bluuebunny/crossref_metadata_2025 huggingface dataset:
Interrogating functional integration between injected pluripotent stem cell-derived cells and surrogate cardiac tissue
Authors: Song Hannah , Yoon Charles , Kattman Steven J. , Dengler Jana , Massé Stéphane , Thavaratnam Thushaanthini , Gewarges Mena , Nanthakumar Kumaraswamy , Rubart Michael , Keller Gordon M. , Radisic Milica , Zandstra Peter W.
Published: October 2009

Myocardial infarction resulting in irreversible loss of cardiomyocytes (CMs) remains a leading cause of heart failure. Although cell transplantation has modestly improved cardiac function, major challenges including increasing cell survival, engraftment, and functional integration with host tissue, remain. Embryonic stem cells (ESCs), which can be differentiated into cardiac progenitors (CPs) and CMs, represent a candidate cell source for cardiac cell therapy. However, it is not known what specific cell type or condition is the most appropriate for transplantation. This problem is exasperated by the lack of efficient and predictive strategies to screen the large numbers of parameters that may impact cell transplantation. We used a cardiac tissue model, engineered heart tissue (EHT), and quantitative molecular and electrophysiological analyses, to test transplantation conditions and specific cell populations for their potential to functionally integrate with the host tissue. In this study, we validated our analytical platform using contractile mouse neonatal CMs (nCMs) and noncontractile cardiac fibroblasts (cFBs), and screened for the integration potential of ESC-derived CMs and CPs (ESC-CMs and -CPs). Consistent with previous in vivo studies, cFB injection interfered with electrical signal propagation, whereas injected nCMs improved tissue function. Purified bioreactor-generated ESC-CMs exhibited a diminished capacity for electrophysiological integration; a result correlated with lower (compared with nCMs) connexin 43 expression. ESC-CPs, however, appeared able to appropriately mature and integrate into EHT, enhancing the amplitude of tissue contraction. Our results support the use of EHT as a model system to accelerate development of cardiac cell therapy strategies.
Role of band 3 in regulating metabolic flux of red blood cells
Authors: Lewis Ian A. , Campanella M. Estela , Markley John L. , Low Philip S.
Published: October 2009

Deoxygenation elevates glycolytic flux and lowers pentose phosphate pathway (PPP) activity in mammalian erythrocytes. The membrane anion transport protein (band 3 or AE1) is thought to facilitate this process by binding glycolytic enzymes (GEs) and inhibiting their activity in an oxygen-dependent manner. However, this regulatory mechanism has not been demonstrated under physiological conditions. In this study, we introduce a
1
H-
13
C NMR technique for measuring metabolic fluxes in intact cells. The role of band 3 in mediating the oxygenated/deoxygenated metabolic transition was examined by treating cells with pervanadate, a reagent that prevents the GE–band 3 complex from forming. We report that pervanadate suppresses oxygen-dependent changes in glycolytic and PPP fluxes. Moreover, these metabolic alterations were not attributable to modulation of bisphosphoglycerate mutase, direct inhibition of GEs by pervanadate, or oxidation, which are the major side effects of pervanadate treatment. These data provide direct evidence supporting the role of band 3 in mediating oxygen-regulated metabolic transitions.
Five-month-old infants' identification of the sources of vocalizations
Authors: Vouloumanos Athena , Druhen Madelynn J. , Hauser Marc D. , Huizink Anouk T.
Published: October 2009

Humans speak, monkeys grunt, and ducks quack. How do we come to know which vocalizations animals produce? Here we explore this question by asking whether young infants expect humans, but not other animals, to produce speech, and further, whether infants have similarly restricted expectations about the sources of vocalizations produced by other species. Five-month-old infants matched speech, but not human nonspeech vocalizations, specifically to humans, looking longer at static human faces when human speech was played than when either rhesus monkey or duck calls were played. They also matched monkey calls to monkey faces, looking longer at static rhesus monkey faces when rhesus monkey calls were played than when either human speech or duck calls were played. However, infants failed to match duck vocalizations to duck faces, even though infants likely have more experience with ducks than monkeys. Results show that by 5 months of age, human infants generate expectations about the sources of some vocalizations, mapping human faces to speech and rhesus faces to rhesus calls. Infants' matching capacity does not appear to be based on a simple associative mechanism or restricted to their specific experiences. We discuss these findings in terms of how infants may achieve such competence, as well as its specificity and relevance to acquiring language.
26G endo-siRNAs regulate spermatogenic and zygotic gene expression in Caenorhabditis elegans
Authors: Han Ting , Manoharan Arun Prasad , Harkins Tim T. , Bouffard Pascal , Fitzpatrick Colin , Chu Diana S. , Thierry-Mieg Danielle , Thierry-Mieg Jean , Kim John K.
Published: October 2009

Endogenous small interfering RNAs (endo-siRNAs) regulate diverse gene expression programs in eukaryotes by either binding and cleaving mRNA targets or mediating heterochromatin formation; however, the mechanisms of endo-siRNA biogenesis, sorting, and target regulation remain poorly understood. Here we report the identification and function of a specific class of germline-generated endo-siRNAs in
Caenorhabditis elegans
that are 26 nt in length and contain a guanine at the first nucleotide position (i.e., 26G RNAs). 26G RNAs regulate gene expression during spermatogenesis and zygotic development, and their biogenesis requires the ERI-1 exonuclease and the RRF-3 RNA-dependent RNA polymerase (RdRP). Remarkably, we identified two nonoverlapping subclasses of 26G RNAs that sort into specific RNA-induced silencing complexes (RISCs) and differentially regulate distinct mRNA targets. Class I 26G RNAs target genes are expressed during spermatogenesis, whereas class II 26G RNAs are maternally inherited and silence gene expression during zygotic development. These findings implicate a class of endo-siRNAs in the global regulation of transcriptional programs required for fertility and development.
Size, shape, and the thermal niche of endotherms
Authors: Porter Warren P. , Kearney Michael
Published: October 2009

