pulmonary vascular bed. Consequently, we investigated the integrated control of pulmonary vasomotor tone by ET and ANG II in 24 chronically instrumented swine (15 female and 9 male) at rest and during graded treadmill exercise. In the systemic circulation, ANG II type 1 (AT1) receptor blockade with irbesartan and mixed ETA/ETB blockade with tezosentan each produced vasodilation. The systemic vasodilator effect of ETA/ETB blockade was enhanced after AT1 blockade in female swine, whereas a trend toward an increase was observed in male swine. In the pulmonary circulation, AT1 receptor blockade had no effect on pulmonary vascular tone in male swine, whereas it resulted in an unexpected increase in pulmonary vasomotor tone in female swine. ETA/ETB receptor blockade did not result in a decrease in pulmonary vasomotor tone at rest but produced a decrease in vasomotor tone during exercise in both genders. This pulmonary vasodilation by ETA/ETB receptor blockade was enhanced after prior AT1 blockade in female swine but not in male swine. In conclusion, in both the systemic and pulmonary circulation of female swine, ANG II inhibits the vasoconstrictor influence of ET. This interaction is gender specific. The observation that plasma ET levels were not altered by AT1 blockade in either gender suggests that the interaction between these vasoconstrictors occurs locally in the vasculature.
Sirolimus inhibits endogenous cholesterol synthesis induced by inflammatory stress in human vascular smooth muscle cells
Authors: Ma Kun L. , Varghese Zac , Ku Yin , Powis Stephen H. , Chen Yaxi , Moorhead John F. , Ruan Xiong Z.
Published: March 2010

Inflammatory stress accelerates the progression of atherosclerosis. Sirolimus, a new immunosuppressive agent, has been shown to have pleiotropic antiatherosclerotic effects. In this study we hypothesized that sirolimus inhibits 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR)-mediated cholesterol synthesis in human vascular smooth muscle cells (VSMCs) under inflammatory stress. Using radioactive assay, we demonstrated that sirolimus inhibited the increase of interleukin-1β (IL-1β)-induced cholesterol synthesis in VSMCs. Further studies showed that sirolimus inhibited both the HMGR gene and protein expression in VSMCs treated with or without IL-1β. These effects were mediated by inhibiting the gene expression of sterol regulatory element-binding protein-2 (SREBP-2) and SREBP-2 cleavage-activating protein (SCAP) as checked by real-time PCR, Western blot analysis, and confocal microscopy for the observation of decreased protein translocation of the SCAP/SREBP-2 complex from the endoplasmic reticulum (ER) to the Golgi. Insulin-induced gene-1 (Insig-1) is a key ER protein controlling the feedback regulation of HMGR at transcriptional and posttranscriptional levels. We demonstrated that sirolimus increased Insig-1 expression which may bind to the SCAP, preventing the exit of SCAP-SREBP complexes from the ER. The increased Insig-1 also accelerated HMGR protein degradation in VSMCs as shown by pulse-chase analysis. In conclusion, sirolimus inhibits cholesterol synthesis induced by inflammatory stress through the downregulation of HMGR expression and the acceleration of HMGR protein degradation. These findings may improve our understanding of the molecular mechanisms of the antiatherosclerosis properties of sirolimus.
The heart rate response to spontaneous arousal from sleep is reduced in children with Down syndrome referred for evaluation of sleep-disordered breathing
Authors: O'Driscoll Denise M. , Horne Rosemary S. C. , Davey Margot J. , Hope Sarah A. , Walker Adrian M. , Nixon Gillian M.
Published: March 2010

Arousal from sleep in healthy adults is associated with a large, transient increase in heart rate (HR). Individuals with Down syndrome (DS) have attenuated cardiovascular responses to autonomic tests during wakefulness. We tested the hypothesis that the HR response to arousal from sleep is reduced in children with DS and obstructive sleep apnea (OSA) compared with healthy children. Twenty children aged 3–17 yr referred for investigation of sleep-disordered breathing (10 DS, and 10 OSA controls) matched for age and obstructive apnea/hypopnea index underwent routine overnight polysomnography. In addition, 10 nonsnoring controls from the general community were studied. Beat-by-beat HR was analyzed from 15 s pre- to 15 s post-spontaneous arousals and compared between groups using two-way ANOVA with repeated measures. Data are presented as means ± SE. For both rapid eye movement (REM) and non-REM (NREM), arousals were associated with a significant increase in HR in all groups (peak response NREM: DS, 118 ± 1% at 3 s; OSA controls, 124 ± 2% at 4 s; and healthy controls, 125 ± 3% at 4 s; and peak response REM: DS, 116 ± 2% at 4 s; OSA controls, 123 ± 3% at 4 s; and healthy controls, 125 ± 4 at 4 s; P < 0.001 for all). Post hoc analysis revealed that HR in the DS group was significantly lower than both control groups at 1–4 s in NREM and at 4 to 5 s in REM ( P < 0.05 for all). In conclusion, the HR response to spontaneous arousal from sleep is reduced in children with DS and OSA compared with healthy children. This attenuated cardiovascular response could be due to reduced sympathetic activation or blunted vagal withdrawal and may have implications for the child with DS and OSA.
Effect of erythrocyte aggregation and flow rate on cell-free layer formation in arterioles
Authors: Ong Peng Kai , Namgung Bumseok , Johnson Paul C. , Kim Sangho
Published: March 2010

