bluuebunny/crossref_metadata_2025 huggingface dataset:
c-Met signaling induces a reprogramming network and supports the glioblastoma stem-like phenotype
Authors: Li Yunqing , Li Angela , Glas Martin , Lal Bachchu , Ying Mingyao , Sang Yingying , Xia Shuli , Trageser Daniel , Guerrero-Cázares Hugo , Eberhart Charles G. , Quiñones-Hinojosa Alfredo , Scheffler Bjorn , Laterra John
Published: June 2011

The tyrosine kinase c-Met promotes the formation and malignant progression of multiple cancers. It is well known that c-Met hyperactivation increases tumorigenicity and tumor cell resistance to DNA damaging agents, properties associated with tumor-initiating stem cells. However, a link between c-Met signaling and the formation and/or maintenance of neoplastic stem cells has not been previously identified. Here, we show that c-Met is activated and functional in glioblastoma (GBM) neurospheres enriched for glioblastoma tumor-initiating stem cells and that c-Met expression/function correlates with stem cell marker expression and the neoplastic stem cell phenotype in glioblastoma neurospheres and clinical glioblastoma specimens. c-Met activation was found to induce the expression of reprogramming transcription factors (RFs) known to support embryonic stem cells and induce differentiated cells to form pluripotent stem (iPS) cells, and c-Met activation counteracted the effects of forced differentiation in glioblastoma neurospheres. Expression of the reprogramming transcription factor Nanog by glioblastoma cells is shown to mediate the ability of c-Met to induce the stem cell characteristics of neurosphere formation and neurosphere cell self-renewal. These findings show that c-Met enhances the population of glioblastoma stem cells (GBM SCs) via a mechanism requiring Nanog and potentially other c-Met–responsive reprogramming transcription factors.
Dual amyloid domains promote differential functioning of the chaplin proteins duringStreptomycesaerial morphogenesis
Authors: Capstick David S. , Jomaa Ahmad , Hanke Chistopher , Ortega Joaquin , Elliot Marie A.
Published: June 2011

The chaplin proteins are functional amyloids found in the filamentousStreptomycesbacteria. These secreted proteins are required for the aerial development ofStreptomyces coelicolor, and contribute to an intricate rodlet ultrastructure that decorates the surfaces of aerial hyphae and spores.S. coelicolorencodes eight chaplin proteins. Previous studies have revealed that only three of these proteins (ChpC, ChpE, and ChpH) are necessary for promoting aerial development, and of these three, ChpH is the primary developmental determinant. Here, we show that the model chaplin, ChpH, contains two amyloidogenic domains: one in the N terminus and one in the C terminus of the mature protein. These domains have different polymerization properties as determined using fluorescence spectroscopy, secondary structure analyses, and electron microscopy. We coupled these in vitro assays with in vivo genetic studies to probe the connection between ChpH amyloidogenesis and its biological function. Using mutational analyses, we demonstrated that both N- and C-terminal amyloid domains of ChpH were required for promoting aerial hypha formation, while the N-terminal domain was dispensable for assembly of the rodlet ultrastructure. These results suggest that there is a functional differentiation of the dual amyloid domains in the chaplin proteins.
Benchmark map of forest carbon stocks in tropical regions across three continents
Authors: Saatchi Sassan S. , Harris Nancy L. , Brown Sandra , Lefsky Michael , Mitchard Edward T. A. , Salas William , Zutta Brian R. , Buermann Wolfgang , Lewis Simon L. , Hagen Stephen , Petrova Silvia , White Lee , Silman Miles , Morel Alexandra
Published: June 2011

Developing countries are required to produce robust estimates of forest carbon stocks for successful implementation of climate change mitigation policies related to reducing emissions from deforestation and degradation (REDD). Here we present a “benchmark” map of biomass carbon stocks over 2.5 billion ha of forests on three continents, encompassing all tropical forests, for the early 2000s, which will be invaluable for REDD assessments at both project and national scales. We mapped the total carbon stock in live biomass (above- and belowground), using a combination of data from 4,079 in situ inventory plots and satellite light detection and ranging (Lidar) samples of forest structure to estimate carbon storage, plus optical and microwave imagery (1-km resolution) to extrapolate over the landscape. The total biomass carbon stock of forests in the study region is estimated to be 247 Gt C, with 193 Gt C stored aboveground and 54 Gt C stored belowground in roots. Forests in Latin America, sub-Saharan Africa, and Southeast Asia accounted for 49%, 25%, and 26% of the total stock, respectively. By analyzing the errors propagated through the estimation process, uncertainty at the pixel level (100 ha) ranged from ±6% to ±53%, but was constrained at the typical project (10,000 ha) and national (>1,000,000 ha) scales atca. ±5% andca. ±1%, respectively. The benchmark map illustrates regional patterns and provides methodologically comparable estimates of carbon stocks for 75 developing countries where previous assessments were either poor or incomplete.
Ancient DNA reveals male diffusion through the Neolithic Mediterranean route
Authors: Lacan Marie , Keyser Christine , Ricaut François-Xavier , Brucato Nicolas , Duranthon Francis , Guilaine Jean , Crubézy Eric , Ludes Bertrand
Published: June 2011