A key challenge in ecology is to define species' niches on the basis of functional traits. Size and shape are important determinants of a species' niche but their causal role is often difficult to interpret. For endotherms, size and shape define the thermal niche through their interaction with core temperature, insulation, and environmental conditions, determining the thermoneutral zone (TNZ) where energy and water costs are minimized. Laboratory measures of metabolic rate used to describe TNZs cannot be generalized to infer the capacity for terrestrial animals to find their TNZ in complex natural environments. Here, we derive an analytical model of the thermal niche of an ellipsoid furred endotherm that accurately predicts field and laboratory data. We use the model to illustrate the relative importance of size and shape on the location of the TNZ under different environmental conditions. The interaction between body shape and posture strongly influences the location of the TNZ and the expected scaling of metabolic rate with size at constant temperature. We demonstrate that the latter relationship has a slope of approximately ½ rather than the commonly expected surface area/volume scaling of ⅔. We show how such functional traits models can be integrated with spatial environmental datasets to calculate null expectations for body size clines from a thermal perspective, aiding mechanistic interpretation of empirical clines such as Bergmann's Rule. The combination of spatially explicit data with biophysical models of heat exchange provides a powerful means for studying the thermal niches of endotherms across climatic gradients.
Bothnia dystrophy is caused by domino-like rearrangements in cellular retinaldehyde-binding protein mutant R234W
Authors: He Xiaoqin , Lobsiger Joel , Stocker Achim
Published: October 2009

Cellular retinaldehyde-binding protein (CRALBP) is essential for mammalian vision by routing 11-
cis
-retinoids for the conversion of photobleached opsin molecules into photosensitive visual pigments. The arginine-to-tryptophan missense mutation in position 234 (R234W) in the human gene
RLBP1
encoding CRALBP compromises visual pigment regeneration and is associated with Bothnia dystrophy. Here we report the crystal structures of both wild-type human CRALBP and of its mutant R234W as binary complexes complemented with the endogenous ligand 11-
cis
-retinal, at 3.0 and 1.7 Å resolution, respectively. Our structural model of wild-type CRALBP locates R234 to a positively charged cleft at a distance of 15 Å from the hydrophobic core sequestering 11-
cis
-retinal. The R234W structural model reveals burial of W234 and loss of dianion-binding interactions within the cleft with physiological implications for membrane docking. The burial of W234 is accompanied by a cascade of side-chain flips that effect the intrusion of the side-chain of I238 into the ligand-binding cavity. As consequence of the intrusion, R234W displays 5-fold increased resistance to light-induced photoisomerization relative to wild-type CRALBP, indicating tighter binding to 11-
cis
-retinal. Overall, our results reveal an unanticipated domino-like structural transition causing Bothnia-type retinal dystrophy by the impaired release of 11-
cis
-retinal from R234W.
Quantitative proteomic analysis of single pancreatic islets
Authors: Waanders Leonie F. , Chwalek Karolina , Monetti Mara , Kumar Chanchal , Lammert Eckhard , Mann Matthias
Published: October 2009

Technological developments make mass spectrometry (MS)-based proteomics a central pillar of biochemical research. MS has been very successful in cell culture systems, where sample amounts are not limiting. To extend its capabilities to extremely small, physiologically distinct cell types isolated from tissue, we developed a high sensitivity chromatographic system that measures nanogram protein mixtures for 8 h with very high resolution. This technology is based on splitting gradient effluents into a capture capillary and provides an inherent technical replicate. In a single analysis, this allowed us to characterize kidney glomeruli isolated by laser capture microdissection to a depth of more than 2,400 proteins. From pooled pancreatic islets of Langerhans, another type of “miniorgan,” we obtained an in-depth proteome of 6,873 proteins, many of them involved in diabetes. We quantitatively compared the proteome of single islets, containing 2,000–4,000 cells, treated with high or low glucose levels, and covered most of the characteristic functions of beta cells. Our ultrasensitive analysis recapitulated known hyperglycemic changes but we also find components up-regulated such as the mitochondrial stress regulator Park7. Direct proteomic analysis of functionally distinct cellular structures opens up perspectives in physiology and pathology.
Microsomal prostaglandin E synthase 1 determines tumor growth in vivo of prostate and lung cancer cells
Authors: Hanaka Hiromi , Pawelzik Sven-Christian , Johnsen John Inge , Rakonjac Marija , Terawaki Kan , Rasmuson Agnes , Sveinbjörnsson Baldur , Schumacher Martin C. , Hamberg Mats , Samuelsson Bengt , Jakobsson Per-Johan , Kogner Per , Rådmark Olof
Published: October 2009

