bluuebunny/crossref_metadata_2025 huggingface dataset:
Differential down-regulation of HLA-DR on monocyte subpopulations during systemic inflammation
Authors: Kim Oh Yoen , Monsel Antoine , Bertrand Michèle , Coriat Pierre , Cavaillon Jean-Marc , Adib-Conquy Minou
Published: May 2010

Introduction

Decreased expression of human leukocyte antigen class II (HLA-DR) on monocytes is a hallmark of altered immune status in patients with a systemic inflammatory response syndrome (SIRS). So far, the analyses were mainly performed without taking into account monocytes subpopulations.

Methods

We studied this modification on CD14HIGH and CD14LOW monocytes of 20 SIRS patients undergoing abdominal aortic surgery (AAS), 20 patients undergoing carotid artery surgery (CAS), and 9 healthy controls, and we investigated mediators and intracellular molecules that may be involved in this process.

Results

HLA-DR on CD14HIGH monocytes started to decrease during surgery, after blood reperfusion, and was further reduced post-surgery. In contrast, HLA-DR expression on CD14LOW cells only decreased after surgery, and to a lesser extent than on CD14HIGH monocytes. Negative correlations were found between the reduction of HLA-DR expression and the change in cortisol levels for both subpopulations, whereas a negative correlation between interleukin-10 (IL-10) levels and HLA-DR modulation was only observed for CD14HIGH cells. In accordance with these ex vivo results, HLA-DR on CD14HIGH and CD14LOW monocytes of healthy donors was reduced following incubation with hydrocortisone, whereas IL-10 only acted on CD14HIGH subpopulation. Furthermore, flow cytometry revealed that the expression of IL-10 receptor was higher on CD14HIGH versus CD14LOW monocytes. In addition, hydrocortisone, and to a lesser extent IL-10, reversed the up-regulation of HLA-DR induced by bacterial products. Finally, membrane-associated RING-CH-1 protein (MARCH1) mRNA, a negative regulator of MHC class II, was up-regulated in monocytes of AAS patients on Day 1 post-surgery, and in those of healthy subjects exposed to hydrocortisone.

Conclusions

This study reveals that HLA-DR expression is modulated differently on CD14HIGH (classical) versus CD14LOW (inflammatory) monocytes after systemic inflammation.
Towards a comprehensive structural variation map of an individual human genome
Authors: Pang Andy W , MacDonald Jeffrey R , Pinto Dalila , Wei John , Rafiq Muhammad A , Conrad Donald F , Park Hansoo , Hurles Matthew E , Lee Charles , Venter J Craig , Kirkness Ewen F , Levy Samuel , Feuk Lars , Scherer Stephen W
Published: May 2010

Background

Several genomes have now been sequenced, with millions of genetic variants annotated. While significant progress has been made in mapping single nucleotide polymorphisms (SNPs) and small (<10 bp) insertion/deletions (indels), the annotation of larger structural variants has been less comprehensive. It is still unclear to what extent a typical genome differs from the reference assembly, and the analysis of the genomes sequenced to date have shown varying results for copy number variation (CNV) and inversions.

Results

We have combined computational re-analysis of existing whole genome sequence data with novel microarray-based analysis, and detect 12,178 structural variants covering 40.6 Mb that were not reported in the initial sequencing of the first published personal genome. We estimate a total non-SNP variation content of 48.8 Mb in a single genome. Our results indicate that this genome differs from the consensus reference sequence by approximately 1.2% when considering indels/CNVs, 0.1% by SNPs and approximately 0.3% by inversions. The structural variants impact 4,867 genes, and >24% of structural variants would not be imputed by SNP-association.

Conclusions

Our results indicate that a large number of structural variants have been unreported in the individual genomes published to date. This significant extent and complexity of structural variants, as well as the growing recognition of their medical relevance, necessitate they be actively studied in health-related analyses of personal genomes. The new catalogue of structural variants generated for this genome provides a crucial resource for future comparison studies.
A human functional protein interaction network and its application to cancer data analysis
Authors: Wu Guanming , Feng Xin , Stein Lincoln
Published: May 2010

Background

One challenge facing biologists is to tease out useful information from massive data sets for further analysis. A pathway-based analysis may shed light by projecting candidate genes onto protein functional relationship networks. We are building such a pathway-based analysis system.

Results

We have constructed a protein functional interaction network by extending curated pathways with non-curated sources of information, including protein-protein interactions, gene coexpression, protein domain interaction, Gene Ontology (GO) annotations and text-mined protein interactions, which cover close to 50% of the human proteome. By applying this network to two glioblastoma multiforme (GBM) data sets and projecting cancer candidate genes onto the network, we found that the majority of GBM candidate genes form a cluster and are closer than expected by chance, and the majority of GBM samples have sequence-altered genes in two network modules, one mainly comprising genes whose products are localized in the cytoplasm and plasma membrane, and another comprising gene products in the nucleus. Both modules are highly enriched in known oncogenes, tumor suppressors and genes involved in signal transduction. Similar network patterns were also found in breast, colorectal and pancreatic cancers.

