bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks
Authors: Yan Koon-Kiu , Fang Gang , Bhardwaj Nitin , Alexander Roger P. , Gerstein Mark
Published: May 2010

The genome has often been called the operating system (OS) for a living organism. A computer OS is described by a regulatory control network termed the call graph, which is analogous to the transcriptional regulatory network in a cell. To apply our firsthand knowledge of the architecture of software systems to understand cellular design principles, we present a comparison between the transcriptional regulatory network of a well-studied bacterium (
Escherichia coli
) and the call graph of a canonical OS (Linux) in terms of topology and evolution. We show that both networks have a fundamentally hierarchical layout, but there is a key difference: The transcriptional regulatory network possesses a few global regulators at the top and many targets at the bottom; conversely, the call graph has many regulators controlling a small set of generic functions. This top-heavy organization leads to highly overlapping functional modules in the call graph, in contrast to the relatively independent modules in the regulatory network. We further develop a way to measure evolutionary rates comparably between the two networks and explain this difference in terms of network evolution. The process of biological evolution via random mutation and subsequent selection tightly constrains the evolution of regulatory network hubs. The call graph, however, exhibits rapid evolution of its highly connected generic components, made possible by designers’ continual fine-tuning. These findings stem from the design principles of the two systems: robustness for biological systems and cost effectiveness (reuse) for software systems.
Ultraviolet A does not induce melanomas in a
Xiphophorus
hybrid fish model
Authors: Mitchell David L. , Fernandez André A. , Nairn Rodney S. , Garcia Rachel , Paniker Lakshmi , Trono David , Thames Howard D. , Gimenez-Conti Irma
Published: May 2010

We examined the wavelength dependence of ultraviolet (UV) ra-diation (UVR)-induced melanoma in a
Xiphophorus
backcross hybrid model previously reported to be susceptible to melanoma induction by ultraviolet A (UVA) and visible light. Whereas ultraviolet B (UVB) irradiation of neonates yielded high frequencies of melanomas in pigmented fish, UVA irradiation resulted in melanoma frequencies that were not significantly different from unirradiated fish. Spontaneous and UV-induced melanoma frequencies correlated with the degree of pigmentation as expected from previous studies, and the histopathology phenotypes of the melanomas were not found in significantly different proportions in UV-treated and -untreated tumor-bearing fish. Our results support the conclusion that a brief early-life exposure to UVB radiation causes melanoma formation in this animal model. These data are consistent with an essential role for direct DNA damage, including cyclobutane dimers and (6-4) photoproducts, in the etiology of melanoma.
Dnmt3b recruitment through E2F6 transcriptional repressor mediates germ-line gene silencing in murine somatic tissues
Authors: Velasco Guillaume , Hubé Florent , Rollin Jérôme , Neuillet Damien , Philippe Cathy , Bouzinba-Segard Haniaa , Galvani Angélique , Viegas-Péquignot Evani , Francastel Claire
Published: May 2010

Methylation of cytosine residues within the CpG dinucleotide in mammalian cells is an important mediator of gene expression, genome stability, X-chromosome inactivation, genomic imprinting, chromatin structure, and embryonic development. The majority of CpG sites in mammalian cells is methylated in a nonrandom fashion, raising the question of how DNA methylation is distributed along the genome. Here, we focused on the functions of DNA methyltransferase-3b (Dnmt3b), of which deregulated activity is linked to several human pathologies. We generated Dnmt3b hypomorphic mutant mice with reduced catalytic activity, which first revealed a deregulation of
Hox
genes expression, consistent with the observed homeotic transformations of the posterior axis. In addition, analysis of deregulated expression programs in Dnmt3b mutant embryos, using DNA microarrays, highlighted illegitimate activation of several germ-line genes in somatic tissues that appeared to be linked directly to their hypomethylation in mutant embryos. We provide evidence that these genes are direct targets of Dnmt3b. Moreover, the recruitment of Dnmt3b to their proximal promoter is dependant on the binding of the E2F6 transcriptional repressor, which emerges as a common hallmark in the promoters of genes found to be up-regulated as a consequence of impaired Dnmt3b activity. Therefore, our results unraveled a coordinated regulation of genes involved in meiosis, through E2F6-dependant methylation and transcriptional silencing in somatic tissues.
A prehydrolysis state of an AAA+ ATPase supports transcription activation of an enhancer-dependent RNA polymerase
Authors: Burrows Patricia C. , Joly Nicolas , Buck Martin
Published: May 2010

ATP hydrolysis-dependent molecular machines and motors often drive regulated conformational transformations in cell signaling and gene regulation complexes. Conformational reorganization of a gene regulation complex containing the major variant form of bacterial RNA polymerase (RNAP), Eσ
54
, requires engagement with its cognate ATP-hydrolyzing activator protein. Importantly, this activated RNAP is essential for a number of adaptive responses, including those required for bacterial pathogenesis. Here we characterize the initial encounter between the enhancer-dependent Eσ
54
and its cognate activator AAA+ ATPase protein, before ADP+P
i
formation, using a small primed RNA (spRNA) synthesis assay. The results show that in a prehydrolysis state, sufficient activator-dependent rearrangements in Eσ
54
have occurred to allow engagement of the RNAP active site with single-stranded promoter DNA to support spRNA synthesis, but not to melt the promoter DNA. This catalytically competent transcription intermediate has similarity with the open promoter complex, in that the RNAP dynamics required for DNA scrunching should be occurring. Significantly, this work highlights that prehydrolysis states of ATPases are functionally important in the molecular transformations they drive.
Real-time multidimensional NMR follows RNA folding with second resolution
Authors: Lee Mi-Kyung , Gal Maayan , Frydman Lucio , Varani Gabriele
Published: May 2010