Formation of a cell-free layer is an important dynamic feature of microcirculatory blood flow, which can be influenced by rheological parameters, such as red blood cell aggregation and flow rate. In this study, we investigate the effect of these two rheological parameters on cell-free layer characteristics in the arterioles (20–60 μm inner diameter). For the first time, we provide here the detailed temporal information of the arteriolar cell-free layer in various rheological conditions to better describe the characteristics of the layer variation. The rat cremaster muscle was used to visualize arteriolar flows, and the extent of aggregation was raised by dextran 500 infusion to levels seen in normal human blood. Our results show that cell-free layer formation in the arterioles is enhanced by a combination of flow reduction and red blood cell aggregation. A positive relation ( P < 0.005) was found between mean cell-free layer widths and their corresponding SDs for all conditions. An analysis of the frequency and magnitudes of cell-free layer variation from their mean value revealed that the layer deviated with significantly larger magnitudes into the red blood cell core after flow reduction and dextran infusion ( P < 0.05). In accordance, the disparity of cell-free layer width distribution found in opposite radial directions from its mean became greater with aggregation in reduced flow conditions. This study shows that the cell-free layer width in arterioles is dependent on both flow rate and red blood cell aggregability, and that the temporal variations in width are asymmetric with a greater excursion into the red blood cell core than toward the vessel wall.
Identification of triptolide, a natural diterpenoid compound, as an inhibitor of lung inflammation
Authors: Hoyle Gary W. , Hoyle Christine I. , Chen Jing , Chang Weiyuan , Williams Ronald W. , Rando Roy J.
Published: March 2010

Inflammation is associated with various pulmonary diseases and contributes to the pathogenesis of acute lung injury. We previously identified a proinflammatory signaling pathway triggered by G protein-coupled receptors (GPCRs) in which stimulation of Gq-coupled GPCRs results in activation of the transcription factor NF-κB. Because damage to the lung causes the release of multiple mediators acting through Gq-coupled GPCRs, this signaling pathway is likely to contribute to inflammatory processes in the injured lung. In an effort to identify novel inhibitors of lung inflammation, the National Institutes of Health Clinical Collection, a library of 446 compounds, was screened for inhibitory activity toward production of IL-8 induced by stimulation of the Gq-coupled tachykinin 1 receptor with substance P in A549 cells. Twenty-eight compounds that significantly inhibited substance P-induced IL-8 production were identified. The most potent inhibitor was triptolide, a diterpenoid compound from Tripterygium wilfordii Hook F, a vine used in traditional Chinese medicine for the treatment of autoimmune diseases. Triptolide inhibited IL-8 production induced by substance P with an IC50 of 2.3 × 10−8 M and inhibited NF-κB activation in response to an agonist of the protease-activated receptor 2 with an IC50 of 1.4 × 10−8 M. Anti-inflammatory effects of triptolide were assessed in vivo using a chlorine gas lung injury model in mice. Triptolide inhibited neutrophilic inflammation and the production of KC (Cxcl1) in the lungs of chlorine-exposed mice. The results demonstrate that triptolide exhibits anti-inflammatory activity in cultured lung cells and in an in vivo model of acute lung injury.
Mechanotransduction by GEF-H1 as a novel mechanism of ventilator-induced vascular endothelial permeability
Authors: Birukova Anna A. , Fu Panfeng , Xing Junjie , Yakubov Bakhtiyor , Cokic Ivan , Birukov Konstantin G.
Published: March 2010

Pathological lung overdistention associated with mechanical ventilation at high tidal volumes (ventilator-induced lung injury; VILI) compromises endothelial cell (EC) barrier leading to development of pulmonary edema and increased morbidity and mortality. We have previously shown involvement of microtubule (MT)-associated Rho-specific guanine nucleotide exchange factor GEF-H1 in the agonist-induced regulation of EC permeability. Using an in vitro model of human pulmonary EC exposed to VILI-relevant magnitude of cyclic stretch (18% CS) we tested a hypothesis that CS-induced alterations in MT dynamics contribute to the activation of Rho-dependent signaling via GEF-H1 and mediate early EC response to pathological mechanical stretch. Acute CS (30 min) induced disassembly of MT network, cell reorientation, and activation of Rho pathway, which was prevented by MT stabilizer taxol. siRNA-based GEF-H1 knockdown suppressed CS-induced disassembly of MT network, abolished Rho signaling, and attenuated CS-induced stress fiber formation and EC realignment compared with nonspecific RNA controls. Depletion of GEF-H1 in the murine two-hit model of VILI attenuated vascular leak induced by lung ventilation at high tidal volume and thrombin-derived peptide TRAP6. These data show for the first time the critical involvement of microtubules and microtubule-associated GEF-H1 in lung vascular endothelial barrier dysfunction induced by pathological mechanical strain.
Regulation of heme oxygenase-1 gene by peptidoglycan involves the interaction of Elk-1 and C/EBPα to increase expression
Authors: Hung Chi-Chih , Liu Xiaoli , Kwon Min-Young , Kang Young-Ho , Chung Su Wol , Perrella Mark A.
Published: March 2010

