bluuebunny/crossref_metadata_2025 huggingface dataset:
RTX cytotoxins recognize β
2
integrin receptors through N-linked oligosaccharides
Authors: Morova Jana , Osicka Radim , Masin Jiri , Sebo Peter
Published: March 2008

Bordetella pertussis
adenylate cyclase (AC) toxin–hemolysin (Hly) (CyaA, ACT, or AC-Hly) is a cytotoxin of the RTX (repeat in toxin) family. It delivers into target cells an AC domain that catalyzes uncontrolled conversion of ATP to cAMP, a key signaling molecule subverting phagocyte functions. CyaA utilizes a heavily N-glycosylated β
2
integrin receptor CD11b/CD18 (α
M
β
2
, Mac-1, or CR3). We show that deglycosylation of cell surface proteins by glycosidase treatment, or inhibition of protein N-glycosylation by tunicamycin, ablates CyaA binding and penetration of CD11b-expressing cells. Furthermore, binding of CyaA to cells was strongly inhibited in the presence of free saccharides occurring as building units of integrin oligosaccharide complex, whereas saccharides absent from integrin oligosaccharide chains failed to inhibit CyaA binding to CD11b/CD18-expressing cells. CyaA, hence, selectively recognized sugar residues of N-linked oligosaccharides of integrins. Moreover, glycosylation of CD11a/CD18, another receptor of the β
2
integrin family, was also essential for cytotoxic action of other RTX cytotoxins, the leukotoxin of
Aggregatibacter actinomycetemcomitans
(LtxA) and the
Escherichia coli
α-Hly (HlyA). These results show that binding and killing of target cells by CyaA, LtxA, and HlyA depends on recognition of N-linked oligosaccharide chains of β
2
integrin receptors. This sets a new paradigm for action of RTX cytotoxins.
Anthropogenic increase in carbon dioxide compromises plant defense against invasive insects
Authors: Zavala Jorge A. , Casteel Clare L. , DeLucia Evan H. , Berenbaum May R.
Published: March 2008

Elevated levels of atmospheric carbon dioxide (CO
2
), a consequence of anthropogenic global change, can profoundly affect the interactions between crop plants and insect pests and may promote yet another form of global change: the rapid establishment of invasive species. Elevated CO
2
increased the susceptibility of soybean plants grown under field conditions to the invasive Japanese beetle (
Popillia japonica
) and to a variant of western corn rootworm (
Diabrotica virgifera virgifera
) resistant to crop rotation by down-regulating gene expression related to defense signaling [lipoxygenase 7 (
lox7
), lipoxygenase 8 (
lox8
), and 1-aminocyclopropane-1-carboxylate synthase (
acc-s
)]. The down-regulation of these genes, in turn, reduced the production of cysteine proteinase inhibitors (CystPIs), which are specific deterrents to coleopteran herbivores. Beetle herbivory increased CystPI activity to a greater degree in plants grown under ambient than under elevated CO
2
. Gut cysteine proteinase activity was higher in beetles consuming foliage of soybeans grown under elevated CO
2
than in beetles consuming soybeans grown in ambient CO
2
, consistent with enhanced growth and development of these beetles on plants grown in elevated CO
2
. These findings suggest that predicted increases in soybean productivity under projected elevated CO
2
levels may be reduced by increased susceptibility to invasive crop pests.
Discovery of a widely distributed toxin biosynthetic gene cluster
Authors: Lee Shaun W. , Mitchell Douglas A. , Markley Andrew L. , Hensler Mary E. , Gonzalez David , Wohlrab Aaron , Dorrestein Pieter C. , Nizet Victor , Dixon Jack E.
Published: March 2008

Bacteriocins represent a large family of ribosomally produced peptide antibiotics. Here we describe the discovery of a widely conserved biosynthetic gene cluster for the synthesis of thiazole and oxazole heterocycles on ribosomally produced peptides. These clusters encode a toxin precursor and all necessary proteins for toxin maturation and export. Using the toxin precursor peptide and heterocycle-forming synthetase proteins from the human pathogen
Streptococcus pyogenes
, we demonstrate the
in vitro
reconstitution of streptolysin S activity. We provide evidence that the synthetase enzymes, as predicted from our bioinformatics analysis, introduce heterocycles onto precursor peptides, thereby providing molecular insight into the chemical structure of streptolysin S. Furthermore, our studies reveal that the synthetase exhibits relaxed substrate specificity and modifies toxin precursors from both related and distant species. Given our findings, it is likely that the discovery of similar peptidic toxins will rapidly expand to existing and emerging genomes.
Nonrandom connectivity of the epileptic dentate gyrus predicts a major role for neuronal hubs in seizures
Authors: Morgan Robert J. , Soltesz Ivan
Published: March 2008