Conformational transitions and structural rearrangements are central to the function of many RNAs yet remain poorly understood. We have used ultrafast multidimensional NMR techniques to monitor the adenine-induced folding of an adenine-sensing riboswitch in real time, with nucleotide-resolved resolution. By following changes in 2D spectra at rates of approximately 0.5 Hz, we identify distinct steps associated with the ligand-induced folding of the riboswitch. Following recognition of the ligand, long range loop-loop interactions form and are then progressively stabilized before the formation of a fully stable complex over approximately 2–3 minutes. The application of these ultrafast multidimensional NMR methods provides the opportunity to determine the structure of RNA folding intermediates and conformational trajectories.
Single residue within the antigen translocation complex TAP controls the epitope repertoire by stabilizing a receptive conformation
Authors: Baldauf Christoph , Schrodt Susanne , Herget Meike , Koch Joachim , Tampé Robert
Published: May 2010

The recognition of virus infected or malignantly transformed cells by cytotoxic T lymphocytes critically depends on the transporter associated with antigen processing (TAP), which delivers proteasomal degradation products into the endoplasmic reticulum lumen for subsequent loading of major histocompatibility complex class I molecules. Here we have identified a single cysteinyl residue in the TAP complex that modulates peptide binding and translocation, thereby restricting the epitope repertoire. Cysteine 213 in human TAP2 was found to be part of a newly uncovered substrate-binding site crucial for peptide recognition. This residue contacts the peptide in the binding pocket in an orientated manner. The translocation complex can be reversibly inactivated by thiol modification of this cysteinyl residue. As part of an unexpected mechanism, this residue is crucial in complementing the binding pocket for a given subset of epitopes as well as in maintaining a substrate-receptive conformation of the translocation complex.
Behavioral insensitivity to DEET in
Aedes aegypti
is a genetically determined trait residing in changes in sensillum function
Authors: Stanczyk Nina M. , Brookfield John F. Y. , Ignell Rickard , Logan James G. , Field Linda M.
Published: May 2010

N,N
-Diethyl-
m
-toluamide (DEET) is one of the most effective and commonly used mosquito repellents. However, during laboratory trials a small proportion of mosquitoes are still attracted by human odors despite the presence of DEET. In this study behavioral assays identified
Aedes aegypti
females that were insensitive to DEET, and the selection of either sensitive or insensitive groups of females with males of unknown sensitivity over several generations resulted in two populations with different proportions of insensitive females. Crossing experiments showed the “insensitivity” trait to be dominant. Electroantennography showed a reduced response to DEET in the selected insensitive line compared with the selected sensitive line, and single sensillum recordings identified DEET-sensitive sensilla that were nonresponders in the insensitive line. This study suggests that behavioral insensitivity to DEET in
A. aegypti
is a genetically determined dominant trait and resides in changes in sensillum function.
A distinct DGAT with
sn
-3 acetyltransferase activity that synthesizes unusual, reduced-viscosity oils in
Euonymus
and transgenic seeds
Authors: Durrett Timothy P. , McClosky Daniel D. , Tumaney Ajay W. , Elzinga Dezi A. , Ohlrogge John , Pollard Mike
Published: May 2010

Endosperm and embryo tissues from the seeds of
Euonymus alatus
(Burning Bush) accumulate high levels of 3-acetyl-1,2-diacyl-
sn
-glycerols (acTAGs) as their major storage lipids. In contrast, the aril tissue surrounding the seed produces long-chain triacylglycerols (lcTAGs) typical of most other organisms. The presence of the
sn
-3 acetyl group imparts acTAGs with different physical and chemical properties, such as a 30% reduction in viscosity, compared to lcTAGs. Comparative transcriptome analysis of developing endosperm and aril tissues using pyrosequencing technology was performed to isolate the enzyme necessary for the synthesis of acTAGs. An uncharacterized membrane-bound
O
-acyltransferase (MBOAT) family member was the most abundant acyltransferase in the endosperm but was absent from the aril. Expression of this MBOAT in yeast resulted in the accumulation of acTAGs but not lcTAG; hence, the enzyme was named EaDAcT (
Euonymus alatus d
iacylglycerol
ac
etyl
t
ransferase). Yeast microsomes expressing EaDAcT possessed acetyl-CoA diacylglycerol acetyltransferase activity but lacked long-chain acyl-CoA diacylglycerol acyltransferase activity. Expression of EaDAcT under the control of a strong, seed-specific promoter in
Arabidopsis
resulted in the accumulation of acTAGs, up to 40 mol % of total TAG in the seed oil. These results demonstrate the utility of deep transcriptional profiling with multiple tissues as a gene discovery strategy for low-abundance proteins. They also show that EaDAcT is the acetyltransferase necessary and sufficient for the production of acTAGs in
Euonymus
seeds, and that this activity can be introduced into the seeds of other plants, allowing the evaluation of these unusual TAGs for biofuel and other applications.
A mechanistic account of value computation in the human brain
Authors: Philiastides Marios G. , Biele Guido , Heekeren Hauke R.
Published: May 2010

