bluuebunny/crossref_metadata_2025 huggingface dataset:
Overweight in medical paediatric inpatients: Detection and parent expectations
Authors: McLean Karen , Wake Melissa , McCallum Zoe
Published: April 2007

Aims:  (i) To determine prevalence and rates of detection of overweight/obesity among general paediatric inpatients. (ii) To explore parental expectations regarding detection and management of overweight/obesity during admission.

Methods:  This is a cross‐sectional survey conducted in the Royal Children’s Hospital, Melbourne, Australia. A total of 102 children aged 2–12 years admitted to a general paediatric unit at the Royal Children’s Hospital and their parents participated in the survey. The main outcome measures are body mass index (BMI); documentation of weight, height and BMI in patient notes; parent description of child’s weight, parent concern about child’s weight, and parent opinion about detection and management of overweight.

Results:  Twelve of 102 children (11.7%, 95% confidence intervals 6.2%, 19.7%) were overweight or obese. All children had a documented weight, two children (2.0%) had a documented height and none had BMI documented. Seven of 12 parents of overweight children described their child’s weight as healthy; five of 12 parents of overweight children were not concerned about their child’s weight. Eight of 12 parents of overweight children believed all admitted children should have their BMI calculated. All parents thought the hospital should take action if a child was found to be overweight.

Conclusions:  Although prevalence of overweight was lower than expected, documentation of overweight did not occur for any patient in the study. Parents of overweight children with acute illnesses believed that the hospital should screen for overweight and discuss it with parents. Further studies are required to determine expectations among other patient populations.
Ki‐67 proliferative index predicts clinical outcome in patients with atypical or anaplastic meningioma
Authors: Bruna Jordi , Brell Marta , Ferrer Isidre , Gimenez‐Bonafe Pepita , Tortosa Avelina
Published: April 2007

Meningiomas represent the second most common central nervous system neoplasms in adults and account for 26% of all primary brain tumors. Although most are benign, between 5% and 15% of meningiomas are atypical (grade II) whereas 1–2% are anaplastic meningiomas (grade III). Although histological grade is the most relevant prognostic factor, there are some unusual cases in which establishing a diagnosis of high‐grade meningioma following 2000 World Health Organization (WHO) histological criteria is extremely difficult. Therefore, the aim of the present study was to evaluate the predictive value of Ki‐67 labeling index and its contribution to current WHO classification in predicting tumor recurrence and overall survival in patients with high‐grade meningiomas. A total of 28 patients (with 16 atypical meningiomas and 12 anaplastic meningiomas) were evaluated for demographic, clinical, radiological and therapeutic variables, and for Ki‐67 immunohistochemistry. Median Ki‐67 labeling index in the whole series was 7.0 (0.5–31.5) with no differences with respect to the histological grade (P = 0.87). In the univariate analysis, Ki‐67 labeling index and postoperative Karnofsky performance status were identified as significant prognostic factors of tumor recurrence and overall survival. The multivariate analysis demonstrated that Ki‐67 labeling index is the only independent predictor of both tumor recurrence and overall survival. More importantly, this predictive value was maintained in both patients with atypical and patients with anaplastic meningioma.
Diagnosis of rickets and reassessment of prevalence among rural children in northern China
Authors: STRAND MARK A. , PERRY JUDITH , JIN MEIMEI , TRACER DAVID P. , FISCHER PHILIP R. , ZHANG PEIYING , XI WEIPING , LI SIHAN
Published: April 2007

Background: Rates of rickets from 15.9 to 26.7% have been reported in China.

Methods: Combining the methods of epidemiology and the behavioral sciences, this study investigated the prevalence of rickets in children in rural Shanxi Province, China. A total of 250 children age 12–24 months were examined physically for the presence of rickets, blood was drawn for laboratory analysis, and X‐rays were taken of each child’s wrists.

Results: Vitamin D deficiency in the spring was found among 65.3% of children. Rickets diagnosis relying on clinical signs alone determined a rickets prevalence of 41.6%, declining to 17.0% in the fall after a summer of sun exposure (χ2 = 8.356, P = 0.004). But an integrated diagnostic method exploiting clinical signs, X‐ray and alkaline phosphatase levels found the prevalence of active rickets to be 3.7%. Furthermore, it was demonstrated that only five clinical signs reflect active rickets – wide wrists, frontal bossing, rachitic rosary, Harrison’s sulcus, and bowed legs.

Conclusions: The prevalence of active rickets in young children in northern China is lower than previously reported. Even in poor countries, simple tests such as X‐rays and alkaline phosphatase can be added to physical examination to more accurately diagnose active rickets.
Prognosis and pathological characteristics of five children with non‐Shiga toxin‐mediated hemolytic uremic syndrome
Authors: KAMIOKA ICHIRO , NOZU KANDAI , FUJITA TERUO , KAITO HIROSHI , TANAKA RYOJIRO , YOSHIYA KUNIHIKO , IIJIMA KAZUMOTO , NAKANISHI KOICHI , YOSHIKAWA NORISHIGE , MATSUO MASAFUMI
Published: April 2007

Background: The three major signs of hemolytic uremic syndrome (HUS) are hemolytic anemia, thrombopenia and acute renal failure. HUS is classified into Shiga toxin‐mediated HUS (Stx‐HUS) and non‐Shiga toxin‐mediated HUS (nStx‐HUS). The prognosis of nStx‐HUS is reported to be less favorable than that of Stx‐HUS. Although the association between the prognosis and pathological characteristics of HUS have been reported such that the prognosis was considered to be poor for thrombotic microangiopathy (TMA) with predominant arterial involvement (arterial TMA), good for TMA with predominant glomerular involvement (glomerular TMA) and dependent on the extent of necrosis in cases of renal cortical necrosis, it is not yet clear whether pathological findings are also related to the renal prognosis of nStx‐HUS cases. Therefore the purpose of the present paper was to analyze renal biopsy findings and prognosis for five children with nStx‐HUS.

