bluuebunny/crossref_metadata_2025 huggingface dataset:
Frequent Mutation of Apc Gene in Rat Colon Tumors and Mucin-Depleted Foci, Preneoplastic Lesions in Experimental Colon Carcinogenesis
Authors: Femia Angelo Pietro , Dolara Piero , Giannini Augusto , Salvadori Maddalena , Biggeri Annibale , Caderni Giovanna
Published: January 2007

Mucin-depleted foci (MDF) are microscopic dysplastic lesions induced in the colon of rodents by specific colon carcinogens. Most MDF show Wnt pathway activation, whereas only a subset shows mutations in the Ctnnb1 gene, coding for β-catenin. Because Apc is a member of the Wnt pathway and the most frequent mutated gene in human colon cancer, we tested whether MDF harbor Apc mutations. F344 rats were treated twice with 150 mg/kg of 1,2-dimethylhydrazine. After 15 or 28 weeks, MDF, aberrant crypt foci (ACF), and tumors were collected. We screened a segment of the Apc gene comprising the region homologous to the mutation cluster region (MCR) of human APC, which frequently shows mutations in experimental colon tumors. Mutations were identified by PCR amplification and sequencing in 6:24 MDF (25%), 7:23 tumors (30%), 0:24 ACF (0%). Most of the mutations (92%) in MDF and tumors were localized in a region upstream from the MCR. All mutations were single-base substitutions and mainly formed by G:C → A:T and C:G → T:A transitions. The pattern of nucleotide changes was similar in MDF and tumors, and, interestingly, the same mutation in codon 1047 was found in two MDF and in three tumors. Four out of the six mutations found in MDF were nonsense mutations, and two were missense. All mutations in tumors determined a protein truncation. These results show that Apc mutations are present in MDF with a frequency similar to that of tumors, strengthening the evidence that they are precancerous lesions in colon carcinogenesis. [Cancer Res 2007;67(2):445–9]
Nuclear factor-κB p65 small interfering RNA or proteasome inhibitor bortezomib sensitizes head and neck squamous cell carcinomas to classic histone deacetylase inhibitors and novel histone deacetylase inhibitor PXD101
Authors: Duan Jianming , Friedman Jay , Nottingham Liesl , Chen Zhong , Ara Gulshan , Van Waes Carter
Published: January 2007

Histone deacetylase inhibitors (HDI) can inhibit proliferation and enhance apoptosis in a wide range of malignancies. However, HDIs show relatively modest activity in head and neck squamous cell carcinomas (HNSCC), in which we have shown the activation of nuclear factor-κB (NF-κB; NF-κB1/RelA or p50/p65), a transcription factor that promotes expression of proliferative and antiapoptotic genes. In this study, we examined if HDIs enhance activation of NF-κB and target genes and if genetic or pharmacologic inhibition of NF-κB can sensitize HNSCC to HDIs. Limited activity of classic HDIs trichostatin A and sodium butyrate was associated with enhanced activation of NF-κB reporter activity in a panel of six HNSCC cell lines. HDIs enhanced NF-κB p50/p65 DNA binding and acetylation of the RelA p65 subunit. Transfection of small interfering RNAs targeting p65 strongly inhibited NF-κB expression and activation, induced cell cycle arrest and cell death, and further sensitized HNSCC cells when combined with HDIs. The p65 small interfering RNA inhibited HDI-enhanced expression of several NF-κB–inducible genes implicated in oncogenesis of HNSCC, such as p21, cyclin D1, and BCL-XL. Bortezomib, an inhibitor of proteasome-dependent NF-κB activation, also increased sensitization to trichostatin A, sodium butyrate, and a novel HDI, PXD101, in vitro, and to the antitumor effects of PXD101 in bortezomib-resistant UMSCC-11A xenografts. However, gastrointestinal toxicity, weight loss, and mortality of the combination were dose limiting and required parenteral fluid administration. We conclude that HDI-enhanced NF-κB activation is one of the major mechanisms of resistance of HNSCC to HDIs. The combination of HDI and proteasome inhibitor produced increased antitumor activity. Low starting dosages for clinical studies combining HDIs with proteasome inhibitors and IV fluid support may be warranted. [Mol Cancer Ther 2007;6(1):37–50]
Tinder, Spark, Oxygen, and Fuel: The Mysterious Rise of the Taliban
Authors: Sullivan Daniel P.
Published: January 2007

Though the Taliban has become one of the best-known fundamentalist groups in the world, its origins remain a mystery. This article argues an explanatory narrative for the rise of the Taliban comprised of three steps in a causal sequence. The first stage consists of causal factors identified in the literature on the rise of the Taliban, including state failure, ethnicity, prevailing poor socio-economic conditions, generational memory of young disaffected males, the fundamentalist teachings of a system of madrasas, and the disappointment of rising expectations (J-curve). These factors are explored individually and then categorized in more detail. J-curve disappointment is found to be a spark that set off a second stage in the causal sequence through the violent mobilization of the Taliban ideology. In this stage, the unique religious ideology acted as the effective oxygen feeding the fire of the Taliban rise. A third stage, in which external support fueled the spread of the Taliban, explains how it was able to spread to over 90% of Afghanistan. The details of this explanatory narrative are brought out by looking at the rise of the Taliban through the lenses of ideology and external support, those factors argued to be of greatest explanatory importance. This analysis identifies the dangers of the large cadres of disaffected young males throughout the Muslim world and the need to provide not only improved socio-economic opportunities but also educational and community-network alternatives to the madrasas used so effectively by the Taliban.
A Liberal Peace in Asia?
Authors: Goldsmith Benjamin E.
Published: January 2007