The Neolithic is a key period in the history of the European settlement. Although archaeological and present-day genetic data suggest several hypotheses regarding the human migration patterns at this period, validation of these hypotheses with the use of ancient genetic data has been limited. In this context, we studied DNA extracted from 53 individuals buried in a necropolis used by a French local community 5,000 y ago. The relatively good DNA preservation of the samples allowed us to obtain autosomal, Y-chromosomal, and/or mtDNA data for 29 of the 53 samples studied. From these datasets, we established close parental relationships within the necropolis and determined maternal and paternal lineages as well as the absence of an allele associated with lactase persistence, probably carried by Neolithic cultures of central Europe. Our study provides an integrative view of the genetic past in southern France at the end of the Neolithic period. Furthermore, the Y-haplotype lineages characterized and the study of their current repartition in European populations confirm a greater influence of the Mediterranean than the Central European route in the peopling of southern Europe during the Neolithic transition.
Multilineage-differentiating stress-enduring (Muse) cells are a primary source of induced pluripotent stem cells in human fibroblasts
Authors: Wakao Shohei , Kitada Masaaki , Kuroda Yasumasa , Shigemoto Taeko , Matsuse Dai , Akashi Hideo , Tanimura Yukihiro , Tsuchiyama Kenichiro , Kikuchi Tomohiko , Goda Makoto , Nakahata Tatsutoshi , Fujiyoshi Yoshinori , Dezawa Mari
Published: June 2011

The stochastic and elite models have been proposed for the mechanism of induced pluripotent stem (iPS) cell generation. In this study we report a system that supports the elite model. We previously identified multilineage-differentiating stress-enduring (Muse) cells in human dermal fibroblasts that are characterized by stress tolerance, expression of pluripotency markers, self-renewal, and the ability to differentiate into endodermal-, mesodermal-, and ectodermal-lineage cells from a single cell. They can be isolated as stage-specific embryonic antigen-3/CD105 double-positive cells. When human fibroblasts were separated into Muse and non-Muse cells and transduced with
Oct3/4
,
Sox2
,
Klf4
, and
c-Myc
, iPS cells were generated exclusively from Muse cells but not from non-Muse cells. Although some colonies were formed from non-Muse cells, they were unlike iPS cells. Furthermore, epigenetic alterations were not seen, and some of the major pluripotency markers were not expressed for the entire period during iPS cell generation. These findings were confirmed further using cells transduced with a single polycistronic virus vector encoding all four factors. The results demonstrate that in adult human fibroblasts a subset of preexisting adult stem cells whose properties are similar in some respects to those of iPS cells selectively become iPS cells, but the remaining cells make no contribution to the generation of iPS cells. Therefore this system seems to fit the elite model rather than the stochastic model.
One-dimensional polaritons with size-tunable and enhanced coupling strengths in semiconductor nanowires
Authors: van Vugt Lambert K. , Piccione Brian , Cho Chang-Hee , Nukala Pavan , Agarwal Ritesh
Published: June 2011

Strong coupling of light with excitons in direct bandgap semiconductors leads to the formation of composite photonic-electronic quasi-particles (polaritons), in which energy oscillates coherently between the photonic and excitonic states with the vacuum Rabi frequency. The light-matter coherence is maintained until the oscillator dephases or the photon escapes. Exciton-polariton formation has enabled the observation of Bose-Einstein condensation in the solid-state, low-threshold polariton lasing and is also useful for terahertz and slow-light applications. However, maintaining coherence for higher carrier concentration and temperature applications still requires increased coupling strengths. Here, we report on size-tunable, exceptionally high exciton-polariton coupling strengths characterized by a vacuum Rabi splitting of up to 200 meV as well as a reduction in group velocity, in surface-passivated, self-assembled semiconductor nanowire cavities. These experiments represent systematic investigations on light-matter coupling in one-dimensional optical nanocavities, demonstrating the ability to engineer light-matter coupling strengths at the nanoscale, even in non-quantum-confined systems, to values much higher than in bulk.
Visualization of the nanospring dynamics of the IκBα ankyrin repeat domain in real time
Authors: Lamboy Jorge A. , Kim Hajin , Lee Kyung Suk , Ha Taekjip , Komives Elizabeth A.
Published: June 2011

IκBα is a crucial regulator of NFκB transcription. NFκB-mediated gene activation is robust because levels of free IκBα are kept extremely low by rapid, ubiquitin-independent degradation of newly synthesized IκBα. IκBα has a weakly folded ankyrin repeat 5–6 (AR5–6) region that is critical in establishing its short intracellular half-life. The AR5–6 region of IκBα folds upon binding to NFκB. The NFκB-bound IκBα has a long half-life and requires ubiquitin-targeted degradation. We present single molecule FRET evidence that the native state of IκBα transiently populates an intrinsically disordered state characterized by a more extended structure and fluctuations on the millisecond time scale. Binding to NFκB or introduction of stabilizing mutations in AR 6 suppressed the fluctuations, whereas higher temperature or small amounts of urea increased them. The results reveal that intrinsically disordered protein regions transition between collapsed and extended conformations under native conditions.
Mannose receptor polyubiquitination regulates endosomal recruitment of p97 and cytosolic antigen translocation for cross-presentation
Authors: Zehner Matthias , Chasan Achmet Imam , Schuette Verena , Embgenbroich Maria , Quast Thomas , Kolanus Waldemar , Burgdorf Sven
Published: June 2011