Methods: Clinical records of five cases of nStx‐HUS among 74 cases of diagnosed HUS were reviewed, and information and data were summarized.

Results: Histological examination of the kidney led to the diagnosis of arterial TMA in three cases, and glomerular TMA and severe renal cortical necrosis in one case each. Analysis of the relationship between renal histological findings and the prognosis found that three patients with arterial TMA and one patient with severe renal cortical necrosis later developed end‐stage renal failure while one patient with glomerular TMA has continued to show normal renal function.

Conclusions: These findings indicate that pathological findings are closely related to the prognosis in cases of nStx‐HUS.
Matrix metalloproteinase‐1 promoter polymorphism and epithelial ovarian cancer: Does ethnicity matter?
Authors: Ju Woong , Kim Jae Weon , Park Noh‐Hyun , Song Yong‐Sang , Kim Seung‐Cheol , Kang Soon‐Beom , Lee Hyo‐Pyo
Published: April 2007

Aim:  To estimate the relationship between matrix metalloproteinase (MMP)‐1 promoter ‐1607 bp polymorphism and the risk of epithelial ovarian cancer (EOC) in Korean women and to clarify the ethnic difference in genotype distribution of this polymorphism.

Methods:  Single nucleotide polymorphism (SNP) of MMP‐1 promoter ‐1607 region in 133 EOC patients and 332 cancer‐free patients were investigated. Then the associations of this polymorphism with EOC or its clinicopathological parameters were analyzed. In addition, genotype distributions of this polymorphism in Korean women were compared with those of other races by extracting data from the previously published literature.

Results:  We found no relationship between MMP‐1 promoter ‐1607 bp polymorphism and epithelial ovarian cancer in a Korean population. Furthermore, we found ethnicity‐dependent differences in genotype distributions and allele frequencies by comparison with previous articles on this topic. We report significant ethnic differences in the genotype distributions and allele frequencies of the MMP‐1 promoter ‐1607 bp polymorphism.

Conclusion:  Our results indicate that MMP‐1‐1607 bp polymorphism shows ethnic diversity, and that the hypothesis that this polymorphism is associated with epithelial ovarian cancer is not supported by this study in a Korean population. Moreover, this finding concurs with results obtained in white Americans and Europeans.
The Role of Local Depositors in Controlling Expenses in Small‐Scale Financial Intermediation: An Empirical Analysis
Authors: HOLLIS AIDAN , SWEETMAN ARTHUR
Published: April 2007

Using data on Irish loan funds, a nineteenth‐century quasi‐bank system, we explore how the capital structure affects managerial agency to impact non‐interest expenses. These organizations had no equity‐holders and were financed by deposits and ‘capital’, comprising donations and accumulated profits, creating problems of managerial moral hazard. Higher net income (before non‐interest expenses) is associated with higher salaries and other non‐interest expenses. More surprisingly, higher ‘capital’–deposit ratios led to higher expenses even after controlling for net income. While this institution is unique, the findings suggest that depositors could assist in controlling expenses in microfinance organizations.
Thatcher's Legacy
Authors: Jenkins Simon
Published: April 2007

At the time of Margaret Thatcher's fall, conventional wisdom held that Thatcherism was a leadership style that had departed with its author. In significant respects, Thatcher's economic reforms were incomplete, and she and her ideas had never enjoyed a popular majority. But subsequent events have made clear that 1979 was a new point of departure. Thatcher's legacy can be described as two revolutions. The first revolution was an assault on the size of the state sector, including the introduction of privatisation and lower taxes. The second was the centralisation of power in Whitehall; necessary for the achievement of the first, but ultimately in conflict with it. John Major and Tony Blair were strong proponents of both revolutions. Britain now requires a third revolution to decentralise, localise, and pluralise the state.
Banality in Politics: Margaret Thatcher and the Biographers
Authors: Garnett Mark
Published: April 2007

There are numerous biographies of Margaret Thatcher, but as yet no full-length study has been written by a political scientist. This is a disappointing omission from the literature, and reflects a general tendency to undervalue biographical studies. One result has been the production of scholarly work on the Conservative party between 1975 and 1990 which is unduly abstract and often misleading. Equally, although some excellent biographies have been produced – and Thatcher's memoirs are among the best of their genre – the unique perspectives of political science can yield some fascinating insights into her career, her party and the changing nature of British government. This article traces some of the crucial interactions which influenced Thatcher – her family background, her experiences within the Conservative party, her electioneering and her conduct of government. It concludes that although Thatcher's personality developed as a result of these encounters, as an adult she affected institutions far more than they affected her. This raises interesting, but not insuperable challenges for political scientists. Individuals do matter, and their influence can be appraised within a broader context. Ironically, it seems that complex characters conform more readily to generalisable norms of political conduct; Thatcher, by contrast, broke many of the accepted rules precisely because her personality was so banal.
Theology in its Spatial Turn: Space, Place and Built Environments Challenging and Changing the Images of God
Authors: Bergmann Sigurd
Published: April 2007