There is strong evidence for a role of prostaglandin E
2
(PGE
2
) in cancer cell proliferation and tumor development. In PGE
2
biosynthesis, cyclooxygenases (COX-1/COX-2) convert arachidonic acid to PGH
2
, which can be isomerized to PGE
2
by microsomal PGE-synthase-1 (MPGES-1). The human prostate cancer cell line DU145 expressed high amounts of MPGES-1 in a constitutive manner. MPGES-1 expression also was detectable in human prostate cancer tissues, where it appeared more abundant compared with benign hyperplasia. By using shRNA, we established stable and practically complete knockdown of MPGES-1, both in DU145 cells with high constitutive expression and in the non-small cell lung cancer cell line A549, where MPGES-1 is inducible. For microsomes prepared from knockdown clones, conversion of PGH
2
to PGE
2
was reduced by 85–90%. This resulted in clear phenotypic changes: MPGES-1 knockdown conferred decreased clonogenic capacity and slower growth of xenograft tumors (with disintegrated tissue structure) in nude mice. For DU145 cells, MPGES-1 knockdown gave increased apoptosis in response to genotoxic stress (adriamycin), which could be rescued by exogenous PGE
2
. The results suggest that MPGES-1 is an alternative therapeutic target in cancer cells expressing this enzyme.
PTEN dosage is essential for neurofibroma development and malignant transformation
Authors: Gregorian Caroline , Nakashima Jonathan , Dry Sarah M. , Nghiemphu P. Leia , Smith Kate Barzan , Ao Yan , Dang Julie , Lawson Gregory , Mellinghoff Ingo K. , Mischel Paul S. , Phelps Michael , Parada Luis F. , Liu Xin , Sofroniew Michael V. , Eilber Fritz C. , Wu Hong
Published: October 2009

Patients with neurofibromatosis type 1 (NF1) carry approximately a 10% lifetime risk of developing a malignant peripheral nerve sheath tumor (MPNST). Although the molecular mechanisms underlying NF1 to MPNST malignant transformation remain unclear, alterations of both the RAS/RAF/MAPK and PI3K/AKT/mTOR signaling pathways have been implicated. In a series of genetically engineered murine models, we perturbed RAS/RAF/MAPK or/and PTEN/PI3K/AKT pathway, individually or simultaneously, via conditional activation ofK-rasoncogene or deletion ofNf1orPtentumor suppressor genes. Only K-Ras activation in combination with a singlePtenallele deletion led to 100% penetrable development of NF lesions and subsequent progression to MPNST. Importantly, loss or decrease in PTEN expression was found in all murine MPNSTs and a majority of human NF1-associated MPNST lesions, suggesting that PTEN dosage and its controlled signaling pathways are critical for transformation of NFs to MPNST. Using noninvasive in vivo PET-CT imaging, we demonstrated that FDG can be used to identify the malignant transformation in both murine and human MPNSTs. Our data suggest that combined inhibition of RAS/RAF/MAPK and PTEN/PI3K/AKT pathways may be beneficial for patients with MPNST.
A role for the ventral premotor cortex beyond performance monitoring
Authors: Pardo-Vazquez Jose L. , Leboran Victor , Acuña Carlos
Published: October 2009

Depending on the circumstances, decision making requires either comparing current sensory information with that showed recently or with that recovered from long-term memory (LTM). In both cases, to learn from past decisions and adapt future ones, memories and outcomes have to be available after the report of a decision. The ventral premotor cortex (PMv) is a good candidate for integrating memory traces and outcomes because it is involved in working-memory, decision-making, and encoding the outcomes. To test this hypothesis we recorded the extracellular unit activity while monkeys performed 2 variants of a visual discrimination task. In one task, the decision was based on the comparison of the orientation of a current stimulus with that of another stimulus recently shown. In the other task, the monkeys had to compare the current orientation of the stimulus with the correct one retrieved from LTM. Here, we report that when the task required retrieval of the stimulus and its use in the following trials, the neurons continue encoding this internal representation together with the outcomes after the monkey has emitted the motor response. However, this codification did not occur when the stimulus was shown recently and updated every trial. These results suggest that the PMv activity represents the information needed to evaluate the consequences of a decision. We interpret these results as evidence that the PMv plays a role in evaluating the outcomes that can serve to learn and thus adapt future decision to environmental demands.
Paper-supported 3D cell culture for tissue-based bioassays
Authors: Derda Ratmir , Laromaine Anna , Mammoto Akiko , Tang Sindy K. Y. , Mammoto Tadanori , Ingber Donald E. , Whitesides George M.
Published: October 2009

Fundamental investigations of human biology, and the development of therapeutics, commonly rely on 2D cell-culture systems that do not accurately recapitulate the structure, function, or physiology of living tissues. Systems for 3D cultures exist but do not replicate the spatial distributions of oxygen, metabolites, and signaling molecules found in tissues. Microfabrication can create architecturally complex scaffolds for 3D cell cultures that circumvent some of these limitations; unfortunately, these approaches require instrumentation not commonly available in biology laboratories. Here we report that stacking and destacking layers of paper impregnated with suspensions of cells in extracellular matrix hydrogel makes it possible to control oxygen and nutrient gradients in 3D and to analyze molecular and genetic responses. Stacking assembles the “tissue”, whereas destacking disassembles it, and allows its analysis. Breast cancer cells cultured within stacks of layered paper recapitulate behaviors observed both in 3D tumor spheroids in vitro and in tumors in vivo: Proliferating cells in the stacks localize in an outer layer a few hundreds of microns thick, and growth-arrested, apoptotic, and necrotic cells concentrate in the hypoxic core where hypoxia-sensitive genes are overexpressed. Altering gas permeability at the ends of stacks controlled the gradient in the concentration of the O
2
and was sufficient by itself to determine the distribution of viable cells in 3D. Cell cultures in stacked, paper-supported gels offer a uniquely flexible approach to study cell responses to 3D molecular gradients and to mimic tissue- and organ-level functions.
Annual Incidence of Latent Tuberculosis Infection among Newly Employed Nurses at a Tertiary Care University Hospital
Authors: Lee Kwangha , Han Min Kyoung , Choi Hye Ran , Choi Chang-Min , Oh Yeon-Mok , Lee Sang Do , Kim Woo Sung , Kim Dong Soon , Woo Jun Hee , Shim Tae Sun
Published: October 2009

Objective.

