bluuebunny/crossref_metadata_2025 huggingface dataset:
A Single
dicer
Gene Is Required for Efficient Gene Silencing Associated with Two Classes of Small Antisense RNAs in
Mucor circinelloides
Authors: de Haro Juan P. , Calo Silvia , Cervantes María , Nicolás Francisco E. , Torres-Martínez Santiago , Ruiz-Vázquez Rosa M.
Published: August 2009

RNA silencing in the zygomycete
Mucor circinelloides
exhibits uncommon features, such as induction by self-replicative sense transgenes and the accumulation of two size classes of antisense small interfering RNAs (siRNAs). To investigate whether this silencing phenomenon follows the rules of a canonical RNA-silencing mechanism, we used hairpin RNA (hpRNA)-producing constructs as silencing triggers and analyzed the efficiency and stability of silencing in different genetic backgrounds. We show here that the dsRNA-induced silencing mechanism is also associated with the accumulation of two sizes of antisense siRNAs and that this mechanism is not mediated by the previously known
dcl-1
(
dicer
-like) gene, which implies the existence of an additional
dicer
gene. An
M. circinelloides dcl-2
gene was cloned and characterized, and the corresponding null mutant was generated by gene replacement. This mutant is severely impaired in the silencing mechanism induced by self-replicative sense or inverted-repeat transgenes, providing the first genetic evidence of a canonical silencing mechanism in this class of fungus and pointing to a role for
dcl-2
in the mechanism. Moreover, a functional
dcl-2
gene is required for the normal accumulation of the two sizes of antisense RNAs, as deduced from the analysis of
dcl-2

−

transformants containing hpRNA-expressing plasmids. In addition to its critical role in transgene-induced silencing, the
dcl-2
gene seems to play a role in the control of vegetative development, since the
dcl-2
null mutants showed a significant decrease in their production of asexual spores.
Generation of Metabolically Diverse Strains ofStreptococcus pyogenesduring Survival in Stationary Phase
Authors: Wood Daniel N. , Weinstein Kathryn E. , Podbielski Andreas , Kreikemeyer Berndt , Gaughan John P. , Valentine Samara , Buttaro Bettina A.
Published: August 2009

Streptococcus pyogenes, in addition to causing fulminant disease, can be carried asymptomatically and may survive in the host without causing disease. Long-term stationary-phase cultures were used to characterize the metabolism of cultures surviving after glucose depletion. Survival of stationary-phase cultures in glucose-depleted rich medium was truncated by switching the cells to phosphate-buffered saline or by the addition of antibiotics, suggesting that survival depended on the presence of nutrients and metabolic activity. The metabolites of the pyruvate-to-acetate (PA) pathway (acetate and formate) and amino acid catabolic pathways (ammonia) accumulated throughout long-term stationary phase (12 weeks). Acid and ammonia production was balanced so that the culture pH was maintained above pH 5.6. Strains isolated from long-term stationary-phase cultures accumulated mutations that resulted in unique exponential-phase metabolisms, with some strains expressing the PA pathway, some strains producing ammonia, and some strains expressing both in the presence of glucose. Strains expressing high levels of PA pathway activity during exponential growth were unable to survive when regrown in pure culture due to the production of excess acid. These data suggest thatS. pyogenesdiversifies during survival in stationary phase into distinct strains with different metabolisms and that complementary metabolism is required to control the pH in stationary-phase cultures. One of three survivor strains isolated from tonsillar discard material from patients expressed high levels of the PA pathway during exponential growth. Sequencing of multiple group A streptococcus regulators revealed two different mutations in two different strains, suggesting that random mutation occurs during survival.
GuaA and GuaB Are Essential forBorrelia burgdorferiSurvival in the Tick-Mouse Infection Cycle
Authors: Jewett Mollie W. , Lawrence Kevin A. , Bestor Aaron , Byram Rebecca , Gherardini Frank , Rosa Patricia A.
Published: August 2009

Pathogens lacking the enzymatic pathways for de novo purine biosynthesis are required to salvage purines and pyrimidines from the host environment for synthesis of DNA and RNA. Two key enzymes in purine salvage pathways are IMP dehydrogenase (GuaB) and GMP synthase (GuaA), encoded by theguaBandguaAgenes, respectively. While these genes are typically found on the chromosome in most bacterial pathogens, theguaABoperon ofBorrelia burgdorferiis present on plasmid cp26, which also harbors a number of genes critical forB. burgdorferiviability. Using molecular genetics and an experimental model of the tick-mouse infection cycle, we demonstrate that the enzymatic activities encoded by theguaABoperon are essential forB. burgdorferimouse infectivity and provide a growth advantage to spirochetes in the tick. These data indicate that the GuaA and GuaB proteins are critical for the survival ofB. burgdorferiin the infection cycle and highlight a potential difference in the requirements for purine salvage in the disparate mammalian and tick environments.
Autonomous and FliK-Dependent Length Control of the Flagellar Rod in
Salmonella enterica
Authors: Takahashi Noriko , Mizuno Shino , Hirano Takanori , Chevance Fabienne F. V. , Hughes Kelly T. , Aizawa Shin-Ichi
Published: August 2009

Salmonella flgG
point mutations produce filamentous rod structures whose lengths are determined by FliK. FliK length variants produce rods with lengths proportional to the corresponding FliK molecular size, suggesting that FliK controls the length of not only the hook but also the rod by the same molecular mechanism.
The
Escherichia coli
Azoreductase AzoR Is Involved in Resistance to Thiol-Specific Stress Caused by Electrophilic Quinones
Authors: Liu Guangfei , Zhou Jiti , Fu Q. Shiang , Wang Jing
Published: August 2009

