bluuebunny/crossref_metadata_2025 huggingface dataset:
Herminiimonas arsenicoxydans sp. nov., a metalloresistant bacterium
Authors: Muller Daniel , Simeonova Diliana D. , Riegel Philippe , Mangenot Sophie , Koechler Sandrine , Lièvremont Didier , Bertin Philippe N. , Lett Marie-Claire
Published: August 2006

An arsenite-oxidizing bacterium, designated strain ULPAs1T, was isolated from industrial sludge heavily contaminated with arsenic. Cells of this isolate were Gram-negative, curved rods, motile by means of a polar flagellum. The strain was positive for oxidase and catalase activities, was able to reduce nitrate to nitrite, used acetate, lactate and peptone as organic carbon sources under aerobic conditions and was able to oxidize arsenite (As[III]) to arsenate (As[V]). 16S rRNA gene sequence analysis and the absence of dodecanoic fatty acids suggested that this strain represents a member of the genusHerminiimonasof the familyOxalobacteraceae, orderBurkholderialesin theBetaproteobacteria. Genomic DNA–DNA hybridization between strain ULPAs1TandHerminiimonas fonticolaS-94Tand between strain ULPAs1TandHerminiimonas aquatilisCCUG 36956Trevealed levels of relatedness of <10 %, well below the recommended 70 % species cut-off value. Thus, strain ULPAs1T(=CCM 7303T=DSM 17148T=LMG 22961T) is the type strain of a novel species ofHerminiimonas, for which the nameHerminiimonas arsenicoxydanssp. nov. is proposed.
Alistipes onderdonkii sp. nov. and Alistipes shahii sp. nov., of human origin
Authors: Song Yuli , Könönen Eija , Rautio Merja , Liu Chengxu , Bryk Anne , Eerola Erkki , Finegold Sydney M.
Published: August 2006

Two groups of previously unknown Gram-negative, strictly anaerobic, pigment-producing, rod-shaped bacteria, which phenotypically and phylogenetically displayed a close association with the recently described species Alistipes finegoldii, were characterized using phenotypic and molecular taxonomic methods. A 16S rRNA gene sequence divergence of approximately 3 % between the two unknown bacteria and A. finegoldii, as well as distinguishable biochemical characteristics, demonstrates that these organisms are genotypically and phenotypically distinct and that each group represents a previously unknown subline within the genus Alistipes. Chromosomal DNA–DNA reassociation studies further confirmed the separateness of the unidentified bacteria and A. finegoldii. On the basis of the phenotypic and phylogenetic findings, two novel species, Alistipes onderdonkii sp. nov. and Alistipes shahii sp. nov., are proposed. The type strains of A. onderdonkii and A. shahii are WAL 8169T (=CCUG 48946T=ATCC BAA-1178T) and WAL 8301T (=CCUG 48947T=ATCC BAA-1179T), respectively; their DNA G+C contents are 58 and 56 mol%, respectively.
Dyadobacter ginsengisoli sp. nov., isolated from soil of a ginseng field
Authors: Liu Qing-Mei , Im Wan-Taek , Lee Myungjin , Yang Deok-Chun , Lee Sung-Taik
Published: August 2006

A Gram-negative, aerobic, non-motile, non-spore-forming and rod-shaped bacterium, strain Gsoil 043T, was isolated from soil from a ginseng field in Pocheon province, South Korea. The novel isolate was characterized in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain Gsoil 043T was shown to belong to the family ‘Flexibacteraceae’ and was related to Dyadobacter fermentans (96.7 %), Dyadobacter crusticola (96.3 %) and Dyadobacter hamtensis (95.8 %). The 16S rRNA gene sequence similarity of the novel strain to other recognized species within the family ‘Flexibacteraceae’ was less than 87.0 %. The G+C content of genomic DNA was 48 mol%. Phenotypic and chemotaxonomic data (major menaquinone, MK-7; major fatty acids, C16 : 1
ω7c, iso-C15 : 0 and C16 : 0) supported the affiliation of strain Gsoil 043T to the genus Dyadobacter. The results of physiological and biochemical tests enabled strain Gsoil 043T to be differentiated genotypically and phenotypically from the three Dyadobacter species with validly published names. The novel isolate therefore represents a novel species for which the name Dyadobacter ginsengisoli sp. nov. is proposed, with the type strain Gsoil 043T (=KCTC 12589T=LMG 23409T).
Shewanella loihica sp. nov., isolated from iron-rich microbial mats in the Pacific Ocean
Authors: Gao Haichun , Obraztova Anna , Stewart Nathan , Popa Radu , Fredrickson James K. , Tiedje James M. , Nealson Kenneth H. , Zhou Jizhong
Published: August 2006