The molecular mechanisms regulating noncanonical protein transport across cellular membranes are poorly understood. Cross-presentation of exogenous antigens on MHC I molecules by dendritic cells (DCs) generally requires antigen translocation from the endosomal compartment into the cytosol for proteasomal degradation. In this study, we demonstrate that such translocation is controlled by the endocytic receptor and regulated by ubiquitination. Antigens internalized by the mannose receptor (MR), an endocytic receptor that targets its ligands specifically toward cross-presentation, were translocated into the cytosol only after attachment of a lysin48-linked polyubiquitin chain to the cytosolic region of the MR. Furthermore, we identify TSG101 as a central regulator of MR ubiquitination and antigen translocation. Importantly, we demonstrate that MR polyubiquitination mediates the recruitment of p97, a member of the ER-associated degradation machinery that provides the driving force for antigen translocation, toward the endosomal membrane, proving the central role of the endocytic receptor and its ubiquitination in antigen translocation.
Defects in coatomer protein I (COPI) transport cause blood feeding-induced mortality in Yellow Fever mosquitoes
Authors: Isoe Jun , Collins Jennifer , Badgandi Hemant , Day W. Anthony , Miesfeld Roger L.
Published: June 2011

Blood feeding by vector mosquitoes provides the entry point for disease pathogens and presents an acute metabolic challenge that must be overcome to complete the gonotrophic cycle. Based on recent data showing that coatomer protein I (COPI) vesicle transport is involved in cellular processes beyond Golgi–endoplasmic reticulum retrograde protein trafficking, we disrupted COPI functions in the Yellow Fever mosquito
Aedes aegypti
to interfere with blood meal digestion. Surprisingly, we found that decreased expression of the γCOPI coatomer protein led to 89% mortality in blood-fed mosquitoes by 72 h postfeeding compared with 0% mortality in control dsRNA-injected blood-fed mosquitoes and 3% mortality in γCOPI dsRNA-injected sugar-fed mosquitoes. Similar results were obtained using dsRNA directed against five other COPI coatomer subunits (α, β, β′, δ, and ζ). We also examined midgut tissues by EM, quantitated heme in fecal samples, and characterized feeding-induced protein expression in midgut, fat body, and ovary tissues of COPI-deficient mosquitoes. We found that COPI defects disrupt epithelial cell membrane integrity, stimulate premature blood meal excretion, and block induced expression of several midgut protease genes. To study the role of COPI transport in ovarian development, we injected γCOPI dsRNA after blood feeding and found that, although blood digestion was normal, follicles in these mosquitoes were significantly smaller by 48 h postinjection and lacked eggshell proteins. Together, these data show that COPI functions are critical to mosquito blood digestion and egg maturation, a finding that could also apply to other blood-feeding arthropod vectors.
Leisure Cards in England: An Unusual Combination of Commercial and Social Marketing?
Authors: Collins Michael Frank
Published: June 2011

The article examines how the mechanism of local Leisure Cards (LCs) operated by local authorities in England and Wales interestingly combine both commercial and social marketing functions. However, they could be much more potent in promoting sport in a sedentary and obesogenic society. Methods include national survey, case studies, and policy analysis. The article describes the quasicommercial marketing of the residents' tier of LCs, using loyalty devices, and the social marketing tier to attract deprived groups. It shows how tokenistic most card operations are, with few dedicated resources, and how the most effective cards carefully segment and target their markets; they offer a choice of sport, arts, and commercial activities, thereby attracting female and older users. The article argues that improved resources and clearer strategies could help usage of facilities and make a better contribution to very challenging government targets for increasing participation. It ponders the conundrum as to why social marketing has not been seen as useful in a field well used to commercial marketing. The article suggests that, unusually, LCs can combine commercial benefits to public leisure providers, and wider social benefits to frequently excluded groups. Although many cities offer tourists packages of discounts, and some social promotion program, there seems little or no research on their impact or efficacy in what is the most free-choice area of social life.
Using Social Marketing to Improve Breast-Feeding Rates in a Low Socioeconomic Area
Authors: Lowry Ray , Austin Julia , Patterson Molly
Published: June 2011

Breast-feeding rates have declined and remained low, especially in populations from low socioeconomic areas of the United Kingdom. The objective was to improve breast-feeding rates in a low socioeconomic area by using social marketing. Front-line clinical staff re-engineered the service they provided to potential breast-feeding women in their care using insights gained and skills developed with social marketing. In just three months, breast-feeding rates improved in the test community by 5% compared to controls. Using social marketing to develop a better breast-feeding product/service works effectively and quickly. Social marketing is often conflated with social advertising. This study shows that product/service development works well and that face-to-face promotion can achieve quick improvements in both outcomes and customer/staff satisfaction.
Investigation of structural and optical anisotropy of m-plane InN films grown on γ-LiAlO2(1 0 0) by metal organic chemical vapour deposition
Authors: Fu D , Zhang R , Liu B , Xie Z L , Xiu X Q , Gu S L , Lu H , Zheng Y D , Chen Y H , Wang Z G
Published: June 2011

