bluuebunny/crossref_metadata_2025 huggingface dataset:
Movements of the western rock lobster (Panulirus cygnus) within shallow coastal waters using acoustic telemetry
Authors: MacArthur L. D. , Babcock R. C. , Hyndes G. A.
Published: July 2008

Understanding the residency and movement patterns of major consumers, such as lobsters, in coastal waters is important for the management of coastal habitats and their fisheries. In the present study, we tagged 34 Panulirus cygnus with acoustic transmitters on a shallow coastal reef in south-western Australia and monitored their movements using fixed and manual receivers between November and May 2005–2006 and 2006–2007. We determined the proportion of ‘white’ (migratory-phase) lobsters emigrating from the reef between November and January and also characterised the large-scale movements of ‘red’ (residential-phase) and white lobsters. We undertook tank experiments to determine the effect of tagging and handling on P. cygnus behaviour. Counter to our expectation, 50% of white lobsters were detected on the reef after the migration period, whereas only a small proportion (13.6%) of white lobsters were tracked leaving the reef and only one individual displayed directional offshore movement. This limited movement indicates that coastal no-take zones may build up legal-sized 4–5+ year old lobsters because many of these are likely to remain resident over the migration season. Laboratory experiments and field observations suggest that tagging and handling affect lobster behaviour and movement for a few days post tagging, potentially confounding conclusions on dispersal and movement patterns in some studies.
Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment
Authors: Biddle Jennifer F. , Fitz-Gibbon Sorel , Schuster Stephan C. , Brenchley Jean E. , House Christopher H.
Published: July 2008

The subseafloor marine biosphere may be one of the largest reservoirs of microbial biomass on Earth and has recently been the subject of debate in terms of the composition of its microbial inhabitants, particularly on sediments from the Peru Margin. A metagenomic analysis was made by using whole-genome amplification and pyrosequencing of sediments from Ocean Drilling Program Site 1229 on the Peru Margin to further explore the microbial diversity and overall community composition within this environment. A total of 61.9 Mb of genetic material was sequenced from sediments at horizons 1, 16, 32, and 50 m below the seafloor. These depths include sediments from both primarily sulfate-reducing methane-generating regions of the sediment column. Many genes of the annotated genes, including those encoding ribosomal proteins, corresponded to those from the Chloroflexi and Euryarchaeota. However, analysis of the 16S small-subunit ribosomal genes suggests that Crenarchaeota are the abundant microbial member. Quantitative PCR confirms that uncultivated Crenarchaeota are indeed a major microbial group in these subsurface samples. These findings show that the marine subsurface is a distinct microbial habitat and is different from environments studied by metagenomics, especially because of the predominance of uncultivated archaeal groups.
Polycomb-group complex 1 acts as an E3 ubiquitin ligase for Geminin to sustain hematopoietic stem cell activity
Authors: Ohtsubo Motoaki , Yasunaga Shin'ichiro , Ohno Yoshinori , Tsumura Miyuki , Okada Satoshi , Ishikawa Nobutsune , Shirao Kenichiro , Kikuchi Akira , Nishitani Hideo , Kobayashi Masao , Takihara Yoshihiro
Published: July 2008

Polycomb
-group (
Pc
G) genes encode multimeric nuclear protein complexes, PcG complex 1 and 2. PcG complex 2 was proved to induce transcription repression and to further methylate histone H3 at lysine-27 (H3K27). Subsequently PcG complex 1 is recruited through recognition of methylated H3K27 and maintains the transcription silencing by mediating monoubiquitination of histone H2A at lysine-119. Genetic evidence demonstrated a crucial role for PcG complex 1 in stem cells, and Bmi1, a member of PcG complex 1, was shown to sustain adult stem cells through direct repression of the
INK4a
locus encoding cyclin-dependent kinase inhibitor, p16CKI, and p19ARF. The molecular functions of PcG complex 1, however, remain insufficiently understood. In our study, deficiency of Rae28, a member of PcG complex 1, was found to impair ubiquitin-proteasome-mediated degradation of Geminin, an inhibitor of DNA replication licensing factor Cdt1, and to increase protein stability. The resultant accumulation of Geminin, based on evidence from retroviral transduction experiments, presumably eliminated hematopoietic stem cell activity in
Rae28
-deficient mice. Rae28 mediates recruiting Scmh1, which provides PcG complex 1 an interaction domain for Geminin. Moreover, PcG complex 1 acts as the E3 ubiquitin ligase for Geminin, as we demonstrated
in vivo
as well as
in vitro
by using purified recombinant PcG complex 1 reconstituted in insect cells. Our findings suggest that PcG complex 1 supports the activity of hematopoietic stem cells, in which high-level Geminin expression induces quiescence securing genome stability, by enhancing cycling capability and hematopoietic activity through direct regulation of Geminin.
ATF6α-Rheb-mTOR signaling promotes survival of dormant tumor cells
in vivo
Authors: Schewe Denis M. , Aguirre-Ghiso Julio A.
Published: July 2008