To make decisions based on the value of different options, we often have to combine different sources of probabilistic evidence. For example, when shopping for strawberries on a fruit stand, one uses their color and size to infer—with some uncertainty—which strawberries taste best. Despite much progress in understanding the neural underpinnings of value-based decision making in humans, it remains unclear how the brain represents different sources of probabilistic evidence and how they are used to compute value signals needed to drive the decision. Here, we use a visual probabilistic categorization task to show that regions in ventral temporal cortex encode probabilistic evidence for different decision alternatives, while ventromedial prefrontal cortex integrates information from these regions into a value signal using a difference-based comparator operation.
Visualization and structural analysis of the bacterial magnetic organelle magnetosome using atomic force microscopy
Authors: Yamamoto Daisuke , Taoka Azuma , Uchihashi Takayuki , Sasaki Hideaki , Watanabe Hiroki , Ando Toshio , Fukumori Yoshihiro
Published: May 2010

The unique ability of magnetotactic bacteria to navigate along a geomagnetic field is accomplished with the help of prokaryotic organelles, magnetosomes. The magnetosomes have well-ordered chain-like structures, comprising membrane-enveloped, nano-sized magnetic crystals, and various types of specifically associated proteins. In this study, we applied atomic force microscopy (AFM) to investigate the spatial configuration of isolated magnetosomes from
Magnetospirillum magneticum
AMB-1 in near-native buffer conditions. AFM observation revealed organic material with a ∼7-nm thickness surrounding a magnetite crystal. Small globular proteins, identified as magnetosome-associated protein MamA, were distributed on the mica surface around the magnetosome. Immuno-labeling with AFM showed that MamA is located on the magnetosome surface. In vitro experiments showed that MamA proteins interact with each other and form a high molecular mass complex. These findings suggest that magnetosomes are covered with MamA oligomers in near-native environments. Furthermore, nanodissection revealed that magnetosomes are built with heterogeneous structures that comprise the organic layer. This study provides important clues to the supramolecular architecture of the bacterial organelle, the magnetosome, and insight into the function of the proteins localized in the organelle.
The Copenhagen Accord for limiting global warming: Criteria, constraints, and available avenues
Authors: Ramanathan Veerabhadran , Xu Yangyang
Published: May 2010

At last, all the major emitters of greenhouse gases (GHGs) have agreed under the Copenhagen Accord that global average temperature increase should be kept below 2 °C. This study develops the criteria for limiting the warming below 2 °C, identifies the constraints imposed on policy makers, and explores available mitigation avenues. One important criterion is that the radiant energy added by human activities should not exceed 2.5 (range: 1.7–4) watts per square meter (Wm
−2
) of the Earth's surface. The blanket of man-made GHGs has already added 3 (range: 2.6–3.5) Wm
−2
. Even if GHG emissions peak in 2015, the radiant energy barrier will be exceeded by 100%, requiring simultaneous pursuit of three avenues: (
i
) reduce the rate of thickening of the blanket by stabilizing CO
2
concentration below 441 ppm during this century (a massive decarbonization of the energy sector is necessary to accomplish this Herculean task), (
ii
) ensure that air pollution laws that reduce the masking effect of cooling aerosols be made radiant energy-neutral by reductions in black carbon and ozone, and (
iii
) thin the blanket by reducing emissions of short-lived GHGs. Methane and hydrofluorocarbons emerge as the prime targets. These actions, even if we are restricted to available technologies for avenues
ii
and
iii
, can reduce the probability of exceeding the 2 °C barrier before 2050 to less than 10%, and before 2100 to less than 50%. With such actions, the four decades we have until 2050 should be exploited to develop and scale-up revolutionary technologies to restrict the warming to less than 1.5 °C.
Pregnancy induces a fetal antigen-specific maternal T regulatory cell response that contributes to tolerance
Authors: Kahn Daniel A. , Baltimore David
Published: May 2010

A fetus is inherently antigenic to its mother and yet is not rejected. The T regulatory (Treg) subset of CD4+T cells can limit immune responses and has been implicated in maternal tolerance of the fetus. Using virgin inbred mice undergoing a first syngenic pregnancy, in which only the male fetuses are antigenic, we demonstrate a maternal splenocyte proliferative response to the CD4+T cell restricted epitope of the male antigen (H-Y) in proportion to the fetal antigen load. A portion of the maternal immune response to fetal antigens is Treg in nature. The bystander suppressive function of pregnancy-generated Tregs requires the presence of the fetal antigen, demonstrating their inherent antigen specificity. In vivo targeting of diphtheria toxin to kill Tregs leads to a lower fraction of live male offspring and a selective reduction in mass of the surviving males. Thus, Tregs generated in the context of pregnancy function in an antigen-specific manner to limit the maternal immune response to the fetus in a successful pregnancy.
Electrophilic tuning of the chemoprotective natural product sulforaphane
Authors: Ahn Young-Hoon , Hwang Yousang , Liu Hua , Wang Xiu Jun , Zhang Ying , Stephenson Katherine K. , Boronina Tatiana N. , Cole Robert N. , Dinkova-Kostova Albena T. , Talalay Paul , Cole Philip A.
Published: May 2010