In this paper a systematic investigation of structural and optical anisotropy of m-plane InN film grown on γ-LiAlO2(1 0 0) substrate by metal organic chemical vapour deposition, which is believed to be much more difficult than molecular beam epitaxy, is presented. The InN film showed pure m-plane phase as confirmed by x-ray diffraction ω/2θ scan together with polarized Raman spectroscopy. The epitaxial relationship between the m-plane InN and the substrate was found to be [0 0 0 1]InN ∥ [0 1 0]LAO and [1 1 − 2 0]InN ∥ [0 0 1]LAO. The inherent film mosaic anisotropy was studied by x-ray rocking curve analysis. Atomic force microscopy revealed that stripe-like features appear on the surface of the m-plane InN film, which originated from the replication of the surface morphological anisotropy of the substrate. Scanning electron microscopy showed blocky surface structures that were indicative of three-dimensional growth mode, which was related to the anisotropic structural mismatch of the film and the foreign substrate. A small direct band gap of ∼0.7 eV of the m-plane InN film was confirmed by low-temperature photoluminescence spectra, which showed evident polarization anisotropy in terms of both intensity and peak energy. Finally, a blue-shift of absorption edge as compared with the photoluminescence peak energy was observed and fully accounted for by the Burstein–Moss effect.
Almost periodic solutions to some second-order nonautonomous differential equations
Authors: Diagana Toka
Published: June 2011

This paper is concerned with the existence of almost periodic mild solutions to some second-order equations. Using dichotomy tools and the Schauder fixed point theorem, the existence of almost periodic mild solutions to those second-order evolution equations is established. To illustrate our abstract results, the existence of almost periodic solutions to a damped second-order boundary value problem is also discussed.
Principles of opioid titration
Authors: Fallon Marie , McConnell Sandra
Published: May 2011

There is great variation in the dose of opioid required by individual patients. Doses must be tailored to the individual’s need and should start low and then be adjusted (titrated) according to response-up or down. Short acting opioids should be used during the initial titration period and then converted to longer acting formulations when the required dose to achieve pain control is reached. Opioids are useful for neuropathic pain. Adjuvants have an important role in controlling some types of pain where opioids give insufficient analgesia or where adverse effects become intolerable.
Cardiovascular therapy techniques
Authors: Singer Mervyn , Webb Andrew R.
Published: May 2011

Abstracts and keywords to be supplied.
Oncological critical care
Authors: Singer Mervyn , Webb Andrew R.
Published: May 2011

Abstracts and keywords to be supplied.
Stem Cell Therapy Post-AMI
Authors: Menasché Philippe
Published: May 2011

• Experimental studies suggest that bone marrow-derived stem cells can improve function of infarcted myocardium

• This benefit seems to involve paracrine signalling and limitation of left ventricular remodelling rather than true regeneration of cardiomyocytes from donor cells

• These experimental findings have been translated in the clinical setting into significant, although moderate, improvements in cardiac function and LV remodelling but the extent to which these benefits impact on event-free long term survival remains to be determined

• Optimisation of this therapeutic strategy will require a more comprehensive characterisation of cell functionality and an improvement in the methods used in cell transfer, engraftment, survival and integration.
Corticosteroid Exposure Not Associated With Long‐term Bone Mineral Density in Pediatric Liver Transplantation
Authors: Nightingale Scott , McEwan‐Jackson Fiona D. , Hawker Gillian A. , Macarthur Colin , Khambalia Amina Z. , Lo Lisha , Fecteau Annie , Ng Vicky L.
Published: June 2011

Objectives:

The aim of the study was to examine the association of corticosteroid exposure and other skeletal risk factors with bone mineral density (BMD) and fractures following pediatric liver transplantation (LT) at a large single center.

Patients and Methods:

Lumbar spine BMD, measured using dual‐energy x‐ray absorptiometry (DXA), was corrected for bone age in 52 ambulatory children ages 4 to 18 years, at least 1 year post‐LT. Potential risk factors for skeletal health such as corticosteroid exposure, dietary and lifestyle factors, and growth and fracture occurrence, were related to BMD using univariate and multivariate regression analyses.

Results:

The prevalence of low BMD (z score <−2) and post‐LT fractures was 3 of 52 (5.8%) and 11 of 52 (21%), respectively. Univariate analysis revealed age >10 years at LT and body mass index (BMI) <85th percentile at time of DXA were significantly associated with BMD (both P = 0.02). BMD did not correlate with corticosteroid dosage in the first year post‐LT, the year before DXA or cumulative lifetime exposure. A cholestatic primary LT indication, acute rejection episodes, and fractures post‐LT were not associated with BMD. Extracurricular physical activity, vitamin D, and calcium intake were not associated with BMD or fractures. Multivariate linear regression revealed increased time post‐LT (P = 0.04) and higher BMI z score at time of DXA (P = 0.02) as the strongest independent variables associated with greater BMD.