To investigate the annual rate of tuberculosis (TB) infection among newly employed nurses using both tuberculin skin test (TST) and QuantiFERON-TB Gold (QFT-G; Cellestis Limited) assay.

Design.

A prospective cohort study involving newly employed nurses.

Setting.

A tertiary care university hospital in South Korea.

Methods.

All participants (n = 196) were tested with the TST and QFT-G assay at baseline. After 1 year, the TST and QFT-G assay were reperformed for subjects who had negative TST results at baseline and for all subjects, respectively.

Results.

The baseline TST and QFT-G assays were positive for 101 subjects (51.5%) and 28 subjects (14.3%), respectively; 22 subjects (11.2%) had positive results of both tests. Although the overall between-test agreement was 54.9% (κ = 0.151 [95% confidence interval, 0.047–0.245]), agreement improved to 78.5% (κ = 0.462 [95% confidence interval, 0.007–0.917]) for subjects who had not received bacille Calmette-Guérin vaccination. After 1 year, the TST yielded positive results for 16 (21.3%) of 75 nurses with negative baseline results, and the QFT-G assay yielded positive results for 21 (14.4%) of 146 subjects with negative baseline Results. Collectively, 5 subjects (3.0%) experienced conversion to positive results with both tests, and 32 subjects (18.9%) experienced conversion to positive results with one of the tests. Neither the employing hospital department nor exposure to patients with TB affected test conversion status.

Conclusions.

The poor overall agreement between TST and QFT-G results may have been caused by the confounding effect of bacille Calmette-Guérin vaccination. The annual risk of TB infection among newly employed nurses was at least 3% on the basis of results of both the TST and QFT-G test. Stricter preventive strategies against TB spread should be implemented in our hospital.
Measurement of Influenza Vaccination Coverage among Healthcare Personnel in US Hospitals
Authors: Lindley Megan C. , Yonek Juliet , Ahmed Faruque , Perz Joseph F. , Torres Gretchen Williams
Published: October 2009

Objective.

To characterize practices related to measuring influenza vaccination rates among healthcare personnel in US hospitals.

Design.

Descriptive survey.

Setting.

Nonfederal, short-stay hospitals that provide general medical and surgical services, identified by use of the 2004 American Hospital Association Annual Survey Database.

Participants.

Healthcare personnel from 996 randomly sampled US hospitals stratified by region and bed size.

Methods.

A self-administered questionnaire was distributed in 2006 to infection control coordinators to gather data on policies and practices related to the provision of the influenza vaccine and on the measurement and reporting of influenza vaccination rates. Descriptive statistics and associations were calculated, and logistic regression was conducted.

Results.

The response rate was 56% (ie, 555 of 996 US hospitals responded to the questionnaire). Weighting accounted for sampling design and nonresponse. Most hospitals provided the influenza vaccine to employees (100%), credentialed medical staff (ie, independent practitioners; 94%), volunteers (86%), and contract staff (83%); provision for students and residents was less frequent (58%). Only 69% of hospitals measured vaccination rates (mean coverage rate, 55%). Most hospitals that measured coverage included employees (98%) in the vaccination rates, whereas contract staff (53%), credentialed medical staff (56%), volunteers (56%), and students and residents (30%) were less commonly included. Among hospitals measuring coverage, 44% included persons for which vaccine was contraindicated, and 51% included persons who refused vaccination. After adjustment for region and size, hospitals with vaccination plans written into policy (odds ratio, 2.0 [95% confidence interval, 1.22–7.67]) or that addressed internally reporting coverage (odds ratio, 4.8 [95% confidence interval, 2.97–7.66]) were more likely to measure coverage than were hospitals without such plans.

Conclusions.

Hospitals vary in terms of the groups of individuals included in influenza vaccination coverage measurements. Standardized measures may improve comparability of hospital-reported vaccination rates. Measuring coverage in a manner that facilitates identification of occupational groups with low vaccination rates may inform development of targeted interventions.
Identification of a Pseudo-Outbreak ofClostridium difficileInfection (CDI) and the Effect of Repeated Testing, Sensitivity, and Specificity on Perceived Prevalence of CDI
Authors: Litvin Marina , Reske Kimberly A. , Mayfield Jennie , McMullen Kathleen M. , Georgantopoulos Peter , Copper Susan , Hoppe-Bauer Joan E. , Fraser Victoria J. , Warren David K. , Dubberke Erik R.
Published: October 2009

Objective.

To describe a pseudo-outbreak ofClostridium difficileinfection (CDI) caused by a faulty toxin assay lot and to determine the effect of sensitivity, specificity, and repeated testing forC. difficileon perceived CDI burden, positive predictive value, and false-positive results.

Design.

Outbreak investigation and criterion standard.

Patients.