Conclusions

We have built a highly reliable functional interaction network upon expert-curated pathways and applied this network to the analysis of two genome-wide GBM and several other cancer data sets. The network patterns revealed from our results suggest common mechanisms in the cancer biology. Our system should provide a foundation for a network or pathway-based analysis platform for cancer and other diseases.
Short RNA half-lives in the slow-growing marine cyanobacterium Prochlorococcus
Authors: Steglich Claudia , Lindell Debbie , Futschik Matthias , Rector Trent , Steen Robert , Chisholm Sallie W
Published: May 2010

Background

RNA turnover plays an important role in the gene regulation of microorganisms and influences their speed of acclimation to environmental changes. We investigated whole-genome RNA stability of Prochlorococcus, a relatively slow-growing marine cyanobacterium doubling approximately once a day, which is extremely abundant in the oceans.

Results

Using a combination of microarrays, quantitative RT-PCR and a new fitting method for determining RNA decay rates, we found a median half-life of 2.4 minutes and a median decay rate of 2.6 minutes for expressed genes - twofold faster than that reported for any organism. The shortest transcript half-life (33 seconds) was for a gene of unknown function, while some of the longest (approximately 18 minutes) were for genes with high transcript levels. Genes organized in operons displayed intriguing mRNA decay patterns, such as increased stability, and delayed onset of decay with greater distance from the transcriptional start site. The same phenomenon was observed on a single probe resolution for genes greater than 2 kb.

Conclusions

We hypothesize that the fast turnover relative to the slow generation time in Prochlorococcus may enable a swift response to environmental changes through rapid recycling of nucleotides, which could be advantageous in nutrient poor oceans. Our growing understanding of RNA half-lives will help us interpret the growing bank of metatranscriptomic studies of wild populations of Prochlorococcus. The surprisingly complex decay patterns of large transcripts reported here, and the method developed to describe them, will open new avenues for the investigation and understanding of RNA decay for all organisms.
Delayed administration of anti-PD-1 antibody reverses immune dysfunction and improves survival during sepsis
Authors: Brahmamdam Pavan , Inoue Shigeaki , Unsinger Jacqueline , Chang Katherine C , McDunn Jonathan E , Hotchkiss Richard S
Published: May 2010

Blocking the negative co-stimulatory molecule PD-1 prevents immune suppression, blocks apoptosis, and improves survival in sepsis.

There is increasing recognition that a major pathophysiologic event in sepsis is the progression to an immunosuppressive state in which the host is unable to eradicate invading pathogens. Although there are likely numerous causes for the immunosuppression, expression of negative costimulatory molecules on immune effector cells is a likely contributing factor. PD-1 is a recently described, negative costimulatory molecule that has potent effects to inhibit T cell activation, cytokine production, and cytotoxic functions. PD-1 plays a critical role in the host response to specific pathogens, but relatively little work has been done on the possible effects of PD-1 in sepsis. We hypothesized that the anti-PD-1 antibody would improve survival in sepsis. Mice underwent CLP, and PD-1 expression was quantitated. Additionally, the effects of anti-PD-1 antibody on lymphocyte apoptosis, cytokine production, host immunity, and survival were determined. PD-1 expression increased beginning 48 h after sepsis, and >20% of CD4 and CD8 T cells were positive by 7 days. Anti-PD-1 antibody administered 24 h after sepsis prevented sepsis-induced depletion of lymphocytes and DCs, increased Bcl-xL, blocked apoptosis, and improved survival. Anti-PD-1 also prevented the loss in DTH, a key indicator of immunocompetence in sepsis. Thus, delayed administration of anti-PD-1 antibody, an important therapeutic advantage, was effective in sepsis. Furthermore, these results add to the growing body of evidence that modulation of the positive and negative costimulatory pathways on immune cells represents a viable therapeutic approach in reversing immunosuppression and improving sepsis survival.
Immune cell recruitment to inflammatory loci is impaired in mice deficient in basement membrane protein laminin α4
Authors: Kenne Ellinor , Soehnlein Oliver , Genové Guillem , Rotzius Pierre , Eriksson Einar E , Lindbom Lennart
Published: May 2010

Mice lacking basement membrane laminin-411 show im-paired leukocyte recruitment to extravascular tissue due to defective migration through the vessel wall.

For leukocytes to penetrate the vessel wall, they need to interact sequentially with the endothelial lining and the perivascular BM. The matrix protein laminin-411 is a major constituent of the vascular BM. The laminin α4 chain is a component of laminin-411 and has structural and signaling functions. Here, we addressed the role of BM laminin α4 in leukocyte recruitment to inflammatory loci. We used several recruitment models in Lam4−/− and WT mice to determine whether lack of laminin-411 in the perivascular BM influences extravasation of inflammatory cells. Recruitment of all major leukocyte subsets (neutrophils, monocytes, and lymphocytes) was reduced in Lam4−/− mice compared with WT. With the use of intravital microscopy, we concluded that this decrease was a result of impaired diapedesis through the vessel wall, as neither leukocyte adhesion to the endothelial lining nor migration in extravascular tissue was hampered in Lam4−/− mice. Collectively, our data suggest a reduced ability of immune cells to penetrate the vessel wall in mice deficient in laminin α4.
Technical Advance: Generation of human pDC equivalents from primary monocytes using Flt3-L and their functional validation under hypoxia
Authors: Sekar Divya , Brüne Bernhard , Weigert Andreas
Published: May 2010

Method for the generation of human pDC equivalents ex vivo from primary monocytes, whose differentiation can be manipulated by environmental stimuli such as hypoxia.