Conclusions:

Neither corticosteroid exposure nor a cholestatic primary indication for LT influenced BMD, which was largely normal in this ambulatory group. Children and adolescents undergoing LT after the age of 10 years and those with low BMI post‐LT may be at greatest risk of poor skeletal health later in life, and thus a potential target patient population to benefit from preventive interventions.
William Ernest Burcham CBE. 1 August 1913 — 5 November 2008
Authors: Dowell J. D. , Griffith J. A. R. , Vinen W. F.
Published: June 2011

William Ernest Burcham, known almost always as Bill, was an experimental nuclear physicist whose research was chiefly concerned with nuclear reactions and with radioactive β-decay. As an undergraduate, research student and postdoctoral student he worked in the Cavendish Laboratory in Cambridge during the last few years of Lord Rutherford’s life. During World War II he was one of those who pioneered the use of centimetre wavelengths in airborne radar. As a university teacher after the war, first in Cambridge and then in Birmingham, he helped for more than 30 years to re-establish nuclear studies as an academic discipline in the UK.
Epidemiological game-theory dynamics of chickenpox vaccination in the USA and Israel
Authors: Liu Jingzhou , Kochin Beth F. , Tekle Yonas I. , Galvani Alison P.
Published: June 2011

The general consensus from epidemiological game-theory studies is that vaccination coverage driven by self-interest (Nash vaccination) is generally lower than group-optimal coverage (utilitarian vaccination). However, diseases that become more severe with age, such as chickenpox, pose an exception to this general consensus. An individual choice to be vaccinated against chickenpox has the potential to harm those not vaccinated by increasing the average age at infection and thus the severity of infection as well as those already vaccinated by increasing the probability of breakthrough infection. To investigate the effects of these externalities on the relationship between Nash and utilitarian vaccination coverages for chickenpox, we developed a game-theory epidemic model that we apply to the USA and Israel, which has different vaccination programmes, vaccination and treatment costs, as well as vaccination coverage levels. We find that the increase in chickenpox severity with age can reverse the typical relationship between utilitarian and Nash vaccination coverages in both the USA and Israel. Our model suggests that to obtain herd immunity of chickenpox vaccination, subsidies or external regulation should be used if vaccination costs are high. By contrast, for low vaccination costs, improving awareness of the vaccine and the potential cost of chickenpox infection is crucial.
Probing mechanical principles of focal contacts in cell–matrix adhesion with a coupled stochastic–elastic modelling framework
Authors: Gao Huajian , Qian Jin , Chen Bin
Published: June 2011

Cell–matrix adhesion depends on the collective behaviours of clusters of receptor–ligand bonds called focal contacts between cell and extracellular matrix. While the behaviour of a single molecular bond is governed by statistical mechanics at the molecular scale, continuum mechanics should be valid at a larger scale. This paper presents an overview of a series of recent theoretical studies aimed at probing the basic mechanical principles of focal contacts in cell–matrix adhesion via stochastic–elastic models in which stochastic descriptions of molecular bonds and elastic descriptions of interfacial traction–separation are unified in a single modelling framework. The intention here is to illustrate these principles using simple analytical and numerical models. The aim of the discussions is to provide possible clues to the following questions: why does the size of focal adhesions (FAs) fall into a narrow range around the micrometre scale? How can cells sense and respond to substrates of varied stiffness via FAs? How do the magnitude and orientation of mechanical forces affect the binding dynamics of FAs? The effects of cluster size, cell–matrix elastic modulus, loading direction and cytoskeletal pretension on the lifetime of FA clusters have been investigated by theoretical arguments as well as Monte Carlo numerical simulations, with results showing that intermediate adhesion size, stiff substrate, cytoskeleton stiffening, low-angle pulling and moderate cytoskeletal pretension are factors that contribute to stable FAs. From a mechanistic point of view, these results provide possible explanations for a wide range of experimental observations and suggest multiple mechanisms by which cells can actively control adhesion and de-adhesion via cytoskeletal contractile machinery in response to mechanical properties of their surroundings.
William Gilbert and ‘Magnetization by Percussion’
Authors: Mills Allan
Published: June 2011

In his
De Magnete
William Gilbert claims that it is possible to make a magnet by hammering a red-hot bar of wrought iron arranged north–south on an anvil. This is contrary to modern ideas concerning the ‘Curie temperature’ (770°C for carbon steel), and to the recognized susceptibility of steel magnets to mechanical abuse. It has proved impossible to replicate Gilbert's technique experimentally. Only lengthy cold hammering of hardened carbon steel specimens on a large ferrous anvil produced weak permanent magnets.
Prospective isolation of a bipotential clonogenic liver progenitor cell in adult mice
Authors: Dorrell Craig , Erker Laura , Schug Jonathan , Kopp Janel L. , Canaday Pamela S. , Fox Alan J. , Smirnova Olga , Duncan Andrew W. , Finegold Milton J. , Sander Maike , Kaestner Klaus H. , Grompe Markus
Published: June 2011