Many complex neuronal circuits have been shown to display nonrandom features in their connectivity. However, the functional impact of nonrandom network topologies in neurological diseases is not well understood. The dentate gyrus is an excellent circuit in which to study such functional implications because proepileptic insults cause its structure to undergo a number of specific changes in both humans and animals, including the formation of previously nonexistent granule cell-to-granule cell recurrent excitatory connections. Here, we use a large-scale, biophysically realistic model of the epileptic rat dentate gyrus to reconnect the aberrant recurrent granule cell network in four biologically plausible ways to determine how nonrandom connectivity promotes hyperexcitability after injury. We find that network activity of the dentate gyrus is quite robust in the face of many major alterations in granule cell-to-granule cell connectivity. However, the incorporation of a small number of highly interconnected granule cell hubs greatly increases network activity, resulting in a hyperexcitable, potentially seizure-prone circuit. Our findings demonstrate the functional relevance of nonrandom microcircuits in epileptic brain networks, and they provide a mechanism that could explain the role of granule cells with hilar basal dendrites in contributing to hyperexcitability in the pathological dentate gyrus.
The effects of low attainment on young people's outcomes at age 22‐23 in Scotland
Authors: Howieson Cathy , Iannelli Cristina
Published: March 2008

A common concern among policy makers in Europe is the low level of qualifications of some school leavers and the possible consequences of this for their life chances and for countries' economic prosperity. This article considers the impact of young people's low levels of educational attainment on their later life chances, especially on labour market participation. It identifies the long‐term negative effects of low attainment and explores the extent to which family background also continues to influence young people's outcomes. It examines the outcomes of low attainment among young men and women and considers whether low attainment has a different impact on the prospects of young men and women. The article also investigates whether staying on at school improves longer‐term chances and opportunities for low attainers. These questions have strong policy relevance, and are explored using data from a nationally representative survey of Scottish school leavers.
Distinguishing Mother–Infant Interaction From Stranger–Infant Interaction at 2, 4, and 6 Months of Age
Authors: Bigelow Ann E. , Power Michelle , Mcquaid Nancy , Ward Ashley , Rochat Philippe
Published: March 2008

Observers watched videotaped face‐to‐face mother–infant and stranger–infant interactions of 12 infants at 2, 4, or 6 months of age. Half of the observers saw each mother paired with her own infant and another infant of the same age (mother tapes) and half saw each infant paired with his or her mother and with a stranger (infant tapes). Observers were asked to judge which was the mother–infant dyad in each pair. Observers' accuracy improved as infants aged and was above chance for both mother and infant tapes when infants were 6 months. Differences between mother–infant and stranger–infant dyadic communication patterns also emerged as the infants aged. At 6 months, mother–infant dyads had more symmetrical communication and less asymmetrical communication than stranger–infant dyads.
Gap Junction Channels Exhibit Connexin-specific Permeability to Cyclic Nucleotides
Authors: Kanaporis Giedrius , Mese Gulistan , Valiuniene Laima , White Thomas W. , Brink Peter R. , Valiunas Virginijus
Published: March 2008

Gap junction channels exhibit connexin dependent biophysical properties, including selective intercellular passage of larger solutes, such as second messengers and siRNA. Here, we report the determination of cyclic nucleotide (cAMP) permeability through gap junction channels composed of Cx43, Cx40, or Cx26 using simultaneous measurements of junctional conductance and intercellular transfer of cAMP. For cAMP detection the recipient cells were transfected with a reporter gene, the cyclic nucleotide-modulated channel from sea urchin sperm (SpIH). cAMP was introduced via patch pipette into the cell of the pair that did not express SpIH. SpIH-derived currents (Ih) were recorded from the other cell of a pair that expressed SpIH. cAMP diffusion through gap junction channels to the neighboring SpIH-transfected cell resulted in a five to sixfold increase in Ih current over time. Cyclic AMP transfer was observed for homotypic Cx43 channels over a wide range of conductances. However, homotypic Cx40 and homotypic Cx26 exhibited reduced cAMP permeability in comparison to Cx43. The cAMP/K+ permeability ratios were 0.18, 0.027, and 0.018 for Cx43, Cx26, and Cx40, respectively. Cx43 channels were ∼10 to 7 times more permeable to cAMP than Cx40 or Cx26 (Cx43 > Cx26 ≥ Cx40), suggesting that these channels have distinctly different selectivity for negatively charged larger solutes involved in metabolic/biochemical coupling. These data suggest that Cx43 permeability to cAMP results in a rapid delivery of cAMP from cell to cell in sufficient quantity before degradation by phosphodiesterase to trigger relevant intracellular responses. The data also suggest that the reduced permeability of Cx26 and Cx40 might compromise their ability to deliver cAMP rapidly enough to cause functional changes in a recipient cell.
Infection Control Experience in a Cooperative Care Center for Transplant Patients
Authors: Nusair Ahmad , Jourdan Dawn , Medcalf Sharon , Marion Nedra , Iwen Peter C. , Fey Paul D. , Reed Elizabeth , Langnas Alan , Rupp Mark E.
Published: March 2008

Objective.

To characterize infection control experience during a 6.5-year period in a cooperative care center for transplant patients.

Design.

Descriptive analysis.

Setting.

A cooperative care center for transplanted patients, in which patients and care partners are housed in a homelike environment, and care partners assume responsibility for patient care duties.

Patients.

Nine hundred ninety one transplant patients.

Methods.

Infection control definitions from the Centers for Disease Control and Prevention were used to ascertain infection rates. Environmental cultures were used to detect methicillin-resistantStaphylococcus aureus(MRSA), vancomycin-resistantEnterococcus(VRE),Clostridium difficile,and fungi during the first 18 months. Surveillance cultures were performed for a subset of patients and care partners.

