bluuebunny/crossref_metadata_2025 huggingface dataset:
Serological and molecular characterization of Vibrio parahaemolyticus marine strains carrying pandemic genetic markers
Authors: Caburlotto Greta , Gennari Micol , Ghidini Valentina , Tafi MariaCarla , Lleo Maria M
Published: April 2010

In 2005, pandemic Vibrio parahaemolyticus was reported to have been introduced in Europe: O3:K6 strains were isolated from clinical cases in France and Spain, and were found to be associated with consumption of contaminated seafood. On the contrary, pandemic strains were not isolated from seafood or from the environment itself. Analysis of two V. parahaemolyticus strains isolated in May 2007 from Northern Italy seawater and plankton samples revealed the presence of the virulence gene tdh and the pandemic-specific markers orf8 and toxRS/new sequence (group-specific PCR). The two strains showed serotypes not included in the ‘pandemic group’, but their molecular typing proved that they represent a single clone showing a genetic profile very similar to that of pandemic O3:K6 reference isolates. Moreover, the two marine strains carried three virulence-related genes associated with clinical strains and, to date, hardly ever or never detected in environmental strains. The presence, in strains isolated from the marine environment, of genetic pandemic markers and virulence genes normally associated with clinical isolates proves that marine strains might constitute a public health concern.
The functional potential of high Arctic permafrost revealed by metagenomic sequencing, qPCR and microarray analyses
Authors: Yergeau Etienne , Hogues Hervé , Whyte Lyle G , Greer Charles W
Published: April 2010

The fate of the carbon stocked in permafrost following global warming and permafrost thaw is of major concern in view of the potential for increased CH4 and CO2 emissions from these soils. Complex carbon compound degradation and greenhouse gas emissions are due to soil microbial communities, but no comprehensive study has yet addressed their composition and functional potential in permafrost. Here, a 2-m deep permafrost sample and its overlying active layer soil were subjected to metagenomic sequencing, quantitative PCR (qPCR) and microarray analyses. The active layer soil and the 2-m permafrost microbial community structures were very similar, with Actinobacteria being the dominant phylum. The two samples also possessed a highly similar spectrum of functional genes, especially when compared with other already published metagenomes. Key genes related to methane generation, methane oxidation and organic matter degradation were highly diverse for both samples in the metagenomic libraries and some (for example, pmoA) showed relatively high abundance in qPCR assays. Genes related to nitrogen fixation and ammonia oxidation, which could have important roles following climatic change in these nitrogen-limited environments, showed low diversity but high abundance. The 2-m permafrost showed lower abundance and diversity for all the assessed genes and taxa. Experimental biases were also evaluated using qPCR and showed that the whole-community genome amplification technique used caused representational biases in the metagenomic libraries by increasing the abundance of Bacteroidetes and decreasing the abundance of Actinobacteria. This study describes for the first time the detailed functional potential of permafrost-affected soils.
Reducing Anti‐Fat Prejudice in Preservice Health Students: A Randomized Trial
Authors: O'Brien Kerry S. , Puhl Rebecca M. , Latner Janet D. , Mir Azeem S. , Hunter John A.
Published: April 2010

Anti‐fat sentiment is increasing, is prevalent in health professionals, and has health and social consequences. There is no evidence for effective obesity prejudice reduction techniques in health professionals. The present experiment sought to reduce implicit and explicit anti‐fat prejudice in preservice health students. Health promotion/public health bachelor degree program students (n = 159) were randomized to one of three tutorial conditions. One condition presented an obesity curriculum on the controllable reasons for obesity (i.e., diet/exercise). A prejudice reduction condition presented evidence on the uncontrollable reasons for obesity (i.e., genes/environment); whereas a neutral (control) curriculum focused on alcohol use in young people. Measures of implicit and explicit anti‐fat prejudice, beliefs about obese people, and dieting, were taken at baseline and postintervention. Repeated measures analyses showed decreases in two forms of implicit anti‐fat prejudice (decreases of 27 and 12%) in the genes/environment condition relative to other conditions. The diet/exercise condition showed a 27% increase in one measure of implicit anti‐fat prejudice. Reductions in explicit anti‐fat prejudice were also seen in the genes/environment condition (P = 0.006). No significant changes in beliefs about obese people or dieting control beliefs were found across conditions. The present results show that anti‐fat prejudice can be reduced or exacerbated depending on the causal information provided about obesity. The present results have implications for the training of health professionals, especially given their widespread negativity toward overweight and obesity.
Molecular insights into mechanisms of intramembrane proteolysis through signal peptide peptidase (SPP)
Authors: Schröder Bernd , Saftig Paul
Published: April 2010

The processing of membrane-anchored signalling molecules and transcription factors by RIP (regulated intramembrane proteolysis) is a major signalling paradigm in eukaryotic cells. Intramembrane cleaving proteases liberate fragments from membrane-bound precursor proteins which typically fulfil functions such as cell signalling and regulation, immunosurveillance and intercellular communication. Furthermore, they are thought to be involved in the development and propagation of several diseases, such as Alzheimer's disease and hepatitis C virus infection. In this issue of the Biochemical Journal, Schrul and colleagues investigate the interaction of the endoplasmic reticulum-resident intramembrane cleaving SPP (signal peptide peptidase) with different type II oriented transmembrane proteins. A combination of co-immunoprecipitation experiments using wild-type and a dominant-negative SPP with electrophoretic protein separations under native conditions revealed selectivity of the interaction. Depending on the interacting protein, SPP formed complexes of different sizes. SPP could build tight interactions not only with signal peptides, but also with pre- and mis-folded proteins. Whereas signal peptides are direct substrates for SPP proteolysis, the study suggests that SPP may be involved in the controlled sequestration of possibly toxic membrane protein species in a proteolysis-independent manner. These large oligomeric membrane protein aggregates may then be degraded by the proteasome or autophagy.
Generation of cylindrical converging shock waves based on shock dynamics theory
Authors: Zhai Zhigang , Liu Cangli , Qin Fenghua , Yang Jiming , Luo Xisheng
Published: April 2010