The pathways that allow quiescent disseminated cancer cells to survive during prolonged dormancy periods are unknown. Here, we identify the transcription factor ATF6α as a pivotal survival factor for quiescent but not proliferative squamous carcinoma cells. ATF6α is essential for the adaptation of dormant cells to chemotherapy, nutritional stress, and, most importantly, the
in vivo
microenvironment. Mechanism analysis showed that MKK6 and p38α/β contribute to regulating nuclear translocation and transcriptional activation of ATF6α in dormant cancer cells. Downstream, ATF6α induces survival through the up-regulation of Rheb and activation of mTOR signaling independent of Akt. Down-regulation of ATF6α or Rheb reverted dormant tumor cell resistance to rapamycin and induced pronounced killing only of dormant cancer cells
in vivo
. Knocking down ATF6α also prolonged the survival of nude mice bearing dormant tumor cells. Targeting survival signaling by the ATF6α-Rheb-mTOR pathway in dormant tumor cells may favor the eradication of residual disease during dormancy periods.
Extracting function from a β-trefoil folding motif
Authors: Gosavi Shachi , Whitford Paul C. , Jennings Patricia A. , Onuchic José N.
Published: July 2008

Despite having remarkably similar three-dimensional structures and stabilities, IL-1β promotes signaling, whereas IL-1Ra inhibits it. Their energy landscapes are similar and have coevolved to facilitate competitive binding to the IL-1 receptor. Nevertheless, we find that IL-1Ra folds faster than IL-1β. A structural alignment of the proteins shows differences mainly in two loops, a β-bulge of IL-1β and a loop in IL-1Ra that interacts with residue K145 and connects β-strands 11 and 12. Bioassays indicate that inserting the β-bulge from IL-1β confers partial signaling capability onto a K145D mutant of IL-1Ra. Based on the alignment, mutational assays and our computational folding results, we hypothesize that functional regions are not central to the β-trefoil motif and cause slow folding. The IL-1β β-bulge facilitates activity and replacing it by the IL-1Ra β-turn results in a hybrid protein that folds faster than IL-1β. Inserting the β11–β12 connecting-loop, which aids inhibition, into either IL-1β or the hybrid protein slows folding. Thus, regions that aid function (either through activity or inhibition) can be inferred from folding traps via structural differences. Mapping functional properties onto the numerous folds determined in structural genomics efforts is an area of intense interest. Our studies provide a systematic approach to mapping the functional genomics of a fold family.
RNA, but not protein partners, is directly responsible for translational silencing by a bacterial Hfq-binding small RNA
Authors: Maki Kimika , Uno Kanako , Morita Teppei , Aiba Hiroji
Published: July 2008

SgrS is an Hfq-binding small RNA that is induced under glucose phosphate stress in
Escherichia coli
. It forms a specific ribo nucleo protein complex with Hfq and RNase E resulting in translational repression and rapid degradation of
ptsG
mRNA, encoding the glucose transporter. Here, we report translational silencing of
ptsG
mRNA in a defined
in vitro
system. We demonstrate that SgrS and Hfq are the minimum components for translational silencing to faithfully reproduce the reaction in cells. We show that
ptsG
-SgrS base pairing is sufficient to cause translational repression when the
ptsG
mRNA is forced to base pair with SgrS without the help of Hfq. The extent of translational repression correlates with the extent of duplex formation. We conclude that base pairing itself but not Hfq is directly responsible for translational silencing and the major role of Hfq in gene silencing is to stimulate the base pairing between SgrS and
ptsG
mRNA. This simple mechanism is in striking contrast to miRNA action in eukaryote in which the RNA is believed to act only as a guide of protein partners.
High mobility group protein B1 enhances DNA repair and chromatin modification after DNA damage
Authors: Lange Sabine S. , Mitchell David L. , Vasquez Karen M.
Published: July 2008

High mobility group protein B1 (HMGB1) is a multifunctional protein with roles in chromatin structure, transcriptional regulation, V(D)J recombination, and inflammation. HMGB1 also binds to and bends damaged DNA, but the biological consequence of this interaction is not clearly understood. We have shown previously that HMGB1 binds cooperatively with nucleotide excision repair damage recognition proteins to triplex-directed psoralen DNA interstrand cross-links (ICLs). Thus, we hypothesized that HMGB1 modulates the repair of DNA damage in mammalian cells. We demonstrate here that mammalian cells lacking HMGB1 are hypersensitive to DNA damage induced by psoralen plus UVA irradiation (PUVA) or UVC radiation, showing less survival and increased mutagenesis. In addition, nucleotide excision repair efficiency is significantly decreased in the absence of HMGB1 as assessed by the repair and removal of UVC lesions from genomic DNA. We also explored the role of HMGB1 in chromatin remodeling upon DNA damage. Immunoblotting demonstrated that, in contrast to HMGB1 proficient cells, cells lacking HMGB1 showed no histone acetylation upon DNA damage. Additionally, purified HMGB1 protein enhanced chromatin formation in an
in vitro
chromatin assembly system. These results reveal a role for HMGB1 in the error-free repair of DNA lesions. Its absence leads to increased mutagenesis, decreased cell survival, and altered chromatin reorganization after DNA damage. Because strategies targeting HMGB1 are currently in development for treatment of sepsis and rheumatoid arthritis, our findings draw attention to potential adverse side effects of anti-HMGB1 therapy in patients with inflammatory diseases.
Sperm cross-over activity in regions of the human genome showing extreme breakdown of marker association
Authors: Webb Adam J. , Berg Ingrid L. , Jeffreys Alec
Published: July 2008