Results.

From June 1999 through December 2005, there were 19,365 patient-days observed. The most common healthcare-associated infection encountered was intravascular catheter-related bloodstream infection, with infection rates of 5.74 and 4.94 cases per 1,000 patient-days for hematopoietic stem cell transplant (HSCT) and solid organ transplant (SOT) patients, respectively. G difficile-associated diarrhea was observed more frequentiy in HSCT patients than in SOT patients (3.97 vs 0.57 cases per 1000 patient-days;P<.0001 ). There was no evidence of environmental contamination with MRSA, VRE, or C.difficile.Acquisition of MRSA was not observed. Acquisition of VRE was documented.

Conclusion.

This study documented that cooperative care was associated with some risk of healthcare-associated infection, most notably intravascular catheter-associated bloodstream infection and C. difficile-associated diarrhea, it appears the incidences of these infections were roughly commensurate with those in other care settings.
Outbreak of Multidrug-Resistant Serratia marcescens Infection in a Neonatal Intensive Care Unit
Authors: Maragakis Lisa L. , Winkler Amy , Tucker Margaret G. , Cosgrove Sara E. , Ross Tracy , Lawson Edward , Carroll Karen C. , Perl Trish M.
Published: March 2008

Background.

Serratia marcescens causes healthcare-associated infections and significant morbidity and mortality in neonatal intensive care units (NICUs). We report the investigation and control of an outbreak of multidrug-resistant (MDR) S. marcescens infection at an NICU.

Methods.

An outbreak investigation and a case-control study were undertaken at a 36-bed NICU in a tertiary care hospital in Baltimore, Maryland, for the period from October 2004 through February 2005. The outbreak investigation included case identification, review of medical records, environmental cultures, patient surveillance cultures, personnel hand cultures, and pulsed-field gel electrophoresis (PFGE). The case-control study included case identification and review of medical records. Infection control measures were implemented. Eighteen NICU neonates had cultures that grew MDR S. marcescens during the study period. The case-control study included 16 patients with the outbreak strain or an unidentified strain of MDR S. marcescens and 32 control patients not infected and/or colonized with MDR S. marcescens, treated in the NICU for at least 48 hours during the study period.

Results.

PFGE analysis identified a single strain of MDR S. marcescens that infected or colonized 15 patients. Two patients had unique strains, and 1 patient's isolate could not be subtyped. An unrelated MDR S. marcescens isolate was recovered from a sink drain. Exposure to inhalational therapy was an independent risk factor for MDR S. marcescens acquisition after adjusting for birth weight. Extensive investigation failed to reveal a point source for the outbreak.

Conclusion.

A single epidemic strain of MDR S. marcescens spread rapidly and threatened to become endemic in this NICU. Transient carriage on the hands of healthcare personnel or on respiratory care equipment was the likely mode of transmission. Cohorting patients and staff, at the cost of bed closures and additional personnel, interrupted transmission and halted the outbreak.
Pluripotency and nuclear reprogramming
Authors: Yamanaka Shinya
Published: March 2008

Embryonic stem cells are promising donor cell sources for cell transplantation therapy, which may in the future be used to treat various diseases and injuries. However, as is the case for organ transplantation, immune rejection after transplantation is a potential problem with this type of therapy. Moreover, the use of human embryos presents serious ethical difficulties. These issues may be overcome if pluripotent stem cells are generated from patients' somatic cells. Here, we review the molecular mechanisms underlying pluripotency and the currently known methods of inducing pluripotency in somatic cells.
Epigenetic mechanisms regulating fate specification of neural stem cells
Authors: Namihira Masakazu , Kohyama Jun , Abematsu Masahiko , Nakashima Kinichi
Published: March 2008

Neural stem cells (NSCs) possess the ability to self-renew and to differentiate along neuronal and glial lineages. These processes are defined by the dynamic interplay between extracellular cues including cytokine signalling and intracellular programmes such as epigenetic modification. There is increasing evidence that epigenetic mechanisms involving, for example, changes in DNA methylation, histone modification and non-coding RNA expression are closely associated with fate specification of NSCs. These epigenetic alterations could provide coordinated systems for regulating gene expression at each step of neural cell differentiation. Here we review the roles of epigenetics in neural fate specification in the mammalian central nervous system.
Genetic pattern of the recent recovery of European otters in southern France
Authors: Janssens Xavier , Fontaine Michaël C. , Michaux Johan R. , Libois Roland , De Kermabon Jean , Defourny Pierre , Baret Philippe V.
Published: March 2008