A novel marine bacterial strain, PV-4T, isolated from a microbial mat located at a hydrothermal vent of Loihi Seamount in the Pacific Ocean, has been characterized. This micro-organism is orangey in colour, Gram-negative, polarly flagellated, facultatively anaerobic and psychrotolerant (temperature range, 0–42 °C). No growth was observed with nitrate, nitrite, DMSO or thiosulfate as the electron acceptor and lactate as the electron donor. The major fatty acid detected in strain PV-4Twas iso-C15 : 0. Strain PV-4Thad ubiquinones consisting mainly of Q-7 and Q-8, and possessed menaquinone MK-7. The DNA G+C content of the strain was 53.8 mol% and the genome size was about 4.5 Mbp. Phylogenetic analyses based on 16S rRNA gene sequences placed PV-4Twithin the genusShewanella. PV-4Texhibited 16S rRNA gene sequence similarity levels of 99.6 and 97.5 %, respectively, with respect to the type strains ofShewanella aquimarinaandShewanella marisflavi. DNA from strain PV-4Tshowed low mean levels of relatedness to the DNAs ofS. aquimarina(50.5 %) andS. marisflavi(8.5 %). On the basis of phylogenetic and phenotypic characteristics, the bacterium was classified in the genusShewanellawithin a distinct novel species, for which the nameShewanella loihicasp. nov. is proposed. The type strain is PV-4T(=ATCC BAA-1088T=DSM 17748T).
Burkholderia silvatlantica sp. nov., a diazotrophic bacterium associated with sugar cane and maize
Authors: Perin L. , Martínez-Aguilar L. , Paredes-Valdez G. , Baldani J. I. , Estrada-de los Santos P. , Reis V. M. , Caballero-Mellado J.
Published: August 2006

In a previous study, nitrogen-fixing isolates were recovered from the rhizosphere of maize and from surface-sterilized leaves of sugar cane cultivated in Rio de Janeiro, Brazil. On the basis of 16S rRNA gene sequence similarities, these isolates were identified as belonging to the genusBurkholderia, and whole-cell-protein profiles demonstrated that they are closely related to each other. In the present study, novel isolates were recovered from the roots of different sugar-cane varieties cultivated in diverse geographical regions of Brazil. Twenty-one nitrogen-fixing isolates were analysed using polyphasic taxonomy criteria, including DNA–DNA relatedness, 16S rRNA gene sequence similarities, fatty acid profiles, whole-cell-protein patterns and multilocus enzyme electrophoresis profiles, as well as morphological, physiological and biochemical characterization. The analysis confirmed that these isolates belong to a novel species within the genusBurkholderia, for which the nameBurkholderia silvatlanticasp. nov. is proposed. The type strain, SRMrh-20T(=LMG 23149T=ATCC BAA-1244T), was isolated from the rhizosphere of maize var. Avantis A2345 cultivated in Seropédica, Rio de Janeiro.
STAC: A method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments
Authors: Diskin Sharon J. , Eck Thomas , Greshock Joel , Mosse Yael P. , Naylor Tara , Stoeckert Christian J. , Weber Barbara L. , Maris John M. , Grant Gregory R.
Published: August 2006

Regions of gain and loss of genomic DNA occur in many cancers and can drive the genesis and progression of disease. These copy number aberrations (CNAs) can be detected at high resolution by using microarray-based techniques. However, robust statistical approaches are needed to identify nonrandom gains and losses across multiple experiments/samples. We have developed a method called Significance Testing for Aberrant Copy number (STAC) to address this need. STAC utilizes two complementary statistics in combination with a novel search strategy. The significance of both statistics is assessed, and P-values are assigned to each location on the genome by using a multiple testing corrected permutation approach. We validate our method by using two published cancer data sets. STAC identifies genomic alterations known to be of clinical and biological significance and provides statistical support for 85% of previously reported regions. Moreover, STAC identifies numerous additional regions of significant gain/loss in these data that warrant further investigation. The P-values provided by STAC can be used to prioritize regions for follow-up study in an unbiased fashion. We conclude that STAC is a powerful tool for identifying nonrandom genomic amplifications and deletions across multiple experiments. A Java version of STAC is freely available for download at http://cbil.upenn.edu/STAC.
Predicting essential genes in fungal genomes
Authors: Seringhaus Michael , Paccanaro Alberto , Borneman Anthony , Snyder Michael , Gerstein Mark
Published: August 2006

Essential genes are required for an organism's viability, and the ability to identify these genes in pathogens is crucial to directed drug development. Predicting essential genes through computational methods is appealing because it circumvents expensive and difficult experimental screens. Most such prediction is based on homology mapping to experimentally verified essential genes in model organisms. We present here a different approach, one that relies exclusively on sequence features of a gene to estimate essentiality and offers a promising way to identify essential genes in unstudied or uncultured organisms. We identified 14 characteristic sequence features potentially associated with essentiality, such as localization signals, codon adaptation, GC content, and overall hydrophobicity. Using the well-characterized baker's yeast Saccharomyces cerevisiae, we employed a simple Bayesian framework to measure the correlation of each of these features with essentiality. We then employed the 14 features to learn the parameters of a machine learning classifier capable of predicting essential genes. We trained our classifier on known essential genes in S. cerevisiae and applied it to the closely related and relatively unstudied yeast Saccharomyces mikatae. We assessed predictive success in two ways: First, we compared all of our predictions with those generated by homology mapping between these two species. Second, we verified a subset of our predictions with eight in vivo knockouts in S. mikatae, and we present here the first experimentally confirmed essential genes in this species.
Hemizygous subtelomeres of an African trypanosome chromosome may account for over 75% of chromosome length
Authors: Callejas Sergio , Leech Vanessa , Reitter Christopher , Melville Sara
Published: August 2006