Population diversity data have recently provided profound, albeit inferential, insights into meiotic recombination across the human genome, revealing a landscape dominated by thousands of cross-over hotspots. However, very few of these putative hotspots have been directly analyzed for cross-over activity. We now describe a search for very active hotspots, by using extreme breakdown of marker association as a guide for high-resolution sperm cross-over analysis. This strategy has led to the isolation of the most active cross-over hotspots yet described. Their morphology, sequence attributes, and cross-over processes are very similar to those seen at less active hotspots, but their activity in sperm is poorly predicted from population diversity information. Several of these hotspots showed evidence for biased gene conversion accompanying cross-over, in some cases associated with variation between men in cross-over activity and with two hotspots showing complete presence/absence polymorphism in different men. Hotspot polymorphism is very common at less active hotspots but curiously was not seen at any of the most active hotspots. This contrasts with the prediction that extreme hotspots should be the most vulnerable to attenuation by meiotic drive in favor of mutations that suppress recombination and should therefore show rapid rate evolution and thus variation in activity between men. Finally, these very intense hotspots provide a valuable resource for dissecting meiotic recombination processes and pathways in humans.
Targeted rescue of a destabilized mutant of p53 by an
in silico
screened drug
Authors: Boeckler Frank M. , Joerger Andreas C. , Jaggi Gaurav , Rutherford Trevor J. , Veprintsev Dmitry B. , Fersht Alan R.
Published: July 2008

The tumor suppressor p53 is mutationally inactivated in ≈50% of human cancers. Approximately one-third of the mutations lower the melting temperature of the protein, leading to its rapid denaturation. Small molecules that bind to those mutants and stabilize them could be effective anticancer drugs. The mutation Y220C, which occurs in ≈75,000 new cancer cases per annum, creates a surface cavity that destabilizes the protein by 4 kcal/mol, at a site that is not functional. We have designed a series of binding molecules from an
in silico
analysis of the crystal structure using virtual screening and rational drug design. One of them, a carbazole derivative (PhiKan083), binds to the cavity with a dissociation constant of ≈150 μM. It raises the melting temperature of the mutant and slows down its rate of denaturation. We have solved the crystal structure of the protein–PhiKan083 complex at 1.5-Å resolution. The structure implicates key interactions between the protein and ligand and conformational changes that occur on binding, which will provide a basis for lead optimization. The Y220C mutant is an excellent “druggable” target for developing and testing novel anticancer drugs based on protein stabilization. We point out some general principles in relationships between binding constants, raising of melting temperatures, and increase of protein half-lives by stabilizing ligands.
When Is a Brain Like the Planet?
Authors: Glymour Clark
Published: July 2008

Time series of macroscopic quantities that are aggregates of microscopic quantities, with unknown one-many relations between macroscopic and microscopic states, are common in applied sciences, from economics to climate studies. When such time series of macroscopic quantities are claimed to be causal, the causal relations postulated are representable by a directed acyclic graph and associated probability distribution—sometimes called a dynamical Bayes net. Causal interpretations of such series imply claims that hypothetical manipulations of macroscopic variables have unambiguous effects on variables “downstream” in the graph, and such macroscopic variables may be predictably produced or altered even while particular microstates are not. This paper argues that such causal time series of macroscopic aggregates of microscopic processes are the appropriate model for mental causation.
Only Five of 10 Strictly Conserved Disulfide Bonds Are Essential for Folding and Eight for Function of the HIV-1 Envelope Glycoprotein
Authors: van Anken Eelco , Sanders Rogier W. , Liscaljet I. Marije , Land Aafke , Bontjer Ilja , Tillemans Sonja , Nabatov Alexey A. , Paxton William A. , Berkhout Ben , Braakman Ineke
Published: July 2008

Protein folding in the endoplasmic reticulum goes hand in hand with disulfide bond formation, and disulfide bonds are considered key structural elements for a protein's folding and function. We used the HIV-1 Envelope glycoprotein to examine in detail the importance of its 10 completely conserved disulfide bonds. We systematically mutated the cysteines in its ectodomain, assayed the mutants for oxidative folding, transport, and incorporation into the virus, and tested fitness of mutant viruses. We found that the protein was remarkably tolerant toward manipulation of its disulfide-bonded structure. Five of 10 disulfide bonds were dispensable for folding. Two of these were even expendable for viral replication in cell culture, indicating that the relevance of these disulfide bonds becomes manifest only during natural infection. Our findings refine old paradigms on the importance of disulfide bonds for proteins.
An RNA Interference Screen Identifies a Novel Regulator of Target of Rapamycin That Mediates Hypoxia Suppression of Translation inDrosophilaS2 Cells
Authors: Lee Soo-Jung , Feldman Renny , O'Farrell Patrick H.
Published: July 2008