Space and place have been marginalised or even absent in theology for long periods of its history. Christian theology, hereby, mirrors a strong characteristic of the so‐called ‘Western culture and its history’, which consequently has placed time over space. In the twentieth century's last years, however, space/place reflections have moved out from the margins to several sectors of sciences and the humanities in what has been summarised as ‘the spatial turn’. Spatial metaphors and the central image of the Earth as ‘our home’ are at the heart of environmentalism. This article starts with a discussion whether the spatial turn represents just a new theme or a necessity at theology's own depth and argues for the later. Theology's reflections about space and place provide a deep challenge and an urgent necessity for theology to become aware of its embeddedness in the existential spatiality of life. Thereafter its first section presents in detail those approaches that recently have regarded the theme of space and place explicitly as a central dimension of theology. Among the profiled approaches we find reflections about themes such as the space of Creation, God's spatiality, the loss of place, and spiritual practices as well as justice, redemption and aesth/ethics in the built environment and the ecological city. A second section maps some of the substantial subthemes in the dynamically emerging agenda. Among the many themes we find are God in the city, lived religion, architecture, eco‐feminism, geography and religion, land, new religiosities, pilgrimage, movement and mobility. In general one can identify two directions of theology in its spatial turn: on the one hand theologians explore what Christian images and practices in space and at place mean for theology's classical questions; on the other hand, they move, slowly but safely, into other discourses by experimenting with theological contributions to other disciplines and public discourses. This article shows how a constructive understanding of theology, which does not only focus on religion's destructive capacity, is fertilised and assisted by the self‐critical reflexiveness in academic theology that embeds the space/place reflection in a broader ecological horizon. Thanks to the embedding of theology in a broader ecological perception and understanding of Creation, the new plastic and spatial theology increases it strength to operate on different scales of nature, society and culture. The overview ends with an open question: Can space set free theology?
Epilithic Cyanobacterial Communities of a Marine Tropical Beach Rock (Heron Island, Great Barrier Reef): Diversity and Diazotrophy
Authors: Díez Beatriz , Bauer Karolina , Bergman Birgitta
Published: April 2007

The diversity and nitrogenase activity of epilithic marine microbes in a Holocene beach rock (Heron Island, Great Barrier Reef, Australia) with a proposed biological calcification “microbialite” origin were examined. Partial 16S rRNA gene sequences from the dominant mat (a coherent and layered pink-pigmented community spread over the beach rock) and biofilms (nonstratified, differently pigmented microbial communities of small shallow depressions) were retrieved using denaturing gradient gel electrophoresis (DGGE), and a clone library was retrieved from the dominant mat. The 16S rRNA gene sequences and morphological analyses revealed heterogeneity in the cyanobacterial distribution patterns. The nonheterocystous filamentous genus
Blennothrix
sp., phylogenetically related to
Lyngbya
, dominated the mat together with unidentified nonheterocystous filaments of members of the
Pseudanabaenaceae
and the unicellular genus
Chroococcidiopsis
. The dominance and three-dimensional intertwined distribution of these organisms were confirmed by nonintrusive scanning microscopy. In contrast, the less pronounced biofilms were dominated by the heterocystous cyanobacterial genus
Calothrix
, two unicellular
Entophysalis
morphotypes,
Lyngbya
spp., and members of the
Pseudanabaenaceae
family.
Cytophaga
-
Flavobacterium
-
Bacteroides
and
Alphaproteobacteria
phylotypes were also retrieved from the beach rock. The microbial diversity of the dominant mat was accompanied by high nocturnal nitrogenase activities (as determined by in situ acetylene reduction assays). A new DGGE
nifH
gene optimization approach for cyanobacterial nitrogen fixers showed that the sequences retrieved from the dominant mat were related to nonheterocystous uncultured cyanobacterial phylotypes, only distantly related to sequences of nitrogen-fixing cultured cyanobacteria. These data stress the occurrence and importance of nonheterocystous epilithic cyanobacteria, and it is hypothesized that such epilithic cyanobacteria are the principal nitrogen fixers of the Heron Island beach rock.
RecombinantSaccharomyces cerevisiaeStrain Expressing a Model Cytochrome P450 in the Rat Digestive Environment: Viability and Bioconversion Activity
Authors: Garrait G. , Jarrige J. F. , Blanquet S. , Beyssac E. , Alric M.
Published: April 2007

An innovative “biodrug” concept, based on the oral administration of living recombinant microorganisms, has recently emerged for the prevention or treatment of various diseases. An engineeredSaccharomyces cerevisiaestrain expressing plant P450 73A1 (cinnamate-4-hydroxylase [CA4H] activity) was used, and its survival and ability to converttrans-cinnamic acid (CIN) intop-coumaric acid (COU) were investigated in vivo. In rats, the recombinant yeast was resistant to gastric and small intestinal secretions but was more sensitive to the conditions found in the large intestine. After oral administration of yeast and CIN, the CA4H activity was shown in vivo, with COU being found throughout the rat's digestive tract and in its urine. The bioconversion reaction occurred very fast, with most of the COU being produced within the first 5 min. The gastrointestinal sac technique demonstrated that the recombinant yeast was able to convert CIN into COU (conversion rate ranging from 2 to 5%) in all the organs of the rat's digestive tract: stomach, duodenum, jejunum, ileum, cecum, and colon. These results promise new opportunities for the development of drug delivery systems based on engineered yeasts catalyzing a bioconversion reaction directly in the digestive tract.
Novel Methods for Genetic Transformation of Natural
Bacillus subtilis
Isolates Used To Study the Regulation of the Mycosubtilin and Surfactin Synthetases
Authors: Duitman Erwin H. , Wyczawski Dobek , Boven Ludolf G. , Venema Gerard , Kuipers Oscar P. , Hamoen Leendert W.
Published: April 2007