Patients hospitalized at a tertiary care hospital who had at least 1 toxin assay for detection ofC. difficileperformed during the period from July 1, 2004, through June 30, 2006.

Methods.

The run control chart method and thex2test were used to compare CDI rates and the proportion of positive test results before, during, and after the pseudo-outbreak. The effect of repeated testing was evaluated by using 3 hypothetical models with a sample of 10,000 patients and various assay sensitivity and specificity estimates.

Results.

In November of 2005, the CDI rate at the hospital increased from 1.5 to 2.6 cases per 1,000 patient-days (P< .01), and the proportion of positive test results increased from 13.6% to 22.1% (P< .01). An investigation revealed a pseudo-outbreak caused by a faulty toxin assay lot. A decrease of only 1.2% in the specificity of the toxin assay would result in a 32% increase in perceived incidence of CDI at this institution. When calculated by use of the manufacturer's stated specificity and sensitivity and this institution's testing practices, the positive predictive value of the test decreased from 80.6% to 4.1% for patients who received 3 tests.

Conclusion.

Specificity is as important as sensitivity when testing for CDI. False-positive CDI cases can drain hospital resources and adversely affect patients. Repeated testing forC. difficileshould be performed with caution.
Temporal behaviour of toroidal rotation velocity in the TCABR tokamak
Authors: Severo J.H.F. , Nascimento I.C. , Kuznetsov Yu.K. , Galvão R.M.O. , Guimarães-Filho Z.O. , Borges F.O. , Usuriaga O.C. , Elizondo J.I. , de Sá W.P. , Sanada E.K. , Tendler M.
Published: October 2009

A new method for determining the temporal evolution of plasma rotation is reported in this work. The method is based upon the detection of two different portions of the spectral profile of a plasma impurity line, using a monochromator with two photomultipliers installed at the exit slits. The plasma rotation velocity is determined by the ratio of the two detected signals. The measured toroidal rotation velocities of C III (4647.4 Å) and C VI (5290.6 Å), at different radial positions in TCABR discharges, show good agreement, within experimental uncertainty, with previous results (Severo et al
2003 Nucl. Fusion
43 1047). In particular, they confirm that the plasma core rotates in the direction opposite to the plasma current, while near the plasma edge (r/a > 0.9) the rotation is in the same direction. This technique was also used to investigate the dependence of toroidal rotation on the poloidal position of gas puffing. The results show that there is no dependence for the plasma core, while for plasma edge (r/a > 0.9) some dependence is observed.
Simulating ITER plasma startup and rampdown scenarios in the DIII-D tokamak
Authors: Jackson G.L. , Casper T.A. , Luce T.C. , Humphreys D.A. , Ferron J.R. , Hyatt A.W. , Leuer J.A. , Petrie T.W. , Turco F. , West W.P.
Published: October 2009

DIII-D experiments have investigated ITER startup scenarios, including an initial phase where the plasma was limited on low field side poloidal bumper limiters. In addition, l
i feedback control has been tested with the goal of producing discharges in ITER within the capabilities of the poloidal field coil set and favourable to the intended mode of operations in the subsequent constant current (flattop) phase. These discharges have been modelled using the Corsica free boundary equilibrium code. High performance hybrid scenario discharges (βN = 2.8, H
98,y2 = 1.4) and ITER H-mode baseline discharges (βN > 1.6, H
98,y2 = 1–1.2) have been obtained experimentally in an ITER similar shape after the ITER-relevant startup. Studies have been initiated to develop a reliable scenario for exiting the burn phase and ramping down the plasma current in ITER without disruptions.
Mitochondrial Reactive Oxygen Species Mediate GPCR–induced TACE/ADAM17-dependent Transforming Growth Factor-α Shedding
Authors: Myers Timothy J. , Brennaman Leann H. , Stevenson Mary , Higashiyama Shigeki , Russell William E. , Lee David C. , Sunnarborg Susan Wohler
Published: October 2009

Epidermal growth factor receptor (EGFR) activation by GPCRs regulates many important biological processes. ADAM metalloprotease activity has been implicated as a key step in transactivation, yet the regulatory mechanisms are not fully understood. Here, we investigate the regulation of transforming growth factor-α (TGF-α) shedding by reactive oxygen species (ROS) through the ATP-dependent activation of the P2Y family of GPCRs. We report that ATP stimulates TGF-α proteolysis with concomitant EGFR activation and that this process requires TACE/ADAM17 activity in both murine fibroblasts and CHO cells. ATP-induced TGF-α shedding required calcium and was independent of Src family kinases and PKC and MAPK signaling. Moreover, ATP-induced TGF-α shedding was completely inhibited by scavengers of ROS, whereas calcium-stimulated shedding was partially inhibited by ROS scavenging. Hydrogen peroxide restored TGF-α shedding after calcium chelation. Importantly, we also found that ATP-induced shedding was independent of the cytoplasmic NADPH oxidase complex. Instead, mitochondrial ROS production increased in response to ATP and mitochondrial oxidative complex activity was required to activate TACE-dependent shedding. These results reveal an essential role for mitochondrial ROS in regulating GPCR-induced growth factor shedding.
Neuronal IP33-Kinase is an F-actin–bundling Protein: Role in Dendritic Targeting and Regulation of Spine Morphology
Authors: Johnson Hong W. , Schell Michael J.
Published: October 2009