The division of labor between DC subsets is evolutionarily well-defined. mDC are efficient in antigen presentation, whereas pDC act as rheostats of the immune system. They activate NK cells, cause bystander activation of mDC, and interact with T cells to induce tolerance. This ambiguity positions pDC at the center of inflammatory diseases, such as cancer, arthritis, and autoimmune diseases. The ability to generate human mDC ex vivo made it possible to engineer them to suit therapy needs. Unfortunately, a similar, easily accessible system to generate human pDC is not available. We describe a method to generate human pDC equivalents ex vivo, termed mo-pDC from peripheral blood monocytes using Flt3-L. mo-pDC showed a characteristic pDC profile, such as high CD123 and BDCA4, but low CD86 and TLR4 surface expression and a low capacity to induce autologous lymphocyte proliferation and to phagocytose apoptotic debris in comparison with mDC. Interestingly, mo-pDC up-regulated the pDC lineage-determining transcription factor E2-2 as well as expression of BDCA2, which is under the transcriptional control of E2-2 but not its inhibitor ID2, during differentiation. mo-pDC produced high levels of IFN-α when pretreated overnight with TNF-α. Under hypoxia, E2-2 was down-regulated, and ID2 was induced in mo-pDC, whereas surface expression of MHCI, CD86, and BDCA2 was decreased. Furthermore, mo-pDC produced high levels of inflammatory cytokines when differentiated under hypoxia compared with normoxia. Hence, mo-pDC can be used to study differentiation and functions of human pDC under microenvironmental stimuli.
Non-conducting function of the Kv2.1 channel enables it to recruit vesicles for release in neuroendocrine and nerve cells
Authors: Feinshreiber Lori , Singer-Lahat Dafna , Friedrich Reut , Matti Ulf , Sheinin Anton , Yizhar Ofer , Nachman Rachel , Chikvashvili Dodo , Rettig Jens , Ashery Uri , Lotan Ilana
Published: May 2010

Regulation of exocytosis by voltage-gated K+ channels has classically been viewed as inhibition mediated by K+ fluxes. We recently identified a new role for Kv2.1 in facilitating vesicle release from neuroendocrine cells, which is independent of K+ flux. Here, we show that Kv2.1-induced facilitation of release is not restricted to neuroendocrine cells, but also occurs in the somatic-vesicle release from dorsal-root-ganglion neurons and is mediated by direct association of Kv2.1 with syntaxin. We further show in adrenal chromaffin cells that facilitation induced by both wild-type and non-conducting mutant Kv2.1 channels in response to long stimulation persists during successive stimulation, and can be attributed to an increased number of exocytotic events and not to changes in single-spike kinetics. Moreover, rigorous analysis of the pools of released vesicles reveals that Kv2.1 enhances the rate of vesicle recruitment during stimulation with high Ca2+, without affecting the size of the readily releasable vesicle pool. These findings place a voltage-gated K+ channel among the syntaxin-binding proteins that directly regulate pre-fusion steps in exocytosis.
Spatio-temporal Rho GTPase signaling – where are we now?
Authors: Pertz Olivier
Published: May 2010

Rho-family GTPases are molecular switches that transmit extracellular cues to intracellular signaling pathways. Their regulation is likely to be highly regulated in space and in time, but most of what is known about Rho-family GTPase signaling has been derived from techniques that do not resolve these dimensions. New imaging technologies now allow the visualization of Rho GTPase signaling with high spatio-temporal resolution. This has led to insights that significantly extend classic models and call for a novel conceptual framework. These approaches clearly show three things. First, Rho GTPase signaling dynamics occur on micrometer length scales and subminute timescales. Second, multiple subcellular pools of one given Rho GTPase can operate simultaneously in time and space to regulate a wide variety of morphogenetic events (e.g. leading-edge membrane protrusion, tail retraction, membrane ruffling). These different Rho GTPase subcellular pools might be described as ‘spatio-temporal signaling modules’ and might involve the specific interaction of one GTPase with different guanine nucleotide exchange factors (GEFs), GTPase-activating proteins (GAPs) and effectors. Third, complex spatio-temporal signaling programs that involve precise crosstalk between multiple Rho GTPase signaling modules regulate specific morphogenetic events. The next challenge is to decipher the molecular circuitry underlying this complex spatio-temporal modularity to produce integrated models of Rho GTPase signaling.
Sarcolemmal nNOS anchoring reveals a qualitative difference between dystrophin and utrophin
Authors: Li Dejia , Bareja Akshay , Judge Luke , Yue Yongping , Lai Yi , Fairclough Rebecca , Davies Kay E. , Chamberlain Jeffrey S. , Duan Dongsheng
Published: May 2010

Duchenne muscular dystrophy (DMD) is a lethal muscle disease caused by dystrophin deficiency. In normal muscle, dystrophin helps maintain sarcolemmal stability. Dystrophin also recruits neuronal nitric oxide synthase (nNOS) to the sarcolemma. Failure to anchor nNOS to the membrane leads to functional ischemia and aggravates muscle disease in DMD. Over the past two decades, a great variety of therapeutic modalities have been explored to treat DMD. A particularly attractive approach is to increase utrophin expression. Utrophin shares considerable sequence, structural and functional similarity with dystrophin. Here, we test the hypothesis that utrophin also brings nNOS to the sarcolemma. Full-length utrophin cDNA was expressed in dystrophin-deficient mdx mice by gutted adenovirus or via transgenic overexpression. Subcellular nNOS localization was determined by immunofluorescence staining, in situ nNOS activity staining and microsomal preparation western blot. Despite supra-physiological utrophin expression, we did not detect nNOS at the sarcolemma. Furthermore, transgenic utrophin overexpression failed to protect mdx muscle from exercise-associated injury. Our results suggest that full-length utrophin cannot anchor nNOS to the sarcolemma. This finding might have important implications for the development of utrophin-based DMD therapies.
Experimental analysis of friction-induced vibrations at the finger contact surface
Authors: Fagiani R , Massi F , Chatelet E , Berthier Y , Sestieri A
Published: May 2010

When a finger moves to scan the surface of an object, the sliding contact generates vibrations that propagate in the finger skin and transmit the information about the object characteristics to mechanoreceptors. Mechanoreceptors convert vibrations into electric impulses sent to the brain.