The molecular identification of adult hepatic stem/progenitor cells has been hampered by the lack of truly specific markers. To isolate putative adult liver progenitor cells, we used cell surface-marking antibodies, including MIC1-1C3, to isolate subpopulations of liver cells from normal adult mice or those undergoing an oval cell response and tested their capacity to form bilineage colonies in vitro. Robust clonogenic activity was found to be restricted to a subset of biliary duct cells antigenically defined as CD45−/CD11b−/CD31−/MIC1-1C3+/CD133+/CD26−, at a frequency of one of 34 or one of 25 in normal or oval cell injury livers, respectively. Gene expression analyses revealed that Sox9 was expressed exclusively in this subpopulation of normal liver cells and was highly enriched relative to other cell fractions in injured livers. In vivo lineage tracing using Sox9creERT2-R26RYFP mice revealed that the cells that proliferate during progenitor-driven liver regeneration are progeny of Sox9-expressing precursors. A comprehensive array-based comparison of gene expression in progenitor-enriched and progenitor-depleted cells from both normal and DDC (3,5-diethoxycarbonyl-1,4-dihydrocollidine or diethyl1,4-dihydro-2,4,6-trimethyl-3,5-pyridinedicarboxylate)-treated livers revealed new potential regulators of liver progenitors.
Reading TE leaves: New approaches to the identification of transposable element insertions
Authors: Ray David A. , Batzer Mark A.
Published: June 2011

Transposable elements (TEs) are a tremendous source of genome instability and genetic variation. Of particular interest to investigators of human biology and human evolution are retrotransposon insertions that are recent and/or polymorphic in the human population. As a consequence, the ability to assay large numbers of polymorphic TEs in a given genome is valuable. Five recent manuscripts each propose methods to scan whole human genomes to identify, map, and, in some cases, genotype polymorphic retrotransposon insertions in multiple human genomes simultaneously. These technologies promise to revolutionize our ability to analyze human genomes for TE-based variation important to studies of human variability and human disease. Furthermore, the approaches hold promise for researchers interested in nonhuman genomic variability. Herein, we explore the methods reported in the manuscripts and discuss their applications to aspects of human biology and the biology of other organisms.
Genome-wide identification of conserved regulatory function in diverged sequences
Authors: Taher Leila , McGaughey David M. , Maragh Samantha , Aneas Ivy , Bessling Seneca L. , Miller Webb , Nobrega Marcelo A. , McCallion Andrew S. , Ovcharenko Ivan
Published: June 2011

Plasticity of gene regulatory encryption can permit DNA sequence divergence without loss of function. Functional information is preserved through conservation of the composition of transcription factor binding sites (TFBS) in a regulatory element. We have developed a method that can accurately identify pairs of functional noncoding orthologs at evolutionarily diverged loci by searching for conserved TFBS arrangements. With an estimated 5% false-positive rate (FPR) in approximately 3000 human and zebrafish syntenic loci, we detected approximately 300 pairs of diverged elements that are likely to share common ancestry and have similar regulatory activity. By analyzing a pool of experimentally validated human enhancers, we demonstrated that 7/8 (88%) of their predicted functional orthologs retained in vivo regulatory control. Moreover, in 5/7 (71%) of assayed enhancer pairs, we observed concordant expression patterns. We argue that TFBS composition is often necessary to retain and sufficient to predict regulatory function in the absence of overt sequence conservation, revealing an entire class of functionally conserved, evolutionarily diverged regulatory elements that we term “covert.”
From IMGT-ONTOLOGY IDENTIFICATION Axiom to IMGT Standardized Keywords: For Immunoglobulins (IG), T Cell Receptors (TR), and Conventional Genes
Authors: Lefranc Marie-Paule
Published: June 2011

INTRODUCTION

IMGT standardized keywords have been defined for the identification of immunoglobulins (IG) and T cell receptors (TR) and conventional genes. These keywords are based on the concepts of identification, generated from the IDENTIFICATION axiom of the Formal IMGT-ONTOLOGY or IMGT-Kaleidoscope that postulates that any molecule, cell, tissue, organ, organism, or population, any process and any relation, has to be identified. Most of the IMGT standardized keywords used for the identification of sequences and structures are names of IMGT-ONTOLOGY leafconcepts (a leafconcept is a concept that corresponds to the finest level of granularity). IMGT standardized keywords have been essential for the data entries into the IMGT databases and tools, and particularly into IMGT/LIGM-DB, the first and the largest IMGT database that contains IG and TR nucleotide sequences and the translation of annotated sequences. IMGT standardized keywords for IG, TR, and conventional genes are defined in the context of the IMGT-ONTOLOGY concepts of identification.
IMGT Unique Numbering for the Variable (V), Constant (C), and Groove (G) Domains of IG, TR, MH, IgSF, and MhSF
Authors: Lefranc Marie-Paule
Published: June 2011