Drawing on recent liberal peace and Asian security research, this article assesses the relevance of prominent ‘Kantian’ hypotheses for understanding the international politics of Asia. While there is some evidence that the dynamics of war and peace are different in Asia than in other parts of the world, this does not mean that liberal theories are irrelevant. There is at best weak support for the pacific effects of democracy or international institutions in Asia. But liberal expectations, and those of some Asia analysts, about the importance of economic interdependence for reducing conflict in Asia are robustly confirmed. This result obtains even with a control for the simultaneous trade-dampening effect of conflict using structural equations. But the strong intra-Asian effect of trade interdependence does not translate into a robust pacific effect between Asian states and those outside the region. A more nuanced picture emerges; the democratic peace appears most relevant for interactions between Asian states and the rest of the world. The findings show that analysts can rely neither on beliefs that Asia is sui generis nor on purely realist models as guides to Asian security issues. Kantian and realist theories are both relevant. The results also indicate that some common assumptions of analysts, especially regarding the importance of alliances and institutions, are not in accord with the regularities of conflict and peace in Asia.
The ‘User’: Friend, foe or fetish?: A critical exploration of user involvement in health and social care
Authors: Cowden Stephen , Singh Gurnam
Published: January 2007

‘User Involvement’ has become the new mantra in Public Services with professionals constantly being reminded that ‘user knows best’. The pur pose of this paper is to ask where the preoccupation with ‘the User’ comes from and to pose some questions about what ‘User Involvement’ actually means. Within our paper we see three issues as central within this. The first is a consideration of the historical antecedents of the discourse of ‘User Involvement’, focusing in on the struggles over British welfare that took place around the late 1970s–early 1980s. This forms the context from which we seek to understand and critique the New Labour project in relation to the massive expansion of regulatory frame works. We argue that, far from enabling the delivery of high quality integrated services that truly reflect the interests of current and future users, these policies represent the further commodification of basic human needs and welfare. Finally, it has become apparent the current ‘User’ discourse has assumed contradictory manifestations, in particular the emergence of groupings of ‘professional users’ who participate in the formation of state policy as ‘expert consultants’. We conclude by arguing for an approach in which user perspectives are neither privileged nor subjugated, but are situated in a process of creative critical dialogue with professionals, which is linked to the development of a concept of welfare driven by emancipatory rather than regulatory imperatives.
With friends like these: The liberalization of queer family policy
Authors: Wilson Angelia Ruth
Published: January 2007

The last ten years have seen a historic shift in policies regulating the lives of lesbian and gay citizens, including most recently civil partnerships. In addition, the Human Fertilisation and Embryology Act (1990) made it possible for lesbians and gay men to access fertility treatments in private clinics. The 2003 review prompted Mary Warnock to argue that such access should be extended to treatment on the National Health Service. In these changing times, Anthony Giddens maintains that lesbian and gay relationships may reflect ideally the ‘pure relationship’. Mary Warnock is not so sure and thinks the state should play a more active role in regulating the lives of those wishing to become parents. This article considers the philosophical justifications for policies affecting lesbian and gay couples and their children, deconstructing the assumptions made by Giddens and Warnock about choices and family and questioning the ‘friendly’ foundation of ‘queer family policy’.
Outdoor play spaces in Canada: The safety dance of standards as policy
Authors: Herrington Susan , Nicholls Jamie
Published: January 2007

Over the past decade the outdoor play spaces designed for children in Canada have been largely shaped by fear and profit, rather than by what we know about children's play and development. Since the early 1980s the Canadian Standards Association (CSA) has played an increasingly important role in this transformation as their technical standards for children's outdoor play spaces have been gradually adapted as policy by local and regional agencies. While the CSA has historically regulated industrial and commercial projects that enable international trade and harmonization with countries such as the United States, their extension of influence to early childhood is problematic; particularly when applied to childcare centres. The following describes some of the issues that arise from the use of safety standards as policy, and the problems these standards cause when applied to childcare centres.
Comparative British Central-Local Relations
Authors: Laffin Martin
Published: January 2007

This article examines three key, possible post-devolution trends relating to central-local relations in England, Scotland and Wales. First, the Scottish and Welsh cases indicate that devolution does not inevitably lead to regional centralism and that central-local relations at the regional or intermediate levels are less competitive and more collaborative where a power balance or symmetry exists between the intermediate and the local level. Second, post-devolution differences in how the public services are being restructured in England, Scotland and Wales suggest that the trend towards governance is not immutable but at least partly a matter of political choice. Third, even so the post-devolution policy similarities between the metropolitan centre and the two devolved territories remain pronounced with a pattern of continued policy tracking, through which the dominance of the metropolitan centre is maintained indirectly rather than directly.
The Framework of Ethical Compliance in the UK
Authors: O’Toole Barry J.
Published: January 2007