In addition to its central role in energy production, oxygen has pervasive regulatory actions. Hypoxia (oxygen limitation) triggers the shutdown of major cellular processes, including gene expression. We carried out a genome-wide RNA interference (RNAi) screen in Drosophila S2 cells for functions required to down-regulate translation during hypoxia. RNAi knockdown of specific genes allowed induction of a green fluorescent protein (GFP) reporter gene and continued protein synthesis during hypoxia. Among the identified genes, Tsc1 and Tsc2, which together form the tuberose sclerosis complex that negatively regulates target of rapamycin (TOR) kinase, gave an especially strong effect. This finding is consistent with the involvement of TOR in promoting translation. Another gene required for efficient inhibition of protein translation during hypoxia, the protein tyrosine phosphatase 61F (Ptp61F), down-regulates TOR activity under hypoxia. Lack of Ptp61F or Tsc2 improves cell survival under prolonged hypoxia in a TOR-dependent manner. Our results identify Ptp61F as a novel modulator of TOR activity and suggest that its function during hypoxia contributes to the down-regulation of protein synthesis.
Enriched random forests
Authors: Amaratunga Dhammika , Cabrera Javier , Lee Yung-Seop
Published: July 2008

Although the random forest classification procedure works well in datasets with many features, when the number of features is huge and the percentage of truly informative features is small, such as with DNA microarray data, its performance tends to decline significantly. In such instances, the procedure can be improved by reducing the contribution of trees whose nodes are populated by non-informative features. To some extent, this can be achieved by prefiltering, but we propose a novel, yet simple, adjustment that has demonstrably superior performance: choose the eligible subsets at each node by weighted random sampling instead of simple random sampling, with the weights tilted in favor of the informative features. This results in an ‘enriched random forest’. We illustrate the superior performance of this procedure in several actual microarray datasets.

Contact:  damaratu@prdus.jnj.com
GenoSNP: a variational Bayes within-sample SNP genotyping algorithm that does not require a reference population
Authors: Giannoulatou Eleni , Yau Christopher , Colella Stefano , Ragoussis Jiannis , Holmes Christopher C.
Published: July 2008

Summary: Current genotyping algorithms typically call genotypes by clustering allele-specific intensity data on a single nucleotide polymorphism (SNP) by SNP basis. This approach assumes the availability of a large number of control samples that have been sampled on the same array and platform. We have developed a SNP genotyping algorithm for the Illumina Infinium SNP genotyping assay that is entirely within-sample and does not require the need for a population of control samples nor parameters derived from such a population. Our algorithm exhibits high concordance with current methods and >99% call accuracy on HapMap samples. The ability to call genotypes using only within-sample information makes the method computationally light and practical for studies involving small sample sizes and provides a valuable independent quality control metric for other population-based approaches.

Availability:  http://www.stats.ox.ac.uk/~giannoul/GenoSNP/

Contact:  cholmes@stats.ox.ac.uk
Strength of electromagnetic, acoustic and Schrödinger reflections
Authors: Mokhov Sergiy , Zeldovich Boris Ya
Published: July 2008

The notion of reflection strength
S
of a plane wave by an arbitrary non-absorbing layer is introduced, so that the intensity of reflection is
R
=tanh
2
S
. We have shown that the total strength of reflection by a sequence of elements is expressed through particular element strengths and mutual phases between them by a simple addition rule; in particular, its possible maximum is the sum of the absolute strengths of constituents. We show that the standard Fresnel reflection may be understood in terms of variable
S
as a sum or difference of two separate contributions, due to an impedance step and a speed step. Strength of reflection for propagating acoustic and quantum mechanical waves is also discussed.
Natural selection for least action
Authors: Kaila Ville R.I , Annila Arto
Published: July 2008

The second law of thermodynamics is a powerful imperative that has acquired several expressions during the past centuries. Connections between two of its most prominent forms, i.e. the evolutionary principle by natural selection and the principle of least action, are examined. Although no fundamentally new findings are provided, it is illuminating to see how the two principles rationalizing natural motions reconcile to one law. The second law, when written as a differential equation of motion, describes evolution along the steepest descents in energy and, when it is given in its integral form, the motion is pictured to take place along the shortest paths in energy. In general, evolution is a non-Euclidian energy density landscape in flattening motion.
On a connection between the polylogarithm function and the Bass diffusion model
Authors: Jodrá Pedro
Published: July 2008

The purpose of this paper is to establish a connection between the polylogarithm function and a continuous probability distribution. We provide closed-form expressions in terms of the polylogarithm function for all the moments of a continuous random variable related to the Bass diffusion model, which was introduced by Bass and is widely used in marketing science. In addition, a new integral representation of the polylogarithm of order
n
is achieved from a probabilistic formulation.
Thermal oscillations in rat kidneys: an infrared imaging study
Authors: Gorbach Alexander M , Wang Hengliang , Elster Eric
Published: July 2008