African trypanosomes are parasitic protozoa that infect a wide range of mammals, including humans. These parasites remain extracellular in the mammalian bloodstream, where antigenic variation allows them to survive the immune response. The Trypanosoma brucei nuclear genome sequence has been published recently. However, the significant chromosome size polymorphism observed among strains and subspecies of T. brucei, where total DNA content may vary up to 30%, necessitates a comparative study to determine the underlying basis and significance of such variation between parasites. In addition, the sequenced strain (Tb927) presents one of the smallest genomes analyzed among T. brucei isolates; therefore, establishing polymorphic regions will provide essential complementary information to the sequencing project. We have developed a Tb927 high-resolution DNA microarray to study DNA content variation along chromosome I, one of the most size-variable chromosomes, in different strains and subspecies of T. brucei. Results show considerable copy number polymorphism, especially at subtelomeres, but are insufficient to explain the observed size difference. Additional sequencing reveals that >50% of a larger chromosome I consists of arrays of variant surface glycoprotein genes (VSGs), involved in avoidance of acquired immunity. In total, the subtelomeres appear to be three times larger than the diploid core. These results reveal that trypanosomes can utilize subtelomeres for amplification and divergence of gene families to such a remarkable extent that they may constitute most of a chromosome, and that the VSG repertoire may be even larger than reported to date. Further experimentation is required to determine if these results are applicable to all size-variable chromosomes.
Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events
Authors: Zhaxybayeva Olga , Gogarten J. Peter , Charlebois Robert L. , Doolittle W. Ford , Papke R. Thane
Published: August 2006

Using 1128 protein-coding gene families from 11 completely sequenced cyanobacterial genomes, we attempt to quantify horizontal gene transfer events within cyanobacteria, as well as between cyanobacteria and other phyla. A novel method of detecting and enumerating potential horizontal gene transfer events within a group of organisms based on analyses of “embedded quartets” allows us to identify phylogenetic signal consistent with a plurality of gene families, as well as to delineate cases of conflict to the plurality signal, which include horizontally transferred genes. To infer horizontal gene transfer events between cyanobacteria and other phyla, we added homologs from 168 available genomes. We screened phylogenetic trees reconstructed for each of these extended gene families for highly supported monophyly of cyanobacteria (or lack of it). Cyanobacterial genomes reveal a complex evolutionary history, which cannot be represented by a single strictly bifurcating tree for all genes or even most genes, although a single completely resolved phylogeny was recovered from the quartets’ plurality signals. We find more conflicts within cyanobacteria than between cyanobacteria and other phyla. We also find that genes from all functional categories are subject to transfer. However, in interphylum as compared to intraphylum transfers, the proportion of metabolic (operational) gene transfers increases, while the proportion of informational gene transfers decreases.
Breeding seasonality and population dynamics of three rodent species in the Magamba Forest Reserve, Western Usambara Mountains, north‐east Tanzania
Authors: Makundi Rhodes H. , Massawe Apia W. , Mulungu Loth S.
Published: August 2006

We investigated breeding seasonality and population dynamics of three rodent species, Lophuromys flavopuncatus, Grammomys dolichurus and Praomys delectorum, in the Magamba Forest, Western Usambara Mountains, north‐east Tanzania. Capture–mark–recapture studies were conducted in 2002–2004. Reproductive conditions of males and females showed temporal variations, an indication of breeding seasonality. Animals were reproductively active between February and May. Rainfall in November–January was instrumental for the onset of breeding and continued throughout the wet season. The recruitment of new individuals born during the season led to highest population densities between end of May and August. Populations declined progressively towards the end of the dry season (September–October). Only P. delectorum showed a marked density increase during January–February, indicating greater survival and/or recruitment during the November–January rains. The study shows that despite a relatively stable environment of the forest reserve, rainfall has strong influence on reproduction and population dynamics, probably because of its effect on primary food resources.
Comparative phenology and growth of four Cenchrus ciliaris L. accessions established under arid bioclimate in Tunisia
Authors: Lobna Mnif , Mohamed Chaieb
Published: August 2006

A phenological study is one of the first steps in understanding the function of ecosystems. This is because phenological events reflect the way in which the species exploit the so‐called favourable periods in order to gain carbon and to allocate photosynthetic products for growth and reproduction. The objective of the present work was to examine the phenology of reproduction and the above‐ground growth of several Cenchrus ciliaris accessions, growing under the arid bioclimate in Tunisia. These accessions collected in the south of Tunisia are: Bou Hedma (P1), Tozeur (P2), Raas Jedir (P3) and Sidi Toui (P4). It was demonstrated that an important phenological variability exists within the different accessions studied. The statistical analysis (correlation and principal component analysis) showed that the accession from Bou Hedma (P1) was the most precocious and vigorous one.
Population genetic structure of the common warthog (Phacochoerus africanus) in Uganda: evidence for a strong philopatry among warthogs and social structure breakdown in a disturbed population
Authors: Muwanika Vincent B. , Nyakaana Silvester , Siegismund Hans R. , Arctander Peter
Published: August 2006