This article raises questions about whether the system for ethical compliance in the public services of the UK is proportionate to the perceived problem of unethical behaviour. The article uses examples from local government, the civil service and Ministers of the Crown. More research needs to be undertaken on these interconnected topics, but problems identified here include: the possibility that the ethical compliance system for local councillors is overly burdensome, and potentially inimical to the democratic process; that changes in the management of the civil service and the increasing influence of special advisers may mean that the ethical compliance system for civil servants is not as robust as it might be; and that for Ministers of the Crown there is not an ethical compliance system in place at all.
The Absent Breast: Speaking of the Mastectomied Body
Authors: Manderson Lenore , Stirling Lesley
Published: January 2007

Worldwide, approximately 1 in 11 women have breast cancer at some time in their lifetime. The majority are successfully treated with surgery, then radiotherapy and/or chemo-therapy. Survival brings its own problems, however, including an underlying ontological problem: What is the part of the body left after a mastectomy? Women talking about their experiences of mastectomy are faced with complex referential tasks with regard to their bodies at different stages of the past and present, within different discourses (medical, sexual, maternal), and from different perspectives (the individual and the generic, their own perspective and that of their medical professionals). Drawing on anthropological research conducted among Australian women, we illustrate how women resolve difficulties of reference to the site of the mastectomy, and examine the shifts in perspective that are marked by different lexical choices.
Lesbians and Bisexual Women in the Eyes of Scientific Psychology
Authors: Lee I-Ching , Crawford Mary
Published: January 2007

Social science research has contributed to the destigmatization of homosexuality which, in turn, has affected the topics researchers choose to study. We examined psychological research that focused on lesbians and bisexual women from 1975 to 2001 to determine if the frequency and content of this research reflect the increasingly positive view of sexual minorities in society. The results indicate that non-heterosexual people were included in less than 1 percent of published research, and lesbians and bisexual women were significantly less likely to be studied than gay and bisexual men. Content analysis of 533 abstracts followed by cluster analysis of 520 abstracts revealed four conceptual frameworks that characterized this body of research: Gender Identity, Attitudes towards Lesbians, Lesbians as Problems, and Life in Heterosexist Society. Together, changes over time in the quantity and emphasis of research shed light on how lesbianism and bisexuality have been constructed in psychological studies and highlight the politics of lesbian-bisexual visibility.
NMDA Receptors in Glia
Authors: Verkhratsky Alexei , Kirchhoff Frank
Published: January 2007

The amino acid L-Glutamate acts as the most ubiquitous mediator of excitatory synaptic transmission in the central nervous system. Glutamatergic transmission is central for diverse brain functions, being particularly important for learning, memory, and cognition. In brain pathology, excessive release of glutamate triggers excitotoxic neural cell death through necrotic or apoptotic pathways. Glutamate effects are mediated by several classes of glutamate receptors, expressed in virtually all cells of neural origin. Specifically important for both physiological information processing and cell damage are glutamate receptors of NMDA ( N-methyl-D-aspartate) type, which, for a long time, were considered to be expressed exclusively in neurons. Recent studies have found functional NMDA receptors in brain macroglia, in astrocytes, and oligodendrocytes. Glial and neuronal NMDA receptors are functionally and structurally different; the glial receptors are weakly (if at all) sensitive to the extracellular magnesium block, which may indicate a predominant expression of the NR3 receptor subunit. In the cortex, astroglial NMDA receptors are activated upon physiological synaptic transmission. The physiological relevance of NMDA receptors in the white matter remains unknown; their activation upon ischemia triggers Ca2+-dependent damage of oligodendrocytes and myelin. The discovery of glial NMDA receptors further indicates the complex nature of intercellular signaling mechanisms in the brain, which involve all types of neural cells, connected through diverse types of chemical and electrical synapses.
Evolution of Cognitive Function via Redeployment of Brain Areas
Authors: Anderson Michael L.
Published: January 2007

The creative reuse of existing neural components may have played a significant role in the evolutionary development of cognition. There are obvious evolutionary advantages to such redeployment, and the data presented here confirm three important empirical predictions of this account of the development of cognition: 1) A typical brain area will be used by many cognitive functions in diverse task categories, (2) evolutionarily older brain areas will be deployed in more cognitive functions, and (3) more recent cognitive functions will use more, and more widely scattered, brain areas. These findings have implications not just for our understanding of the evolutionary origins of cognitive function but also for the practice of both clinical and experimental neuroscience.
Polydendrocytes: NG2 Cells with Many Roles in Development and Repair of the CNS
Authors: Nishiyama Akiko
Published: January 2007