A high-resolution infrared (IR) camera was used to assess rhythmicity in localized renal blood flow, including the extent of regions containing nephrons with spontaneous oscillations in their individual blood flow. The IR imaging was able to follow changes in rat renal perfusion during baseline conditions, during occlusion of the main renal artery and during the administration of either saline or papaverine. Concurrent recordings were made of tubular pressure in superficial nephrons. Spontaneous vascular oscillations centred around 0.02–0.05 Hz and approximately 0.01 Hz could be detected reproducibly by IR imaging. Their spectral characteristics and their response to papaverine were in line with tubular pressure measurements. The intensity of and synchrony between thermal signals from different local areas of the kidney may allow, after surgical exposure, non-invasive imaging of functional clusters involved in renal cortical blood flow. Through visualization of the spatial extent of thermal oscillations, IR imaging holds promise in assessing kidney autoregulatory mechanisms.
Genome-Wide Analysis of Transposon Insertion Polymorphisms Reveals Intraspecific Variation in Cultivated Rice
Authors: Huang Xuehui , Lu Guojun , Zhao Qiang , Liu Xiaohui , Han Bin
Published: July 2008

Insertions and precise eliminations of transposable elements generated numerous transposon insertion polymorphisms (TIPs) in rice (Oryza sativa). We observed that TIPs represent more than 50% of large insertions and deletions (>100 bp) in the rice genome. Using a comparative genomic approach, we identified 2,041 TIPs between the genomes of two cultivars, japonica Nipponbare and indica 93-11. We also identified 691 TIPs between Nipponbare and indica Guangluai 4 in the 23-Mb collinear regions of chromosome 4. Among them, retrotransposon-based insertion polymorphisms were used to reveal the evolutionary relationships of these three cultivars. Our conservative estimates suggest that the TIPs generated approximately 14% of the genomic DNA sequence differences between subspecies indica and japonica. It was also found that more than 10% of TIPs were located in expressed gene regions, representing an important source of genetic variation. Transcript evidence implies that these TIPs induced a series of genetic differences between two subspecies, including interrupting host genes, creating different expression forms, drastically changing intron length, and affecting expression levels of adjacent genes. These analyses provide genome-wide insights into evolutionary history and genetic variation of rice.
Pharmacokinetic interaction of flecainide and paroxetine in relation to the CYP2D6*10 allele in healthy Korean subjects
Authors: Lim Kyoung Soo , Cho Joo‐Youn , Jang In‐Jin , Kim Bo‐Hyung , Kim JaeWoo , Jeon Ji‐Young , Tae Yu‐Mi , Yi SoJeong , Eum SoYoung , Shin Sang‐Goo , Yu Kyung‐Sang
Published: July 2008

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• The only existing study of CYP2D6*10‐associated alterations in flecainide pharmacokinetics was retrospective.

• Paroxetine has been known as a strong inhibitor of CYP2D6.

WHAT THIS STUDY ADDS

• This study reports that the extent of drug interaction between flecainide and paroxetine is influenced by the CYP2D6*10 allele in healthy subjects, which is frequent in Asians.

AIMS

The objectives were to evaluate the effect of CYP2D6 genetic polymorphism on the pharmacokinetics of flecainide, and also on the extent of drug interaction with paroxetine as a CYP2D6 inhibitor after a single oral administration in healthy subjects.

METHODS

An open‐label, two‐period, single‐sequence, cross‐over study was performed in 21 healthy Korean male volunteers (seven for CYP2D6*1/*1 or *1/*2, group 1; seven for CYP2D6*1/*10, group 2; seven for CYP2D6*10/*10 or *10/*36, group 3). Subjects were administered 200 mg of flecainide on day 1. After a 7‐day wash‐out period, subjects were administered 20 mg of paroxetine from day 8 to 14, and 200 mg of flecainide on day 15. Blood sampling was performed up to 72 h after flecainide administration.

RESULTS

Terminal elimination half‐life and mean residence time (MRT) were significantly different among three genotype groups after a single oral administration of flecainide (P = 0.021, 0.011, respectively). Area under the concentration–time curve, terminal elimination half‐life and MRT increased significantly after paroxetine co‐administration only in groups 1 and 2.

CONCLUSIONS

This study reports that the extent of drug interaction between flecainide and paroxetine is influenced by the CYP2D6*10 allele in healthy subjects, which is frequent in Asians.
New diagnostic reporting format for endometrial cytology based on cytoarchitectural criteria
Authors: Yanoh K. , Norimatsu Y. , Hirai Y. , Takeshima N. , Kamimori A. , Nakamura Y. , Shimizu K. , Kobayashi T. K. , Murata T. , Shiraishi T.
Published: July 2008

Objective:  The aim of this study was to develop a new reporting format for endometrial cytology that would standardize the diagnostic criteria and the terminology used for reporting.

Methods:  In previous studies, cytoarchitectural criteria were found to be useful for the cytological assessment of endometrial lesions. To apply these criteria, an appropriate cytological specimen is imperative. In this article, the requirements of an adequate endometrial cytological specimen for the new diagnostic criteria are first discussed. Then, the diagnostic criteria, standardized on a combination of conventional and cytoarchitectural criteria, are presented. Third, terminology that could be used, not only for reporting the histopathological diagnosis, but also for providing better guidance for the gynaecologist to determine further clinical action, is introduced. The proposed reporting format was investigated using endometrial cytology of 58 cases that were cytologically underestimated or overestimated compared to the histopathological diagnosis made on the subsequent endometrial biopsy or surgical specimens.