A simple but effective technique is proposed to generate cylindrical converging shock waves. The shock dynamics is employed to design a curved wall profile of the test section in a shock tube. When a planar shock wave propagates forward along the curved wall, the disturbances produced by the curved wall would continuously propagate along the shock surface and bend the shock wave. As an example, the wall profile for an incident shock Mach number of M0=1.2 and a converging angle of 15° is tested numerically and experimentally. Both numerical and experimental results show a perfect circular shock front, which validates our method.
The Dielectric Constant of Water and Debye-Hückel Limiting Law Slopes
Authors: Archer Donald G. , Wang Peiming
Published: April 2010

Experimental values of the dielectric constant of water suggest that, for temperatures greater than 400 K, the integral in the Kirkwood dielectric-constant equation, which involves the intermolecular potential function, is a simpler function of temperature and pressure than of temperature and density. An equation has been fitted to values of this integral calculated from experimental values of the dielectric constant for temperatures from 238.15 K to 823.15 K and to pressures of approximately 500 MPa for temperatures greater than 273 K. The equation of ε thus has explicit variables T, ρ, p and gives a good representation of the available experimental results. The quality of representation of the experimental results has been compared to that of previous correlations of the dielectric constant. The new equation is applicable through wider regions of independent variables than the previous equations and is capable of sufficient accuracy to provide values of Debye–Hückel limiting law slopes which are as accurate as the experimental results allow. Values of Debye-Hückel limiting-law slopes are tabulated.
Rate Constants for Reactions of Peroxyl Radicals in Fluid Solutions
Authors: Neta P. , Huie Rober E. , Ross Alberta B.
Published: April 2010

Absolute rate constants for reactions of alkylperoxyl and substituted alkylperoxyl radicals with inorganic and organic compounds in aqueous and non-aqueous fluid solutions have been compiled. The radicals have been generated by radiolysis or photolysis and their rate constants were determined generally by kinetic spectrophotometry or esr. Rate constants are included also for formation of peroxyl radicals by reaction of alkyl radicals with oxygen and for decay of peroxyl radicals by radical-radical reactions.
Renewable Energy and Sociotechnical Change: Imagined Subjectivities of ‘the Public’ and Their Implications
Authors: Walker Gordon , Cass Noel , Burningham Kate , Barnett Julie
Published: April 2010

‘The public’ are potentially implicated in processes of sociotechnical change as political actors who welcome or resist technology development in general, or in particular places and settings. We argue in this paper that the potential influence of public subjectivities on sociotechnical change is realised not only through moments of active participation and protest, but also through ‘the public’ being imagined, given agency, and invoked for various purposes by actors in technical–industrial and policy networks. As a case study we explore the significance of an imagined and anticipated public subjectivity for the development of renewable energy technologies in the UK. We use interviews with a diversity of industry and policy actors to explore how imaginaries of the public are constructed from first-hand and mediated experience and knowledge, and the influence these imagined public subjectivities may have on development trajectories and on actor strategies and activities. We show how the shared expectation of an ever present latent but conditional public hostility to renewable energy project development is seen as shaping the material forms of the technologies, their evolving spatiality, and practices of public engagement involved in obtaining project consent. Implications for the actors we are interested in and for broader questions of democratic practice are considered.
Quantitative analysis of intact apolipoproteins in human HDL by top-down differential mass spectrometry
Authors: Mazur Matthew T. , Cardasis Helene L. , Spellman Daniel S. , Liaw Andy , Yates Nathan A. , Hendrickson Ronald C.
Published: April 2010

Top-down mass spectrometry holds tremendous potential for the characterization and quantification of intact proteins, including individual protein isoforms and specific posttranslationally modified forms. This technique does not require antibody reagents and thus offers a rapid path for assay development with increased specificity based on the amino acid sequence. Top-down MS is efficient whereby intact protein mass measurement, purification by mass separation, dissociation, and measurement of product ions with ppm mass accuracy occurs on the seconds to minutes time scale. Moreover, as the analysis is based on the accurate measurement of an intact protein, top-down mass spectrometry opens a research paradigm to perform quantitative analysis of “unknown” proteins that differ in accurate mass. As a proof of concept, we have applied differential mass spectrometry (dMS) to the top-down analysis of apolipoproteins isolated from human HDL
3
. The protein species at 9415.45 Da demonstrates an average fold change of 4.7 (p-value 0.017) and was identified as an
O
-glycosylated form of apolipoprotein C-III [NANA-(2 → 3)-Gal-
β
(1 → 3)-GalNAc, +656.2037 Da], a protein associated with coronary artery disease. This work demonstrates the utility of top-down dMS for quantitative analysis of intact protein mixtures and holds potential for facilitating a better understanding of HDL biology and complex biological systems at the protein level.
α-Synuclein Delays Endoplasmic Reticulum (ER)-to-Golgi Transport in Mammalian Cells by Antagonizing ER/Golgi SNAREs
Authors: Thayanidhi Nandhakumar , Helm Jared R. , Nycz Deborah C. , Bentley Marvin , Liang Yingjian , Hay Jesse C.
Published: April 2010