The physiological role of
Escherichia coli
azoreductase AzoR was studied. It was found that AzoR was capable of reducing several benzo-, naphtho-, and anthraquinone compounds, which were better substrates for AzoR than the model azo substrate methyl red. The
ΔazoR
mutant displayed reduced viability when exposed to electrophilic quinones, which are capable of depleting cellular reduced glutathione (GSH). Externally added GSH can partially restore the impaired growth of the
ΔazoR
mutant caused by 2-methylhydroquinone. The transcription of
azoR
was induced by electrophiles, including 2-methylhydroquinone, catechol, menadione, and diamide. A transcription start point was identified 44 bp upstream from the translation start point. These data indicated that AzoR is a quinone reductase providing resistance to thiol-specific stress caused by electrophilic quinones.
Bacillus subtilisHomologs of MviN (MurJ), the PutativeEscherichia coliLipid II Flippase, Are Not Essential for Growth
Authors: Fay Allison , Dworkin Jonathan
Published: August 2009

Although peptidoglycan synthesis is one of the best-studied metabolic pathways in bacteria, the mechanism underlying the membrane translocation of lipid II, the undecaprenyl-disaccharide pentapeptide peptidoglycan precursor, remains mysterious. Recently, it was proposed that the essentialEscherichia coli mviNgene encodes the lipid II flippase.Bacillus subtiliscontains four proteins that are putatively homologous to MviN, including SpoVB, previously reported to be necessary for spore cortex peptidoglycan synthesis during sporulation. MviN complemented the sporulation defect of a ΔspoVBmutation, and SpoVB and another of theB. subtilishomologs, YtgP, complemented the growth defect of anE. colistrain depleted for MviN. Thus, theseB. subtilisproteins are likely to be MviN homologs. However,B. subtilisstrains lacking these four proteins have no defects in growth, indicating that they likely do not serve as lipid II flippases in this organism.
Vibrio cholerae
LexA Coordinates CTX Prophage Gene Expression
Authors: Kimsey Harvey H. , Waldor Matthew K.
Published: August 2009

The filamentous bacteriophage CTXΦ transmits the cholera toxin genes by infecting and lysogenizing its host,
Vibrio cholerae
. CTXΦ genes required for virion production initiate transcription from the strong
P
A
promoter, which is dually repressed in lysogens by the phage-encoded repressor RstR and the host-encoded SOS repressor LexA. Here we identify the neighboring divergent
rstR
promoter,
P
R
, and show that RstR both positively and negatively autoregulates its own expression from this promoter. LexA is absolutely required for RstR-mediated activation of
P
R
transcription. RstR autoactivation occurs when RstR is bound to an operator site centered 60 bp upstream of the start of transcription, and the coactivator LexA is bound to a 16-bp SOS box centered at position −23.5, within the
P
R
spacer region. Our results indicate that LexA, when bound to its single site in the CTXΦ prophage, both represses transcription from
P
A
and coactivates transcription from the divergent
P
R
. We propose that LexA coordinates
P
A
and
P
R
prophage transcription in a gene regulatory circuit. This circuit is predicted to display transient switch behavior upon induction of CTXΦ lysogens.
Characterization of Alanine Catabolism inPseudomonas aeruginosaand Its Importance for Proliferation In Vivo
Authors: Boulette Megan L. , Baynham Patricia J. , Jorth Peter A. , Kukavica-Ibrulj Irena , Longoria Aissa , Barrera Karla , Levesque Roger C. , Whiteley Marvin
Published: August 2009

The opportunistic pathogenPseudomonas aeruginosacauses a variety of infections in immunocompromised individuals, including individuals with the heritable disease cystic fibrosis. Like the carbon sources metabolized by many disease-causing bacteria, the carbon sources metabolized byP. aeruginosaat the host infection site are unknown. We recently reported thatl-alanine is a preferred carbon source forP. aeruginosaand that two genes potentially involved in alanine catabolism (dadAanddadX) are induced during in vivo growth in the rat peritoneum and during in vitro growth in sputum (mucus) collected from the lungs of individuals with cystic fibrosis. The goals of this study were to characterize factors required for alanine catabolism inP. aeruginosaand to assess the importance of these factors for in vivo growth. Our results reveal thatdadAanddadXare arranged in an operon and are required for catabolism ofl-alanine. Thedadoperon is inducible byl-alanine,d-alanine, andl-valine, and induction is dependent on the transcriptional regulator Lrp. Finally, we show that a mutant unable to catabolizedl-alanine displays decreased competitiveness in a rat lung model of infection.
Evaluation of a Prototype Real-Time PCR Assay for Carcinogenic Human Papillomavirus (HPV) Detection and Simultaneous HPV Genotype 16 (HPV16) and HPV18 Genotyping
Authors: Castle Philip E. , Sadorra Mark , Lau Tiffany , Aldrich Carrie , Garcia Francisco A. R. , Kornegay Janet
Published: August 2009