Results:  Of the 58 cases, 12 were reassessed as being unsatisfactory for evaluation. Among the remaining 46 cases, 25 of the 27 cases, which had been underestimated and subsequently diagnosed as having endometrial carcinoma or a precursor stage on histopathological examination,were reassessed as recommended for endometrial biopsy. On the other hand, 19 cases overestimated by cytology were all reassessed as not requiring biopsy.

Conclusions:  The reporting format for endometrial cytology proposed in this article may improve diagnostic accuracy and reduce the number of patients managed inappropriately.
Control of stream insect assemblages: roles of spatial configuration and local environmental factors
Authors: HEINO JANI , MYKRÄ HEIKKI
Published: July 2008

Abstract1. Current views in ecology emphasise that community structure is the sum of multiple processes, with imprints of both regional and local drivers. However, the degree to which stream insect assemblages are structured by spatial configuration (complying with the dispersal‐based neutral hypothesis) and local environmental features (complying with the niche‐based species sorting hypothesis) has not been rigorously examined based on surveys in multiple years.

2. Stream sites in a boreal drainage system were surveyed during three consecutive years and the relative contribution of spatial configuration and local environmental variables to aquatic insect assemblage structure (characterised by both abundance and presence–absence data) was assessed. Separate analyses were conducted for mayflies (Ephemeroptera), stoneflies (Plecoptera), caddisflies (Trichoptera), and non‐biting midges (Diptera: Chironomidae) in each year.

3. There were no relationships between the spatial location and local environmental features of streams in Mantel tests, facilitating exploration of their independent effects on assemblage structure. The study found virtually no effects of spatial location on stream insect assemblages across the study drainage system, as evidenced by Mantel tests and canonical correspondence analyses (CCA). The environmental variables were also rather weakly associated with assemblage structure, with the total amount of explained variation ranging from 9.8% to 31.7% in the CCAs. There were no appreciable differences in the amount of environment‐related explained variation in assemblage structure between mayflies, stoneflies, caddisflies, and midges, but some between‐year differences were noticeable in most insect groups. The environmental variables that were significantly related to assemblage structure exhibited some between‐group and between‐year variability. In general, patterns shown by abundance and presence–absence data were highly similar.

4. It appears that stream insect assemblages comply with the niche‐based species sorting hypothesis in the context of metacommunity ecology. In contrast, the absence of spatial structuring suggests that stream insect assemblages do not comply with the neutral hypothesis, being not strongly dispersal limited at the within‐drainage basin scale.
Polyphagy, flightlessness, and reproductive output of females: a case study with bagworms (Lepidoptera: Psychidae)
Authors: RHAINDS MARC , LEATHER SIMON R. , SADOF CLIFFORD
Published: July 2008

Abstract 1. We evaluated the relation between plant‐mediated larval traits and the fitness of female bagworms, Thyridopteryx ephemeraeformis Haworth (Lepidoptera: Psychidae) by sampling 29 populations of bagworms on five plant genera (Thuja, Pinus, Picea, Juniperus, and Gleditsia).

2. Compared with those on other genera of plants, female larvae on Thuja attained a larger size at pupation and developed faster. The superior quality of Thuja as a larval food plant resulted in a higher potential fitness of females, as indicated by a low level of pupal mortality and high fecundity.

3. The fecundity of females increased with pupal size on different plant genera, and the effect of host plant genus was negligible compared with pupal size.

4. The mating success of females varied among different populations (0–37% unmated females), but neither host plant, emergence time, nor the size of females had a significant influence on the proportion of mated females.

5. The conversion of adult biomass into reproductive tissue, measured as the ratio between the biomass of eggs divided by the biomass of calling females, increased with the pupal size of females and approached 90% for large females. The high rate of egg conversion in bagworms may be related to the neoteny of short‐lived females that invest little in somatic tissue.
Wetland degradation leads to homogenization of the biota at local and landscape scales
Authors: LOUGHEED VANESSA L. , MCINTOSH MOLLIE D. , PARKER CHRISTIAN A. , STEVENSON R. JAN
Published: July 2008

1. We examined whether the anthropogenic degradation of wetlands leads to homogenization of the biota at local and/or landscape scales and, if so, what specific factors account for such an effect. We compared 16 isolated wetlands (Michigan, U.S.A.) that varied in surrounding land use: half had developed, and half undeveloped, riparian zones. Samples of macrophytes, epiphytic diatoms, zooplankton, macroinvertebrates and water chemistry were collected along three transects in each wetland.

2. Developed wetlands were more nutrient‐rich with higher Cl concentrations. The plant community at developed sites was dominated by Lemnaceae (duckweed), while undeveloped wetlands were dominated by rooted, floating‐leaved vegetation and sensitive plant species. Undeveloped wetlands contained heterogeneous and species‐rich plant communities, greater species richness of zooplankton and diatoms, and heterogeneous zooplankton distributions as compared to developed sites.

3. A comparison among wetlands showed that diatom and zooplankton assemblages in developed wetlands were nested subsets of richer biota found in less developed wetlands. Conversely, plant communities were more heterogeneously distributed among developed wetlands at the landscape level. This may be attributable to patchy invasions by exotic species, which were a feature of the degraded wetlands within developed landscapes.