Heme oxygenase (HO)-1 is a cytoprotective enzyme with anti-inflammatory properties. HO-1 is induced during a systemic inflammatory response, and expression of HO-1 is beneficial during sepsis of a Gram-positive source. Systemic infection from Gram-positive organisms has emerged as an important cause of sepsis, with Staphylococcus aureus as a common etiology. An important mediator of Gram-positive infections is peptidoglycan (PGN), a cell wall component of these organisms. Here, we demonstrate that HO-1 played an important, protective role in vivo, as mice deficient in HO-1 were very sensitive to the lethal effects of PGN derived from S. aureus. PGN induced HO-1 protein and mRNA levels, and this regulation occurred at the level of gene transcription. The PGN-responsive region of the HO-1 promoter (from −117 to −66 bp) contains a functional EBS, and Ets proteins are known to be involved in the regulation of inflammatory responses. We showed previously that Ets factors (activators Ets-2 and Ets-1 and repressor Elk-3) regulate HO-1 expression by Gram-negative endotoxin. However, during exposure to a Gram-positive stimulus in the present study, Elk-1 was a potent activator of HO-1 in conjunction with PGN. The ability of Elk-1 to induce HO-1 promoter activity was independent of direct DNA binding, but rather occurred by interacting with the CCAAT/enhancer-binding protein-α (C/EBPα), which binds to DNA. Moreover, silencing of C/EBPα in macrophages prevented induction of HO-1 promoter activity by either Elk-1 or PGN. These data provide further insight into the regulation and function of HO-1 by a mediator of Gram-positive bacteria.
TNF Induces Choroid Plexus Epithelial Cell Barrier Alterations by Apoptotic and Nonapoptotic Mechanisms
Authors: Schwerk Christian , Rybarczyk Kasia , Essmann Frank , Seibt Annette , Mölleken Marie-Louise , Zeni Patrick , Schroten Horst , Tenenbaum Tobias
Published: March 2010

The choroid plexus epithelium constitutes the structural basis of the blood-cerebrospinal fluid barrier. Since the cytokine TNF is markedly increased during inflammatory diseases in the blood and the central nervous system, we investigated by which mechanisms TNF induces barrier alteration in porcine choroid plexus epithelial cells. We found a dose-dependent decrease of transepithelial electrical resistance, increase of paracellular inulin-flux, and induction of histone-associated DNA fragmentation and caspase-3 activation after TNF stimulation. This response was strongly aggravated by the addition of cycloheximide and could partially be inhibited by the NF-B inhibitor CAPE, but most effectively by the pan-caspase-inhibitor zVAD-fmk and not by the JNK inhibitor SP600125. Partial loss of cell viability could also be attenuated by CAPE. Immunostaining showed cell condensation and nuclear binding of high-mobility group box 1 protein as a sign of apoptosis after TNF stimulation. Taken together our findings indicate that TNF compromises PCPEC barrier function by caspase and NF-B dependent mechanisms.
Three Years of Experience with the STELLA Robotic Observatory
Authors: Granzer Thomas , Weber Michael , Strassmeier Klaus G.
Published: March 2010

Since May 2006, the two STELLA robotic telescopes at the Izaña observatory
in Tenerife, Spain, delivered an almost uninterrupted stream of scientific data.
To achieve such a high level of autonomous operation, the replacement of all
troubleshooting skills of a regular observer in software was required. Care
must be taken on error handling issues and on robustness of the algorithms
used. In the current paper, we summarize the approaches we followed in the
STELLA observatory.
Primary Hepatic Actinomycosis
Authors: Cetinkaya Ziya , Kocakoc Ercan , Coskun Serdar , Ozercan Ibrahim Hanefi
Published: March 2010

Objectives: To present a case of primary hepatic actinomycosis. Clinical Presentation: A-40-year-old man was admitted to the general surgery clinic with a 1-month history of abdominal pain and weight loss. Liver transaminase, bilirubin levels and white blood cell counts were increased. Abdominal ultrasound and CT revealed cystic lesions with necrotic debris involving the posterior segment of the right lobe of the liver and the medial segment of the left lobe. Intervention: The patient underwent surgery under general anesthesia. On exploration, three cavities were found within the liver containing necrotic material. Surgical debridement and drainage was performed. Histopathological examination revealed actinomycotic colonies with a surrounding suppurative granulomatous reaction. The patient was treated with penicillin for 3 months. Conclusion: This case showed that histological examination of biopsy or surgical material or anaerobic cultures was needed for definitive diagnosis and that hepatic actinomycosis should be included in the differential diagnosis of solitary or multiple hypodense liver lesions.