Results from a prototype real-time PCR assay that separately detected human papillomavirus genotype 16 (HPV16), HPV18, and 12 other carcinogenic HPV genotypes in aggregate (cobas 4800 HPV test) and results from a PCR assay that detects 37 HPV genotypes individually (Linear Array) were compared using a convenience sample of cervical specimens (
n
= 531). The percentage of total agreement between the two assays was 94.7% (95% confidence interval, 92.5 to 96.5%). The Linear Array test was more likely than cobas 4800 HPV test to test positive for the 12 other carcinogenic HPV genotypes among women without evidence of cervical disease (
P
= 0.004).
Impact of a Short Period of Pre-Enrichment on Detection and Bacterial Loads of Methicillin-Resistant
Staphylococcus aureus
from Screening Specimens
Authors: Van Heirstraeten L. , Abrahantes J. Cortiñas , Lammens C. , Lee A. , Harbarth S. , Molenberghs G. , Aerts M. , Goossens H. , Malhotra-Kumar S.
Published: August 2009

We compared the impacts of direct plating on a chromogenic medium and of plating after enrichment (4 h and overnight) on the detection of methicillin-resistant
Staphylococcus aureus
(MRSA) from 52 patient screening samples. MRSA colony counts for ≈70% of samples after overnight pre-enrichment were >20-fold higher than the counts after the other two treatments. The qualitative differences (sample was MRSA positive/negative) between the results of the direct plating and 4-h pre-enrichment treatments were not significant, indicating no advantage of the latter; however, the number of samples positive for MRSA increased significantly after an overnight sample pre-enrichment (
P
< 0.005).
Evaluation of PCR-Based Testing for Surveillance of KPC-Producing Carbapenem-Resistant Members of the
Enterobacteriaceae
Family
Authors: Schechner Vered , Straus-Robinson Keren , Schwartz David , Pfeffer Iris , Tarabeia Jalal , Moskovich Rina , Chmelnitsky Inna , Schwaber Mitchell J. , Carmeli Yehuda , Navon-Venezia Shiri
Published: August 2009

The spread of carbapenem-resistant members of the
Enterobacteriaceae
family (CRE) harboring carbapenemases is an emerging public health threat. As KPC-producing
Klebsiella
species are endemic in our tertiary care hospital, we aimed to evaluate a PCR-based surveillance test for identification of rectal carriage of KPC-producing CRE. We conducted a surveillance study between May and December 2007. Rectal swabs were collected from patients known to harbor CRE and from contacts of newly discovered patients harboring CRE. Specimens were evaluated by culture and by PCR analysis for
bla
KPC
and were defined as positive if CRE was cultured and
bla
KPC
was identified. Discrepant results between the culture and PCR analysis were resolved by subculturing, repeating the PCR, and performing a hydrolysis assay. Positive CRE cultures prior or subsequent to the time of sampling for the study were also taken into consideration. Sensitivity, specificity, and time to result were calculated. A total of 755 swabs were included. Concordant results were documented for 735 specimens; 51 were positive as determined by both PCR and culture. Discrepancies existed for 20 swabs; 9 were
bla
KPC
negative and CRE culture positive, and 11 were
bla
KPC
positive and CRE culture negative. After repeat testing, a total of 64 samples were classified as
bla
KPC
-positive CRE. The sensitivity and specificity of the PCR analysis were 92.2% and 99.6%, respectively, and those of the culture were 87.5% and 99.4%, respectively. Over the last 3 months of the study, the sensitivity of the PCR improved to 96.3%, versus 77.8% for culture. Time to result was 30 h for the PCR and 60 h (negative) and 75 h (positive) for the CRE culture.
bla
KPC
PCR-based testing is a useful method for the surveillance of KPC-producing CRE. Its main advantage over culturing is a shorter time to result, and it may prove to be more sensitive.
Validity, reliability and responsiveness of patient-reported outcome questionnaires when assessing hip and groin disability: a systematic review
Authors: Thorborg K , Roos EM , Bartels EM , Petersen J , Hölmich P
Published: August 2009

Background

Novel treatment interventions are advancing rapidly in the management of hip and groin disability in the physically active young to middle-aged population.

Objective

To recommend the most suitable patient-reported outcome (PRO) questionnaires for the assessment of hip and groin disability based on a systematic review of evidence of validity, reliability and responsiveness of these instruments.

Methods

MEDLINE, EMBASE, CINAHL, Cochrane Central Register of Controlled Trials, PsycINFO, SportsDiscus and Web of Science were all searched up to January 2009. Two reviewers independently rated measurement properties of the PRO questionnaires in the included studies, according to a standardised criteria list.

Results

The computerised search identified 2737 publications. Forty-one publications investigating measurement properties of PRO questionnaires assessing hip or groin disability were included in the study. Twelve different questionnaires designed for patients with hip disability and one questionnaire for patients with groin disability were identified. Hip dysfunction and Osteoarthritis Outcome Score (HOOS) contains adequate measurement qualities to evaluate patients with hip osteoarthritis (OA) or total hip replacement (THR). Hip Outcome Score (HOS) is the best available questionnaire for evaluating hip arthroscopy, but the Inguinal Pain Questionnaire, the only identified questionnaire evaluating groin disability, does not contain adequate measurement qualities.

Conclusions

HOOS is recommended for evaluating patients with hip OA undergoing non-surgical treatment and surgical interventions such as THR. HOS is recommended for evaluating patients undergoing hip arthroscopy. Current and new PRO questionnaires should also be evaluated in younger patients (age <50) with hip and/or groin disability, including surgical and non-surgical patients.
Ultrasonographic tissue characterisation of human Achilles tendons: quantification of tendon structure through a novel non-invasive approach
Authors: van Schie H T M , de Vos R J , de Jonge S , Bakker E M , Heijboer M P , Verhaar J A N , Tol J L , Weinans H
Published: August 2009

Objective

To assess whether three-dimensional imaging of the Achilles tendon by ultrasonographic tissue characterisation (UTC) can differentiate between symptomatic and asymptomatic tendons.