In this context, by appropriate experiments, a frequency analysis of the signal characterizing the surface scanning can be carried out to investigate the vibration spectrum measured on the finger and to highlight how the tactile sense is connected to the measured frequency spectra. Although the correlation between the surface roughness with respect to the tactile sensation is deeply analysed in the literature, the vibration spectra induced by the finger—surface scanning and the consequent activation of mechanoreceptors on the skin were rarely investigated. In particular, in this paper, interests will be focused on the changes shown in the vibration spectra, caused by variations in the characteristic contact parameters such as scanning velocity and roughness.
Axially Chiral Anilido–Aldimine Aluminum Complexes with a Pseudobinaphthyl Skeleton
Authors: Hayashi Kazuhiro , Nakajima Yumiko , Ozawa Fumiyuki , Kawabata Takeo
Published: May 2010

Axially chiral anilido–aldimine aluminum complexes with a pseudobinaphthyl skeleton 3a and 3b have been prepared. X-ray analysis indicates that complex 3b adopts a conformation similar to that of 1,1′-binaphthyls. The racemization barrier of 3a was determined to be 23.0 kcal mol−1, which was higher by ca. 4 kcal mol−1 than the corresponding diarylamine precursor with an N–H–N hydrogen bond.
Photostability of Water-dispersible CdTe Quantum Dots: Capping Ligands and Oxygen
Authors: Emin Saim , Loukanov Alexandre , Wakasa Masanobu , Nakabayashi Seiichiro , Kaneko Yasuko
Published: May 2010

Here we report the effect of various capping ligands on the optical properties and photostability of CdTe quantum dots in aqueous solutions. Ligand exchange procedure is used to prepare water dispersive CdTe nanocrystals capped with aminoethanethiol, 3-mercaptopropionic and dihydrolipoic acids. The dynamics of photoexcited states is examined by transient photoluminescent spectroscopy. Our results demonstrate that the luminescence intensity of water-dispersible CdTe quantum dots is strongly influenced by molecular oxygen under light irradiation.
Truthful Revelation Mechanisms for Simultaneous Common Agency Games
Authors: Pavan Alessandro , Calzolari Giacomo
Published: May 2010

We introduce new revelation mechanisms for simultaneous common agency games which, although they do not always permit a complete equilibrium characterization, do facilitate the characterization of the equilibrium outcomes that are typically of interest in applications. We then show how these mechanisms can be used in applications such as menu auctions, competition in nonlinear tariffs, and moral hazard settings. Lastly, we show how one can enrich the revelation mechanisms, albeit at a cost of an increase in complexity, to characterize all possible equilibrium outcomes, including those sustained by non-Markov strategies and/or mixed-strategy profiles. (JEL C72, D82, D86)
The Pricing of Academic Journals: A Two-Sided Market Perspective
Authors: Jeon Doh-Shin , Rochet Jean-Charles
Published: May 2010

More and more academic journals are adopting an open access policy by which articles are accessible free of charge, while publication costs are recovered through author fees. We study the consequences of this open access policy on the quality standard of an electronic academic journal. If the journal's objective were to maximize social welfare, open access would be optimal. However, we show that if the journal has a different objective (such as maximizing readers' utility, the impact of the journal, or its profit), open access tends to induce it to choose a quality standard below the socially efficient level. (JEL L11, L82)
Open Access and Dynamic Efficiency
Authors: Klumpp Tilman , Su Xuejuan
Published: May 2010

In our model, production of a final good requires access to an excludable resource owned by an integrated firm. The quality of the resource depends on an investment by the owner and impacts the downstream demand curve. Under open access, the owner must share the resource with downstream competitors at a regulated tariff. We show that quality exceeds the monopoly level, and increases with the number of competitors, if the access tariff is set according to a principle we call revenue neutrality. Our results contradict the notion that dynamic efficiency must be sacrificed for gains in static (allocative) efficiency. (JEL D21, D43, D45, L24, O34)
The First of the Month Effect: Consumer Behavior and Store Responses
Authors: Hastings Justine , Washington Ebonya
Published: May 2010

Previous research has demonstrated that benefit recipients decrease expenditures on, and consumption of, food throughout the benefit month. Using detailed grocery store scanner data, we ask two questions: whether cycling is due to a desire for variety that leads to within-month substitution across product quality, and whether cycling is driven by countercyclical retail pricing. We find that the decrease in food expenditures is largely driven by reductions in quantity, not quality, and that prices for foods purchased by benefit households vary pro-cyclically with demand, implying that households could save money by delaying their food purchases until later in the month. (JEL D12, I38)
Estimating the Effect of Student Aid on College Enrollment: Evidence from a Government Grant Policy Reform
Authors: Nielsen Helena Skyt , Sørensen Torben , Taber Christopher
Published: May 2010