The actin microstructure in dendritic spines is involved in synaptic plasticity. Inositol trisphosphate 3-kinase A (ITPKA) terminates Ins(1,4,5)P3signals emanating from spines and also binds filamentous actin (F-actin) through its amino terminal region (amino acids 1-66, N66). Here we investigated how ITPKA, independent of its kinase activity, regulates dendritic spine F-actin microstructure. We show that the N66 region of the protein mediates F-actin bundling. An N66 fusion protein bundled F-actin in vitro, and the bundling involved N66 dimerization. By mutagenesis we identified a point mutation in a predicted helical region that eliminated both F-actin binding and bundling, rendering the enzyme cytosolic. A fusion protein containing a minimal helical region (amino acids 9-52, N9-52) bound F-actin in vitro and in cells, but had lower affinity. In hippocampal neurons, GFP-tagged N66 expression was highly polarized, with targeting of the enzyme predominantly to spines. By contrast, N9-52-GFP expression occurred in actin-rich structures in dendrites and growth cones. Expression of N66-GFP tripled the length of dendritic protrusions, induced longer dendritic spine necks, and induced polarized actin motility in time-lapse assays. These results suggest that, in addition to its ability to regulate intracellular Ca2+via Ins(1,4,5)P3metabolism, ITPKA regulates structural plasticity.
Exploring the Roles of Diaphanous and Enabled Activity in Shaping the Balance between Filopodia and Lamellipodia
Authors: Homem Catarina C.F. , Peifer Mark
Published: October 2009

During migration cell protrusions power cell extension and sample the environment. Different cells produce different protrusions, from keratocytes dominated by lamellipodia, to growth cones combining filopodia and lamellipodia, to dendritic spines. One key challenge is to determine how the toolkit of actin regulators are coordinated to generate these diverse protrusive arrays. Here we use Drosophila leading-edge (LE) cells to explore how Diaphanous (Dia)-related formins and Ena/VASP proteins cooperate in this process. We first dissect the Dia regulatory region, revealing novel roles for the GTPase-binding and FH3 domains in cortical localization, filopodial initiation, and lengthening. Second, we provide evidence that activating Dia mobilizes Ena from storage places near the LE to act at the LE. Further, Dia and Ena coIP and can recruit one another to new locations, suggesting cooperation is key to their mechanisms of action. Third, we directly explore the functional relationship between Dia and Ena, varying their levels and activity separately in the same cell type. Surprisingly, although each is sufficient to induce filopodia, together they induce lamellipodia. Our data suggest they work together in a complex and nonadditive way, with the ratio between active Dia and Ena being one factor that modulates the balance between filopodia and lamellipodia.
MBP-1 Suppresses Growth and Metastasis of Gastric Cancer Cells through COX-2
Authors: Hsu Kai-Wen , Hsieh Rong-Hong , Wu Chew-Wun , Chi Chin-Wen , Lee Yan-Hwa Wu , Kuo Min-Liang , Wu Kou-Juey , Yeh Tien-Shun
Published: October 2009

The c-Myc promoter binding protein 1 (MBP-1) is a transcriptional suppressor of c-myc expression and involved in control of tumorigenesis. Gastric cancer is one of the most frequent neoplasms and lethal malignancies worldwide. So far, the regulatory mechanism of its aggressiveness has not been clearly characterized. Here we studied roles of MBP-1 in gastric cancer progression. We found that cell proliferation was inhibited by MBP-1 overexpression in human stomach adenocarcinoma SC-M1 cells. Colony formation, migration, and invasion abilities of SC-M1 cells were suppressed by MBP-1 overexpression but promoted by MBP-1 knockdown. Furthermore, the xenografted tumor growth of SC-M1 cells was suppressed by MBP-1 overexpression. Metastasis in lungs of mice was inhibited by MBP-1 after tail vein injection with SC-M1 cells. MBP-1 also suppressed epithelial-mesenchymal transition in SC-M1 cells. Additionally, MBP-1 bound on cyclooxygenase 2 (COX-2) promoter and downregulated COX-2 expression. The MBP-1-suppressed tumor progression in SC-M1 cells were through inhibition of COX-2 expression. MBP-1 also exerted a suppressive effect on tumor progression of other gastric cancer cells such as AGS and NUGC-3 cells. Taken together, these results suggest that MBP-1–suppressed COX-2 expression plays an important role in the inhibition of growth and progression of gastric cancer.
Bone Morphogenetic Protein-6 Promotes Cerebellar Granule Neurons Survival by Activation of the MEK/ERK/CREB Pathway
Authors: Barneda-Zahonero Bruna , Miñano-Molina Alfredo , Badiola Nahuai , Fadó Rut , Xifró Xavier , Saura Carlos A. , Rodríguez-Alvarez José
Published: October 2009

Bone morphogenetic proteins (BMPs) have been implicated in the generation and postnatal differentiation of cerebellar granule cells (CGCs). Here, we examined the eventual role of BMPs on the survival of these neurons. Lack of depolarization causes CGC death by apoptosis in vivo, a phenomenon that is mimicked in vitro by deprivation of high potassium in cultured CGCs. We have found that BMP-6, but not BMP-7, is able to block low potassium–mediated apoptosis in CGCs. The neuroprotective effect of BMP-6 is not accompanied by an increase of Smad translocation to the nucleus, suggesting that the canonical pathway is not involved. By contrast, activation of the MEK/ERK/CREB pathway by BMP-6 is necessary for its neuroprotective effect, which involves inhibition of caspase activity and an increase in Bcl-2 protein levels. Other pathways involved in the regulation of CGC survival, such as the c-Jun terminal kinase and the phosphatidylinositol 3-kinase (PI3K)-Akt/PKB, were not affected by BMP-6. Moreover, failure of BMP-7 to activate the MEK/ERK/CREB pathway could explain its inability to protect CGCs from low potassium–mediated apoptosis. Thus, this study demonstrates that BMP-6 acting through the noncanonical MEK/ERK/CREB pathway plays a crucial role on CGC survival.
CRISPI: a CRISPR interactive database
Authors: Rousseau Christine , Gonnet Mathieu , Le Romancer Marc , Nicolas Jacques
Published: October 2009