Design

Case-control study.

Setting

Sports Medical Department of the Hague Medical Centre.

Patients

Twenty-six tendons from patients with chronic midportion Achilles tendinopathy were included. The “matched” control group consisted of 26 asymptomatic tendons.

Interventions

Symptomatic and asymptomatic tendons were scanned using the UTC procedure. One researcher performed the ultrasonographic data collection. These blinded data were randomised, and outcome measures were determined by two independent observers.

Main outcome measurements

The raw ultrasonographic images were analysed with a customdesigned algorithm that quantifies the three-dimensional stability of echo patterns, qua intensity and distribution over contiguous transverse images. This threedimensional stability was related to tendon structure in previous studies. UTC categorises four different echotypes that represent (I) highly stable; (II) medium stable; (III) highly variable and (IV) constantly low intensity and variable distribution. The percentages of echo-types were calculated, and the maximum tendon thickness was measured. Finally, the inter-observer reliability of UTC was determined.

Results

Symptomatic tendons showed less pixels in echo-types I and II than asymptomatic tendons (51.5% vs 76.6%, p<0.001), thus less three-dimensional stability of the echo pattern. The mean maximum tendon thickness was 9.2 mm in the symptomatic group and 6.8 mm in the asymptomatic group (p<0.001). The Intraclass Correlation Coefficient (ICC) for the interobserver reliability of determining the echo-types I+II was 0.95. The ICC for tendon thickness was 0.84.

Conclusion

UTC can quantitatively evaluate tendon structure and thereby discriminate symptomatic and asymptomatic tendons. As such, UTC might be useful to monitor treatment protocols.
Use of NSAIDs in triathletes: prevalence, level of awareness and reasons for use
Authors: Gorski T , Cadore E Lusa , Pinto S Santana , da Silva E Marczwski , Correa C Silva , Beltrami F Gabe , Kruel L F Martins
Published: August 2009

Objective

To determine the level of awareness regarding nonsteroidal anti-inflammatory drugs (NSAIDs) and the prevalence and reasons for their consumption among athletes competing at the 2008 Brazil Ironman Triathlon (3.8 km swim, 180 km cycle and 42.2 km run).

Design

Survey study.

Setting

2008 Brazil Ironman Triathlon, Florianópolis, Brazil, May 2008.

Participants

327 Of the 1250 athletes competing at the 2008 Brazil Ironman Triathlon were enrolled in the study.

Main Outcome

Measures Athletes answered a questionnaire about NSAID effects, side effects and consumption at the bike checkout or awards lunch.

Results

196 (59.9%) Athletes reported using NSAIDs in the previous 3 months; of these, 25.5% (n=50), 17.9% (n=35) and 47.4% (n=93) consumed NSAIDs the day before, immediately before and during the race, respectively. Among NSAID users, 48.5% (n=95) consumed them without medical prescription. The main reason given for NSAID consumption in the previous 3 months was the treatment of injuries, while the main reason given for consuming NSAIDs during the race was pain prevention. Despite anti-inflammatory and analgesic effects, most athletes were unaware of the effects of NSAIDs, and the only adverse effects known by most athletes were the gastrointestinal complications.

Conclusions

This study found a high prevalence of NSAID consumption, limited awareness of the effects and side effects of them and a high rate of nonprescribed use. It is suggested that long-distance triathlon events include in their programmes educational devices such as talks or folders about NSAID use, effects and side effects.
Coenzyme-dependent alcohol dehydrogenases in Candida guilliermondii Y4
Authors: Indrati Retno , Naito Junko , Ohta Yoshiyuki
Published: August 2009

Candida guilliermondii Y4 is capable of synthesizing two different alcohol dehydrogenases. ADH1 is constitutive on different carbon sources under shaking or settling conditions and its activity is prominent on gel electrophoresis. ADH2 is only synthesized under shaking condition. Two types of mutants were isolated using an allyl alcohol selection technique. ADH1-deficient mutants had 2.7% ADH activity of the wild type, while ADH2-deficient mutants had an ADH activity as high as that of the wild-type ADH activity. The alcohol dehydrogenases of the mutants differ from those of the wild type in their relative oxidation rates of alcohols. ADH1 appears to possess a functional role mainly in the production of ethanol from acetaldehyde, while ADH2 functions mainly in the oxidation of ethanol to acetaldehyde. However, both enzymes seem to be capable of carrying out the reverse reactions, since mutants lacking either of them still grew satisfactorily on different carbon sources. Key words: Candida guilliermondii, alcohol dehydrogenase, ADH1-deficient mutant, ADH2-deficient mutant.
Intracellular location of enzymes involved in citrate production by Aspergillus niger
Authors: Jaklitsch Walter M. , Kubicek Christian P. , Scrutton Michael C.
Published: August 2009