Toxicity of human α-synuclein when expressed in simple organisms can be suppressed by overexpression of endoplasmic reticulum (ER)-to-Golgi transport machinery, suggesting that inhibition of constitutive secretion represents a fundamental cause of the toxicity. Whether similar inhibition in mammals represents a cause of familial Parkinson's disease has not been established. We tested elements of this hypothesis by expressing human α-synuclein in mammalian kidney and neuroendocrine cells and assessing ER-to-Golgi transport. Overexpression of wild type or the familial disease-associated A53T mutant α-synuclein delayed transport by up to 50%; however, A53T inhibited more potently. The secretory delay occurred at low expression levels and was not accompanied by insoluble α-synuclein aggregates or mistargeting of transport machinery, suggesting a direct action of soluble α-synuclein on trafficking proteins. Co-overexpression of ER/Golgi arginine soluble N-ethylmaleimide-sensitive factor attachment protein receptors (R-SNAREs) specifically rescued transport, indicating that α-synuclein antagonizes SNARE function. Ykt6 reversed α-synuclein inhibition much more effectively than sec22b, suggesting a possible neuroprotective role for the enigmatic high expression of ykt6 in neurons. In in vitro reconstitutions, purified α-synuclein A53T protein specifically inhibited COPII vesicle docking and fusion at a pre-Golgi step. Finally, soluble α-synuclein A53T directly bound ER/Golgi SNAREs and inhibited SNARE complex assembly, providing a potential mechanism for toxic effects in the early secretory pathway.
EphrinBs/EphBs Signaling Is Involved in Modulation of Spinal Nociceptive Processing through a Mitogen-activated Protein Kinases-dependent Mechanism
Authors: Ruan Jia-Ping , Zhang Hong-Xing , Lu Xian-Fu , Liu Yue-Peng , Cao Jun-Li
Published: April 2010

Background

Our previous studies have demonstrated that EphBs receptors and ephrinBs ligands were involved in modulation of spinal nociceptive information. However, the downstream mechanisms that control this process are not well understood. The aim of this study was to further investigate whether mitogen-activated protein kinases (MAPKs), as the downstream effectors, participate in modulation of spinal nociceptive information related to ephrinBs/EphBs.

Methods

Thermal hyperalgesia and mechanical allodynia were measured using radiant heat and von Frey filaments test. Immunofluorescence staining was used to detect the expression of p-MAPKs and of p-MAPKs/neuronal nuclei, or p-MAPKs/glial fibrillary acidic protein double label. C-Fos expression was determined by immunohistochemistry. The expression of p-MAPKs was also determined by Western blot assay.

Results

Intrathecal injection of ephrinB1-Fc produced a dose- and time-dependent thermal and mechanical hyperalgesia, accompanied by the increase of spinal p-MAPKs and c-Fos expression. Immunofluorescence staining revealed that p-MAPKs colocalized with the neuronal marker (neuronal nuclei) and the astrocyte marker (glial fibrillary acidic protein). Inhibition of MAPKs prevented and reversed pain behaviors and the increase of spinal c-Fos expression induced by intrathecal injection of ephrinB1-Fc. Inhibition of EphBs receptors by intrathecal injection of EphB1-Fc reduced formalin-induced inflammation and chronic constrictive injury-induced neuropathic pain behaviors accompanied by decreased expression of spinal p-MAPKs and c-Fos protein. Furthermore, pretreatment with MK-801, an N-methyl-d-aspartate receptor antagonist, prevented behavioral hyperalgesia and activation of spinal MAPKs induced by intrathecal injection of ephrinB1-Fc.

Conclusions

These results demonstrated that activation of MAPKs contributed to modulation of spinal nociceptive information related to ephrinBs/EphBs.
Hydrocortisone Supplementation Enhances Hemodynamic Stability in Brain-dead Patients
Authors: Nicolas-Robin Armelle , Barouk Jérome D. , Amour Julien , Coriat Pierre , Riou Bruno , Langeron Olivier
Published: April 2010

Background

Hemodynamic instability is frequent in brain-dead patients and may result, in part, from absolute or relative adrenal insufficiency. Corticosteroid supplementation is widely used to restore hemodynamic stability in septic shock and to reduce the time of shock resolution. The authors verified that supplementation with hydrocortisone may enhance hemodynamic stability in brain-dead patients.

Methods

All consecutive brain-dead patients with hypotension requiring vasopressor agents were included in this single-center noninterventional clinical observation study. Assessment of baseline and adrenocorticotropic hormone (ACTH)-stimulated plasma cortisol concentrations was performed. Immediately after, patients were systematically treated with a single intravenous injection of hydrocortisone (50 mg), and norepinephrine administration was adjusted every 15 min to maintain mean arterial pressure between 65 and 90 mmHg. Adrenal insufficiency was defined as baseline plasma cortisol concentration less than 15 microg/dl and/or delta plasma cortisol concentration less than 9 microg/dl. Patients were considered as ACTH responders when delta cortisol concentration was more than 9 microg/dl 30 min after ACTH injection.