We investigated how landscape affects the population genetic structure and the dispersal of the elusive European otterLutra lutrain a contemporary colonization context, over several generations and at the level of hydrographic basins. Our study area included 10 basins located in the Cévennes National Park (CNP), at the southern front of the natural otter recovery in France. Each basin comprised 50 to 300 km of permanent rivers that were surveyed for otter presence from 1991 to 2005. Faecal samples collected in 2004 and 2005 in this area were genotyped at 9 microsatellite loci, resulting in the identification of 70 genetically distinct individuals. Bayesian clustering methods were used to infer genetic structure of the populations and to compare recent gene flow to the observed colonization. At the regional level, we identified 2 distinct genetic clusters (NE and SW; FST=0.102) partially separated by ridges, suggesting that the CNP was recolonized by 2 genetically distinct otter populations. At the basin level, the genetic distance between groups of individuals in different basins was positively correlated to the mean slope separating these basins. The probable origins and directions of individual movements (i.e. migration between clusters and basin colonization inside clusters) were inferred from assignment tests. This approach shows that steep and dry lands can stop, impede or divert the dispersal of a mobile carnivore such as the otter.
Spider assemblages in winter oilseed rape affected by landscape and site factors
Authors: Drapela Thomas , Moser Dietmar , Zaller Johann G. , Frank Thomas
Published: March 2008

Spiders are an abundant and diverse group of generalist predators in arable fields. Knowledge on what landscape and site factors affect this group can be valuable for efforts to reduce biodiversity loss in agricultural landscapes and can have implications for natural pest control. We investigated the impact of landscape and site factors on epigeic spiders in 29 winter oilseed rape fields (Brassica napus, OSR) embedded in differently structured landscapes in an agricultural region east of Vienna (Austria). Landscape factors included proportions of non‐crop areas, woody areas and fallows, lengths of road‐side strips and hedges, and landscape diversity at different spatial scales (r=250–2000 m). Site factors included OSR stand density, soil index, soil cultivation intensity, nitrogen fertilisation level, OSR vegetation cover in late autumn, and insecticide applications. Data were analysed using regression, ordination, and variation partitioning. Different characteristics of spider assemblages responded to different landscape factors at different spatial scales. Observed species richness showed the strongest positive reponse to proportions of woody areas at rather small scale (radius 500 m), but the relation remained significant up to the 1250 m radius. Standardised species richness was positively related to non‐crop area at the smallest scale (radius 250 m). Activity density was positively related to length of road‐side strips with maximum effects at large scale (radius 1750 m) and non‐crop area (radius 750 m). Site characteristics (stand density, insecticide applications, and late autumn ground cover) and landscape factors (woody areas and fallows at radius 500 m) were similarly important for explaining species composition. We interpret the scale‐dependency of relations as the result of differences in dispersal power of the studied spider species. These results demonstrate the important, scale dependent influence of natural and semi‐natural habitats on spider assemblages in arable fields.
Multi‐scale spatial patterns of three seagrass species with different growth dynamics
Authors: Kendrick Gary A. , Holmes Karen W. , Van Niel Kimberly P.
Published: March 2008

Knowledge of landscape spatial patterns of seagrasses and their rates of loss and natural colonization is critical for understanding the ecology of this group of submerged aquatic plants. Seagrasses form extensive meadows that occupy sheltered coastal seas of the world. In this paper, we examine the multi‐scale variability of three seagrass species over a large near‐shore region (42 km2) in Western Australia. Geostatistical non‐parametric methods were used to explore spatial variation in presence ofAmphibolis griffithii,Posidonia coriaceaandP. sinuosa, and to identify the spatial scales at which distinct patterns in the species distributions occur: <50, 50–610 and >610 m. Each species showed unique variance structure across local (<50 and 50–610 m) and regional scales (>610 m), suggesting differences in species biology, environmental requirements, inter‐species interactions, and their ability to modify their environment. These observations reflect that 1) seagrass landscapes are created by processes that independently act on each seagrass species at different spatial scales; 2) the species’ distributions differ in their hydrodynamic forcing, and; 3) seagrass species distributions reflect colonization history such that related species are separated in space because they have different places in the successional sequence. This cross‐scale study demonstrates that shoot studies only partly address the spatial structure of seagrass landscapes and further large‐scale spatially‐explicit research is required before we can interpret the driving processes.
Dynamics of mycorrhizae during development of riparian forests along an unregulated river
Authors: Piotrowski Jeff S. , Lekberg Ylva , Harner Mary J. , Ramsey Philip W. , Rillig Matthias C.
Published: March 2008

In this study, we explore two mycorrhizal groups during development of riparian soils along a freely‐flowing river. We provide the first documentation of a shift in abundance between arbuscular mycorrhizae and ectomycorrhizae during floodplain succession. We used a chronosequence spanning 0–70 yr along a river in northwestern Montana, USA, to test the hypothesis that abundance of arbuscular mycorrhizal fungi (AMF) is greatest in early stages of soil development, and abundance of ectomycorrhizal fungi (ECMF) is greatest later in floodplain succession. We also measured the AMF‐mediated process of formation of soil aggregates during site development. AMF colonization of the dominant tree (black cottonwood,Populus trichocarpa) remained low (<5%), while AMF colonization of understory species was high (45–90%), across the chronosequence. Mycorrhizal inoculum potential (MIP) and hyphal length of AMF in soil peaked within the first 13 yr of succession and then declined. No single variable significantly correlated with AMF abundance, but AMF tended to decline as litter and soil organic matter increased. Density of ectomycorrhizal root tips in soil increased linearly throughout the chronosequence, and ectomycorrhizal colonization of cottonwood roots increased rapidly in early stages of succession. These patterns suggest that ECMF are not limited by dispersal, but rather influenced by abundance of host plants. Formation of water stable aggregates increased rapidly during the first third of the chronosequence, which was the period of greatest AMF abundance in the soil. The peak in AMF infectivity and hyphal length during early succession suggests that regular flooding and establishment of new sites promotes AMF abundance in this ecosystem. Regulation of rivers that eliminates creation of new sites may reduce contributions of AMF to riparian areas.
Fire, native species, and soil resource interactions influence the spatio‐temporal invasion pattern of Bromus tectorum
Authors: Gundale Michael J. , Sutherland Steve , DeLuca Thomas H.
Published: March 2008

