bluuebunny/crossref_metadata_2025 huggingface dataset:
Angiogenesis pattern of native and cross‐linked collagen membranes: an immunohistochemical study in the rat
Authors: Schwarz Frank , Rothamel Daniel , Herten Monika , Sager Martin , Becker Jürgen
Published: June 2006

Abstract: The aim of the present study was to immunohistochemically evaluate angiogenesis pattern of native and cross‐linked collagen membranes after subcutaneous implantation in rats. Five commercially available and three experimental membranes (VN) were included: (1) BioGide® (BG), (2) BioMend® (BM), (3) BioMend Extend® (BME), (4) Ossix® (OS), (5) TutoDent® (TD), and (6–8) VN(1–3). Specimens were randomly allocated in unconnected subcutaneous pouches (n=4) separated surgically on the back of 40 wistar rats, which were divided into five groups (2, 4, 8, 16, and 24 weeks), including eight animals each. Pattern of angiogenesis was labelled using primary mouse monoclonal antibody to transglutaminase II. For each membrane, the period of time, needed for a complete and homogeneous transmembraneous vascularization, was assessed immunohistomorhometrically. Differences between the membranes were found regarding the initial pattern of transmembraneous angiogenesis, as evaluated 2 weeks following implantation. Mean cross‐ and longitudinal‐sectional area of blood vessels (%) was highest for VN(3) (5.27±2.73), followed by BG (2.45±0.88), VN(1) (2.07±0.29), VN(2) (1.91±0.55), TD (1.44±0.53), BME (0.35±0.29) and BM (0.25±0.4). In contrast to BG and VN(1–3), BM, BME and TD exhibited a homogeneous transmembraneous formation of blood vessels merely 4–8 weeks following implantation. OS, however, exhibited no signs of angiogenesis throughout the whole study period. Within the limits of the present study, it may be concluded that pattern of transmembraneous angiogenesis markedly differs among the membranes investigated.
Comparison of early telescope loading of non‐submerged ITI implants in irradiated and non‐irradiated oral cancer patients
Authors: Landes Constantin Alexander , Kovács Adorján Ferenc
Published: June 2006

Objective: To compare early dental implant loading in irradiated and non‐irradiated oral cancer patients in order to accelerate masticatory function improvement and quality of life.

Patients and methods: One hundred and fourteen non‐submerged interforaminal ITI implants were early loaded in 30 patients after 3 weeks in situ (telescoped overdenture). Nineteen patients received 72 implants (63%) after local irradiation; 11 non‐irradiated patients received 42 implants (37%) with a 24‐month follow‐up.

Results: At 24 month follow‐up, one early failure had occurred in an irradiated patient (=99% functioning implants in situ). Peri‐implant bleeding and plaque index were similarly high in both groups (40 to 68% average).The Results of other measured parameters were as follows (values for mean; irradiated; non‐irradiated patients with respective standard deviations; significance of comparison): bone loss (0.9±0.9; 1.4±0.9; 0.4±0.5 mM; P<0.01); Periotest® score (−2.7±2.7; −2.4±2.2; −3.1±3.3; P<0.2); gingival recession (0.6±0.7 mM; 0.8±0.9 mM; 0.4±0.5 mM, P<0.02); and peri‐implant probing depths (3±1.2; 2.6±0.6; 3.4±1.7 mM; P<0.002).

Conclusion: The results suggest reliable non‐submerged implantation and early loading. However, bone loss in irradiated mandibles, combined with higher average Periotest values and gingival recession in an oral environment of altered saliva quantity, quality, microflora and local scarring, requires extended follow‐up.
Influence of smoking on osseointegrated implant failure: a meta‐analysis
Authors: Hinode Daisuke , Tanabe Shin‐ichi , Yokoyama Masaaki , Fujisawa Kenji , Yamauchi Eiji , Miyamoto Youji
Published: June 2006

Abstract: The aim of this study was to examine the influence of smoking on osseointegrated implant failure by performing a meta‐analysis. A computerized literature search using PubMed database (in English) and Japana Centra Revuo Medicina (in Japanese) was carried out to identify all relevant studies. Among 175 studies identified and chosen for detailed review, 19 were appropriate for inclusion in our meta‐analysis. When smokers were compared with non‐smokers, odds ratio (OR) for osseointegrated implant failure was significantly elevated (OR 2.17, 95% confidence intervals (CI), 1.67–2.83). Seven studies were appropriate to examine the influence of intra‐oral location (maxillary arch vs. mandibular arch) of implant failure on smoking. The OR for implant failure occurring in the maxillary arch was significantly elevated (OR 2.06, 95% CI, 1.61–2.65), whereas the OR in the mandibular arch did not demonstrate a significant increased risk associated with smoking (OR 1.32, 95% CI, 0.72–2.4). Our meta‐analysis revealed a significant relationship between smoking and the risk of osseointegrated implant failure, more particularly those implants located in the maxillary arch.
Quality and quantity of bone following alveolar distraction osteogenesis in the human mandible
Authors: Chiapasco Matteo , Lang Niklaus P. , Bosshardt Dieter D.
Published: June 2006

Purpose: The purpose of this prospective study on humans were to evaluate (a) the clinical outcome of alveolar distraction osteogenesis for the correction of vertically deficient edentulous mandibular ridges, (b) the clinical outcome of dental implants placed in the distracted areas, and (c) the quality and quantity of the bone that had formed in the distraction gap.