The intracellular distribution and maximal activities of nine enzymes involved in the biosynthesis and degradation of citric acid in Aspergillus niger were determined under conditions of growth and of citric acid production. Under these conditions the intracellular location of the enzymes in most cases resembled that described for other filamentous fungi. Pyruvate carboxylase was found predominantly or exclusively in the cytosol. A single isoenzyme of NADP–isocitrate dehydrogenase was present, which appeared to be localised in the mitochondrion. No significant differences in maximal enzyme activities were observed except for NADP–isocitrate dehydrogenase, which showed decreased activity in production-phase mycelia. The results obtained support the scheme proposed by C. P. Kubicek for the intracellular organisation of citric acid formation but provide little evidence that this process is controlled at the level of the biosynthesis of any of the enzymes examined here. Key words: pyruvate carboxylase, citric acid production, enzyme compartmentation, Aspergillus niger.
An electroporation-based system for high-efficiency transformation of germinated conidia of filamentous fungi
Authors: Chakraborty B. N. , Patterson N. A. , Kapoor M.
Published: August 2009

A rapid and efficient electroporation procedure has been developed for transformation of germinating conidia of filamentous fungi. Pretreatment of conidial preparations with a cell wall weakening agent, such as β-glucuronidase, was found to be essential for successful transformation. Using the qa-2+ gene of Neurospora crassa, encoding the catabolic dehydroquinase, as a selectable marker with a double-mutant host strain, auxotrophic for aromatic amino acids, integration of the plasmid was observed to be predominantly at ectopic chromosomal sites. Cotransformation with the qa-2+ gene and a plasmid containing a heat shock gene sequence (hsp70 of N. crassa) suggested integration site preference. High efficiencies of transformation to hygromycin resistance were achieved employing the bacterial hygromycin B phosphotransferase gene with N. crassa, the patulin-producer Penicillium urticae, and the causal agent of blackleg disease of crucifers, Leptosphaeria maculans. The economically important species Aspergillus oryzae was similarly transformed to benomyl resistance with the benomyl-resistant β-tubulin gene of N. crassa as a dominant selectable marker. Key words: transformation, Neurospora, Aspergillus, Penicillium, Leptosphaeria, electroporation.
Conditions for soft rot of wood
Authors: Worrall J. J. , Anagnost S. E. , Wang C. J. K.
Published: August 2009

Conditions leading to optimal development of soft rot of wood were studied in vitro. Rates of weight loss generally remained more or less constant for 12 weeks, after which they decreased. Use of Petri dishes as decay chambers, saturation of blocks with a reduced nutrient solution containing micronutrients and vitamins, and use of a thick nylon mesh as a support between the agar and blocks generally gave better results than alternative conditions. Depending on experimental conditions, decay was either superficial or more or less uniform throughout the block. The uniform pattern was associated with higher weight losses than the superficial pattern. These and other results suggest that, although soft rot is most readily apparent as a surface decay of near-saturated wood in service, moisture conditions for optimal development may be no different than for decays caused by basidiomycetes. Key words: wood decay, moisture, Chaetomium globosum.
Biomass distribution in a subarctic Piceamariana – Cladoniaalpestris woodland
Authors: Rencz Andrew N. , Auclair Allan N. D.
Published: August 2009

A study of 15 lichen woodlands in the subarctic of eastern Canada indicated a strong dominance by Piceamariana and Cladoniaalpestris.Mean tree density was 556 trees per hectare. Over 75% of all tree stems were Piceamariana. Piceaglauca and Larixlaricina were only minor components.Total shrub and ground cover was 120%. Lichen covered 97% of the surface area. Cladoniaalpestris alone represented 78% of total lichen cover. Shrubs covered 17% of the surface area. Moss and club moss species (6% cover) were minor.Total live biomass on a representative site was 46 291 kg•ha−1. Piceamariana and Cladoniaalpestris formed 75% of the total. The only other significant species was Betidaglandulosa (12 % of total).Biomass was distributed between tree, shrub, and ground layer species in the approximate ratio of 3:1:1. Lichen and leaf tissue represented one-third (31%) of the total biomass. Stem and roots constituted 40% and 28% of total biomass, respectively. Piceamariana contained 76% of all stem tissue. Shrub root mass (39% of shrub dry weight) was high in comparison with tree root mass (34% of P. mariana dry weight). Evergreen vascular species had three times more shoot mass relative to root mass than deciduous forms.Comparison of biomass levels and tissue distribution indicated the lichen woodland studied was similar to others in the immediate area and to Larix woodlands in the USSR. Lichen woodland had much lower total biomass, had high root–shoot ratios, and high shrub and ground layer biomass compared with boreal conifer and temperate deciduous forest.
Kraft-pulping evaluation of decayed trembling aspen (Populustremuloides) from Ontario
Authors: Hunt K. , Basham J. T. , Kemperman J. A.
Published: August 2009

Kraft-pulping data of sound and decayed trembling aspen (Populustremuloides Michx.) samples from five clones in Ontario are reported. From each clone, samples consisted of one sound bolt and three bolts from each of three major types of stem decay of aspen in central Canada, caused by Fomesigniarius (L. ex Fr.) Kichx., Radulumcasearium (Morg.) Lloyd, and Peniophorapolygonia (Pers. ex Fr.) Bourd.Average yields for sound and decayed woods were 57.5 and 51.9% ovendry wood, respectively; equivalent to an average decrease of 9.7% ovendry pulp due to decay. A decrease of 11.5% was obtained when only advanced decays were considered.Screen rejects were greater for both sound and decayed wood than in previous studies, even at low permanganate numbers. They appeared to be dependent on the type of decay.Pulp strengths from incipient-decayed wood differed little from those of sound wood, but those from the advance-decayed wood showed substantial decreases. Tear factor was the most affected (20–29% lower), and breaking length least affected, by decay (13–9% lower).
Southern pine stem form defined through principal component analysis
Authors: Liu C. J. , Keister T. D.
Published: August 2009