Fine‐scale genetic structure of large mammals is rarely analysed. Yet it is potentially important in estimating gene flow between the now fragmented wildlife habitats and in predicting re‐colonization following local extinction events. In this study, we examined the extent to which warthog populations from five localities in Uganda are genetically structured using both mitochondrial control region sequence and microsatellite allele length variation. Four of the localities (Queen Elizabeth, Murchison Falls, Lake Mburo and Kidepo Valley) are national parks with relatively good wildlife protection practices and the other (Luwero), not a protected area, is characterized by a great deal of hunting. In the total sample, significant genetic differentiation was observed at both the mtDNA locus (FST = 0.68;P < 0.001) and the microsatellite loci (FST = 0.14;P < 0.001). Despite the relatively short geographical distances between populations, significant genetic differentiation was observed in all pair‐wise population comparisons at the two marker sets (mtDNAFST = 0.21–0.79,P < 0.001; microsatelliteFST = 0.074–0.191,P < 0.001). Significant heterozygote deficiency was observed at most loci within protected areas while no significant deviation from Hardy–Weinberg expectation was observed in the unprotected Luwero population. We explain these results in terms of: (i) a strong philopatry among warthogs, (ii) a Wahlund effect resulting from the sampling regime and (iii) break down of social structure in the disturbed Luwero population.
Expression of TCL1 and CD27 in primary cutaneous B‐cell lymphomas
Authors: Pescarmona E , Remotti D , Perez M , Monaco S , Pacchiarotti A , Faraggiana T , Russo G , Baroni C D
Published: August 2006

Aims To investigate by immunohistochemical analysis the expression of the TCL1 oncogene product and of CD27 in 25 cases of primary cutaneous B‐cell lymphomas (PCBCL) classified according to the World Health Organization–European Organization for Research and Treatment of Cancer classification of cutaneous lymphomas. In B‐cell ontogenesis TCL1 is mainly expressed by ‘naive’ B lymphocytes and by a subset of germinal centre B cells, whereas CD27 is expressed by a subset of germinal centre B cells, ‘memory’ B lymphocytes and plasma cells, suggesting that their expression in physiological conditions is mutually exclusive.

Methods and results Overall, TCL1 was expressed in 5/25 cases (20%) and CD27 in 15/25 cases (60%). Furthermore, 7/25 cases (28%) were TCL1– and CD27– and 2/25 cases (8%) were TCL1+ and CD27+. In particular, primary cutaneous follicle‐centre lymphomas (10 cases) showed a variable expression of both TCL1 and CD27, whereas primary cutaneous marginal‐zone B‐cell lymphomas (eight cases) showed, with the exception of a single case, a definite CD27+/TCL1– profile.

Conclusions These findings indicate: (i) the TCL1 oncogene product is uncommonly expressed in PCBCL (20% of cases, mainly of the follicle‐centre subtype); (ii) in contrast, CD27 is often expressed in PCBCL (60% of cases), mainly of the marginal‐zone subtype; (iii) the coexpression of TCL1 and CD27 may be seldom observed in PCBCL (8% of cases); (iv) PCBCL does not seem to show, in terms of either TCL1 or CD27 expression, significant differences compared with its systemic counterparts.
Synovitis score: discrimination between chronic low‐grade and high‐grade synovitis
Authors: Krenn V , Morawietz L , Burmester G‐R , Kinne R W , Mueller‐Ladner U , Muller B , Haupl T
Published: August 2006

Aims : To standardize the histopathological assessment of synovial membrane specimens in order to contribute to the diagnostics of rheumatic and non‐rheumatic joint diseases.

Methods and results : Three features of chronic synovitis (enlargement of lining cell layer, cellular density of synovial stroma, leukocytic infiltrate) were semiquantitatively evaluated (from 0, absent to 3, strong) and each feature was graded separately. The sum provided the synovitis score, which was interpreted as follows: 0–1, no synovitis; 2–4, low‐grade synovitis; 5–9, high‐grade synovitis. Five hundred and fifty‐nine synovectomy specimens were graded by two independent observers. Clinical diagnoses were osteoarthrosis (n = 212), post‐traumatic arthritis (n = 21), rheumatoid arthritis (n = 246), psoriatic arthritis (n = 22), reactive arthritis (n = 9), as well as controls (n = 49) from autopsies of patients without joint damage. Median synovitis scores when correlated with clinical diagnoses were: controls 1.0, osteoarthritis 2.0, post‐traumatic arthritis 2.0, psoriatic arthritis 3.5, reactive arthritis 5.0 and rheumatoid arthritis 5.0. The scores differed significantly between most disease groups, especially between degenerative and rheumatic diseases. A high‐grade synovitis was strongly associated with rheumatic joint diseases (P < 0.001, sensitivity 61.7%, specificity 96.1%). The correlation between the two observers was high (r = 0.941).

Conclusion : The proposed synovitis score is based on well‐defined, reproducible histopathological criteria and may contribute to diagnosis in rheumatic and non‐rheumatic joint diseases.
Encouraging fruit consumption in primary schoolchildren: a pilot study in North Wales, UK
Authors: Yeo S. T. , Edwards R. T.
Published: August 2006

Objective  To explore the feasibility and cost of promoting fruit consumption among primary schoolchildren across Anglesey, a region in North Wales, UK.

Design, setting and subjects  A postal survey of the head teachers of all 51 primary schools across Anglesey to ascertain their attitudes to promoting fruit consumption and current initiatives in place was conducted. This was followed by a 1‐week pilot study in a single primary school to assess parents’ support and willingness to bear or share costs, to determine children's fruit preferences, and to calculate fruit waste. Finally, the cost to local government of providing a piece of fruit to each primary schoolchild daily was calculated.