Natural isolates of
Bacillus subtilis
are often difficult to transform due to their low genetic competence levels. Here we describe two methods that stimulate natural transformation. The first method uses plasmid pGSP12, which expresses the competence transcription factor ComK and stimulates competence development about 100-fold. The second method stimulates Campbell-type recombination of DNA ligation mixtures in
B. subtilis
by the addition of polyethylene glycol. We employed these novel methods to study the regulation of the synthetases for the lipopeptide antibiotics mycosubtilin (
myc
) and surfactin (
srfA
) in
B. subtilis
strain ATCC 6633. By means of
lacZ
reporter fusions, it was shown that the expression of
srfA
is >100 times lower in strain ATCC 6633 than in the laboratory strain
B. subtilis
168. Expression of the
myc
operon was highest in rich medium, whereas
srfA
expression reached maximal levels in minimal medium. Further genetic analyses showed that the
srfA
operon is mainly regulated by the response regulator ComA, while the
myc
operon is primarily regulated by the transition-state regulator AbrB. Although there is in vitro evidence for a synergistic activity of mycosubtilin and surfactin, the expression of both lipopeptide antibiotics is clearly not coordinated.
Eap1p, an Adhesin That Mediates
Candida albicans
Biofilm Formation In Vitro and In Vivo
Authors: Li Fang , Svarovsky Michael J. , Karlsson Amy J. , Wagner Joel P. , Marchillo Karen , Oshel Philip , Andes David , Palecek Sean P.
Published: April 2007

Candida albicans
is the leading cause of systemic fungal infections in immunocompromised humans. The ability to form biofilms on surfaces in the host or on implanted medical devices enhances
C. albicans
virulence, leading to antimicrobial resistance and providing a reservoir for infection. Biofilm formation is a complex multicellular process consisting of cell adhesion, cell growth, morphogenic switching between yeast form and filamentous states, and quorum sensing. Here we describe the role of the
C. albicans EAP1
gene, which encodes a glycosylphosphatidylinositol-anchored, glucan-cross-linked cell wall protein, in adhesion and biofilm formation in vitro and in vivo. Deleting
EAP1
reduced cell adhesion to polystyrene and epithelial cells in a gene dosage-dependent manner. Furthermore,
EAP1
expression was required for
C. albicans
biofilm formation in an in vitro parallel plate flow chamber model and in an in vivo rat central venous catheter model.
EAP1
expression was upregulated in biofilm-associated cells in vitro and in vivo. Our results illustrate an association between Eap1p-mediated adhesion and biofilm formation in vitro and in vivo.
Stable Preanaphase Spindle Positioning Requires Bud6p and an Apparent Interaction between the Spindle Pole Bodies and the Neck
Authors: Haarer Brian K. , Helfant Astrid Hoes , Nelson Scott A. , Cooper John A. , Amberg David C.
Published: April 2007

Faithful partitioning of genetic material during cell division requires accurate spatial and temporal positioning of nuclei within dividing cells. In
Saccharomyces cerevisiae
, nuclear positioning is regulated by an elegant interplay between components of the actin and microtubule cytoskeletons. Regulators of this process include Bud6p (also referred to as the actin-interacting protein Aip3p) and Kar9p, which function to promote contacts between cytoplasmic microtubule ends and actin-delimited cortical attachment points. Here, we present the previously undetected association of Bud6p with the cytoplasmic face of yeast spindle pole bodies, the functional equivalent of metazoan centrosomes. Cells lacking Bud6p show exaggerated movements of the nucleus between mother and daughter cells and display reduced amounts of time a given spindle pole body spends in close association with the neck region of budding cells. Furthermore, overexpression of
BUD6
greatly enhances interactions between the spindle pole body and mother-bud neck in a spindle alignment-defective dynactin mutant. These results suggest that association of either spindle pole body with neck components, rather than simply entry of a spindle pole body into the daughter cell, provides a positive signal for the progression of mitosis. We propose that Bud6p, through its localization at both spindle pole bodies and at the mother-bud neck, supports this positive signal and provides a regulatory mechanism to prevent excessive oscillations of preanaphase nuclei, thus reducing the likelihood of mitotic delays and nuclear missegregation.
Structural Properties of Periplasmic SodCI That Correlate with Virulence in
Salmonella enterica
Serovar Typhimurium
Authors: Krishnakumar Radha , Kim Byoungkwan , Mollo Elizabeth A. , Imlay James A. , Slauch James M.
Published: April 2007

Salmonella enterica
strains survive and propagate in macrophages by both circumventing and resisting the antibacterial effectors normally delivered to the phagosome. An important aspect of
Salmonella
resistance is the production of periplasmic superoxide dismutase to combat phagocytic superoxide.
S. enterica
serovar Typhimurium strain 14028 produces two periplasmic superoxide dismutases: SodCI and SodCII. Both enzymes are produced during infection, but only SodCI contributes to virulence in the animal. Although 60% identical to SodCII at the amino acid level with very similar enzymatic properties, SodCI is dimeric, protease resistant, and tethered within the periplasm via a noncovalent interaction. In contrast, SodCII is monomeric and protease sensitive and is released from the periplasm normally by osmotic shock. We have constructed an enzymatically active monomeric SodCI enzyme by site-directed mutagenesis. The resulting protein was released by osmotic shock and sensitive to protease and could not complement the loss of wild-type dimeric SodCI during infection. To distinguish which property is most critical during infection, we cloned and characterized related SodC proteins from a variety of bacteria.
Brucella abortus
SodC was monomeric and released by osmotic shock but was protease resistant and could complement SodCI in the animal. These data suggest that protease resistance is a critical property that allows SodCI to function in the harsh environment of the phagosome to combat phagocytic superoxide. We propose a model to account for the various properties of SodCI and how they contribute to bacterial survival in the phagosome.
σ
E
Regulates and Is Regulated by a Small RNA in
Escherichia coli
Authors: Thompson Karl M. , Rhodius Virgil A. , Gottesman Susan
Published: April 2007