Material and methods: Seven patients presenting vertically deficient edentulous ridges were treated by means of distraction osteogenesis with an intraoral alveolar distractor. Approximately 3 months after consolidation of the distracted segments, 20 ITI solid screw SLA implants were placed in the distracted areas. Three to 4 months later, abutments were connected and prosthetic loading of the implants started. During implant site preparation, bone biopsies were taken at the implant sites with trephine burrs for histologic and histometric analyses.

Results: The mean follow‐up after the initial prosthetic loading was 18 months (range 12–24 months). The mean bone gain obtained at the end of distraction was 7 mm (range 5–9 mm). The cumulative success rate of implants 2 years after the onset of prosthetic loading was 95%, whereas the survival rate of implants was 100%. The newly formed bone consisted of woven bone reinforced by parallel‐fibered bone with bone marrow spaces between the bone trabeculae. The bone area fraction in the distraction region ranged from 21.6% to 57.8% (38.5±11.7%).

Discussion and conclusions: Results from this study showed that (a) distraction osteogenesis is a reliable technique for the correction of vertically deficient edentulous ridges, (b) the regenerated bone withstood the functional demands of implant loading, (c) survival and success rates of implants placed in the distracted areas were consistent with those of implants placed in native bone, and (d) there is sufficient bone volume and maturity in the distracted region for primary stability of the implant.
Early implant failure. Prognostic capacity of Periotest®: retrospective study of a large sample
Authors: Noguerol Blas , Muñoz Ricardo , Mesa Francisco , De Dios Luna Juan , O'Valle Francisco
Published: June 2006

Objectives: The objectives of this study were to determine the accuracy of Periotest® to monitor primary implant stability at first‐stage surgery, to identify by multivariate analysis the variables associated with early implant failure and to compare Periotest® with radiographic study in the diagnosis of implant stability at second‐stage surgery (during osseointegration period).

Material and methods: A 10‐year retrospective study was conducted on 1084 Brånemark® implants placed in 316 patients. Clinical variables, implant diameter and length, Periotest® values (PTVs) and radiological variables were analyzed in bivariate and multivariate studies in order to determine their influence on early implant failure.

Results: After examination of the sensitivity and specificity values obtained for different PTV cutoff points, a cutoff PTV of −2 was selected (84% sensitivity and 39% specificity). In the bivariate analysis, early failure was significantly related to smoking habits, implant location, bone type, implant features and PTVs (−2 and ≥−2). In the final multiple logistic model, only age (odds ratio (OR)=4.53; 95% confidence interval (CI), 1.34–15.27), smoking habits (OR=2.5; 95% CI, 1.3–4.79), bone type (OR=1.93; 95% CI, 1.01–3.7) and PTV at first surgery (OR=3.01; 95% CI, 1.5–6.02) were independently related to early failure.

Conclusions: The Periotest® (with −2 cutoff) at first surgery offers high sensitivity in the prognosis of early implant loss and shows a greater capacity to evaluate stability during the osseointegration period compared with radiographic study.
Biomechanical aspects of initial intraosseous stability and implant design: a quantitative micro‐morphometric analysis
Authors: Akça Kιvanç , Chang Ting‐Ling , Tekdemir İbrahim , Fanuscu Mete I.
Published: June 2006

Purpose: The objective of this biomechanical study was to explore the effect of bone micro‐morphology on initial intraosseous stability of implants with different designs.

Material and methods: Straumann and Astra Tech dental implants were placed into anterior and posterior regions of completely edentulous maxilla and mandible of a human cadaver. Experiments were undertaken to quantify initial implant stability and bone micro‐morphology. Installation torque values (ITVs) and implant stability quotients (ISQs) were measured to determine initial intraosseous implant stability. For quantification of relative bone volume and micro‐architecture, sectioned implant–bone and bone core specimens of each implant placement site were consecutively scanned and trabecular bone was analyzed in a micro‐computed tomography (micro‐CT) unit. Experimental outcomes were evaluated for correlations among implant designs, initial intraosseous implant stability and bone micro‐structural parameters.

Results: ITVs correlated higher with bone volume fraction (BV/TV) than ISQs, at 88.1% and 68.9% levels, respectively. Correlations between ITVs and micro‐morphometric parameters were significant at the 95% confidence level (P<0.05) while ISQs were not. Differences in ITVs, ISQs and BV/TV data in regards to implant designs used were not significant at the 95% confidence level (P>0.05).

Conclusion: Bone micro‐morphology has a prevailing effect over implant design on intraosseus initial implant stability, and ITV is more sensitive in terms of revealing biomechanical properties at the bone–implant interface in comparison with ISQ.
What is the biological basis of pattern formation of skin lesions?
Authors: Paus Ralf , Chuong C. M. , Dhouailly D. , Gilmore S. , Forest L. , Shelley W. B. , Stenn K. S. , Maini P. , Michon F. , Parimoo S. , Cadau S. , Demongeot J. , Zheng Y. , Paus R. , Happle R.
Published: June 2006