Sulforaphane [1-isothiocyanato-4-(methylsulfinyl)butane], a naturally occurring isothiocyanate derived from cruciferous vegetables, is a highly potent inducer of phase 2 cytoprotective enzymes and can protect against electrophiles including carcinogens, oxidative stress, and inflammation. The mechanism of action of sulforaphane is believed to involve modifications of critical cysteine residues of Keap1, which lead to stabilization of Nrf2 to activate the antioxidant response element of phase 2 enzymes. However, the dithiocarbamate functional group formed by a reversible reaction between isothiocyanate of sulforaphane and sulfhydryl nucleophiles of Keap1 is kinetically labile, and such modification in intact cells has not yet been demonstrated. Here we designed sulforaphane analogs with replacement of the reactive isothiocyanate by the more gentle electrophilic sulfoxythiocarbamate group that also selectively targets cysteine residues in proteins but forms stable thiocarbamate adducts. Twenty-four sulfoxythiocarbamate analogs were synthesized that retain the structural features important for high potency in sulforaphane analogs: the sulfoxide or keto group and its appropriate distance to electrophilic functional group. Evaluation in various cell lines including hepatoma cells, retinal pigment epithelial cells, and keratinocytes as well as in mouse skin shows that these analogs maintain high potency and efficacy for phase 2 enzyme induction as well as the inhibitory effect on lipopolysaccharide-induced nitric oxide formation like sulforaphane. We further show in living cells that a sulfoxythiocarbamate analog can label Keap1 on several key cysteine residues as well as other cellular proteins offering new insights into the mechanism of chemoprotection.
Hepatitis B virus core antigen determines viral persistence in a C57BL/6 mouse model
Authors: Lin Yi-Jiun , Huang Li-Rung , Yang Hung-Chih , Tzeng Horng-Tay , Hsu Ping-Ning , Wu Hui-Lin , Chen Pei-Jer , Chen Ding-Shinn
Published: May 2010

We recently developed a mouse model of hepatitis B virus (HBV) persistence, in which a single i.v. hydrodynamic injection of HBV DNA to C57BL/6 mice allows HBV replication and induces a partial immune response, so that about 20–30% of the mice carry HBV for more than 6 months. The model was used to identify the viral antigen crucial for HBV persistence. We knocked out individual HBV genes by introducing a premature termination codon to the HBV core, HBeAg, HBx, and polymerase ORFs. The specific-gene-deficient HBV mutants were hydrodynamically injected into mice and the HBV profiles of the mice were monitored. About 90% of the mice that received the HBcAg-mutated HBV plasmid exhibited high levels of hepatitis B surface antigenemia and maintained HBsAg expression for more than 6 months after injection. To map the region of HBcAg essential for viral clearance, we constructed a set of serial HBcAg deletion mutants for hydrodynamic injection. We localized the essential region of HBcAg to the carboxyl terminus, specifically to the 10 terminal amino acids (HBcAg176–185). The majority of mice receiving this HBV mutant DNA did not elicit a proper HBcAg-specific IFN-γ response and expressed HBV virions for 6 months. These results indicate that the immune response triggered in mice by HBcAg during exposure to HBV is important in determining HBV persistence.
Christine Jacobs-Wagner: Drawing the bacterial organizational chart
Authors: Short Ben
Published: May 2010

Jacobs-Wagner has been at the forefront of a revolution in bacterial cell biology.
Mutant huntingtin impairs Ku70-mediated DNA repair
Authors: Enokido Yasushi , Tamura Takuya , Ito Hikaru , Arumughan Anup , Komuro Akihiko , Shiwaku Hiroki , Sone Masaki , Foulle Raphaele , Sawada Hirohide , Ishiguro Hiroshi , Ono Tetsuya , Murata Miho , Kanazawa Ichiro , Tomilin Nikolai , Tagawa Kazuhiko , Wanker Erich E. , Okazawa Hitoshi
Published: May 2010

DNA repair defends against naturally occurring or disease-associated DNA damage during the long lifespan of neurons and is implicated in polyglutamine disease pathology. In this study, we report that mutant huntingtin (Htt) expression in neurons causes double-strand breaks (DSBs) of genomic DNA, and Htt further promotes DSBs by impairing DNA repair. We identify Ku70, a component of the DNA damage repair complex, as a mediator of the DNA repair dysfunction in mutant Htt–expressing neurons. Mutant Htt interacts with Ku70, impairs DNA-dependent protein kinase function in nonhomologous end joining, and consequently increases DSB accumulation. Expression of exogenous Ku70 rescues abnormal behavior and pathological phenotypes in the R6/2 mouse model of Huntington’s disease (HD). These results collectively suggest that Ku70 is a critical regulator of DNA damage in HD pathology.
Tbx1 regulatesVegfr3and is required for lymphatic vessel development
Authors: Chen Li , Mupo Annalisa , Huynh Tuong , Cioffi Sara , Woods Matthew , Jin Chengliu , McKeehan Wallace , Thompson-Snipes LuAnn , Baldini Antonio , Illingworth Elizabeth
Published: May 2010

Lymphatic dysfunction causes several human diseases, and tumor lymphangiogenesis is implicated in cancer spreading. TBX1 is the major gene for DiGeorge syndrome, which is associated with multiple congenital anomalies. Mutation of Tbx1 in mice recapitulates the human disease phenotype. In this study, we use molecular, cellular, and genetic approaches to show, unexpectedly, that Tbx1 plays a critical role in lymphatic vessel development and regulates the expression of Vegfr3, a gene that is essential for lymphangiogenesis. Tbx1 activates Vegfr3 transcription in endothelial cells (ECs) by binding to an enhancer element in the Vegfr3 gene. Conditional deletion of Tbx1 in ECs causes widespread lymphangiogenesis defects in mouse embryos and perinatal death. Using the mesentery as a model tissue, we show that Tbx1 is not required for lymphatic EC differentiation; rather, it is required for the growth and maintenance of lymphatic vessels. Our findings reveal a novel pathway for the development of the lymphatic vessel network.
N-cadherin mediates plasticity-induced long-term spine stabilization
Authors: Mendez Pablo , De Roo Mathias , Poglia Lorenzo , Klauser Paul , Muller Dominique
Published: May 2010