Bromus tectorum (cheatgrass) is an invasive annual that occupies perennial grass and shrub communities throughout the western United States. Bronus tectorum exhibits an intriguing spatio‐temporal pattern of invasion in low elevation ponderosa pine Pinus ponderosa/bunchgrass communities in western Montana where it forms dense rings beneath solitary pines following fire. This pattern provides a unique opportunity to investigate several indirect effects of native vegetation that influence the invasion pattern of B. tectorum, and specifically how native species, disturbance, and soil resources interact to influence the spatio‐temporal pattern of invasion. We established four replicate field sites, each containing burned‐tree, burned‐grass, unburned‐tree, and unburned‐grass sampling locations, and initiated a series of field sampling and greenhouse experiments utilizing these locations. The objective of our first greenhouse experiment was to identify whether belowground factors contributed to the pattern of B. tectorum biomass observed in these field locations. This experiment generated a B. tectorum biomass response that was nearly identical to the invasion pattern observed in the field, suggesting further investigation of belowground factors was necessary. We measured resin‐sorbed NH4+ and NO3− during one generation of B. tectorum, and measured a suite of P fractions through a sequential extraction procedure from these soils. These data revealed that a resource island of high N and P exists beneath pine trees. Through a second greenhouse experiment, we determined that N limited B. tectorum biomass in tree soil, whereas P limited biomass in bunchgrass soil. Finally, through a germination experiment we determined that pine litter strongly inhibited B. tectorum germination. These data suggest B. tectorum is regulated by P in bunchgrass soil, and by N and inhibition by pine litter beneath trees, effects that are likely alleviated by fire. These data demonstrate the combined role of direct and indirect interactions between native and invasive species in regulating biological invasions.
Determinants of species richness, endemism and turnover in European longhorn beetles
Authors: Baselga Andrés
Published: March 2008

This study assessed the diversity patterns of a large family of beetles, Cerambycidae, in Europe and tested the following hypotheses: 1) richness gradients of this hyperdiverse taxon are driven by water and energy variables; 2) endemism is explained by the same factors, but variation between areas also reflects post‐glacial re‐colonization processes; and 3) faunal composition is determined by the same climatic variables and, therefore, beta diversity (species turnover) is related to richness gradients. Species richness, endemism and beta diversity were modelled using inventories of 37 European territories, built from a database containing the distributions of 609 species. Area, spatial position, and nine topographical and climatic variables were used as predictors in regression and constrained analysis of principal coordinates modelling.

Species richness was mostly explained by a temperature gradient, which produced a south‐to‐north decreasing richness gradient. Endemism followed the same pattern, but was also determined by longitudinal variation, peaking in the southwestern and southeastern corners of the continent. Faunal turnover was explained by an important purely spatial pattern and a spatially structured environmental gradient. Thus, contrary to other groups, cerambycid richness was mostly explained by environmental energy, but not by water availability. Endemism was concentrated in the Iberian and Greek peninsulas, but not in Italy. Thus, the latter area may have been the major source of post‐glacial re‐colonization for European longhorn beetles or, otherwise, a poor refuge during glaciations. Turnover patterns were independent of the richness gradient, because northern faunas are nested in southern ones. Turnover, in contrast to richness, was driven by both the independent effects of climate and geographic constraints that might reflect dispersal limitation or stochastic colonization events, suggesting that richness gradients are more environmentally deterministic phenomena than turnover patterns.
Deep‐sea nematode biodiversity in the Mediterranean basin: testing for longitudinal, bathymetric and energetic gradients
Authors: Danovaro Roberto , Gambi Cristina , Lampadariou Nikolaos , Tselepides Anastasios
Published: March 2008

The knowledge of the processes controlling the spatial distribution of species diversity is one of the main challenges of the present ecological research. Spatial patterns of benthic biodiversity in the deep sea are poorly known in comparison with other ecosystems and this limits our understanding of the mechanisms controlling the distribution and maintenance of high biodiversity in the largest ecosystems of our biosphere. Although the Mediterranean basin covers <1% of the world ocean surface, none the less it hosts >7.5% of the global biodiversity. The high biogeographic complexity and the presence of steep ecological gradients contribute in making the Mediterranean a region of very high diversity. Here we report the results of an investigation on the patterns of nematode biodiversity in the deep‐Mediterranean Sea, in relation with bathymetric, longitudinal and energetic gradients. Our results indicate that benthic biodiversity in the deep‐Mediterranean decreases significantly with increasing depth. Moreover, at equally deep sites, nematode diversity decreased from the western to the eastern basin and longitudinal gradients were evident when comparing sites at 4000‐m depth, with 3000‐m depth. The analysis of the available energy (measured as labile organic matter content of the sediments) suggests that biodiversity patterns are not controlled by the amounts of food resources, but instead bio‐availability is the key factor. A more detailed analysis revealed an extremely high deep‐sea beta‐diversity (turnover diversity), both among sites at different depths as well as at similar depths of different longitude or within the same basin. This new finding has not only important implications on the estimates of the overall regional diversity (gamma diversity), but also suggests the presence of high biogeographic complexity in the deep benthic domain of the Mediterranean Sea.
Wnt signaling inside the nucleus
Authors: Shitashige Miki , Hirohashi Setsuo , Yamada Tesshi
Published: March 2008