Abstract:  Pattern recognition is at the heart of clinical dermatology and dermatopathology. Yet, while every practitioner of the art of dermatological diagnosis recognizes the supreme value of diagnostic cues provided by defined patterns of ‘efflorescences’, few contemplate on the biological basis of pattern formation in and of skin lesions. Vice versa, developmental and theoretical biologists, who would be best prepared to study skin lesion patterns, are lamentably slow to discover this field as a uniquely instructive testing ground for probing theoretical concepts on pattern generation in the human system. As a result, we have at best scraped the surface of understanding the biological basis of pattern formation of skin lesions, and widely open questions dominate over definitive answer. As a symmetry‐breaking force, pattern formation represents one of the most fundamental principles that nature enlists for system organization. Thus, the peculiar and often characteristic arrangements that skin lesions display provide a unique opportunity to reflect upon – and to experimentally dissect – the powerful organizing principles at the crossroads of developmental, skin and theoretical biology, genetics, and clinical dermatology that underlie these – increasingly less enigmatic – phenomena. The current ‘Controversies’ feature offers a range of different perspectives on how pattern formation of skin lesions can be approached. With this, we hope to encourage more systematic interdisciplinary research efforts geared at unraveling the many unsolved, yet utterly fascinating mysteries of dermatological pattern formation. In short: never a dull pattern!
Immunohistochemical study of small integrin‐binding ligand, N‐linked glycoproteins in reactionary dentin of rat molars at different ages
Authors: Moses Kyle D. , Butler William T. , Qin Chunlin
Published: June 2006

Small integrin‐binding ligand, N‐linked glycoproteins (SIBLING) are believed to play key roles in the process of biomineralization. Reactionary dentin (RD), formed by odontoblasts in response to external stimuli, differs morphologically from primary dentin (PD). To test our hypothesis that the microscopic changes reflect variations in molecular mechanisms involved in formation of the two forms of dentin, and to characterize RD further, we compared the distributions of four SIBLING proteins [bone sialoprotein (BSP), osteopontin (OPN), dentin matrix protein 1 (DMP‐1) and dentin sialophosphoprotein (DSPP)] in naturally occurring RD with those in PD. Molars of rats aged 12, 18, 24 and 36 wk were analyzed using immunohistochemistry with antibodies against BSP, OPN, DMP‐1, and dentin sialoprotein (a fragment of DSPP). Differences in the distribution of the four SIBLING proteins were evident. Bone sialoprotein, not seen in PD, was consistently observed in RD. Osteopontin, almost absent from PD, was clearly observed in RD. The expression levels of DMP‐1 and DSP in RD were lower than in PD. Elevated expression of BSP and OPN, along with a marked decrease of dentin sialoprotein and DMP‐1 in RD, suggests a difference in the mechanism of formation of the two forms of dentin.
Masticatory function with mandibular implant‐supported overdentures fitted with different attachment types
Authors: Van Der Bilt Andries , Van Kampen Frits M. C. , Cune Marco S.
Published: June 2006

Oral rehabilitation by means of implant‐retained mandibular overdentures is known to improve the oral function. The improvement may depend on the degree of retention and stability of the denture and thus on the type of attachment. In this within‐patient cross‐over clinical trial, we examined the hypothesis that more retention and stability of the overdenture improves the masticatory function. Eighteen patients received two permucosal implants, a new overdenture, and, successively, three different suprastructure modalities: a magnet, a ball, and a bar‐clip attachment. We quantified aspects of the oral function by measuring the electromyographic activity of the jaw muscles and the jaw movement during chewing. The muscle activity was significantly lower for the unsupported new mandibular denture compared with values for the supported new denture. No significant differences in muscle activity were observed among the three attachment types. Furthermore, we did not observe significant differences in jaw muscle activity between the old unsupported denture and the new supported denture, despite significant differences in masticatory performance. Measuring muscle activity during chewing will thus not provide adequate information about masticatory function. Thus, subjects chewed more efficiently after implant treatment. No changes in cycle duration or in jaw movement parameters were observed among the various measurement moments.
Dental beliefs: evaluation of the Swedish version of the revised Dental Beliefs Survey in different patient groups and in a non‐clinical student sample
Authors: Abrahamsson Kajsa H. , Hakeberg Magnus , Stenman Jane , Öhrn Kerstin
Published: June 2006

The aim of this study was to evaluate and to test the psychometric properties of a Swedish version of the revised Dental Beliefs Survey (DBS‐R) in different patient groups and in a non‐clinical sample of students. It was hypothesized that negative dental beliefs, assessed using the DBS‐R, would discriminate between fearful and non‐fearful study groups. The questionnaire was distributed together with the Dental Anxiety Scale (DAS). The sample included 550 adults who responded to the questionnaires (206 students, 177 general dental patients, 105 periodontal patients and 62 patients at a waiting list for dental‐fear treatment). The internal drop‐out rate was low. The results confirmed that the DBS‐R discriminates well between fearful patients and the other study groups. The DBS‐R had a high internal consistency in all the study groups. Furthermore, the DBS‐R correlated significantly with age (higher values in younger age groups) and the DAS. Regression analyses showed that the DBS‐R subdimensions of ‘communication’ and ‘control’/or ‘trust’, respectively, were significant predictors for dental fear. The results suggest that the DBS‐R is a reliable and valid instrument for use in different Swedish patient‐ and non‐clinical population groups in order to assess attitudes to dentists. However, the underlying factor structure of the DBS‐R needs to be further explored and established.
Downregulation of Human Endometrial IL‐18 by Exogenous Ovarian Steroids
Authors: Lédée Nathalie , Dubanchet Sylvie , Lombroso Raoul , Ville Yves , Chaouat Gérard
Published: June 2006

Problem

To evaluate the influence of ovarian steroids on IL‐18, IL‐15 and angiopoietin‐2 mRNA expression in the endometrium in the mid luteal phase.