NG2 cells, or polydendrocytes, are defined as glial cells that express the NG2 proteoglycan and represent a fourth major glial cell population in the mammalian central nervous system. They are morphologically, antigenically, and functionally distinct from mature astrocytes, oligodendrocytes, and microglia. Although they are most often equated with oligodendrocyte progenitor cells, they exhibit some properties that are not commonly associated with those of progenitor cells that generate myelinating cells. This review discusses recent observations and unanswered issues related to their lineage and their role in remyelination, neural signaling, and axonal growth.
Magnetic Resonance Imaging of Alzheimer's Pathology in the Brains of Living Transgenic Mice: A New Tool in Alzheimer's Disease Research
Authors: Jack Clifford R. , Marjanska Malgorzata , Wengenack Thomas M. , Reyes Denise A. , Curran Geoffrey L. , Lin Joseph , Preboske Gregory M. , Poduslo Joseph F. , Garwood Michael
Published: January 2007

Alzheimer's disease (AD) is the most common cause of dementia in the elderly. Cardinal pathologic features of AD are amyloid plaques and neurofibrillary tangles, and most in the field believe that the initiating events ultimately leading to clinical AD center on disordered metabolism of amyloid beta protein. Mouse models of AD have been created by inserting one or more human mutations associated with disordered amyloid metabolism and that cause early onset familial AD into the mouse genome. Human-like amyloid plaque formation increases dramatically with age in these transgenic mice. Amyloid reduction in humans is a major therapeutic objective, and AD transgenic mice allow controlled study of this biology. Recent work has shown that amyloid plaques as small as 35 μm can be detected using in vivo magnetic resonance microimaging (MRMI) at high magnetic field (9.4 T). In addition, age-dependent changes in metabolite concentration analogous to those that have been identified in human AD patients can be detected in these transgenic mice using single-voxel 1H magnetic resonance spectroscopy (1H MRS) at high magnetic field. These MR-based techniques provide a new set of tools to the scientific community engaged in studying the biology of AD in transgenic models of the disease. For example, an obvious application is evaluating therapeutic modification of disease progression. Toward the end of this review, the authors include results from a pilot study demonstrating feasibility of using MRMI to detect therapeutic modification of plaque progression in AD transgenic mice.
How Humans Reach: Distinct Cortical Systems for Central and Peripheral Vision
Authors: Clavagnier Simon , Prado Jérôme , Kennedy Henry , Perenin Marie-Thérèse
Published: January 2007

Lesions of the posterior parietal cortex in humans can produce a specific disruption of visually guided hand movements termed optic ataxia. The fact that the deficit mainly occurs in peripheral vision suggests that reaching in foveal and extrafoveal vision relies on two different anatomical substrates. Using fMRI in healthy subjects, the authors demonstrated the existence of two systems, differently modulated by the two reaching conditions. Reaching in central vision involves a restricted network, including the medial intraparietal sulcus (mIPS) and the caudal part of the dorsal premotor cortex (PMd). Reaching in peripheral vision engages a more extensive network, including the parieto-occipital junction (POJ). Interestingly, POJ corresponds to the site of the lesion overlap that the authors recently found to be responsible for optic ataxia. These two sets of results converge to show that there is not a unique cortical network for reaching control but instead two systems engaged in reaching to targets in the central and peripheral visual field.
Estrogens and Epilepsy: Why Are We So Excited?
Authors: Velíšková Jana
Published: January 2007

Estrogens are essential for normal brain function throughout life. The source of estrogens is not only from the periphery, but local production has also been demonstrated in the CNS. Actions of estrogens involve a variety of effects, which include modulation of gene expression, regulation of neurotransmitter release, or direct inter-actions with neurotransmitter receptors. By these effects, estrogens affect neuronal excitability and thus may play an important role in seizure disorders. Although the original clinical as well as animal studies suggest that estrogens have exclusively proconvulsant properties, it has now become clear that estrogens also produce anticonvulsant effects. These opposite effects of estrogens on seizures may depend on treatment duration, latency prior to seizure testing, mode of administration, estrogen dose and hormonal status, estrogenic species, the region/neurotransmitter system involved, seizure type/model used, and sex. Animal data also suggest that estrogens, specifically β-estradiol, have neuroprotective effects on seizure-induced hippocampal damage. Further studies are necessary to understand the role of estrogens in seizure disorders. Such under-standing is important, especially for women with epilepsy, to make qualified decisions regarding administration of contraceptives and hormonal replacement therapy as well as for the design of new therapeutic strategies for better seizure control and prevention of seizure-induced neuronal damage.
Development of Cortical Maps: Perspectives From the Barrel Cortex
Authors: Inan Melis , Crair Michael C.
Published: January 2007