Excitatory synapses on dendritic spines are dynamic structures whose stability can vary from hours to years. However, the molecular mechanisms regulating spine persistence remain essentially unknown. In this study, we combined repetitive imaging and a gain and loss of function approach to test the role of N-cadherin (NCad) on spine stability. Expression of mutant but not wild-type NCad promotes spine turnover and formation of immature spines and interferes with the stabilization of new spines. Similarly, the long-term stability of preexisting spines is reduced when mutant NCad is expressed but enhanced in spines expressing NCad-EGFP clusters. Activity and long-term potentiation (LTP) induction selectively promote formation of NCad clusters in stimulated spines. Although activity-mediated expression of NCad-EGFP switches synapses to a highly stable state, expression of mutant NCad or short hairpin RNA–mediated knockdown of NCad prevents LTP-induced long-term stabilization of synapses. These results identify NCad as a key molecular component regulating long-term synapse persistence.
N-cadherin: stabilizing synapses
Authors: Arikkath Jyothi
Published: May 2010

Spines are sites of excitatory synapse formation in central neurons. Alterations in spine structure and function are widely believed to actively contribute to the cellular mechanisms of learning and memory. In this issue, Mendez et al. (2010. J. Cell Biol. doi:10.1083/jcb.201003007) demonstrate a pivotal role for the cell adhesion molecule N-cadherin in activity-mediated spine stabilization, offering a new mechanism for how spine dynamics and stability are regulated by activity in central neurons.
Regulation of learning and memory by meningeal immunity: a key role for IL-4
Authors: Derecki Noël C. , Cardani Amber N. , Yang Chun Hui , Quinnies Kayla M. , Crihfield Anastasia , Lynch Kevin R. , Kipnis Jonathan
Published: May 2010

Proinflammatory cytokines have been shown to impair cognition; consequently, immune activity in the central nervous system was considered detrimental to cognitive function. Unexpectedly, however, T cells were recently shown to support learning and memory, though the underlying mechanism was unclear. We show that one of the steps in the cascade of T cell–based support of learning and memory takes place in the meningeal spaces. Performance of cognitive tasks led to accumulation of IL-4–producing T cells in the meninges. Depletion of T cells from meningeal spaces skewed meningeal myeloid cells toward a proinflammatory phenotype. T cell–derived IL-4 was critical, as IL-4−/− mice exhibited a skewed proinflammatory meningeal myeloid cell phenotype and cognitive deficits. Transplantation of IL-4−/− bone marrow into irradiated wild-type recipients also resulted in cognitive impairment and proinflammatory skew. Moreover, adoptive transfer of T cells from wild-type into IL-4−/− mice reversed cognitive impairment and attenuated the proinflammatory character of meningeal myeloid cells. Our results point to a critical role for T cell–derived IL-4 in the regulation of cognitive function through meningeal myeloid cell phenotype and brain-derived neurotrophic factor expression. These findings might lead to the development of new immune-based therapies for cognitive impairment associated with immune decline.
Transcription factors Foxo3a and Foxo1 couple the E3 ligase Cbl-b to the induction of Foxp3 expression in induced regulatory T cells
Authors: Harada Yohsuke , Harada Yasuyo , Elly Chris , Ying Ge , Paik Ji-Hye , DePinho Ronald A. , Liu Yun-Cai
Published: May 2010

The transcription factor Foxp3 is essential for optimal regulatory T (T reg) cell development and function. Here, we show that CD4+ T cells from Cbl-b RING finger mutant knockin or Cbl-b–deficient mice show impaired TGF-β–induced Foxp3 expression. These T cells display augmented Foxo3a phosphorylation, but normal TGF-β signaling. Expression of Foxo3a rescues Foxp3 expression in Cbl-b–deficient T cells, and Foxo3a deficiency results in defective TGF-β–driven Foxp3 induction. A Foxo3a-binding motif is present in a proximal region of the Foxp3 promoter, and is required for Foxo3a association. Foxo1 exerts similar effects as Foxo3a on Foxp3 expression. This study reveals that Foxo factors promote transcription of the Foxp3 gene in induced T reg cells, and thus provides new mechanistic insight into Foxo-mediated T cell regulation.
Deuteration distribution estimation with improved sequence coverage for HX/MS experiments
Authors: Lou Xinghua , Kirchner Marc , Renard Bernhard Y. , Köthe Ullrich , Boppel Sebastian , Graf Christian , Lee Chung-Tien , Steen Judith A. J. , Steen Hanno , Mayer Matthias P. , Hamprecht Fred A.
Published: May 2010

Motivation: Time-resolved hydrogen exchange (HX) followed by mass spectrometry (MS) is a key technology for studying protein structure, dynamics and interactions. HX experiments deliver a time-dependent distribution of deuteration levels of peptide sequences of the protein of interest. The robust and complete estimation of this distribution for as many peptide fragments as possible is instrumental to understanding dynamic protein-level HX behavior. Currently, this data interpretation step still is a bottleneck in the overall HX/MS workflow.

Results: We propose HeXicon, a novel algorithmic workflow for automatic deuteration distribution estimation at increased sequence coverage. Based on an L1-regularized feature extraction routine, HeXicon extracts the full deuteration distribution, which allows insight into possible bimodal exchange behavior of proteins, rather than just an average deuteration for each time point. Further, it is capable of addressing ill-posed estimation problems, yielding sparse and physically reasonable results. HeXicon makes use of existing peptide sequence information, which is augmented by an inferred list of peptide candidates derived from a known protein sequence. In conjunction with a supervised classification procedure that balances sensitivity and specificity, HeXicon can deliver results with increased sequence coverage.

Availability: The entire HeXicon workflow has been implemented in C++ and includes a graphical user interface. It is available at http://hci.iwr.uni-heidelberg.de/software.php.