Method of study

We quantified IL‐18/GAPDH, IL‐18 BP/GAPDH, IL‐15/GAPDH and angiopoietin‐2/GAPDH in the endometrium by quantitative polymerase chain reaction on day 21 of the cycle. We first compared cytokines expression over two natural cycles (n = 15) then between natural and oestrogen–progestin replacement treatment (n = 18).

Results

Endometrial IL‐18, IL‐18 BP, IL‐15 and angiopoietin‐2 mRNA expression did not change over two natural cycles. Addition of exogenous hormones significantly decreased IL‐18 and IL‐18 BP mRNA expression but not influence IL‐15 or angiopoietin‐2 ratios. This was also observed with immunohistochemistry.

Conclusion

Exogenous oestro‐progestative hormones influence endometrial IL‐18 system expression involved in angiogenesis and in the uterine natural killer (uNK) cell activation pathway during the implantation process.
Purine‐induced expression of urate oxidase and enzyme activity in Atlantic salmon (Salmo salar)
Authors: Andersen Øivind , Aas Turid s. , Skugor Stanko , Takle Harald , van Nes Solveig , Grisdale‐Helland Barbara , Helland Ståle J. , Terjesen Bendik F.
Published: June 2006

The peroxisomal enzyme urate oxidase plays a pivotal role in the degradation of purines in both prokaryotes and eukaryotes. However, knowledge about the purine‐induced expression of the encoding gene is lacking in vertebrates. These are the first published sequences of fish urate oxidase, which were predicted from PCR amplified liver cDNAs of Atlantic salmon (Salmo salar), Atlantic cod (Gadus morhua), Atlantic halibut (Hippoglossus hippoglossus) and African lungfish (Protopterus annectens). Sequence alignment of different vertebrate urate oxidases revealed amino acid substitutions of putative functional importance in the enzyme of chicken and lungfish. In the adult salmon, expression of urate oxidase mRNA predominated in liver, but was also identified in several nonhepatic organs including brain, but not in skeletal muscle and kidney. Juvenile salmon fed diets containing bacterial protein meal (BPM) rich in nucleic acids showed a significant increase in liver urate oxidase enzyme activity, and urea concentrations in plasma, muscle and liver were elevated. Whereas salmon fed the 18% BPM diet showed a nonsignificant increase in liver mRNA levels of urate oxidase compared with the 0% BPM‐fed fish, no further increase in mRNA levels was found in fish receiving 36% BPM. The discrepancy between urate oxidase mRNA and enzyme activity was explained by rapid mRNA degradation or alternatively, post‐translational control of the activity. Although variable plasma and liver levels of urate were detected, the substrate increased only slightly in 36% BPM‐fed fish, indicating that the uricolytic pathway of Atlantic salmon is intimately regulated to handle high dietary purine levels.
Surface density of cellobiohydrolase on crystalline celluloses
Authors: Igarashi Kiyohiko , Wada Masahisa , Hori Ritsuko , Samejima Masahiro
Published: June 2006

The enzymatic kinetics of glycoside hydrolase family 7 cellobiohydrolase (Cel7A) towards highly crystalline celluloses at the solid–liquid interface was evaluated by applying the novel concept of surface density (ρ) of the enzyme, which is defined as the amount of adsorbed enzyme divided by the maximum amount of adsorbed enzyme. When the adsorption levels of Trichoderma viride Cel7A on cellulose Iα from Cladophora and cellulose Iβ from Halocynthia were compared, the maximum adsorption of the enzyme on cellulose Iβ was ∼1.5 times higher than that on cellulose Iα, although the rate of cellobiose production from cellulose Iβ was lower than that from cellulose Iα. This indicates that the specific activity (k) of Cel7A adsorbed on cellulose Iα is higher than that of Cel7A adsorbed on cellulose Iβ. When k was plotted versus ρ, a dramatic decrease of the specific activity was observed with the increase of surface density (ρ‐value), suggesting that overcrowding of enzyme molecules on a cellulose surface lowers their activity. An apparent difference of the specific activity was observed between crystalline polymorphs, i.e. the specific activity for cellulose Iα was almost twice that for cellulose Iβ. When cellulose Iα was converted to cellulose Iβ by hydrothermal treatment, the specific activity of Cel7A decreased and became similar to that of native cellulose Iβ at the same ρ‐value. These results indicate that the hydrolytic activity (rate) of bound Cel7A depends on the nature of the crystalline cellulose polymorph, and an analysis that takes surface density into account is an effective means to evaluate cellulase kinetics at a solid–liquid interface.
Human mesotrypsin exhibits restricted S1′ subsite specificity with a strong preference for small polar side chains
Authors: Szepessy Edit , Sahin‐Tóth Miklós
Published: June 2006