RybB is a small, Hfq-binding noncoding RNA originally identified in a screen of conserved intergenic regions in
Escherichia coli
. Fusions of the
rybB
promoter to
lacZ
were used to screen plasmid genomic libraries and genomic transposon mutants for regulators of
rybB
expression. A number of plasmids, including some carrying
rybB
, negatively regulated the fusion. An insertion in the
rep
helicase and one upstream of
dnaK
decreased expression of the fusion. Multicopy suppressors of these insertions led to identification of two plasmids that stimulated the fusion. One contained the gene for the response regulator OmpR; the second contained
mipA
, encoding a murein hydrolase. The involvement of MipA and OmpR in cell surface synthesis suggested that the
rybB
promoter might be dependent on σ
E
. The sequence upstream of the +1 of
rybB
contains a consensus σ
E
promoter. The activity of
rybB
-
lacZ
was increased in cells lacking the RseA anti-sigma factor and when σ
E
was overproduced from a heterologous promoter. The activity of
rybB
-
lacZ
and the detection of RybB were totally abolished in an
rpoE
-null strain. In vitro, σ
E
efficiently transcribes from this promoter. Both a
rybB
mutation and an
hfq
mutation significantly increased expression of both
rybB
-
lacZ
and
rpoE
-
lacZ
fusions, consistent with negative regulation of the σ
E
response by RybB and other small RNAs. Based on the plasmid screens, NsrR, a repressor sensitive to nitric oxide, was also found to negatively regulate σ
E
-dependent promoters in an RseA-independent fashion.
The Phosphotransferase System Formed by PtsP, PtsO, and PtsN Proteins Controls Production of Polyhydroxyalkanoates in
Pseudomonas putida
Authors: Velázquez Francisco , Pflüger Katharina , Cases Ildefonso , De Eugenio Laura I. , de Lorenzo Víctor
Published: April 2007

The genome of
Pseudomonas putida
KT2440 encodes five proteins of the phosphoenolpyruvate-carbohydrate phosphotransferase system. Two of these (FruA and FruB) form a dedicated system for fructose intake, while enzyme I
Ntr
(EI
Ntr
; encoded by
ptsP
), NPr (
ptsO
), and EII
Ntr
(
ptsN
) act in concert to control the intracellular accumulation of polyhydroxyalkanoates, a typical product of carbon overflow.
Identification of the σBRegulon ofBacillus cereusand Conservation of σB-Regulated Genes in Low-GC-Content Gram-Positive Bacteria
Authors: van Schaik Willem , van der Voort Menno , Molenaar Douwe , Moezelaar Roy , de Vos Willem M. , Abee Tjakko
Published: April 2007

The alternative sigma factor σBhas an important role in the acquisition of stress resistance in many gram-positive bacteria, including the food-borne pathogenBacillus cereus. Here, we describe the identification of the set of σB-regulated genes inB. cereusby DNA microarray analysis of the transcriptome upon a mild heat shock. Twenty-four genes could be identified as being σBdependent as witnessed by (i) significantly lower expression levels of these genes in mutants with a deletion ofsigBandrsbY(which encode the alternative sigma factor σBand a crucial positive regulator of σBactivity, respectively) than in the parental strainB. cereusATCC 14579 and (ii) increased expression of these genes upon a heat shock. Newly identified σB-dependent genes inB. cereusinclude a histidine kinase and two genes that have predicted functions in spore germination. This study shows that the σBregulon ofB. cereusis considerably smaller than that of other gram-positive bacteria. This appears to be in line with phylogenetic analyses where σBof theB. cereusgroup was placed close to the ancestral form of σBin gram-positive bacteria. The data described in this study and previous studies in which the complete σBregulon of the gram-positive bacteriaBacillus subtilis,Listeria monocytogenes, andStaphylococcus aureuswere determined enabled a comparison of the sets of σB-regulated genes in the different gram-positive bacteria. This showed that only three genes (rsbV,rsbW, andsigB) are conserved in their σBdependency in all four bacteria, suggesting that the σBregulon of the different gram-positive bacteria has evolved to perform niche-specific functions.
In Vitro Biosynthesis of Ether-Type Glycolipids in the Methanoarchaeon
Methanothermobacter thermautotrophicus
Authors: Morii Hiroyuki , Eguchi Tadashi , Koga Yosuke
Published: April 2007