Results  A 53% response rate was obtained in the postal survey of primary school head teachers. All respondents expressed an interest in participating in future fruit promotion programmes. Of 27 primary schools, 26 that responded (96.3%) had programmes in place in which 18 had adopted specific food policies. In the pilot study at the single Anglesey primary school, a response rate of 97% from parents who expressed support for fruit promotion in school was obtained. Parents expressed their willingness to pay at least 15 pence per day towards fruit provision at break time for their children if such a service was not provided by local government. If local government was to invest in this initiative, the total cost of providing one piece of fruit per day to all primary school children in Anglesey would be £211 000 per annum (2004 prices; 19 pence per child per day).

Conclusion  This pilot study shows support by teachers and parents for initiatives to encourage primary schoolchildren to eat more fruit. Waste can be minimized by choosing fruit that children prefer, in this study, grapes, apples and oranges. The decision as to whether local government or parents are asked to pay for fruit provision is political, depending on local socioeconomic circumstances, local government priorities, national education and nutrition policies.
Underestimation and overestimation of personal weight status: associations with socio‐demographic characteristics and weight maintenance intentions
Authors: Brug J. , Wammes B. , Kremers S. , Giskes K. , Oenema A.
Published: August 2006

Objective  Unwarranted underestimation and overestimation of personal weight status may prevent weight maintenance behaviour. The present study reports on correlates of under‐ and overestimation of personal weight status and the association with weight maintenance intentions and self‐reported action.

Design  Comparison of three cross‐sectional surveys, representing different population groups.

Subjects  Survey 1: 1694 adolescents 13–19 years of age; survey 2: 979 nonobese adults 25–35 years of age; survey 3: 617 adults 21–62 years of age.

Measurements  Self‐administered written questionnaires (surveys 1 and 3) and telephone‐administered questionnaires (survey 2); self‐reported BMI, self‐rated weight status, intentions and self‐reported actions to avoid weight gain or to lose weight, sex, age, education and ethnic background. Respondents were classified as people who are realistic about personal body weight status or people who under‐ and overestimate their body weight status, based on BMI and self‐rated weight status.

Results  Most respondents in the three survey populations were realistic about their weight status. Overestimation of weight status was consistently more likely among women, whereas underestimation was more likely among men, older respondents and respondents from ethnic minorities. Self‐rated weight status was a stronger correlate of intentions and self‐report actions to avoid weight gain than weight status based on Body Mass Index.

Conclusions  Relevant proportions of the study populations underestimated or overestimated their bodyweight status. Overestimation of personal weight status may lead to unwarranted weight maintenance actions, whereas underestimation may result in lack of motivation to avoid further weight gain.
Differences in weaning practice, food and nutrient intake between breast‐ and formula‐fed 4‐month‐old infants in England
Authors: Noble S. , Emmett P.
Published: August 2006

Background  Breastfed infants may grow more slowly in the second half of infancy than formula‐fed infants, differences in weaning practice may contribute.

Methods  Dietary intakes of 4‐month‐old infants have been investigated cross‐sectionally. Diet was assessed using a structured 1‐day un‐weighed dietary record in 852 white singletons (72% of those invited) from a random sub‐sample of infants taking part in Avon Longitudinal Study of Parents and Children. Nutrient intakes of formula‐fed infants were compared by sex and with UK reference values. Estimated mean energy and nutrient intakes, mean bodyweight and daily quantities of food consumed were compared by weaning practice.

Results  In formula‐fed infants mean energy intakes and intakes of most nutrients were adequate. There were significant differences in intakes of most nutrients by weaning practice; however, mean energy intake and body weight of breastfed infants was similar to formula‐fed infants. Infants given formula milk were less likely to consume vegetables and fruit, and more likely to consume commercial infant drinks, compared with infants who were breastfed. In breastfed infants breast milk intake was lower if solids were given (905 g versus 818 g; P = 0.01); however, nutrient intake was not compromised. In formula‐fed infants milk intake was not different in those having solids compared to those having milk only (810 g versus 795 g; P = 0.649).

Conclusions  Differences in weaning practice and patterns of food consumption were seen between breast‐ and formula‐fed infants, these may contribute to later growth differences.
Demonstration of lanthanum in liver cells by energy‐dispersive X‐ray spectroscopy, electron energy loss spectroscopy and high‐resolution transmission electron microscopy
Authors: YANG Z. , SCHRYVERS D. , ROELS F. , D’HAESE P. C. , DE BROE M. E.
Published: August 2006

The appearance of lanthanum in liver cells as a result of the injection of lanthanum chloride into rats is investigated by advanced transmission electron microscopy techniques, including electron energy loss spectroscopy and high‐resolution transmission electron microscopy. It is demonstrated that the lysosomes contain large amounts of lanthanum appearing in a granular form with particle dimensions between 5 and 25 nm, whereas no lanthanum could be detected in other surrounding cellular components.
A novel real‐time confocal imaging technique for examining host–implant interfacial shear failure patterns
Authors: COOK R. J. , THOMPSON I. D. , ROBINSON P. D. , WATSON T. F.
Published: August 2006