Mesotrypsin, an inhibitor‐resistant human trypsin isoform, does not activate or degrade pancreatic protease zymogens at a significant rate. These observations led to the proposal that mesotrypsin is a defective digestive protease on protein substrates. Surprisingly, the studies reported here with α1‐antitrypsin (α1AT) revealed that, even though mesotrypsin was completely resistant to this serpin‐type inhibitor, it selectively cleaved the Lys10–Thr11 peptide bond at the N‐terminus. Analyzing a library of α1AT mutants in which Thr11 was mutated to various amino acids, we found that mesotrypsin hydrolyzed lysyl peptide bonds containing Thr or Ser at the P1′ position with relatively high specificity (kcat/KM∼105 m−1·s−1). Compared with Thr or Ser, P1′ Gly or Met inhibited cleavage 13‐ and 25‐fold, respectively, whereas P1′ Asn, Asp, Ile, Phe or Tyr resulted in 100–200‐fold diminished rates of proteolysis, and Pro abolished cleavage completely. Consistent with the Ser/Thr P1′ preference, mesotrypsin cleaved the Arg358–Ser359 reactive‐site peptide bond of α1AT Pittsburgh and was rapidly inactivated by the serpin mechanism (ka∼106 m−1 s−1). Taken together, the results indicate that mesotrypsin is not a defective protease on polypeptide substrates in general, but exhibits a relatively high specificity for Lys/Arg–Ser/Thr peptide bonds. This restricted, thrombin‐like subsite specificity explains why mesotrypsin cannot activate pancreatic zymogens, but might activate certain proteinase‐activated receptors. The observations also identify α1AT Pittsburgh as an effective mesotrypsin inhibitor and the serpin mechanism as a viable stratagem to overcome the inhibitor‐resistance of mesotrypsin.
Revisiting the prediction of protein function at CASP6
Authors: Pellegrini‐Calace Marialuisa , Soro Simonetta , Tramontano Anna
Published: June 2006

The ability to predict the function of a protein, given its sequence and/or 3D structure, is an essential requirement for exploiting the wealth of data made available by genomics and structural genomics projects and is therefore raising increasing interest in the computational biology community. To foster developments in the area as well as to establish the state of the art of present methods, a function prediction category was tentatively introduced in the 6th edition of the Critical Assessment of Techniques for Protein Structure Prediction (CASP) worldwide experiment. The assessment of the performance of the methods was made difficult by at least two factors: (a) the experimentally determined function of the targets was not available at the time of assessment; (b) the experiment is run blindly, preventing verification of whether the convergence of different predictions towards the same functional annotation was due to the similarity of the methods or to a genuine signal detectable by different methodologies. In this work, we collected information about the methods used by the various predictors and revisited the results of the experiment by verifying how often and in which cases a convergent prediction was obtained by methods based on different rationale. We propose a method for classifying the type and redundancy of the methods. We also analyzed the cases in which a function for the target protein has become available. Our results show that predictions derived from a consensus of different methods can reach an accuracy as high as 80%. It follows that some of the predictions submitted to CASP6, once reanalyzed taking into account the type of converging methods, can provide very useful information to researchers interested in the function of the target proteins.
Characterization of the lipopolysaccharide and β‐glucan of the fish pathogen Francisella victoria
Authors: Kay William , Petersen Bent O. , Duus Jens Ø. , Perry Malcolm B. , Vinogradov Evgeny
Published: June 2006

Lipopolysaccharide (LPS) and β‐glucan from Francisella victoria, a fish pathogen and close relative of highly virulent mammal pathogen Francisella tularensis, have been analyzed using chemical and spectroscopy methods. The polysaccharide part of the LPS was found to contain a nonrepetitive sequence of 20 monosaccharides as well as alanine, 3‐aminobutyric acid, and a novel branched amino acid, thus confirming F. victoria as a unique species. The structure identified composes the largest oligosaccharide elucidated by NMR so far, and was possible to solve using high field NMR with cold probe technology combined with the latest pulse sequences, including the first application of H2BC sequence to oligosaccharides. The non‐phosphorylated lipid A region of the LPS was identical to that of other Francisellae, although one of the lipid A components has not been found in Francisella novicida. The heptoseless core‐lipid A region of the LPS contained a linear pentasaccharide fragment identical to the corresponding part of F. tularensis and F. novicida LPSs, differing in side‐chain substituents. The linkage region of the O‐chain also closely resembled that of other Francisella. LPS preparation contained two characteristic glucans, previously observed as components of LPS preparations from other strains of Francisella: amylose and the unusual β‐(1–6)‐glucan with (glycerol)2phosphate at the reducing end.
A nonribosomal peptide synthetase (Pes1) confers protection against oxidative stress in Aspergillus fumigatus
Authors: Reeves Emer P. , Reiber Kathrin , Neville Claire , Scheibner Olaf , Kavanagh Kevin , Doyle Sean
Published: June 2006