4. Our results indicate that several taxonomic groups showed similar, probably inter‐dependent, responses to wetland degradation and habitat homogenization at both the local and landscape scales. This change in community structure from a species‐rich and heterogeneous community dominated by floating‐leaved plants in undeveloped wetlands, to nutrient‐rich wetlands dominated by duckweed may represent a shift to an alternate stable state.
Impact of past and present land‐management on the C‐balance of a grassland in the Swiss Alps
Authors: ROGIERS NELE , CONEN FRANZ , FURGER MARKUS , STÖCKLI RETO , EUGSTER WERNER
Published: July 2008

Grasslands cover about 40% of the ice‐free global terrestrial surface, but their quantitative importance in global carbon exchange with the atmosphere is still highly uncertain, and thus their potential for carbon sequestration remains speculative. Here, we report on CO2 exchange of an extensively used mountain hay meadow and pasture in the Swiss pre‐Alps on high‐organic soils (7–45% C by mass) over a 3‐year period (18 May 2002–20 September 2005), including the European summer 2003 heat‐wave period. During all 3 years, the ecosystem was a net source of CO2 (116–256 g C m−2 yr−1). Harvests and grazing cows (mostly via C export in milk) further increased these C losses, which were estimated at 355 g C m−2 yr−1 during 2003 (95% confidence interval 257–454 g C m−2 yr−1). Although annual carbon losses varied considerably among years, the CO2 budget during summer 2003 was not very different from the other two summers. However, and much more importantly, the winter that followed the warm summer of 2003 observed a significantly higher carbon loss when there was snow (133±6 g C m−2) than under comparable conditions during the other two winters (73±5 and 70±4 g C m−2, respectively). The continued annual C losses can most likely be attributed to the long‐term effects of drainage and peat exploitation that began 119 years ago, with the last significant drainage activities during the Second World War around 1940. The most realistic estimate based on depth profiles of ash content after combustion suggests that there is an 500–910 g C m−2 yr−1 loss associated with the decomposition of organic matter. Our results clearly suggest that putting efforts into preserving still existing carbon stocks may be more successful than attempts to increase sequestration rates in such high‐organic mountain grassland soils.
Interannual variation in soil CO2 efflux and the response of root respiration to climate and canopy gas exchange in mature ponderosa pine
Authors: IRVINE J. , LAW B. E. , MARTIN J. G. , VICKERS D.
Published: July 2008

We examined a 6‐year record of automated chamber‐based soil CO2 efflux (Fs) and the underlying processes in relation to climate and canopy gas exchange at an AmeriFlux site in a seasonally drought‐stressed pine forest. Interannual variability of Fs was large (CV=17%) with a range of 427 g C m−2 yr−1 around a mean annual Fs of 811 g C m−2 yr−1. On average, 76% of the variation of daily mean Fs could be quantified using an empirical model with year‐specific basal respiration rate that was a linear function of tree basal area increment (BAI) and modulated by a common response to soil temperature and moisture. Interannual variability in Fs could be attributed almost equally to interannual variability in BAI (a proxy for above‐ground productivity) and interannual variability in soil climate. Seasonal total Fs was twice as sensitive to soil moisture variability during the summer months compared with temperature variability during the same period and almost insensitive to the natural range of interannual variability in spring temperatures. A strong seasonality in both root respiration (Rr) and heterotrophic respiration (Rh) was observed with the fraction attributed to Rr steadily increasing from 18% in mid‐March to 50% in early June through early July before dropping rapidly to 10% of Fs by mid‐August. The seasonal pattern in Rr (10‐day averages) was strongly linearly correlated with tree transpiration (r2=0.90, P<0.01) as measured using sap flux techniques and gross ecosystem productivity (GEP, r2=0.83, P<0.01) measured by the eddy‐covariance approach. Rr increased by 0.43 g C m−2 day−1 for every 1 g C m−2 day−1 increase in GEP. The strong linear correlation of Rr to seasonal changes in GEP and transpiration combined with longer‐term interannual variability in the base rate of Fs, as a linear function of BAI (r2=0.64, P=0.06), provides compelling justification for including canopy processes in future models of Fs.
Effects of tractor wheeling on root morphology and yield of lucerne (Medicago sativa L.)
Authors: Głąb T.
Published: July 2008

The purpose of this study was to determine the effect of soil compaction on the herbage yield and root growth of lucerne (Medicago sativa L.). A field experiment was conducted on a silty loam Mollic Fluvisols soil in 2003–2006. Herbage yield and root morphology, in terms of root length density, mean root diameter, specific root length and distribution of dry matter (DM) in roots, were measured. Four compaction treatments were applied three times annually by tractor using the following number of passes: control without experimental traffic, two passes, four passes and six passes. The tractor traffic changed the physical properties of the soil by increasing bulk density and penetration resistance. Soil compaction also improved its water retention properties. These changes were associated with changes in root morphology and distribution of the DM in roots. Soil compaction resulted in higher proportions of the DM in roots, especially in the upper, 0–10 cm, soil horizon. Decreases in the root length density were observed in a root diameter range of 0·1–1·0 mm. It was also found that roots in a more compacted soil were significantly thicker. An effect of the root system of lucerne on soil compaction was observed. The root system of lucerne decreased the effects of soil compaction that had been recorded in the first and the second year of the experiment. An increase in the number of passes resulted in a decrease in the DM yield of herbage in the second and third harvests each year.
Enhanced secretion of interferon‐γ by bovine γδ T cells induced by coculture with Mycobacterium bovis‐infected dendritic cells: evidence for reciprocal activating signals
Authors: Price Sally J. , Hope Jayne C.
Published: July 2008