In clinical practice, implant failure usually occurs at the biomaterial–host tissue interface, typically involving both biomechanical and biochemical mechanisms. By definition, any new ‘bioactive’ material will bond to living bone but, prior to clinical use, interface formation, performance, longevity and failure pattern characterizations are necessary. The common missing link in many biomaterial interface investigations is imaging at the point of presumed loaded failure. The novel real‐time confocal technique described here allows bond strength, formation rate, longevity and bone–material interface failure pattern characterization for a wide range of biomaterials capable of forming tissue interfaces, in one real‐time imaged microshear stress process, conducted using imaging frame matched load/displacement data acquisition under relatively normal near in vivo environmental conditions. The technique, validated by post‐failure scanning electron microscopy imaging, revealed that more slowly reacting melt‐derived 45S5 glass materials produced stronger and more stable long‐term interfaces than faster reacting microporous bioactive sol‐gel glasses.
Electron microscopy and diffraction of radiation‐sensitive nanostructured materials
Authors: SCHAPER A. K. , YOSHIOKA T. , OGAWA T. , TSUJI M.
Published: August 2006

Soft matter research of natural organic and synthetic nanomaterials is an area in nanoscience and technology that has been growing particularly quickly in recent years. The materials under investigation are sensitive to high‐energy electrons. Any structure characterization using electron microscopy thus requires special care. First, we illustrated this on naturally grown nanotubes observed by normal and cryogenic scanning electron microscopy. Second, we studied the ordering and orientation of the mesophase in template‐grown nanotubes and nanorods containing discotic liquid crystals without and with doping, as desired. For these studies, we mainly used transmission electron diffraction and microscopy at low‐dose conditions, high‐efficiency image acquisition, and cryoprotection of the structures at liquid helium temperature. Additional analytical information was obtained by electron energy filtering observations.
Statistical analysis of reduced pair correlation functions of capillaries in the prostate gland
Authors: MATTFELDT T. , ECKEL S. , FLEISCHER F. , SCHMIDT V.
Published: August 2006

Blood capillaries are thread‐like structures that may be considered as an example of a spatial fibre process in three dimensions. At light microscopy, the capillary profiles appear as a planar point process on sections. It has recently been shown that the observed pair correlation function g(r) of the centres of the fibre profiles on two‐dimensional sections may be used to estimate the reduced pair correlation function of stationary and isotropic fibre processes in three dimensions. In the present study, we explored how this approach may be extended to statistical analysis of reduced g‐functions of capillaries from multiple specimens of different groups and with replicated observations. The methods were applied to normal prostatic tissue compared with prostate cancer. Confidence intervals for the mean reduced g‐functions of groups were estimated for fixed r‐values parametrically using the t‐distribution, and by bootstrap methods. Each estimated reduced g‐function was furthermore characterized in terms of its first maximum and minimum. The mean length of capillaries per unit tissue volume was significantly higher in prostate cancer tissue than in normal prostate tissue. Significant differences between the mean reduced g‐functions of malignant and benign lesions could be demonstrated for two domains of r‐values. In general, bootstrap‐based confidence intervals were slightly wider than parametrically estimated confidence intervals. Falsely negative lower bounds of the intervals, which sometimes arose using the parametric approach, could be avoided by the bootstrap method. Testing of group mean values for significant differences by the bootstrap method yielded more conservative results than multiple t‐tests. The functional value of the first maximum of the reduced g‐function and a global statistical parameter of short‐range ordering was significantly reduced in the carcinoma group. Prostate cancer tissue is more densely supplied with capillaries than normal prostate tissue and the three‐dimensional arrangement of the vessels differs with respect to interaction at various distance ranges. In the local approach used here, bootstrap methods can be used as a robust statistical tool for the computation of confidence intervals and group comparisons of mean reduced g‐functions at specific ranges of interaction.
A flexible instrument control and image acquisition system for a scanning electron microscope
Authors: KAPP O. H. , SMITH D. R. , JENDRASZKIEWICZ G. , GORODEZKY I. , KIM KWANG‐JE , CREWE A. V.
Published: August 2006

We have developed an instrument control and image acquisition system for use with scanning electron microscopes. By making the system flexible over a wide range of operating voltages, scan generation and image acquisition modes can be easily accommodated to a wide range of instruments. We show the implementation of this system for use with a custom‐built low‐voltage scanning electron microscope. We then explore the simple modifications that are required for control of two instruments intended for use as free electron lasers.
Wavelength division scanning for two‐photon excitation fluorescence imaging
Authors: SHI K. , YIN S. , LIU Z.
Published: August 2006

We investigate wavelength division scanning for two‐photon excitation fluorescence imaging. Two‐photon imaging using lateral wavelength division scanning is demonstrated. In addition, we theoretically analyse the spatial and temporal properties of a femtosecond laser beam focused by a Fresnel lens and investigate the feasibility of axial scanning using wavelength division.
Use of confocal linescan to document ciliary beat frequency
Authors: DOYLE R. T. , MONINGER T. , DEBAVALYA N. , HSU W. H.
Published: August 2006

We present a method to document ciliary beat frequency with the linescan function of a scanning confocal microscope, using ciliated tracheal cells and free‐swimming rotifers as examples. Depending on the clarity of the original data, the ciliary beat frequency can be determined from the confocal linescan directly or from an intensity linescan analysis of the original data. Fast Fourier transform treatment of the data can be used to verify the derived ciliary beat frequency. The linescan approach allows analysis of simple ciliary movements displayed by the ciliated tracheal cells, as well as complex movements performed by free‐swimming rotifers while feeding.
Chronic Prenatal Ethanol Exposure Increases Glucocorticoid‐Induced Glutamate Release in the Hippocampus of the Near‐Term Foetal Guinea Pig
Authors: Iqbal U. , Brien J. F. , Kapoor A. , Matthews S. G. , Reynolds J. N.
Published: August 2006