Aspergillus fumigatus is an important human fungal pathogen. The Aspergillus fumigatus genome contains 14 nonribosomal peptide synthetase genes, potentially responsible for generating metabolites that contribute to organismal virulence. Differential expression of the nonribosomal peptide synthetase gene, pes1, in four strains of Aspergillus fumigatus was observed. The pattern of pes1 expression differed from that of a putative siderophore synthetase gene, sidD, and so is unlikely to be involved in iron acquisition. The Pes1 protein (expected molecular mass 698 kDa) was partially purified and identified by immunoreactivity, peptide mass fingerprinting (36% sequence coverage) and MALDI LIFT‐TOF/TOF MS (four internal peptides sequenced). A pes1 disruption mutant (Δpes1) of Aspergillus fumigatus strain 293.1 was generated and confirmed by Southern and western analysis, in addition to RT‐PCR. The Δpes1 mutant also showed significantly reduced virulence in the Galleria mellonella model system (P < 0.001) and increased sensitivity to oxidative stress (P = 0.002) in culture and during neutrophil‐mediated phagocytosis. In addition, the mutant exhibited altered conidial surface morphology and hydrophilicity, compared to Aspergillus fumigatus 293.1. It is concluded that pes1 contributes to improved fungal tolerance against oxidative stress, mediated by the conidial phenotype, during the infection process.
Aggregative organization enhances the DNA end‐joining process that is mediated by DNA‐dependent protein kinase
Authors: Takahagi Masahiko , Tatsumi Kouichi
Published: June 2006

The occurrence of DNA double‐strand breaks in the nucleus provokes in its structural organization a large‐scale alteration whose molecular basis is still mostly unclear. Here, we show that double‐strand breaks trigger preferential assembly of nucleoproteins in human cellular fractions and that they mediate the separation of large protein–DNA aggregates from aqueous solution. The interaction among the aggregative nucleoproteins presents a dynamic condition that allows the effective interaction of nucleoproteins with external molecules like free ATP and facilitates intrinsic DNA end‐joining activity. This aggregative organization is functionally coacervate‐like. The key component is DNA‐dependent protein kinase (DNA‐PK), which can be characterized as a DNA‐specific aggregation factor as well as a nuclear scaffold/matrix‐interactive factor. In the context of aggregation, the kinase activity of DNA‐PK is essential for efficient DNA end‐joining. The massive and functional concentration of nucleoproteins on DNA in vitro may represent a possible status of nuclear dynamics in vivo, which probably includes the DNA‐PK‐dependent response to multiple double‐strand breaks.
H i 21 cm absorption at z ∼ 2.347 towards PKS B0438-436
Authors: Kanekar N. , Subrahmanyan R. , Ellison S. L. , Lane W. M. , Chengalur J. N.
Published: June 2006

We report the detection of redshifted H i 21-cm absorption in the z∼ 2.347 damped Lyman a absorber (DLA) towards PKS B0438-436 with the Green Bank Telescope. This is the second-highest redshift at which 21-cm absorption has been detected in a DLA. The absorption extends over ∼60 km s-1 and has two distinct components, at z= 2.347 477(12) and z= 2.347 869(20). A similar velocity structure is seen in optical metal lines, although the peak absorption here is offset by ∼11 km s-1 from the peak in the 21-cm line. We obtain a high spin temperature Ts∼ (886 ± 248) × (f/0.58) K, using a covering factor estimated from 2.3-GHz very long baseline interferometry data. However, the current data cannot rule out a low spin temperature. The non-detection of CO 3-2 absorption places the upper limit NCO < 3.8 × 1015 (Tx/10) cm-2 on the CO column density.
The Lyman α forest and WMAP year three
Authors: Viel Matteo , Haehnelt Martin G. , Lewis Antony
Published: June 2006

A combined analysis of cosmic microwave background (CMB) and Lyman a forest data can constrain the matter power spectrum from small scales of about 1 h-1 Mpc all the way to the horizon scale. The long lever arm and complementarity provided by such an analysis have previously led to a significant tightening of the constraints on the shape and the amplitude of the power spectrum of primordial density fluctuations. We present here a combined analysis of the WMAP three-year results with Lyman a forest data. The amplitude of the matter power spectrum s8 and the spectral index ns inferred from the joint analysis of high- and low-resolution Lyman a forest data as analysed by Viel & Haehnelt are consistent with the new WMAP results to within 1s. The joint analysis with the mainly low-resolution data as analysed by McDonald et al. suggests a value of s8 that is ~2s higher than that inferred from the WMAP three-year data alone. The joint analysis of the three-year WMAP and the Lyman a forest data also does not favour a running of the spectral index. The best-fitting values for a combined analysis of the three-year WMAP data, other CMB data, 2-degree Field (2dF) data and the Lyman a forest data are (s8, ns) = (0.78 ± 0.03, 0.96 ± 0.01).
Phosphorus partitioning in a shallow lake: implications for water quality management
Authors: Spears B. M. , Carvalho L. , Paterson D. M.
Published: June 2006

This paper describes the seasonal partitioning of phosphorus (P) across the sediment–water interface in Loch Leven, Scotland, and discusses the implications for future lake management strategy with respect to recovery from eutrophication. In a 10‐month survey, surface water total phosphorus (TP) concentrations were highest in late summer and lowest in early spring. In contrast, sediment TP concentrations were highest in mid‐winter and lowest in late summer. Water discharge at the main outflow of the loch was highest when water‐column TP was low and sediment TP high, and vice versa. Monthly sediment P uptake/release values showed significant cycling between the water‐column and the sediment and showed seasonal variation in four release‐sensitive P pools. Regulating the water level to increase flushing during sediment release periods and decrease flushing during uptake periods has the potential to significantly enhance the recovery of shallow lakes and reservoirs following historic nutrient loading.
Effect of dispersal at range edges on the structure of species ranges
Authors: Bahn Volker , J. O'Connor Raymond , B. Krohn William
Published: June 2006