The biosynthesis of archaeal ether-type glycolipids was investigated in vitro using
Methanothermobacter thermautotrophicus
cell-free homogenates. The sole sugar moiety of glycolipids and phosphoglycolipids of the organism is the β-
d
-glucosyl-(1→6)-
d
-glucosyl (gentiobiosyl) unit. The enzyme activities of archaeol:UDP-glucose β-glucosyltransferase (monoglucosylarchaeol [MGA] synthase) and MGA:UDP-glucose β-1,6-glucosyltransferase (diglucosylarchaeol [DGA] synthase) were found in the methanoarchaeon. The synthesis of DGA is probably a two-step glucosylation: (i) archaeol + UDP-glucose → MGA + UDP, and (ii) MGA + UDP-glucose → DGA + UDP. Both enzymes required the addition of K
+
ions and archaetidylinositol for their activities. DGA synthase was stimulated by 10 mM MgCl
2
, in contrast to MGA synthase, which did not require Mg
2+
. It was likely that the activities of MGA synthesis and DGA synthesis were carried out by different proteins because of the Mg
2+
requirement and their cellular localization. MGA synthase and DGA synthase can be distinguished in cell extracts greatly enriched for each activity by demonstrating the differing Mg
2+
requirements of each enzyme. MGA synthase preferred a lipid substrate with the
sn
-2,3 stereostructure of the glycerol backbone on which two saturated isoprenoid chains are bound at the
sn
-2 and
sn
-3 positions. A lipid substrate with unsaturated isoprenoid chains or
sn
-1,2-dialkylglycerol configuration exhibited low activity. Tetraether-type caldarchaetidylinositol was also actively glucosylated by the homogenates to form monoglucosyl caldarchaetidylinositol and a small amount of diglucosyl caldarchaetidylinositol. The addition of Mg
2+
increased the formation of diglucosyl caldarchaetidylinositol. This suggested that the same enzyme set synthesized the sole sugar moiety of diether-type glycolipids and tetraether-type phosphoglycolipids.
Purification and Characterization of Mycobacterial Phospholipase A: an Activity Associated with Mycobacterial Cutinase
Authors: Parker Sarah K. , Curtin Kathryn M. , Vasil Michael L.
Published: April 2007

We describe mycobacterial phospholipase A activity (MPLA) and, using reverse genetics, have associated this activity with putative mycobacterial cutinase. PLAs, which hydrolyze fatty acids on phospholipids, play a significant role in human inflammatory states and disease pathogenesis. In prokaryotes, the recognition of their role in virulence is more recent. Cutinases are serine esterases whose primary substrate is cutin, the waxy exterior layer of plants.
Mycobacterium tuberculosis
has maintained seven putative cutinases, though it should not encounter cutin; we demonstrate that known cutinases and MPLA cleave phospholipids in a PLA-type manner and also hydrolyze Tween. We analyzed cutinase motifs in mycobacteria and found the motif very prevalent. All mycobacteria tested had MPLA activity. These studies suggest an alternative use for putative cutinases by the
M. tuberculosis
group that is likely related to MPLA activity and lipid metabolism.
Characterization of a C—C Bond Hydrolase fromSphingomonas wittichiiRW1 with Novel Specificities towards Polychlorinated Biphenyl Metabolites
Authors: Seah Stephen Y. K. , Ke Jiyuan , Denis Geoffroy , Horsman Geoff P. , Fortin Pascal D. , Whiting Cheryl J. , Eltis Lindsay D.
Published: April 2007

Sphingomonas wittichiiRW1 degrades chlorinated dibenzofurans and dibenzo-p-dioxins viametacleavage. We used inverse PCR to amplifydxnB2, a gene encoding one of threemeta-cleavage product (MCP) hydrolases identified in the organism that are homologues of BphD involved in biphenyl catabolism. Purified DxnB2 catalyzed the hydrolysis of 8-OH 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate (HOPDA) approximately six times faster than for HOPDA at saturating substrate concentrations. Moreover, the specificity of DxnB2 for HOPDA (kcat/Km= 1.2 × 107M−1s−1) was about half that of the BphDs ofBurkholderia xenovoransLB400 andRhodococcus globerulusP6, two potent polychlorinated biphenyl (PCB)-degrading strains. Interestingly, DxnB2 transformed 3-Cl and 4-OH HOPDAs, compounds that inhibit the BphDs and limit PCB degradation. DxnB2 had a higher specificity for 9-Cl HOPDA than for HOPDA but a lower specificity for 8-Cl HOPDA (kcat/Km= 1.7 × 106M−1s−1), the chlorinated analog of 8-OH HOPDA produced during dibenzofuran catabolism. Phylogenetic analyses based on structure-guided sequence alignment revealed that DxnB2 belongs to a previously unrecognized class of MCP hydrolases, evolutionarily divergent from the BphDs although the physiological substrates of both enzyme types are HOPDAs. However, both classes of enzymes have mainly small hydrophobic residues lining the subsite that binds the C-6 phenyl of HOPDA, in contrast to the bulky hydrophobic residues (Phe106, Phe135, Trp150, and Phe197) found in the class II enzymes that prefer substrates possessing a C-6 alkyl. Thr196 and/or Asn203 appears to be an important determinant of specificity for DxnB2, potentially forming hydrogen bonds with the 8-OH substituent. This study demonstrates that the substrate specificities of evolutionarily divergent hydrolases may be useful for degrading mixtures of pollutants, such as PCBs.
Flagellar Motility Is Critical forListeria monocytogenesBiofilm Formation
Authors: Lemon Katherine P. , Higgins Darren E. , Kolter Roberto
Published: April 2007

The food-borne pathogenListeria monocytogenesattaches to environmental surfaces and forms biofilms that can be a source of food contamination, yet little is known about the molecular mechanisms of its biofilm development. We observed that nonmotile mutants were defective in biofilm formation. To investigate how flagella might function during biofilm formation, we compared the wild type with flagellum-minus and paralyzed-flagellum mutants. Both nonmotile mutants were defective in biofilm development, presumably at an early stage, as they were also defective in attachment to glass during the first few hours of surface exposure. This attachment defect could be significantly overcome by providing exogenous movement toward the surface via centrifugation. However, this centrifugation did not restore mature biofilm formation. Our results indicate that it is flagellum-mediated motility that is critical for both initial surface attachment and subsequent biofilm formation. Also, any role forL. monocytogenesflagella as adhesins on abiotic surfaces appears to be either minimal or motility dependent under the conditions we examined.
AN FPTAS FOR COMPUTING THE SIMILARITY OF THREE-DIMENSIONAL POINT SETS
Authors: KIRCHNER STEFAN
Published: April 2007