In this paper, we estimate the response of college enrollment to changes in student aid arising from a Danish reform. We separately identify the effect of aid from that of other observed and unobserved variables such as parental income. We exploit the combination of a kinked aid scheme and a reform to identify the effect of direct costs on enrollment. To allow for potential biases due to borrowing constraints, we use detailed information on parents' assets. We find that enrollment is less responsive than found in other studies and that borrowing constraints only deter college enrollment to a minor extent. (JEL H52, I22, I23)
Significant Sirolimus and Dronedarone Interaction in a Kidney Transplant Recipient
Authors: Tichy Eric M , Medwid Andrew J , Mills Elizabeth A , Formica Richard N , Kulkarni Sanjay
Published: May 2010

Objective:

To report the potential clinically significant pharmacokinetic interaction between sirolimus and dronedarone.

Case Summary:

A 67-year-old man status post-kidney transplant in 2004 was maintained on an immunosuppressive regimen consisting of sirolimus, mycophenolate mofetil, and prednisone. He had been maintained for more than 1 year on a stable dose of sirolimus (5 mg/day), with concentrations ranging between 5 and 13.5 ng/mL. The patient was admitted to the hospital with a complaint of bloody diarrhea; shortly after admission, he developed atrial fibrillation for which dronedarone 400 mg twice daily was initiated. Sirolimus concentrations obtained 3 days after initiation of dronedarone revealed a trough concentration that was increased by more than 3-fold (38.6 ng/mL) from his baseline trough concentration. After sirolimus was held for 6 days, the trough concentration was 7.8 ng/mL. The dosage was reduced to 1 mg/day; there was no need for further adjustment.

Discussion:

While the potential for an interaction between sirolimus and dronedarone is listed in the package insert of dronedarone, there are no documented reports of this interaction in the peer-reviewed literature. Since sirolimus is a narrow therapeutic index medication, information about the severity and magnitude of the interaction with dronedarone may help clinicians avoid therapeutic misadventures when this combination is employed. Our case clearly demonstrates a significant pharmacokinetic interaction between sirolimus and dronedarone. The Horn Drug Interaction Probability Scale indicates that the occurrence of an interaction between sirolimus and dronedarone in our case is probable.

Conclusions:

Due to the potential for sirolimus toxicity and excessive immunosuppression, the concurrent use of dronedarone and sirolimus should be avoided when possible. If concurrent administration cannot be avoided, we suggest close monitoring and a 50–75% dose reduction of sirolimus prior to dronedarone initiation.
miR-221/222 suppression protects against endoplasmic reticulum stress-induced apoptosis via p27Kip1- and MEK/ERK-mediated cell cycle regulation
Authors: Dai Rongyang , Li Juan , Liu Youping , Yan Dongmei , Chen Shaokun , Duan Chunyan , Liu Xiaoyan , He Tao , Li Hong
Published: May 2010

Cancer cells are relatively resistant to endoplasmic reticulum (ER) stress-induced apoptosis. However, the underlying mechanisms remain largely unclear. We observed that the microRNAs miR-221/222 are associated with apoptosis regulation under ER stress in human hepatocellular carcinoma (HCC) cells. Induction of ER stress does not trigger significant apoptosis but obviously causes downregulation of miR-221/222 in HCC cells. In these cells, ER stress-induced apoptosis is enhanced by miR-221/222 mimics and attenuated by miR-221/222 inhibitors. miR-221/222 promoted-apoptosis under ER stress is associated with p27Kip1- and MEK/ERK-mediated cell cycle regulation. Our results suggest that suppression of miR-221/222 plays a crucial role in the protection against apoptosis induced by ER stress in HCC cells.
Human SepSecS or SLA/LP: selenocysteine formation and autoimmune hepatitis
Authors: Palioura Sotiria , Herkel Johannes , Simonović Miljan , Lohse Ansgar W. , Söll Dieter
Published: May 2010

Selenocysteine, the 21st genetically encoded amino acid, is the major form of the antioxidant trace element selenium in the human body. In eukaryotes and archaea its synthesis proceeds through a phosphorylated intermediate in a tRNA-dependent fashion. The final step of selenocysteine formation is catalyzed byO-phosphoseryl-tRNA:selenocysteinyl-tRNA synthase (SepSecS) that converts phosphoseryl-tRNASecto selenocysteinyl-tRNASec. The human SepSecS protein is also known as soluble liver antigen/liver pancreas (SLA/LP), which represents one of the antigens of autoimmune hepatitis. Here we review the discovery of human SepSecS and the current understanding of the immunogenicity of SLA/LP in autoimmune hepatitis.
The type III secretion injectisome, a complex nanomachine for intracellular ‘toxin’ delivery
Authors: Cornelis Guy R.
Published: May 2010

The type III secretion injectisome is a nanomachine that delivers bacterial proteins into the cytosol of eukaryotic target cells. It consists of a cylindrical basal structure spanning the two bacterial membranes and the peptidoglycan, connected to a hollow needle, eventually followed by a filament (animal pathogens) or to a long pilus (plant pathogens). Export employs a type III pathway. During assembly, all the protein subunits of external elements are sequentially exported by the basal structure itself, implying that the export apparatus can switch its substrate specificity over time. The length of the needle is controlled by a protein that it also secreted during assembly and presumably acts as a molecular ruler.
Tissue kallikrein promotes prostate cancer cell migration and invasion via a protease-activated receptor-1-dependent signaling pathway
Authors: Gao Lin , Smith Robert S. , Chen Li-Mei , Chai Karl X. , Chao Lee , Chao Julie
Published: May 2010