Accumulation of the β‐catenin protein and transactivation of a certain set of T‐cell factor (TCF)‐4 target genes by accumulated β‐catenin have been considered crucial in colorectal carcinogenesis. In the present review, we summarize nuclear proteins that interact with, and regulate, the β‐catenin and TCF and lymphoid enhancer factor (LEF) transcriptional complexes. Our recent series of proteomic studies has also revealed that various classes of nuclear proteins participate in the β‐catenin–TCF‐4 complex and modulate its transcriptional activity. Furthermore, the protein composition of the TCF‐4‐containing nuclear complex is not fixed, but is regulated dynamically by endogenous programs associated with intestinal epithelial cell differentiation and exogenous stimuli. Restoration of the loss‐of‐function mutation of the adenomatous polyposis coli (APC) gene in colorectal cancer cells does not seem to be a realistic approach with currently available medical technologies, and only signaling molecules downstream of the APC gene product can be considered as targets of pharmacological intervention. Nuclear proteins associated with the β‐catenin–TCF‐4 complex may include feasible targets for molecular therapy against colorectal cancer. Recently, an inhibitor of the interaction between CREB‐binding protein and β‐catenin was shown to efficiently shut down the transcriptional activity of TCF‐4 and induce apoptosis of colorectal cancer cells. We also summarize current strategies in the development of drugs against Wnt signaling. (Cancer Sci 2008; 99: 631–637)
Molecular biomarkers in urothelial bladder cancer
Authors: Kim Wun‐Jae , Bae Suk‐Chul
Published: March 2008

Bladder cancers are a mixture of heterogeneous cell populations, and numerous factors are likely to be involved in dictating their recurrence, progression, and the patient's survival. For any candidate prognostic marker to have considerable clinical relevance, it must add some predictive capacity beyond that offered by the conventional clinical and pathological parameters. None of the biomarkers reported to date have shown sufficient sensitivity and specificity for detecting the whole spectrum of bladder cancer diseases in routine clinical practice. The limitations of established prognostic markers requires us to identify better molecular parameters that could be of interest in predicting the prognosis of bladder cancer patients, in particular, the high‐risk patient groups that are at risk of progression and recurrence. Recent progress in epigenetic modification and gene silencing opened a new avenue for the identification of epigenetic markers, which appears to be more useful for cancer diagnosis and prognosis. Although epigenetic markers also have limitations, the combined epigenetic marker approach may increase sensitivity and reliability. The epigenetic silencing of tumor‐suppressor genes is interesting from a clinical standpoint because of the possibility of reversing epigenetic changes and restoring gene function in a cell. In addition, microarray technology provides us with additional tools for the analysis of global gene‐expression analysis of tumor samples. Future microarray analyses are likely to reveal particular gene‐expression signatures that predict the likelihood of bladder cancer progression and recurrence, as well as a patient's survival and responsiveness to different anticancer therapies, with great specificity and sensitivity. (Cancer Sci 2008; 99: 646–652)
Down regulation of BRCA2 causes radio‐sensitization of human tumor cells in vitro and in vivo
Authors: Yu Dong , Sekine Emiko , Fujimori Akira , Ochiya Takahiro , Okayasu Ryuichi
Published: March 2008

In order to study the role of BRCA2 protein in homologous recombination repair and radio‐sensitization, we utilized RNA interference strategy in vitro and in vivo with human tumor cells. HeLa cells transfected with small‐interfering BRCA2 NA (BRCA2 siRNA) (Qiagen) as well as negative‐control siRNA for 48 h were irradiated, and several critical end points were examined. The radiation cell survival level was significantly reduced in HeLa cells with BRCA2 siRNA when compared with mock‐ or negative‐control siRNA transfected cells. DNA double strand break repair as measured by constant field gel‐electrophoresis showed a clear inhibition in cells with BRCA2 siRNA, while little inhibition was observed in cells with negative control siRNA. Our immuno‐staining experiments revealed a significant delay in Rad51 foci formation in cells with BRCA2 siRNA when compared with the control populations. However, none of the non‐homologous end joining proteins nor the phosphorylation of DNA‐dependent protein kinase catalytic subunit was affected in cells transfected with BRCA2 siRNA. In addition, the combined treatment with radiation and BRCA2 siRNA in xenograft model with HeLa cells showed an efficient inhibition of in vivo tumor growth. Our results demonstrate down‐regulation of BRCA2 leads to radio‐sensitization mainly through the inhibition of homologous recombination repair type double‐strand break repair; a possibility of using BRCA2 siRNA as an effective radiosensitizer in tumor radiotherapy may arise. (Cancer Sci 2008; 99: 810–815)
Translational microarray systems for outcome prediction of hepatocellular carcinoma
Authors: Iizuka Norio , Hamamoto Yoshihiko , Tsunedomi Ryouichi , Oka Masaaki
Published: March 2008