One approach to examining how higher sensory, motor, and cognitive faculties emerge in the neocortex is to elucidate the underlying wiring principles of the brain during development. The mammalian neocortex is a layered structure generated from a sheet of proliferating ventricular cells that progressively divide to form specific functional areas, such as the primary somatosensory (S1) and motor (M1) cortices. The basic wiring pattern in each of these functional areas is based on a similar framework, but is distinct in detail. Functional specialization in each area derives from a combination of molecular cues within the cortex and neuronal activity-dependent cues provided by innervating axons from the thalamus. One salient feature of neocortical development is the establishment of topographic maps in which neighboring neurons receive input relayed from neighboring sensory afferents. Barrels, which are prominent sensory units in the somatosensory cortex of rodents, have been examined in detail, and data suggest that the initial, gross formation of the barrel map relies on molecular cues, but the refinement of this topography depends on neuronal activity. Several excellent reviews have been published on the patterning and plasticity of the barrel cortex and the precise targeting of ventrobasal thalamic axons. In this review, the authors will focus on the formation and functional maturation of synapses between thalamocortical axons and cortical neurons, an event that coincides with the formation of the barrel map. They will briefly review cortical patterning and the initial targeting of thalamic axons, with an emphasis on recent findings. The rest of the review will be devoted to summarizing their understanding of the cellular and molecular mechanisms underlying thalamocortical synapse maturation and its role in barrel map formation.
Multiple myeloma–reactive T cells recognize an activation-induced minor histocompatibility antigen encoded by the ATP-dependent interferon-responsive (ADIR) gene
Authors: van Bergen Cornelis A. M. , Kester Michel G. D. , Jedema Inge , Heemskerk Mirjam H. M. , van Luxemburg-Heijs Simone A. P. , Kloosterboer Freke M. , Marijt W. A. Erik , de Ru Arnoud H. , Schaafsma M. Ron , Willemze Roel , van Veelen Peter A. , Falkenburg J. H. Frederik
Published: January 2007

Minor histocompatibility antigens (mHags) play an important role in both graft-versus-tumor effects and graft-versus-host disease (GVHD) after allogeneic stem cell transplantation. We applied biochemical techniques and mass spectrometry to identify the peptide recognized by a dominant tumor-reactive donor T-cell reactivity isolated from a patient with relapsed multiple myeloma who underwent transplantation and entered complete remission after donor lymphocyte infusion. A frequently occurring single nucleotide polymorphism in the human ATP-dependent interferon-responsive (ADIR) gene was found to encode the epitope we designated LB-ADIR-1F. Although gene expression could be found in cells from hematopoietic as well as nonhematopoietic tissues, the patient suffered from only mild acute GVHD despite high percentages of circulating LB-ADIR-1F–specific T cells. Differential recognition of nonhematopoietic cell types and resting hematopoietic cells as compared with activated B cells, T cells, and tumor cells was demonstrated, illustrating variable LB-ADIR-1F expression depending on the cellular activation state. In conclusion, the novel mHag LB-ADIR-1F may be a suitable target for cellular immunotherapy when applied under controlled circumstances.
Temporal genetic program following B-cell receptor cross-linking: altered balance between proliferation and death in healthy and malignant B cells
Authors: Vallat Laurent D. , Park Yuhyun , Li Cheng , Gribben John G.
Published: January 2007

Gene expression in cells is a dynamic process but is usually examined at a single time point. We used gene expression profiling over time to build temporal models of gene transcription after B-cell receptor (BCR) signaling in healthy and malignant B cells and chose this as a model since BCR cross-linking induces both cell proliferation and apoptosis, with increased apoptosis in chronic lymphocytic leukemia (CLL) compared to healthy B cells. To determine the basis for this, we examined the global temporal gene expression profile for BCR stimulation and developed a linear combination method to summarize the effect of BCR simulation over all the time points for all patients. Functional learning identified common early events in healthy B cells and CLL cells. Although healthy and malignant B cells share a common genetic pattern early after BCR signaling, a specific genetic program is engaged by the malignant cells at later time points after BCR stimulation. These findings identify the molecular basis for the different functional consequences of BCR cross-linking in healthy and malignant B cells. Analysis of gene expression profiling over time may be used to identify genes that might be rational targets to perturb these pathways.
EDGEdb: a transcription factor-DNA Interaction database for the analysis of C. elegans differential gene expression
Authors: Barrasa M Inmaculada , Vaglio Philippe , Cavasino Fabien , Jacotot Laurent , Walhout Albertha JM
Published: January 2007

Background

Transcription regulatory networks are composed of protein-DNA interactions between transcription factors and their target genes. A long-term goal in genome biology is to map protein-DNA interaction networks of all regulatory regions in a genome of interest. Both transcription factor -and gene-centered methods can be used to systematically identify such interactions. We use high-throughput yeast one-hybrid assays as a gene-centered method to identify protein-DNA interactions between regulatory sequences (e.g. gene promoters) and transcription factors in the nematode Caenorhabditis elegans. We have already mapped several hundred protein-DNA interactions and analyzed the transcriptional consequences of some by examining differential gene expression of targets in the presence or absence of an upstream regulator. The rapidly increasing amount of protein-DNA interaction data at a genome scale requires a database that facilitates efficient data storage, retrieval and integration.

Description

Here, we report the implementation of a C.

e

legans
d ifferential g ene e xpression d atab ase (EDGEdb). This database enables the storage and retrieval of protein-DNA interactions and other data that relate to differential gene expression. Specifically, EDGEdb contains: i) sequence information of regulatory elements, including gene promoters, ii) sequence information of all 934 predicted transcription factors, their DNA binding domains, and, where available, their dimerization partners and consensus DNA binding sites, iii) protein-DNA interactions between regulatory elements and transcription factors, and iv) expression patterns conferred by regulatory elements, and how such patterns are affected by interacting transcription factors.