Principal component analysis, a multivariate statistical procedure, was used to develop equations for defining stem taper of loblolly (Pinustaeda L.) and slash pine (P. elliottii Engelm.) in Louisiana, U.S.A. Four sets of data were used (three of loblolly and one of slash pine). Data included individual tree diameter measurements at the ground line, 0.02, 0.04, 0.06, 0.08, and at each 0.1 of total height. Thus each data-set i included ni trees, each with 14 diameter measurements. Principal component analysis was applied to each data set and in every case a single eigenvalue absorbed more than 99% of the total variance. A graph of the elements of the eigenvector associated with the principal eigenvalue, plotted over the appropriate proportional height, resembled the mean stem taper of the trees in the data set. Within a data set, no differences were found in stem form among diameter at breast height (dbh) or height classes but trees with crown ratios greater than 0.51 did appear to have more taper in the upper 0.3 of the bole. Apparent differences in stem form were noted among trees growing in different areas of the state, and between the two species when growing in the same area. The first eigenvector can be interpolated by various methods to obtain a model for stem taper. We used a regression technique, with the first eigenvector as the dependent variable, and the corresponding proportional heights and their powers as independent variables. The equations thus developed are useful for determining volumes. We believe that the curve of the eigenvector for the first principal component is, at least, an approximation of a descriptive law of stem taper.
Changes in the organic layers under a black spruce stand fertilized with urea and triple superphosphate
Authors: Mahendrappa M. K.
Published: August 2009

Changes in the levels of soil nutrients and decomposition of organic matter under a black spruce (Piceamariana (Mill.) B.S.P.) stand treated with urea and triple superphosphate were studied over five growing seasons.The application of both N and P increased organic matter decomposition as indicated by decreases in the weights of L and F layers in fertilized plots and by the calculated values for the decomposition rate factors. Added urea moved down through the organic horizon and changed both physical and chemical characteristics of the organic material, particularly the F and H layers, which became greasy to touch as compared with those in the untreated plots. The thickness of the organic horizons was decreased in most of the urea-treated plots. Treatment effects on the levels of exchangeable ammonium N were detectable at the end of five growing seasons. Differences in the levels of ammoniacal N were greater in the L layers at the end of first growing season (1968) and in the F and H layers after 5 years (1972). The concentration of available P, however, showed treatment effects in 1968 but not in 1972. Addition of P with urea retarded the movement of N.
FRACTAL FLUCTUATIONS AND STATISTICAL NORMAL DISTRIBUTION
Authors: SELVAM A. M.
Published: August 2009

Dynamical systems in nature exhibit self-similar fractal fluctuations and the corresponding power spectra follow inverse power law form signifying long-range space-time correlations identified as self-organized criticality. The physics of self-organized criticality is not yet identified. The Gaussian probability distribution used widely for analysis and description of large data sets underestimates the probabilities of occurrence of extreme events such as stock market crashes, earthquakes, heavy rainfall, etc. The assumptions underlying the normal distribution such as fixed mean and standard deviation, independence of data, are not valid for real world fractal data sets exhibiting a scale-free power law distribution with fat tails. A general systems theory for fractals visualizes the emergence of successively larger scale fluctuations to result from the space-time integration of enclosed smaller scale fluctuations. The model predicts a universal inverse power law incorporating the golden mean for fractal fluctuations and for the corresponding power spectra, i.e., the variance spectrum represents the probabilities, a signature of quantum systems. Fractal fluctuations therefore exhibit quantum-like chaos. The model predicted inverse power law is very close to the Gaussian distribution for small-scale fluctuations, but exhibits a fat long tail for large-scale fluctuations. Extensive data sets of Dow Jones index, human DNA, Takifugu rubripes (Puffer fish) DNA are analyzed to show that the space/time data sets are close to the model predicted power law distribution.
GENERAL CODING METHOD ON RANDOM SELF-SIMILAR TREE COMPOSED OF MULTIPLE BASIC PATTERNS
Authors: HUNG CHUN-PO
Published: August 2009

This work discusses the random self-similar tree generation by employing multiple basic patterns, and investigates the character code and standardization algorithm for multiple basic patterns. With reference to the wide range of various basic patterns in natural shapes, the general coding method and the corresponding algorithm to calculate the topological distance is developed for random self-similar tree with multiple basic patterns. To assess the adaptability of the process, the general coding method is applied to transfer the generated river network to a code series and the corresponding algorithm for calculating topological distance of the links is used to determine the width function of the pattern. Finally, the width-function based geomorphologic instantaneous unit hydrograph (WF-GIUH) model is then applied to estimate the runoff of the Po-bridge watershed in northern Taiwan. The results reveal that the random self-similar tree with multiple basic patterns proposed in this study can be implemented successfully to calculate hydrologic responses.
THE SMALLEST ENCLOSING DISC OF AN AFFINE IFS FRACTAL
Authors: MARTYN TOMASZ
Published: August 2009

We present a novel approach to approximate the smallest disc to enclose an affine IFS attractor at any accuracy. The approach is efficient and characterized by very low memory requirements. It is based on a concept of spanning points we introduce to describe the extent of an IFS attractor. We give the formal definition of these points and show how to construct them efficiently in practice. A proof that the smallest disc to enclose the spanning points includes the smallest enclosing disc of the IFS attractor is given. We also show that the former disc approximates the latter with an error depending on parameters relevant to the construction of the points. The main benefit of using the spanning points is that their number is usually small even for high approximation accuracies. Thus, we can apply with success one of the known, smallest enclosing disc algorithms to the spanning points. The enclosed experimental results obtained for popular IFS fractals confirm the theoretical assertions of the paper, by showing that our method performs well in practice.
A Class of Bound Entangled States of Two Qutrits
Authors: Jurkowski Jacek , Chruściński Dariusz , Rutkowski Adam
Published: August 2009