Contact:  fred.hamprecht@iwr.uni-heidelberg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Regulation of the Expression of Plant Resistance Gene SNC1 by a Protein with a Conserved BAT2 Domain
Authors: Li Yingzhong , Tessaro Mark J. , Li Xin , Zhang Yuelin
Published: May 2010

Plant Resistance (R) genes encode immune receptors that recognize pathogens and activate defense responses. Because of fitness costs associated with maintaining R protein-mediated resistance, expression levels of R genes have to be tightly regulated. However, mechanisms on how R-gene expression is regulated are poorly understood. Here we show that MODIFIER OF snc1, 1 (MOS1) regulates the expression of SUPPRESSOR OF npr1-1, CONSTITUTIVE1 (SNC1), which encodes a Toll/interleukin receptor-nucleotide binding site-leucine-rich repeat type of R protein in Arabidopsis (Arabidopsis thaliana). In the mos1 loss-of-function mutant plants, snc1 expression is repressed and constitutive resistance responses mediated by snc1 are lost. The repression of snc1 expression in mos1 is released by knocking out DECREASE IN DNA METHYLATION1. In mos1 mutants, DNA methylation in a region upstream of SNC1 is altered. Furthermore, expression of snc1 transgenes using the native promoter does not require MOS1, indicating that regulation of SNC1 expression by MOS1 is at the chromatin level. Map-based cloning of MOS1 revealed that it encodes a novel protein with a HLA-B ASSOCIATED TRANSCRIPT2 (BAT2) domain that is conserved in plants and animals. Our study on MOS1 suggests that BAT2 domain-containing proteins may function in regulation of gene expression at chromatin level.
Identification and Application of a Rice Senescence-Associated Promoter
Authors: Liu Li , Zhou Yong , Szczerba Mark W. , Li Xianghua , Lin Yongjun
Published: May 2010

SAG39 is a rice (Oryza sativa) gene that encodes a cysteine protease. SAG39 shares 55% homology with the Arabidopsis (Arabidopsis thaliana) senescence-associated protein SAG12. The promoter for SAG39 (PSAG39) was isolated, and SAG39 expression was determined to be relatively low in mature leaves, while not expressed in the endosperm. SAG39 mRNA levels increased as senescence progressed, with maximum accumulation of transcripts at late senescence stages. Gel retardation assays indicated that two cis-acting elements in PSAG39, HBOXCONSENSUSPVCHS and WRKY71OS, responded to leaf senescence. To test if PSAG39 could be useful for increasing rice yields by increasing cytokinin content and delaying senescence, homozygous transgenic plants were obtained by linking PSAG39 to the ipt gene and introducing it into Zhonghua 11. The chlorophyll level of the flag leaf was used to monitor senescence, confirming the stay-green phenotype in PSAG39:ipt transgenic rice versus wild-type plants. Changes in the cytokinin content led to early flowering and a greater number of emerged panicles 70 d after germination in the transgenic rice. Measurements of sugar and nitrogen contents in flag leaves demonstrated a transition in the source-sink relationship in transgenic plants triggered at the onset of leaf senescence, with the nitrogen content decreasing more slowly, while sugars were removed more rapidly than in wild-type plants. The importance of these changes to rice physiology, yield, and early maturation will be discussed.
Activation of ASC induces apoptosis or necrosis, depending on the cell type, and causes tumor eradication
Authors: Motani Kou , Kawase Kouji , Imamura Ryu , Kinoshita Takeshi , Kushiyama Hiroko , Suda Takashi
Published: May 2010

The adaptor protein ASC (also called TMS1) links certain NLR proteins (e.g., NLRC4, NLRP3) and caspases. It is involved in the chemosensitivity of tumor cells and inflammation. Here, we found that ASC activation using NLRC4 mimicry or an autoinflammatory disease‐associated NLRP3 mutant induced necrosis in COLO205 colon adenocarcinoma cells, but induced caspase‐8‐dependent apoptosis in NUGC‐4 stomach cancer cells. As the Fas ligand induced caspase‐8‐dependent apoptosis in COLO205 cells, caspase‐8 was intact in this cell line. ASC‐mediated necrosis was preceded by lysosomal leakage, and diminished by inhibitors for vacuolar H+‐ATPase, cathepsins, and calpains but not by inhibitors for caspase‐8, or aspartic proteases, suggesting that lysosomes and certain proteases were involved in this process. Finally, growing tumors of transplanted human cancer cells in nude mice were eradicated by the activation of endogenous ASC in the tumor cells, irrespective of the form of cell death. Thus, ASC mediates distinct forms of cell death in different cell types, and is a promising target for cancer therapy. (Cancer Sci 2010)
Staphylococcal enterotoxin A induction of pro‐inflammatory cytokines and lethality in mice is primarily dependent on MyD88
Authors: Kissner Teri L. , Cisney Emily D. , Ulrich Robert G. , Fernandez Stefan , Saikh Kamal U.
Published: May 2010