We recently demonstrated that tissue kallikrein (TK) promotes keratinocyte migration through activation of protease-activated receptor-1 (PAR1) and transactivation of the epi-dermal growth factor receptor (EGFR). In this study, we investigated the potential role of PAR1in mediating the effect of TK on cancer cell migration, invasion and proliferation. Our results show that TK promotes DU145 prostate cancer cell migration in a concentration-dependent manner, but has no effect on A549 lung cancer cells. Active TK markedly increases DU145 cell migration and invasion, which are blocked by aprotinin but minimally affected by icatibant; kinin treatment has little effect. TK-induced cell migration and invasion are abolished by inhibition of PAR1using a pharmacological inhibitor or RNA interference. The effect of TK on cell migration and invasion are also blocked by inhibitors of protein kinase C, c-Src, matrix metalloproteinase, EGFR and extracellular signal-regulated kinase (ERK). Moreover, TK stimulates ERK phosphorylation, which is inhibited by an EGFR antagonist. Additionally, TK but not kinin stimulates DU145 cell proliferation through activation of the kinin B2 receptor, but not PAR1and EGFR. These results indicate differential signaling pathways mediated by TK in promoting prostate cancer cell migration and invasion via PAR1activation, and proliferation via kinin B2 receptor stimulation.
Cathepsin E enhances anticancer activity of doxorubicin on human prostate cancer cells showing resistance to TRAIL-mediated apoptosis
Authors: Yasukochi Atsushi , Kawakubo Tomoyo , Nakamura Seiji , Yamamoto Kenji
Published: May 2010

We previously described that cathepsin E specifically induces growth arrest and apoptosis in several human prostate cancer cell linesin vitroby catalyzing the proteolytic release of soluble tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) from the tumor cell surface. It also prevents tumor growth and metastasisin vivothrough multiple mechanisms, including induction of apoptosis, angiogenesis inhibition and enhanced immune responses. Using the prostate cancer cell line PPC-1, which is relatively resistant to cell death by doxorubicin (40–50% cytotoxicity), we first report that a combination treatment with cathepsin E can overcome resistance of the cells to this agent.In vitrostudies showed that combined treatment of PPC-1 cells with the two agents synergistically induces viability loss, mainly owing to down-regulation of a short form of the FLICE inhibitory protein FLIP. The enhanced antitumor activity was corroborated byin vivostudies with athymic mice bearing PPC-1 xenografts. Intratumoral application of cathepsin E in doxorubicin-treated mice results in tumor cell apoptosis and tumor regression in xenografts by enhanced TRAIL-induced apoptosis through doxorubicin-induced c-FLIP down-regulation and by a decrease in tumor cell proliferation. These results indicate that combination of cathepsin E and doxorubicin is sufficient to overcome resistance to TRAIL-mediated apoptosis in chemoresistant prostate cancer PPC-1 cells, thus indicating therapeutic potential for clinical use.
Decoding transcription and microRNA-mediated translation control in Drosophila development
Authors: Gaul Ulrike
Published: May 2010

The spatio-temporal regulation of gene expression lies at the heart of animal development. In this article we present an overview of our recent work to apply systems biological approaches to the study of transcription and microRNA-mediated translation control in Drosophila development. We have identified many new cis-regulatory elements within the segmentation gene network, a transcriptional hierarchy governing pattern formation along the antero-posterior axis of the embryo, and developed a novel thermodynamic model to predict their expression. A similar thermodynamic approach that takes into account the secondary structure of the target mRNA significantly improves the prediction of microRNA binding sites.
Converging on the function of intrinsically disordered nucleoporins in the nuclear pore complex
Authors: Peleg Orit , Lim Roderick Y.H.
Published: May 2010

Several biological mechanisms involve proteins or proteinaceous components that are intrinsically disordered. A case in point pertains to the nuclear pore complex (NPC), which regulates molecular transport between the nucleus and the cytoplasm. NPC functionality is dependent on unfolded domains rich in Phe-Gly (FG) repeats (i.e., FG-domains) that collectively act to promote or hinder cargo translocation. To a large extent, our understanding of FG-domain behavior is limited to in vitro investigations given the difficulty to resolve them directly in the NPC. Nevertheless, recent findings indicate a collective convergence towards rationalizing FG-domain function. This review aims to glean further insight into this fascinating problem by taking an objective look at the boundary conditions and contextual details underpinning FG-domain behavior in the NPC. Here, we treat the FG-domains as being commensurate with polymeric chains to address ambiguities such as for instance, how FG-domains tethered to the central channel of the NPC would behave differently as compared with their free-floating counterparts in solution. By bringing such fundamental questions to the fore, this review seeks to illuminate the importance of how such parameters can hold influence over the structure-function relation of intrinsically disordered proteins in the NPC and beyond.
Towards molecular systems biology of gene transcription and regulation
Authors: Cramer Patrick
Published: May 2010

Ten years after the determination of the RNA polymerase II structure, the basic mechanism of mRNA synthesis during gene transcription is known. In the future, the initiation and regulation of transcription must be studied with a combination of structural biology, biochemistry, functional genomics, and computational methods. In this article, the efforts of our laboratory to move from an integrated structural biology of gene transcription towards molecular systems biology of gene regulation are reviewed.
Assessment of the Nova StatSensor whole blood point-of-care creatinine analyzer for the measurement of kidney function in screening for chronic kidney disease
Authors: Shephard Mark , Peake Michael , Corso Olivia , Shephard Anne , Mazzachi Beryl , Spaeth Brooke , Barbara Jeffrey , Mathew Timothy
Published: May 2010

Background: Point-of-care testing for creatinine using a fingerprick sample and resultant estimated glomerular filtration rate has potential for screening for chronic kidney disease in community settings. This study assessed the applicability of the Nova StatSensor creatinine analyzer for this purpose.