DNA microarray technology has revolutionized our understanding of the molecular basis of hepatocellular carcinoma (HCC), one of the most fatal human cancers with a high recurrence rate. Many researchers have used DNA microarray technology to reclassify HCC with respect to metastatic potential and to develop predictors for the outcome of HCC. However, developed predictors have reached the level only of small retrospective studies, and their current status is far from that required for clinical use. This is due to the lack of transparent data, the high cost and data instability associated with the high dimensionality of the technique, the infancy of bioinformatics, and the complicated nature of recurrent HCC. This comprehensive review summarizes: (i) class comparison studies to identify genes or pathways involved in HCC metastasis (ii) class discovery studies that have resulted in the identification of a new molecular subclass of HCC with respect to metastasis, and (iii) class prediction studies to develop multidimensional predictors for HCC outcome. We also discuss issues that need to be addressed so that the power of array‐based predictors can be estimated prospectively in large independent cohorts of HCC patients. (Cancer Sci 2008; 99: 659–665)
Tumor promoting properties of a cigarette smoke prevalent polycyclic aromatic hydrocarbon as indicated by the inhibition of gap junctional intercellular communication via phosphatidylcholine‐specific phospholipase C
Authors: Upham Brad L. , Bláha Ludek , Babica Pavel , Park Joon‐Suk , Sovadinova Iva , Pudrith Charles , Rummel Alisa M. , Weis Liliane M. , Sai Kimie , Tithof Patti K. , Gužvić Miodrag , Vondráček Jan , Machala Miroslav , Trosko James E.
Published: March 2008

Inhibition of gap junctional intercellular communication (GJIC) and the activation of intracellular mitogenic pathways are common hallmarks of epithelial derived cancer cells. We previously determined that the 1‐methyl and not the 2‐methyl isomer of anthracene, which are prominent cigarette smoke components, activated extracellular receptor kinase, and inhibited GJIC in WB‐F344 rat liver epithelial cells. Using these same cells, we show that an immediate upstream response to 1‐methylanthracene was a rapid (<1 min) release of arachidonic acid. Inhibition of phosphatidylcholine‐specific phospholipase C prevented the inhibition of GJIC by 1‐methylanthracene. In contrast, inhibition of phosphatidylinositol specific phospholipase C, phospholipase A2, diacylglycerol lipase, phospholipase D, protein kinase C, and tyrosine protein kinases had no effect on 1‐methylanthracene‐induced inhibition of GJIC. Inhibition of protein kinase A also prevented inhibition of GJIC by 1‐methylanthracene. Direct measurement of phosphatidylcholine‐specific phospholipase C and sphingomyelinase indicated that only phosphatidylcholine‐specific phospholipase C was activated in response to 1‐methylanthracene, while 2‐methylanthracene had no effect. 1‐methylanthracene also activated p38‐mitogen activated protein kinase; however, like extracellular kinase, its activation was not involved in 1‐methylanthracene‐induced regulation of GJIC, and this activation was independent of phosphatidylcholine‐specific phospholipase C. Although mitogen activated protein kinases were activated, Western blot analyzes indicated no change in connexin43 phosphorylation status. Our results indicate that phosphatidylcholine‐specific phospholipase C is an important enzyme in the induction of a tumorigenic phenotype, namely the inhibition of GJIC; whereas mitogen activated protein kinases triggered in response to 1‐methylanthracene, were not involved in the deregulation of GJIC. (Cancer Sci 2008; 99: 696–705)
Heat shock protein 90 inhibition is cytotoxic to primary AML cells expressing mutant FLT3 and results in altered downstream signalling
Authors: Al Shaer Laila , Walsby Elisabeth , Gilkes Amanda , Tonks Amanda , Walsh Valerie , Mills Ken , Burnett Alan , Rowntree Clare
Published: March 2008

Activating mutations of the FMS‐like tyrosine kinase 3 gene (FLT3) occur in approximately one‐third of patients with acute myeloid leukaemia (AML) and predict for a poor outcome. Heat shock protein 90 (Hsp90) is a molecular chaperone that is frequently used by cancer cells to stabilise mutant oncoproteins. Mutant FLT3 is chaperoned by Hsp90 in primary AML blasts whereas unmutated FLT3 is not, making Hsp90 inhibitors potentially useful therapeutically. The present study showed that inhibition of Hsp90 by 17‐allylamino‐17‐demethoxygeldanamycin (17‐AAG) was cytotoxic to primary AML cells expressing mutant FLT3. Inhibition of Hsp90 results in altered downstream signalling effects in primary AML cells with disruption of Janus kinase–signal transducer and activator of transcription (JAK‐STAT), mitogen‐activated protein kinase and phosphatidylinositol 3/AKT signalling pathways. Co‐treatment of blasts with 17‐AAG and cytarabine resulted in a synergistic or additive effect in approximately 50% of AML cases tested. Our results confirm that Hsp90 is a valid molecular target in the therapy of AML. Inhibition of Hsp90 in parallel with conventional AML therapies may have particular benefit in those patients with the poor prognostic FLT3 mutant disease.
The prognostic significance of cytopenia in chronic lymphocytic leukaemia/small lymphocytic lymphoma
Authors: Zent Clive S. , Ding Wei , Schwager Susan M. , Reinalda Megan S. , Hoyer James D. , Jelinek Diane F. , Tschumper Renee C. , Bowen Deborah A. , Call Timothy G. , Shanafelt Tait D. , Kay Neil E. , Slager Susan L.
Published: March 2008