Exposure to high cortisol concentration can injure the developing brain, possibly via an excitotoxic mechanism involving glutamate (Glu). The present study tested the hypothesis that chronic prenatal ethanol exposure (CPEE) activates the foetal hypothalamic‐pituitary‐adrenal axis to produce high cortisol exposure in the foetal compartment and alters sensitivity to glucocorticoid‐induced Glu release in the foetal hippocampus. Pregnant guinea pigs received daily oral administration of ethanol (4 g/kg maternal body weight/day) or isocaloric‐sucrose/pair‐feeding from gestational day (GD) 2 until GD 63 (term, approximately GD 68) at which time they were euthanised, 1 h after their final treatment. Adrenocorticotrophic hormone (ACTH) and cortisol concentrations were determined in foetal plasma. Basal and electrically stimulated Glu and γ‐aminobutyric acid (GABA) efflux in the presence or absence of dexamethasone (DEX), a selective glucocorticoid‐receptor agonist, were determinedex vivoin foetal hippocampal slices. Glucocorticoid receptor (GR), mineralocorticoid receptor (MR) andN‐methyl‐d‐aspartate (NMDA) receptor NR1 subunit mRNA expression were determinedin situin the hippocampus and dentate gyrus. In the near‐term foetus, CPEE increased foetal plasma ACTH and cortisol concentrations. Electrically stimulated glutamate, but not GABA, release was increased in CPEE foetal hippocampal slices. Low DEX concentration (0.3 µM) decreased stimulated glutamate, but not GABA, release in both CPEE and control foetal hippocampal slices. High DEX concentration (3.0 µM) increased basal release of Glu, but not GABA, in CPEE foetal hippocampal slices. GR, but not MR, mRNA expression was elevated in the hippocampus and dentate gyrus, whereas NR1 mRNA expression was increased in the CA1 and CA3 fields of the foetal hippocampus. These data demonstrate that CPEE increases high glucocorticoid concentration‐induced Glu release in the foetal hippocampus, presumably as a consequence of increased GR expression. These effects of CPEE, coupled with increased glutamate release and increased NMDA receptor expression, may predispose the near‐term foetal hippocampus to GR and Glu‐NMDA receptor‐mediated neurodevelopmental toxicity.
Dorsal Hippocampal Administration of Triiodothyronine Enhances Long‐Term Memory for Trace Cued and Delay Contextual Fear Conditioning in Rats
Authors: Sui L. , Wang F. , Liu F. , Wang J. , Li B. M.
Published: August 2006

Thyroid hormones play critical roles in brain maturation and cognitive functions. The present study investigated the role of thyroid hormone in emotional learning and memory using trace and delay contextual and cued fear conditioning tasks, respectively. Rats were administered triiodothyronine (T3) into the dorsal hippocampal area 10 min before training or immediately after training, and were scored for freezing behaviour in the same context and in a novel context with and without an auditory cue that had been paired previously with an aversive stimulus, a foot shock. Rats administered T3 before and after training both exhibited significantly increased long‐term fear memory in the trace cued and the delay contextual fear conditioning procedures compared to their control groups. The T3‐administered rats were not significantly different from their respective controls on the acquisition and short‐term fear memory in the trace and delay fear conditioning tasks. No significant difference on long‐term trace contextual and delay cued fear memory, respectively, was found. These results indicate that the observed T3‐induced enhancement of long‐term contextual and cued fear memory was specific to the hippocampus‐dependent conditioning tasks. These findings are the first to demonstrate that infusion of T3 into the dorsal hippocampus can improve performance on an emotional memory task.
Effects of pergolide on severe sleep bruxism in a patient experiencing oral implant failure
Authors: VAN DER ZAAG J. , LOBBEZOO F. , VAN DER AVOORT P.G.G.L. , WICKS D.J. , HAMBURGER H.L. , NAEIJE M.
Published: August 2006

summary  In the patient described in this study, oral implants failed as a probable consequence of severe, polysomnographically confirmed sleep bruxism. As this patient had the wish to be re‐implanted after this failure, we decided to try diminishing the frequency of bruxism and duration first. To that end, two management strategies were used. Their efficacy was evaluated polysomnographically, yielding a total of six overnight recordings. Of the selected management strategies, the administration of low doses of the dopamine D1/D2 receptor agonist pergolide finally resulted in a substantial and lasting reduction in the bruxism outcome measures under study. This result supports the previous suggestion that central neurochemicals like dopamine may be involved in the modulation of sleep bruxism. The case report also illustrates the importance of an extensive history taking (questionnaires as well as oral) and clinical examination of oral implant patients for the presence of severe bruxism before the implant procedure is started. In case of doubt, polysomnography may be considered to definitively confirm or rule out the presence of severe sleep bruxism.
Interfacial ultramorphology of single‐step adhesives: nanoleakage as a function of time
Authors: REIS A. F. , BEDRAN‐RUSSO A. K. B. , GIANNINI M. , PEREIRA P. N. R.
Published: August 2006