Results

Among the 31 patients included, the incidence of adrenal insufficiency was 87% [95% CI, 70-96%]. A significant (> or =30%) decrease in norepinephrine dose was obtained 180 min after hydrocortisone injection in 18 (59%) patients, from 0.31 [0.16-0.44] microg . kg(-1) . min(-1) to 0.18 [0.10-0.24] microg . kg(-1) . min(-1) (P < 0.01). The incidence of hemodynamic response was greater in ACTH nonresponders than in ACTH responders: 86% versus 50%, respectively, P < 0.05.

Conclusions

Adrenal insufficiency with hemodynamic instability is frequent in brain-dead patients. After ACTH stimulation testing and hydrocortisone infusion, hemodynamic stability is enhanced especially in patients with true adrenal nonfunction.
Face Mask Ventilation in Edentulous Patients
Authors: Racine Stéphane X. , Solis Audrey , Hamou Nora Ait , Letoumelin Philippe , Hepner David L. , Beloucif Sadek , Baillard Christophe
Published: April 2010

Background

In edentulous patients, it may be difficult to perform face mask ventilation because of inadequate seal with air leaks. Our aim was to ascertain whether the "lower lip" face mask placement, as a new face mask ventilation method, is more effective at reducing air leaks than the standard face mask placement.

Methods

Forty-nine edentulous patients with inadequate seal and air leak during two-hand positive-pressure ventilation using the ventilator circle system were prospectively evaluated. In the presence of air leaks, defined as a difference of at least 33% between inspired and expired tidal volumes, the mask was placed in a lower lip position by repositioning the caudal end of the mask above the lower lip while maintaining the head in extension. The results are expressed as mean +/- SD or median (25th-75th percentiles).

Results

Patient characteristics included age (71 +/- 11 yr) and body mass index (24 +/- 4 kg/m2). By using the standard method, the median inspired and expired tidal volumes were 450 ml (400-500 ml) and 0 ml (0-50 ml), respectively, and the median air leak was 400 ml (365-485 ml). After placing the mask in the lower lip position, the median expired tidal volume increased to 400 ml (380-490), and the median air leak decreased to 10 ml (0-20 ml) (P < 0.001 vs. standard method). The lower lip face mask placement with two hands reduced the air leak by 95% (80-100%).

Conclusions

In edentulous patients with inadequate face mask ventilation, the lower lip face mask placement with two hands markedly reduced the air leak and improved ventilation.
Effects on Brain Edema of Crystalloid and Albumin Fluid Resuscitation after Brain Trauma and Hemorrhage in the Rat
Authors: Jungner Mårten , Grände Per-Olof , Mattiasson Gustav , Bentzer Peter
Published: April 2010

Background

It has been hypothesized that resuscitation with crystalloids after brain trauma increases brain edema compared with colloids, but previous studies on the subject have been inconclusive. To test this hypothesis, the authors compared groups resuscitated with either colloid or crystalloid.

Methods

After fluid percussion injury, rats were subjected to a controlled hemorrhage of 20 ml/kg and were randomized to 5% albumin at 20 ml/kg (A20), isotonic Ringer's acetate at 50 ml/kg (C50), or 90 ml/kg (C90). After 3 or 24 h, water content in the injured cortex was determined using a wet/dry weight method. Blood volume was calculated from plasma volume, measured by 125I-albumin dilution, and hematocrit. Oncotic pressure and osmolality were measured with osmometers.

Results

At 3 h, blood volume was equal in the A20 and C90 groups and lower in the C50 group. Oncotic pressure was reduced by 35-40% in the crystalloid groups and unchanged in the albumin group. Cortical water content in the A20 group was lower than in the C90 group (81.3 +/- 0.5% vs. 82.1 +/- 1.1%, P < 0.05), but it was not different from the C50 group (81.8 +/- 1.1%). At 24 h, oncotic pressure and blood volume were normalized in all groups, and cortical water content was significantly lower in the albumin group than in the crystalloid groups. Osmolality and arterial pressure were equal in all groups throughout the experiment.

Conclusions

When given to the same intravascular volume expansion, isotonic crystalloids caused greater posttraumatic brain edema than 5% albumin at 3 and 24 h after trauma.
Effects of Intrathecal Ketorolac on Human Experimental Pain
Authors: Eisenach James C. , Curry Regina , Tong Chuanyao , Houle Timothy T. , Yaksh Tony L.
Published: April 2010

Background

Nonsteroidal antiinflammatory drugs, the most commonly used analgesics, reduce pain not only by inhibiting cyclooxygenase at peripheral sites of inflammation but also by potentially inhibiting cyclooxygenase in the central nervous system, especially the spinal cord. Animal studies suggest that products of cyclooxygenase in the spinal cord do not alter pain responses to acute noxious stimuli but reduce pain and sensitization after peripheral inflammation. We used a spinal injection of small doses of the cyclooxygenase inhibitor ketorolac to survey the role of spinal cyclooxygenase in human experimental pain and hypersensitivity states.

Methods

After regulatory agency approval and informed consent, we examined the effect of 2.0 mg intrathecal ketorolac in 41 healthy volunteers to acute noxious thermal stimuli in normal skin and to mechanical stimuli in skin sensitized by topical capsaicin or ultraviolet burn. We also examined the effect of intravenous ketorolac.

Results

Intrathecal ketorolac reduced hypersensitivity when it was induced by a combination of ultraviolet burn plus intermittent heat and, according to one of the two analytical strategies, when it was induced by ultraviolet burn alone.