INTRODUCTION

The “IMGT unique numbering” (or “IMGT_unique_numbering”) concept is a major concept of numerotation (generated from the NUMEROTATION axiom) of IMGT-ONTOLOGY, the global reference in immunogenetics and immunoinformatics, built by IMGT, the international ImMunoGeneTics information system. The “IMGT unique numbering” concept, described here, allows one to number domain types that are characteristic of protein superfamilies, whatever the species, the molecule type or the chain type. Three leafconcepts (a leafconcept is a concept that corresponds to the finest level of granularity) have been defined, respectively, for the variable (V) domain and constant (C) domain of the immunoglobulin superfamily (IgSF) and for the groove (G) domain of the major histocompatibility (MH) superfamily (MhSF). The IMGT unique numbering concept has been a great breakthrough in immunogenetics and systems biology in allowing, for the first time, the bridging of the gap between amino acid (and nucleotide) sequences of any V, C, or G domain and their two-dimensional (2D) and three-dimensional (3D) structures. The IMGT unique numbering concept has been fundamental in the creation of the IMGT Collier de Perles and in the standardization of the description of mutations, amino acid changes, polymorphisms, and contact analysis in the IMGT databases, tools, and web resources.
iTRAQ-Labeled Yeast Peptide Clean-Up Using a Reversed-Phase Column
Authors: Simon Eric S.
Published: June 2011

INTRODUCTION

A commercial reagent, known as the isobaric tag for relative and absolute quantification (iTRAQ), makes it possible to analyze multiple samples simultaneously. The ability of iTRAQ to compare relative protein abundances across as many as eight samples is a significant advantage over other stable isotope strategies, such as stable isotope labeling by amino acids in cell culture (SILAC) and isotope-coded affinity tag (ICAT). The iTRAQ protocol set compares the proteome of Saccharomyces cerevisiae under two different metabolic states (fermentation versus respiration) with the goal of determining the proteins involved in each of the activated pathways by measuring their relative abundances using iTRAQ. Before using isoelectric focusing (IEF) to fractionate the iTRAQ-labeled peptides, the sample needs to be cleaned up because it contains a high concentration of buffer (500 mM triethylammonium bicarbonate), excess reagents from the reduction and alkylation of the proteins, and degradation products of the iTRAQ reagents. All of these are incompatible with IEF. To remove them, the sample is passed over a reversed-phase C18 column. This protocol describes this procedure.
Isoelectric Focusing of iTRAQ-Labeled Yeast
Authors: Simon Eric S.
Published: June 2011

INTRODUCTION

A commercial reagent, known as the isobaric tag for relative and absolute quantification (iTRAQ), makes it possible to analyze multiple samples simultaneously. The ability of iTRAQ to compare relative protein abundances across as many as eight samples is a significant advantage over other stable isotope strategies, such as stable isotope labeling by amino acids in cell culture (SILAC) and isotope-coded affinity tag (ICAT). The iTRAQ protocol set compares the proteome of Saccharomyces cerevisiae under two different metabolic states (fermentation versus respiration) with the goal of determining the proteins involved in each of the activated pathways by measuring their relative abundances using iTRAQ. This protocol describes fractionation of the iTRAQ-labeled proteins by isoelectric focusing (IEF) on immobilized pH gradient (IPG) strips using an OFFGEL Fractionator.
IMGT/V-QUEST: IMGT Standardized Analysis of the Immunoglobulin (IG) and T Cell Receptor (TR) Nucleotide Sequences
Authors: Giudicelli Véronique , Brochet Xavier , Lefranc Marie-Paule
Published: June 2011

INTRODUCTION

IMGT/V-QUEST is the integrated online IMGT tool for the standardized analysis of the immunoglobulin (IG) or antibody and T cell receptor (TR) rearranged nucleotide sequences. The analysis of these antigen receptors represents a crucial challenge for the study of the adaptative immune response in normal and disease-related situations. The expressed IG and TR repertoires represent a potential of 1012 IG and 1012 TR per individual. This huge diversity results from mechanisms that occur at the DNA level during IG molecular synthesis, including the combinatorial rearrangement of the variable (V), diversity (D), and joining (J) genes, the N diversity (V, D, and J exonuclease trimming and addition at random of nucleotides by the terminal deoxynucleotidyl transferase during the V-(D)-J rearrangement) and, for IG, somatic hypermutations. IMGT/V-QUEST, as described here, identifies the V, D, J genes and alleles by alignment with the germline IG and TR gene and allele sequences of the IMGT reference directory. The tool describes the V-REGION mutations and identifies the hot spot positions in the closest germline V gene. IMGT/V-QUEST integrates IMGT/JunctionAnalysis for a detailed analysis of the V-J and V-D-J junctions and IMGT/Automat for a complete sequence annotation of the sequences, and provides IMGT Collier de Perles.
Arabidopsis Pht1;5 Mobilizes Phosphate between Source and Sink Organs and Influences the Interaction between Phosphate Homeostasis and Ethylene Signaling
Authors: Nagarajan Vinay K. , Jain Ajay , Poling Michael D. , Lewis Anthony J. , Raghothama Kashchandra G. , Smith Aaron P.
Published: June 2011