Staphylococcal enterotoxin (SE) ‐induced toxic shock is triggered by inflammatory cytokine signal amplification after SE binding to major histocompatibility complex class II molecules on antigen‐presenting cells and T‐cell receptors. Identifying host cellular elements contributing to this pro‐inflammatory signal amplification is critical for developing a strategy for therapeutic intervention. Myeloid differentiation primary‐response protein 88 (MyD88) is an intracellular signalling adaptor protein primarily known for mediating pro‐inflammatory cytokine responses. We investigated the role of MyD88 in staphylococcal enterotoxin A (SEA) ‐treated cell cultures and mouse models of toxic shock. Our results demonstrated that elevated levels of tumour necrosis factor‐α, interferon‐γ, interleukin‐1α/β (IL‐1α/β), IL‐2 and IL‐6 production correlated with up‐regulation of MyD88 after treatment of spleen cells and mice with SEA alone or in combination with lipopolysaccharide (LPS). The SEA‐induced lethality was also observed in (LPS‐independent) d‐galactosamine‐sensitized mice. While LPS potentiated SEA‐induced cytokine responses, d‐galactosamine treatment had no additive effect. Most importantly, our results demonstrated that MyD88−/− mice were resistant to SEA‐induced toxic shock and had reduced pro‐inflammatory cytokine responses. These results suggest that SEA‐induced lethality is primarily dependent on MyD88. Our findings offer an important insight on potential therapeutic treatment of SEA‐induced toxic shock targeting MyD88.
Patient‐reported outcomes following islet cell or pancreas transplantation (alone or after kidney) in Type 1 diabetes: a systematic review
Authors: Speight J. , Reaney M. D. , Woodcock A. J. , Smith R. M. , Shaw J. A. M.
Published: May 2010

Diabet. Med. 27, 812–822 (2010)

Aims  For selected individuals with complex Type 1 diabetes, pancreatic islet transplantation (IT) offers the potential of excellent glycaemic control without significant hypoglycaemia, balanced by the need for ongoing systemic immunosuppression. Increasingly, patient‐reported outcomes (PROs) are considered alongside biomedical outcomes as a measure of transplant success. PROs in IT have not previously been compared directly with the closest alternate treatment option, pancreas transplant alone (PTA) or pancreas after kidney (PAK).

Methods  We used a Population, Intervention, Comparisons, Outcomes (PICO) strategy to search Scopus and screened 314 references for inclusion.

Results  Twelve studies [including PRO assessment of PAK, PTA, islet‐after kidney (IAK) and islet transplant alone (ITA); n = 7–205] used a total of nine specified and two unspecified PRO measures. Results were mixed but identified some benefits which remained apparent up to 36 months post‐transplant, including improvements in fear of hypoglycaemia, as well as some aspects of diabetes‐specific quality of life (QoL) and general health status. Negative outcomes included short‐term pain associated with the procedure, immunosuppressant side effects and depressed mood associated with loss of graft function.

Conclusions  The mixed results may be attributable to limited sample sizes. Also, some PRO measures may lack sensitivity to detect actual changes, as they exclude issues and domains of life likely to be important for QoL post‐transplantation and when patients may no longer perceive themselves to have diabetes. Thus, the full impact of islet/pancreas transplantation (alone or after kidney) on QoL is unknown. Furthermore, no studies have assessed patient satisfaction, which may highlight further advantages and disadvantages of transplantation.
WHO'S ARGUING? A CALL FOR REFLEXIVITY IN BIOETHICS
Authors: IVES JONATHAN , DUNN MICHAEL
Published: May 2010

In this paper we set forth what we believe to be a relatively controversial argument, claiming that ‘bioethics’ needs to undergo a fundamental change in the way it is practised. This change, we argue, requires philosophical bioethicists to adopt reflexive practices when applying their analyses in public forums, acknowledging openly that bioethics is an embedded socio‐cultural practice, shaped by the ever‐changing intuitions of individual philosophers, which cannot be viewed as a detached intellectual endeavour. This said, we argue that in order to manage the personal, social and cultural embeddedness of bioethics, philosophical bioethicists should openly acknowledge how their practices are constructed and should, in their writing, explicitly deal with issues of bias and conflict of interest, just as empirical scientists are required to do.
THE FUTURE OF BIOETHICS: THREE DOGMAS AND A CUP OF HEMLOCK
Authors: DAWSON ANGUS
Published: May 2010

In this paper I argue that bioethics is in crisis and that it will not have a future unless it begins to embrace a more Socratic approach to its leading assumptions. The absence of a critical and sceptical spirit has resulted in little more than a dominant ideology. I focus on three key issues. First, that too often bioethics collapses into medical ethics. Second, that medical ethics itself is beset by a lack of self‐reflection that I characterize here as a commitment to three dogmas. Third, I offer a more positive perspective by suggesting how bioethics may benefit from looking towards public health ethics as a new source of inspiration and direction.
Ownership and the Value of Political Connections: Evidence from China
Authors: Wu Wenfeng , Wu Chongfeng , Rui Oliver M.
Published: May 2010

Research has found that political connectedness can have both positive and negative effects on firm value. To resolve these mixed findings, we investigate the impact of political ties conditional on ownership for a sample of Chinese firms over the period 1999–2006. We find that private firms with politically connected managers have a higher value and obtain more government subsidies than those without connected managers, whereas local state‐owned enterprises with connected managers have a lower value and employ more surplus labour than those without connected managers. Our results indicate that the effect of political ties is subject to firm ownership.
High concentrations of dexmedetomidine inhibit compound action potentials in frog sciatic nerves without α2adrenoceptor activation
Authors: Kosugi Toshifumi , Mizuta Kotaro , Fujita Tsugumi , Nakashima Mikio , Kumamoto Eiichi
Published: May 2010

BACKGROUND AND PURPOSEDexmedetomidine, an α2‐adrenoceptor agonist, exhibits anti‐nociceptive actions at the spinal cord and enhances the effect of local anaesthetics in the peripheral nervous system. Although the latter action may be attributed in part to inhibition of nerve conduction produced by dexmedetomidine, this has not been fully examined yet.