Conclusion

EDGEdb provides a protein-DNA -and protein-protein interaction resource for C. elegans transcription factors and a framework for similar databases for other organisms. The database is available at http://edgedb.umassmed.edu.
Identification of candidate genes associated with cell wall digestibility and eQTL (expression quantitative trait loci) analysis in a Flint × Flint maize recombinant inbred line population
Authors: Shi Chun , Uzarowska Anna , Ouzunova Milena , Landbeck Matthias , Wenzel Gerhard , Lübberstedt Thomas
Published: January 2007

Background

Cell-wall digestibility is the major target for improving the feeding value of forage maize. An understanding of the molecular basis for cell-wall digestibility is crucial towards breeding of highly digestible maize.

Results

865 candidate ESTs for cell-wall digestibility were selected according to the analysis of expression profiles in 1) three sets of brown-midrib isogenic lines in the genetic background of inbreds 1332 (1332 and 1332 bm3), 5361 (5361 and 5361 bm3), and F2 (F2, F2 bm1, F2 bm2, and F2 bm3), 2) the contrasting extreme lines of FD (Flint × Dent, AS08 × AS 06), DD1 (Dent × Dent, AS11 × AS09), and DD2 (Dent × Dent, AS29 × AS30) mapping populations, and 3) two contrasting isogenic inbreds, AS20 and AS21. Out of those, 439 ESTs were assembled on our "Forage Quality Array", a small microarray specific for cell wall digestibility related experiments. Transcript profiles of 40 lines of a Flint × Flint population were monitored using the Forage Quality Array, which were contrasting for cell wall digestibility. Using t-tests (p < 0.01), the expression patterns of 102 ESTs were significantly different between high and low quality groups. Using interval mapping, eQTL (LOD ≥ 2.4) were detected for 20% (89 of 439) of the spotted ESTs. On average, these eQTL explained 39% of the transcription variation of the corresponding ESTs. Only 26% (23 of 89) ESTs detected a single eQTL. eQTL hotspots, containing greater than 5% of the total number of eQTL, were located in chromosomal bins 1.07, 1.12, 3.05, 8.03, and 9.04, respectively. Bin 3.05 was co-localized with a cell-wall digestibility related QTL cluster.

Conclusion

102 candidate genes for cell-wall digestibility were validated by genetical genomics approach. Although the cDNA array highlights gene types (the tested gene and any close family members), trans-acting factors or metabolic bottlenecks seem to play the major role in controlling heritable variation of gene expression related to cell-wall digestibility, since no in silico mapped ESTs were in the same location as their own eQTL. Transcriptional variation was generally found to be oligogenic rather than monogenic inherited due to only 26% ESTs detected a single eQTL in the present study. One eQTL hotspot was co-localized with cell wall digestibility related QTL cluster on bins 3.05, implying that in this case the gene(s) underlying QTL and eQTL are identical. As the field of genetical genomics develops, it is expected to significantly improve our knowledge about complex traits, such as cell wall degradability. Comprehensive knowledge of the lignin pathway and cell wall biogenesis will allow plant breeders to choose the best genomic targets controlling these characters, for improving forage digestibility through genetic engineering or marker-assisted selection.
Integration of regulatory signals through involvement of multiple global regulators: control of the Escherichia coli gltBDF operon by Lrp, IHF, Crp, and ArgR
Authors: Paul Ligi , Mishra Pankaj K , Blumenthal Robert M , Matthews Rowena G
Published: January 2007

Background

The glutamate synthase operon (gltBDF) contributes to one of the two main pathways of ammonia assimilation in Escherichia coli. Of the seven most-global regulators, together affecting expression of about half of all E. coli genes, two were previously shown to exert direct, positive control on gltBDF transcription: Lrp and IHF. The involvement of Lrp is unusual in two respects: first, it is insensitive to the usual coregulator leucine, and second, Lrp binds more than 150 bp upstream of the transcription starting point. There was indirect evidence for involvement of a third global regulator, Crp. Given the physiological importance of gltBDF, and the potential opportunity to learn about integration of global regulatory signals, a combination of in vivo and in vitro approaches was used to investigate the involvement of additional regulatory proteins, and to determine their relative binding positions and potential interactions with one another and with RNA polymerase (RNAP).

Results

Crp and a more local regulator, ArgR, directly control gltBDF transcription, both acting negatively. Crp-cAMP binds a sequence centered at -65.5 relative to the transcript start. Mutation of conserved nucleotides in the Crp binding site abolishes the Crp-dependent repression. ArgR also binds to the gltBDF promoter region, upstream of the Lrp binding sites, and decreases transcription. RNAP only yields a defined DNAse I footprint under two tested conditions: in the presence of both Lrp and IHF, or in the presence of Crp-cAMP. The DNAse I footprint of RNAP in the presence of Lrp and IHF is altered by ArgR.