We provide a new class of states of two qutrits displaying the so-called bound entanglement. We investigate the states using various versions of computable cross-norm and realignment criteria recently introduced in [7].
Distilling Entanglement from Fermions
Authors: Keyl Michael
Published: August 2009

Since fermions are based on anti-commutation relations, their entanglement cannot be studied in the usual way, such that the available theory has to be modified appropriately. Recent publications consider in particular the structure of separable and of maximally entangled states. In this paper we want to discuss local operations and entanglement distillation from bipartite fermionic systems. To this end we apply an algebraic point of view where algebras of local observables, rather than tensor product Hilbert spaces play the central role. We apply our scheme in particular to fermionic Gaussian states, where the whole discussion can be reduced to properties of the covariance matrix. Finally, the results are demonstrated with free fermions on an infinite, one-dimensional lattice.
Remarks on the Structure of Clifford Quantum Cellular Automata
Authors: Schlingemann Dirk-Michael
Published: August 2009

We report here on the structure of reversible quantum cellular automata with the additional restriction that these are also Clifford operations. This means that tensor products of Weyl operators (projective representation of a finite abelian symplectic group) are mapped to multiples of tensor products of Weyl operators. Therefore Clifford quantum cellular automata are induced by symplectic cellular automata in phase space. We characterize these symplectic cellular automata and find that all possible local rules must be, up to some global shift, reflection-invariant with respect to the origin. In the one-dimensional case we also find that all 1D Clifford quantum cellular automata are generated by a few elementary operations.
Vitamin K promotes mineralization, osteoblast-to-osteocyte transition, and an anticatabolic phenotype by γ-carboxylation-dependent and -independent mechanisms
Authors: Atkins Gerald J. , Welldon Katie J. , Wijenayaka Asiri R. , Bonewald Lynda F. , Findlay David M.
Published: August 2009

The vitamin K family members phylloquinone (vitamin K1) and the menaquinones (vitamin K2) are under study for their roles in bone metabolism and as potential therapeutic agents for skeletal diseases. We have investigated the effects of two naturally occurring homologs, phytonadione (vitamin K1) and menatetrenone (vitamin K2), and those of the synthetic vitamin K, menadione (vitamin K3), on human primary osteoblasts. All homologs promoted in vitro mineralization by these cells. Vitamin K1-induced mineralization was highly sensitive to warfarin, whereas that induced by vitamins K2 and K3 was less sensitive, implying that γ-carboxylation and other mechanisms, possibly genomic actions through activation of the steroid xenobiotic receptor, are involved in the effect. The positive effect on mineralization was associated with decreased matrix synthesis, evidenced by a decrease from control in expression of type I collagen mRNA, implying a maturational effect. Incubation in the presence of vitamin K2 or K3 in a three-dimensional type I collagen gel culture system resulted in increased numbers of cells with elongated cytoplasmic processes resembling osteocytes. This effect was not warfarin sensitive. Addition of calcein to vitamin K-treated cells revealed vitamin K-dependent deposition of mineral associated with cell processes. These effects are consistent with vitamin K promoting the osteoblast-to-osteocyte transition in humans. To test whether vitamin K may also act on mature osteocytes, we tested the effects of vitamin K on MLO-Y4 cells. Vitamin K reduced receptor activator of NF-κB ligand expression relative to osteoprotegerin by MLO-Y4 cells, an effect also seen in human cultures. Together, our findings suggest that vitamin K promotes the osteoblast-to-osteocyte transition, at the same time decreasing the osteoclastogenic potential of these cells. These may be mechanisms by which vitamin K optimizes bone formation and integrity in vivo and may help explain the net positive effect of vitamin K on bone formation.
Role of PSD95 in membrane association and catalytic activity of nNOSα in nitrergic varicosities in mice gut
Authors: Chaudhury Arun , He Xue-Dao , Goyal Raj K.
Published: August 2009

We have recently shown that membrane association of neuronal nitric oxide synthase-α (nNOSα) is critical in the regulation of synthesis of NO during nitrergic neurotransmission. The purpose of this study was to examine the role of the synapse-associated proteins (SAPs) in membrane association of nNOSα. Varicosities (swellings on terminal axons) were isolated from mice gastrointestinal tract and examined for nNOSα, postsynaptic density protein 95 (PSD95), and membrane interactions by coimmunoprecipitation and SDS-PAGE. Our results show that PSD95 protein was present in the membrane fraction of the nerve varicosity, whereas both PSD95 and SAP97 were present in the cytosol. nNOSα was associated with PSD95 but not SAP97. nNOSα-PSD95 complex was bound to the membrane via palmitoylation of PSD95. Depalmitoylation of PSD95 with 2-bromopalmitate dislocates nNOSα and PSD95 from the varicosity membrane and abolishes NO production. These studies show that palmitoylation of PSD95 anchors nNOSα to the varicosity membrane and that it is obligatory for NO production by the enzyme. Palmitoylation of PSD95 may provide a novel target for regulation of nitrergic neurotransmission.
Phasic contractions of rat mesenteric lymphatics increase basal and phasic nitric oxide generation in vivo
Authors: Bohlen H. Glenn , Wang Wei , Gashev Anatoliy , Gasheva Olga , Zawieja Dave
Published: August 2009