EXPERIMENTAL APPROACHWe examined the effects of various adrenoceptor agonists including dexmedetomidine, and tetracaine, a local anaesthetic, on compound action potentials (CAPs) recorded from the frog sciatic nerve, using the air‐gap method.

KEY RESULTSDexmedetomidine reversibly and concentration‐dependently reduced the peak amplitude of CAPs (IC50= 0.40 mmol·L−1). This action was not antagonized by two α2‐adrenoceptor antagonists, yohimbine and atipamezole; the latter antagonist itself reduced CAP peak amplitude. Clonidine and oxymetazoline, two other α2‐adrenoceptor agonists, also inhibited CAPs; the maximum effect of clonidine was only 20%, while oxymetazoline was less potent (IC50= 1.5 mmol·L−1) than dexmedetomidine. On the other hand, (±)‐adrenaline, (±)‐noradrenaline, α1‐adrenoceptor agonist (‐)‐phenylephrine and β‐adrenoceptor agonist (‐)‐isoprenaline (each 1 mmol·L−1) had no effect on CAPs. Tetracaine reversibly reduced CAP peak amplitude (IC50of 0.014 mmol·L−1).

CONCLUSIONS AND IMPLICATIONSDexmedetomidine reduced CAP peak amplitude without α2‐adrenoceptor activation (at concentrations >1000‐fold higher than those used as α2adrenoceptor agonist), with a lower potency than tetracaine. CAPs were inhibited by other α2adrenoceptor agonists, oxymetazoline and clonidine, and also an α2adrenoceptor antagonist atipamezole. Thus, some drugs acting on α2adrenoceptors are able to block nerve conduction.
Irbesartan treatment up‐regulates hepatic expression of PPARα and its target genes in obese Koletsky (fak/fak) rats: a link to amelioration of hypertriglyceridaemia
Authors: Rong X , Li Y , Ebihara K , Zhao M , Kusakabe T , Tomita T , Murray M , Nakao K
Published: May 2010

BACKGROUND AND PURPOSE

Hypertriglyceridaemia is associated with an increased risk of cardiovascular disease. Irbesartan, a well‐established angiotensin II type 1 receptor (AT1) blocker, improves hypertriglyceridaemia in rodents and humans but the underlying mechanism of action is unclear.

EXPERIMENTAL APPROACH

Male obese Koletsky (fak/fak) rats, which exhibit spontaneous hypertension and metabolic abnormalities, received irbesartan (40 mg·kg−1·day−1) or vehicle by oral gavage over 7 weeks. Adipocyte‐derived hormones in plasma were measured by ELISA. Gene expression in liver and other tissues was assessed by real‐time PCR and Western immunoblotting.

KEY RESULTS

In Koletsky (fak/fak) rats irbesartan lowered plasma concentrations of triglycerides and non‐esterified fatty acids, and decreased plasma insulin concentrations and the homeostasis model assessment of insulin resistance index. However, this treatment did not affect food intake, body weight, epididymal white adipose tissue weight, adipocyte size and plasma leptin concentrations, although plasma adiponectin was decreased. Irbesartan up‐regulated hepatic expression of mRNAs corresponding to peroxisome proliferator‐activated receptor (PPAR)α and its target genes (carnitine palmitoyltransferase‐1a, acyl‐CoA oxidase and fatty acid translocase/CD36) that mediate hepatic fatty acid uptake and oxidation; the increase in hepatic PPARα expression was confirmed at the protein level. In contrast, irbesartan did not affect expression of adipose PPARγ and its downstream genes or hepatic genes that mediate fatty acid synthesis.

CONCLUSIONS AND IMPLICATIONS

These findings demonstrate that irbesartan treatment up‐regulates PPARα and several target genes in liver of obese spontaneously hypertensive Koletsky (fak/fak) rats and offers a novel insight into the lipid‐lowering mechanism of irbesartan.
Stimulatory effects of the multi‐kinase inhibitor sorafenib on human bladder cancer cells
Authors: Rose A , Grandoch M , vom Dorp F , Rübben H , Rosenkranz A , Fischer JW , Weber A‐A
Published: May 2010

BACKGROUND AND PURPOSESorafenib is an inhibitor of several intracellular signalling kinases with anti‐proliferative, anti‐angiogenic and pro‐apoptotic effects in tumour cells. Sorafenib is used in the therapy of advanced renal cell carcinoma, and several phase II clinical trials are being carried out in patients with urothelial carcinomas.

EXPERIMENTAL APPROACHUsing a panel of human bladder cancer cell lines (RT4, T24, J82), we characterized systematically the effects of sorafenib on intracellular signalling, migration, proliferation and apoptosis.

KEY RESULTSWe demonstrated that at low concentrations (<1 µM), sorafenib is capable of significantly stimulating migration and proliferation of the bladder cancer cells. We hypothesize that these stimulatory effects on tumour cell functions might be explained by an activation of the Ras/ERK‐1/2 signal transduction pathway. In addition, the comparison of different bladder cancer cell lines not only revealed a different biology (e.g. cell migration), but also a differential susceptibility to the anti‐apoptotic effects of sorafenib. Finally, we confirmed in different bladder cancer cell lines the known inhibitory actions of sorafenib in pharmacological concentrations (≥3 µM) on ERK‐1/2 phosphorylation, migration and proliferation, as well as the pro‐apoptotic effects of the compound.

CONCLUSIONS AND IMPLICATIONSTaken together, these findings suggest that although sorafenib has the potential to be used in the treatment of urothelial carcinoma, this compound might also activate bladder cancer cells at low concentrations. This should be relevant for dosing regiments to optimize the treatment with this promising anti‐tumour drug.