Conclusion

The involvement of nearly half of E. coli's most-global regulatory proteins in the control of gltBDF transcription is striking, but seems consistent with the central metabolic role of this operon. Determining the mechanisms of activation and repression for gltBDF was beyond the scope of this study. However the results are consistent with a model in which IHF bends the DNA to allow stabilizing contacts between Lrp and RNAP, ArgR interferes with such contacts, and Crp introduces an interfering bend in the DNA and/or stabilizes RNAP in a poised but inactive state.
Transcriptional changes associated with breast cancer occur as normal human mammary epithelial cells overcome senescence barriers and become immortalized
Authors: Li Yizheng , Pan Jing , Li Jian-Liang , Lee Jee Hyung , Tunkey Chris , Saraf Katie , Garbe James C , Whitley Maryann Z , Jelinsky Scott A , Stampfer Martha R , Haney Steven A
Published: January 2007

Background

Human mammary epithelial cells (HMEC) overcome two well-characterized genetic and epigenetic barriers as they progress from primary cells to fully immortalized cell lines in vitro. Finite lifespan HMEC overcome an Rb-mediated stress-associated senescence barrier (stasis), and a stringent, telomere-length dependent, barrier (agonescence or crisis, depending on p53 status). HMEC that have overcome the second senescence barrier are immortalized.

Methods

We have characterized pre-stasis, post-selection (post-stasis, with p16 silenced), and fully immortalized HMEC by transcription profiling and RT-PCR. Four pre-stasis and seven post-selection HMEC samples, along with 10 representatives of fully immortalized breast epithelial cell lines, were profiled using Affymetrix U133A/B chips and compared using both supervised and unsupervised clustering. Datasets were validated by RT-PCR for a select set of genes. Quantitative immunofluorescence was used to assess changes in transcriptional regulators associated with the gene expression changes.

Results

The most dramatic and uniform changes we observed were in a set of about 30 genes that are characterized as a "cancer proliferation cluster," which includes genes expressed during mitosis (CDC2, CDC25, MCM2, PLK1) and following DNA damage. The increased expression of these genes was particularly concordant in the fully immortalized lines. Additional changes were observed in IFN-regulated genes in some post-selection and fully immortalized cultures. Nuclear localization was observed for several transcriptional regulators associated with expression of these genes in post-selection and immortalized HMEC, including Rb, Myc, BRCA1, HDAC3 and SP1.

Conclusion

Gene expression profiles and cytological changes in related transcriptional regulators indicate that immortalized HMEC resemble non-invasive breast cancers, such as ductal and lobular carcinomas in situ, and are strikingly distinct from finite-lifespan HMEC, particularly with regard to genes involved in proliferation, cell cycle regulation, chromosome structure and the DNA damage response. The comparison of HMEC profiles with lines harboring oncogenic changes (e.g. overexpression of Her-2neu, loss of p53 expression) identifies genes involved in tissue remodeling as well as proinflamatory cytokines and S100 proteins. Studies on carcinogenesis using immortalized cell lines as starting points or "normal" controls need to account for the significant pre-existing genetic and epigenetic changes inherent in such lines before results can be broadly interpreted.
Improved glucose tolerance in acyl CoA:diacylglycerol acyltransferase 1-null mice is dependent on diet
Authors: Wang Steven JY , Cornick Claire , O'Dowd Jacqueline , Cawthorne Michael A , Arch Jonathan R S
Published: January 2007

Background

Mice that lack acyl CoA:diacylglycerol acyltransferase (Dgat1
-/- mice) are reported to have a reduced body fat content and improved glucose tolerance and insulin sensitivity. Studies so far have focussed on male null mice fed a high fat diet and there are few data on heterozygotes. We compared male and female Dgat1
-/-, Dgat1
+/- and Dgat1
+/+ C57Bl/6 mice fed on either standard chow or a high fat diet.

Results

Body fat content was lower in the Dgat1
-/- than the Dgat1
+/+ mice in both experiments; lean body mass was higher in male Dgat1
-/- than Dgat1
+/+ mice fed on the high fat diet. Energy intake and expenditure were higher in male Dgat1
-/- than Dgat1
+/+ mice; these differences were less marked or absent in females. The body fat content of female Dgat1
+/- mice was intermediate between that of Dgat1
-/- and Dgat1
+/+ mice, whereas male Dgat1+/- mice were similar to or fatter than Dgat1
+/+ mice. Glucose tolerance was improved and plasma insulin reduced in Dgat1
-/- mice fed on the high fat diet, but not on the chow diet. Both male and female Dgat1
+/- mice had similar glucose tolerance to Dgat1
+/+ mice.

Conclusion

These results suggest that although ablation of DGAT1 improves glucose tolerance by preventing obesity in mice fed on a high fat diet, it does not improve glucose tolerance in mice fed on a low fat diet.
Five-year predictors of physical activity decline among adults in low-income communities: a prospective study
Authors: Weiss Deborah R , O'Loughlin Jennifer L , Platt Robert W , Paradis Gilles
Published: January 2007

Background

Obesity in North America is now endemic, and increased understanding of the determinants of physical inactivity is critical. This analysis identified predictors of declines in physical activity over 5 years among adults in low-income, inner-city neighbourhoods.

Methods

Data on leisure time physical activity were collected in telephone interviews in 1992 and 1997 from 765 adults (47% of baseline respondents), as part of the evaluation of a community-based cardiovascular disease risk reduction program.