Range edges are of particular interest to ecology because they hold key insights into the limits of the realized niche and associated population dynamics. A recent feature of Oikos summarized the state of the art on range edge ecology. While the typical question is what causes range edges, another important question is how range edges influence the distribution of abundances across a species geographic range when dispersal is present. We used a single species population dynamics model on a coupled‐lattice to determine the effects of dispersal on peripheral populations as compared to populations at the core of the range. In the absence of resource gradients, the reduced neighborhood and thus lower connectivity or higher isolation among populations at the range edge alone led to significantly lower population sizes in the periphery of the range than in the core. Lower population sizes mean higher extinction risks and lower adaptability at the range edge, which could inhibit or slow range expansions, and thus effectively stabilize range edges. The strength of this effect depended on the potential population growth rate and the maximum dispersal distance. Lower potential population growth rates led to a stronger effect of dispersal resulting in a higher difference in population sizes between the two areas. The differential effect of dispersal on population sizes at the core and periphery of the range in the absence of resource gradients implies that traditional, habitat‐based distribution models could result in misleading conclusions about the habitat quality in the periphery. Lower population sizes at the periphery are also relevant to conservation, because habitat removal not only eliminates populations but also creates new edges. Populations bordering these new edges may experience declines, due to their increased isolation.
Species richness peaks for intermediate levels of biomass in a fractal succession with quasi‐neutral interactions
Authors: Mouillot David , Mouquet Nicolas
Published: June 2006

The mechanisms that promote species richness, including net community interactions, are considered central to the investigation of the consequences of biodiversity loss for ecosystem functioning. Recently, some empirical studies at large spatiotemporal scales suggest that increasing species richness within natural communities results in a finer division of biomass among species rather than an increase in total biomass. In parallel, the most common pattern observed in nature is the peaked relationship between diversity and productivity estimated as total biomass. Thus, the aim of our study is to provide model predictions for the diversity–biomass relationship with various levels of net species interactions within communities: negative, neutral, quasi‐neutral and positive. Using a scaling relationship between the number of species and total community biomass, we propose a new self‐similar process of biomass partitioning during a community assembly process. At each step of the succession, K more species appear that are A times less abundant on average giving K=Ad; the parameter d being a fractal dimension related to the nature of interactions among coexisting species. Our results, compared to those from meta‐analyses about empirical diversity–productivity relationships, illustrate that quasi‐neutral interactions among coexisting species lead to the most commonly observed pattern: an ‘envelope’ where diversity peaks at intermediate values of total biomass, i.e. that the area below the hump‐backed line (considered as the upper boundary) is filled with data points.
Early Agglomeration Recognition System (EARS)
Authors: Korbee R. , van Ommen J. R. , Lensselink J. , Nijenhuis J. , Kiel J. H. A. , van den Bleek C. M.
Published: June 2006

In fluidized-bed combustion and gasification of biomass and waste, agglomeration of bed/ash particles is a major problem area. This paper deals with a new method for monitoring and controlling fluidized-bed hydrodynamics, which enables the recognition of agglomeration in an early stage and provides control measures to prevent further agglomeration and defluidization. The method, called early agglomeration recognition system (EARS), is based on recognizing significant differences between reference time series of pressure fluctuations and successive time series measured during prolonged plant operation. The early recognition provides a time interval for taking dedicated actions to counteract the agglomeration. Thus, EARS can be a tool to help plant operators prevent agglomeration-induced plant shutdowns and minimize bed material makeup and residue production. Results are presented of small-scale experiments showing the effectiveness and selectivity of the early agglomeration recognition. Subsequently, the development of control strategies is discussed.
The Performance of a Loop Seal in a CFB Boiler
Authors: Johansson Andreas , Johnsson Filip , Andersson Bengt-Åke
Published: June 2006

High in-bed heat transfer and low corrosive environment imply that the loop seal of a circulating fluidized bed (CFB) boiler is an advantageous location for superheaters. In order to increase the knowledge on the flow pattern and the heat transfer distribution to the tubes within a loop seal, measurements were performed in the loop seal of a 30MW CFB boiler as well as in a 1∕3 scaled-down seal operated according to simplified scaling laws. The scale model measurements show that the solids recirculation flux can be maintained with a substantial decrease of the fluidization flow in the seal compared to that currently used at full load conditions. It was also possible to significantly decrease the fraction of the bottom of the seal that was fluidized without affecting the solids flux through the seal. A gradient in the solids flow were detected in the vertical direction.
Identification of a Copper-Inducible Promoter for Use in Ectopic Expression in the Fungal Pathogen
Histoplasma capsulatum
Authors: Gebhart Dana , Bahrami Adam K. , Sil Anita
Published: June 2006

Despite the existence of a number of genetic tools to study the fungal pathogen
Histoplasma capsulatum
, strategies for conditional gene expression have not been developed. We used microarray analysis to identify genes that are transcriptionally induced or repressed by the addition of copper sulfate (CuSO
4
) to
H. capsulatum
yeast cultures. One of these genes,
CRP1
, encodes a putative copper efflux pump that is significantly induced in the presence of CuSO
4
. The upstream regulatory region of
CRP1
was sufficient to drive copper-regulated expression of two reporter genes,
lacZ
and the gene encoding green fluorescent protein. Microarray experiments were performed to determine a copper concentration that triggers accumulation of the
CRP1
transcript without significant perturbation of global gene expression. These studies show that the
CRP1
upstream regulatory region can be used for ectopic expression of heterologous genes in
H. capsulatum
. Furthermore, they demonstrate the strategic use of microarrays to identify conditional promoters that confer induction in the absence of large-scale shifts in gene expression.
Investigation of the Mechanism of Meiotic DNA Cleavage by
VMA1
-Derived Endonuclease Uncovers a Meiotic Alteration in Chromatin Structure around the Target Site
Authors: Fukuda Tomoyuki , Ohta Kunihiro , Ohya Yoshikazu
Published: June 2006