Summary: The CRISPR genomic structures (Clustered Regularly Interspaced Short Palindromic Repeats) form a family of repeats that is largely present in archaea and frequent in bacteria. On the basis of a formal model of CRISPR using very few parameters, a systematic study of all their occurrences in all available genomes of Archaea and Bacteria has been carried out. This has resulted in a relational database, CRISPI, which also includes a complete repertory of associated CRISPR-associated genes (CAS). A user-friendly web interface with many graphical tools and functions allows users to extract results, find CRISPR in personal sequences or calculate sequence similarity with spacers.

Availability: CRISPI free access at http://crispi.genouest.org

Contact:  croussea@irisa.fr; jnicolas@irisa.fr;
G-compass: a web-based comparative genome browser between human and other vertebrate genomes
Authors: Kawahara Yoshihiro , Sakate Ryuichi , Matsuya Akihiro , Murakami Katsuhiko , Sato Yoshiharu , Zhang Hao , Gojobori Takashi , Itoh Takeshi , Imanishi Tadashi
Published: October 2009

Summary: G-compass is designed for efficient comparative genome analysis between human and other vertebrate genomes. The current version of G-compass allows us to browse two corresponding genomic regions between human and another species in parallel. One-to-one evolutionarily conserved regions (i.e. orthologous regions) between species are highlighted along the genomes. Information such as locations of duplicated regions, copy number variations and mammalian ultra-conserved elements is also provided. These features of G-compass enable us to easily determine patterns of genomic rearrangements and changes in gene orders through evolutionary time. Since G-compass is a satellite database of H-InvDB, which is a comprehensive annotation resource for human genes and transcripts, users can easily refer to manually curated functional annotations and other abundant biological information for each human transcript. G-compass is expected to be a valuable tool for comparing human and model organisms and promoting the exchange of functional information.

Availability: G-compass is freely available at http://www.h-invitational.jp/g-compass/.

Contact:  t.imanishi@aist.go.jp
Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere
Authors: Yu Jian , Zhou Yong , Tanaka Isao , Yao Min
Published: October 2009

Motivation: Prediction of ligand binding sites of proteins is significant as it can provide insight into biological functions and reaction mechanisms of proteins. It is also a prerequisite for protein–ligand docking and an important step in structure-based drug design.

Results: We present a new algorithm, Roll, implemented in a program named POCASA, which can predict binding sites by detecting pockets and cavities of proteins with a rolling sphere. To evaluate the performance of POCASA, a test with the same data set as used in several existing methods was carried out. POCASA achieved a high success rate of 77%. In addition, the test results indicated that POCASA can predict good shapes of ligand binding sites.

Availability:A web version of POCASA is freely available at http://altair.sci.hokudai.ac.jp/g6/Research/POCASA_e.html

Contact:  yao@castor.sci.hokudai.ac.jp

Supplementary information:  Supplementary data are available at Bioinformatics online.
Targeted interrogation of copy number variation using SCIMMkit
Authors: Zerr Troy , Cooper Gregory M. , Eichler Evan E. , Nickerson Deborah A.
Published: October 2009

Summary: Copy number variants (CNVs) contribute substantially to human genomic diversity, and development of accurate and efficient methods for CNV genotyping is a central problem in exploring human genotype–phenotype associations. SCIMMkit provides a robust, integrated implementation of three previously validated algorithms [SCIMM (SNP-Conditional Mixture Modeling), SCIMM-Search and SCOUT (SNP-Conditional OUTlier detection)] for targeted interrogation of CNVs using Illumina Infinium II and GoldenGate SNP assays. SCIMMkit is applicable to standardized genome-wide SNP arrays and customized multiplexed SNP panels, providing economy, efficiency and flexibility in experimental design.

Availability: Source code and documentation are available for noncommercial use at http://droog.gs.washington.edu/scimmkit.

Contact:  troyz@u.washington.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Inbreeding depression in adaptive plasticity under predation risk in a freshwater snail
Authors: Auld Josh R. , Relyea Rick A.
Published: October 2009

While much attention has been paid to the effects of inbreeding on fitness, this has mostly come from a genetic perspective. Consequently, the interaction between inbreeding and the environment is less well understood. To understand the effects of inbreeding in natural populations where environmental conditions are variable, we need to examine not only how the effects of inbreeding change among environments but also how inbreeding may affect the ability to respond to environmental conditions (i.e. phenotypic plasticity). We reared selfed and outcrossed hermaphroditic snails (Physa acuta) in the presence and absence of chemical cues from predatory crayfish and quantified expression of an inducible defence, an adaptively plastic response to predation risk. Overall, inbred snails exhibited reduced defences, but more importantly, inbreeding reduced the expression of predator-induced adaptive plasticity. Inbreeding depression in defensive morphology was 26 per cent and inbreeding depression in the plasticity of this trait was 48 per cent. Inbreeding depression in adaptive plasticity may be important to understanding the effects of inbreeding in nature.
Do female ornaments indicate quality in eider ducks?
Authors: Lehikoinen Aleksi , Jaatinen Kim , Öst Markus
Published: October 2009