Conclusions

These data suggest a more limited role for spinal cord cyclooxygenase in human pain states than predicted by studies in animals.
Role of Spinal Cyclooxygenase in Human Postoperative and Chronic Pain
Authors: Eisenach James C. , Curry Regina , Rauck Richard , Pan Peter , Yaksh Tony L.
Published: April 2010

Background

Nonsteroidal antiinflammatory drugs are commonly used to treat postoperative and chronic pain. Animal studies suggest that these drugs act, in part, by blocking prostaglandin production in the spinal cord. The authors tested intrathecal ketorolac in patients with chronic or postoperative pain.

Methods

After approval of the institutional review board and the Food and Drug Administration, three clinical studies were performed. First, 15 patients receiving chronic intrathecal morphine received 0.5-2.0 mg of intrathecal ketorolac. Second, 12 patients receiving chronic intrathecal morphine received, in a double-blinded, randomized, cross-over design, intrathecal saline or 2.0 mg of ketorolac, with pain intensity as the primary outcome measure. Third, 30 patients undergoing total vaginal hysterectomy received, in a double-blinded, randomized, controlled design, intrathecal saline or 2.0 mg of ketorolac, with bupivacaine with time to first morphine dose after surgery as the primary outcome measure.

Results

Patients with chronic pain had many symptoms before intrathecal injection, without worsening of these symptoms from ketorolac. Pain intensity was reduced by intrathecal ketorolac, but this did not differ from placebo. In the first study, pain was reduced by intrathecal ketorolac in patients with high cerebrospinal fluid prostaglandin E2 concentrations but not in those with normal concentrations. Intrathecal ketorolac did not alter time to first morphine after surgery.

Conclusions

Intrathecal ketorolac did not relieve chronic pain or extend anesthesia or analgesia from intrathecal bupivacaine administered at the beginning of surgery. Under the conditions of these studies, it seems that spinal cylcooxygenase activity does not contribute to chronic or postoperative pain.
Social insects inspire human design
Authors: Holbrook C. Tate , Clark Rebecca M. , Moore Dani , Overson Rick P. , Penick Clint A. , Smith Adrian A.
Published: April 2010

The international conference ‘Social Biomimicry: Insect Societies and Human Design’, hosted by Arizona State University, USA, 18–20 February 2010, explored how the collective behaviour and nest architecture of social insects can inspire innovative and effective solutions to human design challenges. It brought together biologists, designers, engineers, computer scientists, architects and businesspeople, with the dual aims of enriching biology and advancing biomimetic design.
Inbreeding tolerance and fitness costs in wild bottlenose dolphins
Authors: Frère Céline H. , Krützen Michael , Kopps Anna M. , Ward Patrick , Mann Janet , Sherwin William B.
Published: April 2010

In wild populations, inbreeding tolerance is expected to evolve where the cost of avoidance exceeds that of tolerance. We show that in a wild population of bottlenose dolphins found in East Shark Bay, Western Australia, levels of inbreeding are higher than expected by chance alone, and demonstrate that inbreeding is deleterious to female fitness in two independent ways. We found that inbred females, and females with inbred calves, have reduced fitness (lower calving success). We further show that one of the costs of inbreeding is extended weaning age, and that females' earlier calves are more likely to be inbred. While the exact causes of inbreeding remain obscure, our results indicate that one factor is female age, and thus experience. Any inbreeding avoidance mechanisms such as female evasion of kin, or male dispersal, do not seem to be completely effective in this population, which supports the view that inbreeding avoidance does not always evolve wherever inbreeding incurs a cost.
Calcification provides mechanical reinforcement to whale baleen α-keratin
Authors: Szewciw L. J. , de Kerckhove D. G. , Grime G. W. , Fudge D. S.
Published: April 2010

Hard α-keratins such as hair, nail, wool and horn are stiff epidermal appendages used by mammals in a variety of functions including thermoregulation, feeding and intraspecific competition. Hard α-keratins are fibre-reinforced structures consisting of cytoskeletal elements known as ‘intermediate filaments’ embedded in an amorphous protein matrix. Recent research has shown that intermediate filaments are soft and extensible in living keratinocytes but become far stiffer and less extensible in keratinized cells, and this stiffening may be mediated by air-drying. Baleen, the keratinous plates used by baleen whales during filter feeding, is an unusual mammalian keratin in that it never air dries, and in some species, it represents the most heavily calcified of all the hard α-keratins. We therefore tested the hypothesis that whale baleen is stiffened by calcification. Here, we provide, to our knowledge, the first comprehensive description of baleen material properties and show that calcification contributes to overcoming the shortcomings of stiffening this hard α-keratin without the benefit of air-drying. We also demonstrate striking interspecies differences in the calcification patterns among three species of baleen whales and provide novel insights into the function and evolution of this unusual biomaterial.
A FOXO–Pak1 transcriptional pathway controls neuronal polarity
Authors: de la Torre-Ubieta Luis , Gaudillière Brice , Yang Yue , Ikeuchi Yoshiho , Yamada Tomoko , DiBacco Sara , Stegmüller Judith , Schüller Ulrich , Salih Dervis A. , Rowitch David , Brunet Anne , Bonni Azad
Published: April 2010