Multiple investigators have shown interdependence of lymphatic contractions on nitric oxide (NO) activity by pharmacological and traumatic suppression of endothelial NO synthase (eNOS). We demonstrated that lymphatic diastolic relaxation is particularly sensitive to NO from the lymphatic endothelium. The predicted mechanism is shear forces produced by the lymph flow during phasic pumping, activating eNOS in the lymphatic endothelium to produce NO. We measured [NO] during phasic contractions using microelectrodes on in situ mesenteric lymphatics in anesthetized rats under basal conditions and with an intravenous saline bolus (0.5 ml/100 g) or infusion (0.5 ml·100 g−1·h−1). Under basal conditions, [NO] measured on the tubular portions of the lymphatics was ∼200–250 nM, slightly higher than in the adjacent adipocyte microvasculature, whereas [NO] measured on the lymphatic bulb surface was ∼400 nM. Immunohistochemistry of eNOS in isolated lympathics indicated a much greater expression in the lymph valves and surrounding bulb area than in the tubular regions. During phasic lymphatic contractions, the valve and tubular [NO] increased with each contraction, and during intravenous saline infusion, [NO] increased in proportion to the contraction frequency and, presumably, lymph flow. The partial blockade of eNOS over ∼1 cm length with Nω-nitro-l-arginine methyl ester lowered the [NO]. These in vivo data document for the first time that both valvular and tubular lymphatic segments increase NO generation during each phasic contraction and that [NO] summated with increased contraction frequency. The combined data predict regional variations in eNOS and [NO] in the tubular and valve areas, plus the summated NO responses dependent on contraction frequency provide for a complex relaxation mechanism involving NO.
Poor trunk flexibility is associated with arterial stiffening
Authors: Yamamoto Kenta , Kawano Hiroshi , Gando Yuko , Iemitsu Motoyuki , Murakami Haruka , Sanada Kiyoshi , Tanimoto Michiya , Ohmori Yumi , Higuchi Mitsuru , Tabata Izumi , Miyachi Motohiko
Published: August 2009

Flexibility is one of the components of physical fitness as well as cardiorespiratory fitness and muscular strength and endurance. Flexibility has long been considered a major component in the preventive treatment of musculotendinous strains. The present study investigated a new aspect of flexibility. Using a cross-sectional study design, we tested the hypothesis that a less flexible body would have arterial stiffening. A total of 526 adults, 20 to 39 yr of age (young), 40 to 59 yr of age (middle-aged), and 60 to 83 yr of age (older), participated in this study. Subjects in each age category were divided into either poor- or high-flexibility groups on the basis of a sit-and-reach test. Arterial stiffness was assessed by brachial-ankle pulse wave velocity (baPWV). Two-way ANOVA indicated a significant interaction between age and flexibility in determining baPWV ( P < 0.01). In middle-aged and older subjects, baPWV was higher in poor-flexibility than in high-flexibility groups (middle-aged, 1,260 ± 141 vs. 1,200 ± 124 cm/s, P < 0.01; and older, 1,485 ± 224 vs. 1,384 ± 199 cm/s, P < 0.01). In young subjects, there was no significant difference between the two flexibility groups. A stepwise multiple-regression analysis ( n = 316) revealed that among the components of fitness (cardiorespiratory fitness, muscular strength, and flexibility) and age, all components and age were independent correlates of baPWV. These findings suggest that flexibility may be a predictor of arterial stiffening, independent of other components of fitness.
Disruption of endothelial peroxisome proliferator-activated receptor-γ reduces vascular nitric oxide production
Authors: Kleinhenz Jennifer M. , Kleinhenz Dean J. , You Shaojin , Ritzenthaler Jeffrey D. , Hansen Jason M. , Archer David R. , Sutliff Roy L. , Hart C. Michael
Published: August 2009

Vascular endothelial cells express the ligand-activated transcription factor, peroxisome proliferator-activated receptor-γ (PPARγ), which participates in the regulation of metabolism, cell proliferation, and inflammation. PPARγ ligands attenuate, whereas the loss of function mutations in PPARγ stimulate, endothelial dysfunction, suggesting that PPARγ may regulate vascular endothelial nitric oxide production. To explore the role of endothelial PPARγ in the regulation of vascular nitric oxide production in vivo, mice expressing Cre recombinase driven by an endothelial-specific promoter were crossed with mice carrying a floxed PPARγ gene to produce endothelial PPARγ null mice (ePPARγ−/−). When compared with littermate controls, ePPARγ−/−animals were hypertensive at baseline and demonstrated comparable increases in systolic blood pressure in response to angiotensin II infusion. When compared with those of control animals, aortic ring relaxation responses to acetylcholine were impaired, whereas relaxation responses to sodium nitroprusside were unaffected in ePPARγ−/−mice. Similarly, intact aortic segments from ePPARγ−/−mice released less nitric oxide than those from controls, whereas endothelial nitric oxide synthase expression was similar in control and ePPARγ−/−aortas. Reduced nitric oxide production in ePPARγ−/−aortas was associated with an increase in the parameters of oxidative stress in the blood and the activation of nuclear factor-κB in aortic homogenates. These findings demonstrate that endothelial PPARγ regulates vascular nitric oxide production and that the disruption of endothelial PPARγ contributes to endothelial dysfunction in vivo.