VMA1
-derived endonuclease (VDE), a homing endonuclease in
Saccharomyces cerevisiae
, is encoded by the mobile intein-coding sequence within the nuclear
VMA1
gene. VDE recognizes and cleaves DNA at the 31-bp VDE recognition sequence (VRS) in the
VMA1
gene lacking the intein-coding sequence during meiosis to insert a copy of the intein-coding sequence at the cleaved site. The mechanism underlying the meiosis specificity of
VMA1
intein-coding sequence homing remains unclear. We studied various factors that might influence the cleavage activity in vivo and found that VDE binding to the VRS can be detected only when DNA cleavage by VDE takes place, implying that meiosis-specific DNA cleavage is regulated by the accessibility of VDE to its target site. As a possible candidate for the determinant of this accessibility, we analyzed chromatin structure around the VRS and revealed that local chromatin structure near the VRS is altered during meiosis. Although the meiotic chromatin alteration exhibits correlations with DNA binding and cleavage by VDE at the
VMA1
locus, such a chromatin alteration is not necessarily observed when the VRS is embedded in ectopic gene loci. This suggests that nucleosome positioning or occupancy around the VRS by itself is not the sole mechanism for the regulation of meiosis-specific DNA cleavage by VDE and that other mechanisms are involved in the regulation.
PneumocystisMelanins Confer Enhanced Organism Viability
Authors: Icenhour Crystal R. , Kottom Theodore J. , Limper Andrew H.
Published: June 2006

Pneumocystiscontinues to represent an important opportunistic fungal pathogen of those with compromised immunity. Thus, it is crucial to identify factors that affect its viability and pathogenicity. We previously reported the first identification of melanins inPneumocystis. In the present study, we sought to further characterize these components and define the function for these melanins. Melanins extracted fromPneumocystisand melanizedPneumocystiscells were analyzed by electron spin resonance spectroscopy, revealing spectra consistent with melanins from other fungi. Immunofluorescence assays using anti-melanin monoclonal antibodies showed that melanins are widely present acrossPneumocystishost species, including mouse-, ferret-, and human-derivedPneumocystisorganisms, as well asPneumocystis cariniiderived from rat. Using immunoelectron microscopy, melanins were found to localize to the cell wall and cytoplasm ofP. cariniicysts, as well as to intracystic bodies within mature cysts. Next, the role of melanins on the maintenance ofPneumocystisviability was determined by using quantitative reverse transcription-PCR measurement of the heat shock protein mRNA under adverse environmental conditions. Using a new method to promote the melanization ofPneumocystis, we observed that strongly melanizedPneumocystisretained viability to a greater degree when exposed to UV irradiation or desiccation compared to less-pigmented organisms. These studies support our previous identification ofPneumocystismelanins across the genus, further characterize thesePneumocystiscomponents, and demonstrate that melanins protectPneumocystisfrom environmental stressors.
Lipid Raft-Based Membrane Compartmentation of a Plant Transport Protein Expressed in
Saccharomyces cerevisiae
Authors: Grossmann Guido , Opekarova Miroslava , Novakova Linda , Stolz Jürgen , Tanner Widmar
Published: June 2006

The hexose-proton symporter HUP1 shows a spotty distribution in the plasma membrane of the green alga
Chlorella kessleri. Chlorella
cannot be transformed so far. To study the membrane localization of the HUP1 protein in detail, the symporter was fused to green fluorescent protein (GFP) and heterologously expressed in
Saccharomyces cerevisiae
and
Schizosaccharomyces pombe
. In these organisms, the HUP1 protein has previously been shown to be fully active. The GFP fusion protein was exclusively targeted to the plasma membranes of both types of fungal cells. In
S. cerevisiae
, it was distributed nonhomogenously and concentrated in spots resembling the patchy appearance observed previously for endogenous H
+
symporters. It is documented that the
Chlorella
protein colocalizes with yeast proteins that are concentrated in 300-nm raft-based membrane compartments. On the other hand, it is completely excluded from the raft compartment housing the yeast H
+
/ATPase. As judged by their solubilities in Triton X-100, the HUP1 protein extracted from
Chlorella
and the GFP fusion protein extracted from
S. cerevisiae
are detergent-resistant raft proteins.
S. cerevisiae
mutants lacking the typical raft lipids ergosterol and sphingolipids showed a homogenous distribution of HUP1-GFP within the plasma membrane. In an ergosterol synthesis (
erg6
) mutant, the rate of glucose uptake was reduced to less than one-third that of corresponding wild-type cells. In
S. pombe
, the sterol-rich plasma membrane domains can be stained in vivo with filipin.
Chlorella
HUP1-GFP accumulated exactly in these domains. Altogether, it is demonstrated here that a plant membrane protein has the property of being concentrated in specific raft-based membrane compartments and that the information for its raft association is retained between even distantly related organisms.