Methods: Fingerprick samples from 100 patients (63 renal, 37 healthy volunteers; range 46–962 μmol/L) were assayed using two StatSensor analyzers. Lithium heparin venous plasma samples collected simultaneously were assayed in duplicate using the isotope dilution mass spectrometry-aligned Roche Creatinine Plus enzymatic assay on a Hitachi Modular P unit. Method comparison statistics and the ability of the StatSensor to correctly categorise estimated glomerular filtration rate above or below 60 mL/min were calculated pre- and post-alignment with the laboratory method.

Results: StatSensor 1 creatinine results (y) were much lower than the laboratory (y=0.75x+10.2, average bias –47.3, 95% limits of agreement –208 to +113 μmol/L). For estimated glomerular filtration rates above or below 60 mL/min, 100% and 87% of results respectively agreed with the laboratory estimated glomerular filtration rate (79% and 96% post-alignment). StatSensor 2 statistics were similar. The 95% limits of agreement between StatSensor creatinine results were –35 to +34 μmol/L.

Conclusions: Isotope dilution mass spectrometry alignment of the StatSensor will identify most patients with estimated glomerular filtration rate <60 mL/min, but there will be many falsely low estimated glomerular filtration rate results that require laboratory validation. Creatinine results need improvement.

Clin Chem Lab Med 2010;48:1113–9.
Singing-Related Neural Activity Distinguishes Two Putative Pallidal Cell Types in the Songbird Basal Ganglia: Comparison to the Primate Internal and External Pallidal Segments
Authors: Goldberg Jesse H. , Adler Avital , Bergman Hagai , Fee Michale S.
Published: May 2010

The songbird area X is a basal ganglia homolog that contains two pallidal cell types—local neurons that project within the basal ganglia and output neurons that project to the thalamus. Based on these projections, it has been proposed that these classes are structurally homologous to the primate external (GPe) and internal (GPi) pallidal segments. To test the hypothesis that the two area X pallidal types are functionally homologous to GPe and GPi neurons, we recorded from neurons in area X of singing juvenile male zebra finches, and directly compared their firing patterns to neurons recorded in the primate pallidus. In area X, we found two cell classes that exhibited high firing (HF) rates (>60 Hz) characteristic of pallidal neurons. HF-1 neurons, like most GPe neurons we examined, exhibited large firing rate modulations, including bursts and long pauses. In contrast, HF-2 neurons, like GPi neurons, discharged continuously without bursts or long pauses. To test whether HF-2 neurons were the output neurons that project to the thalamus, we next recorded directly from pallidal axon terminals in thalamic nucleus DLM, and found that all terminals exhibited singing-related firing patterns indistinguishable from HF-2 neurons. Our data show that singing-related neural activity distinguishes two putative pallidal cell types in area X: thalamus-projecting neurons that exhibit activity similar to the primate GPi, and non-thalamus-projecting neurons that exhibit activity similar to the primate GPe. These results suggest that song learning in birds and motor learning in mammals use conserved basal ganglia signaling strategies.
Postnatal Switch from Synaptic to Extrasynaptic Transmission between Interneurons and NG2 Cells
Authors: Vélez-Fort Mateo , Maldonado Paloma P. , Butt Arthur M. , Audinat Etienne , Angulo María Cecilia
Published: May 2010

NG2 cells, oligodendrocyte precursors, play a critical role in myelination during postnatal brain maturation, but a pool of these precursors is maintained in the adult and recruited to lesions in demyelinating diseases. NG2 cells in immature animals have recently been shown to receive synaptic inputs from neurons, and these have been assumed to persist in the adult. Here, we investigated the GABAergic synaptic activity of NG2 cells in acute slices of the barrel cortex of NG2-DsRed transgenic mice during the first postnatal month, which corresponds to the period of active myelination in the neocortex. Our data demonstrated that the frequency of spontaneous and miniature GABAergic synaptic activity of cortical NG2 cells dramatically decreases after the second postnatal week, indicating a decrease in the number of synaptic inputs onto NG2 cells during development. However, NG2 cells still receive GABAergic inputs from interneurons in the adult cortex. These inputs do not rely on the presence of functional synapses but involve a form of GABA spillover. This GABA volume transmission allows interneurons to induce phasic responses in target NG2 cells through the activation of extrasynaptic GABAAreceptors. Hence, after development is complete, volume transmission allows NG2 cells to integrate neuronal activity patterns at frequencies occurring duringin vivosensory stimulation.
Glutamatergic Signaling by Mesolimbic Dopamine Neurons in the Nucleus Accumbens
Authors: Tecuapetla Fatuel , Patel Jyoti C. , Xenias Harry , English Daniel , Tadros Ibrahim , Shah Fulva , Berlin Joshua , Deisseroth Karl , Rice Margaret E. , Tepper James M. , Koos Tibor
Published: May 2010