summary  The aim of this study was to examine the effectiveness of single‐step self‐etching adhesives in preventing nanoleakage over a 90‐day water‐storage period, and analyse the ultramorphological characteristics of resin–dentin interfaces. Three single‐step self‐etching adhesives were evaluated: Adper Prompt L‐Pop – LP (3M ESPE), iBond – iB (Heraeus Kulzer), and Clearfil Tri‐S Bond – S3 (Kuraray). Bonded specimens were sectioned into 0·9‐mm thick slabs and stored in water for 1, 60 or 90 days. After the storage periods, a silver tracer solution was used to reveal nanometer‐sized spaces and evidence of degradation within resin–dentin interfaces. Epoxy resin‐embedded sections were prepared, and the interfaces observed with the TEM. Nanoleakage patterns were compared among adhesives and storage periods using image analysis software. Data were statistically analysed by two‐way anova and Tukey test. Nanoleakage was observed in all resin–dentin interfaces produced by the single‐step self‐etching adhesives. Results showed that LP presented the lowest silver deposition means at 1 day. However, after 60 and 90 days, the area of silver deposition significantly increased for LP. iB presented intense silver deposition after 1 day and a small increase after 90 days. S3 presented the lowest silver deposition means after 60 and 90 days of water‐storage.
Relationship between tooth contacts in the retruded contact position and mandibular positioning during retrusion
Authors: YAMASHITA S. , AI M. , HASHII K. , AKIYAMA S. , KOIKE H. , NUMAO H.
Published: August 2006

summary  We conducted a series of studies with the purpose to investigate the locations of tooth contacts in the retruded contact position (RCP) and to discuss their significance in the stomatognathic system. In the present study, the relationship between the locations of RCP contacts and mandibular positioning during retrusion was examined. Thirty dentists and clinical residents were selected as subjects. One specialist in prosthetic dentistry examined each subject for the location of the RCP contacts. The mandibular positioning during retrusion was measured using a mandibular movement analysis system with six degrees of freedom. Originally programmed software was developed. Five reference points were selected: the central lower incisor (point I), the first molars on both sides (points RM and LM) and the condyles on both sides (points RC and LC). Tooth contact was observed most frequently at the second molar, followed by the first premolar. Points I, RM and LM all moved in an inferior‐posterior direction, whereas points RC and LC moved in various directions ranging from superior‐posterior to inferior‐posterior. When the subjects were divided into two groups according to the most anterior tooth of occlusion in the RCP, the condylar positioning tended to be more superior in the group with molar contact than that with premolar contact. These results suggest that the locations of RCP contacts could be an important factor in jaw guidance during retrusion.
All three chaperonin genes in the archaeon Haloferax volcanii are individually dispensable
Authors: Kapatai Georgia , Large Andrew , Benesch Justin L. P. , Robinson Carol V. , Carrascosa José L. , Valpuesta José M. , Gowrinathan Preethy , Lund Peter A.
Published: August 2006

The Hsp60 or chaperonin class of molecular chaperones is divided into two phylogenetic groups: group I, found in bacteria, mitochondria and chloroplasts, and group II, found in eukaryotic cytosol and archaea. Group I chaperonins are generally essential in bacteria, although when multiple copies are found one or more of these are dispensable. Eukaryotes contain eight genes for group II chaperonins, all of which are essential, and it has been shown that these proteins assemble into double‐ring complexes with eightfold symmetry where all proteins occupy specific positions in the ring. In archaea, there are one, two or three genes for the group II chaperonins, but whether they are essential for growth is unknown. Here we describe a detailed genetic, structural and biochemical analysis of these proteins in the halophilic archaeon, Haloferax volcanii. This organism contains three genes for group II chaperonins, and we show that all are individually dispensable but at least one must be present for growth. Two of the three possible double mutants can be constructed, but only one of the three genes is capable of fully complementing the stress‐dependent phenotypes that these double mutants show. The chaperonin complexes are made up of hetero‐oligomers with eightfold symmetry, and the properties of the different combinations of subunits derived from the mutants are distinct. We conclude that, although they are more homologous to eukaryotic than prokaryotic chaperonins, archaeal chaperonins have some redundancy of function.
Cyclitols and carbohydrates in leaves and roots of 13 Eucalyptus species suggest contrasting physiological responses to water deficit
Authors: MERCHANT ANDREW , TAUSZ MICHAEL , ARNDT STEFAN K. , ADAMS MARK A.
Published: August 2006

In many tree species, physiological adaptations to drought include the accumulation of osmotically active substances and/or the presence of particular compatible solutes, among them cyclitols. Recently, the cyclitol quercitol was identified in species of Eucalyptus, a diverse genus whose speciation is probably driven by adaptation to water availability.

We subjected seedlings of 13 Eucalyptus species from different ecosystems (‘mesic’ and ‘xeric’) and different sub‐generic taxonomic groups to 10 weeks of water deficit (WD) treatment. Pre‐dawn water potentials (ψpdwn) and relative water content (RWC) were determined in shoots, and total osmolality, soluble low‐molecular‐weight carbohydrates and cyclitols were measured in leaves and roots.

Responses to water deficit followed two distinct patterns: Eucalyptus species from ‘mesic’ environments adjusted concentrations of sucrose (through increased levels of sucrose and decreases in RWC) in response to water deficit, whereas ‘xeric’ species increased concentrations of quercitol (through reductions in RWC). In root tissues, only species from xeric environments contained high levels of quercitol and mannitol, increasing under WD conditions.

We suggest that the former (mesic) strategy may be beneficial to respond to short‐lasting drought conditions, because sucrose is easily metabolized, whereas the latter (xeric) strategy may relate to an effective acclimation to longer‐lasting drought. These physiological response groups are also related to taxonomic groups within the genus.