Neuronal polarity is essential for normal brain development and function. However, cell-intrinsic mechanisms that govern the establishment of neuronal polarity remain to be identified. Here, we report that knockdown of endogenous FOXO proteins in hippocampal and cerebellar granule neurons, including in the rat cerebellar cortex in vivo, reveals a requirement for the FOXO transcription factors in the establishment of neuronal polarity. The FOXO transcription factors, including the brain-enriched protein FOXO6, play a critical role in axo–dendritic polarization of undifferentiated neurites, and hence in a switch from unpolarized to polarized neuronal morphology. We also identify the gene encoding the protein kinase Pak1, which acts locally in neuronal processes to induce polarity, as a critical direct target gene of the FOXO transcription factors. Knockdown of endogenous Pak1 phenocopies the effect of FOXO knockdown on neuronal polarity. Importantly, exogenous expression of Pak1 in the background of FOXO knockdown in both primary neurons and postnatal rat pups in vivo restores the polarized morphology of neurons. These findings define the FOXO proteins and Pak1 as components of a cell-intrinsic transcriptional pathway that orchestrates neuronal polarity, thus identifying a novel function for the FOXO transcription factors in a unique aspect of neural development.
Transcriptional silencing of γ-globin by BCL11A involves long-range interactions and cooperation with SOX6
Authors: Xu Jian , Sankaran Vijay G. , Ni Min , Menne Tobias F. , Puram Rishi V. , Kim Woojin , Orkin Stuart H.
Published: April 2010

The developmental switch from human fetal (γ) to adult (β) hemoglobin represents a clinically important example of developmental gene regulation. The transcription factor BCL11A is a central mediator of γ-globin silencing and hemoglobin switching. Here we determine chromatin occupancy of BCL11A at the human β-globin locus and other genomic regions in vivo by high-resolution chromatin immunoprecipitation (ChIP)–chip analysis. BCL11A binds the upstream locus control region (LCR), ɛ-globin, and the intergenic regions between γ-globin and δ-globin genes. A chromosome conformation capture (3C) assay shows that BCL11A reconfigures the β-globin cluster by modulating chromosomal loop formation. We also show that BCL11A and the HMG-box-containing transcription factor SOX6 interact physically and functionally during erythroid maturation. BCL11A and SOX6 co-occupy the human β-globin cluster along with GATA1, and cooperate in silencing γ-globin transcription in adult human erythroid progenitors. These findings collectively demonstrate that transcriptional silencing of γ-globin genes by BCL11A involves long-range interactions and cooperation with SOX6. Our findings provide insight into the mechanism of BCL11A action and new clues for the developmental gene regulatory programs that function at the β-globin locus.
The shape of the DNA minor groove directs binding by the DNA-bending protein Fis
Authors: Stella Stefano , Cascio Duilio , Johnson Reid C.
Published: April 2010

The bacterial nucleoid-associated protein Fis regulates diverse reactions by bending DNA and through DNA-dependent interactions with other control proteins and enzymes. In addition to dynamic nonspecific binding to DNA, Fis forms stable complexes with DNA segments that share little sequence conservation. Here we report the first crystal structures of Fis bound to high- and low-affinity 27-base-pair DNA sites. These 11 structures reveal that Fis selects targets primarily through indirect recognition mechanisms involving the shape of the minor groove and sequence-dependent induced fits over adjacent major groove interfaces. The DNA shows an overall curvature of ∼65°, and the unprecedented close spacing between helix–turn–helix motifs present in the apodimer is accommodated by severe compression of the central minor groove. In silico DNA structure models show that only the roll, twist, and slide parameters are sufficient to reproduce the changes in minor groove widths and recreate the curved Fis-bound DNA structure. Models based on naked DNA structures suggest that Fis initially selects DNA targets with intrinsically narrow minor grooves using the separation between helix–turn–helix motifs in the Fis dimer as a ruler. Then Fis further compresses the minor groove and bends the DNA to generate the bound structure.
The Changing Fate of a Secretory Glycoprotein in Developing Maize Endosperm
Authors: Arcalis Elsa , Stadlmann Johannes , Marcel Sylvain , Drakakaki Georgia , Winter Verena , Rodriguez Julian , Fischer Rainer , Altmann Friedrich , Stoger Eva
Published: April 2010

Zeins are the major storage proteins in maize (Zea mays) endosperm, and their accumulation in zein bodies derived from the endoplasmic reticulum is well characterized. In contrast, relatively little is known about post-Golgi compartments or the trafficking of vacuolar proteins in maize endosperm, specifically the presence of globulins in structures resembling protein storage vacuoles that appear in early to mid-stage seed development. We investigated this pathway by expressing and analyzing a recombinant reporter glycoprotein during endosperm maturation, using a combination of microscopy and sensitive glycopeptide analysis. Specific N-glycan acceptor sites on the protein were followed through the stages of grain development, revealing a shift from predominantly paucimannosidic vacuolar glycoforms to predominantly trimmed glycan structures lacking fucose. This was accompanied by a change in the main subcellular localization of the protein from large protein storage vacuole-like post-Golgi organelles to the endoplasmic reticulum and zein bodies. The endogenous storage proteins corn α-globulin and corn legumin-1 showed a similar spatiotemporal profile both in transgenic plants expressing the reporter glycoprotein and in wild-type plants. This indicates that the shift of the intracellular trafficking route, as observed with our reporter glycoprotein, may be a common strategy in maize seed development.
Robin: An Intuitive Wizard Application for R-Based Expression Microarray Quality Assessment and Analysis
Authors: Lohse Marc , Nunes-Nesi Adriano , Krüger Peter , Nagel Axel , Hannemann Jan , Giorgi Federico M. , Childs Liam , Osorio Sonia , Walther Dirk , Selbig Joachim , Sreenivasulu Nese , Stitt Mark , Fernie Alisdair R. , Usadel Björn
Published: April 2010