We present an FPTAS for a combinatorial optimization problem which is motivated by a problem in drug-design. The problem is as follows. One is given two finite subsets A,B of points in three-dimensional space which represent the centers of atoms of two molecules. The objective function is large if there are an appropriate rigid motion M, subsets S ⊂ A and T ⊂ B of the same size and a bijective function f from S to M(T) such that |S| is sufficiently large and the root mean squared distance between S and f(S) is small. The object is to find M and f such that the objective function is maximized. The corresponding maximum value defines the similarity score between two molecules.
UNIVERSAL ROUTING AND PERFORMANCE ASSURANCE FOR DISTRIBUTED NETWORKS
Authors: CHEN KEVIN F. , SHA EDWIN H.-M.
Published: April 2007

We show that universal routing can be achieved with low overhead in distributed networks. The validity of our results rests on a new network called the fat-stack. We show that from a routing perspective the fat-stack is efficient and is suitable for use as a baseline distributed network and as a crucial benchmark architecture for evaluating the performance of specific distributed networks. We show that the fat-stack is efficient by proving it is universal. A requirement for the fat-stack to be universal is that link capacities double up the levels of the network. We use methods developed in the areas of VLSI and processor interconnect for much of our analysis. We then show how to scale the fat-stack from a VLSI graph layout to a large-scale distributed topology and how the network can be an effective benchmark architecture. Our universality proofs show that a fat-stack of area Θ(A) can simulate any competing network of area A with [Formula: see text] overhead independently of wire delay. The universality result implies that the fat-stack of a given size is nearly the best routing network of that size. The fat-stack is also the minimal universal network for an [Formula: see text] overhead in terms of number of links. Actual simulations show that the fat-stack outperforms a mesh-based distributed network of comparable hardware usage. Our work helps explain why some deployed networks function in the way they do in terms of routing. It also provides an exemplary network of proven efficiency and scalability for building new distributed systems.
FLOW ON DATA NETWORK AND A POSITIVE SEMIDEFINITE REPRESENTABLE DELAY FUNCTION
Authors: GALTER JÉRÔME , LAUGIER ALEXANDRE
Published: April 2007

Data networks are subject to congestion, thereby the delay to go across the network may be large enough in order to dishearten customers to keep on using such a network. In this paper we address the problem of determining in a given network a routing which minimizes the delay or keeps it under a certain bound. This problem was already shown as [Formula: see text] complete. Our main contribution is to study it in the special context of the positive semidefinite programming and we present a column generation approach to solve the underlying problem.
Electrical parameters and ion species for active transport in human esophageal stratified squamous epithelium and Barrett's specialized columnar epithelium
Authors: Tobey N. A. , Argote C. M. , Vanegas X. C. , Barlow W. , Orlando R. C.
Published: April 2007

The human esophagus is lined by stratified squamous epithelium (ESSE), and in some subjects with reflux disease the distal esophagus becomes lined by Barrett's specialized columnar epithelium (BSCE). ESSE and BSCE differ both histologically and functionally, the latter evident by differences in their in vivo transmural electrical potential difference (PD), ESSE averaging −15 mV and BSCE being greater than −25 mV. In this report we examine the basis for this difference in PD. This is done by mounting endoscopic biopsies of ESSE from 25 subjects without esophageal disease and BSCE from 19 with Barrett's esophagus in mini-Ussing chambers for electrical recordings basally and after bathing solution ion replacement. The results show that the PD of human ESSE reflects a low level of active ion transport (5.1 ± 0.8 μA/cm2) combined with a high level of tissue (electrical) resistance (344 ± 34 Ω·cm2) and that of BSCE reflects a high level of active transport (43.6 ± 11.6 μA/cm2) combined with a low level of resistance (69 ± 8 Ω·cm2). Furthermore, active transport in ESSE was principally due to sodium absorption whereas in BSCE it was equally divided between sodium absorption and anion (chloride/bicarbonate) secretion, the latter through an apical membrane, 4-acetamido4′-isothiocyano-2,2′-stilbenedisulfonic acid-sensitive anion channel. As an anion-secreting tissue with bicarbonate secretory capacity more than fivefold greater than ESSE, BSCE is better suited than ESSE for defense of the esophagus against reflux disease.
Exendin-4, but not dipeptidyl peptidase IV inhibition, increases small intestinal mass in GK rats
Authors: Simonsen Lotte , Pilgaard Sofie , Orskov Cathrine , Rosenkilde Mette M. , Hartmann Bolette , Holst Jens J. , Deacon Carolyn F.
Published: April 2007