The development of cytopenia in chronic lymphocytic leukaemia (CLL) patients can predict poor prognosis. All CLL patients seen in the Division of Hematology at Mayo Clinic Rochester from 1 January 1995 to 31 December 2004 (n = 1750) were evaluated for cytopenia, aetiology of cytopenia and clinical outcome. Cytopenia occurred in 423 (24·2%) patients and was attributable to CLL in 303 (17·3%) cases, with 228 (75%) of these having bone marrow (BM) failure and 75 (25%) having autoimmune disease (AID). Survival from onset of cytopenia was significantly better for patients with AID (median 9·1 years) compared to patients with BM failure (median 4·4 years, P < 0·001). Patients with AID diagnosed within 1 year of the diagnosis of CLL (n = 35) had similar survival from diagnosis compared to patients without CLL‐related cytopenia (median 9·3 vs. 9·7 years, P = 0·881). Although cytopenia caused by BM failure predicted a poorer prognosis in CLL, cytopenia caused by AID was not an adverse prognostic factor. These findings suggest that patients with cytopenia due to AID cannot be meaningfully classified by the current clinical staging systems. Revisions of the National Cancer Institute Working Group 96 criteria should consider the aetiology of cytopenia in staging CLL patients.
Toll‐like receptor‐4‐mediated macrophage activation is differentially regulated by progesterone via the glucocorticoid and progesterone receptors
Authors: Jones Leigh A. , Anthony Jean‐Paul , Henriquez Fiona L. , Lyons Russell E. , Nickdel Mohammad B. , Carter Katharine C. , Alexander James , Roberts Craig W.
Published: March 2008

Macrophage function has been demonstrated to be subject to modulation by progesterone. However, as this steroid hormone can act through the glucocorticoid receptor as well as the progesterone receptor, the mechanism of action has not been precisely characterized. To determine the mode of action, we compared the ability of progesterone, norgestrel (a synthetic progesterone‐receptor‐specific agonist) and dexamethasone (a synthetic glucocorticoid receptor agonist) to modulate macrophage function following stimulation of the Toll‐like receptor‐4 (TLR‐4) ligand lipopolysaccharide (LPS). The results demonstrate that following stimulation of TLR‐4 with LPS and cotreatment with either progesterone or dexamethasone, but not norgestrel, there is a significant reduction in nitric oxide (NO) production, indicating that this progesterone‐mediated effect is through ligation of the glucocorticoid receptor. In contrast, LPS‐induced interleukin‐12 (IL‐12) production could be downregulated by all three steroids, indicating that ligation by progesterone of either the glucocorticoid or the progesterone receptors or both could mediate this effect. While progesterone downmodulated NO‐mediated killing of Leishmania donovani by activated macrophages in vitro, most probably via the glucocorticoid receptor, it had little effect on Toxoplasma gondii growth in these cells. This would suggest that progesterone‐mediated increased susceptibility to T. gondii during pregnancy is more likely to be related to the ability of the hormone to downregulate IL‐12 production and a type‐1 response utilizing the progesterone as well as the glucocorticoid receptors.
Spermatogonial morphology, kinetics and niches in hamsters exposed to short‐ and long‐photoperiod
Authors: Do Nascimento H. F. , Drumond A. L. , De França L. R. , Chiarini‐Garcia H.
Published: March 2008

Previous studies have shown that under short photoperiod exposure spermatogenesis in golden hamster regresses leading to sexual inactivity. It is known that this regression is related to changes in somatic and germ cells (spermatocytes and spermatids). However, the photoperiod effects on spermatogonial biology have not been studied in detail yet. In this regard, this study was carried out to investigate the morphology, kinetics and niches of different spermatogonial types in golden hamsters under long‐ and short‐photoperiod. Six spermatogonial generations such as type A undifferentiated (Aund), type A differentiating (A1, A2, A3), intermediate (In) and type B spermatogonia were characterized, and were morphologically similar irrespective of the photoperiod exposure. The short photoperiod was inhibitory to Aundspermatogonia and preleptotene but had no effect on the number of differentiating (A1to B) spermatogonia. In golden hamsters exposed to stimulatory‐photoperiod, the interstitial components were positioned mainly in triangular areas around the seminiferous tubules and, in this situation, the Aundspermatogonia were clearly positioned in niches (p < 0.05) in all stages studied. On the other hand, during the inhibitory‐photoperiod where the seminiferous tubules have smaller diameter, the interstitial components were more homogenously distributed and the triangular areas were not clearly observed. In this case, the niches were identified only at stage VII (p < 0.05), although there was a trend of being positioned in niches area in all the stages studied. Thus, these findings suggest that the Aundspermatogonia location in the seminiferous epithelium and the niche position are directly related to the position of the interstitial components.