The wide application of high-throughput transcriptomics using microarrays has generated a plethora of technical platforms, data repositories, and sophisticated statistical analysis methods, leaving the individual scientist with the problem of choosing the appropriate approach to address a biological question. Several software applications that provide a rich environment for microarray analysis and data storage are available (e.g. GeneSpring, EMMA2), but these are mostly commercial or require an advanced informatics infrastructure. There is a need for a noncommercial, easy-to-use graphical application that aids the lab researcher to find the proper method to analyze microarray data, without this requiring expert understanding of the complex underlying statistics, or programming skills. We have developed Robin, a Java-based graphical wizard application that harnesses the advanced statistical analysis functions of the R/BioConductor project. Robin implements streamlined workflows that guide the user through all steps of two-color, single-color, or Affymetrix microarray analysis. It provides functions for thorough quality assessment of the data and automatically generates warnings to notify the user of potential outliers, low-quality chips, or low statistical power. The results are generated in a standard format that allows ready use with both specialized analysis tools like MapMan and PageMan and generic spreadsheet applications. To further improve user friendliness, Robin includes both integrated help and comprehensive external documentation. To demonstrate the statistical power and ease of use of the workflows in Robin, we present a case study in which we apply Robin to analyze a two-color microarray experiment comparing gene expression in tomato (Solanum lycopersicum) leaves, flowers, and roots.
DNA Is Taken Up by Root Hairs and Pollen, and Stimulates Root and Pollen Tube Growth
Authors: Paungfoo-Lonhienne Chanyarat , Lonhienne Thierry G.A. , Mudge Stephen R. , Schenk Peer M. , Christie Michael , Carroll Bernard J. , Schmidt Susanne
Published: April 2010

Phosphorus (P) enters roots as inorganic phosphate (Pi) derived from organic and inorganic P compounds in the soil. Nucleic acids can support plant growth as the sole source of P in axenic culture but are thought to be converted into Pi by plant-derived nucleases and phosphatases prior to uptake. Here, we show that a nuclease-resistant analog of DNA is taken up by plant cells. Fluorescently labeled S-DNA of 25 bp, which is protected against enzymatic breakdown by its phosphorothioate backbone, was taken up and detected in root cells including root hairs and pollen tubes. These results indicate that current views of plant P acquisition may have to be revised to include uptake of DNA into cells. We further show that addition of DNA to Pi-containing growth medium enhanced the growth of lateral roots and root hairs even though plants were P replete and had similar biomass as plants supplied with Pi only. Exogenously supplied DNA increased length growth of pollen tubes, which were studied because they have similar elongated and polarized growth as root hairs. Our results indicate that DNA is not only taken up and used as a P source by plants, but ironically and independent of Pi supply, DNA also induces morphological changes in roots similar to those observed with P limitation. This study provides, to our knowledge, first evidence that exogenous DNA could act nonspecifically as signaling molecules for root development.
Inhibition of Auxin Transport from the Ovary or from the Apical Shoot Induces Parthenocarpic Fruit-Set in Tomato Mediated by Gibberellins
Authors: Serrani Juan Carlos , Carrera Esther , Ruiz-Rivero Omar , Gallego-Giraldo Lina , Peres LÁzaro EustÁquio Pereira , García-Martínez José Luis
Published: April 2010

Fruit-set in tomato (Solanum lycopersicum) depends on gibberellins and auxins (GAs). Here, we show, using the cv MicroTom, that application of N-1-naphthylphthalamic acid (NPA; an inhibitor of auxin transport) to unpollinated ovaries induced parthenocarpic fruit-set, associated with an increase of indole-3-acetic acid (IAA) content, and that this effect was negated by paclobutrazol (an inhibitor of GA biosynthesis). NPA-induced ovaries contained higher content of GA1 (an active GA) and transcripts of GA biosynthetic genes (SlCPS, SlGA20ox1, and -2). Interestingly, application of NPA to pollinated ovaries prevented their growth, potentially due to supraoptimal IAA accumulation. Plant decapitation and inhibition of auxin transport by NPA from the apical shoot also induced parthenocarpic fruit growth of unpollinated ovaries. Application of IAA to the severed stump negated the plant decapitation effect, indicating that the apical shoot prevents unpollinated ovary growth through IAA transport. Parthenocarpic fruit growth induced by plant decapitation was associated with high levels of GA1 and was counteracted by paclobutrazol treatment. Plant decapitation also produced changes in transcript levels of genes encoding enzymes of GA biosynthesis (SlCPS and SlGA20ox1) in the ovary, quite similar to those found in NPA-induced fruits. All these results suggest that auxin can have opposing effects on fruit-set, either inducing (when accumulated in the ovary) or repressing (when transported from the apical shoot) that process, and that GAs act as mediators in both cases. The effect of NPA application and decapitation on fruit-set induction was also observed in MicroTom lines bearing introgressed DWARF and SELF-PRUNING wild-type alleles.
Misorientations induced by deformation twinning in titanium
Authors: Bozzolo Nathalie , Chan Lisa , Rollett Anthony D.
Published: April 2010