Evidence suggests that γδ T cells form part of the innate immune response to Mycobacterium bovis infection. Dendritic cells (DCs) are capable of secreting high levels of interleukin‐12 (IL‐12) following infection with mycobacteria and can induce interferon‐γ (IFN‐γ) secretion by natural killer and γδ T cells We investigated the innate interactions occurring between WC1+γδ T cells and M. bovis‐infected DCs. Following coculture with M. bovis‐infected DCs, secretion of IFN‐γ and expression of CD25 and major histocompatibility complex class II on WC1+γδ T cells were significantly enhanced. Reciprocal enhancement of IL‐12 secretion by the DCs was also observed and this interaction was found to be contact dependent. We hypothesize that there is an early, transient signal between the WC1+γδ T cells and the DCs, which promotes the synthesis of biologically active IL‐12, and which is dependent upon cell–cell contact. Reciprocal signals including IL‐12 are then delivered to WC1+γδ cells, which leads to the enhanced secretion of IFN‐γ, and the up‐regulation of activation markers and antigen presentation molecules by the WC1+γδ T cells. These interactions are likely to form a critical part of the T helper type 1‐conditioning response of DCs to M. bovis.
Differential expression of CD26 on virus‐specific CD8+ T cells during active, latent and resolved infection
Authors: Ibegbu Chris C. , Xu Yong‐Xian , Fillos Dimitri , Radziewicz Henry , Grakoui Arash , Kourtis Athena P.
Published: July 2008

The hallmark of effective establishment of immune memory is the long‐term memory cell that persists in the absence of antigen. To explore its characteristics, we investigated the differences between a resolved successful immune response, such as after influenza (flu) vaccination, and the state of chronic infection with persistent antigen, such as with cytomegalovirus (CMV), Epstein–Barr virus (EBV) or human immunodeficiency virus (HIV), which leads to defective T‐cell memory. Immunophenotypic analyses using multi‐parameter flow cytometry and tetramer technology identified a unique pattern of CD26high expression among influenza‐specific CD8+ T cells, but not among CD8+ T cells specific for CMV, EBV (three different epitopes) or HIV. The median percentage of CD8+ T cells expressing CD26 was 95·5% for influenza, but for cells specific for CMV, EBV and HIV it was 10·5%, 12%–19%, and 13·2%, respectively. These findings suggest that expression of CD26high may be a characteristic of a memory cell. CD26high expression correlates with expression of CD127, a marker of memory cells. Furthermore, CD26high cells can produce interleukin‐2. These findings offer insight into the dynamics of T‐cell differentiation, and they may offer a specific marker of a successfully developed memory CD8+ T cell, that of CD26high. This marker has the potential to be useful in studies of immune responses to infectious agents, and to new vaccine candidates.
Endogenous DNA damage and testicular germ cell tumors
Authors: Cook M. B. , Sigurdson A. J. , Jones I. M. , Thomas C. B. , Graubard B. I. , Korde L. , Greene M. H. , McGlynn K. A.
Published: July 2008

Testicular germ cell tumors are comprised of two histologic groups, seminomas and non‐seminomas. We postulated that the possible divergent pathogeneses of these histologies may be partially explained by variable levels of net endogenous DNA damage. To test our hypothesis, we conducted a case–case analysis of 51 seminoma and 61 non‐seminoma patients using data and specimens from the Familial Testicular Cancer study and the U.S. Radiologic Technologists cohort. A lymphoblastoid cell line was cultured for each patient and the alkaline comet assay was used to determine four parameters: tail DNA, tail length, comet distributed moment (CDM) and Olive tail moment (OTM). Odds ratios (OR) and 95% confidence intervals (95% CI) were estimated using logistic regression. Values for tail length, tail DNA, CDM and OTM were modelled as categorical variables using the 50th and 75th percentiles of the seminoma group. Tail DNA was significantly associated with non‐seminoma compared with seminoma (OR50th percentile = 3.31, 95% CI: 1.00, 10.98; OR75th percentile = 3.71, 95% CI: 1.04, 13.20; p for trend = 0.039). OTM exhibited similar, albeit statistically non‐significant, risk estimates (OR50th percentile = 2.27, 95% CI: 0.75, 6.87; OR75th percentile = 2.40, 95% CI: 0.75, 7.71; p for trend = 0.12) whereas tail length and CDM showed no association. In conclusion, the results for tail DNA and OTM indicate that net endogenous levels are higher in patients who develop non‐seminoma compared with seminoma. This may partly explain the more aggressive biology and younger age‐of‐onset of this histologic subgroup compared with the relatively less aggressive, later‐onset seminoma.