Long-term treatment with dipeptidyl peptidase IV inhibitors (DPPIV-I) or glucagon-like peptide (GLP)-1 analogs may potentially affect intestinal growth by down- or upregulating the intestinotrophic hormone GLP-2. This study compared the intestinotrophic effects of 12-wk administration of vehicle, exendin-4 (Ex-4; 5 nmol/kg bid sc), or DPPIV-I (NN-7201, 10 mg/kg qd orally) in GK rats. Some animals were observed additionally for 9 wk after the end of treatment. Both treatments lowered glycated hemoglobin A1c at wk 12 vs. control (Ex-4, −0.8%; DPPIV-I, −0.4%). Body weight was reduced by Ex-4 compared with control (361 ± 4 vs. 399 ± 5 g; P < 0.001) because of reduced food intake, whereas neither parameter was affected by DPPIV-I. Linear bone growth was unaffected by either treatment. After treatment end, food intake in Ex-4 animals increased, and, by wk 21, body weight was identical in all groups. The small intestine of Ex-4-treated animals was larger at wk 12 compared with control (length, 135.6 ± 1.6 vs. 124.5 ± 2.3 cm, P < 0.001; absolute weight, 8.4 ± 0.2 vs. 6.4 ± 0.4 g, P < 0.001), being most pronounced proximally, where the absolute cross-sectional area related to body weight increased by 24% because of increased mucosal thickness. These effects were reversible, and 9 wk after the end of treatment, no differences between Ex-4 and control were apparent. Plasma GLP-2 concentrations were unaltered by either treatment, and Ex-4 had no agonistic or antagonistic effects on the transfected GLP-2 receptor. DPPIV-I had no intestinal effects. In conclusion, the continued presence of Ex-4 is necessary to maintain weight loss in GK rats. Effective antihyperglycemic treatment with Ex-4 increases intestinal mass reversibly, whereas DPPIV-I lacks intestinal effects.
Rho kinase-mediated local cold-induced cutaneous vasoconstriction is augmented in aged human skin
Authors: Thompson-Torgerson Caitlin S. , Holowatz Lacy A. , Flavahan Nicholas A. , Larry Kenney W.
Published: April 2007

Cutaneous vasoconstriction (VC), a critical thermoregulatory response to cold, is generally impaired with aging. However, the effects of aging on local cooling-induced VC and its underlying mechanisms are poorly understood. We tested whether aged skin exhibits attenuated localized cold-induced VC and whether Rho kinase-mediated cold-induced VC is augmented with age. Skin blood flow was monitored with laser Doppler flowmetry (LDF) on seven young and seven older subjects. Cutaneous vascular conductance (CVC; LDF/mean arterial pressure) was expressed as percentage change from baseline (%ΔCVCbase). In protocol 1, two forearm skin sites were cooled to six temperatures (31.5–19°C) for 10 min each or two temperatures (29°C, 24°C) for 30 min each, with no age differences in the magnitude of VC. In protocol 2, three forearm skin sites were instrumented for intradermal microdialysis and cooled to 24°C for 40 min. During minutes 1–5, there was no age difference in CVC responses at control sites (young: −45 ± 6% vs. older: −46 ± 3%, P > 0.9). Adrenoceptor antagonism (yohimbine + propranolol) abolished VC in young (to +15 ± 13%, P < 0.05) but only partially inhibited VC in older subjects (to −23 ± 6%, P < 0.05). Rho kinase inhibition plus adrenoceptor antagonism (yohimbine + propranolol + fasudil) abolished VC in both groups. During minutes 35–40, there was no age difference in control (young: −77 ± 4% vs. older: −70 ± 2%, P > 0.3) or adrenoceptor-antagonized responses (young: −61 ± 3% vs. older: −55 ± 2%, P > 0.3); however, Rho kinase inhibition plus adrenoceptor antagonism blocked more VC in older compared with young subjects (−19 ± 11% vs. −35 ± 3%, P < 0.05). Although its magnitude remains unaffected, cold-induced VC becomes less dependent on adrenergic and more dependent on Rho kinase signaling with advancing age.
Enhanced cardioprotection against ischemia-reperfusion injury with a dipyridamole and low-dose atorvastatin combination
Authors: Ye Yumei , Lin Yu , Perez-Polo Regino , Huang Ming-He , Hughes Michael G. , McAdoo David J. , Manickavasagam Saraswathy , Uretsky Barry F. , Birnbaum Yochai
Published: April 2007

Atorvastatin (ATV) limits infarct size (IS) by activating Akt and ecto-5-nucleotidase, which generates adenosine. Activated Akt and adenosine activate endothelial nitric oxide synthase (eNOS). When given orally, high doses (10 mg/kg) are needed to achieve full protection. We determined whether dipyridamole (DIP), by preventing the reuptake of adenosine, has a synergistic effect with ATV in reducing myocardial IS. In this study, rats received 3-days of the following: water, ATV (2 mg·kg−1·day−1), DIP (6 mg·kg−1·day−1), or ATV + DIP. In addition, rats received 3-days of the following: aminophylline (Ami; 10 mg·kg−1·day−1) or Ami + ATV + DIP. Rats underwent 30 min of myocardial ischemia followed by 4 h of reperfusion (IS protocol), or hearts were explanted for immunoblotting. As a result, IS in the controls was 34.0 ± 2.8% of the area at risk. ATV (33.1 ± 2.1%) and DIP (30.5 ± 1.5%) did not affect IS, whereas ATV + DIP reduced IS (12.2 ± 0.5%; P < 0.001 vs. each of the other groups). There was no difference in IS between the Ami alone (48.1 ± 0.8%) and the Ami + ATV + DIP (45.8 ± 2.9%) group ( P = 0.422), suggesting that Ami completely blocked the protective effect. Myocardial adenosine level in the controls was 30.6 ± 3.6 pg/μl. ATV (51.0 ± 4.9 pg/μl) and DIP (51.5 ± 6.8 pg/μl) caused a small increase in adenosine levels, whereas ATV + DIP caused a greater increase in adenosine levels (66.4 ± 3.1 pg/μl). ATV and DIP alone did not affect myocardial Ser473 phosphorylated-Akt and Ser1177 phosphorylated-eNOS levels, whereas ATV + DIP significantly increased them. In conclusion, low-dose ATV and DIP had synergistic effects in reducing myocardial IS and activation of Akt and eNOS. This combination may have a potential benefit in augmenting the eNOS-mediated pleiotropic effects of statins.