The misorientations induced by cold-rolling in commercially pure titanium by twinning and multiple twinning were investigated by electron backscatter diffraction. Three main types of twins occur: compressive twins (64.6° 〈1\overline 100〉) which are predominant, followed by tensile twins of type 1 (84.8° [11\overline 20]) and a few of type 2 (35.1° 〈1\overline 100〉). The main multiple twinning configurations are (i) several variants of a given type of twin inside a given grain and (ii) second-generation tensile twins inside primary compressive twins. All possible misorientations resulting from the combination of two out of the three main twinning systems have been calculated and compared with the experimentally observed twin configurations. This facilitated interpretation of the peak found at 41° 〈5\overline 1\overline 43〉 in the misorientation distribution as the result of double twinning (tensile twins inside primary compressive twins).
Modeling of kinematic diffraction from a thin silicon film illuminated by a coherent, focused X-ray nanobeam
Authors: Ying Andrew , Osting Braxton , Noyan I. C. , Murray Conal E. , Holt Martin , Maser Jörg
Published: April 2010

A rigorous model of a diffraction experiment utilizing a coherent, monochromatic, X-ray beam, focused by a Fresnel zone plate onto a thin, perfect, single-crystal layer is presented. In this model, first the coherent wave emanating from an ideal zone plate equipped with a direct-beam stop and order-sorting aperture is computed. Then, diffraction of the focused wavefront by a thin silicon film positioned at the primary focal spot is calculated. This diffracted wavefront is propagated to the detector position, and the intensity distribution at the detector plane is extracted. The predictions of this model agree quite well with experimental data measured at the Center for Nanoscale Materials nanoprobe instrument at Sector 26 of the Advanced Photon Source.
An investigation of goethite-seeded Al(OH)3precipitation usingin situX-ray diffraction and Rietveld-based quantitative phase analysis
Authors: Webster Nathan A. S. , Madsen Ian C. , Loan Melissa J. , Knott Robert B. , Naim Fatima , Wallwork Kia S. , Kimpton Justin A.
Published: April 2010

Anin situX-ray diffraction investigation of goethite-seeded Al(OH)3precipitation from synthetic Bayer liquor at 343 K has been performed. The presence of iron oxides and oxyhydroxides in the Bayer process has implications for alumina reversion, which causes significant process losses through unwanted gibbsite precipitation, and is also relevant for the nucleation and growth of scale on mild steel process equipment. The gibbsite, bayerite and nordstrandite polymorphs of Al(OH)3precipitated from the liquor; gibbsite appeared to precipitate first, with subsequent formation of bayerite and nordstrandite. A Rietveld-based approach to quantitative phase analysis was implemented for the determination of absolute phase abundances as a function of time, from which kinetic information for the formation of the Al(OH)3phases was determined.
Optimization of a bent perfect Si(111) monochromator at a small take-off angle for use in a stress instrument
Authors: Seong Baek-Seok , Em Vyacheslav , Mikula Pavol , Šaroun Jan , Kang Mi-Hyun
Published: April 2010

The reflectivity and resolution properties of focusing cylindrically bent perfect crystal Si(111) monochromators of different diffraction geometries were tested with the aim of evaluating their possible use in a stress instrument with an unusually small take-off angle (2θM≃ 30°). The experiments showed that an Si crystal with reflecting planes (111) in the symmetric diffraction geometry provides a maximum figure of merit for accuracy in the peak position that is comparable to that achieved previously from an optimized Si(220) monochromator at 2θM≃ 55°.
Identification of QTL for dorso‐caudal chronic pleuritis in 12 crossbred porcine families
Authors: Gregersen V. R. , Sørensen K. K. , Christensen O. F. , Busch M. E. , Vingborg R. K. K. , Velander I. H. , Lund M. S. , Bendixen C.
Published: April 2010

Pleuropneumonia is a major problem in pig production. At the time of slaughter, chronic pleuritis (CP) developed from pleuropneumonia is a common finding, and breeding for a reduced incidence of CP using marker‐assisted selection (MAS) would be advantageous. Before applying MAS, quantitative trait loci (QTL) or markers associated with the prevalence of CP should be identified. In this study, 7470 pigs from crosses between 12 Danish Duroc boars and 604 sows (Danish Landrace × Danish Large White) were evaluated for CP located on the dorso‐caudal part of the lungs. Quantitative trait loci were identified within boar families using both a Binomial logistic regression method and a chi‐square test of association. Significant QTL for CP were detected onSus scrofachromosomes (SSC) 2, 8, 12, 13, 14 and 18 using both methods. One QTL on SSC 8 was also detected across families. For the QTL identified within families, the odds‐ratio of having CP was approximately twice as high for the unfavourable allele compared to the favourable one. These QTL and closely linked markers show promise for the development of gene‐specific markers associated with a reduced incidence of CP located on the dorso‐caudal part of the lungs.
Origin of Hungarian indigenous chicken breeds inferred from mitochondrial DNA D‐loop sequences
Authors: Revay T. , Bodzsar N. , Mobegi V. E. , Hanotte O. , Hidas A.
Published: April 2010

In this study, we assessed the maternal origin of six Hungarian indigenous chicken breeds using mitochondrial DNA information. Sequences of Hungarian chickens were compared with the D‐loop chicken sequences annotated in the GenBank and to nine previously described reference haplotypes representing the main haplogroups of chicken. The first 530 bases of the D‐loop region were sequenced in 74 chickens of nine populations. Eleven haplotypes (HIC1‐HIC11) were observed from 17 variable sites. Three sequences (HIC3, HIC8 and HIC9) of our chickens were found as unique to Hungary when searched against the NCBI GenBank database. Hungarian domestic chicken mtDNA sequences could be assigned into three clades and probably two maternal lineages. Results indicated that 86% of the Hungarian haplotypes are related to the reference sequence that likely originated from the Indian subcontinent, while the minor part of our sequences presumably derive from South East Asia, China and Japan.