The fitness consequences of female ornamentation remain little studied and the results are often contradictory. Female ornamentation may be an artefact of a genetic correlation with male ornamentation, but this possibility can be disregarded if the ornament only occurs in females. Female-specific white wing bars in eiders (
Somateria mollissima
) have been suggested to indicate individual quality, and we studied size variation in this trait in relation to key fitness components and quality attributes. We found that clutch size, body condition, female age, hatching date and success were unrelated to female ornament size; ornament size was explained by its size in the previous year. In contrast, good body condition was associated with hatching success. These results suggest that the breadth of the white wing bars does not indicate individual quality in our study population.
Nanoparticle interaction with model lung surfactant monolayers
Authors: Harishchandra Rakesh Kumar , Saleem Mohammed , Galla Hans-Joachim
Published: October 2009

One of the most important functions of the lung surfactant monolayer is to form the first line of defence against inhaled aerosols such as nanoparticles (NPs), which remains largely unexplored. We report here, for the first time, the interaction of polyorganosiloxane NPs (AmorSil20: 22 nm in diameter) with lipid monolayers characteristic of alveolar surfactant. To enable a better understanding, the current knowledge about an established model surface film that mimics the surface properties of the lung is reviewed and major results originating from our group are summarized. The pure lipid components dipalmitoylphosphatidylcholine and dipalmitoylphosphatidylglycerol have been used to study the biophysical behaviour of their monolayer films spread at the air–water interface in the presence of NPs. Film balance measurements combined with video-enhanced fluorescence microscopy have been used to investigate the formation of domain structures and the changes in the surface pattern induced by NPs. We are able to show that NPs are incorporated into lipid monolayers with a clear preference for defect structures at the fluid–crystalline interface leading to a considerable monolayer expansion and fluidization. NPs remain at the air–water interface probably by coating themselves with lipids in a self-assembly process, thereby exhibiting hydrophobic surface properties. We also show that the domain structure in lipid layers containing surfactant protein C, which is potentially responsible for the proper functioning of surfactant material, is considerably affected by NPs.
Bioresponsive nanosensors in medical imaging
Authors: Schellenberger Eyk
Published: October 2009

Superparamagnetic iron oxide nanoparticles have been established as sensitive probes for magnetic resonance imaging (MRI). While the majority of specific nanosensors are based on sterically stabilized iron oxide particles, the focus of this review is on the use of very small iron oxide particles (VSOPs) that are electrostatically stabilized by an anionic citrate acid shell. We used VSOPs to develop target-specific as well as protease-activatable nanosensors for molecular MRI.
On the thermodynamic entropy of fatigue fracture
Authors: Naderi M. , Amiri M. , Khonsari M. M.
Published: October 2009

Entropy production during the fatigue process can serve as a measure of degradation. We postulate that the thermodynamic entropy of metals undergoing repeated cyclic load reaching the point of fracture is a constant, independent of geometry, load and frequency. That is, the necessary and sufficient condition for the final fracture of a metal undergoing fatigue load corresponds to a constant irreversible entropy gain. To examine validity, we present the results of an extensive set of both experimental tests and analytical predictions that involve bending, torsion and tension-compression of aluminium 6061-T6 and stainless steel 304 specimens. The concept of tallying up the entropy generation has application in determining the fatigue life of components undergoing cyclic bending, torsion and tension-compression.
An analytical model for dispersion of pollutants from a continuous source in the atmospheric boundary layer
Authors: Kumar Pramod , Sharan Maithili
Published: October 2009

For the dispersion of a pollutant released from a continuous source in the atmospheric boundary layer (ABL), a generalized analytical model describing the crosswind-integrated concentrations is presented. An analytical scheme is described to solve the resulting two-dimensional steady-state advection–diffusion equation for horizontal wind speed as a generalized function of vertical height above the ground and eddy diffusivity as a function of both downwind distance from the source and vertical height. Special cases of this model are deduced and an extensive analysis is carried out to compare the model with the known analytical models by taking the particular forms of wind speed and vertical eddy diffusivity.

The proposed model is evaluated with the observations obtained from Copenhagen diffusion experiments in unstable conditions and Hanford and Prairie Grass experiments in stable conditions. In evaluation of the model, a recently proposed formulation for the wind speed in the entire ABL is used. It is concluded that the present model is performing well with the observations and can be used to predict the short-range dispersion from a continuous release. Further, it is shown that the accurate parameterizations of wind speed and eddy diffusivity provide a significant improvement in the agreement between computed and observed concentrations.
A progressive simultaneous iteration solution for dynamic element vibration analysis
Authors: Gupta K. K. , Lawson C. L.
Published: October 2009

Development and employment of dynamic elements can result in substantial gain in solution convergence for vibration analysis, when compared with the usual finite element discretization. Efficient solution of the associated quadratic matrix eigenproblem is crucial in achieving a superior and relatively economical solution. This paper first describes a novel eigensolution of the quadratic matrix equation by a progressive simultaneous iteration method. Free vibration analysis results of a rectangular prestressed membrane are next presented in detail that provides an assessment of relative solution convergence and computing expenses of the two idealization procedures.