Results

One-third of 527 participants who were physically active at baseline, were inactive in 1997. Predictors of becoming inactive included female sex (OR = 1.63 95% CI (1.09, 2.43)), older age (1.02 (1.01, 1.04)), higher BMI (1.57 (1.03, 2.40)), poor self-rated health (1.39 (1.05, 1.84)), lower self-efficacy for physical activity (1.46 (1.00, 2.14)), and not using a neighborhood facility for physical activity (1.61 (1.02, 2.14)).

Conclusion

These results highlight the fact that a variety of variables play a role in determining activity level, from demographic variables such as age and sex, to psychosocial and environmental variables. In addition, these results highlight the important role that other health-related variables may play in predicting physical activity level, in particular the observed association between baseline BMI and the increased risk of becoming inactive over time. Lastly, these results demonstrate the need for multi-component interventions in low-income communities, which target a range of issues, from psychosocial factors, to features of the physical environment.
Intracranial pressure monitoring in intensive care: clinical advantages of a computerized system over manual recording
Authors: Zanier Elisa Roncati , Ortolano Fabrizio , Ghisoni Laura , Colombo Angelo , Losappio Sabina , Stocchetti Nino
Published: January 2007

Introduction

The presence of intracranial hypertension (HICP) after traumatic brain injury (TBI) affects patient outcome. Intracranial pressure (ICP) data from electronic monitoring equipment are usually calculated and recorded hourly in the clinical chart by trained nurses. Little is known, however, about how precisely this method reflects the real patterns of ICP after severe TBI. In this study, we compared hourly manual recording with a validated and continuous computerized reference standard.

Methods

Thirty randomly selected patients with severe TBI and HICP admitted to the neuroscience intensive care unit (Policlinico University Hospital, Milan, Italy) were retrospectively studied. A 24-hour interval with ICP monitoring was randomly selected for each patient. The manually recorded data available for analysis covered 672 hours corresponding to 36,492 digital data points. The two methods were evaluated using the correlation coefficient and the Bland and Altman method. We used the proportion test to analyze differences in the number of episodes of HICP (ICP > 20 mm Hg) detected with the two methods and the paired t test to analyze differences in the percentage of time of HICP.

Results

There was good agreement between the digitally collected ICP and the manual recordings of the end-hour values. Bland and Altman analysis confirmed a mean difference between the two methods of 0.05 mm Hg (standard deviation 3.66); 96% of data were within the limits of agreement (+7.37 and -7.28). The average percentages of time of ICP greater than 20 mm Hg were 39% calculated from the digital measurements and 34% from the manual observations. From the continuous digital recording, we identified 351 episodes of ICP greater than 20 mm Hg lasting at least five minutes and 287 similar episodes lasting at least ten minutes. Conversely, end-hour ICP of greater than 20 mm Hg was observed in only 204 cases using manual recording methods.

Conclusion

Although manually recorded end-hour ICP accurately reflected the computerized end-hour and mean hour values, the important omission of a number of episodes of high ICP, some of long duration, results in a clinical picture that is not accurate or informative of the true pattern of unstable ICP in patients with TBI.
Efficient generation of CD34+ progenitor-derived dendritic cells from G-CSF-mobilized peripheral mononuclear cells does not require hematopoietic stem cell enrichment
Authors: Paczesny Sophie , Li Yin-Ping , Li Na , Latger-Cannard Véronique , Marchal Luc , Ou-Yang Jing-Ping , Bordigoni Pierre , Stoltz Jean-François , Eljaafari Assia
Published: January 2007

As a result of their potent antigen-presentation function, dendritic cells (DC) are important tools for cell therapy programs. In vitro-generated DC from enriched CD34+ hematopoietic stem cells (HSC; enriched CD34 DC) have already proven their efficiency in Phase I/II clinical trials. Here, we investigated whether enrichment of CD34+ HSC before the onset of culture was absolutely required for their differentiation into DC. With this aim, we developed a new two-step culture method. PBMC harvested from G-CSF-mobilized, healthy patients were expanded for 7 days during the first step, with early acting cytokines, such as stem cell factor, fetal liver tyrosine kinase 3 ligand (Flt-3L), and thrombopoietin. During the second step, expanded cells were then induced to differentiate into mature DC in the presence of GM-CSF, Flt-3L, and TNF-α for 8 days, followed by LPS exposure for 2 additional days. Our results showed that the rate of CD34+/CD38+/lineageneg cells increased 19.5 ± 10-fold (mean±sd) during the first step, and the expression of CD14, CD1a, CD86, CD80, and CD83 molecules was up-regulated markedly following the second step. When compared with DC generated from enriched CD34+ cells, which were expanded for 7 days before differentiation, DC derived from nonenriched peripheral blood stem cells showed a similar phenotye but higher yields of production. Accordingly, the allogeneic stimulatory capacity of the two-step-cultured DC was as at least as efficient as that of enriched CD34 DC. In conclusion, we report herein a new two-step culture method that leads to high yields of mature DC without any need of CD34+ HSC enrichment.