Phosphorus (P) remobilization in plants is required for continuous growth and development. The Arabidopsis (Arabidopsis thaliana) inorganic phosphate (Pi) transporter Pht1;5 has been implicated in mobilizing stored Pi out of older leaves. In this study, we used a reverse genetics approach to study the role of Pht1;5 in Pi homeostasis. Under low-Pi conditions, Pht1;5 loss of function (pht1;5-1) resulted in reduced P allocation to shoots and elevated transcript levels for several Pi starvation-response genes. Under Pi-replete conditions, pht1;5-1 had higher shoot P content compared with the wild type but had reduced P content in roots. Constitutive overexpression of Pht1;5 had the opposite effect on P distribution: namely, lower P levels in shoots compared with the wild type but higher P content in roots. Pht1;5 overexpression also resulted in altered Pi remobilization, as evidenced by a greater than 2-fold increase in the accumulation of Pi in siliques, premature senescence, and an increase in transcript levels of genes involved in Pi scavenging. Furthermore, Pht1;5 overexpressors exhibited increased root hair formation and reduced primary root growth that could be rescued by the application of silver nitrate (ethylene perception inhibitor) or aminoethoxyvinylglycine (ethylene biosynthesis inhibitor), respectively. Together, these data indicate that Pht1;5 plays a critical role in mobilizing Pi from P source to sink organs in accordance with developmental cues and P status. The study also provides evidence for a link between Pi and ethylene signaling pathways.
The Pepper E3 Ubiquitin Ligase RING1 Gene,CaRING1, Is Required for Cell Death and the Salicylic Acid-Dependent Defense Response
Authors: Lee Dong Hyuk , Choi Hyong Woo , Hwang Byung Kook
Published: June 2011

Ubiquitination is essential for ubiquitin/proteasome-mediated protein degradation in plant development and defense. Here, we identified a novel E3 ubiquitin ligase RING1 gene, CaRING1, from pepper (Capsicum annuum). In pepper, CaRING1 expression is induced by avirulent Xanthomonas campestris pv vesicatoria infection. CaRING1 contains an amino-terminal transmembrane domain and a carboxyl-terminal RING domain. In addition, it displays in vitro E3 ubiquitin ligase activity, and the RING domain is essential for E3 ubiquitin ligase activity in CaRING1. CaRING1 also localizes to the plasma membrane. In pepper plants, virus-induced gene silencing of CaRING1 confers enhanced susceptibility to avirulent X. campestris pv vesicatoria infection, which is accompanied by compromised hypersensitive cell death, reduced expression of PATHOGENESIS-RELATED1, and lowered salicylic acid levels in leaves. Transient expression of CaRING1 in pepper leaves induces cell death and the defense response that requires the E3 ubiquitin ligase activity of CaRING1. By contrast, overexpression of CaRING1 in Arabidopsis (Arabidopsis thaliana) confers enhanced resistance to hemibiotrophic Pseudomonas syringae pv tomato and biotrophic Hyaloperonospora arabidopsidis infections. Taken together, these results suggest that CaRING1 is involved in the induction of cell death and the regulation of ubiquitination during the defense response to microbial pathogens.
Global research neglect of population‐based approaches to smoking cessation: time for a more rigorous science of population health interventions
Authors: Lawrence David , Mitrou Francis , Zubrick Stephen R.
Published: June 2011

It has been argued that the preponderance of studies into individual smoking cessation therapies seems grossly out of proportion to the number of people who use these therapies to quit smoking, and that this imbalance is due to factors such as the role of the pharmaceutical industry in funding research and a general bias towards individual‐ rather than population‐based approaches to medical and health problems. We believe that there are other significant factors that affect the balance of research in smoking cessation, such as the higher standards of evidence required to justify the implementation of individual medical therapies compared with population‐based interventions. We argue that research practitioners in the area of population tobacco control are well placed to address this imbalance by setting more rigorous standards of evidence for population health interventions. This could be achieved by setting aside a small proportion of funds from population health and advocacy activities to invest in studying their effectiveness. We believe that this would potentially return information of sufficient value to justify increasing overall population investment beyond the cost of the additional research component. Additional benefits would be gained from increased research in this area, such as better understanding of how to translate tobacco control initiatives to developing countries with high smoking rates, and how to target disadvantaged and marginalized populations more effectively in developed countries that continue to have high rates of smoking and low rates of smoking cessation, despite the existence of broad population‐based strategies.
A policy‐oriented review of strategies for improving the outcomes of services for substance use disorder patients*
Authors: Humphreys Keith , McLellan A. Thomas
Published: June 2011

Aims  To inform policy makers on available options for improving the effectiveness of treatments for substance use disorders and to stimulate debate about treatment improvement strategies among public officials, clinical providers, care managers, service users, families and researchers.

Methods  We draw on the scientific literature and our public policy experiences in two countries (the United Kingdom and the United States) to give an overview of policies which may improve care for individuals with substance use disorders. We divide such policies into ‘process‐focused quality improvement strategies’ that attempt to change some aspect of treatment (e.g. increased retention, greater use of evidence‐based practices) and ‘patient‐focused strategies’ that attempt to reward outcomes directly (e.g. contingency management for patients, payment by results for providers).

Findings  Many policies of both types are poorly developed, have shown poor results, or both. The evidence is clear that process‐focused quality improvement strategies can change what providers do and how treatment programs work, but such changes have thus far demonstrated only minimal impact on patient outcomes. Patient‐focused strategies face challenges including treatment providers avoiding hard‐to‐treat patients or spending inordinate time relocating patients after treatment to assess outcome. However, policies that reward in‐treatment outcomes and policies that allow the patient to purchase desired recovery support services show more promise. As policy makers go forward in this endeavor, they can do an enormous service to their countries and the field by embedding careful evaluation studies alongside new treatment outcome improvement initiatives.