Recent evidence suggests the intriguing possibility that midbrain dopaminergic (DAergic) neurons may use fast glutamatergic transmission to communicate with their postsynaptic targets. Because of technical limitations, direct demonstration of the existence of this signaling mechanism has been limited to experiments using cell culture preparations that often alter neuronal function including neurotransmitter phenotype. Consequently, it remains uncertain whether glutamatergic signaling between DAergic neurons and their postsynaptic targets exists under physiological conditions. Here, using an optogenetic approach, we provide the first conclusive demonstration that mesolimbic DAergic neurons in mice release glutamate and elicit excitatory postsynaptic responses in projection neurons of the nucleus accumbens. In addition, we describe the properties of the postsynaptic glutamatergic responses of these neurons during experimentally evoked burst firing of DAergic axons that reproduce the reward-related phasic population activity of the mesolimbic projection. These observations indicate that, in addition to DAergic mechanisms, mesolimbic reward signaling may involve glutamatergic transmission.
Presenilin 1 Mutants Impair the Self-Renewal and Differentiation of Adult Murine Subventricular Zone-Neuronal Progenitors via Cell-Autonomous Mechanisms Involving Notch Signaling
Authors: Veeraraghavalu Karthikeyan , Choi Se Hoon , Zhang Xiaoqiong , Sisodia Sangram S.
Published: May 2010

The vast majority of pedigrees with familial Alzheimer's disease (FAD) are caused by inheritance of mutations in thePSEN1 1gene. While genetic ablation studies have revealed a role for presenilin 1 (PS1) in embryonic neurogenesis, little information has emerged regarding the potential effects of FAD-linked PS1 variants on proliferation, self-renewal and differentiation, key events that control cell fate commitment of adult brain neural progenitors (NPCs). We used adult brain subventricular zone (SVZ)-derived NPC cultures transduced with recombinant lentivirus as a means to investigate the effects of various PS1 mutants on self-renewal and differentiation properties. We now show that viral expression of several PS1 mutants in NPCs leads to impaired self-renewal and altered differentiation toward neuronal lineage,in vitro. In line with these observations, diminished constitutive proliferation and steady-state SVZ progenitor pool size was observedin vivoin transgenic mice expressing the PS1ΔE9 variant. Moreover, NPC cultures established from the SVZ of adult mice expressing PS1ΔE9 exhibit reduced self-renewal capacity and premature exit toward neuronal fates. To these findings, we show that both the levels of endogenous Notch/CBF-1-transcriptional activity and transcripts encoding Notch target genes are diminished in SVZ NPCs expressing PS1ΔE9. The deficits in self-renewal and multipotency are restored by expression of Notch1-ICD or a downstream target of the Notch pathway, Hes1. Hence, we argue that a partial reduction in PS-dependent γ-secretase processing of the Notch, at least in part, accounts for the impairments observed in SVZ NPCs expressing the FAD-linked PS1ΔE9 variant.
Action Potentials Initiate in the Axon Initial Segment and Propagate through Axon Collaterals Reliably in Cerebellar Purkinje Neurons
Authors: Foust Amanda , Popovic Marko , Zecevic Dejan , McCormick David A.
Published: May 2010

Purkinje neurons are the output cells of the cerebellar cortex and generate spikes in two distinct modes, known as simple and complex spikes. Revealing the point of origin of these action potentials, and how they conduct into local axon collaterals, is important for understanding local and distal neuronal processing and communication. By using a recent improvement in voltage-sensitive dye imaging technique that provided exceptional spatial and temporal resolution, we were able to resolve the region of spike initiation as well as follow spike propagation into axon collaterals for each action potential initiated on single trials. All fast action potentials, for both simple and complex spikes, whether occurring spontaneously or in response to a somatic current pulse or synaptic input, initiated in the axon initial segment. At discharge frequencies of less than ∼250 Hz, spikes propagated faithfully through the axon and axon collaterals, in a saltatory manner. Propagation failures were only observed for very high frequencies or for the spikelets associated with complex spikes. These results demonstrate that the axon initial segment is a critical decision point in Purkinje cell processing and that the properties of axon branch points are adjusted to maintain faithful transmission.
Mechanistic Basis for the Failure of Cone Transducin to Translocate: Why Cones Are Never Blinded by Light
Authors: Lobanova Ekaterina S. , Herrmann Rolf , Finkelstein Stella , Reidel Boris , Skiba Nikolai P. , Deng Wen-Tao , Jo Rebecca , Weiss Ellen R. , Hauswirth William W. , Arshavsky Vadim Y.
Published: May 2010

The remarkable ability of our vision to function under ever-changing conditions of ambient illumination is mediated by multiple molecular mechanisms regulating the light sensitivity of rods and cones. One such mechanism involves massive translocation of signaling proteins, including the G-protein transducin, into and out of the light-sensitive photoreceptor outer segment compartment. Transducin translocation extends the operating range of rods, but in cones transducin never translocates, which is puzzling because cones typically function in much brighter light than rods. Using genetically manipulated mice in which the rates of transducin activation and inactivation were altered, we demonstrate that, like in rods, transducin translocation in cones can be triggered when transducin activation exceeds a critical level, essentially saturating the photoresponse. However, this level is never achieved in wild-type cones: their superior ability to tightly control the rates of transducin activation and inactivation, responsible for avoiding saturation by light, also accounts for the prevention of transducin translocation at any light intensity.